Ecology

Falkowski, P. G., Fenchel, T. & Delong, E. F. The microbial engines that drive Earth’s biogeochemical cycles. Science (New York, N.Y.) 320, 1034–1039 (2008).ADS 
CAS 

Google Scholar 
Jørgensen, B. B. & Kasten, S. in Marine Geochemistry, edited by H. D. Schulz & M. Zabel (Springer, 2006), 271–309.Broman, E., Sjöstedt, J., Pinhassi, J. & Dopson, M. Shifts in coastal sediment oxygenation cause pronounced changes in microbial community composition and associated metabolism. Microbiome 5, 96 (2017).PubMed 
PubMed Central 

Google Scholar 
Billerbeck, M. et al. Surficial and deep pore water circulation governs spatial and temporal scales of nutrient recycling in intertidal sand flat sediment. Mar. Ecol. Prog. Ser. 326, 61–76 (2006).ADS 
CAS 

Google Scholar 
Booth, J. M., Fusi, M., Marasco, R., Mbobo, T. & Daffonchio, D. Fiddler crab bioturbation determines consistent changes in bacterial communities across contrasting environmental conditions. Sci. Rep. 9, 3749 (2019).ADS 
PubMed 
PubMed Central 

Google Scholar 
Torti, A., Lever, M. A. & Jørgensen, B. B. Origin, dynamics, and implications of extracellular DNA pools in marine sediments. Mar. Genom. 24(Pt 3), 185–196 (2015).
Google Scholar 
Starke, R., Pylro, V. S. & Morais, D. K. 16S rRNA gene copy number normalization does not provide more reliable conclusions in metataxonomic surveys. Microb. Ecol. 81, 535–539 (2021).CAS 
PubMed 

Google Scholar 
Blazewicz, S. J., Barnard, R. L., Daly, R. A. & Firestone, M. K. Evaluating rRNA as an indicator of microbial activity in environmental communities: Limitations and uses. ISME J. 7, 2061–2068 (2013).CAS 
PubMed 
PubMed Central 

Google Scholar 
de Vrieze, J., Pinto, A. J., Sloan, W. T. & Ijaz, U. Z. The active microbial community more accurately reflects the anaerobic digestion process: 16S rRNA (gene) sequencing as a predictive tool. Microbiome 6, 63 (2018).PubMed 
PubMed Central 

Google Scholar 
Zhang, Y., Zhao, Z., Dai, M., Jiao, N. & Herndl, G. J. Drivers shaping the diversity and biogeography of total and active bacterial communities in the South China Sea. Mol. Ecol. 23, 2260–2274 (2014).CAS 
PubMed 
PubMed Central 

Google Scholar 
Meyer, K. M., Petersen, I. A. B., Tobi, E., Korte, L. & Bohannan, B. J. M. Use of RNA and DNA to identify mechanisms of bacterial community homogenization. Front. Microbiol. 10, 2066 (2019).PubMed 
PubMed Central 

Google Scholar 
Petro, C., Starnawski, P., Schramm, A. & Kjeldsen, K. U. Microbial community assembly in marine sediments. Aquat. Microb. Ecol. 79, 177–195 (2017).
Google Scholar 
Walsh, E. A. et al. Relationship of bacterial richness to organic degradation rate and sediment age in subseafloor sediment. Appl. Environ. Microbiol. 82, 4994–4999 (2016).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Dinsdale, E. A. et al. Microbial ecology of four coral atolls in the Northern Line Islands. PLoS ONE 3, e1584 (2008).ADS 
PubMed 
PubMed Central 

Google Scholar 
Schmitt, S. et al. Salinity, microbe and carbonate mineral relationships in brackish and hypersaline lake sediments: A case study from the tropical Pacific coral atoll of Kiritimati. Depositional Rec. 5, 212–229 (2019).
Google Scholar 
Schneider, D., Arp, G., Reimer, A., Reitner, J. & Daniel, R. Phylogenetic analysis of a microbialite-forming microbial mat from a hypersaline lake of the Kiritimati atoll, Central Pacific. PLoS ONE 8, e66662 (2013).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Zhang, B. et al. Sediment microbial communities and their potential role as environmental pollution indicators in Xuande Atoll, South China Sea. Front. Microbiol. 11, 1011 (2020).PubMed 
PubMed Central 

Google Scholar 
Galand, P. E. et al. Phylogenetic and functional diversity of Bacteria and Archaea in a unique stratified lagoon, the Clipperton atoll (N Pacific). FEMS Microbiol. Ecol. 79, 203–217 (2012).CAS 
PubMed 

Google Scholar 
Stoddart, D. R. The conservation of Aldabra. Geogr. J. 134, 471 (1968).
Google Scholar 
Farrow, G. E. & Brander, K. M. Tidal studies on Aldabra. Phil. Trans. R. Soc. Lond. B 260, 93–121 (1971).ADS 

Google Scholar 
Gaillard, C., Bernier, P. & Gruet, Y. L. lagon d’Aldabra (Seychelles, Océan indien), un modèle pour le paléoenvironnement de Cerin (Kimméridgien supérieur, Jura méridional, France). Geobios 27, 331–348 (1994).
Google Scholar 
Hamylton, S., Spencer, T. & Hagan, A. B. Spatial modelling of benthic cover using remote sensing data in the Aldabra lagoon, western Indian Ocean. Mar. Ecol. Prog. Ser. 460, 35–47 (2012).ADS 

Google Scholar 
Braithwaite, C. J. R. Last interglacial changes in sea level on Aldabra, western Indian Ocean. Sedimentology 67, 3236–3258 (2020).
Google Scholar 
Haverkamp, P. J. et al. Giant tortoise habitats under increasing drought conditions on Aldabra Atoll—Ecological indicators to monitor rainfall anomalies and related vegetation activity. Ecol. Ind. 80, 354–362 (2017).
Google Scholar 
Hughes, R. N. & Gamble, J. C. A quantitative survey of the biota of intertidal soft substrata on Aldabra Atoll, Indian Ocean. Phil. Trans. R. Soc. Lond. B 279, 327–355 (1977).ADS 

Google Scholar 
Braithwaite, C., Casanova, J., Frevert, T. & Whitton, B. A. Recent stromatolites in landlocked pools on Aldabra, Western Indian Ocean. Palaeogeogr. Palaeoclimatol. Palaeoecol. 69, 145–165 (1989).
Google Scholar 
Potts, M. & Whitton, B. A. Nitrogen fixation by blue-green algal communities in the intertidal zone of the lagoon of Aldabra Atoll. Oecologia 27, 275–283 (1977).ADS 
CAS 
PubMed 

Google Scholar 
Potts, M. & Whitton, B. A. Vegetation of the intertidal zone of the lagoon of Aldabra, with particular reference to the photosynthetic prokaryotic communities. Proc. R. Soc. Lond. B. 208, 13–55 (1980).ADS 

Google Scholar 
Meyers, P. A. Preservation of elemental and isotopic source identification of sedimentary organic matter. Chem. Geol. 114, 289–302 (1994).ADS 
CAS 

Google Scholar 
Choi, A., Lee, K., Oh, H.-M., Feng, J. & Cho, J.-C. Litoricola marina sp. nov.. Int. J. Syst. Evolut. Microbiol. 60, 1303–1306 (2010).CAS 

Google Scholar 
Durham, B. P. et al. Draft genome sequence of marine alphaproteobacterial strain HIMB11, the first cultivated representative of a unique lineage within the Roseobacter clade possessing an unusually small genome. Stand Genom. Sci. 9, 632–645 (2014).
Google Scholar 
Boehm, A. B., Yamahara, K. M. & Sassoubre, L. M. Diversity and transport of microorganisms in intertidal sands of the California coast. Appl. Environ. Microbiol. 80, 3943–3951 (2014).ADS 
PubMed 
PubMed Central 

Google Scholar 
Probandt, D., Eickhorst, T., Ellrott, A., Amann, R. & Knittel, K. Microbial life on a sand grain: From bulk sediment to single grains. ISME J. 12, 623–633 (2018).PubMed 

Google Scholar 
Wong, H. L., Smith, D.-L., Visscher, P. T. & Burns, B. P. Niche differentiation of bacterial communities at a millimeter scale in Shark Bay microbial mats. Sci. Rep. 5, 15607 (2015).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Dupraz, C., Visscher, P. T., Baumgartner, L. K. & Reid, R. P. Microbe-mineral interactions: Early carbonate precipitation in a hypersaline lake (Eleuthera Island, Bahamas). Sedimentology 51, 745–765 (2004).ADS 
CAS 

Google Scholar 
Diaz, M. R., Piggot, A. M., Eberli, G. P. & Klaus, J. S. Bacterial community of oolitic carbonate sediments of the Bahamas Archipelago. Mar. Ecol. Prog. Ser. 485, 9–24 (2013).ADS 

Google Scholar 
Cui, H., Yang, K., Pagaling, E. & Yan, T. Spatial and temporal variation in enterococcal abundance and its relationship to the microbial community in Hawaii beach sand and water. Appl. Environ. Microbiol. 79, 3601–3609 (2013).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Petriglieri, F., Nierychlo, M., Nielsen, P. H. & McIlroy, S. J. In situ visualisation of the abundant Chloroflexi populations in full-scale anaerobic digesters and the fate of immigrating species. PLoS ONE 13, e0206255 (2018).CAS 
PubMed 
PubMed Central 

Google Scholar 
Wietz, M., Gram, L., Jørgensen, B. & Schramm, A. Latitudinal patterns in the abundance of major marine bacterioplankton groups. Aquat. Microb. Ecol. 61, 179–189 (2010).
Google Scholar 
Wemheuer, B. et al. Impact of a phytoplankton bloom on the diversity of the active bacterial community in the southern North Sea as revealed by metatranscriptomic approaches. FEMS Microbiol. Ecol. 87, 378–389 (2014).CAS 
PubMed 

Google Scholar 
Heywood, K. J., Stevens, D. P. & Bigg, G. R. Eddy formation behind the tropical island of Aldabra. Deep Sea Res. Part I 43, 555–578 (1996).
Google Scholar 
Pérez-Cataluña, A. et al. Revisiting the taxonomy of the genus Arcobacter: Getting order from the chaos. Front. Microbiol. 9, 2077 (2018).PubMed 
PubMed Central 

Google Scholar 
Revsbech, N. P. & Jørgensen, B. B. Microelectrodes: Their Use in Microbial Ecology. In Advances in Microbial Ecology (ed. Marshall, K. C.) 293–352 (Springer, 1989).
Google Scholar 
Watson, J. et al. Reductively debrominating strains of Propionigenium maris from burrows of bromophenol-producing marine infauna. Int. J. Syst. Evol. Microbiol. 50(Pt 3), 1035–1042 (2000).CAS 
PubMed 

Google Scholar 
Sasi, J. T. S., Rahul, K., Ramaprasad, E. V. V., Sasikala, C. & Ramana, C. V. Arcobacter anaerophilus sp. nov., isolated from an estuarine sediment and emended description of the genus Arcobacter. Int. J. Syst. Evolut. Microbiol. 63, 4619–4625 (2013).
Google Scholar 
Rinke, C. et al. High genetic similarity between two geographically distinct strains of the sulfur-oxidizing symbiont ‘Candidatus Thiobios zoothamnicoli’. FEMS Microbiol. Ecol. 67, 229–241 (2009).CAS 
PubMed 

Google Scholar 
Vartoukian, S. R., Palmer, R. M. & Wade, W. G. The division “Synergistes”. Anaerobe 13, 99–106 (2007).CAS 
PubMed 

Google Scholar 
Janssen, P. H. & Liesack, W. Succinate decarboxylation by Propionigenium maris sp. nov., a new anaerobic bacterium from an estuarine sediment. Arch. Microbiol. 164, 29–35 (1995).CAS 
PubMed 

Google Scholar 
Shiozaki, T. et al. Nitrification and its influence on biogeochemical cycles from the equatorial Pacific to the Arctic Ocean. ISME J. 10, 2184–2197 (2016).CAS 
PubMed 
PubMed Central 

Google Scholar 
González-Domenech, C. M., Martínez-Checa, F., Béjar, V. & Quesada, E. Denitrification as an important taxonomic marker within the genus Halomonas. Syst. Appl. Microbiol. 33, 85–93 (2010).PubMed 

Google Scholar 
Farmer, J. J., Michael, J. J., Brenner, F. W., Cameron, D. N. & Birkhead, K. M. The Book. In Bergey’s Manual of Systematics of Archaea and Bacteria (eds Whitman, W. B. et al.) 1–79 (Wiley, 2016).
Google Scholar 
Ventosa, A. & Haba, R. R. in Bergey’s Manual of Systematics of Archaea and Bacteria, edited by W. B. Whitman, et al. (Wiley, 2015), 1–16.Lloyd, K. G. Time as a microbial resource. Environ. Microbiol. Rep. 13, 18–21 (2021).PubMed 

Google Scholar 
Holguin, G., Vazquez, P. & Bashan, Y. The role of sediment microorganisms in the productivity, conservation, and rehabilitation of mangrove ecosystems: An overview. Biol. Fertil. Soils 33, 265–278 (2001).CAS 

Google Scholar 
Nanca, C. L., Neri, K. D., Ngo, A. C. R., Bennett, R. M. & Dedeles, G. R. Degradation of polycyclic aromatic hydrocarbons by moderately halophilic bacteria from Luzon salt beds. J. Health Pollut. 8, 180915 (2018).PubMed 
PubMed Central 

Google Scholar 
Bird, J. T. et al. Uncultured microbial phyla suggest mechanisms for multi-thousand-year subsistence in Baltic Sea sediments. MBio 10, 1002 (2019).
Google Scholar 
Moulton, O. M. et al. Microbial associations with macrobiota in coastal ecosystems: Patterns and implications for nitrogen cycling. Front. Ecol. Environ. 14, 200–208 (2016).
Google Scholar 
Park, S., Park, J.-M., Kang, C.-H. & Yoon, J.-H. Aestuariispira insulae gen. nov., sp. nov., a lipolytic bacterium isolated from a tidal flat. Int. J. Syst. Evol. Microbiol. 64, 1841–1846 (2014).CAS 
PubMed 

Google Scholar 
Evans, M. V. et al. Members of Marinobacter and Arcobacter influence system biogeochemistry during early production of hydraulically fractured natural gas wells in the Appalachian Basin. Front. Microbiol. 9, 2646 (2018).PubMed 
PubMed Central 

Google Scholar 
Wilhelm, R. C. Following the terrestrial tracks of Caulobacter – redefining the ecology of a reputed aquatic oligotroph. ISME J. 12, 3025–3037 (2018).PubMed 
PubMed Central 

Google Scholar 
Suzuki, D., Ueki, A., Amaishi, A. & Ueki, K. Desulfopila aestuarii gen. nov., sp. nov., a Gram-negative, rod-like, sulfate-reducing bacterium isolated from an estuarine sediment in Japan. Int. J. Syst. Evol. Microbiol. 57, 520–526 (2007).CAS 
PubMed 

Google Scholar 
Dawson, K. S., Scheller, S., Dillon, J. G. & Orphan, V. J. Stable isotope phenotyping via cluster analysis of nanoSIMS data as a method for characterizing distinct microbial ecophysiologies and sulfur-cycling in the environment. Front. Microbiol. 7, 774 (2016).PubMed 
PubMed Central 

Google Scholar 
Fadhlaoui, K. et al. Fusibacter fontis sp. nov., a sulfur-reducing, anaerobic bacterium isolated from a mesothermic Tunisian spring. Int. J. Syst. Evol. Microbiol. 65, 3501–3506 (2015).CAS 
PubMed 

Google Scholar 
Kjeldsen, K. U. et al. Diversity of sulfate-reducing bacteria from an extreme hypersaline sediment, Great Salt Lake (Utah). FEMS Microbiol. Ecol. 60, 287–298 (2007).CAS 
PubMed 

Google Scholar 
Schneider, D., Wemheuer, F., Pfeiffer, B. & Wemheuer, B. Extraction of total DNA and RNA from marine filter samples and generation of a cDNA as universal template for marker gene studies. Methods Mol. Biol. Clifton N J 1539, 13–22 (2017).CAS 

Google Scholar 
Klindworth, A. et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 41, e1 (2013).CAS 
PubMed 

Google Scholar 
Berkelmann, D., Schneider, D., Hennings, N., Meryandini, A. & Daniel, R. Soil bacterial community structures in relation to different oil palm management practices. Sci. Data 7, 421 (2020).CAS 
PubMed 
PubMed Central 

Google Scholar 
von Hoyningen-Huene, A. J. E. et al. Bacterial succession along a sediment porewater gradient at Lake Neusiedl in Austria. Sci. data 6, 163 (2019).
Google Scholar 
Tange, O. Gnu parallel-the command-line power tool. login: The USENIX Mag. 36, 42–47 (2011).Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: An ultra-fast all-in-one FASTQ preprocessor. Bioinformatics (Oxford, England) 34, i884–i890 (2018).
Google Scholar 
Zhang, J., Kobert, K., Flouri, T. & Stamatakis, A. PEAR: A fast and accurate Illumina paired-end read merger. Bioinformatics (Oxford, England) 30, 614–620 (2014).CAS 

Google Scholar 
Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet j. 17, 10 (2011).
Google Scholar 
Rognes, T., Flouri, T., Nichols, B., Quince, C. & Mahé, F. VSEARCH: A versatile open source tool for metagenomics. PeerJ 4, e2584 (2016).Edgar, R. C. UNOISE2: Improved error-correction for Illumina 16S and ITS amplicon sequencing (2016).Quast, C. et al. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596 (2013).CAS 
PubMed 

Google Scholar 
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 

Google Scholar 
SILVAngs. SILVAngs – rDNA-based microbial community analysis using next-generation sequencing (NGS) data – user guide. Available at https://www.arb-silva.de/fileadmin/silva_databases/sngs/SILVAngs_User_Guide.pdf (2017).McDonald, D. et al. The Biological Observation Matrix (BIOM) format or: How I learned to stop worrying and love the ome-ome. GigaScience 1, 7 (2012).PubMed 
PubMed Central 

Google Scholar 
Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).CAS 
PubMed 
PubMed Central 

Google Scholar 
Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2–approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).ADS 
PubMed 
PubMed Central 

Google Scholar 
Rambaut, A. FigTree – tree figure drawing tool (2018).R Core Team. R: A language and environment for statistical computing. (R Foundation for Statistical Computing, 2020).RStudio Team. RStudio: integrated development for R (RStudio Inc., 2021).Chen, L. et al. GMPR: A robust normalization method for zero-inflated count data with application to microbiome sequencing data. PeerJ 6, e4600 (2018).PubMed 
PubMed Central 

Google Scholar 
Pereira, M. B., Wallroth, M., Jonsson, V. & Kristiansson, E. Comparison of normalization methods for the analysis of metagenomic gene abundance data. BMC Genom. 19, 274 (2018).
Google Scholar 
Andersen, K. S., Kirkegaard, R. H., Karst, S. M. & Albertsen, M. ampvis2: an R package to analyse and visualise 16S rRNA amplicon data (2018).Oksanen, J. et al. vegan: Community ecology package (2018).Wickham, H. ggplot2: Elegant Graphics for Data Analysis (Springer, 2016).Kembel, S. W. et al. Picante: R tools for integrating phylogenies and ecology. Bioinformatics (Oxford, England) 26, 1463–1464 (2010).CAS 

Google Scholar 
Harrel Jr, F. E., with contributions from Charles Dupont and many others. Hmisc: Harrell Miscellaneous (2021).Wei, T. & Simko, V. R package “corrplot”: Visualization of a Correlation (2021).de Cáceres, M. & Legendre, P. Associations between species and groups of sites: Indices and statistical inference. Ecology 90, 3566–3574 (2009).PubMed 

Google Scholar 
Shannon, P. et al. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498–2504 (2003).CAS 
PubMed 
PubMed Central 

Google Scholar 
Esri Inc. ArcGIS Desktop (Esri Inc., 2019).Inkscape Developers. Inkscape (2020).Fussmann, D. et al. Authigenic formation of Ca–Mg carbonates in the shallow alkaline Lake Neusiedl, Austria. Biogeosciences 17, 2085–2106 (2020).ADS 
CAS 

Google Scholar 
Parkhurst, D. L. & Appelo, C. A. in U.S. Geological Survey Techniques and Methods (2013), Vol. 6, pp. 2328–7055. More

Slade, C. & Law, B. The other half of the coastal State Forest estate in New South Wales; The value of informal forest reserves for conservation. Aust. Zool. 39, 359–370. https://doi.org/10.7882/AZ.2016.011 (2017).Article 

Google Scholar 
Munks, S. A., Chuter, A. E. & Koch, A. J. ‘Off-reserve’ management in practice: Contributing to conservation of biodiversity over 30 years of Tasmania’s forest practices system. For. Ecol. Manag. 465, 117941. https://doi.org/10.1016/j.foreco.2020.117941 (2020).Article 

Google Scholar 
Lande, R. Demographic models of the northern spotted owl (Strix occidentalis caurina). Oecologia 75, 601–607 (1988).ADS 
CAS 
Article 

Google Scholar 
Franklin, C. M. A., Macdonald, S. E. & Nielsen, S. E. Can retention harvests help conserve wildlife? Evidence for vertebrates in the boreal forest. Ecosphere 10(3), e02632 (2019).Article 

Google Scholar 
McAlpine, C. A. et al. Conserving koalas: A review of the contrasting regional trends, outlooks and policy challenges. Biol. Conserv. 192, 226–236. https://doi.org/10.1016/j.biocon.2015.09.020 (2015).Article 

Google Scholar 
Kavanagh, R. P. & Stanton, M. A. Koalas use young Eucalyptus plantations in an agricultural landscape on the Liverpool Plains, New South Wales. Ecol. Manag. Restor. 13, 297–305. https://doi.org/10.1111/emr.12005 (2012).Article 

Google Scholar 
Matthews, A., Lunney, D., Gresser, S. & Maitz, W. Movement patterns of koalas in remnant forest after fire. Aust. Mammal. 38, 91–104. https://doi.org/10.1071/AM14010 (2016).Article 

Google Scholar 
McAlpine, C. A. et al. The importance of forest area and configuration relative to local habitat factors for conserving forest mammals: A case study of koalas in Queensland, Australia. Biol. Conserv. 132, 153–165. https://doi.org/10.1016/j.biocon.2006.03.021 (2006).Article 

Google Scholar 
Beyer, H. L. et al. Management of multiple threats achieves meaningful koala conservation outcomes. J. Appl. Ecol. 55, 1966–1975. https://doi.org/10.1111/1365-2664.13127 (2018).Article 

Google Scholar 
Kavanagh, R. P., Stanton, M. A. & Brassil, T. E. Koalas continue to occupy their previous home-ranges after selective logging in Callitris–Eucalyptus forest. Wildl. Res. 34, 94–107. https://doi.org/10.1071/WR06126 (2007).Article 

Google Scholar 
Kavanagh, R. P., Debus, S., Tweedie, T. & Webster, R. Distribution of nocturnal forest birds and mammals in north-eastern New South Wales: Relationships with environmental variables and management history. Wildl. Res. 22, 359–377. https://doi.org/10.1071/WR9950359 (1995).Article 

Google Scholar 
Roberts, P. Associations Between Koala Faecal Pellets and Trees at Dorrigo, M.Sc. Thesis (University of New England, 1998).
Google Scholar 
Smith, A. P. Koala conservation and habitat requirements in a timber production forest in north-east New South Wales. In Conservation of Australia’s Forest Fauna (ed. Lunney, D.) 591–611 (Royal Zoological Society of New South Wales, 2004).Chapter 

Google Scholar 
Radford Miller, S. Aspects of the ecology of the koala, Phascolarctos cinereus, in a tall coastal production forest in north eastern New South Wales. PhD thesis (Southern Cross University, 2012).Law, B. S. et al. Passive acoustics and sound recognition provide new insights on status and resilience of an iconic endangered marsupial (koala Phascolarctos cinereus) to timber harvesting. PLoS One 13(10), e0205075. https://doi.org/10.1371/journal.pone.0205075 (2018).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Ellis, W. et al. Koala habitat use and population density: Using field data to test the assumptions of ecological models. Aust. Mammal. 35, 160–165. https://doi.org/10.1071/AM12023 (2013).Article 

Google Scholar 
Ashman, K. R., Rendall, A. R., Symonds, M. R. E. & Whisson, D. Understanding the role of plantations in the abundance of an arboreal folivore. Landsc. Urban Plan. 193, 103684. https://doi.org/10.1016/j.landurbplan.2019.103684 (2020).Article 

Google Scholar 
Cristescu, R. H., Rhodes, J., Frere, C. & Banks, P. B. Is restoring flora the same as restoring fauna? Lessons learned from koalas and mining rehabilitation. J. Appl. Ecol. 50(2), 423–431. https://doi.org/10.1111/1365-2664.12046 (2013).Article 

Google Scholar 
Chandler, R. B. & Royle, J. A. Spatially explicit models for inference about density in unmarked or partially marked populations. Ann. Appl. Stat. 7(2), 936–954. https://doi.org/10.1214/12-AOAS610 (2013).MathSciNet 
Article 
MATH 

Google Scholar 
Law, B., Gonsalves, L., Burgar, J., Brassil, T., Kerr, I., Wilmott, L., Madden, K., Smith, M., Mella, V., Crowther, M., Krockenberger, M., Rus, A., Pietsch, R., Truskinger, A., Eichinski, P. & Roe, P. Validation of spatial count models to estimate koala Phascolarctos cinereus density from acoustic arrays. Wildl. Res. (in press).MacKenzie, D. I. et al. Occupancy Estimation and Modeling: Inferring Patterns and Dynamics of Species Occurrence (Elsevier, 2006).MATH 

Google Scholar 
Smith, M. Behaviour of the Koala, Phascolarctos cinereus (Goldfuss), in Captivity III. Vocalisations. Wildl. Res. 7, 13–34. https://doi.org/10.1071/WR9800013 (1980).Article 

Google Scholar 
Ellis, W. et al. Koala bellows and their association with the spatial dynamics of free-ranging koalas. Behav. Ecol. 22, 372–377. https://doi.org/10.1093/beheco/arq216 (2011).Article 

Google Scholar 
Ellis, W. et al. The role of bioacoustic signals in koala sexual selection: Insights from seasonal patterns of associations revealed with gps-proximity units. PLoS One 10(7), e0130657. https://doi.org/10.1371/journal.pone.0130657 (2015).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Martin, R. W. Overbrowsing and decline of a population of the koala, Phascolarctos cinereus, in Victoria II. Population condition. Aust. Wildl. Res. 12, 367–375 (1985).ADS 
Article 

Google Scholar 
Penn, A. M. et al. Demographic forecasting in koala conservation. Conserv. Biol. 14(3), 629–638. https://doi.org/10.1046/j.1523-1739.2000.99385.x (2000).Article 

Google Scholar 
Watchorn, D. J. & Whisson, D. A. Quantifying the interactions between koalas in a high-density population during the breeding period. Aust. Mammal. 42(1), 28–37. https://doi.org/10.1071/AM18027 (2019).Article 

Google Scholar 
Crowther, M. S. et al. Comparison of three methods of estimating the population size of an arboreal mammal in a fragmented rural landscape. Wildl. Res. 48, 105–114. https://doi.org/10.1071/WR19148 (2020).Article 

Google Scholar 
Witt, R. R. et al. Real-time drone derived thermal imagery outperforms traditional survey methods for an arboreal forest mammal. PLoS One 15(11), e0242204. https://doi.org/10.1371/journal.pone.0242204 (2020).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Law, B.S, Gonsalves, L., Burgar, J., Brassil, T., Kerr I. & O’Loughlin C. Fire severity and its local extent are key to assessing impacts of Australian mega-fires on koala (Phascolarctos cinereus) density. Glob. Ecol. Biogeogr. 00, 1–13. https://doi.org/10.1111/geb.13458 (2022).Hynes, E. F., Whisson, D. A. & Di Stefano, J. Response of an arboreal species to plantation harvest. For. Ecol. Manag. 490, 119092. https://doi.org/10.1016/j.foreco.2021.119092 (2021).Article 

Google Scholar 
Law, B., Gonsalves, L., Burgar, J., Brassil, T., Kerr, I., O’Loughlin, C., Eichinski, P. & Roe, P. Regulated timber harvesting does not reduce koala density in north-east forests of New South Wales. Unpubl. Report to NSW (Natural Resources Commission, 2021).Phillips, S. Aversive behaviour by koalas (Phascolarctos cinereus) during the course of a music festival in northern New South Wales, Australia. Aust. Mammal. 38(2), 158–163. https://doi.org/10.1071/AM15006 (2016).Article 

Google Scholar 
Fedrowitz, K. et al. Can retention forestry help conserve biodiversity? A meta-analysis. J. Appl. Ecol. 51, 1669–1679. https://doi.org/10.1111/1365-2664.12289 (2014).Article 
PubMed 
PubMed Central 

Google Scholar 
Mori, A. S. & Kitagawa, R. Retention forestry as a major paradigm for safeguarding forest biodiversity in productive landscapes: A global meta-analysis. Biol. Conserv. 175, 65–73. https://doi.org/10.1016/j.biocon.2014.04.016 (2014).Article 

Google Scholar 
Law, B. et al. Development and field validation of a regional, management-scale habitat model: A koala Phascolarctos cinereus case study. Ecol. Evol. 7, 7475–7489. https://doi.org/10.1002/ece3.3300 (2017).Article 
PubMed 
PubMed Central 

Google Scholar 
Phillips, S., Wallis, K. & Lane, A. Quantifying the impacts of bushfire on populations of wild koalas (Phascolarctos cinereus): Insights from the 2019/20 fire season. Ecol. Manag. Restor. 22, 80–88. https://doi.org/10.1111/emr.12458 (2021).Article 

Google Scholar 
Kramer, A. et al. California spotted owl habitat selection in a fire-managed landscape suggests conservation benefit of restoring historical fire regimes. For. Ecol. Manag. 479, 118576 (2021).Article 

Google Scholar 
Jones, G. M. et al. Megafire causes persistent loss of an old-forest species. Anim. Conserv. 24, 925–936. https://doi.org/10.1111/acv.12697 (2021).Article 

Google Scholar 
Hagens, S. V., Rendall, A. R. & Whisson, D. A. Passive acoustic surveys for predicting species’ distributions: Optimising detection probability. PLoS One 13(7), e0199396. https://doi.org/10.1371/journal.pone.0199396 (2018).Article 
PubMed 
PubMed Central 

Google Scholar 
Law, B. et al. Using passive acoustic recording and automated call identification to survey koalas in the southern forests of New South Wales. Aust. Zool. 40, 477–486 (2019).Article 

Google Scholar 
Towsey, M., Planitz, B., Nantes, A., Wimmer, J. & Roe, P. A toolbox for animal call recognition. Bioacoustics 21, 107–125. https://doi.org/10.1080/09524622.2011.648753 (2012).Article 

Google Scholar 
Royle, J. A. & Dorazio, R. M. Parameter-expanded data augmentation for Bayesian analysis of capture–recapture models. J. Ornithol. 152(2), 521–537 (2012).Article 

Google Scholar 
Royle, J. A., Chandler, R. B., Sollmann, R. & Gardner, B. Spatial Capture–Recapture 1st edn. (Elsevier, 2014). https://doi.org/10.1016/B978-0-12-405939-9.00020-7.Book 

Google Scholar 
Clark, J. D. Comparing clustered sampling designs for spatially explicit estimation of population density. Popul. Ecol. 61(1), 93–101. https://doi.org/10.1002/1438-390X.1011 (2019).Article 

Google Scholar 
Sun, C. C., Fuller, A. K. & Royle, J. A. Trap configuration and spacing influences parameter estimates in spatial capture-recapture models. PLoS One 9(2), e88025. https://doi.org/10.1371/journal.pone.0088025 (2014).ADS 
CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Plummer, M. JAGS: A program for analysis of Bayesian graphical models using Gibbs sampling. In Proceedings of the 3rd International Workshop on Distributed Statistical Computing, Vol. 124(125.10), pp. 1–10 (2003).Plummer, M. rjags: Bayesian graphical models using MCMC. R package version 4(6) (2016).Burgar, J. M., Stewart, F. E., Volpe, J. P., Fisher, J. T. & Burton, A. C. Estimating density for species conservation: Comparing camera trap spatial count models to genetic spatial capture-recapture models. Glob. Ecol. Conserv. 15, e00411. https://doi.org/10.1016/j.gecco.2018.e00411 (2018).Article 

Google Scholar 
Stewart-Oaten, A., Murdoch, W. W. & Parker, K. R. Environmental impact assessment: “Pseudoreplication” in time?. Ecology 67(4), 929–940. https://doi.org/10.2307/1939815 (1986).Article 

Google Scholar 
Stewart-Oaten, A. & Bence, J. R. Temporal and spatial variation in environmental impact assessment. Ecol. Monogr. 71(2), 305–339. https://doi.org/10.1890/0012-9615(2001)071[0305:TASVIE]2.0.CO;2 (2001).Article 

Google Scholar  More

IPCC. Climate change 2013: The Physical Science Basis. Contribution of Working Group I to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change (Cambridge University Press, 2013).
Google Scholar 
Pachauri, R. K. et al. Climate change 2014: Synthesis report. Contribution of Working Groups I, II and III to the fifth assessment report of the Intergovernmental Panel on Climate Change (IPCC, 2014).
Google Scholar 
Reay, D. S. et al. Global agriculture and nitrous oxide emissions. Nat. Clim. Change 2, 410–416 (2012).ADS 
CAS 

Google Scholar 
Jassal, R. S., Black, T. A., Roy, R. & Ethier, G. Effect of nitrogen fertilization on soil CH4 and N2O fluxes, and soil and bole respiration. Geoderma 162, 182–186 (2011).ADS 
CAS 

Google Scholar 
Hu, H. W., Chen, D. & He, J. Z. Microbial regulation of terrestrial nitrous oxide formation: Understanding the biological pathways for prediction of emission rates. FEMS Microbiol. Rev. 39, 729–749 (2015).CAS 
PubMed 

Google Scholar 
Bateman, E. J. & Baggs, E. M. Contributions of nitrification and denitrification to N2O emissions from soils at different water-filled pore space. Biol. Fertil. Soils 41, 379–388 (2005).CAS 

Google Scholar 
Yang, Y. D., Hu, Y. G., Wang, Z. M. & Zeng, Z. H. Variations of the nirS-, nirK-, and nosZ-denitrifying bacterial communities in a northern Chinese soil as affected by different long-term irrigation regimes. Environ. Sci. Pollut. Res. 25, 14057–14067 (2018).CAS 

Google Scholar 
Pan, Y., Ye, L., Ni, B. & Yuan, Z. Effect of pH on N2O reduction and accumulation during denitrification by methanol utilizing denitrifiers. Water Res. 46, 4832–4840 (2012).CAS 
PubMed 

Google Scholar 
Hallin, S., Philippot, L., Loffler, F. E., Sanford, R. A. & Jones, C. M. Genomics and ecology of novel N2O-reducing microorganisms. Trends Microbiol. 1485, 43–55 (2017).
Google Scholar 
Yang, L., Zhang, X. & Ju, X. Linkage between N2O emission and functional gene abundance in an intensively managed calcareous fluvo-aquic soil. Sci. Rep. 7, 43283 (2017).ADS 
PubMed 
PubMed Central 

Google Scholar 
Cui, P. Y. et al. Long-term organic and inorganic fertilization alters temperature sensitivity of potential N2O emissions and associated microbes. Soil Biol. Biochem. 93, 131–141 (2016).CAS 

Google Scholar 
Gerber, J. S. et al. Spatially explicit estimates of N2O emissions from croplands suggest climate mitigation opportunities from improved fertilizer management. Glob. Change Biol. 22, 3383–3394 (2016).ADS 

Google Scholar 
Shcherbak, I., Millar, N. & Robertson, G. P. Global metaanalysis of the nonlinear response of soil nitrous oxide (N2O) emissions to fertilizer nitrogen. Proc. Natl. Acad. Sci. 111, 9199–9204 (2014).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Wang, J., Chadwick, D. R., Cheng, Y. & Yan, X. Global analysis of agricultural soil denitrification in response to fertilizer nitrogen. Sci. Total Environ. 616, 908–917 (2018).ADS 
PubMed 

Google Scholar 
Albanito, F. et al. Direct nitrous oxide emissions from tropical and sub-tropical agricultural systems—A review and modelling of emission factors. Sci. Rep. 7, 44235 (2017).ADS 
PubMed 
PubMed Central 

Google Scholar 
Wolsing, M. & Priemé, A. Observation of high seasonal variation in community structure of denitrifying bacteria in arable soil receiving artificial fertilizer and cattle manure by determining T-RFLP of nir gene fragments. FEMS Microbiol. Ecol. 48, 261–271 (2004).CAS 
PubMed 

Google Scholar 
Akiyama, H., McTaggart, I. P., Ball, B. C. & Scott, A. N2O, NO, and NH3 emissions from soil after the application of organic fertilizers, urea and water. Water Air Soil Pollut. 156, 113–129 (2004).ADS 
CAS 

Google Scholar 
Wang, Y. Y. et al. Responses of N2O reductase gene (nosZ)-denitrifer communities to long-term fertilization follow a depth pattern in calcareous purplish paddy soil. J. Integr. Agric. 16, 2597–2611 (2017).CAS 

Google Scholar 
Fernandez-Luqueno, F. et al. Emission of CO2 and N2O from soil cultivated with common bean (Phaseolus vulgaris L.) fertilized with different N sources. Sci. Total Environ. 407, 4289–4296 (2009).ADS 
CAS 
PubMed 

Google Scholar 
Yin, C. et al. Different denitrification potential of aquic brown soil in Northeast China under inorganic and organic fertilization accompanied by distinct changes of nirS-and nirK-denitrifying bacterial community. Eur. J. Soil Biol. 65, 47–56 (2014).CAS 

Google Scholar 
Harter, J. et al. Linking N2O emissions from biochar-amended soil to the structure and function of the N-cycling microbial community. ISME J. 8, 660–674 (2013).PubMed 
PubMed Central 

Google Scholar 
Hai, B. et al. Quantification of key genes steering the microbial nitrogen cycle in the rhizosphere of sorghum cultivars in tropical agroecosystems. Appl. Environ. Microbiol. 75, 4993–5000 (2009).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Huang, R. et al. Nitrous oxide emission and the related denitrifier community: A short-term response to organic manure substituting chemical fertilizer. Ecotoxicol. Environ. Saf. 192, 110291 (2020).CAS 
PubMed 

Google Scholar 
Xu, X. et al. NosZ clade II rather than clade I determine in situ N2O emissions with different fertilizer types under simulated climate change and its legacy. Soil Biol. Biochem. 150, 107974 (2020).CAS 

Google Scholar 
Henderson, S. L. et al. Changes in denitrifier abundance, denitrification gene mRNA levels, nitrous oxide emissions, and denitrification in anoxic soil microcosms amended with glucose and plant residues. Appl. Environ. Microbiol. 76, 2155–2164 (2010).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Palmer, K., Biasi, C. & Horn, M. A. Contrasting denitrififier communities relate to contrasting N2O emission patterns from acidic peat soils in arctic tundra. ISME J. 6, 1058–1077 (2012).CAS 
PubMed 

Google Scholar 
Dandie, C. E. et al. Abundance, diversity and functional gene expression of denitrifier communities in adjacent riparian and agricultural zones. FEMS Microbiol. Ecol. 77, 69–82 (2011).CAS 
PubMed 

Google Scholar 
Avrahami, S., Conrad, R. & Braker, G. Effect of soil ammonium concentration on N2O release and on the community structure of ammonia oxidizers and denitrifiers. Appl. Environ. Microbiol. 68, 5685–5692 (2002).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Yang, Y. J. et al. Compost supplementation with nitrogen loss and greenhouse gas emissions during pig manure composting. Bioresour. Technol. 297, 122435 (2019).PubMed 

Google Scholar 
Yang, Y. J. et al. Exploring the microbial mechanisms of organic matter transformation during pig manure composting amended with bean dregs and biochar. Bioresour. Technol. 313, 123647 (2020).CAS 
PubMed 

Google Scholar 
Yang, J. H., Wang, C. L. & Dai, H. L. Agricultural Soil Analysis and Environmental Monitoring (China Land Press, 2008) (in Chinese).
Google Scholar 
Wang, Q. R., Li, Y. C. & Klassen, W. Changes of soil microbial biomass carbon and nitrogen with cover crops and irrigation in a tomato field. J. Plant Nutr. 30, 623–639 (2007).CAS 

Google Scholar 
Moore, J. M., Klose, S. & Tabatabai, M. A. Soil microbial biomass carbon and nitrogen as affected by cropping systems. Biol. Fertil. Soils 31, 200–210 (2000).CAS 

Google Scholar 
Jones, D. L. & Willett, V. B. Experimental evaluation of methods to quantify dissolved organic nitrogen (DON) and dissolved organic carbon (DOC) in soil. Soil Biol. Biochem. 38, 991–999 (2006).CAS 

Google Scholar 
Ghani, A., Dexter, M. & Perrott, K. W. Hot-water extractable carbon in soils: A sensitive measurement for determining impacts of fertilization, grazing and cultivation. Soil Biol. Biochem. 35, 1231–1243 (2003).CAS 

Google Scholar 
Huang, R. et al. Variation in N2O emission and N2O related microbial functional genes in straw- and biochar-amended and non-amended soils. Appl. Soil. Ecol. 137, 57–68 (2019).
Google Scholar 
Yang, Y. J. et al. Soil organic carbon transformation and dynamics of microorganisms under different organic amendments. Sci. Total Environ. 750, 141719 (2021).ADS 
CAS 
PubMed 

Google Scholar 
López-Fernández, S. et al. Effects of fertiliser type and the presence or absence of plants on nitrous oxide emissions from irrigated soils. Nutr. Cycl. Agroecosyst. 78, 279–289 (2007).
Google Scholar 
Wallenstein, M. D., Myrold, D. D., Firestone, M. & Voytek, M. Environmental controls on denitrifying communities and denitrification rates: insights from molecular methods. Ecol. Appl. 16, 2143–2152 (2006).PubMed 

Google Scholar 
Ciarlo, E., Conti, M., Bartoloni, N. & Rubio, G. Soil N2O emissions and N2O/(N2O+N2) ratio as affected by different fertilization practices and soil moisture. Biol. Fertil. Soils 44, 991–995 (2008).CAS 

Google Scholar 
Dandie, C. E. et al. Changes in bacterial denitrifier community abundance over time in an agricultural field and their relationship with denitrification activity. Appl. Environ. Microbiol. 74, 5997–6005 (2008).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Francis, C. A., O’Mullan, G. D., Cornwell, J. C. & Ward, B. B. Transitions in nirS-type denitrifier diversity, community composition, and biogeochemical activity along the Chesapeake Bay estuary. Front. Microbiol. 4, 237 (2013).PubMed 
PubMed Central 

Google Scholar 
Lin, W. et al. Evaluation of N2O sources after fertilizers application in vegetable soil by dual isotopocule plots approach. Environ. Res. 188, 109818 (2020).CAS 
PubMed 

Google Scholar 
Chen, M. M. et al. Nitrosospira cluster 3 lineage of AOB and nirK of Rhizobiales respectively dominated N2O emissions from nitrification and denitrification in organic and chemical N fertilizer treated soils. Ecol. Indic. 127, 107722 (2021).CAS 

Google Scholar 
Malghani, S., Kim, J., Lee, S. H., Yoo, G. Y. & Kang, H. Application of two contrasting rice-residue-based biochars triggered gaseous loss of nitrogen under denitrification-favoring conditions: a short-term study based on acetylene inhibition technique. Appl. Soil Ecol. 127, 112–119 (2018).
Google Scholar 
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 (2015).
Google Scholar 
Philippot, L., Andert, J., Jones, C. M., Bru, D. & Hallin, S. Importance of denitrifiers lacking the genes encoding the nitrous oxide reductase for N2O emissions from soil. Glob. Change Biol. 17, 1497–1504 (2011).ADS 

Google Scholar 
Chen, Z. et al. Differentiated response of denitrifying communities to fertilization regime in paddy soil. Microb. Ecol. 63, 446–459 (2012).PubMed 

Google Scholar 
Yoshida, M., Ishii, S., Otsuka, S. & Senoo, K. nirK-harboring denitrifiers are more responsive to denitrification-inducing conditions in rice paddy soil than nirS-harboring bacteria. Microbes Environ. 25, 45–48 (2010).PubMed 

Google Scholar 
Yin, C. et al. Denitrification potential under different fertilization regimes is closely coupled with changes in the denitrifying community in a black soil. Appl. Microbiol. Biotechnol. 99, 5719–5729 (2015).CAS 
PubMed 

Google Scholar 
Barrett, M. et al. Carbon amendment and soil depth affect the distribution and abundance of denitrifiers in agricultural soils. Environ. Sci. Pollut. Res. 23, 7899–7910 (2016).CAS 

Google Scholar 
Yoshida, M., Ishii, S., Otsuka, S. & Senoo, K. Temporal shifts in diversity and quantity of nirS and nirK in a rice paddy field soil. Soil Biol. Biochem. 41, 2044–2051 (2009).CAS 

Google Scholar 
Kandeler, E., Deiglmayr, K., Tscherko, D., Bru, D. & Philippot, L. Abundance of narG, nirS, nirK, and nosZ genes of denitrifying bacteria during primary successions of a glacier foreland. Appl. Environ. Microbiol. 72, 5957–5962 (2006).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar  More

PlasticsEurope. Plastics – the Facts 2019, Avenue E. van Nieuwenhuyse 4/3, 1160 Brussels. Belgium: PlasticsEurope. https://www.plasticseurope.org/de/resources/publications/4312-plastics-facts-2020 (2020).Mattsson, K., Jocic, S., Doverbratt, I. & Hansson, L. A. In Nanoplastics in the Aquatic Environment: Microplastic Contamination in Aquatic Environments (ed. Zheng, E. Y.) 379–399 (Elsevier, 2018).Chapter 

Google Scholar 
Lusher, A. L., Tirelli, V., O’Connor, I. & Officer, R. Microplastics in Arctic polar waters: The first reported values of particles in surface and sub-surface samples. Sci. Rep. 5, 14947. https://doi.org/10.1038/srep14947 (2015).ADS 
CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Waller, C. L. et al. Microplastics in the Antarctic marine system: An emerging area of research. Sci. Total. Environ. 598, 220–227. https://doi.org/10.1016/j.scitotenv.2017.03.283 (2017).ADS 
CAS 
Article 
PubMed 

Google Scholar 
Thompson, R. C. et al. Lost at sea: where is all the plastic?. Sci. 304, 838–838 (2004).CAS 
Article 

Google Scholar 
Gall, S. C. & Thompson, R. C. The impact of debris on marine life. Mar. Pollut. Bull. 92, 170–179. https://doi.org/10.1016/j.marpolbul.2014.12.041 (2015).CAS 
Article 
PubMed 

Google Scholar 
Kroon, F. J., Motti, C. E., Jensen, L. H. & Berry, K. L. Classification of marine microdebris: A review and case study on fish from the Great Barrier Reef, Australia. Sci. Rep. 8, 1–15. https://doi.org/10.1038/s41598-018-34590-6 (2018).CAS 
Article 

Google Scholar 
Cunningham, E. M. & Sigwart, J. D. Environmentally accurate microplastic levels and their absence from exposure studies. Integr. Comp. Biol. 59, 1485–1496. https://doi.org/10.1093/icb/icz068 (2019).Article 
PubMed 

Google Scholar 
Welden, N. A. & Cowie, P. R. Long-term microplastic retention causes reduced body condition in the langoustine Nephrops norvegicus. Environ. Pollut. 218, 895–900. https://doi.org/10.1016/j.envpol.2016.08.020 (2016).CAS 
Article 
PubMed 

Google Scholar 
Green, D. S., Colgan, T. J., Thompson, R. C. & Carolan, J. C. Exposure to microplastics reduces attachment strength and alters the haemolymph proteome of blue mussels (Mytilus edulis). Environ. Pollut. 246, 423–434. https://doi.org/10.1016/j.envpol.2018.12.017 (2019).CAS 
Article 
PubMed 

Google Scholar 
Schéré, C. M., Dawson, T. P. & Schreckenberg, K. Multiple conservation designations: what impact on the effectiveness of marine protected areas in the Irish Sea?. Int. J. Sustain. Dev. 27, 596–610. https://doi.org/10.1080/13504509.2019.1706058 (2020).Article 

Google Scholar 
Ungfors, A. et al. Nephrops fisheries in European waters. In Advances in Marine Biology 247–314 (Academic Press, 2013).
Google Scholar 
ICES. Celtic Seas Ecosystem—Fisheries Overview. In Report of the ICES Advisory Committee, 2019. ICES Advice 2019, Section 7.2. 40 pp https://doi.org/10.17895/ices.advice.5708. (2019).Becker, C., Dick, J. T., Cunningham, E. M., Schmitt, C. & Sigwart, J. D. The crustacean cuticle does not record chronological age: New evidence from the gastric mill ossicles. Arthropod. Struct. Dev. 47, 498–512. https://doi.org/10.1016/j.asd.2018.07.002 (2018).Article 
PubMed 

Google Scholar 
Woodall, L. C. et al. The deep sea is a major sink for microplastic debris. R. Soc. Open Sci. 1, 140317. https://doi.org/10.1098/rsos.140317 (2014).ADS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Yin, J., Li, J. Y., Craig, N. J. & Su, L. Microplastic pollution in wild populations of decapod crustaceans: A review. Chemosphere https://doi.org/10.1016/j.chemosphere.2021.132985 (2021).Article 
PubMed 
PubMed Central 

Google Scholar 
Cau, A. et al. Benthic crustacean digestion can modulate the environmental fate of microplastics in the deep sea. Environ. Sci. Technol. 54, 4886–4892. https://doi.org/10.1021/acs.est.9b07705 (2020).ADS 
CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Hara, J., Frias, J. & Nash, R. Quantification of microplastic ingestion by the decapod crustacean Nephrops norvegicus from Irish waters. Mar. Pollut. Bull. 152, 110905. https://doi.org/10.1016/j.marpolbul.2020.110905 (2020).CAS 
Article 
PubMed 

Google Scholar 
Hill, A. E., Durazo, R. & Smeed, D. A. Observations of a cyclonic gyre in the western Irish Sea. Cont. Shelf Res. 14, 479–490. https://doi.org/10.1016/0278-4343(94)90099-X (1994).ADS 
Article 

Google Scholar 
Horsburgh, K. J. & Hill, A. E. A three-dimensional model of density-driven circulation in the Irish Sea. J. Phys. Oceanogr. 33, 343–365. https://doi.org/10.1175/1520-0485(2003)033%3c0343:ATDMOD%3e2.0.CO;2 (2003).ADS 
Article 

Google Scholar 
Hill, A.E., Brown, J., & Fernand, L. The western Irish Sea gyre: a retention system for Norway lobster (Nephrops norvegicus)? Oceanol. Acta. 19, 357–368. (1996). https://archimer.ifremer.fr/doc/00094/20493/Lebreton, L. et al. Evidence that the great pacific garbage patch is rapidly accumulating plastic. Sci. Rep. 8, 1–15. https://doi.org/10.1038/s41598-018-22939-w (2018).CAS 
Article 

Google Scholar 
Charlesworth, M., Mitchell, S. H. & Oliver, W. T. Metals in surficial sediments of the north-west Irish Sea. Bull. Environ. Contam. Toxicol. 62, 40–47. https://doi.org/10.1007/s001289900839 (1999).CAS 
Article 
PubMed 

Google Scholar 
Charlesworth, M. E., Service, M. & Gibson, C. E. The distribution and transport of Sellafield derived 137Cs and 241Am to western Irish Sea sediments. Sci. Total. Environ. 354, 83–92. https://doi.org/10.1016/j.scitotenv.2004.12.062 (2006).ADS 
CAS 
Article 
PubMed 

Google Scholar 
Global Monitoring and Forecasting Center. Atlantic-European North West Shelf – Ocean Physics Analysis and Forecast, E.U Copernicus Marine Service Information . Available at: https://resources.marine.copernicus.eu/product-detail/NORTHWESTSHELF_ANALYSIS_FORECAST_PHY_004_013/INFORMATION (Accessed: 8th December 2021).Cunningham, E. M. et al. High abundances of microplastic pollution in deep-sea sediments: Evidence from antarctica and the Southern Ocean. Environ. Sci. Technol. 54, 13661–13671. https://doi.org/10.1021/acs.est.0c03441 (2020).ADS 
CAS 
Article 
PubMed 

Google Scholar 
Zhang, S. et al. A simple method for the extraction and identification of light density microplastics from soil. Sci. Total. Environ. 616, 1056–1065. https://doi.org/10.1016/j.scitotenv.2017.10.213 (2018).ADS 
CAS 
Article 
PubMed 

Google Scholar 
Martin, J., Lusher, A., Thompson, R. C. & Morley, A. The deposition and accumulation of microplastics in marine sediments and bottom water from the Irish continental shelf. Sci. Rep. 7, 10772. https://doi.org/10.1038/s41598-017-11079-2 (2017).ADS 
CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
R Core Development Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2018).
Google Scholar 
Nor, N. H. M. & Obbard, J. P. Microplastics in Singapore’s coastal mangrove ecosystems. Mar. Pollut. Bullet. 79, 278–283. https://doi.org/10.1016/j.marpolbul.2013.11.025 (2014).CAS 
Article 

Google Scholar 
Lacerda, A. L. D. F. et al. Plastics in sea surface waters around the Antarctic Peninsula. Sci. Rep. 9, 1–12. https://doi.org/10.1038/s41598-019-40311-4 (2019).MathSciNet 
CAS 
Article 

Google Scholar 
Tata, T., Belabed, B. E., Bououdina, M. & Bellucci, S. Occurrence and characterization of surface sediment microplastics and litter from North African coasts of Mediterranean Sea: Preliminary research and first evidence. Sci. Total. Environ. 713, 136664. https://doi.org/10.1016/j.scitotenv.2020.136664 (2020).ADS 
CAS 
Article 
PubMed 

Google Scholar 
Lorenz, C. et al. Spatial distribution of microplastics in sediments and surface waters of the southern North Sea. Environ. Pollut. 252, 1719–1729 (2019).CAS 
Article 

Google Scholar 
Chouchene, K. et al. Microplastics on Barra beach sediments in Aveiro, Portgal. Mar. Pollut. Bull. 167, 112264. https://doi.org/10.1016/j.marpolbul.2021.112264 (2021).CAS 
Article 
PubMed 

Google Scholar 
Kane, I. A. et al. Seafloor microplastic hotspots controlled by deep-sea circulation. Science 368, 1140–1145. https://doi.org/10.1126/science.aba5899 (2020).ADS 
CAS 
Article 
PubMed 

Google Scholar 
Gaylarde, C. C., Neto, J. A. B. & da Fonseca, E. M. Paint fragments as polluting microplastics: A brief review. Mar. Pollut. Bull. 162, 111847. https://doi.org/10.1016/j.marpolbul.2020.111847 (2021).CAS 
Article 
PubMed 

Google Scholar 
Sait, S. T. L. et al. Microplastic fibres from synthetic textiles: Environmental degradation and additive chemical content. Environ. Pollut. 268, 115745. https://doi.org/10.1016/j.envpol.2020.115745 (2021).CAS 
Article 
PubMed 

Google Scholar 
Chen, Q. et al. Bioassay guided analysis coupled with non-target chemical screening in polyethylene plastic shopping bag fragments after exposure to simulated gastric juice of Fish. J. Hazard. Mater. 401, 123421. https://doi.org/10.1016/j.jhazmat.2020.123421 (2021).CAS 
Article 
PubMed 

Google Scholar 
Wu, X. et al. Photo aging and fragmentation of polypropylene food packaging materials in artificial seawater. Water. Res. 188, 116456. https://doi.org/10.1016/j.watres.2020.116456 (2021).CAS 
Article 
PubMed 

Google Scholar 
Zabaniotou, A. & Kassidi, E. Life cycle assessment applied to egg packaging made from polystyrene and recycled paper. J. Clean. Prod. 11, 549–559. https://doi.org/10.1016/S0959-6526(02)00076-8 (2003).Article 

Google Scholar 
Tanaka, K. & Takada, H. Microplastic fragments and microbeads in digestive tracts of planktivorous fish from urban coastal waters. Sci. Rep. 6, 34351. https://doi.org/10.1038/srep34351 (2016).ADS 
CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Biamis, C., O’Driscoll, K. & Hardiman, G. Microplastic toxicity: A review of the role of marine sentinel species in assessing the environmental and public health impacts. CSCEE. https://doi.org/10.1016/j.cscee.2020.100073 (2020).Article 

Google Scholar 
Bakir, A., Rowland, S. J. & Thompson, R. C. Transport of persistent organic pollutants by microplastics in estuarine conditions. Estuar. Coast. 140, 14–21. https://doi.org/10.1016/j.ecss.2014.01.004 (2014).CAS 
Article 

Google Scholar 
Nelson, A. M. & Long, T. E. A perspective on emerging polymer technologies for bisphenol-A replacement. Polym. Int. 61, 1485–1491. https://doi.org/10.1002/pi.4323 (2012).CAS 
Article 

Google Scholar 
Le Bihanic, F. et al. Organic contaminants sorbed to microplastics affect marine medaka fish early life stages development. Mar. Pollut. Bull. 154, 111059. https://doi.org/10.1016/j.marpolbul.2020.111059 (2020).CAS 
Article 
PubMed 

Google Scholar 
Murray, F. & Cowie, P. R. Plastic contamination in the decapod crustacean Nephrops norvegicus (Linnaeus, 1758). Mar. Pollut. Bull. 62, 1207–1217. https://doi.org/10.1016/j.marpolbul.2011.03.032 (2011).CAS 
Article 
PubMed 

Google Scholar 
Cobb, J. S. & Phillips, B. F. (eds) The Biology and Management of Lobsters, Physiology and Behaviour 2–61 (Academic Press Inc., 1980).
Google Scholar 
Quintana, M. M., Motova, A., Wilkie, O., Patience, N. Seafish: Economics of the UK fishing fleet 2020. Seafish Report No. SR758. Edinburgh, UK. https://www.seafish.org/document/?id=d9e7982d-e374-4de7-85a4-ca80c35f5666 (2021). More

Lawrence, J.M. Sea urchins: biology and ecology. Amsterdam, The Netherlands: Elsevier B.V. (2020)Purcell, S.W., Samyn, Y. & Conand, C. Commercially important sea cucumbers of the world. Rome, Italy: FAO. (2012)Yorke, C. E., Page, H. M. & Miller, R. J. Sea urchins mediate the availability of kelp detritus to benthic consumers. Proc. R. Soc. B. 286(1906), 20190846 (2019).CAS 
Article 

Google Scholar 
Dethier, M. N. et al. Feces as food: The nutritional value of urchin feces and implications for benthic food webs. J. Exp. Mar. Biol. Ecol. 514, 95–102 (2019).Article 

Google Scholar 
Purcell, S. W. et al. Ecological roles of exploited sea cucumbers. Oceanogr. Mar. Biol. 54, 367–386 (2017).
Google Scholar 
Hamel, J. F. & Mercier, A. Early development, settlement, growth, and spatial distribution of the sea cucumber Cucumaria frondosa (Echinodermata: Holothuroidea). Can. J. Fish. Aquat. Sci. 53(2), 253–271 (1996).Article 

Google Scholar 
Grosso, L. et al. Integrated Multi-Trophic Aquaculture (IMTA) system combining the sea urchin Paracentrotus lividus, as primary species, and the sea cucumber Holothuria tubulosa as extractive species. Aquaculture 534, 736268 (2021)Gabara, S.S., Konar, B.H. & Edwards, M.S. Biodiversity loss leads to reductions in community-wide trophic complexity. Ecosphere 12(2), e03361 (2021)Duffy, J. E. et al. The functional role of biodiversity in ecosystems: Incorporating trophic complexity. Ecol. Lett. 10(6), 522–538 (2010).ADS 
Article 

Google Scholar 
Miller, R. J. et al. Giant kelp, Macrocystis pyrifera, increases faunal diversity through physical engineering. Proc. R. Soc. B. 285(1874), 20172571 (2018).Article 

Google Scholar 
Soulsby, P. G., Lowthion, D. & Houston, M. Effects of macroalgal mats on the ecology of intertidal mudflats. Mar. Pollut. Bull. 13(5), 162–166 (1982).Article 

Google Scholar 
Filbee-Dexter, K. & Scheibling, R.E. Sea urchin barrens as alternative stable states of collapsed kelp ecosystems. Mar. Ecol.: Prog. Ser. 495(1), 1–25 (2014)Hendler, G., Miller, J. E., Pawson, D. L. & Kier, P. M. Sea stars, sea urchins and allies: echinoderms of Florida and the Caribbean (Smithsonian Institution Press, 1995).
Google Scholar 
James, D. B. Sea cucumber and sea urchin resources. CMFRI Bull. 34, 85–93 (1983).
Google Scholar 
Muthiga, N.A. & Kawaka, J.A. The effects of temperature and light on the gametogenesis and spawning of four sea urchin and one sea cucumber species on coral reefs in Kenya. Proceedings of the 11th international coral reef symposium. Fort Lauderdale, Florida pp 356–360 (2008)Byrnes, J., Cardinale, B. & Reed, D. Interactions between sea urchin grazing and prey diversity on temperate rocky reef communities. Ecology 94(7), 1636–1646 (2013).Article 

Google Scholar 
Vanderklift, M.A. & Kendrick, G.A. Contrasting influence of sea urchins on attached and drift macroalgae. Mar. Ecol.: Prog. Ser. 299, 101–110 (2005)Duggins, D. O. Interspecific facilitation in a guild of benthic marine herbivores. Oecologia 48(2), 157–163 (1981).ADS 
Article 

Google Scholar 
Bonaviri, C. et al. Fish versus starfish predation in controlling sea urchin populations in Mediterranean rocky shores. Mar. Ecol.: Prog. Ser. 382(1), 129–138 (2009)Purcell, S. W. & Simutoga, M. Spatio-temporal and size-dependent variation in the success of releasing cultured sea cucumbers in the wild. Rev. Fish. Sci. 16, 204–214 (2008).Article 

Google Scholar 
Scheibling, R. E. & Robinson, M. C. Settlement behaviour and early post-settlement predation of the sea urchin Strongylocentrotus droebachiensis. J. Exp. Mar. Biol. Ecol. 365(1), 59–66 (2008).Article 

Google Scholar 
Francour, P. Predation on holothurians: a literature review. Invertebr. Biol. 116(1), 52–60 (1997).Article 

Google Scholar 
Scheibling, R. E. & Hamm, J. Interactions between sea urchins (Strongylocentrotus droebachiensis) and their predators in field and laboratory experiments. Mar. Biol. 110(1), 105–116 (1991).Article 

Google Scholar 
Bartumeus, F., Romero, J. & Alcoverro, T. The scent of fear makes sea urchins go ballistic. Mov. Ecol. 9(1), 1–12 (2021).Article 

Google Scholar 
Campbell, A.C. & Coppard, S., Tudor-Thomas CD. Escape and aggregation responses of three echinoderms to conspecific stimuli. Biol. Bull. 201(2), 175–185 (2001)Chi, X. et al. Conspecific alarm cues are a potential effective barrier to regulate foraging behavior of the sea urchin Mesocentrotus nudus. Mar. Environ. Res. 171(8), 105476 (2021)Chi, X. et al. Foraging behavior of the sea urchin Mesocentrotus nudus exposed to conspecific alarm cues in various conditions. Sci. Rep. 11(1), 1–6 (2021).Article 

Google Scholar 
Zhadan, P.M. & Vaschenko, M.A. Long-term study of behaviors of two cohabiting sea urchin species, Mesocentrotus nudus and Strongylocentrotus intermedius, under conditions of high food quantity and predation risk in situ. PeerJ 7(1), e8087 (2019)Bshary, R. & Noë, R. Red colobus and Diana monkeys provide mutual protection against predators. Anim. Behav. 54(6), 1461–1474 (1997).CAS 
Article 

Google Scholar 
Peres, C. A. Anti-predation benefits in a mixed-species group of Amazonian tamarins. Folia Primatol. 61(2), 61–76 (1993).CAS 
Article 

Google Scholar 
Fuji, A. Ecological studies on the growth and food consumption of Japanese common littoral sea urchin, Strongylocentrotus intermedius (A. Agassiz). Mem. Fac. Fish. Hokkaido Univ. 15(2), 83–160 (1967)Chang, Y., Ding, J., Song, J. & Yang, W. Biology and aquaculture of sea cucumbers and sea urchins (Ocean Press, 2004).
Google Scholar 
Yang, H., Hamel, J. F. & Mercier, A. The sea cucumber Apostichopus japonicus: history, biology and aquaculture (Elsevier Inc., 2015).
Google Scholar 
Zhao, C. et al. Carryover effects of short-term UV-B radiation on fitness related traits of the sea urchin Strongylocentrotus intermedius. Ecotoxicol. Environ. Saf. 164, 659–664 (2018).CAS 
Article 

Google Scholar 
Zhang, L. et al. Effects of long-term elevated temperature on covering, sheltering and righting behaviors of the sea urchin Strongylocentrotus intermedius. PeerJ 5, e3122 (2017)Zhao, C. et al. Effects of covering behavior and exposure to a predatory crab Charybdis japonica on survival and HSP70 expression of juvenile sea urchins Strongylocentrotus intermedius. PloS One 9(5), e97840 (2014)Kawai, T. & Agatsuma, Y. Predators on released seed of the sea urchin Strongylocentrotus intermedius at Shiribeshi, Hokkaido, Japan. Fish. Sci. (Tokyo, Jpn.) 62(2), 317–318 (1996)Hatanaka, H. Experimental studies on the predation of juvenile sea cucumber, Stichopus japonicus by sea star Asterina pectinifera. Aquacult. Sci. 42(4), 563–566 (1994).
Google Scholar 
Guidetti, P. & Mori, M. Morpho-functional defences of Mediterranean sea urchins, Paracentrotus lividus and Arbacia lixula, against fish predators. Mar. Biol. 147(3), 797–802 (2005).Article 

Google Scholar 
Moitoza, D.J & Phillips, D.W. Prey defense, predator preference, and nonrandom diet: the interactions between Pycnopodia helianthoides and two species of sea urchins. Mar. Biol. 53(4), 299–304 (1979)Williams, J.P. et al. Sea urchin mass mortality rapidly restores kelp forest communities. Mar. Ecol.: Prog. Ser. 664, 117–131 (2021)Pearse, J. Ecological role of purple sea urchins. Science 314(5801), 940–941 (2006).ADS 
CAS 
Article 

Google Scholar 
Vadas, R. L. Preferential feeding: an optimization strategy in sea urchins. Ecol. Monogr. 47(4), 337–371 (1977).Article 

Google Scholar 
Lowe, A. T. et al. Sedentary urchins influence benthic community composition below the macroalgal zone. Mar. Biol. 36(2), 129–140 (2015).
Google Scholar 
Layton, C. et al. Kelp Forest Restoration in Australia. Front. Mar. Sci. 7(74) (2020)Eger, A.M. et al. Global Kelp forest restoration: Past lessons, status, and future goals. Preprint. EcoEvoRxiv. https://doi.org/10.32942/osf.io/emaz2 (2021)Ritson-Williams, R. & Paul, V. J. Marine benthic invertebrates use multimodal cues for defense against reef fish. Mar. Ecol. Prog. Ser. 340, 29–39 (2007).ADS 
Article 

Google Scholar 
Hu, F. et al. Effects of artificial reefs on selectivity and behaviors of the sea cucumber Apostichopus japonicas: New insights into the pond culture. Aquacult. Rep. 21(3), 100842 (2021)Sun, J. et al. Light intensity regulates phototaxis, foraging and righting behaviors of the sea urchin Strongylocentrotus intermedius. PeerJ 7, e8001 (2019)Bi, S., Shi, J. & Liu, A. Exploitation and utilization of Ulva lactuca L. Mod. Fish. Inf. 11, 21–23 (1993).
Google Scholar 
Chang, Y. Q., Wang, Z. C. & Wang, G. J. Effect of temperature and algae on feeding and growth in sea urchin Strongylocentrotus intermedius. J. Fish. China 23(1), 69–76 (1999).
Google Scholar 
Dumont, C., Himmelman, J.H. & Russell, M.P. Size-specific movement of green sea urchins Strongylocentrotus droebachiensis on urchin barrens in eastern Canada. Mar. Ecol.: Prog. Ser. 276, 93–101 (2004)Sun, J. et al. Interaction among sea urchins in response to food cues. Sci. Rep. 11(1), 1–9 (2021).ADS 
Article 

Google Scholar 
Węglarczyk, S. Kernel density estimation and its application. ITM Web Conf. 23(2), 00037 (2018).Article 

Google Scholar  More

Price, P. W. Evolutionary Biology of Parasites (Princeton University Press, 1980).
Google Scholar 
Lima, L. B., Bellay, S., Giacomini, H. C., Isaac, A. & Lima-Junior, D. P. Influence of host diet and phylogeny on parasite sharing by fish in a diverse tropical floodplain. Parasitology 143, 343–349 (2016).CAS 
PubMed 

Google Scholar 
Eizaguirre, C., Lenz, T. L., Kalbe, M. & Milinski, M. Rapid and adaptive evolution of MHC genes under parasite selection in experimental vertebrate populations. Nat. Commun. 3, 1–6 (2012).
Google Scholar 
Bashey, F. Within-host competitive interactions as a mechanism for the maintenance of parasite diversity. Philos. Trans. R. Soc. B Biol. Sci. 370, 20140301 (2015).
Google Scholar 
Jolles, J. W., Mazué, G. P. F., Davidson, J., Behrmann-Godel, J. & Couzin, I. D. Schistocephalus parasite infection alters sticklebacks’ movement ability and thereby shapes social interactions. Sci. Rep. 10, 12282 (2020).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Demandt, N. et al. Parasite-infected sticklebacks increase the risk-taking behaviour of uninfected group members. Proc. R. Soc. B Biol. Sci. 285, 20180956 (2018).
Google Scholar 
Poulin, R. Parasite manipulation of host behavior: An update and frequently asked questions. Adv. Study Behav. 41, 151–186 (2010).
Google Scholar 
Terui, A., Ooue, K., Urabe, H. & Nakamura, F. Parasite infection induces size-dependent host dispersal: Consequences for parasite persistence. Proc. R. Soc. B Biol. Sci. 284, 20171491 (2017).
Google Scholar 
Raeymaekers, J. A. M. et al. Contrasting parasite communities among allopatric colour morphs of the Lake Tanganyika cichlid Tropheus. BMC Evol. Biol. 13, 41 (2013).PubMed 
PubMed Central 

Google Scholar 
Meyer, B. S. et al. An exploration of the links between parasites, trophic ecology, morphology, and immunogenetics in the Lake Tanganyika cichlid radiation. Hydrobiologia 832, 215–233 (2019).PubMed 

Google Scholar 
Gobbin, T. P. et al. Temporally consistent species differences in parasite infection but no evidence for rapid parasite-mediated speciation in Lake Victoria cichlid fish. J. Evol. Biol. 33, 556–575 (2020).PubMed 
PubMed Central 

Google Scholar 
Karvonen, A., Wagner, C. E., Selz, O. M. & Seehausen, O. Divergent parasite infections in sympatric cichlid species in Lake Victoria. J. Evol. Biol. 31, 1313–1329 (2018).PubMed 

Google Scholar 
Bush, S. E. et al. Host defense triggers rapid adaptive radiation in experimentally evolving parasites. Evol. Lett. 3, 120–128 (2019).PubMed 
PubMed Central 

Google Scholar 
Waid, R. M., Raesly, R. L., Mckaye, K. R. & McCrary, J. Zoogeografía íctica de lagunas cratéricas de Nicaragua. Encuentro 51, 65–80 (1999).
Google Scholar 
Barluenga, M., Stölting, K., Salzburger, W., Muschick, M. & Meyer, A. Sympatric speciation in Nicaraguan crater lake cichlid fish. Nature 439, 719–723 (2006).ADS 
CAS 
PubMed 

Google Scholar 
Elmer, K. R., Lehtonen, T. K., Fan, S. & Meyer, A. Crater lake colonization by neotropical cichlid fishes. Evolution 67, 281–288 (2012).PubMed 

Google Scholar 
Kautt, A. F. et al. Contrasting signatures of genomic divergence during sympatric speciation. Nature 588, 106–111 (2020).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Elmer, K. R., Lehtonen, T. K., Kautt, A. F., Harrod, C. & Meyer, A. Rapid sympatric ecological differentiation of crater lake cichlid fishes within historic times. BMC Biol. 8, 1–15 (2010).
Google Scholar 
Kautt, A. F., Machado-Schiaffino, G., Torres-Dowdall, J. & Meyer, A. Incipient sympatric speciation in Midas cichlid fish from the youngest and one of the smallest crater lakes in Nicaragua due to differential use of the benthic and limnetic habitats? Ecol. Evol. 6, 5342–5357 (2016).PubMed 
PubMed Central 

Google Scholar 
Barluenga, M. & Meyer, A. Phylogeography, colonization and population history of the Midas cichlid species complex (Amphilophus spp.) in the Nicaraguan crater lakes. BMC Evol. Biol. 10, 326 (2010).PubMed 
PubMed Central 

Google Scholar 
Elmer, K. R., Lehtonen, T. K. & Meyer, A. Color assortative mating contributes to sympatric divergence of neotropical cichlid fish. Evolution 63, 2750–2757 (2009).PubMed 

Google Scholar 
Kautt, A. F., Machado-Schiaffino, G. & Meyer, A. Lessons from a natural experiment: Allopatric morphological divergence and sympatric diversification in the Midas cichlid species complex are largely influenced by ecology in a deterministic way. Evol. Lett. 2, 323–340 (2018).PubMed 
PubMed Central 

Google Scholar 
Elmer, K. R., Kusche, H., Lehtonen, T. K. & Meyer, A. Local variation and parallel evolution: Morphological and genetic diversity across a species complex of neotropical crater lake cichlid fishes. Philos. Trans. R. Soc. B Biol. Sci. 365, 1763–1782 (2010).
Google Scholar 
Elmer, K. R. et al. Parallel evolution of Nicaraguan crater lake cichlid fishes via non-parallel routes. Nat. Commun. 5, 1–8 (2014).
Google Scholar 
Vanhove, M. P. M. et al. Cichlids: A host of opportunities for evolutionary parasitology. Trends Parasitol. 32, 820–832 (2016).PubMed 

Google Scholar 
Choudhury, A. et al. Trematode diversity in freshwater fishes of the Globe II: ‘New World’. Syst. Parasitol. 93, 271–282 (2016).PubMed 

Google Scholar 
Watson, D. E. Digenea of fishes from Lake Nicaragua. In Investigations of the Ichthyofauna of Nicaraguan Lakes Vol. 15 (ed. Thorson, T. B.) 251–260 (University of Nebraska Press, 1976).
Google Scholar 
Aguirre-Macedo, M. L. et al. Larval helminths parasitizing freshwater fishes from the Atlantic coast of Nicaragua. Comp. Parasitol. 68, 42–51 (2001).
Google Scholar 
Aguirre-Macedo, M. L. et al. Some adult endohelminths parasitizing freshwater fishes from the Atlantic Drainages of Nicaragua. Comp. Parasitol. 68, 190–195 (2001).
Google Scholar 
Mendoza-Franco, E. F., Posel, P. & Dumailo, S. Monogeneans (Dactylogyridae: Ancyrocephalinae) of freshwater fishes from the Caribbean coast of Nicaragua. Comp. Parasitol. 70, 32–41 (2003).
Google Scholar 
Andrade-Gómez, L., Pinacho-Pinacho, C. D. & García-Varela, M. Molecular, morphological, and ecological data of Saccocoelioides Szidat, 1954 (Digenea: Haploporidae) from Middle America supported the reallocation from Culuwiya cichlidorum to Saccocoelioides. J. Parasitol. 103, 257–267 (2017).PubMed 

Google Scholar 
López-Jiménez, A., Pérez-Ponce de León, G. & García-Varela, M. Molecular data reveal high diversity of Uvulifer (Trematoda: Diplostomidae) in Middle America, with the description of a new species. J. Helminthol. 92, 725–739 (2018).PubMed 

Google Scholar 
Vidal-Martínez, V. M., Scholz, T. & Aguirre-Macedo, M. L. Dactylogyridae of cichlid fishes from Nicaragua, Central America, with descriptions of Gussevia herotilapiae sp. n. and three new species of Sciadicleithrum (Monogenea: Ancyrocephalinae). Comp. Parasitol. 68, 76–86 (2001).
Google Scholar 
de Chambrier, A. & Vaucher, C. Proteocephalus gaspari n. sp. (Cestoda: Proteocephalidae), parasite de Lepisosteus tropicus (Gill.) au Lac Managua (Nicaragua). Rev. suisse Zool. 91, 229–233 (1984).
Google Scholar 
González-Solís, A. D. & Jiménez-García, M. I. Parasitic nematodes of freshwater fishes from two nicaraguan crater lakes. Comp. Parasitol. 73, 188–192 (2006).
Google Scholar 
Santacruz, A., Morales-Serna, F. N., Leal-Cardín, M., Barluenga, M. & Pérez-Ponce de León, G. Acusicola margulisae n. sp. (Copepoda: Ergasilidae) from freshwater fishes in a Nicaraguan crater lake based on morphological and molecular evidence. Syst. Parasitol. 97, 165–177 (2020).PubMed 

Google Scholar 
Santacruz, A., Barluenga, M. & Pérez-Ponce de León, G. Taxonomic assessment of the genus Procamallanus (Nematoda) in Middle American cichlids (Osteichthyes) with molecular data, and the description of a new species from Nicaragua and Costa Rica. Parasitol. Res. 120, 1965–1977 (2021).PubMed 

Google Scholar 
Bush, A. O., Lafferty, K. D., Lotz, J. M. & Shostak, A. W. Parasitology meets ecology on its own terms: Margolis et al. revisited. J. Parasitol. 83, 575–583 (1997).CAS 
PubMed 

Google Scholar 
Rózsa, L., Reiczigel, J. & Majoros, G. Quantifying parasites in samples of hosts. J. Parasitol. 86, 228–232 (2000).PubMed 

Google Scholar 
Krebs, C. J. Species diversity measures. In Ecological Methodology (ed. Krebs, C. J.) (Addison-Wesley Educational Publishers, 2014).
Google Scholar 
Dixon, P. VEGAN, a package of R functions for community ecology. J. Veg. Sci. 14, 927–930 (2003).
Google Scholar 
R Core Team. A language and environment for statistical computing. R Found. Stat. Comput. (2018). https://www.R-project.org.Wickham, H. Elegant Graphics for Data Analysis: ggplot2 (Springer, 2008).MATH 

Google Scholar 
Hsieh, T. C., Ma, K. H. & Chao, A. iNEXT-package: Interpolation and extrapolation for species diversity. Methods Ecol. Evol. 7, 1451–1456 (2016).
Google Scholar 
Chao, A. et al. Rarefaction and extrapolation with Hill numbers: A framework for sampling and estimation in species diversity studies. Ecol. Monogr. 84, 45–67 (2014).
Google Scholar 
Poulin, R. Parasite biodiversity revisited: Frontiers and constraints. Int. J. Parasitol. 44, 581–589 (2014).PubMed 

Google Scholar 
Salzburger, W. Understanding explosive diversification through cichlid fish genomics. Nat. Rev. Genet. 19, 705–717 (2018).CAS 
PubMed 

Google Scholar 
Barluenga, M. & Meyer, A. The Midas cichlid species complex: Incipient sympatric speciation in Nicaraguan cichlid fishes? Mol. Ecol. 13, 2061–2076 (2004).CAS 
PubMed 

Google Scholar 
Elmer, K. R. & Meyer, A. Adaptation in the age of ecological genomics: Insights from parallelism and convergence. Trends Ecol. Evol. 26, 298–306 (2011).PubMed 

Google Scholar 
Pérez-Ponce de León, G. & Choudhury, A. Biogeography of helminth parasites of freshwater fishes in Mexico: The search for patterns and processes. J. Biogeogr. 32, 645–659 (2005).
Google Scholar 
Blais, J. et al. MHC adaptive divergence between closely related and sympatric African cichlids. PLoS ONE 2, e734 (2007).ADS 
PubMed 
PubMed Central 

Google Scholar 
Pariselle, A. et al. The monogenean parasite fauna of cichlids: A potential tool for host biogeography. Int. J. Evol. Biol. 2011, 1–15 (2011).
Google Scholar 
Aguilar-Aguilar, R., Salgado-Maldonado, G., Contreras-Medina, R. & Martínez-Aquino, A. Richness and endemism of helminth parasites of freshwater fishes in Mexico. Biol. J. Linn. Soc. 94, 435–444 (2008).
Google Scholar 
Dogiel, V. A. Ecology of parasites of freshwater fish. In Parasitology of Fishes (eds Dogiel, V. A. et al.) 1–47 (Edinburgh Oliver & Boyd, 1961).
Google Scholar 
Poulin, R. & Valtonen, E. T. The predictability of helminth community structure in space: A comparison of fish populations from adjacent lakes. Int. J. Parasitol. 32, 1235–1243 (2002).PubMed 

Google Scholar 
Razo-Mendivil, U., Rosas-Valdez, R. & Pérez-Ponce de León, G. A new Cryptogonimid (Digenea) from the mayan cichlid, Cichlasoma urophthalmus (Osteichthyes: Cichlidae), in several localities of the Yucatán Peninsula, Mexico. J. Parasitol. 94, 1371–1378 (2009).
Google Scholar 
Mendoza-Franco, E. F. et al. Occurrence of Sciadicleithrum mexicanum Kritsky, Vidal-Martinez et Rodríguez-Canul, 1994 (Monogenea: Dactylogyridae) in the Cichlid Cichlasoma urophthalmus from a flooded quarry in Yucatan, Mexico. Mem. Inst. Oswaldo Cruz 90, 319–324 (1995).
Google Scholar 
Blasco-Costa, I. & Poulin, R. Host traits explain the genetic structure of parasites: A meta-analysis. Parasitology 140, 1316–1322 (2013).PubMed 

Google Scholar 
Torchin, M. E., Lafferty, K. D., Dobson, A. P., McKenzie, V. J. & Kuris, A. M. Introduced species and their missing parasites. Nature 421, 628–630 (2003).ADS 
CAS 
PubMed 

Google Scholar 
Salgado-Maldonado, G. et al. Helminth parasites of freshwater fishes of the Balsas River drainage basin of southwestern Mexico. Comp. Parasitol. 68, 196–203 (2001).
Google Scholar 
McCrary, J. K., Murphy, B. R., Stauffer, J. R. & Hendrix, S. S. Tilapia (Teleostei: Cichlidae) status in Nicaraguan natural waters. Environ. Biol. Fishes 78, 107–114 (2007).
Google Scholar 
García-Vásquez, A., Pinacho-Pinacho, C. D., Guzmán-Valdivieso, I., Calixto-Rojas, M. & Rubio-Godoy, M. Morpho-molecular characterization of Gyrodactylus parasites of farmed tilapia and their spillover to native fishes in Mexico. Sci. Rep. 11, 1–17 (2021).
Google Scholar 
Paredes-Trujillo, A., Velázquez-Abunader, I., Torres-Irineo, E., Romero, D. & Vidal-Martínez, V. M. Geographical distribution of protozoan and metazoan parasites of farmed Nile tilapia Oreochromis niloticus (L.) (Perciformes: Cichlidae) in Yucatán, México. Parasit. Vectors 9, 66 (2016).PubMed 
PubMed Central 

Google Scholar 
Zhang, S. et al. Monogenean fauna of alien tilapias (Cichlidae) in south China. Parasite 26, 4 (2019).PubMed 
PubMed Central 

Google Scholar 
Outa, J. O., Dos Santos, Q. M., Avenant-Oldewage, A. & Jirsa, F. Parasite diversity of introduced fish Lates niloticus, Oreochromis niloticus and endemic Haplochromis spp. of Lake Victoria. Kenya. Parasitol. Res. 120, 1583 (2021).PubMed 

Google Scholar 
Smit, N. J., Malherbe, W. & Hadfield, K. A. Alien freshwater fish parasites from South Africa: Diversity, distribution, status and the way forward. Int. J. Parasitol. Parasites Wildl. 6, 386–401 (2017).PubMed 
PubMed Central 

Google Scholar 
Pérez-Ponce de León, G., Lagunas-Calvo, O., García-Prieto, L., Briosio-Aguilar, R. & Aguilar-Aguilar, R. Update on the distribution of the co-invasive Schyzocotyle acheilognathi (= Bothriocephalus acheilognathi), the Asian fish tapeworm, in freshwater fishes of Mexico. J. Helminthol. 92, 279–290 (2018).PubMed 

Google Scholar 
Scholz, T., Šimková, A., Razanabolana, J. R. & Kuchta, R. The first record of the invasive Asian fish tapeworm (Schyzocotyle acheilognathi) from an endemic cichlid fish in Madagascar. Helminthol. 55, 84–87 (2018).CAS 

Google Scholar 
Acosta, A., Carvalho, E. & da Silva, R. First record of Lernaea cyprinacea (copepoda) in a native fish species from a Brazilian river. Neotrop. Helminthol. 7, 7–12 (2013).
Google Scholar 
Choudhury, A. et al. The invasive asian fish tapeworm, Bothriocephalus acheilognathi Yamaguti, 1934, in the chagres river/panama canal drainage, Panama. BioInvas. Rec. 2, 99–104 (2013).
Google Scholar 
Schatz, H. & Behan-Pelletier, V. Global diversity of oribatids (Oribatida: Acari: Arachnida). Hydrobiologia 595, 323–328 (2008).
Google Scholar 
Choudhury, A., Hoffnagle, T. L. & Cole, R. A. Parasites of native and nonnative fishes of the Little Colorado River, Grand Canyon, Arizona. J. Parasitol. 90, 1042–1053 (2004).PubMed 

Google Scholar 
Vanhove, M. P. M. Part 6: Evolutionary parasitology of African freshwater fishes—And its implications for the sustainable management of aquatic resources. In A Guide to the Parasites of African Freshwater Fishes (eds Scholz, T. et al.) 403–412 (Royal Belgian Institute of Natural Sciences, 2018).
Google Scholar 
Catalano, S. R., Whittington, I. D., Donnellan, S. C. & Gillanders, B. M. Parasites as biological tags to assess host population structure: Guidelines, recent genetic advances and comments on a holistic approach. Int. J. Parasitol. Parasites Wildl. 3, 220–226 (2014).PubMed 

Google Scholar 
Baldwin, R. E., Banks, M. A. & Jacobson, K. C. Integrating fish and parasite data as a holistic solution for identifying the elusive stock structure of Pacific sardines (Sardinops sagax). Rev. Fish Biol. Fish. 22, 137–156 (2011).
Google Scholar 
Criscione, C. D. & Blouin, M. S. Parasite phylogeographical congruence with salmon host evolutionarily significant units: Implications for salmon conservation. Mol. Ecol. 16, 993–1005 (2007).CAS 
PubMed 

Google Scholar 
Vanhove, M. P. M. et al. Hidden biodiversity in an ancient lake: Phylogenetic congruence between Lake Tanganyika tropheine cichlids and their monogenean flatworm parasites. Sci. Rep. 5, 1–15 (2015).
Google Scholar 
Matschiner, M., Böhne, A., Ronco, F. & Salzburger, W. The genomic timeline of cichlid fish diversification across continents. Nat. Commun. 11, 1–8 (2020).
Google Scholar 
Choudhury, A., García-Varela, M. & Pérez-Ponce de León, G. Parasites of freshwater fishes and the Great American biotic interchange: A bridge too far? J. Helminthol. 91, 174–196 (2017).CAS 
PubMed 

Google Scholar 
Mendoza-Franco, E. F. & Vidal-Martínez, V. M. Phylogeny of species of Sciadicleithrum (Monogenoidea: Ancyrocephalinae), and their historical biogeography in the Neotropics. J. Parasitol. 91, 253–259 (2005).PubMed 

Google Scholar 
de Chambrier, A., Pinacho-Pinacho, C. D., Hernández-Orts, J. S. & Scholz, T. T. A new genus and two new species of proteocephalidean tapeworms (Cestoda) from cichlid fish (Perciformes: Cichlidae) in the neotropics. J. Parasitol. 103, 83–94 (2017).PubMed 

Google Scholar 
Mendoza-Palmero, C. A., Blasco-Costa, I., Hernández-Mena, D. & Pérez-Ponce de León, G. Parasciadicleithrum octofasciatum n. gen., n. sp. (Monogenoidea: Dactylogyridae), parasite of Rocio octofasciata (Regan) (Cichlidae: Perciformes) from Mexico characterised by morphological and molecular evidence. Parasitol. Int. 66, 152–162 (2017).PubMed 

Google Scholar 
Pinacho-Pinacho, C. D., Hernández-Orts, J. S., Sereno-Uribe, A. L., Pérez-Ponce de León, G. & García-Varela, M. Mayarhynchus karlae n. g., n. sp. (Acanthocephala: Neoechinorhynchidae), a parasite of cichlids (Perciformes: Cichlidae) in southeastern Mexico, with comments on the paraphyly of Neoechynorhynchus Stiles & Hassall, 1905. Syst. Parasitol. 94, 351–365 (2017).PubMed 

Google Scholar 
Razo-Mendivil, U., Vázquez-Domínguez, E., Rosas-Valdez, R., Pérez-Ponce de León, G. & Nadler, S. A. Phylogenetic analysis of nuclear and mitochondrial DNA reveals a complex of cryptic species in Crassicutis cichlasomae (Digenea: Apocreadiidae), a parasite of Middle-American cichlids. Int. J. Parasitol. 40, 471–486 (2010).CAS 
PubMed 

Google Scholar 
Razo-Mendivil, U., Rosas-Valdez, R., Rubio-Godoy, M. & Pérez-Ponce de León, G. The use of mitochondrial and nuclear sequences in prospecting for cryptic species in Tabascotrema verai (Digenea: Cryptogonimidae), a parasite of Petenia splendida (Cichlidae) in Middle America. Parasitol. Int. 64, 173–181 (2015).CAS 
PubMed 

Google Scholar 
Pinacho-Pinacho, C. D., García-Varela, M., Sereno-Uribe, A. L. & Pérez-Ponce de León, G. A hyper-diverse genus of acanthocephalans revealed by tree-based and non-tree-based species delimitation methods: Ten cryptic species of Neoechinorhynchus in Middle American freshwater fishes. Mol. Phylogenet. Evol. 127, 30–45 (2018).PubMed 

Google Scholar 
Martínez-Aquino, A. et al. Detecting a complex of cryptic species within Neoechinorhynchus golvani (Acanthocephala: Neoechinorhynchidae) inferred from ITSs and LSU rDNA gene sequences. J. Parasitol. 95, 1040–1047 (2009).PubMed 

Google Scholar  More

Kumar, N. et al. Peste des petits ruminants virus infection of small ruminants: A comprehensive review. Viruses 6, 2287–2327. https://doi.org/10.3390/v6062287 (2014).Article 
PubMed 
PubMed Central 

Google Scholar 
Zientara, S., Weyer, C. T. & Lecollinet, S. African horse sickness. Rev. Sci. Tech. 34, 315–327. https://doi.org/10.20506/rst.34.2.2359 (2015).CAS 
Article 
PubMed 

Google Scholar 
Rutkowska, D. A., Mokoena, N. B., Tsekoa, T. L., Dibakwane, V. S. & O’Kennedy, M. M. Plant-produced chimeric virus-like particles—A new generation vaccine against African horse sickness. BMC Vet. Res. 15, 1. https://doi.org/10.1016/j.rvsc.2010.05.031 (2019).CAS 
Article 

Google Scholar 
Barnard, B. J. H. Epidemiology of African horse sickness and the role of zebra in South Africa. Arch. Virol. Suppl. 14, 13–19. https://doi.org/10.1007/978-3-7091-6823-3_3 (1998).CAS 
Article 
PubMed 

Google Scholar 
Hamblin, C., Salt, J. S., Mellor, P. S., Graham, S. D. & Wohlsein, P. Donkeys as reservoirs of African horse sickness virus. Arch. Virol. Suppl. 14, 37–47. https://doi.org/10.1007/978-3-7091-6823-3_5 (1998).CAS 
Article 
PubMed 

Google Scholar 
Mellor, P. S., Boorman, J. P. T. & Baylis, M. Culicoides biting midges: their role as arbovirus vectors. Annu. Rev. Entomol. 45, 307–340 (2000).CAS 
Article 

Google Scholar 
Redmond, E. F., Jones, D. & Rushton, J. Economic assessment of african horse sickness vaccine impact. Equine Vet. J. https://doi.org/10.1111/j.2042-3306.1982.tb02404.x (2021).Article 
PubMed 

Google Scholar 
Venter, G. J., Wright, I. M., Linde, T. C. V. D. & Paweska, J. T. The oral susceptibility of South African field populations of Culicoides to African horse sickness virus. Med. Vet. Entomol. 23, 367–378. https://doi.org/10.1111/j.1365-2915.2009.00829.x (2010).Article 

Google Scholar 
Mellor, P. S., Boned, J., Hamblin, C. & Graham, S. D. Isolations of African horse sickness virus from vector insects made during the 1988 epizootic in Spain. Epidemiol. Infect. 105, 447–454. https://doi.org/10.1017/s0950268800048020 (1990).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Meiswinkel, R. & Paweska, J. T. Evidence for a new field Culicoides vector of African horse sickness in South Africa. Prev. Vet. Med. 60, 243–253. https://doi.org/10.1016/s0167-5877(02)00231-3 (2003).CAS 
Article 
PubMed 

Google Scholar 
Howell, P. G. The isolation and identification of further antigenic types of African horsesickness virus. Onderstepoort. J. Vet. Res. 29, 139–149 (1962).
Google Scholar 
Calisher, C. H. & Mertens, P. P. C. Taxonomy of African horse sickness viruses. Arch. Virol. Suppl. 14, 3 (1998).CAS 
PubMed 

Google Scholar 
Rodriguez, M., Hooghuis, H. & Castaño, M. African horse sickness in Spain. Vet. Microbiol. 33, 129–142. https://doi.org/10.1016/0378-1135(92)90041-q (1992).CAS 
Article 
PubMed 

Google Scholar 
Howell, P. G. The 1960 epizootic of African Horsesickness in the Middle East and S.W. Asia (268KB) (268KB). J. South Afr. Vet. Med. Assoc. (1960).King, S., RajkoEnow, P., Ashby, M., Frost, L. & Batten, C. Outbreak of African Horse Sickness in Thailand, 2020. Transbound. Emerg. Dis. (2020).OIE. World Animal Health Information System. https://www.oie.int/wahis_2/public/wahid.php/Reviewreport/Review?page_refer=MapFullEventReport&reportid=33768 (2020).Castillo-Olivares, J. African horse sickness in Thailand: Challenges of Controlling an outbreak by vaccination. Equine Vet. J. (2020).Gibbens, N. Schmallenberg virus: a novel viral disease in northern Europe. Vet. Rec. 170, 58. https://doi.org/10.1136/vr.e292 (2012).Article 
PubMed 

Google Scholar 
Purse, B. V., Brown, H. E., Harrup, L., Mertens, P. & Rogers, D. J. Invasion of bluetongue and other orbivirus infections into Europe: the role of biological and climatic processes. Rev. Sci. Tech. 27, 427–442 (2008).CAS 
Article 

Google Scholar 
Leta, S., Fetene, E., Mulatu, T., Amenu, K. & Revie, C. W. Modeling the global distribution of Culicoides imicola: an Ensemble approach. Sci. Rep. 9, 1 (2019).CAS 
Article 

Google Scholar 
Thepparat, A., Bellis, G., Ketavan, C., Ruangsittichai, J. & Apiwathnasorn, C. T. species of Culicoides Latreille (Diptera: Ceratopogonidae) newly recorded from Thailand. Zootaxa 4033, 48–56. https://doi.org/10.11646/zootaxa.4033.1.2 (2015).Article 
PubMed 

Google Scholar 
Raksakoon, C. & Potiwat, R. Current arboviral threats and their potential vectors in Thailand. Pathogens 10, 80 (2021).CAS 
Article 

Google Scholar 
Gao, S. et al. Transboundary spread of peste des petits ruminants virus in western China: A prediction model. PLoS ONE 16, e0257898–e0257898. https://doi.org/10.1371/journal.pone.0257898 (2021).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Joka, F. R., Van Gils, H., Huang, L. & Wang, X. High probability areas for ASF infection in china along the russian and korean borders. Transbound. Emerg. Dis. https://doi.org/10.1016/j.watres.2015.05.061.Steven et al. Opening the black box: an open-source release of Maxent. Ecography (2017).Gils, H. V., Westinga, E., Carafa, M., Antonucci, A. & Ciaschetti, G. Where the bears roam in Majella National Park, Italy. J. Nat. Conser. 22, 23–34. https://doi.org/10.1016/j.jnc.2013.08.001 (2014).Article 

Google Scholar 
Duque-Lazo, J., Navarro-Cerrillo, R. M., Van Gils, H. & Groen, T. A. Forecasting oak decline caused by Phytophthora cinnamomi in Andalusia : identification of priority areas for intervention. For. Ecol. Manage. 417, 122–136 (2018).Article 

Google Scholar 
Duque-Lazo, J., Gils, H. V., Groen, T. A. & Cerrillo, R. M. N. Transferability of species distribution models: The case of Phytophthora cinnamomi in Southwest Spain and Southwest Australia. Ecol. Model. 320, 62–70 (2016).Article 

Google Scholar 
Zeng, Z., Gao, S., Wang, H.-N., Huang, L.-Y. & Wang, X.-L. A predictive analysis on the risk of peste des petits ruminants in livestock in the Trans-Himalayan region and validation of its transboundary transmission paths. PLoS ONE 16, e0257094–e0257094. https://doi.org/10.1371/journal.pone.0257094 (2021).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Joka, F. R., Wang, H., van Gils, H. & Wang, X. Could wild boar be the Trans-Siberian transmitter of African swine fever?. Transbound. Emerg. Dis. https://doi.org/10.1111/tbed.13814 (2020).Article 
PubMed 

Google Scholar 
Robin, M., Page, P., Archer, D. & Baylis, M. African horse sickness: The potential for an outbreak in disease-free regions and current disease control and elimination techniques. Equine Vet. J. 48, 659–669. https://doi.org/10.1111/evj.12600 (2016).CAS 
Article 
PubMed 

Google Scholar 
Maclachlan, N. J. & Guthrie, A. J. Re-emergence of bluetongue, African horse sickness, and other Orbivirus diseases. Vet. Res. 41, 35. https://doi.org/10.1051/vetres/2010007 (2010).Article 
PubMed 
PubMed Central 

Google Scholar 
M. et al. African horse sickness: The potential for an outbreak in disease-free regions and current disease control and elimination techniques. Equine Vet. J. https://doi.org/10.1111/evj.12600 (2016).Eagles, D., Melville, L., Weir, R. & Davis, S. Long-distance aerial dispersal modelling of Culicoides biting midges: case studies of incursions into Australia. BMC Vet. Res. 10, 1. https://doi.org/10.1186/1746-6148-10-135 (2014).Article 

Google Scholar 
Pedgley, D. E. & Tucker, M. R. Possible spread of African horse sickness on the wind. J. Hygiene 79, 279–298 (1977).CAS 
Article 

Google Scholar 
Riddin, M. A., Venter, G. J., Labuschagne, K. & Villet, M. H. Culicoides species as potential vectors of African horse sickness virus in the southern regions of South Africa. Med. Vet. Entomol. 33, 1 (2019).Article 

Google Scholar 
Carpenter, S., Mellor, P. S., Fall, A. G., Garros, C. & Venter, G. J. African horse sickness Virus: History, transmission, and current status. Annu. Rev. Entomol. 62, 343–358. https://doi.org/10.1146/annurev-ento-031616-035010 (2017).CAS 
Article 
PubMed 

Google Scholar 
https://www.oie.int/wahis_2/public/wahid.php/Countryinformation/Countryreports. (Accessed 12 August 2020).OIE. African horse sickness(updated April 2013). OIE Technical Disease Cards, Paris, France: World Organisation for Animal Health. (2013).Ciss, M. et al. Ecological niche modelling to estimate the distribution of Culicoides, potential vectors of bluetongue virus in Senegal. BMC Ecology 19, doi:https://doi.org/10.1186/s12898-019-0261-9 (2019).Harrup, L. E. et al. Does covering of farm-associated Culicoides larval habitat reduce adult populations in the United Kingdom?. Vet. Parasitol. 201, 137–145. https://doi.org/10.1016/j.vetpar.2013.11.028 (2013).Article 
PubMed 

Google Scholar 
Hoch, A. L., Roberts, D. R. & Pinheiro, F. P. Host-seeking behavior and seasonal abundance of Culicoides paraensis (Diptera: Ceratopogonidae) in Brazil. J. Am. Mosq. Control Assoc. 6, 110–114 (1990).CAS 
PubMed 

Google Scholar 
Carpenter, S., Groschup, M. H., Garros, C., Felippe-Bauer, M. L. & Purse, B. V. Culicoides biting midges, arboviruses and public health in Europe. Antiviral Res. 100, 102–113. https://doi.org/10.1016/j.antiviral.2013.07.020 (2013).CAS 
Article 
PubMed 

Google Scholar 
Carpenter, S., Wilson, A., Barber, J., Veronesi, E. & Gubbins, S. Temperature Dependence of the Extrinsic Incubation Period of Orbiviruses in Culicoides Biting Midges. PLoS ONE 6, e27987. https://doi.org/10.1371/journal.pone.0027987 (2011).ADS 
CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Yanase, T. et al. Molecular Identification of Field-CollectedCulicoidesLarvae in the Southern Part of Japan. J. Med. Entomol. (2013).Meiswinkel, R. Afrotropical Culicoides: C (Avaritia) miombo sp. nov., a widespread species closely allied to C. (A.) imicola Kieffer, 1913 (Diptera: Ceratopogonidae). Onderstepoort. J. Vet. Res. 58, 155–170 (1991).Sloyer, K. E. et al. Ecological niche modeling the potential geographic distribution of four Culicoides species of veterinary significance in Florida, USA. PLoS ONE 14, 1 (2019).Article 

Google Scholar 
Reynolds, D. R., Chapman, J. W. & Harrington, R. The migration of insect vectors of plant and animal viruses. Adv. Virus Res. 67, 453–517 (2006).CAS 
Article 

Google Scholar 
L. et al. Investigating Incursions of Bluetongue Virus Using a Model of Long-Distance Culicoides Biting Midge Dispersal. Transbound. Emerg. Dis. https://doi.org/10.1111/j.1865-1682.2012.01345.x (2013).Notice of the general office of the Ministry of agriculture and rural areas and the general office of the State General Administration of sports on printing and distributing the national horse industry development plan (2020–2025). (Animal Husbandry and Veterinary Bureau, 2020.09.29). More

Mehbub MF, Lei J, Franco C, Zhang W. Marine sponge derived natural products between 2001 and 2010: trends and opportunities for discovery of bioactives. Mar Drugs. 2014;12:4539–77.PubMed 
PubMed Central 

Google Scholar 
Sipkema D, Franssen MCR, Osinga R, Tramper J, Wijffels RH. Marine sponges as pharmacy. Mar Biotechnol. 2005;7:142–62.CAS 

Google Scholar 
Dobson CM. Chemical space and biology. Nature. 2004;432:824–8.CAS 
PubMed 

Google Scholar 
Indraningrat AAG, Micheller S, Runderkamp M, Sauerland I, Becking LE, Smidt H, et al. Cultivation of sponge-associated bacteria from Agelas sventres and Xestospongia muta collected from different depths. Mar Drugs. 2019;17:578.CAS 
PubMed Central 

Google Scholar 
Piel J. Metabolites from symbiotic bacteria. Nat Prod Rep. 2009;26:338–62.CAS 
PubMed 

Google Scholar 
Webster NS, Thomas T. The sponge hologenome. mBio. 2016;7:e00135–16.PubMed 
PubMed Central 

Google Scholar 
de Oliveira MRF, de Maringá UE, da Costa C, Benedito E. Trends and gaps in scientific production on freshwater sponges. Oecologia Austrlis. 2020;24:61–75.
Google Scholar 
Manconi R, Pronzato R. How to survive and persist in temporary freshwater? Adaptive traits of sponges (Porifera: Spongillida): a review. Hydrobiologia. 2016;782:11–22.
Google Scholar 
Manconi R, Pronzato R. Chapter 8 – Phylum Porifera. In: Thorp JH, Rogers DC, editors. Ecology and general biology. Thorp and Covich’s freshwater invertebrates. vol 1 (4th ed.) New York: Academic Press; 2015. p. 133–157.Manconi R, Pronzato R. Chapter 3 – Phylum Porifera. In: Thorp JH, Rogers DC, editors. Keys to Nearctic fauna. Thorp and Covich’s freshwater invertebrates vol 2(4th ed.) San Diego: Academic Press, Elsevier; 2016. p. 39–83.Leidy J. On Spongilla. In: Proceedings of the Academy of Natural Sciences of Philadelphia. Philadelphia: Academy of Natural Sciences of Philadelphia; 1850. p. 278.Smith F. Distribution of the fresh-water sponges of North America. INHS Bull. 1921;14:9–22.
Google Scholar 
Old MC. Environmental selection of the fresh-water sponges (Spongillidae) of Michigan. Trans Am Microsc Soc. 1932;51:129–36.CAS 

Google Scholar 
Ashley JM. Fresh water sponges of Illinois and Michigan. Urbana-Champaign: Master of Arts, University of Illinois; 1913.Jewell ME. An ecological study of the fresh-water sponges of northeastern Wisconsin. Ecol Monogr. 1935;5:461–504.CAS 

Google Scholar 
Kolomyjec SH, Willford RA. The fall 2019 genetics class. Phylogenetic analysis of Michigan’s freshwater sponges (Porifera, Spongillidae) using extended COI mtDNA sequences. bioRxiv. 2020; https://doi.org/10.1101/2020.04.26.062448.Copeland J, Kunigelis S, Tussing J, Jett T, Rich C. Freshwater sponges (Porifera: Spongillida) of Tennessee. Am Midl Nat. 2019;181:310–26.
Google Scholar 
Lauer TE, Spacie A. An association between freshwater sponges and the zebra mussel in a southern Lake Michigan harbor. J Freshw Ecol. 2004;19:631–7.
Google Scholar 
Skelton J, Strand M. Trophic ecology of a freshwater sponge (Spongilla lacustris) revealed by stable isotope analysis. Hydrobiologia. 2013;709:227–35.CAS 

Google Scholar 
Early TA, Glonek T. Zebra mussel destruction by a Lake Michigan sponge: populations, in vivo 31P nuclear magnetic resonance, and phospholipid profiling. Environ Sci Technol. 1999;33:1957–62.CAS 

Google Scholar 
Early TA, Kundrat JT, Schorp T, Glonek T. Lake Michigan sponge phospholipid variations with habitat: A 31P nuclear magnetic resonance study. Comp Biochem Physiol. 1996;114:77–89.
Google Scholar 
Dembitsky VM, Rezanka T, Srebnik M. Lipid compounds of freshwater sponges: family Spongillidae, class Demospongiae. Chem Phys Lipids. 2003;123:117–55.CAS 
PubMed 

Google Scholar 
Řezanka T, Sigler K, Dembitsky VM. Syriacin, a novel unusual sulfated ceramide glycoside from the freshwater sponge Ephydatia syriaca (Porifera, Demospongiae, Spongillidae). Tetrahedron. 2006;62:5937–43.
Google Scholar 
Radnaeva LD, Bazarsadueva SV, Taraskin VV, Tulokhonov AK. First data on lipids and microorganisms of deepwater endemic sponge Baikalospongia intermedia and sediments from hydrothermal discharge area of the Frolikha Bay (North Baikal, Siberia). J Great Lakes Res. 2020;46:67–74.CAS 

Google Scholar 
Manconi R, Piccialli V, Pronzato R, Sica D. Steroids in porifera, sterols from freshwater sponges Ephydatia fluviatilis (L.) and Spongilla lacustris (L.). Comp Biochem Physiol. 1988;91:237–45.
Google Scholar 
Belikov S, Belkova N, Butina T, Chernogor L, Kley AM-V, Nalian A, et al. Diversity and shifts of the bacterial community associated with Baikal sponge mass mortalities. PLoS ONE. 2019;14:e0213926.CAS 
PubMed 
PubMed Central 

Google Scholar 
Costa R, Keller-Costa T, Gomes NCM, da Rocha UN, van Overbeek L, van Elsas JD. Evidence for selective bacterial community structuring in the freshwater sponge Ephydatia fluviatilis. Microb Ecol. 2013;65:232–44.PubMed 

Google Scholar 
Laport MS, Pinheiro U, Rachid CTCC. Freshwater sponge Tubella variabilis presents richer microbiota than marine sponge species. Front Microbiol. 2019;10:2799.PubMed 
PubMed Central 

Google Scholar 
Kenny NJ, Plese B, Riesgo A, Itskovich VB. Symbiosis, selection, and novelty: freshwater adaptation in the unique sponges of Lake Baikal. Mol Biol Evol. 2019;36:2462–80.CAS 
PubMed Central 

Google Scholar 
Gaikwad S, Shouche YS, Gade WN. Microbial community structure of two freshwater sponges using Illumina MiSeq sequencing revealed high microbial diversity. AMB Express. 2016;6:40.PubMed 
PubMed Central 

Google Scholar 
Gernert C, Glöckner FO, Krohne G, Hentschel U. Microbial diversity of the freshwater sponge Spongilla lacustris. Microb Ecol. 2005;50:206–12.CAS 
PubMed 

Google Scholar 
Hernandez A, Nguyen LT, Dhakal R, Murphy BT. The need to innovate sample collection and library generation in microbial drug discovery: a focus on academia. Nat Prod Rep. 2021;38:292–300.CAS 
PubMed 
PubMed Central 

Google Scholar 
Li C-Q, Liu W-C, Zhu P, Yang J-L, Cheng K-D. Phylogenetic diversity of bacteria associated with the marine sponge Gelliodes carnosa collected from the Hainan Island coastal waters of the South China Sea. Microb Ecol. 2011;62:800–12.PubMed 

Google Scholar 
Sipkema D, Schippers K, Maalcke WJ, Yang Y, Salim S, Blanch HW. Multiple approaches to enhance the cultivability of bacteria associated with the marine sponge Haliclona (gellius) sp. Appl Environ Microbiol. 2011;77:2130–40.CAS 
PubMed 
PubMed Central 

Google Scholar 
Montalvo NF, Davis J, Vicente J, Pittiglio R, Ravel J, Hill RT. Integration of culture-based and molecular analysis of a complex sponge-associated bacterial community. PLoS ONE. 2014;9:e90517.PubMed 
PubMed Central 

Google Scholar 
Elfeki M, Alanjary M, Green SJ, Ziemert N, Murphy BT. Assessing the efficiency of cultivation techniques to recover natural product biosynthetic gene populations from sediment. ACS Chem Biol. 2018;13:2074–81.CAS 
PubMed 

Google Scholar 
Dieckmann R, Graeber I, Kaesler I, Szewzyk U, von Döhren H. Rapid screening and dereplication of bacterial isolates from marine sponges of the Sula Ridge by intact-cell-MALDI-TOF mass spectrometry (ICM-MS). Appl Microbiol Biotechnol. 2005;67:539–48.CAS 
PubMed 

Google Scholar 
Costa MS, Clark CM, Ómarsdóttir S, Sanchez LM, Murphy BT. Minimizing taxonomic and natural product redundancy in microbial libraries using MALDI-TOF MS and the bioinformatics pipeline IDBac. J Nat Prod. 2019;82:2167–73.CAS 
PubMed 
PubMed Central 

Google Scholar 
Clark CM, Costa MS, Sanchez LM, Murphy BT. Coupling MALDI-TOF mass spectrometry protein and specialized metabolite analyses to rapidly discriminate bacterial function. Proc Natl Acad Sci USA. 2018;115:4981–6.CAS 
PubMed 
PubMed Central 

Google Scholar 
Clark CM, Costa MS, Conley E, Li E, Sanchez LM, Murphy BT. Using the open-source MALDI TOF-MS IDBac pipeline for analysis of microbial protein and specialized metabolite data. J Vis Exp. 2019;147:e59219.
Google Scholar 
Ryzhov V, Fenselau C. Characterization of the protein subset desorbed by MALDI from whole bacterial cells. Anal Chem. 2001;73:746–50.CAS 
PubMed 

Google Scholar 
Welker M, Moore ERB. Applications of whole-cell matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry in systematic microbiology. Syst Appl Microbiol. 2011;34:2–11.CAS 
PubMed 

Google Scholar 
Sandrin TR, Goldstein JE, Schumaker S. MALDI TOF MS profiling of bacteria at the strain level: a review. Mass Spectrom Rev. 2013;32:188–217.CAS 
PubMed 

Google Scholar 
Seuylemezian A, Aronson HS, Tan J, Lin M, Schubert W, Vaishampayan P. Development of a custom MALDI-TOF MS database for species-level identification of bacterial isolates collected from spacecraft and associated surfaces. Front Microbiol. 2018;9:780.PubMed 
PubMed Central 

Google Scholar 
Strejcek M, Smrhova T, Junkova P, Uhlik O. Whole-cell MALDI-TOF MS versus 16S rRNA gene analysis for identification and dereplication of recurrent bacterial isolates. Front Microbiol. 2018;9:1294.PubMed 
PubMed Central 

Google Scholar 
Giraud-Gatineau A, Texier G, Garnotel E, Raoult D, Chaudet H. Insights into subspecies discrimination potentiality from bacteria MALDI-TOF mass spectra by using data mining and diversity studies. Front Microbiol. 2020;11:1931.PubMed 
PubMed Central 

Google Scholar 
LaMontagne MG, Tran PL, Benavidez A, Morano LD. Development of an inexpensive matrix-assisted laser desorption-time of flight mass spectrometry method for the identification of endophytes and rhizobacteria cultured from the microbiome associated with maize. PeerJ. 2021;9:e11359.PubMed 
PubMed Central 

Google Scholar 
Freiwald A, Sauer S. Phylogenetic classification and identification of bacteria by mass spectrometry. Nat Protoc. 2009;4:732–42.CAS 
PubMed 

Google Scholar 
Croxatto A, Prod’hom G, Greub G. Applications of MALDI-TOF mass spectrometry in clinical diagnostic microbiology. FEMS Microbiol Rev. 2012;36:380–407.CAS 
PubMed 

Google Scholar 
Rodríguez-Sánchez B, Cercenado E, Coste AT, Greub G. Review of the impact of MALDI-TOF MS in public health and hospital hygiene, 2018. Eurosurveillance. 2019;24:1800193. PubMed Central 

Google Scholar 
Rahi P, Vaishampayan P. MALDI-TOF MS application in microbial ecology studies. Front Microbiol. 2019;10:2954.PubMed 

Google Scholar 
Popović NT, Kazazić SP, Strunjak-Perović I, Čož-Rakovac R. Differentiation of environmental aquatic bacterial isolates by MALDI-TOF MS. Environ Res. 2017;152:7–16.PubMed 

Google Scholar 
Rahi P, Prakash O, Shouche YS. Matrix-assisted laser desorption/ionization Time-of-Flight mass-spectrometry (MALDI-TOF MS) based microbial identifications: challenges and scopes for microbial ecologists. Front Microbiol. 2016;7:1359.PubMed 
PubMed Central 

Google Scholar 
Schumann P, Maier T. Chapter 13 – MALDI-TOF mass spectrometry applied to classification and identification of bacteria. In: Methods in microbiology, vol 41, ISSN 0580-9517. Goodfellow M, Sutcliffe I, Chun J, editors. Academic Press; 2014. p. 275–306.Murtagh F, Legendre P. Ward’s hierarchical agglomerative clustering method: which algorithms implement Ward’s criterion? J Classif. 2014;31:274–95.
Google Scholar 
Batagelj V. Generalized Ward and related clustering problems. In: Bock HH, editor. North Holland, Amsterdam: Proceedings of the First Conference of the International Federation of Classification Societies; 1988. p. 67–74.van Santen JA, Jacob G, Singh AL, Aniebok V, Balunas MJ, Bunsko D, et al. The natural products atlas: an open access knowledge base for microbial natural products discovery. ACS Cent Sci. 2019;5:1824–33.PubMed 
PubMed Central 

Google Scholar 
Ghyselinck J, Van Hoorde K, Hoste B, Heylen K, De Vos P. Evaluation of MALDI-TOF MS as a tool for high-throughput dereplication. J Microbiol Meth. 2011;86:327–36.CAS 

Google Scholar 
Pruesse E, Peplies J, Glöckner FO. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics. 2012;28:1823–9.CAS 
PubMed 
PubMed Central 

Google Scholar 
Henson MW, Lanclos VC, Pitre DM, Weckhorst JL, Lucchesi AM, Cheng C, et al. Expanding the diversity of bacterioplankton isolates and modeling isolation efficacy with large-scale dilution-to-extinction cultivation. Appl Environ Microbiol. 2020;86:e00943–20.CAS 
PubMed 
PubMed Central 

Google Scholar 
Hoffmann T, Krug D, Bozkurt N, Duddela S, Jansen R, Garcia R, et al. Correlating chemical diversity with taxonomic distance for discovery of natural products in myxobacteria. Nat Commun. 2018;9:1–10.CAS 

Google Scholar 
Jensen PR, Williams PG, Oh D-C, Zeigler L, Fenical W. Species-specific secondary metabolite production in marine actinomycetes of the genus Salinispora. Appl Environ Microbiol. 2007;73:1146–52.CAS 
PubMed 

Google Scholar 
Ziemert N, Lechner A, Wietz M, Millán-Aguiñaga N, Chavarria KL, Jensen PR. Diversity and evolution of secondary metabolism in the marine actinomycete genus Salinispora. Proc Natl Acad Sci USA. 2014;111:E1130–9.CAS 
PubMed 
PubMed Central 

Google Scholar 
Bruns H, Crüsemann M, Letzel A-C, Alanjary M, McInerney JO, Jensen PR, et al. Function-related replacement of bacterial siderophore pathways. ISME J. 2018;12:320–9.CAS 
PubMed 

Google Scholar 
Chase AB, Sweeney D, Muskat MN, Guillén-Matus DG, Jensen PR. Vertical inheritance facilitates interspecies diversification in biosynthetic gene clusters and specialized metabolites. MBio. 2021;12:e0270021.PubMed 

Google Scholar 
Covington BC, Xu F, Seyedsayamdost MR. A natural product chemist’s guide to unlocking silent biosynthetic gene clusters. Annu Rev Biochem. 2021;90:763–88.CAS 
PubMed 

Google Scholar 
Adamek M, Alanjary M, Sales-Ortells H, Goodfellow M, Bull AT, Winkler A, et al. Comparative genomics reveals phylogenetic distribution patterns of secondary metabolites in Amycolatopsis species. BMC Genomics. 2018;19:426.PubMed 
PubMed Central 

Google Scholar 
Chevrette MG, Currie CR. Emerging evolutionary paradigms in antibiotic discovery. J Ind Microbiol Biotechnol. 2019;46:257–71.CAS 
PubMed 

Google Scholar 
Zdouc MM, Iorio M, Maffioli SI, Crüsemann M, Donadio S, Sosio M. Planomonospora: a metabolomics perspective on an underexplored Actinobacteria genus. J Nat Prod. 2021;84:204–19.CAS 
PubMed 
PubMed Central 

Google Scholar 
Kang D, Shoaie S, Jacquiod S, Sørensen SJ, Ledesma-Amaro R. Comparative genomics analysis of keratin-degrading Chryseobacterium species reveals their keratinolytic potential for secondary metabolite production. Microorganisms. 2021;9:1042.CAS 
PubMed 
PubMed Central 

Google Scholar 
Han S, Van Treuren W, Fischer CR, Merrill BD, DeFelice BC, Sanchez JM, et al. A metabolomics pipeline for the mechanistic interrogation of the gut microbiome. Nature. 2021;595:415–20.CAS 
PubMed 

Google Scholar 
Newman DJ, Cragg GM. Natural products as sources of new drugs over the nearly four decades from 01/1981 to 09/2019. J Nat Prod. 2020;83:770–803.CAS 
PubMed 

Google Scholar 
Demain AL, Sanchez S. Microbial drug discovery: 80 years of progress. J Antibiot. 2009;62:5–16.CAS 

Google Scholar 
Chambers MC, Maclean B, Burke R, Amodei D, Ruderman DL, Neumann S, et al. A cross-platform toolkit for mass spectrometry and proteomics. Nat Biotechnol. 2012;30:918–20.CAS 
PubMed 
PubMed Central 

Google Scholar 
Gibb S, Strimmer K. Mass spectrometry analysis using MALDIquant. In: Datta S, Mertens BJA, editors. Statistical analysis of proteomics, metabolomics, and lipidomics data using mass spectrometry. Cham: Springer International Publishing; 2017. p. 101–24.Gibb S, Strimmer K. MALDIquant: a versatile R package for the analysis of mass spectrometry data. Bioinformatics. 2012;28:2270–1.CAS 
PubMed 

Google Scholar 
Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol. 1991;173:697–703.CAS 
PubMed 
PubMed Central 

Google Scholar  More