More stories

  • in

    Mitogenomic analysis of diversity of key whitefly pests in Kenya and its implication to their sustainable management

    1.Martin, J. H., Mifsud, D. & Rapisarda, C. The whiteflies (Hemiptera: Aleyrodidae) of Europe and the Mediterranean basin. Bull. Entomol. Res. 90, 407–448 (2000).CAS 
    PubMed 
    Article 

    Google Scholar 
    2.Omongo, C. A. et al. African cassava whitefly, Bemisia tabaci, resistance in African and South American cassava genotypes. J. Integr. Agric. 11, 327–336 (2012).Article 

    Google Scholar 
    3.Omongo, C. A. et al. Host plant resistance to African Bemisia tabaci in local landraces and improved cassava mosaic disease resistant genotypes in Uganda. In 6th International Scientific Meeting of the Cassava Biotechnology Network (Abstracts), Vol. 84, 8–14 (2004).4.Legg, J. P., Sseruwagi, P. & Brown, J. Bemisia whiteflies cause physical damage and yield losses to cassava in Africa. In Sixth International Scientific Meeting of the Cassava Biotechnology Network 78 (2004).5.Lloyd, L. L. The control of the greenhouse white fly (Asterochiton vaporariorum) with notes on its biology 1. Ann Appl Biol. 9, 1–32 (1922).Article 

    Google Scholar 
    6.McAuslane, H. J. & Smith, S. A. Sweet Potato Whitefly B Biotype, Bemisia tabaci (Gennadius) (Insecta: Hemiptera: Aleyrodidae) (University of Florida, 2015).
    Google Scholar 
    7.Viscarret, M. M., Botto, E. N. & Polaszek, A. N. Whiteflies (Hemiptera: Aleyrodidae) of economic importance and their natural enemies (Hymenoptera: Aphelinidae, Signiphoridae) in Argentina. Rev. Chil. Entomol. 26, 5–11 (2000).
    Google Scholar 
    8.Abd-Rabou, S. & Simmons, A. M. Survey of natural enemies of whiteflies (Hemiptera: Aleyrodidae) in Egypt with new local and world records. Entomol. News 124, 38–56 (2014).Article 

    Google Scholar 
    9.Roopa, H. K. et al. Phylogenetic analysis of Trialeurodes spp. (Hemiptera: Aleyrodidae) from India based on differences in mitochondrial and nuclear DNA. Fla Entomol. 1, 1086–94 (2012).Article 

    Google Scholar 
    10.De Barro, P. J., Liu, S. S., Boykin, L. M. & Dinsdale, A. B. Bemisia tabaci: a statement of species status. Annu. Rev. Entomol. 7, 1–9 (2011).Article 
    CAS 

    Google Scholar 
    11.Liu, S. S., Colvin, J. & De Barro, P. J. Species concepts as applied to the whitefly Bemisia tabaci systematics: how many species are there? J. Integr. Agric. 11, 176–186 (2012).Article 

    Google Scholar 
    12.CABI/EPPO. Distribution Maps of Quarantine Pests for Europe (eds Smith I. M. & Charles L. M. F.) 768 (CAB International, 1998).13.Brown, J. K. Current status of Bemisia tabaci as a plant pest and virus vector in agroecosystems worldwide. FAO Plant Prot. Bull. 42, 3–2 (1994).
    Google Scholar 
    14.Brown, J. K. Molecular markers for the identification and global tracking of whitefly vector—begomovirus complexes. Virus Res. 71, 233–260 (2000).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    15.Maruthi, M. N., Hillocks, R. J., Rekha, A. R. & Colvin, J. Transmission of Cassava brown streak virus by whiteflies. In Sixth International Scientific Meeting of the Cassava Biotechnology Network—Adding Value to a Small-Farmer Crop 8–14 (2004).16.Mugerwa, H. et al. Genetic diversity and geographic distribution of Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) genotypes associated with cassava in East Africa. Ecol. Evol. 2, 2749–2762 (2012).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    17.Maruthi, M. N. et al. Reproductive incompatibility and cytochrome oxidase I gene sequence variability amongst host-adapted and geographically separate Bemisia tabaci populations (Hemiptera: Aleyrodidae). Syst. Entomol. 29, 560–568 (2004).Article 

    Google Scholar 
    18.Legg, J. P. et al. Comparing the regional epidemiology of the cassava mosaic and cassava brown streak virus pandemics in Africa. Virus Res. 159, 161–170 (2011).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    19.Prijović, M. et al. Genetic variation of the greenhouse whitefly, Trialeurodes vaporariorum (Hemiptera: Aleyrodidae), among populations from Serbia and neighbouring countries, as inferred from COI sequence variability. Bull. Entomol. Res. 104, 357–366 (2014).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    20.Palevsky, E. et al. How specific is the phoretic relationship between broad mite, Polyphagotarsonemus latus (Banks) (Acari: Tarsonemidae), and its insect vectors? Exp. Appl. Acarol. 25, 217–224 (2001).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    21.Mound, L. A. & Halsey, S. H. Whitefly of the World. A Systematic Catalogue of the Aleyrodidae (Homoptera) with Host Plant and Natural Enemy Data (Wiley, 1978).
    Google Scholar 
    22.Legg, J. P., French, R., Rogan, D., Okao-Okuja, G. & Brown, J. K. A distinct Bemisia tabaci (Gennadius) (Hemiptera: Sternorrhyncha: Aleyrodidae) genotype cluster is associated with the epidemic of severe cassava mosaic virus disease in Uganda. Mol. Ecol. 11, 1219–1229 (2002).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    23.Legg, J. P. Epidemiology of a whitefly-transmitted cassava mosaic geminivirus pandemic in Africa. In Bemisia: Bionomics and Management of a Global Pest (eds Stansly, P. A. & Naranjo, S. E.) 233–257 (Springer, 2009).24.Legg, J. P. et al. Spatio-temporal patterns of genetic change amongst populations of cassava Bemisia tabaci whiteflies driving virus pandemics in East and Central Africa. Virus Res. 186, 61–75 (2014).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    25.Delatte, H. et al. A new silverleaf-inducing biotype Ms of Bemisia tabaci (Hemiptera: Aleyrodidae) indigenous to the islands of the south-west Indian Ocean. Bull. Entomol. Res. 95, 29–35 (2005).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    26.Jones, A. L. & Markham, R. H. Whitefly and whitefly-borne viruses in the tropics: building a knowledge base for global action. CIAT 341, 129–140 (2005).
    Google Scholar 
    27.Hodges, G. S. & Evans, G. A. An identification guide to the whiteflies (Hemiptera: Aleyrodidae) of the Southeastern United States. Fla Entomol. 1, 518–534 (2005).Article 

    Google Scholar 
    28.Calvert, L. A. et al. Morphological and mitochondrial DNA marker analyses of whiteflies (Homoptera: Aleyrodidae) colonizing cassava and beans in Colombia. Ann. Entomol. Soc. Am. 94, 512–519 (2001).CAS 
    Article 

    Google Scholar 
    29.Ovalle, T. M., Parsa, S., Hernández, M. P. & Becerra Lopez-Lavalle, L. A. Reliable molecular identification of nine tropical whitefly species. Ecol. Evol. 4, 3778–3787 (2014).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    30.Shatters, R. G. Jr., Powell, C. A., Boykin, L. M., Liansheng, H. E. & McKenzie, C. L. Improved DNA barcoding method for Bemisia tabaci and related Aleyrodidae: development of universal and Bemisia tabaci biotype-specific mitochondrial cytochrome c oxidase I polymerase chain reaction primers. J. Econ. Entomol. 102, 750–758 (2009).CAS 
    PubMed 
    Article 

    Google Scholar 
    31.Alhudaib, K. A., Rezk, A. A., Abdel-Banat, B. M. & Soliman, A. M. Molecular identification of the biotype of whitefly (Bemisia tabaci) inhabiting the eastern region of Saudi Arabia. J. Biol. Sci. 14, 494–500 (2014).Article 
    CAS 

    Google Scholar 
    32.Cavalieri, V., Manglli, A., Tiberini, A., Tomassoli, L. & Rapisarda, C. Rapid identification of Trialeurodes vaporariorum, Bemisia tabaci (MEAM1 and MED) and tomato-infecting criniviruses in whiteflies and in tomato leaves by real-time reverse transcription-PCR assay. Bull. Insectol. 67, 219–225 (2014).
    Google Scholar 
    33.Dickey, A. M., Stocks, I. C., Smith, T., Osborne, L. & McKenzie, C. L. DNA barcode development for three recent exotic whitefly (Hemiptera: Aleyrodidae) invaders in Florida. Fla Entomol. 98, 473–478 (2015).Article 

    Google Scholar 
    34.Brown, J. K. et al. Molecular diagnostic development for begomovirus-betasatellite complexes undergoing diversification: a case study. Virus Res. 241, 29–41 (2017).CAS 
    PubMed 
    Article 

    Google Scholar 
    35.Frohlich, D. R., Torres-Jerez, I., Bedford, I. D., Markham, P. G. & Brown, J. K. A phylogeographical analysis of the Bemisia tabaci species complex based on mitochondrial DNA markers. Mol. Ecol. 8, 1683–1691 (1999).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    36.Folmer, O., Black, M., Hoeh, W., Lutz, R. & Vrijenhoek, R. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol. Mar. Biol. Biotechnol. 3, 294–299 (1994).CAS 
    PubMed 

    Google Scholar 
    37.Xiong, B. & Kocher, T. D. Comparison of mitochondrial DNA sequences of seven morphospecies of black flies (Diptera: Simuliidae). Genome 34, 306–311 (1991).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    38.Narang, S. K., Seawright, J. A. & Suarez, M. F. Genetic structure of natural populations of Anopheles albimanus in Colombia. J. Am. Mosq. Control 7, 437–445 (1991).CAS 

    Google Scholar 
    39.Dinsdale, A., Cook, L., Riginos, C., Buckley, Y. M. & De Barro, P. Refined global analysis of Bemisia tabaci (Hemiptera: Sternorrhyncha: Aleyrodoidea: Aleyrodidae) mitochondrial cytochrome oxidase 1 to identify species level genetic boundaries. Ann. Entomol. Soc. Am. 103, 196–208 (2010).Article 

    Google Scholar 
    40.Berry, S. D. et al. Molecular evidence for five distinct Bemisia tabaci (Homoptera: Aleyrodidae) geographic haplotypes associated with cassava plants in sub-Saharan Africa. Ann. Entomol. Soc. Am. 97, 852–859 (2004).CAS 
    Article 

    Google Scholar 
    41.Brown, J. K. et al. Characterization and distribution of esterase electromorphs in the whitefly, Bemisia tabaci (Genn.) (Homoptera: Aleyrodidae). Biochem. Genet. 33, 205–214 (1995).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    42.De Barro, P. J. & Carver, M. Cabbage whitefly, Aleyrodes proletella (L.) (Hemiptera: Aleyrodidae), newly discovered in Australia. Aust. J. Entomol. 36, 255–256 (1997).Article 

    Google Scholar 
    43.Springate, S. & Colvin, J. Pyrethroid insecticide resistance in British populations of the cabbage whitefly Aleyrodes proletella. Pest. Manag. Sci. 68, 260–267 (2012).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    44.Chen, Z. T., Mu, L. X., Wang, J. R. & Du, Y. Z. Complete mitochondrial genome of the citrus spiny whitefly Aleurocanthus spiniferus (Quaintance) (Hemiptera: Aleyrodidae): implications for the phylogeny of whiteflies. PLoS ONE 11, e0161385 (2016).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    45.Boykin, L. M. et al. Global relationships of Bemisia tabaci (Hemiptera: Aleyrodidae) revealed using Bayesian analysis of mitochondrial COI DNA sequences. Mol. Phylogenet. Evol. 44, 1306–1319 (2007).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    46.Lee, W., Park, J., Lee, G. S., Lee, S. & Akimoto, S. I. Taxonomic status of the Bemisia tabaci complex (Hemiptera: Aleyrodidae) and reassessment of the number of its constituent species. PLoS ONE 8, e63817 (2013).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    47.Manzari, S. & Quicke, D. L. A cladistic analysis of whiteflies, subfamily Aleyrodinae (Hemiptera: Sternorrhyncha: Aleyrodidae). J. Nat. Hist. 40, 2423–2554 (2006).Article 

    Google Scholar 
    48.Gamarra, H., Carhuapoma, P., Mujica, N., Kreuze, J. & Kroschel, J. Greenhouse whitefly, Trialeurodes vaporariorum (Westwood 1956). In Pest Distribution and Risk Atlas for Africa—Potential Global and Regional Distribution and Abundance of Agricultural and Horticultural Pests and Associated Biocontrol Agents Under Current and Future Climates (eds Kroschel, J., Mujica, N., Carhuapoma, P., & Sporleder, M.) 154–168 (International Potato Center (CIP), 2016).49.Khamis, F. M. et al. Insights in the global genetics and gut microbiome of Black Soldier Fly, Hermetia illucens: implications for animal feed safety control. Front. Microbiol. 34, 1538 (2020).Article 

    Google Scholar 
    50.Simon, C. et al. Evolution, weighting, and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved polymerase chain reaction primers. Ann. Entomol. Soc. Am. 87, 651–701 (1994).CAS 
    Article 

    Google Scholar 
    51.Frohlich, D., Torres-Jerez, I., Bedford, I. D., Markham, P. G. & Brown, J. K. A phylogeographic analysis of the Bemisia tabaci species complex based on mitochondrial DNA markers. Mol. Ecol. 8, 1593–1602 (1999).Article 

    Google Scholar 
    52.Xiong, B. & Kocher, T. D. Comparison of mitochondrial DNA sequences of seven morphospecies of black flies (Diptera: Simuliidae). Genome 34, 306–311 (1991).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    53.Kearse, M. et al. Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28, 1647–1649 (2012).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    54.Larkin, M. A. et al. Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947–2948 (2007).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    55.Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35, 1547–1549 (2018).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    56.Kimura, M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16, 111–120 (1980).ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    57.Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    58.Bernt, M. et al. MITOS: improved de novo metazoan mitochondrial genome annotation. Mol. Phylogenet. Evol. 69, 313–319 (2013).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    59.CABI. Invasive Species Compendium (CAB International). Available online at www.cabi.org/isc/datasheet/8925 (2019).60.Fick, S. E. & Hijmans, R. J. Worldclim 2: new 1-km spatial resolution climate surfaces for global land areas. Int. J. Climatol. 37, 4302–4315 (2017).Article 

    Google Scholar 
    61.Taylor, K. E., Stouffer, R. J. & Meeh, G. A. An overview of CMIP5 and the experiment design. Bull. Am. Meteorol. Soc. 93, 485–498 (2012).ADS 
    Article 

    Google Scholar 
    62.Hijmans, R. J., Cameron, S. E., Parra, J. L., Jones, P. G. & Jarvis, A. Very high-resolution interpolated climate surfaces for global land areas. Int. J. Climatol. 25, 1965–1978 (2005).Article 

    Google Scholar 
    63.Kuhn, M. et al. caret: Classification and Regression Training. R package version 6.0-71. https://CRAN.R-project.org/package=caret (2016). More

  • in

    Mucin O-glycans suppress quorum-sensing pathways and genetic transformation in Streptococcus mutans

    1.Hansson, G. C. Mucins and the microbiome. Annu. Rev. Biochem. 89, 769–793 (2020).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    2.Cross, B. W. & Ruhl, S. Glycan recognition at the saliva—oral microbiome interface. Cell. Immunol. 333, 19–33 (2018).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    3.Tabak, L. A. In defense of the oral cavity: structure, biosynthesis, and function of salivary mucins. Annu. Rev. Physiol. 57, 547–564 (1995).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    4.Deng, L. et al. Oral streptococci utilize a Siglec-like domain of serine-rich repeat adhesins to preferentially target platelet sialoglycans in human blood. PLoS Pathog. 10, e1004540 (2014).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    5.Shanker, E. & Federle, M. J. Quorum sensing regulation of competence and bacteriocins in Streptococcus pneumoniae and mutans. Genes 8, 15 (2017).PubMed Central 
    Article 
    CAS 

    Google Scholar 
    6.Nakano, K., Nomura, R. & Ooshima, T. Streptococcus mutans and cardiovascular diseases. Jpn. Dent. Sci. Rev. 44, 29–37 (2008).Article 

    Google Scholar 
    7.Murchison, H. H., Barrett, J. F., Cardineau, G. A. & Curtiss, R. Transformation of Streptococcus mutans with chromosomal and shuttle plasmid (pYA629) DNAs. Infect. Immun. 54, 273–282 (1986).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    8.Villedieu, A. et al. Prevalence of tetracycline resistance genes in oral bacteria. Antimicrob. Agents Chemother. 47, 878–882 (2003).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    9.Chansley, P. E. & Kral, T. A. Transformation of fluoride resistance genes in Streptococcus mutans. Infect. Immun. 57, 1968–1970 (1989).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    10.Hernando-Amado, S., Coque, T. M., Baquero, F. & Martínez, J. L. Defining and combating antibiotic resistance from one health and global health perspectives. Nat. Microbiol. 4, 1432–1442 (2019).CAS 
    PubMed 
    Article 

    Google Scholar 
    11.Villedieu, A. et al. Genetic basis of erythromycin resistance in oral bacteria. Antimicrob. Agents Chemother. 48, 2298–2301 (2004).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    12.Olsen, I., Tribble, G. D., Fiehn, N.-E. & Wang, B.-Y. Bacterial sex in dental plaque. J. Oral Microbiol. 5, 20736 (2013).Article 

    Google Scholar 
    13.Loesche, W. J. Role of Streptococcus mutans in human dental decay. Microbiol. Rev. 50, 353–380 (1986).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    14.Loesche, W. J., Rowan, J., Straffon, L. H. & Loos, P. J. Association of Streptococcus mutans with human dental decay. Infect. Immun. 11, 1252–1260 (1975).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    15.Mathews, S. A., Kurien, B. T. & Scofield, R. H. Oral manifestations of Sjögren’s syndrome. J. Dent. Res. 87, 308–318 (2008).CAS 
    PubMed 
    Article 

    Google Scholar 
    16.Pramanik, R., Osailan, S. M., Challacombe, S. J., Urquhart, D. & Proctor, G. B. Protein and mucin retention on oral mucosal surfaces in dry mouth patients. Eur. J. Oral. Sci. 118, 245–253 (2010).CAS 
    PubMed 
    Article 

    Google Scholar 
    17.Frenkel, E. S. & Ribbeck, K. Salivary mucins in host defense and disease prevention. J. Oral Microbiol. 7, 29759 (2015).PubMed 
    Article 
    CAS 

    Google Scholar 
    18.Ahn, S.-J., Wen, Z. T. & Burne, R. A. Multilevel control of competence development and stress tolerance in Streptococcus mutans UA159. Infect. Immun. 74, 1631–1642 (2006).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    19.Ahn, S.-J., Ahn, S.-J., Wen, Z. T., Brady, L. J. & Burne, R. A. Characteristics of biofilm formation by Streptococcus mutans in the presence of saliva. Infect. Immun. 76, 4259–4268 (2008).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    20.Duarte, S. et al. Influences of starch and sucrose on Streptococcus mutans biofilms. Oral Microbiol. Immunol. 23, 206–212 (2008).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    21.Mitchell, T. J. The pathogenesis of streptococcal infections: from tooth decay to meningitis. Nat. Rev. Microbiol. 1, 219–230 (2003).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    22.Frenkel, E. S. & Ribbeck, K. Salivary mucins protect surfaces from colonization by cariogenic bacteria. Appl. Environ. Microbiol. 81, 332–338 (2015).PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 
    23.Frenkel, E. S. & Ribbeck, K. Salivary mucins promote the coexistence of competing oral bacterial species. ISME J. 11, 1286–1290 (2017).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    24.Levine, M. Salivary proteins may be useful for determining caries susceptibility. J. Evid. Based Dent. Pract. 13, 91–93 (2013).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    25.Thomsson, K. A., Schulz, B. L., Packer, N. H. & Karlsson, N. G. MUC5B glycosylation in human saliva reflects blood group and secretor status. Glycobiology 15, 791–804 (2005).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    26.Ajdic, D. et al. Genome sequence of Streptococcus mutans UA159, a cariogenic dental pathogen. Proc. Natl Acad. Sci. USA 99, 14434–14439 (2002).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    27.Paik, S., Brown, A., Munro, C. L., Cornelissen, C. N. & Kitten, T. The sloABCR operon of Streptococcus mutans encodes an Mn and Fe transport system required for endocarditis virulence and its Mn-dependent repressor. J. Bacteriol. 185, 5967–5975 (2003).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    28.Nicolas, G. G. Detection of putative new mutacins by bioinformatic analysis using available web tools. BioData Min. 4, 22 (2011).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    29.Aframian, N. & Eldar, A. A bacterial tower of Babel: quorum-sensing signaling diversity and its evolution. Annu. Rev. Microbiol. 74, 587–606 (2020).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    30.Merritt, J., Qi, F. & Shi, W. A unique nine-gene comY operon in Streptococcus mutans. Microbiology 151, 157–166 (2005).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    31.Underhill, S. A. M. et al. Intracellular signaling by the comRS system in Streptococcus mutans genetic competence. mSphere 3, e00444-18 (2018).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    32.Dufour, D., Cordova, M., Cvitkovitch, D. G. & Lévesque, C. M. Regulation of the competence pathway as a novel role associated with a streptococcal bacteriocin. J. Bacteriol. 193, 6552–6559 (2011).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    33.Hossain, M. S. & Biswas, I. Mutacins from Streptococcus mutans UA159 are active against multiple streptococcal species. Appl. Environ. Microbiol. 77, 2428–2434 (2011).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    34.Merritt, J. & Qi, F. The mutacins of Streptococcus mutans: regulation and ecology. Mol. Oral. Microbiol 27, 57–69 (2012).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    35.Son, M., Shields, R. C., Ahn, S. J., Burne, R. A. & Hagen, S. J. Bidirectional signaling in the competence regulatory pathway of Streptococcus mutans. FEMS Microbiol. Lett. 362, fnv159 (2015).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    36.Reck, M., Tomasch, J. & Wagner-Döbler, I. The alternative sigma factor SigX controls bacteriocin synthesis and competence, the two quorum sensing regulated traits in Streptococcus mutans. PLoS Genet. 11, e1005353 (2015).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    37.Perry, J. A., Cvitkovitch, D. G. & Lévesque, C. M. Cell death in Streptococcus mutans biofilms: a link between CSP and extracellular DNA. FEMS Microbiol. Lett. 299, 261–266 (2009).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    38.Wenderska, I. B. et al. A novel function for the competence inducing peptide, XIP, as a cell death effector of Streptococcus mutans. FEMS Microbiol. Lett. 336, 104–112 (2012).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    39.Perry, D. & Kuramitsu, H. K. Genetic transformation of Streptococcus mutans. Infect. Immun. 32, 1295–1297 (1981).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    40.Desai, K., Mashburn-Warren, L., Federle, M. J. & Morrison, D. A. Development of competence for genetic transformation of Streptococcus mutans in a chemically defined medium. J. Bacteriol. 194, 3774–3780 (2012).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    41.Khan, R. et al. Extracellular identification of a processed type II ComR/ComS pheromone of Streptococcus mutans. J. Bacteriol. 194, 3781–3788 (2012).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    42.Khan, R. et al. A positive feedback loop mediated by Sigma X enhances expression of the streptococcal regulator ComR. Sci. Rep. 7, 5984 (2017).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    43.Nakano, K. et al. Streptococcus mutans clonal variation revealed by multilocus sequence typing. J. Clin. Microbiol. 45, 2616–2625 (2007).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    44.Mukherjee, S. & Bassler, B. L. Bacterial quorum sensing in complex and dynamically changing environments. Nat. Rev. Microbiol. https://doi.org/10.1038/s41579-019-0186-5 (2019).45.Visch, L. L., Gravenmade, E. J., Schaub, R. M., Van Putten, W. L. & Vissink, A. A double-blind crossover trial of CMC- and mucin-containing saliva substitutes. Int. J. Oral Max. Surg. 15, 395–400 (1986).CAS 
    Article 

    Google Scholar 
    46.Silverman, H. S. et al. In vivo glycosylation of mucin tandem repeats. Glycobiology 11, 459–471 (2001).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    47.Zalewska, A., Zwierz, K., Zółkowski, K. & Gindzieński, A. Structure and biosynthesis of human salivary mucins. Acta Biochim. Pol. 47, 1067–1079 (2000).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    48.Wheeler, K. M. et al. Mucin glycans attenuate the virulence of Pseudomonas aeruginosa in infection. Nat. Microbiol. 4, 2146–2154 (2019).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    49.Werlang, C., Cárcarmo-Oyarce, G. & Ribbeck, K. Engineering mucus to study and influence the microbiome. Nat. Rev. Mater. https://doi.org/10.1038/s41578-018-0079-7 (2019).50.Wang, B. X. et al. Mucin glycans signal through the sensor kinase RetS to inhibit virulence-associated traits in Pseudomonas aeruginosa. Curr. Biol. 31, 90–102 (2021).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    51.Huang, Y., Mechref, Y. & Novotny, M. V. Microscale nonreductive release of O-Linked glycans for subsequent analysis through MALDI mass spectrometry and capillary electrophoresis. Anal. Chem. 73, 6063–6069 (2001).CAS 
    PubMed 
    Article 

    Google Scholar 
    52.Khan, R. et al. Comprehensive transcriptome profiles of Streptococcus mutans UA159 map core streptococcal competence genes. mSystems 1, e00038 (2016).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    53.Rayment, S. A., Liu, B., Offner, G. D., Oppenheim, F. G. & Troxler, R. F. Immunoquantification of human salivary mucins MG1 and MG2 in stimulated whole saliva: factors influencing mucin levels. J. Dent. Res. 79, 1765–1772 (2000).CAS 
    PubMed 
    Article 

    Google Scholar 
    54.Son, M., Ahn, S.-J., Guo, Q., Burne, R. A. & Hagen, S. J. Microfluidic study of competence regulation in Streptococcus mutans: environmental inputs modulate bimodal and unimodal expression of comX. Mol. Microbiol. 86, 258–272 (2012).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    55.Ricomini Filho, A. P., Khan, R., Åmdal, H. A. & Petersen, F. C. Conserved pheromone production, response and degradation by Streptococcus mutans. Front. Microbiol. 10, 2140 (2019).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    56.Hagen, S. J. & Son, M. Origins of heterogeneity in Streptococcus mutans competence: interpreting an environment-sensitive signaling pathway. Phys. Biol. 14, 015001 (2017).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    57.Hillman, J. D., Mo, J., McDonell, E., Cvitkovitch, D. & Hillman, C. H. Modification of an effector strain for replacement therapy of dental caries to enable clinical safety trials. J. Appl. Microbiol. 102, 1209–1219 (2007).CAS 
    PubMed 
    Article 

    Google Scholar 
    58.Singla, D., Sharma, A., Sachdev, V. & Chopra, R. Distribution of Streptococcus mutans and Streptococcus sobrinus in dental plaque of indian pre-school children using PCR and SB-20M agar medium. J. Clin. Diagn. Res. 10, ZC60–ZC63 (2016).PubMed 
    PubMed Central 

    Google Scholar 
    59.Rodriguez, A. M. et al. Physiological and molecular characterization of genetic competence in Streptococcus sanguinis. Mol. Oral Microbiol. 26, 99–116 (2011).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    60.Darch, S. E. et al. Spatial determinants of quorum signaling in a Pseudomonas aeruginosa infection model. Proc. Natl Acad. Sci. USA 115, 4779–4784 (2018).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    61.Wu, C. et al. Regulation of ciaXRH operon expression and identification of the CiaR regulon in Streptococcus mutans. J. Bacteriol. 192, 4669–4679 (2010).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    62.Qi, F., Merritt, J., Lux, R. & Shi, W. Inactivation of the ciaH gene in Streptococcus mutans diminishes mutacin production and competence development, alters sucrose-dependent biofilm formation, and reduces stress tolerance. Infect. Immun. 72, 4895–4899 (2004).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    63.Biswas, S. & Biswas, I. Role of HtrA in surface protein expression and biofilm formation by Streptococcus mutans. Infect. Immun. 73, 6923–6934 (2005).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    64.Senadheera, M. D. et al. A VicRK signal transduction system in Streptococcus mutans affects gtfBCD, gbpB, and ftf expression, biofilm formation, and genetic competence development. J. Bacteriol. 187, 4064–4076 (2005).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    65.Domenech, A. et al. Proton motive force disruptors block bacterial competence and horizontal gene transfer. Cell Host Microbe 27, 544–555 (2020).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    66.Merritt, J., Zheng, L., Shi, W. & Qi, F. Genetic characterization of the hdrRM operon: a novel high-cell-density-responsive regulator in Streptococcus mutans. Microbiology 153, 2765–2773 (2007).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    67.Okinaga, T., Niu, G., Xie, Z., Qi, F. & Merritt, J. The hdrRM operon of Streptococcus mutans encodes a novel regulatory system for coordinated competence development and bacteriocin production. J. Bacteriol. 192, 1844–1852 (2010).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    68.Alves, L. A. et al. PepO is a target of the two-component systems VicRK and CovR required for systemic virulence of Streptococcus mutans. Virulence 11, 521–536 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    69.Underhill, S. A. M., Shields, R. C., Burne, R. A. & Hagen, S. J. Carbohydrate and PepO control bimodality in competence development by Streptococcus mutans. Mol. Microbiol. 112, 1388–1402 (2019).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    70.Kaspar, J. R., Lee, K., Richard, B., Walker, A. R. & Burne, R. A. Direct interactions with commensal streptococci modify intercellular communication behaviors of Streptococcus mutans. ISME J. https://doi.org/10.1038/s41396-020-00789-7 (2020).71.Idone, V. et al. Effect of an orphan response regulator on Streptococcus mutans sucrose-dependent adherence and cariogenesis. Infect. Immun. 71, 4351–4360 (2003).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    72.Nagasawa, R., Sato, T. & Senpuku, H. Raffinose induces biofilm formation by Streptococcus mutans in low concentrations of sucrose by increasing production of extracellular DNA and fructan. Appl. Environ. Microbiol. 83, e00869 (2017).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    73.Suzuki, Y., Nagasawa, R. & Senpuku, H. Inhibiting effects of fructanase on competence-stimulating peptide-dependent quorum sensing system in Streptococcus mutans. J. Infect. Chemother. 23, 634–641 (2017).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    74.Yoshida, A., Ansai, T., Takehara, T. & Kuramitsu, H. K. LuxS-based signaling affects Streptococcus mutans biofilm formation. Appl. Environ. Microbiol. 71, 2372–2380 (2005).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    75.Son, M., Ghoreishi, D., Ahn, S.-J., Burne, R. A. & Hagen, S. J. Sharply tuned pH response of genetic competence regulation in Streptococcus mutans: a microfluidic study of the environmental sensitivity of comX. Appl. Environ. Microbiol. 81, 5622–5631 (2015).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    76.Nielsen, S. S. in Food Analysis Laboratory Manual 137–141 (Springer, 2017).77.Aoki, K. et al. The diversity of O-linked glycans expressed during Drosophila melanogaster development reflects stage- and tissue-specific requirements for cell signaling. J. Biol. Chem. 283, 30385–30400 (2008).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    78.Kumagai, T., Katoh, T., Nix, D. B., Tiemeyer, M. & Aoki, K. In-gel β-elimination and aqueous-organic partition for improved O- and sulfoglycomics. Anal. Chem. 85, 8692–8699 (2013).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    79.Anumula, K. R. & Taylor, P. B. A comprehensive procedure for preparation of partially methylated alditol acetates from glycoprotein carbohydrates. Anal. Biochem. 203, 101–108 (1992).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    80.Liu, Y. et al. The minimum information required for a glycomics experiment (MIRAGE) project: improving the standards for reporting glycan microarray-based data. Glycobiology 27, 280–284 (2017).CAS 
    PubMed 

    Google Scholar 
    81.Clark, K., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J. & Sayers, E. W. GenBank. Nucleic Acids Res. 44, D67–D72 (2016).CAS 
    PubMed 
    Article 

    Google Scholar 
    82.O’Leary, N. A. et al. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res. 44, D733–D745 (2016).Article 
    CAS 

    Google Scholar 
    83.Afgan, E. et al. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Res. 46, W537–W544 (2018).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    84.Huber, W. et al. Orchestrating high-throughput genomic analysis with Bioconductor. Nat. Methods 12, 115–121 (2015).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    85.Anders, S. & Huber, W. Differential expression analysis for sequence count data. Genome Biol. 11, R106 (2010).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    86.Kanehisa, M., Sato, Y., Kawashima, M., Furumichi, M. & Tanabe, M. KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res. 44, D457–D462 (2016).CAS 
    Article 

    Google Scholar 
    87.Thissen, D., Steinberg, L. & Kuang, D. Quick and easy implementation of the Benjamini–Hochberg procedure for controlling the false positive rate in multiple comparisons. J. Educ. Behav. Stat. 27, 77–83 (2002).Article 

    Google Scholar 
    88.Aymanns, S., Mauerer, S., Zandbergen, G., Wolz, C. & Spellerberg, B. High-level fluorescence labeling of Gram-positive pathogens. PLoS ONE 6, e19822 (2011).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    89.Takehara, S., Yanagishita, M., Podyma-Inoue, K. A. & Kawaguchi, Y. Degradation of MUC7 and MUC5B in human saliva. PLoS ONE 8, e69059 (2013).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar  More

  • in

    Author Correction: Short-range interactions govern the dynamics and functions of microbial communities

    AffiliationsDepartment of Environmental Systems Science, ETH Zurich, Zurich, SwitzerlandAlma Dal Co, Simon van Vliet, Daniel Johannes Kiviet, Susan Schlegel & Martin AckermannDepartment of Environmental Microbiology, Eawag, Duebendorf, SwitzerlandAlma Dal Co, Simon van Vliet, Daniel Johannes Kiviet, Susan Schlegel & Martin AckermannDepartment of Zoology, University of British Columbia, British Columbia, Vancouver, CanadaSimon van VlietAuthorsAlma Dal CoSimon van VlietDaniel Johannes KivietSusan SchlegelMartin AckermannCorresponding authorCorrespondence to
    Alma Dal Co. More

  • in

    Fish associations with shallow water subsea pipelines compared to surrounding reef and soft sediment habitats

    1.Parente, V., Ferreira, D., Moutinho dos Santos, E. & Luczynski, E. Offshore decommissioning issues: deductibility and transferability. Energy Policy 34, 1992–2001 (2006).Article 

    Google Scholar 
    2.Macreadie, P. I., Fowler, A. M. & Booth, D. J. Rigs-to-reefs: will the deep sea benefit from artificial habitat?. Front. Ecol. Environ. 9, 455–461 (2011).Article 

    Google Scholar 
    3.Fowler, A. M., Macreadie, P. I., Jones, D. O. B. & Booth, D. J. A multi-criteria decision approach to decommissioning of offshore oil and gas infrastructure. Ocean Coast. Manag. 87, 20–29 (2014).Article 

    Google Scholar 
    4.Hamzah, B. A. International rules on decommissioning of offshore installations: some observations. Mar. Policy 27, 339–348 (2003).Article 

    Google Scholar 
    5.Chandler, J., White, D., Techera, E. J., Gourvenec, S. & Draper, S. Engineering and legal considerations for decommissioning of offshore oil and gas infrastructure in Australia. Ocean Eng. 131, 338–347 (2017).Article 

    Google Scholar 
    6.Claisse, J. T. et al. Oil platforms off California are among the most productive marine fish habitats globally. Proc. Natl. Acad. Sci. U. S. A. 111, 15462–15467 (2014).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    7.Fowler, A. M. & Booth, D. J. Evidence of sustained populations of a small reef fish on artificial structures. Does depth affect production on artificial reefs?. J. Fish Biol. 80, 613–629 (2012).CAS 
    PubMed 
    Article 

    Google Scholar 
    8.Gallaway, B. J., Szedlmayer, S. T. & Gazey, W. J. A life history review for red snapper in the Gulf of Mexico with an evaluation of the importance of offshore petroleum platforms and other artificial reefs. Rev. Fish. Sci. 17, 48–67 (2009).Article 

    Google Scholar 
    9.Love, M. S. et al. Potential use of offshore marine structures in rebuilding an overfished rockfish species, bocaccio (Sebastes paucispinis). Fish. Bull. 104, 383–390 (2006).
    Google Scholar 
    10.Friedlander, A. M., Ballesteros, E., Fay, M. & Sala, E. Marine communities on oil platforms in Gabon, West Africa: high biodiversity oases in a low biodiversity environment. PLoS ONE 9, e103709 (2014).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    11.McLean, D. L., Taylor, M. D., Giraldo Ospina, A. & Partridge, J. C. An assessment of fish and marine growth associated with an oil and gas platform jacket using an augmented remotely operated vehicle. Cont. Shelf Res. 179, 66–84 (2019).ADS 
    Article 

    Google Scholar 
    12.Schramm, K. D. et al. A comparison of stereo-BRUVs and stereo-ROV techniques for sampling shallow water fish communities on and off pipelines. Mar. Environ. Res. 162, 105198 (2020).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    13.Schroeder, D. M. & Love, M. S. Ecological and political issues surrounding decommissioning of offshore oil facilities in the Southern California Bight. Ocean Coast. Manag. 47, 21–48 (2004).Article 

    Google Scholar 
    14.Bull, A. S. & Love, M. S. Worldwide oil and gas platform decommissioning: a review of practices and reefing options. Ocean Coast. Manag. 168, 274–306 (2019).Article 

    Google Scholar 
    15.Department of Industry, Science, Energy and Resources. Offshore Petroleum Decommissioning Guideline 4 (Department of Industry, Science, Energy and Resources, 2018).
    Google Scholar 
    16.Bell, N. & Smith, J. Coral growing on North Sea oil rigs. Nature 402, 601–601 (1999).ADS 
    CAS 
    Article 

    Google Scholar 
    17.APPEA. Scientific Literature Review. Environmental Impacts of Decommissioning Options (APPEA, 2017).
    Google Scholar 
    18.Stolk, P., Markwell, K. & Jenkins, J. M. Artificial reefs as recreational scuba diving resources: a critical review of research. J. Sustain. Tour. 15, 331–350 (2007).Article 

    Google Scholar 
    19.Scarborough-Bull, A., Love, M. S. & Schroeder, D. M. Artificial reefs as fishery conservation tools: contrasting the roles of offshore structures between the Gulf of Mexico and the Southern California Bight. Am. Fish. Soc. Symp. 49, 899–915 (2008).
    Google Scholar 
    20.Moore, C. H. et al. Improving spatial prioritisation for remote marine regions: optimising biodiversity conservation and sustainable development trade-offs. Sci. Rep. 6, 32029 (2016).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    21.Cripps, S. J. & Aabel, J. P. Environmental and socio-economic impact assessment of Ekoreef, a multiple platform rigs-to-reefs development. ICES J. Mar. Sci. 59, 300–308 (2002).Article 

    Google Scholar 
    22.Matthews, K. R. Species similarity and movement of fishes on natural and artificial reefs in Monterey bay, California. Bull. Mar. Sci. 37, 252–270 (1985).ADS 

    Google Scholar 
    23.Grossman, G. D., Jones, G. P. & Seaman, W. J. Jr. Do artificial reefs increase regional fish production? A review of existing data. Fisheries 22, 17–23 (1997).Article 

    Google Scholar 
    24.Bohnsack, J. A. Are high densities of fishes at artificial reefs the result of habitat limitation or behavioral preference?. Bull. Mar. Sci. 44, 631–645 (1989).
    Google Scholar 
    25.Page, H. M., Dugan, J. E., Culver, C. S. & Hoesterey, J. C. Exotic invertebrate species on offshore oil platforms. Mar. Ecol. Prog. Ser. 325, 101–107 (2006).ADS 
    Article 

    Google Scholar 
    26.Pajuelo, J. G. et al. Introduction of non-native marine fish species to the Canary Islands waters through oil platforms as vectors. J. Mar. Syst. 163, 23–30 (2016).Article 

    Google Scholar 
    27.van Elden, S., Meeuwig, J. J., Hobbs, R. J. & Hemmi, J. M. Offshore oil and gas platforms as novel ecosystems: a global perspective. Front. Mar. Sci. 6, 548 (2019).Article 

    Google Scholar 
    28.Rouse, S., Hayes, P. & Wilding, T. A. Commercial fisheries losses arising from interactions with offshore pipelines and other oil and gas infrastructure and activities. ICES J. Mar. Sci. 77, 1148–1156 (2020).Article 

    Google Scholar 
    29.Bond, T. et al. Fish associated with a subsea pipeline and adjacent seafloor of the North West Shelf of Western Australia. Mar. Environ. Res. 141, 53–65 (2018).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    30.Bond, T., Partridge, J. C., Taylor, M. D., Cooper, T. F. & McLean, D. L. The influence of depth and a subsea pipeline on fish assemblages and commercially fished species. PLoS ONE 13, e0207703 (2018).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    31.Bond, T. et al. Diel shifts and habitat associations of fish assemblages on a subsea pipeline. Fish. Res. 206, 220–234 (2018).Article 

    Google Scholar 
    32.McLean, D. L. et al. Using industry ROV videos to assess fish associations with subsea pipelines. Cont. Shelf Res. 141, 76–97 (2017).ADS 
    Article 

    Google Scholar 
    33.McLean, D. L., Vaughan, B. I., Malseed, B. E. & Taylor, M. D. Fish-habitat associations on a subsea pipeline within an Australian Marine Park. Mar. Environ. Res. 153, 104813 (2020).CAS 
    Article 

    Google Scholar 
    34.Love, M. S. & York, A. A comparison of the fish assemblages associated with an oil/gas pipeline and adjacent seafloor in the Santa Barbara Channel, Southern California Bight. Bull. Mar. Sci. 77, 101–118 (2005).ADS 

    Google Scholar 
    35.Arnould, J. P. Y. et al. Use of anthropogenic sea floor structures by Australian fur seals: potential positive ecological impacts of marine industrial development?. PLoS ONE 10, e0130581 (2015).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    36.DMP. Maps and Geospatial Information (Government of Western Australia, Department of Mine, Industry Regulation and Safety, 2020).
    Google Scholar 
    37.McLean, D. L. et al. Distribution, abundance, diversity and habitat associations of fishes across a bioregion experiencing rapid coastal development. Estuar. Coast. Shelf Sci. 178, 36–47 (2016).ADS 
    Article 

    Google Scholar 
    38.Travers, M. J., Clarke, K. R., Newman, S. J., Hall, N. G. & Potter, I. C. To what extents are species richness and abundance of reef fishes along a tropical coast related to latitude and other factors?. Cont. Shelf Res. 167, 99–110 (2018).ADS 
    Article 

    Google Scholar 
    39.Travers, M. J., Newman, S. J. & Potter, I. C. Influence of latitude, water depth, day v. night and wet v. dry periods on the species composition of reef fish communities in tropical Western Australia. J. Fish Biol. 69, 987–1017 (2006).Article 

    Google Scholar 
    40.Travers, M. J., Potter, I. C., Clarke, K. R. & Newman, S. J. Relationships between latitude and environmental conditions and the species richness, abundance and composition of tropical fish assemblages over soft substrata. Mar. Ecol. Prog. Ser. 446, 221–241 (2012).ADS 
    Article 

    Google Scholar 
    41.Chevron. Wheatstone Project: Dredging and Dredge Spoil Placement Environmental Monitoring and Management Plan 234 (Chevron Australia Pty Ltd., 2016).
    Google Scholar 
    42.Gaughan, D. J. et al. (eds) Status Reports of the Fisheries and Aquatic Resources of Western Australia 2017/18: The State of the Fisheries (Department of Primary Industries and Regional Development, 2019).
    Google Scholar 
    43.Ryan, K. L. et al. Statewide Survey of Boat-Based Recreational Fishing in Western Australia 2017/18. Fisheries Research Report No. 297, Department of Primary Industries and Regional Development (2019).44.Harvey, E. S., Goetze, J., McLaren, B., Langlois, T. & Shortis, M. R. Influence of range, angle of view, image resolution and image compression on underwater stereo-video measurements: high-definition and broadcast-resolution video cameras compared. Mar. Technol. Soc. J. 44, 75–85 (2010).Article 

    Google Scholar 
    45.Goetze, J. S. et al. A field and video analysis guide for diver operated stereo-video. Methods Ecol. Evol. 10, 1083–1090 (2019).Article 

    Google Scholar 
    46.Myers, E. M. V., Harvey, E. S., Saunders, B. J. & Travers, M. J. Fine-scale patterns in the day, night and crepuscular composition of a temperate reef fish assemblage. Mar. Ecol. 37, 668–678 (2016).ADS 
    Article 

    Google Scholar 
    47.Sward, D., Monk, J. & Barrett, N. A systematic review of remotely operated vehicle surveys for visually assessing fish assemblages. Front. Mar. Sci. 6, 134 (2019).Article 

    Google Scholar 
    48.Gregoire, T. G. & Valentine, H. T. Sampling Strategies for Natural Resources and the Environment (CRC Press, 2007).
    Google Scholar 
    49.Harvey, E. S. & Shortis, M. R. Calibration stability of an underwater stereo-video system: implications for measurement accuracy and precision. Mar. Technol. Soc. J. 32, 3–17 (1998).
    Google Scholar 
    50.Shortis, M. R. & Harvey, E. S. Design and calibration of an underwater stereo-video system for the monitoring of marine fauna populations. Int. Arch. Photogramm. Remote Sens. 32, 792–799 (1998).
    Google Scholar 
    51.Shortis, M., Harvey, E. & Abdo, D. A review of underwater stereo-image measurement for marine biology and ecology applications. In Oceanography and Marine Biology Vol. 47 (eds Gibson, R. et al.) 257–292 (Taylor & Francis, 2009).
    Google Scholar 
    52.Boutros, N., Shortis, M. R. & Harvey, E. S. A comparison of calibration methods and system configurations of underwater stereo-video systems for applications in marine ecology. Limnol. Oceanogr. Methods 13, 224–236 (2015).Article 

    Google Scholar 
    53.Taylor, R. B. & Willis, T. J. Relationships amongst length, weight and growth of north-eastern New Zealand reef fishes. Mar. Freshw. Res. 49, 255–260 (1998).Article 

    Google Scholar 
    54.Froese, R. & Pauly, D. FishBase. www.fishbase.org, Accessed Sept 2019 (2019).55.Bach, L. L., Saunders, B. J., Newman, S. J., Holmes, T. H. & Harvey, E. S. Cross and long-shore variations in reef fish assemblage structure and implications for biodiversity management. Estuar. Coast. Shelf Sci. 218, 246–257 (2019).ADS 
    Article 

    Google Scholar 
    56.Anderson, M., Gorley, R. & Clarke, K. P. PERMANOVA+ for PRIMER: Guide to Software and Statistical Methods 1st edn. (PRIMER-E, 2008).
    Google Scholar 
    57.Anderson, M. J. A new method for non-parametric multivariate analysis of variance. Austral. Ecol. 26, 32–46 (2001).
    Google Scholar 
    58.Anderson, M. J. Distance-based tests for homogeneity of multivariate dispersions. Biometrics 62, 245–253 (2006).MathSciNet 
    PubMed 
    MATH 
    Article 
    PubMed Central 

    Google Scholar 
    59.Harvey, E. S., Cappo, M., Butler, J. J., Hall, N. & Kendrick, G. A. Bait attraction affects the performance of remote underwater video stations in assessment of demersal fish community structure. Mar. Ecol. Prog. Ser. 350, 245–254 (2007).ADS 
    Article 

    Google Scholar 
    60.Watson, D. L., Harvey, E. S., Anderson, M. J. & Kendrick, G. A. A comparison of temperate reef fish assemblages recorded by three underwater stereo-video techniques. Mar. Biol. 148, 415–425 (2005).Article 

    Google Scholar 
    61.Langlois, T. J. et al. Cost-efficient sampling of fish assemblages: comparison of baited video stations and diver video transects. Aquat. Biol. 9, 155–168 (2010).Article 

    Google Scholar 
    62.Simon, T., Pinheiro, H. T. & Joyeux, J.-C. Target fishes on artificial reefs: evidences of impacts over nearby natural environments. Sci. Total Environ. 409, 4579–4584 (2011).ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    63.Simon, T., Joyeux, J.-C. & Pinheiro, H. T. Fish assemblages on shipwrecks and natural rocky reefs strongly differ in trophic structure. Mar. Environ. Res. 90, 55–65 (2013).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    64.Wulff, J. L. Ecological interactions of marine sponges. Can. J. Zool. 84, 146–166 (2006).Article 

    Google Scholar 
    65.Bohnsack, J. A. & Sutherland, D. L. Artificial reef research: a review with recommendations for future priorities. Bull. Mar. Sci. 37, 11–39 (1985).
    Google Scholar 
    66.Harvey, E. S., Butler, J. J., McLean, D. L. & Shand, J. Contrasting habitat use of diurnal and nocturnal fish assemblages in temperate Western Australia. J. Exp. Mar. Biol. Ecol. 426–427, 78–86 (2012).Article 

    Google Scholar 
    67.Newman, S. J. & Williams, D. M. Mesh size selection and diel variability in catch of fish traps on the central Great Barrier Reef, Australia: a preliminary investigation. Fish. Res. 23, 237–253 (1995).Article 

    Google Scholar 
    68.Nagelkerken, I., Dorenbosch, M., Verberk, W. & van der Cocheret de la Morinière Velde, E. G. Day-night shifts of fishes between shallow-water biotopes of a Caribbean bay, with emphasis on the nocturnal feeding of Haemulidae and Lutjanidae. Mar. Ecol. Prog. Ser. 194, 55–64 (2000).ADS 
    Article 

    Google Scholar 
    69.Currey, L. M., Heupel, M. R., Simpfendorfer, C. A. & Williams, A. J. Assessing fine-scale diel movement patterns of an exploited coral reef fish. Anim. Biotelem. 3, 41 (2015).Article 

    Google Scholar 
    70.Newman, S. J. & Williams, D. M. Spatial and temporal variation in assemblages of Lutjanidae, Lethrinidae and associated fish species among mid-continental shelf reefs in the central Great Barrier Reef. Mar. Freshw. Res. 52, 843–851 (2001).Article 

    Google Scholar 
    71.Layman, C. A., Allgeier, J. E., Yeager, L. A. & Stoner, E. W. Thresholds of ecosystem response to nutrient enrichment from fish aggregations. Ecology 94, 530–536 (2013).PubMed 
    Article 

    Google Scholar 
    72.Shantz, A. A., Ladd, M. C., Schrack, E. & Burkepile, D. E. Fish-derived nutrient hotspots shape coral reef benthic communities. Ecol. Appl. 25, 2142–2152 (2015).PubMed 
    Article 

    Google Scholar 
    73.Marnane, M. J. & Bellwood, D. R. Diet and nocturnal foraging in cardinalfishes (Apogonidae) at One Tree Reef, Great Barrier Reef, Australia. Mar. Ecol. Prog. Ser. 231, 261–268 (2002).ADS 
    Article 

    Google Scholar 
    74.Wen, C. K. C., Pratchett, M. S., Almany, G. R. & Jones, G. P. Patterns of recruitment and microhabitat associations for three predatory coral reef fishes on the southern Great Barrier Reef, Australia. Coral Reefs 32, 389–398 (2013).ADS 
    Article 

    Google Scholar 
    75.Friedlander, A. M. & Parrish, J. D. Habitat characteristics affecting fish assemblages on a Hawaiian coral reef. J. Exp. Mar. Biol. Ecol. 224, 1–30 (1998).Article 

    Google Scholar 
    76.Pradella, N., Fowler, A. M., Booth, D. J. & Macreadie, P. I. Fish assemblages associated with oil industry structures on the continental shelf of north-western Australia. J. Fish Biol. 84, 247–255 (2014).CAS 
    PubMed 
    Article 

    Google Scholar 
    77.McLean, D. L. et al. Fish and habitats on wellhead infrastructure on the north west shelf of Western Australia. Cont. Shelf Res. 164, 10–27 (2018).ADS 
    Article 

    Google Scholar 
    78.Frisch, A. J. Are juvenile coral-trouts (Plectropomus) mimics of poisonous pufferfishes (Canthigaster) on coral reefs?. Mar. Ecol. 27, 247–252 (2006).ADS 
    Article 

    Google Scholar 
    79.Wen, C. K. C., Pratchett, M. S., Almany, G. R. & Jones, G. P. Role of prey availability in microhabitat preferences of juvenile coral trout (Plectropomus: Serranidae). J. Exp. Mar. Biol. Ecol. 443, 39–45 (2013).Article 

    Google Scholar 
    80.Kerry, J. T. & Bellwood, D. R. The effect of coral morphology on shelter selection by coral reef fishes. Coral Reefs 31, 415–424 (2012).ADS 
    Article 

    Google Scholar 
    81.Lindfield, S. J., Harvey, E. S., McIlwain, J. L. & Halford, A. R. Silent fish surveys: bubble-free diving highlights inaccuracies associated with SCUBA-based surveys in heavily fished areas. Methods Ecol. Evol. 5, 1061–1069 (2014).Article 

    Google Scholar 
    82.Kulbicki, M. How the acquired behaviour of commercial reef fishes may influence the results obtained from visual censuses. J. Exp. Mar. Biol. Ecol. 222, 11–30 (1998).Article 

    Google Scholar 
    83.Gray, A. E. et al. Comparison of reef fish survey data gathered by open and closed circuit SCUBA divers reveals differences in areas with higher fishing pressure. PLoS ONE 11, e0167724 (2016).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    84.Guidetti, P., Vierucci, E. & Bussotti, S. Differences in escape response of fish in protected and fished Mediterranean rocky reefs. J. Mar. Biol. Assoc. U. K. 88, 625–627 (2008).Article 

    Google Scholar 
    85.Laidig, T. E., Krigsman, L. M. & Yoklavich, M. M. Reactions of fishes to two underwater survey tools, a manned submersible and a remotely operated vehicle. Fish. Bull. 111, 54–67 (2013).
    Google Scholar 
    86.Sutton, S. G. & Bushnell, S. L. Socio-economic aspects of artificial reefs: considerations for the Great Barrier Reef Marine Park. Ocean Coast. Manag. 50, 829–846 (2007).Article 

    Google Scholar 
    87.Florisson, J. H. et al. King Reef: an Australian first in repurposing oil and gas infrastructure to benefit regional communities. APPEA J. 60, 435–439 (2020).Article 

    Google Scholar 
    88.Rouse, S., Kafas, A., Catarino, R. & Peter, H. Commercial fisheries interactions with oil and gas pipelines in the North Sea: considerations for decommissioning. ICES J. Mar. Sci. 75, 279–286 (2018).Article 

    Google Scholar 
    89.Gratwicke, B. & Speight, M. R. The relationship between fish species richness, abundance and habitat complexity in a range of shallow tropical marine habitats. J. Fish Biol. 66, 650–667 (2005).Article 

    Google Scholar 
    90.Charbonnel, E., Serre, C., Ruitton, S., Harmelin, J.-G. & Jensen, A. Effects of increased habitat complexity on fish assemblages associated with large artificial reef units (French Mediterranean coast). ICES J. Mar. Sci. 59, 208–213 (2002).Article 

    Google Scholar 
    91.Perkol-Finkel, S., Shashar, N. & Benayahu, Y. Can artificial reefs mimic natural reef communities? The roles of structural features and age. Mar. Environ. Res. 61, 121–135 (2006).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    92.Burt, J., Bartholomew, A., Usseglio, P., Bauman, A. & Sale, P. F. Are artificial reefs surrogates of natural habitats for corals and fish in Dubai, United Arab Emirates?. Coral Reefs 28, 663–675 (2009).ADS 
    Article 

    Google Scholar 
    93.Folpp, H., Lowry, M., Gregson, M. & Suthers, I. M. Fish assemblages on estuarine artificial reefs: natural rocky-reef mimics or discrete assemblages?. PLoS ONE 8, e63505 (2014).ADS 
    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar  More

  • in

    Nitrogen has a greater influence than phosphorus on the diazotrophic community in two successive crop seasons in Northeast China

    1.Berthrong, S. T. et al. Nitrogen fertilization has a stronger effect on soil nitrogen-fixing bacterial communities than elevated atmospheric CO2. Appl. Environ. Microb. 80, 3103–3112. https://doi.org/10.1128/AEM.04034-13 (2014).CAS 
    Article 

    Google Scholar 
    2.Millar, N., Robertson, G. P., Grace, P. R., Gehl, R. J. & Hoben, J. P. Nitrogen fertilizer management for nitrous oxide (N2O) mitigation in intensive corn (Maize) production: An emissions reduction protocol for US Midwest agriculture. Mitig. Adapt. Strat. Gl. 15, 185–204. https://doi.org/10.1007/s11027-010-9212-7 (2010).Article 

    Google Scholar 
    3.Zhou, J. et al. Influence of 34-years of fertilization on bacterial communities in an intensively cultivated black soil in northeast China. Soil Biol. Biochem. 90, 42–51. https://doi.org/10.1016/j.soilbio.2015.07.005 (2015).CAS 
    Article 

    Google Scholar 
    4.Ding, J. et al. Influence of inorganic fertilizer and organic manure application on fungal communities in a long-term field experiment of Chinese Mollisols. Appl. Soil Ecol. 111, 114–122. https://doi.org/10.1016/j.apsoil.2016.12.003 (2017).ADS 
    Article 

    Google Scholar 
    5.Zhou, J. et al. Thirty four years of nitrogen fertilization decreases fungal diversity and alters fungal community composition in black soil in northeast China. Soil Biol. Biochem. 95, 135–143. https://doi.org/10.1016/j.soilbio.2015.12.012 (2016).CAS 
    Article 

    Google Scholar 
    6.Liu, J. et al. Diversity and distribution patterns of acidobacterial communities in the black soil zone of northeast China. Soil Biol. Biochem. 95, 212–222. https://doi.org/10.1016/j.soilbio.2015.12.021 (2016).CAS 
    Article 

    Google Scholar 
    7.Pan, H. et al. Organic and inorganic fertilizers respectively drive bacterial and fungal community compositions in a fluvo-aquic soil in northern China. Soil Till. Res. 198, 104540. https://doi.org/10.1016/j.still.2019.104540 (2020).Article 

    Google Scholar 
    8.Ma, M. et al. Chronic fertilization of 37 years alters the phylogenetic structure of soil arbuscular mycorrhizal fungi in Chinese Mollisols. AMB Express 8, 57. https://doi.org/10.1186/s13568-018-0587-2 (2018).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    9.Hu, X. et al. Long-term manure addition reduces diversity and changes community structure of diazotrophs in a neutral black soil of northeast China. J. Soils Sediments 18, 2053–2062. https://doi.org/10.1007/s11368-018-1975-6 (2018).CAS 
    Article 

    Google Scholar 
    10.Liu, J. et al. Ammonia-oxidizing archaea show more distinct biogeographic distribution patterns than ammonia-oxidizing bacteria across the black soil zone of northeast China. Front. Microbial. 9, 171. https://doi.org/10.3389/fmicb.2019.00023 (2018).Article 

    Google Scholar 
    11.Fan, K., Delgado-Baquerizo, M., Guo, X., Wang, D. & Chu, H. Suppressed N fixation and diazotrophs after four decades of fertilization. Microbiome 7, 143. https://doi.org/10.1186/s40168-019-0757-8 (2019).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    12.Kumar, U. et al. Long-term aromatic rice cultivation effect on frequency and diversity of diazotrophs in its rhizosphere. Ecol. Eng. 101, 227–236. https://doi.org/10.1016/j.ecoleng.2017.02.010 (2017).Article 

    Google Scholar 
    13.Gaby, J. C., Rishishwar, L., Valderrama-Aguirre, L. C., Green, S. J. & Kostka, J. E. Diazotroph community characterization via a high-throughput nifH amplicon sequencing and analysis pipeline. Appl. Environ. Microbiol. 84, 01512–01517. https://doi.org/10.1128/AEM.01512-17 (2018).Article 

    Google Scholar 
    14.Wang, J. et al. Temporal variation of diazotrophic community abundance and structure in surface and subsoil under four fertilization regimes during a wheat growing season. Agric. Ecosyst. Environ. 216, 116–124. https://doi.org/10.1016/j.agee.2015.09.039 (2016).CAS 
    Article 

    Google Scholar 
    15.Van Kessel, C. & Hartley, C. Agricultural management of grain legumes: Has it led to an increase in nitrogen fixation?. Field Crops Res. 65, 165–181. https://doi.org/10.1016/S0378-4290(99)00085-4 (2000).Article 

    Google Scholar 
    16.Wang, C. et al. Impact of 25 years of inorganic fertilization on diazotrophic abundance and community structure in an acidic soil in southern China. Soil Biol. Biochem. 113, 240–249. https://doi.org/10.1016/j.soilbio.2017.06.019 (2017).CAS 
    Article 

    Google Scholar 
    17.Feng, M. et al. Long-term fertilization influences community assembly processes of soil diazotrophs. Soil Biol. Biochem. 126, 151–158. https://doi.org/10.1016/j.soilbio.2018.08.021 (2018).CAS 
    Article 

    Google Scholar 
    18.Fan, L. Response of diazotrophic microbial community to nitrogen input and glyphosate application in soils cropped to soybean. (2013).19.Cheng, F. et al. Isolation and application of effective nitrogen fixation rhizobial strains on low-phosphorus acid soils in South China. Chin. Sci. Bull. 54, 412–420. https://doi.org/10.1007/s11434-008-0521-0 (2009).CAS 
    Article 

    Google Scholar 
    20.Qiao, Y. et al. The effect of fertilizer practices on N balance and global warming potential of maize–soybean–wheat rotations in Northeastern China. Field Crops Res. 161, 98–106. https://doi.org/10.1016/j.fcr.2014.03.005 (2014).Article 

    Google Scholar 
    21.Hsu, S. F. & Buckley, D. H. Evidence for the functional significance of diazotroph community structure in soil. ISME J. 3, 124–136. https://doi.org/10.1038/ismej.2008.82 (2009).CAS 
    Article 
    PubMed 

    Google Scholar 
    22.Chen, J., Shen, W., Xu, H., Li, Y. & Luo, T. The composition of nitrogen-fixing microorganisms correlates with soil nitrogen content during reforestation: A comparison between legume and non-legume plantations. Front. Microbiol. 10, 508. https://doi.org/10.3389/fmicb.2019.00508 (2019).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    23.Saleem, M., Law, A. D., Sahib, M. R., Pervaiz, Z. H. & Zhang, Q. Impact of root system architecture on rhizosphere and root microbiome. Rhizosphere 6, 47–51. https://doi.org/10.1016/j.rhisph.2018.02.003 (2018).Article 

    Google Scholar 
    24.Zhang, X. et al. Response of the abundance of key soil microbial nitrogen-cycling genes to multi-factorial global changes. PLoS ONE 8, e76500. https://doi.org/10.1371/journal.pone.0076500 (2013).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    25.Coelho, M. et al. Molecular detection and quantification of nifH gene sequences in the rhizosphere of sorghum (Sorghum bicolor) sown with two levels of nitrogen fertilizer. Appl. Soil Ecol. 42, 48–53. https://doi.org/10.1016/j.apsoil.2009.01.010 (2009).Article 

    Google Scholar 
    26.Wakelin, S. A. et al. The effects of stubble retention and nitrogen application on soil microbial community structure and functional gene abundance under irrigated maize. Fems Microbiol. Ecol. 59, 661–670. https://doi.org/10.1111/j.1574-6941.2006.00235.x (2006).CAS 
    Article 
    PubMed 

    Google Scholar 
    27.Shirani, H., Hajabbasi, M. A., Afyuni, M. & Hemmat, A. Effects of farmyard manure and tillage systems on soil physical properties and corn yield in central Iran. Soil Till. Res. 68, 101–108. https://doi.org/10.1016/S0167-1987(02)00110-1 (2002).Article 

    Google Scholar 
    28.Sheffer, E., Batterman, S. A., Levin, S. A. & Hedin, L. O. Biome-scale nitrogen fixation strategies selected by climatic constraints on nitrogen cycle. Nat. Plants 1, 15182. https://doi.org/10.1038/nplants.2015.182 (2015).CAS 
    Article 
    PubMed 

    Google Scholar 
    29.Guo, J. H. et al. Significant acidification in major Chinese croplands. Science 327, 1008–1010. https://doi.org/10.1126/science.1182570 (2010).ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 
    30.Ding, J. et al. Effect of 35 years inorganic fertilizer and manure amendment on structure of bacterial and archaeal communities in black soil of northeast China. Appl. Soil Ecol. 105, 187–195. https://doi.org/10.1016/j.apsoil.2016.04.010 (2016).Article 

    Google Scholar 
    31.Soman, C., Keymer, D. P. & Kent, A. D. Edaphic correlates of feedstock-associated diazotroph communities. GCB Bioenergy 10, 343–352. https://doi.org/10.1111/gcbb.12502 (2018).CAS 
    Article 

    Google Scholar 
    32.He, D. et al. Evolvement of structure and abundance of soil nitrogen-fixing bacterial community in Phyllostachys edulis plantations with age of time. Acta Pedol. Sin. 52, 934–942. https://doi.org/10.11766/trxb201408070397 (2015).Article 

    Google Scholar 
    33.Ning, Q. et al. Effects of nitrogen deposition rates and frequencies on the abundance of soil nitrogen-related functional genes in temperate grassland of northern China. J. Soils Sediments 15, 694–704. https://doi.org/10.1007/s11368-015-1061-2 (2015).CAS 
    Article 

    Google Scholar 
    34.Huang, J. et al. Responses of soil nitrogen fixation to Spartina alterniflora invasion and nitrogen addition in a Chinese salt marsh. Sci. Rep. 6, 20384. https://doi.org/10.1038/srep20384 (2016).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    35.Zhu, C. et al. N-fertilizer-driven association between the arbuscular mycorrhizal fungal community and diazotrophic community impacts wheat yield. Agric. Ecosyst. Environ. 254, 191–201. https://doi.org/10.1016/j.agee.2017.11.029 (2018).Article 

    Google Scholar 
    36.Coelho, M. et al. Diversity of nifH gene pools in the rhizosphere of two cultivars of sorghum (Sorghum bicolor) treated with contrasting levels of nitrogen fertilizer. FEMS Microbiol. Lett. 111, 114–122. https://doi.org/10.1111/j.1574-6968.2007.00975.x (2007).CAS 
    Article 

    Google Scholar 
    37.Velagaleti, R. R. & Marsh, S. Influence of host cultivars and Bradyrhizobium strains on the growth and symbiotic performance of soybean under salt stress. Plant Soil 119, 133–138. https://doi.org/10.1007/BF02370277 (1989).Article 

    Google Scholar 
    38.Appunu, C. & Dhar, B. Symbiotic effectiveness of acid-tolerant Bradyrhizobium strains with soybean in low pH soil. Afr. J. Biotechnol. https://doi.org/10.5897/AJB06.131 (2006).Article 

    Google Scholar 
    39.Kunert, K. J. et al. Drought stress responses in soybean roots and nodules. Front. Plant Sci. 7, 1015. https://doi.org/10.3389/fpls.2016.01015 (2016).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    40.Ahemad, M. & Khan, M. S. Insecticide-tolerant and plant growth promoting Bradyrhizobium sp. (vigna) improves the growth and yield of greengram [Vigna radiata (L.) Wilczek] in insecticide-stressed soils. Symbiosis 54, 17–27. https://doi.org/10.1007/s13199-011-0122-6 (2011).CAS 
    Article 

    Google Scholar 
    41.Chen, J., Zhou, Z. & Gu, J. Occurrence and diversity of nitrite-dependent anaerobic methane oxidation bacteria in the sediments of the South China Sea revealed by amplification of both 16S rRNA and pmoAgenes. Appl. Microbiol. Biotechnol. 98, 5685–5696. https://doi.org/10.1007/s00253-014-5733-4 (2014).CAS 
    Article 
    PubMed 

    Google Scholar 
    42.Santoscaton, I. R., Caton, T. M. & Schneegurt, M. A. Nitrogen-fixation activity and the abundance and taxonomy of nifH genes in agricultural, pristine, and urban prairie stream sediments chronically exposed to different levels of nitrogen loading. Arch. Microbiol. https://doi.org/10.1007/s00203-018-1475-5 (2018).Article 

    Google Scholar 
    43.Zhou, J. et al. Effects of long term application of urea on ammonia oxidizing archaea community in black soil in Northeast China. Sci. Agric. Sin. 49, 294–304. https://doi.org/10.3864/j.issn.0578-1752.2016.02.010 (2016).CAS 
    Article 

    Google Scholar 
    44.Zhou, J. et al. Consistent effects of nitrogen fertilization on soil bacterial communities in black soils for two crop seasons in China. Sci. Rep. 7, 3267. https://doi.org/10.1038/s41598-017-03539-6 (2017).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    45.Diedrick, K. A. Field Investigations of Nitrogen Fertility on Corn and Soybeans and Foliar Manganese-Glyphosate Interactions on Glyphosate-Tolerant Soybeans in Ohio (The Ohio State University, 2010).
    Google Scholar 
    46.Salamone, I., Bereiner, J., Urquiaga, S. & Boddey, R. Biological nitrogen fixation in Azospirillumstrain-maize genotype associations as evaluated by the 15N isotope dilution technique. Biol. Fertil. Soils 23, 249–256. https://doi.org/10.1007/BF00335952 (1996).Article 

    Google Scholar 
    47.Carelli, M. et al. Genetic diversity and dynamics of sinorhizobium meliloti populations nodulating different alfalfa cultivars in Italiansoils. Appl. Environ. Microbiol. 66, 4785–4789. https://doi.org/10.1128/AEM.66.11.4785-4789.2000 (2000).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    48.Coelho, M. R. et al. Diversity of Paenibacillus spp. in the rhizosphere of four sorghum (Sorghum bicolor) cultivars sown with two contrasting levels of nitrogen fertilizer assessed by rpoB-based PCR-DGGE and sequencing analysis. J. Microbiol. Biotechnol. 17, 753–760. https://doi.org/10.1007/s10295-007-0209-5 (2007).CAS 
    Article 
    PubMed 

    Google Scholar 
    49.Cao, Y., Wang, E., Zhao, L., Chen, W. & Wei, G. Diversity and distribution of rhizobia nodulated with Phaseolus vulgaris in two ecoregions of China. Soil Biol. Biochem. 78, 128–137. https://doi.org/10.1016/j.soilbio.2014.07.026 (2014).CAS 
    Article 

    Google Scholar 
    50.Ahmed, I. H., Francina, L. B., Isabella, H. R. & Galaletsang, S. Nodulation efficacy of Bradyrhizobium japonicum inoculant strain WB74 on soybean (Glycine max L. Merrill) is affected by several limiting factors. Afr. J. Microbiol. Res. 8, 2069–2076. https://doi.org/10.5897/ajmr2014.6709 (2014).Article 

    Google Scholar 
    51.Yan, J. et al. Effects of long-term fertilization strategies on soil productivity and rhizobial diversity in Chinese mollisol. Pedosphere 29, 784–793. https://doi.org/10.1016/S1002-0160(17)60470-3 (2019).Article 

    Google Scholar 
    52.Riffkin, P. A., Quigley, P. E., Kearney, G. A., Cameron, F. J. & Thies, J. E. Factors associated with biological nitrogen fixation in dairy pastures in south-western Victoria. Aust. J. Agric. Res. 50, 261–272. https://doi.org/10.1071/a98035 (1999).Article 

    Google Scholar 
    53.Yang, L. et al. Diazotroph abundance and community structure are reshaped by straw return and mineral fertilizer in rice-rice-green manure rotation. Appl. Soil Ecol. 136, 11–20. https://doi.org/10.1016/j.apsoil.2018.12.015 (2019).Article 

    Google Scholar 
    54.Zou, Y. et al. Effects of different land use patterns on nifH genetic diversity of soil nitrogen-fixing microbial communities in Leymus Chinensis steppe. Acta Ecol. Sin. 31, 150–156 (2011).Article 

    Google Scholar 
    55.Zahran, H. H. Rhizobium-Legume symbiosis and nitrogen fixation under severe conditions and in an arid climate. Microbiol. Mol. Biol. R 63, 968–989. https://doi.org/10.1016/j.chnaes.2011.03.004 (1999).CAS 
    Article 

    Google Scholar 
    56.Tang, Y. et al. Impact of fertilization regimes on diazotroph community compositions and N2-fixation activity in paddy soil. Agriculture, Ecosystems & Environment: An International Journal for Scientific Research on the Relationship of Agriculture and Food Production to the Biosphere (2017).57.Gao, P., Li, Y., Tan, L., Guo, F. & Ma, T. Composition of bacterial and archaeal communities in an alkali-surfactant-polyacrylamide-flooded oil reservoir and the responses of microcosms to nutrients. Front. Microbiol. 10, 2197. https://doi.org/10.3389/fmicb.2019.02197 (2019).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    58.Rösch, C., Mergel, A. & Bothe, H. Biodiversity of denitrifying and dinitrogen-fixing bacteria in an acid forest soil. Appl. Enviro. Microbiol. 68, 3818–3829. https://doi.org/10.1128/AEM.68.8.3818-3829.2002 (2002).CAS 
    Article 

    Google Scholar 
    59.Wei, G. et al. Similar drivers but different effects lead to distinct ecological patterns of soil bacterial and archaeal communities. Soil Biol. Biochem. 144, 107759. https://doi.org/10.1016/j.soilbio.2020.107759 (2020).CAS 
    Article 

    Google Scholar 
    60.Sun, R., Guo, X., Wang, D. & Chu, H. Effects of long-term application of chemical and organic fertilizers on the abundance of microbial communities involved in the nitrogen cycle. Appl. Soil Ecol. 95, 171–178. https://doi.org/10.1016/j.apsoil.2015.06.010 (2015).Article 

    Google Scholar 
    61.Asnicar, F., Weingart, G., Tickle, T. L., Huttenhower, C. & Segata, N. Compact graphical representation of phylogenetic data and metadata with GraPhlAn. PeerJ 3, 1029. https://doi.org/10.7717/peerj.1029 (2015).Article 

    Google Scholar 
    62.Gao, P. et al. Spatial isolation and environmental factors drive distinct bacterial and archaeal communities in different types of petroleum reservoirs in China. Sci. Rep. 6, 20174. https://doi.org/10.1038/srep20174 (2016).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar  More

  • in

    Ecosystem response persists after a prolonged marine heatwave

    1.Overland, J., Rodionov, S., Minobe, S. & Bond, N. North Pacific regime shifts: definitions, issues and recent transitions. Prog. Oceanogr. 77, 92–102. https://doi.org/10.1016/j.pocean.2008.03.016 (2008).ADS 
    Article 

    Google Scholar 
    2.Chavez, F. P., Ryan, J., Lluch-Cota, S. E. & Niquen, M. From anchovies to sardines and back: multidecadal change in the Pacific Ocean. Science 299, 217–221 (2003).ADS 
    CAS 
    Article 

    Google Scholar 
    3.Beaugrand, G. et al. Synchronous marine pelagic regime shifts in the Northern Hemisphere. Philos. Trans. R. Soc. B Biol. Sci. 370, 20130272. https://doi.org/10.1098/rstb.2013.0272 (2015).Article 

    Google Scholar 
    4.Anderson, P. J. & Piatt, J. F. Community reorganization in the Gulf of Alaska following ocean climate regime shift. Mar. Ecol. Prog. Ser. 189, 117–123 (1999).ADS 
    Article 

    Google Scholar 
    5.Hare, S. R. & Mantua, N. J. Empirical evidence for North Pacific regime shifts in 1977 and 1989. Prog. Oceanogr. 47, 103–145. https://doi.org/10.1016/S0079-6611(00)00033-1 (2000).ADS 
    Article 

    Google Scholar 
    6.Litzow, M. A. Climate regime shifts and community reorganization in the Gulf of Alaska: how do recent shifts compare with 1976/1977?. ICES J. Mar. Sci. 63, 1386–1396 (2006).Article 

    Google Scholar 
    7.Hatch, S. A. Kittiwake diets and chick production signal a 2008 regime shift in the Northeast Pacific. Mar. Ecol. Prog. Ser. 477, 271–284. https://doi.org/10.3354/meps10161 (2013).ADS 
    Article 

    Google Scholar 
    8.Mantua, N. J., Hare, S. R., Zhang, Y., Wallace, J. M. & Francis, R. C. A Pacific interdecadal climate oscillation with impacts on salmon production. Bull. Am. Meteor. Soc. 78, 1069–1080 (1997).ADS 
    Article 

    Google Scholar 
    9.Cane, M. A. & Zebiak, S. E. A theory for El-Nino and the Southern oscillation. Science 228, 1085–1087 (1985).ADS 
    CAS 
    Article 

    Google Scholar 
    10.Di Lorenzo, E. et al. North Pacific Gyre oscillation links ocean climate and ecosystem change. Geophys. Res. Lett. 35, 6. https://doi.org/10.1029/2007GL032838 (2008).Article 

    Google Scholar 
    11.Bond, N. A., Overland, J. E., Spillane, M. & Stabeno, P. Recent shifts in the state of the North Pacific. Geophys. Res. Lett. 30, 1–3. https://doi.org/10.1029/2003GL018597 (2003).Article 

    Google Scholar 
    12.Litzow, M. A. et al. Non-stationary climate–salmon relationships in the Gulf of Alaska. Proc. R. Soc. B Biol. Sci. 285, 20181855. https://doi.org/10.1098/rspb.2018.1855 (2018).Article 

    Google Scholar 
    13.Litzow, M. A. et al. The changing physical and ecological meanings of North Pacific Ocean climate indices. Proc. Natl. Acad. Sci. 117, 7665–7671. https://doi.org/10.1073/pnas.1921266117 (2020).CAS 
    Article 
    PubMed 

    Google Scholar 
    14.Peterson, W. T. & Schwing, F. B. A new climate regime in northeast Pacific ecosystems. Geophys. Res. Lett. 30, 1896 (2003).ADS 
    Article 

    Google Scholar 
    15.Litzow, M. A. & Mueter, F. J. Assessing the ecological importance of climate regime shifts: An approach from the North Pacific Ocean. Prog. Oceanogr. 120, 110–119. https://doi.org/10.1016/j.pocean.2013.08.003 (2014).ADS 
    Article 

    Google Scholar 
    16.Puerta, P., Ciannelli, L., Rykaczewski, R., Opiekun, M. & Litzow, M. A. Do Gulf of Alaska fish and crustacean populations show synchronous non-stationary responses to climate?. Prog. Oceanogr. 175, 161–170. https://doi.org/10.1016/j.pocean.2019.04.002 (2019).ADS 
    Article 

    Google Scholar 
    17.IPCC. Summary for policymakers. In: IPCC special report on the ocean and cryosphere in a changing climate [H.- O. Pörtner, D.C. Roberts, V. Masson-Delmotte, P. Zhai, M. Tignor, E. Poloczanska, K. Mintenbeck, M. Nicolai, A. Okem, J. Petzold, B. Rama, N. Weyer (eds.)]. Accessed on 11/5/2019. Accessed on 11/5/2019. https://report.ipcc.ch/srocc/pdf/SROCC_FinalDraft_FullReport.pdf, 2019.18.Oliver, E. C. J. et al. Longer and more frequent marine heatwaves over the past century. Nat. Commun. 9, 1324. https://doi.org/10.1038/s41467-018-03732-9 (2018).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    19.Hobday, A. et al. Categorizing and naming marine heatwaves. Oceanography 31, 162–173. https://doi.org/10.5670/oceanog.2018.205 (2018).Article 

    Google Scholar 
    20.Smale, D. A. et al. Marine heatwaves threaten global biodiversity and the provision of ecosystem services. Nat. Clim. Change 9, 306–312. https://doi.org/10.1038/s41558-019-0412-1 (2019).ADS 
    Article 

    Google Scholar 
    21.Di Lorenzo, E. & Mantua, N. Multi-year persistence of the 2014/15 North Pacific marine heatwave. Nat. Clim. Change 6, 1042–1047. https://doi.org/10.1038/nclimate3082 (2016).ADS 
    Article 

    Google Scholar 
    22.Jackson, J. M., Johnson, G. C., Dosser, H. V. & Ross, T. Warming from recent marine heatwave lingers in deep british columbia fjord. Geophys. Res. Lett. 45, 9757–9764. https://doi.org/10.1029/2018GL078971 (2018).ADS 
    Article 

    Google Scholar 
    23.Cornwall, W. A new ‘Blob’ menaces Pacific ecosystems. Science 365, 1233–1233. https://doi.org/10.1126/science.365.6459.1233 (2019).ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 
    24.Sutherland, K. R., Sorensen, H. L., Blondheim, O. N., Brodeur, R. D. & Galloway, A. W. E. Range expansion of tropical pyrosomes in the northeast Pacific ocean. Ecology 99, 2397–2399. https://doi.org/10.1002/ecy.2429 (2018).Article 
    PubMed 

    Google Scholar 
    25.Batten, S. D. et al. Interannual variability in lower trophic levels on the Alaskan Shelf. Deep Sea Res. Part II 147, 58–68. https://doi.org/10.1016/j.dsr2.2017.04.023 (2018).Article 

    Google Scholar 
    26.Brodeur, R. D., Auth, T. D. & Phillips, A. J. Major shifts in pelagic micronekton and macrozooplankton community structure in an upwelling ecosystem related to an unprecedented marine heatwave. Front. Mar. Sci. 6, 212. https://doi.org/10.3389/fmars.2019.00212 (2019).Article 

    Google Scholar 
    27.Harvell, C. D. et al. Disease epidemic and a marine heat wave are associated with the continental-scale collapse of a pivotal predator (Pycnopodia helianthoides). Sci. Adv. 5, eaau7042, doi:https://doi.org/10.1126/sciadv.aau7042 (2019).28.Piatt, J. F. et al. Extreme mortality and reproductive failure of common murres resulting from the northeast Pacific marine heatwave of 2014–2016. PLoS ONE 15, e0226087. https://doi.org/10.1371/journal.pone.0226087 (2020).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    29.Wade, N. M. et al. Effects of an unprecedented summer heatwave on the growth performance, flesh colour and plasma biochemistry of marine cage-farmed Atlantic salmon (Salmo salar). J. Therm. Biol 80, 64–74. https://doi.org/10.1016/j.jtherbio.2018.12.021 (2019).CAS 
    Article 
    PubMed 

    Google Scholar 
    30.Peterson, C. H. et al. Long-term ecosystem response to the exxon valdez oil spill. Science 302, 2082–2086 (2003).ADS 
    CAS 
    Article 

    Google Scholar 
    31.Esler, D. et al. Timelines and mechanisms of wildlife population recovery following the Exxon Valdez oil spill. Deep Sea Res. Part II 147, 36–42. https://doi.org/10.1016/j.dsr2.2017.04.007 (2018).Article 

    Google Scholar 
    32.Danielson, S. L. et al. A study of marine temperature variations in the northern Gulf of Alaska across years of marine heatwaves and cold spells. Deep Sea Research Part II: Topical Studies in Oceanography (In prep).33.Arimitsu, M. L. et al. Heatwave-induced synchrony within forage fish portfolio disrupts energy flow to top pelagic predators. Glob. Change Biol., in press. https://doi.org/10.1111/gcb.15556 (2021).34.von Biela, V. R. et al. Extreme reduction in nutritional value of a key forage fish during the Pacific marine heatwave of 2014–2016. Mar. Ecol. Progress Ser. 613, 171–182 (2019).35.Sydeman, W. J. et al. Puffins reveal contrasting relationships between forage fish and ocean climate in the North Pacific. Fish. Oceanogr. 26, 379–395. https://doi.org/10.1111/fog.12204 (2017).Article 

    Google Scholar 
    36.Savage, K. 2018 Alaska Region marine mammal stranding summary. 14 (Protected Resources Division, National Marine Fisheries Service, Alaska Region, Juneau, Alaska 99802, 2019).37.Barbeaux, S. J., Holsman, K. & Zador, S. Marine heatwave stress test of ecosystem-based fisheries management in the Gulf of Alaska pacific cod fishery. Front. Mar. Sci. 7, 703. https://doi.org/10.3389/fmars.2020.00703 (2020).Article 

    Google Scholar 
    38.Fisher, J. L., Peterson, W. T. & Rykaczewski, R. R. The impact of El Niño events on the pelagic food chain in the northern California Current. Glob. Change Biol. 21, 4401–4414. https://doi.org/10.1111/gcb.13054 (2015).ADS 
    Article 

    Google Scholar 
    39.McKinstry, C. A. E. & Campbell, R. W. Seasonal variation of zooplankton abundance and community structure in Prince William Sound, Alaska, 2009–2016. Deep Sea Res. Part II 147, 69–78. https://doi.org/10.1016/j.dsr2.2017.08.016 (2018).Article 

    Google Scholar 
    40.Santora, J. A. et al. Spatial ecology of krill, micronekton and top predators in the central California current: implications for defining ecologically important areas. Prog. Oceanogr. 106, 154–174 (2012).ADS 
    Article 

    Google Scholar 
    41.Blake, R. E., Ward, C. L., Hunsicker, M. E., Shelton, A. O. & Hollowed, A. B. Spatial community structure of groundfish is conserved across the Gulf of Alaska. Mar. Ecol. Prog. Ser. 626, 145–160 (2019).ADS 
    Article 

    Google Scholar 
    42.McGowan, D. W., Horne, J. K. & Rogers, L. A. Effects of temperature on the distribution and density of capelin in the Gulf of Alaska. Mar. Ecol. Prog. Ser. 620, 119–138 (2019).ADS 
    Article 

    Google Scholar 
    43.Watson, J. T. & Haynie, A. C. Paths to resilience: Alaska pollock fleet uses multiple fishing strategies to buffer against environmental change in the Bering Sea. Can. J. Fish. Aquat. Sci. 75, 1977–1989. https://doi.org/10.1139/cjfas-2017-0315 (2018).Article 

    Google Scholar 
    44.Beaudreau, A. H. et al. Thirty years of change and the future of Alaskan fisheries: Shifts in fishing participation and diversification in response to environmental, regulatory and economic pressures. Fish Fish. 20, 601–619. https://doi.org/10.1111/faf.12364 (2019).Article 

    Google Scholar 
    45.Barbeaux, S. et al. Assessment of the Pacific cod stock in the Gulf of Alaska. 160 (National Marine Fisheries Service, Alaska Fisheries Science Center, Seattle, Washington, USA, U.S. Department of Commerce, National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Alaska Fisheries Science Center, 2018).46.Laurel, B. J. & Rogers, L. A. Loss of spawning habitat and prerecruits of Pacific cod during a Gulf of Alaska heatwave. Can. J. Fish. Aquat. Sci. 77, 644–650. https://doi.org/10.1139/cjfas-2019-0238 (2020).Article 

    Google Scholar 
    47.Yang, Q. et al. How “The Blob” affected groundfish distributions in the Gulf of Alaska. Fish. Oceanogr. 28, 434–453. https://doi.org/10.1111/fog.12422 (2019).Article 

    Google Scholar 
    48.Fissel, B. et al. Stock assessment and fishery evaluation report for the groundfish fisheries of the Gulf Of Alaska and Bering Sea/Aleutian Islands area: Economic status of the groundfish fisheries off Alaska, 2017. 385 (National Marine Fisheries Service, Alaska Fisheries Science Center, Seattle, Washington, USA, Alaska Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 2019).49.Kasperski, S. & Holland, D. S. Income diversification and risk for fishermen. Proc. Natl. Acad. Sci. 110, 2076–2081. https://doi.org/10.1073/pnas.1212278110 (2013).ADS 
    Article 
    PubMed 

    Google Scholar 
    50.Scyphers, S. B., Picou, J. S. & Grabowski, J. H. Chronic social disruption following a systemic fishery failure. Proc. Natl. Acad. Sci. 116, 22912–22914. https://doi.org/10.1073/pnas.1913914116 (2019).ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 
    51.Curnock, M. I. et al. Shifts in tourists’ sentiments and climate risk perceptions following mass coral bleaching of the Great Barrier Reef. Nat. Clim. Change 9, 535–541. https://doi.org/10.1038/s41558-019-0504-y (2019).ADS 
    Article 

    Google Scholar 
    52.Caputi, N. et al. Factors affecting the recovery of invertebrate stocks from the 2011 Western Australian extreme marine heatwave. Front. Mar. Sci. 6, 484. https://doi.org/10.3389/fmars.2019.0048 (2019).Article 

    Google Scholar 
    53.Chandrapavan, A., Caputi, N. & Kangas, M. I. The decline and recovery of a crab population from an extreme marine heatwave and a changing climate. Front. Mar. Sci. 6, 510. https://doi.org/10.3389/fmars.2019.00510 (2019).Article 

    Google Scholar 
    54.Walsh, J. E. et al. The high latitude marine heat wave of 2016 and its impacts on Alaska. Bull. Am. Meteor. Soc. 99, S39–S43. https://doi.org/10.1175/BAMS-D-17-0118.1 (2018).Article 

    Google Scholar 
    55.Sewall, F., Norcross, B., Vollenweider, J. & Heintz, R. Growth, energy storage, and feeding patterns reveal winter mortality risks for juvenile Pacific herring in Prince William Sound, Alaska, USA. Mar. Ecol. Prog. Ser. 623, 195–208 (2019).ADS 
    Article 

    Google Scholar 
    56.Toresen, R., Skjoldal, H. R., Vikebø, F. & Martinussen, M. B. Sudden change in long-term ocean climate fluctuations corresponds with ecosystem alterations and reduced recruitment in Norwegian spring-spawning herring (Clupea harengus, Clupeidae). Fish Fish. 20, 686–696. https://doi.org/10.1111/faf.12369 (2019).Article 

    Google Scholar 
    57.Duffy-Anderson, J. T. et al. Responses of the northern bering sea and southeastern bering sea pelagic ecosystems following record-breaking low winter sea ice. Geophys. Res. Lett. 46, 9833–9842. https://doi.org/10.1029/2019gl083396 (2019).ADS 
    Article 

    Google Scholar 
    58.Babcock, R. C. et al. Severe continental-scale impacts of climate change are happening now: extreme climate events impact marine habitat forming communities along 45% of Australia’s coast. Front. Mar. Sci. 6, 411. https://doi.org/10.3389/fmars.2019.00411 (2019).Article 

    Google Scholar 
    59.Jacox, M., Tommasi, D., Alexander, M. A., Hervieux, G. & Stock, C. Predicting the evolution of the 2014–16 California Current System marine heatwave from an ensemble of coupled global climate forecasts. Front. Mar. Sci. 6, 497. https://doi.org/10.3389/fmars.2019.00497 (2019).Article 

    Google Scholar 
    60.Francis, R. C., Hare, S. R., Hollowed, A. B. & Wooster, W. S. Effects of interdecadal climate variability on the oceanic ecosystems of the NE Pacific. Fish. Oceanogr. 7, 1–21 (1998).Article 

    Google Scholar 
    61.Rogers, L. A. & Dougherty, A. B. Effects of climate and demography on reproductive phenology of a harvested marine fish population. Glob. Change Biol. 25, 708–720. https://doi.org/10.1111/gcb.14483 (2019).ADS 
    Article 

    Google Scholar 
    62.Laurel, B. J. et al. Regional warming exacerbates match/mismatch vulnerability for cod larvae in Alaska. Prog. Oceanogr. Accepted (2021).63.Hughes, B. B. et al. Long-term studies contribute disproportionately to ecology and policy. Bioscience 67, 271–281. https://doi.org/10.1093/biosci/biw185 (2017).Article 

    Google Scholar 
    64.Lonhart, S. I., Jeppesen, R., Beas-Luna, R., Crooks, J. A. & Lorda, J. Shifts in the distribution and abundance of coastal marine species along the eastern Pacific Ocean during marine heatwaves from 2013 to 2018. Mar. Biodivers. Rec. 12, 13. https://doi.org/10.1186/s41200-019-0171-8 (2019).Article 

    Google Scholar 
    65.Vander Naald, B. P., Sergeant, C. J. & Beaudreau, A. H. Public perception and valuation of long-term ecological monitoring. Ecosphere 10, e02875. https://doi.org/10.1002/ecs2.2875 (2019).Article 

    Google Scholar 
    66.Hollowed, A. B. et al. Recent advances in understanding the effects of climate change on the world’s oceans. ICES J. Mar. Sci. 76, 1215–1220. https://doi.org/10.1093/icesjms/fsz084 (2019).Article 

    Google Scholar 
    67.R: A language and environment for statistical computing. (R: A language and environment for statistical computing. R Foundation for Statistical Computing. Vienna, Austria. https://www.R-project.org/, 2020).68.Zuur, A. F., Fryer, R. J., Jolliffe, I. T., Dekker, R. & Beukema, J. J. Estimating common trends in multivariate time series using dynamic factor analysis. Environmetrics 14, 665–685. https://doi.org/10.1002/env.611 (2003).Article 

    Google Scholar 
    69.Holmes, E., Ward, E., Scheuerell, M. & Wills, L. MARSS: multivariate autoregressive state-space modeling (Northwest Fisheries Science Center NOAA, Seattle, WA, 2018).
    Google Scholar 
    70.Holmes, E. E., Ward, E. J. & Scheuerell, M. D. Analysis of multivariate time-series using the MARSS package, v3.10.10. 284 (Northwest Fisheries Science Center, NOAA, Seattle, WA, USA, 2018).71.Zuur, A. F., Tuck, I. D. & Bailey, N. Dynamic factor analysis to estimate common trends in fisheries time series. Can. J. Fish. Aquat. Sci. 60, 542–552. https://doi.org/10.1139/f03-030 (2003).Article 

    Google Scholar 
    72.Clarke, K. R. & Gorley, R. N. Getting started with PRIMER v7 (PRIMER-E ltd, Plymouth, 2015).
    Google Scholar 
    73.Clarke, K. R., Gorley, R. N., Somerfield, P. J. & Warwick, R. M. Change in marine communities: an approach to statistical analysis and interpretation (PRIMER-E ltd, Plymouth, 2014).
    Google Scholar 
    74.Clarke, K. R., Somerfield, P. J. & Gorley, R. N. Testing of null hypotheses in exploratory community analyses: similarity profiles and biota-environment linkage. J. Exp. Mar. Biol. Ecol. 366, 56–69. https://doi.org/10.1016/j.jembe.2008.07.009 (2008).Article 

    Google Scholar 
    75.Strom, S. L., Fredrickson, K. A. & Bright, K. J. Spring phytoplankton in the eastern coastal Gulf of Alaska: photosynthesis and production during high and low bloom years. Deep Sea Res. Part II 132, 107–121. https://doi.org/10.1016/j.dsr2.2015.05.003 (2016).CAS 
    Article 

    Google Scholar 
    76.Strom, S. L., Fredrickson, K. A. & Bright, K. J. Microzooplankton in the coastal Gulf of Alaska: Regional, seasonal and interannual variations. Deep Sea Res. Part II 165, 192–202. https://doi.org/10.1016/j.dsr2.2018.07.012 (2019).Article 

    Google Scholar 
    77.Mackas, D. L. Interannual variability of the zooplankton community off southern Vancouver Island. Can. Sp. Publ. Fish. Aquat. Sci. 121, 603–615 (1995).
    Google Scholar 
    78.Kimmel, D. G. & Duffy-Anderson, J. T. Zooplankton abundance trends and patterns in Shelikof Strait, western Gulf of Alaska, USA, 1990–2017. J. Plankton Res. 42, 334–354. https://doi.org/10.1093/plankt/fbaa019 (2020).Article 

    Google Scholar 
    79.Richardson, A. J. et al. Using continuous plankton recorder data. Prog. Oceanogr. 68, 27–74. https://doi.org/10.1016/j.pocean.2005.09.011 (2006).ADS 
    Article 

    Google Scholar 
    80.Von Szalay, P. G. & Raring, N. W. Data Report: 2017 Gulf of Alaska bottom trawl survey. U.S. Dep. Commer., NOAA Tech. Memo. NMFS-AFSC-374, 260 p., (2018).81.Matarese, A. C., Blood, D.M., Picquelle, S. J. & J.L., B. Vol. NOAA Prof. Paper NMFS 1, 281 p. 281 (NOAA Professional Paper NMFS 1, 2003).82.Weitzman, B. et al. Changes in rocky intertidal community structure during a marine heatwave in the northern Gulf of Alaska. Front. Mar. Sci., 8. https://www.frontiersin.org/articles/10.3389/fmars.2021.556820/full (2021).83.Bodkin, J. L. et al. Variation in abundance of Pacific Blue Mussel (Mytilus trossulus) in the Northern Gulf of Alaska, 2006–2015. Deep Sea Res. Part II 147, 87–97. https://doi.org/10.1016/j.dsr2.2017.04.008 (2018).Article 

    Google Scholar 
    84.Konar, B. et al. Wasting disease and static environmental variables drive sea star assemblages in the Northern Gulf of Alaska. J. Exp. Mar. Biol. Ecol. 520, 151209. https://doi.org/10.1016/j.jembe.2019.151209 (2019).Article 

    Google Scholar 
    85.Mudge, M. L., Pietrzak, K. W. & Rojek, N. A. Biological monitoring at Chowiet Island, Alaska in 2019. U.S. Fish and Wildl. Serv. Rep., AMNWR 2019/16. Homer, Alaska., 187 (2019).86.Suryan, R. M. & Irons, D. B. Colony and population dynamics of black-legged kittiwakes in a heterogeneous environment. Auk 118, 636–649 (2001).Article 

    Google Scholar 
    87.Harding, A. M. A. et al. Prey density and the behavioral flexibility of a marine predator: the common murre (Uria aalge). Ecology 88, 2024–2033 (2007).Article 

    Google Scholar 
    88.Litzow, M. I., Piatt, J. I., Prichard, A. I. & Roby, D. I. Response of pigeon guillemots to variable abundance of high-lipid and low-lipid prey. Oecologia 132, 286–295 (2002).ADS 
    Article 

    Google Scholar 
    89.Moran, J. R., Heintz, R. A., Straley, J. M. & Vollenweider, J. J. Regional variation in the intensity of humpback whale predation on Pacific herring in the Gulf of Alaska. Deep Sea Res. Part II 147, 187–195. https://doi.org/10.1016/j.dsr2.2017.07.010 (2018).Article 

    Google Scholar 
    90.Robards, M. D., Anthony, J. A., Rose, G. A. & Piatt, J. F. Changes in proximate composition and somatic energy content for Pacific sand lance (Ammodytes hexapterus) from Kachemak Bay, Alaska relative to maturity and season. J. Exp. Mar. Biol. Ecol. 242, 245–258 (1999).Article 

    Google Scholar 
    91.Muradian, M. L., Branch, T. A., Moffitt, S. D. & Hulson, P.-J.F. Bayesian stock assessment of Pacific herring in Prince William Sound Alaska. PLOS ONE 12, e0172153. https://doi.org/10.1371/journal.pone.0172153 (2017).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    92.Moffitt, S. D. Retrospective longitudinal growth history from scales of Pacific herring collected in Prince William Sound. (Exxon Valdez Long-Term Herring Research and Monitoring Program Final Report (Project 13120111-N), Exxon Valdez Oil Spill Trustee Council. Anchorage, AK, Anchorage, AK, 2017).93.Batten, S. D., Moffitt, S., Pegau, W. S. & Campbell, R. Plankton indices explain interannual variability in Prince William Sound herring first year growth. Fish. Oceanogr. 25, 420–432. https://doi.org/10.1111/fog.12162 (2016).Article 

    Google Scholar 
    94.Dorn, M. et al. Assessment of the walleye pollock stock in the Gulf of Alaska. 161 ( North Pacific Fishery Management Council, Anchorage, AK, 2019).95.Barbeaux, S. et al. Assessment of the Pacific cod stock in the Gulf of Alaska. 140 (North Pacific Fishery Management Council, Anchorage, AK, 2019).96.Spies, I., Aydin, K., Ianelli, J. N. & Palsson, N. Assessment of the arrowtooth flounder stock in the Gulf of Alaska (North Pacific Fishery Management Council, Anchorage, AK, 2019).
    Google Scholar 
    97.Hanselman, D. H. et al. Assessment of the Sablefish stock in Alaska. 263 (North Pacific Fishery Management Council, Anchorage, AK, 2019).98.Kettle, A. B. Biological monitoring at East Amatuli Island, Alaska in 2018. U.S. Fish and Wildlife Service Report, AMNWR 2019/13. Homer, Alaska., 84 (2019).99.Coletti, H. et al. Gulf Watch Alaska: Nearshore benthic systems in the Gulf of Alaska. Long-Term Monitoring Program (Gulf Watch Alaska) Final Report (Exxon Valdez Oil Spill Trustee Council Project 16120114-R), Exxon Valdez Oil Spill Trustee Council, Anchorage, Alaska., (2018).100.Bodkin, J. SOP for conducting marine bird and mammal surveys – Version 4.1: Southwest Alaska Inventory and Monitoring Network. Natural Resource Report NPS/SWAN/NRR— 2011/392. National Park Service, Fort Collins, Colorado, USA., (2011).101.Stocking, J., Bishop, M. A. & Arab, A. Spatio-temporal distributions of piscivorous birds in a subarctic sound during the nonbreeding season. Deep Sea Res. Part II 147, 138–147. https://doi.org/10.1016/j.dsr2.2017.07.017 (2018).Article 

    Google Scholar 
    102.102Kuletz, K. J. & Labunski, E. A. Seabird Distribution and Abundance in the Offshore Environment, Final Report. US Dept. of the Interior, Bureau of Ocean Energy Management, Alaska OCS Region. OCS Study BOEM 2017–004. Anchorage, Alaska, USA. 59 pp, plus 400 pages of Appendices (2017).103.Coletti, H. A., Bodkin, J. L., Monson, D. H., Ballachey, B. E. & Dean, T. A. Detecting and inferring cause of change in an Alaska nearshore marine ecosystem. Ecosphere 7, e01489. https://doi.org/10.1002/ecs2.1489 (2016).Article 

    Google Scholar 
    104.Maniscalco, J. M., Springer, A. M., Parker, P. & Adkison, M. D. A longitudinal study of steller sea lion natality rates in the Gulf of Alaska with comparisons to census data. PLoS ONE 9, e111523. https://doi.org/10.1371/journal.pone.0111523 (2014).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    105.Sweeney, K., Fritz, L. W., Towell, R. & Gelatt, T. Results of Steller Sea Lion Surveys in Alaska, June-July 2017. 17 (National Marine Fisheries Service, Alaska Fisheries Science Center, Seattle, Washington, USA, National Marine Fisheries Service, Alaska Fisheries Science Center, Marine Mammal Laboratory, 7600 Sand Point Way NE, Seattle WA 98115, https://www.fisheries.noaa.gov/resource/data/2017-results-steller-sea-lion-surveys-alaska, 2017).106.Straley, J. M. et al. Seasonal presence and potential influence of humpback whales on wintering Pacific herring populations in the Gulf of Alaska. Deep Sea Res. Part II 147, 173–186. https://doi.org/10.1016/j.dsr2.2017.08.008 (2018).Article 

    Google Scholar 
    107.Olsen, D. W., Matkin, C. O., Andrews, R. D. & Atkinson, S. Seasonal and pod-specific differences in core use areas by resident killer whales in the Northern Gulf of Alaska. Deep Sea Res. Part II 147, 196–202. https://doi.org/10.1016/j.dsr2.2017.10.009 (2018).Article 

    Google Scholar 
    108.ADFG. Alaska Department of Fish and Game Statewide electronic fish ticket database 1985 to present. 1st edition. Alaska Department of Fish and Game, Division of Commercial Fisheries. (Accessed October 2019). (2018). More

  • in

    First description of deep benthic habitats and communities of oceanic islands and seamounts of the Nazca Desventuradas Marine Park, Chile

    1.Yesson, C., Clark, M. R., Taylor, M. L. & Rogers, A. D. The global distribution of seamounts based on 30 arc seconds bathymetry data. Deep. Res. Part I Oceanogr. Res. Pap. 58, 442–453 (2011).ADS 
    Article 

    Google Scholar 
    2.Preez, CDu., Curtis, J. M. R. & Clarke, M. E. The structure and distribution of benthic communities on a shallow seamount (Cobb Seamount, Northeast Pacific Ocean). PLoS ONE 11, 1–29 (2016).Article 
    CAS 

    Google Scholar 
    3.Auster, P. J. et al. Definition and detection of vulnerable marine ecosystems on the high seas: problems with the ‘move-on’ rule. ICES J. Mar. Sci. 68, 254–264 (2011).Article 

    Google Scholar 
    4.Watling, L. & Auster, P. J. Seamounts on the high seas should be managed as vulnerable marine ecosystems. Front. Mar. Sci. 4, 1–4 (2017).Article 

    Google Scholar 
    5.Cho, W. W. Faunal Biogeography, Community Structure, and Genetic Connectivity of North Atlantic Seamounts (Massachusetts Institute of Technology & Woods Hole Oceanographic Institution, 2008).6.Rogers, A. D. The Biology of Seamounts: 25 Years on. Advances in Marine Biology vol. 79 (Elsevie, 2018).7.Wagner, D. et al. The Salas y Gómez and Nazca ridges: a global diversity hotspot in need of protection. 28 (2020).8.Kvile, K. O., Taranto, G. H., Pitcher, T. J. & Morato, T. A global assessment of seamount ecosystems knowledge using an ecosystem evaluation framework. Biol. Conserv. 173, 108–120 (2014).Article 

    Google Scholar 
    9.Victorero, L., Robert, K., Robinson, L. F., Taylor, M. L. & Huvenne, V. A. I. Species replacement dominates megabenthos beta diversity in a remote seamount setting. Sci. Rep. 8, 1–11 (2018).CAS 
    Article 

    Google Scholar 
    10.Yesson, C. et al. Improved bathymetry leads to 4000 new seamount predictions in the global ocean. UCL Open Environ. Preprint, 1–12 (2020).11.Gálvez Larach, M. Montes submarinos de Nazca y Salas y Gómez: una revisión para el manejo y conservación. Lat. Am. J. Aquat. Res. 37, 479–500 (2009).Article 

    Google Scholar 
    12.Jarrard, R. D. & Clague, D. A. Implications of Pacific Island and seamount ages for the origin of volcanic chains. Rev. Geophys. 15, 57–76 (1977).ADS 
    Article 

    Google Scholar 
    13.Chave, E. H. & Jones, A. T. Deep-water megafauna of the Kohala and Haleakala slopes, Alenuihaha Channel Hawaii. Deep Sea Res. Part A Oceanogr. Res. Pap. 38, 781–803 (1991).ADS 
    Article 

    Google Scholar 
    14.Kitchingman, A., Lai, S., Morato, T. & Pauly, D. How many seamounts are there and where are they located? In Seamounts: Ecology, Fisheries & Conservation, Series 12 (eds Pitcher, T. J. et al.) 26–40 (Blackwell Publishing, 2008). https://doi.org/10.1002/9780470691953.ch2.
    Google Scholar 
    15.Parin, N. V., Mironov, A. N. & Nesis, K. M. Biology of the Nazca and Sala y Gómez submarine ridges, an outpost of the Indo-West Pacific fauna in the eastern Pacific ocean: composition and distribution of the fauna, its communities and history. Advances in Marine Biology vol. 32 (1997).16.Samadi, S., Schlacher, T. & Richer de Forges, B. Seamount benthos. In Seamounts: Ecology, Fisheries and Conservation (eds Pitcher, T. et al.) 119–140 (Wiley-Blackwell, 2007).
    Google Scholar 
    17.Mironov, A. N., Molodtsova, T. N. & Parin., N. V. Soviet and Russian studies on seamount biology. (2006).18.Fernández, M., Pappalardo, P., Rodríguez-Ruiz, M. C. & Castilla, J. C. Síntesis del estado del conocimiento sobre la riqueza de especies de macroalgas, macroinvertebrados y peces en aguas costeras y oceánicas de Isla de Pascua e Isla Salas y Gómez. Lat. Am. J. Aquat. Res. 42, 760–802 (2014).Article 

    Google Scholar 
    19.Easton, E. E. et al. Chile and the Salas y Gómez Ridge. In Mesophotic Coral Ecosystems 477–490 (Springer, 2019). https://doi.org/10.1007/978-3-319-92735-0_27.20.Friedlander, A. M. et al. Marine biodiversity in Juan Fernández and Desventuradas islands, Chile: global endemism hotspots. PLoS ONE 11, e0145059 (2016).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    21.Sellanes, J., Salisbury, R. A., Tapia, J. M. & Asorey, C. M. A new species of Atrimitra Dall, 1918 (Gastropoda: Mitridae) from seamounts of the recently created Nazca-Desventuradas Marine Park Chile. PeerJ 2019, 1–16 (2019).
    Google Scholar 
    22.Gaymer, C. F. et al. Plan General de Administración y su Valoración Económica. Informe final proyecto FIPA 2016–31 ‘Bases técnicas para la gestión del Parque Marino Nazca-Desventuradas y propuesta de Plan General de Administración’ (2018).23.Clark, M. R. et al. The ecology of seamounts: structure, function, and human impacts. Ann. Rev. Mar. Sci. 2, 253–278 (2010).PubMed 
    Article 

    Google Scholar 
    24.Henry, L. A. et al. Environmental variability and biodiversity of megabenthos on the Hebrides Terrace Seamount (Northeast Atlantic). Sci. Rep. 4, 1–10 (2014).
    Google Scholar 
    25.Jones, C. G., Lawton, J. H. & Shachak, M. Organisms as ecosystem engineers. Oikos 69, 373 (1994).Article 

    Google Scholar 
    26.Morgan, N. B., Goode, S., Roark, E. B. & Baco, A. R. Fine scale assemblage structure of benthic invertebrate megafauna on the North Pacific Seamount Mokumanamana. Front. Mar. Sci. 6, 1–21 (2019).Article 

    Google Scholar 
    27.Davies, J. S. et al. Benthic assemblages of the Anton Dohrn Seamount (NE Atlantic): defining deep-sea biotopes to support habitat mapping and management efforts with a focus on vulnerable marine ecosystems. PLoS ONE 10, 33 (2015).
    Google Scholar 
    28.Auster, P. J., Malatesta, R. J. & Larosa, S. C. Patterns of microhabitat utilization by mobile megafauna on the southern New England (USA) continental shelf and slope. Mar. Ecol. Prog. Ser. 127, 77–85 (1995).ADS 
    Article 

    Google Scholar 
    29.Uzmann, J. R., Cooper, R. A., Theroux, R. B. & Wigley, R. L. Synoptic comparison of three sampling techniques for estimating abundance and distribution of selected megafauna: submersible vs. camera sled vs. otter trawl. Mar. Fish. Rev. 39, 11–19 (1977).
    Google Scholar 
    30.Valentine, J. P. & Edgar, G. J. Impacts of a population outbreak of the urchin Tripneustes gratilla amongst Lord Howe Island coral communities. Coral Reefs 29, 399–410 (2010).ADS 
    Article 

    Google Scholar 
    31.Greene, H. et al. A classification scheme for deep seafloor habitats. Oceanol. Acta 22, 663–678 (1999).Article 

    Google Scholar 
    32.Greene, H., O’Connell, V., Brylinsky, C. & Reynolds, J. Marine Benthic Habitat classification: What’s Best for Alaska? In Marine Habitat Mapping Technology for Alaska (eds Reynolds, J. & Greene, H. G.) 169–184 (Alaska Sea Grant College Program University of Alaska Fairbanks, 2008). https://doi.org/10.4027/mhmta.2008.12.
    Google Scholar 
    33.Naar, D. F., Johnson, K. P., Wessel, D., Duncan, P. & Mahoney, J. Rapa Nui. 2001: Cruise report for Leg 6 of the Drift expedition aboard the R/V Revelle (2001).34.Haase, K. M., Stoffers, P. & Garbe-Schönberg, C. D. The petrogenetic evolution of lavas from Easter Island and neighbouring seamounts, near-ridge hotspot volcanoes in the SE pacific. J. Petrol. 38, 785–813 (1997).ADS 
    CAS 
    Article 

    Google Scholar 
    35.Woods, M. T. & Okal, E. A. The structure of the Nazca Ridge and Sala y Gomez seamount chain from the dispersion of Rayleigh waves. Geophys. J. Int. 117, 205–222 (1994).ADS 
    Article 

    Google Scholar 
    36.Rodrigo, C., Foucher, N., Philippi, N. & Lara, L. E. Morfoestructuras volcánicas y sedimentarias de los montes submarinos de la región de las islas Desventuradas, basadas en el análisis de datos acústicos. 110–115 (2017).37.Mecho, A. et al. Environmental drivers of mesophotic echinoderm assemblages of the Southeastern Pacific Ocean. Front Mar. Sci. 8, 1–15 (2021).Article 

    Google Scholar 
    38.VLC media player – Open Source Multimedia Framework and Player.39.Dyer, B. S. & Westneat, M. W. Taxonomía y biogeografía de los peces costeros del Archipiélago de Juan Fernández y de las islas Desventuradas Chile. Rev. Biol. Mar. Oceanogr. 45, 589–617 (2010).Article 

    Google Scholar 
    40.Pequeño, G. & Lamilla, J. The Littoral Fish Assemblage of the Desventuradas Islands (Chile) Has Zoogeographical Affinities with the Western Pacific. Glob. Ecol. Biogeogr. 9, 431–437 (2000).Article 

    Google Scholar 
    41.Raines, B. & Huber, M. Biodiversity Quadrupled-Revision of Easter Island and Salas y Gómez Bivalves. Zootaxa 106 (2012).42.Retamal, M. A. & Moyano, H. I. Zoogeografía de los crustáceos decápodos chilenos marinos y dulceacuícolas. Lat. Am. J. Aquat. Res. 38, 302–328 (2010).
    Google Scholar 
    43.Sysoev, A. B. Gastropods of the family Turridae (Gastropoda:Toxoglosa) of the Nasca and Sala y Gómez underwater ridges. 124, 245–260 (1990).44.Zarenkov, N. A. Crabs of the familiy Leucosiidae (subfamilies Ebalinae an Iliinae) collected in tropical water of Indian and Pacific oceans waters of Indian and Pacific oceans. Bol. Nauk. 10, 16–26 (1969).
    Google Scholar 
    45.Zarenkov, N. A. Decapods (Stenopodidea, Brachyura, Anomura) of the underwater Nazca and Salas y Gómez Ridges. Tr. Instituta Okeanol. AN USSR 124, 218–244 (1990).
    Google Scholar 
    46.Barriga, E., Salazar, C., Palacios, J., Romero, M. & Rodriguez, A. Distribucion, abundancia y estructura poblacional del langostino rojo de profundidad Haliporoides diomedeae (Crustacea: Decapoda: Solenoceridae). Lat. Am. J. Aquat. Res. 37, 371–380 (2009).
    Google Scholar 
    47.R Core Team. R Core Team (2020). R: A language and environment for statistical computing. version 4.0.3. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/ (2019).48.Oksanen J et al. vegan: Community Ecology Package.R package version 2.5-7. https://cran.r-project.org/package=vegan (2020).49.Jones, D. & Frid, C. L. J. Altering intertidal sediment topography: effects on biodiversity and ecosystem functioning. Mar. Ecol. 30, 83–96 (2009).ADS 
    Article 

    Google Scholar 
    50.Wickham, H. ggplot2: Elegant Graphics for Data Analysis (Springer, 2009).
    Google Scholar 
    51.National Geographic & Oceana. Islas Desventuradas. Biodiversidad marina y propuesta de conservación. 58 (2013).52.Levin, L. A. & Nittrouer, C. A. Textural characteristics of sediment on deep seamounts in the eastern Pacific Ocean between 10°N and 30°N. In Seamounts, Islands and Atolls, 43 (eds Keating, B. et al.) 187–203 (Geophysical Monograph, 1987).
    Google Scholar 
    53.Lourido, A., Parra, S. & Serrano, A. Preliminary Results on the Composition and Structure of Soft-Bottom Macrobenthic Communities of a Seamount: the Galicia Bank (NE Atlantic Ocean). Thalassas 35, 1–9 (2019).Article 

    Google Scholar 
    54.Flach, E., Muthumbi, A. & Heip, C. Meiofauna and macrofauna community structure in relation to sediment composition at the iberian margin compared to the goban spur (NE atlantic). Prog. Oceanogr. 52, 433–457 (2002).ADS 
    Article 

    Google Scholar 
    55.Levin, L. A. & Gooday, A. The deep Atlantic Ocean floor. In Ecosystems of the Deep Oceans (ed. Tyler, P.) 187–203 (Elsevier, 2003).
    Google Scholar 
    56.Thistle, D. The deep-sea floor: an overview. In Ecosystems of the World, Ecosystems of the Deep Sea (ed. Tyler, P. A.) 5–37 (Elsevier, 2003).
    Google Scholar 
    57.Louzao, M. et al. Historical macrobenthic community assemblages in the Avilés Canyon, N Iberian Shelf: Baseline biodiversity information for a marine protected area. J. Mar. Syst. 80, 47–56 (2010).Article 

    Google Scholar 
    58.Kon, K., Tsuchiya, Y., Sato, T., Shinagawa, H. & Yamada, Y. Role of microhabitat heterogeneity in benthic faunal communities in sandy bottom sediments of Oura Bay, Shimoda Japan. Reg. Stud. Mar. Sci. 2, 71–76 (2015).Article 

    Google Scholar 
    59.Clark, M. R., Schlacher, T. A., Rowden, A. A., Stocks, K. I. & Consalvey, M. Science priorities for Seamounts: research links to conservation and management. PLoS ONE 7, e29232 (2012).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    60.Zeppilli, D., Pusceddu, A., Trincardi, F. & Danovaro, R. Seafloor heterogeneity influences the biodiversity-ecosystem functioning relationships in the deep sea. Sci. Rep. 6, 1–12 (2016).Article 
    CAS 

    Google Scholar 
    61.de la Torriente, A. et al. Benthic habitat modelling and mapping as a conservation tool for marine protected areas: a seamount in the western Mediterranean. Aquat. Conserv. Mar. Freshw. Ecosyst. 29, 732–750 (2019).Article 

    Google Scholar 
    62.Gallardo, M., Macpherson, E., Tapia-Guerra, J. M., Asorey, C. M. & Sellanes, J. A new species of Munida Leach, 1820 (Crustacea: Decapoda: Anomura: Munididae) from seamounts of the Nazca-Desventuradas Marine Park. PeerJ https://doi.org/10.7717/peerj.10531 (2021).Article 

    Google Scholar 
    63.Castilla, J. C. Islas oceánicas chilenas: conocimiento científico y necesidades de investigación (Ediciones Universidad Católica de Chile, 1987).64.Bahamonde, N. San Félix y San Ambrosio, las islas llamadas Desventuradas 85–99 (1987).65.Díaz-Díaz, O., Bone, D., Rodríguez, C. T. & Delgado-Blas, V. H. Poliquetos de Sudamérica. Especial d, 149 (2017).66.Díaz-Díaz, O. F., Rozbaczylo, N., Sellanes, J. & Tapia-Guerra, J. M. A new species of Eunice Cuvier, 1817 (Polychaeta: Eunicidae) from the slope of the Desventuradas Islands and seamounts of the Nazca Ridge, southeastern Pacific Ocean. A New Species Cuscus 4860, 211–226 (2020).
    Google Scholar 
    67.Kantor, Y. & Sysoev, A. Latiaxis (Babelomurex) naskensis, a new species of Coralliophilidae (Gastropoda) from South-Eastern Pacific. Ruthenica 2, 163–167 (1992).
    Google Scholar 
    68.Sepulveda, J. I. Peces de las Islas Oceánicas Chilenas. In Islas Oceánicas Chilenas: Conocimiento científico y necesidades de Investigaciones. (ed. Castilla, J.) 225–246 (Ediciones Universidad Católica de Chile, 1987).69.Mironov, A. & Detinova., N. Bottom fauna of the Nazca and Sala y Gomez ridges. Plankton and benthos from the Nazca and Sala y Gomez Submarine Ridges 269–278 (1990).70.Lundsten, L. et al. Benthic invertebrate communities on three seamounts off southern and central California USA. Mar. Ecol. Prog. Ser. 374, 23–32 (2009).ADS 
    Article 

    Google Scholar 
    71.Rex, M. A. et al. Global bathymetric patterns of standing stock and body size in the deep-sea benthos. Mar. Ecol. Prog. Ser. 317, 1–8 (2006).ADS 
    Article 

    Google Scholar 
    72.QGIS.org. QGIS Geographic Information System.QGIS Association. Version 3.10. https://www.qgis.org (2020). More

  • in

    Distribution and altitudinal patterns of carbon and nitrogen storage in various forest ecosystems in the central Yunnan Plateau, China

    1.Sharrow, S. H. & Ismail, S. Carbon and nitrogen storage in agroforests, tree plantations, and pastures in western Oregon, USA. Agrofor. Syst. 60(2), 123–130 (2004).Article 

    Google Scholar 
    2.Yang, L. L. et al. Carbon and nitrogen storage and distribution in four forest ecosystems in Liupan Mountains, Northwestern China. Acta. Ecol. Sin. 35(15), 5215–5227 (2015).
    Google Scholar 
    3.Watson, R. T. et al. Land use, land-use change, and forestry. In: Published for the Intergovernmental Panel on Climate Change. Cambridge University Press, pp. 308 (2000).4.Zhao, M. M. et al. Estimation of China’s forest stand biomass carbon sequestration based on the continuous biomass expansion factor model and seven forest inventories from 1977 to 2013. For. Ecol. Manag. 448, 528–534 (2019).Article 

    Google Scholar 
    5.Dale, V. H. et al. Climate change and forest disturbances. Bioscience 51, 723–734 (2001).Article 

    Google Scholar 
    6.Gunderson, P. Carbon—Nitrogen Interactions in Forest Ecosystems—Final Report. Danish Centre for Forest, Landscape and Planning, Denmark (2006).7.Hook, P. B. & Burke, I. C. Biogeochemistry in a shortgrass landscape: control by topography, soil texture, and microclimate. Ecology 81, 2686–2703 (2000).Article 

    Google Scholar 
    8.Vourlitis, G. L., Zorba, G., Pasquini, S. C. & Mustard, R. Carbon and nitrogen storage in soil and litter of southern Californian semi-arid shrublands. J. Arid Environ. 70, 164–173 (2007).ADS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    9.Bonan, G. B. Forests and climate change: forcings, feedbacks, and the climate benefits of forests. Science 320, 1444–1449 (2008).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    10.Liu, G. H., Fu, B. & Fang, J. Y. Carbon dynamics of Chinese forests and its contribution to global carbon balance. Acta. Ecol. Sin. 20(5), 733–740 (2000).
    Google Scholar 
    11.IPCC. Contribution of Working Group I to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change. Cambridge University Press, Cambridge (2007).12.Phillips, J. et al. Live aboveground carbon stocks in natural forests of Colombia. For. Ecol. Manag. 374, 119–128 (2016).Article 

    Google Scholar 
    13.Gibbs, H. K., Brown, B., Niles, J. O. & Foley, J. A. Monitoring and estimating tropical forest carbon stocks: making REDD a reality. Environ. Res. Lett. 2(4), 1–13 (2007).
    Google Scholar 
    14.Aragão, L. et al. Above- and below-ground net primary productivity across ten Amazonian forests on contrasting soils. Biogeosciences 6, 2759–2778 (2009).ADS 
    Article 

    Google Scholar 
    15.Malhi, Y. et al. Comprehensive assessment of carbon productivity, allocation and storage in three Amazonian forests. Glob. Chang. Biol. 15, 1255–1274 (2009).ADS 
    Article 

    Google Scholar 
    16.Post, W. M. & Kwon, K. C. Soil carbon sequestration and land use change: processes and potential. Glob. Chang. Biol. 6, 317–327 (2000).ADS 
    Article 

    Google Scholar 
    17.Ma, J. et al. Ecosystem carbon storage distribution between plant and soil in different forest types in Northeastern China. Ecol. Eng. 81, 353–362 (2015).Article 

    Google Scholar 
    18.Davidson, E. A., Trumbore, S. E. & Amundson, R. Biogeochemistry—soil warming and organic carbon content. Nature 408, 789–790 (2000).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    19.Chaturvedi, R. K. & Raghubanshi, A. S. Aboveground biomass estimation of small diameter woody species of tropical dry forest. New For. 44, 509–519 (2013).Article 

    Google Scholar 
    20.Wen, D. & He, N. P. Forest carbon storage along the north-south transect of eastern china: spatial patterns, allocation, and influencing factors. Ecol. Indic. 61, 960–967 (2016).CAS 
    Article 

    Google Scholar 
    21.Fan, S. et al. A large terrestrial carbon sink in North America implied by atmospheric andoceanic carbon dioxide data and models. Science 282, 442–446 (1998).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    22.Gough, C. M., Vogel, C. S., Schmid, H. P. & Curtis, P. S. Controls on annual forest carbon storage: lessons from the past and predictions for the future. Bioscience 58, 609–622 (2008).Article 

    Google Scholar 
    23.Van Deusen, P. Carbon sequestration potential of forest land: Management for products and bioenergy versus preservation. Biomass Bioenerg. 34, 1687–1694 (2010).Article 

    Google Scholar 
    24.Bradford, J. B., Jensen, N. R., Domke, G. M. & D’Amato, A. W. Potential increases in natural disturbance rates could offset forest management impacts on ecosystem carbon stocks. For. Ecol. Manag. 308, 178–187 (2013).Article 

    Google Scholar 
    25.Park, A. Carbon storage and stand conversion in a pine-dominated boreal forest landscape. For. Ecol. Manag. 340, 70–81 (2015).Article 

    Google Scholar 
    26.Wang, S. J., Zhao, J. X. & Chen, Q. B. Controlling factors of soil CO2 efflux in Pinusyunnanensis across different stand ages. PLoS ONE 10(5), e0127274. https://doi.org/10.1371/journal.pone.0127274 (2015).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    27.Liu, J. et al. Distinct soil bacterial communities in response to the cropping system in a Mollisol of northeast China. Appl. Soil Ecol. 119, 407–416 (2017).Article 

    Google Scholar 
    28.Kavvadias, V. A. et al. Litterfall, litter accumulation and litter decomposition rates in four forest ecosystems in northern Greece. For. Ecol. Manag. 144, 113–127 (2001).Article 

    Google Scholar 
    29.Dai, W. et al. Spatial pattern of carbon stocks in forest ecosystems of a typical subtropical region of Southeastern China. For. Ecol. Manag. 409, 288–297 (2018).Article 

    Google Scholar 
    30.Liu, S. et al. Carbon and nitrogen storage and distribution in different forest ecosystems in the subalpine of western Sichuan. Acta. Ecol. Sin. 37(4), 1074–1083 (2017).CAS 
    Article 

    Google Scholar 
    31.Kern, J., Giani, L., Teixeira, W., Lanza, G. & Glaser, B. What can we learn from ancient fertile anthropic soil (Amazonian Dark Earths, shell mounds, Plaggen soil) for soil carbon sequestration?. CATENA 172, 104–112 (2019).CAS 
    Article 

    Google Scholar 
    32.Zhang, Z. H., Wang, L. C., Luo, J. X. & Zheng, D. R. Study on tree biomass models of Pinus Yunnanensis Faranch in Northwest Yunnan Province. J. Shandong For. Sci. Technol. 4, 4–6 (2011) ((in Chinese)).ADS 

    Google Scholar 
    33.Chen, C. Biomass and production of the Arbor-Layers in Pinus armandii forests. J. Northwestern Coll. For. 1, 1–18 (1984) ((in Chinese)).
    Google Scholar 
    34.Liu, S. R., Su, Y. M., Cai, X. H. & Ma, Q. Y. Aboveground biomass of quercus aquifolioides shrub community and its responses to altitudinal gradients in balangshan mountain, Shichuan province. Sci. Silvae. Sin. 42, 1–7 (2006) ((in Chinese)).
    Google Scholar 
    35.Li, J. L., Liang, S. C. & Chen, S. Z. A preliminary study on the biomass models of keteleeria davidiana var chien-peii colony in qingyan town of Guizhou province. J. Guizhou Normal Univ. 15, 7–12 (1997) ((in Chinese)).CAS 

    Google Scholar 
    36.Yang, L. L. et al. Carbon and nitrogen storage and distribution in four forest ecosystems in Liupan Mountains, northwestern China. Acta. Ecol. Sin. 35, 5215–5227 (2015) ((in Chinese)).
    Google Scholar 
    37.Xie, S. C., Liu, W. Y., Li, S. C. & Yang, G. P. Preliminary studies on the biomass of middle-mountain moist evergreen broadleaved forests in Ailao Mountain, Yunnan. Acta Phytoecol. Sin. 20, 167–176 (1996) ((in Chinese)).
    Google Scholar 
    38.Shen, Y., Tian, D. L., Yan, W. D. & Xiao, Y. Biomass and its distribution of natural secondary quercus fabri + sassafras tsumu+ cunninghamia lanceolata community in Yuanling county, Hunan province. J. Cent. South Univ. For. Technol. 31, 44–51 (2011) ((in Chinese)).CAS 

    Google Scholar 
    39.Guo, L. B. & Gifford, R. M. Soil carbon stocks and land use change: a meta analysis. Global Change Biol. 8, 345–360 (2002).ADS 
    Article 

    Google Scholar 
    40.Zhou, Y. R., Yu, Z. L. & Zhao, S. D. Carbon storage and budget of major Chinese forest types. Acta. Phytoecol. Sin. 24, 518–522 (2000) ((in Chinese)).
    Google Scholar 
    41.Eslamdoust, J. & Sohrabi, H. Carbon storage in biomass, litter, and soil of different native and introduced fast-growing tree plantations in the South Caspian Sea. J. For. Res. 29, 449–457 (2018).CAS 
    Article 

    Google Scholar 
    42.He, Y. J. et al. Carbon storage capacity of monoculture and mixed-species plantations in subtropical China. For. Ecol. Manag. 295, 193–198 (2013).Article 

    Google Scholar 
    43.Ren, H. et al. Spatial and temporal patterns of carbon storage from 1992 to 2002 in forest ecosystems in Guangdong, Southern China. Plant Soil 363, 123–138 (2013).CAS 
    Article 

    Google Scholar 
    44.Ali, F., Khan, N., Ahmad, A. & Khan, A. A. Structure and biomass carbon of Olea ferruginea forests in the foot hills of Malakand division, Hindukush range mountains of Pakistan. Acta. Ecol. Sin. 39, 261–266 (2019).Article 

    Google Scholar 
    45.Ren, Y. et al. Potential for forest vegetation carbon storage in Fujian Province, China, determined from forest inventories. Plant Soil 345, 125–140 (2011).CAS 
    Article 

    Google Scholar 
    46.Fu, W. J. et al. Spatial variation of biomass carbon density in a subtropical region of Southeastern China. Forests 6, 1966–1981 (2015).Article 

    Google Scholar 
    47.Fonseca, W., Alice, F. E. & Rey-Benayas, J. M. Carbon accumulation in aboveground and belowground biomass and soil of different age native forest plantations in the humid tropical lowlands of Costa Rica. New For. 43, 197–211 (2012).Article 

    Google Scholar 
    48.Nelson, A., Saunders, M., Wagner, R. & Weiskittel, A. Early stand production of hybrid poplar and white spruce in mixed and monospecific plantations in eastern Maine. New For. 43, 519–534 (2012).Article 

    Google Scholar 
    49.Gao, Y., Cheng, J., Ma, Z., Zhao, Y. & Su, J. Carbon storage in biomass, litter, and soil of different plantations in a semiarid temperate region of northwest China. Ann. For. Sci. 71, 427–435 (2014).Article 

    Google Scholar 
    50.Fortier, J., Gagnon, D., Truax, B. & Lambert, F. Biomass and volume yield after 6 years in multiclonal hybrid poplar riparian buffer strips. Biomass Bioenerg. 34, 1028–1040 (2010).Article 

    Google Scholar 
    51.González-Rodríguez, H. et al. Litterfall deposition and leaf litter nutrient return in different locations at Northeastern Mexico. Plant Ecol. 212, 1747–1757 (2011).Article 

    Google Scholar 
    52.Pan, Y. et al. A large and persistent carbon sink in the world’s forests. Science https://doi.org/10.1126/science.1201609 (2011).Article 
    PubMed 

    Google Scholar 
    53.Bradford, J. B., Birdsey, R. A., Joyce, L. A. & Ryan, M. G. Tree age, disturbance history and carbon stocks and fluxes in subalpine rocky mountain forests. Global Change Biol. 14, 2882–2897 (2008).ADS 
    Article 

    Google Scholar 
    54.Zhang, C. N., Yan, X. D. & Yang, J. H. Estimation of nitrogen reserves in forest soils of China. J. Southwest Agric. Univ. 26, 572-575+579 (2004) ((in Chinese)).
    Google Scholar 
    55.Lee, K. L., Ong, K. H., King, P. J. H., Chubo, J. K. & Su, D. S. A. Stand productivity, carbon content, and soil nutrients in different stand ages of Acacia mangium in Sarawak, Malaysia. Turk. J. Agric. For. 39, 154–161 (2015).CAS 
    Article 

    Google Scholar 
    56.Cao, B., Domke, G. M., Russell, M. B. & Walters, B. F. Spatial modeling of litter and soil carbon stocks on forest land in the conterminous United States. Sci. Total Environ. 654, 94–106 (2019).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    57.Deng, L., Wang, K. B., Chen, M. L., Shangguan, Z. P. & Sweeney, S. Soil organic carbon storage capacity positively related to forest succession on the Loess Plateau, China. CATENA 110, 1–7 (2013).CAS 
    Article 

    Google Scholar 
    58.Zhu, B. et al. Altitudinal changes in carbon storage of temperate forests on Mt Changbai, Northeast China. J. Plant Res. 123, 439–452 (2010).PubMed 
    Article 

    Google Scholar 
    59.Xie, X. L., Sun, B., Zhou, H. Z. & Li, A. B. Soil organic carbon storage in China. Pedosphere 14, 491–500 (2004).CAS 

    Google Scholar 
    60.Leuschner, C., Moser, G., Bertsch, C., Röderstein, M. & Hertel, D. Large altitudinal increase in tree root/shoot ratio in tropical mountain forests of Ecuador. Basic Appl. Ecol. 8, 219–230 (2007).Article 

    Google Scholar 
    61.Singh, S. P., Adhikari, B. S. & Zobel, D. B. Biomass, productivity, leaf longevity, and forest structure in the central Himalaya. Ecol. Monog. 64, 401–421 (1994).Article 

    Google Scholar 
    62.Kirschbaum, M. U. F. Will changes in soil organic carbon act as a positive or negative feedback on global warming?. Biogeochemistry 27, 753–760 (2000).Article 

    Google Scholar 
    63.Raich, J. W., Russel, A. E., Kitayama, K., Parton, W. J. & Vitousek, P. M. Temperature influences carbon accumulation in moist tropical forests. Ecology 87, 76–87 (2006).PubMed 
    Article 

    Google Scholar  More