More stories

  • in

    Dynamics of rumen microbiome in sika deer (Cervus nippon yakushimae) from unique subtropical ecosystem in Yakushima Island, Japan

    Gruninger, R. J., Ribeiro, G. O., Cameron, A. & McAllister, T. A. Invited review: Application of meta-omics to understand the dynamic nature of the rumen microbiome and how it responds to diet in ruminants. Animal 13, 1843–1854 (2019).CAS 

    Google Scholar 
    Morgavi, D. P., Kelly, W. J., Janssen, P. H. & Attwood, G. T. Rumen microbial (meta)genomics and its application to ruminant production. Animal 7, 184–201 (2013).CAS 

    Google Scholar 
    Bergman, E. N. Energy contributions of volatile fatty acids from the gastrointestinal tract in various species. Physiol. Rev. 70, 567–590 (1990).CAS 

    Google Scholar 
    Flint, H. J. The rumen microbial ecosystem—Some recent developments. Trends Microbiol. 5, 483–488 (1997).CAS 

    Google Scholar 
    Hobson, P. N. & Stewart, C. S. The Rumen Microbial Ecosystem. (Springer, 2012).Moraïs, S. & Mizrahi, I. The road not taken: The rumen microbiome, functional groups, and community states. Trends Microbiol. 27, 538–549 (2019).
    Google Scholar 
    Cheng, K. J., Forsberg, C. W., Minato, H. & Costerton, J. W. in Physiological Aspects of Digestion and Metabolism in Ruminants (eds T. Tsuda, Y. Sasaki, & R. Kawashima) 595–624 (Academic Press, 1991).McSweeney, C. S., Palmer, B., McNeill, D. M. & Krause, D. O. Microbial interactions with tannins: Nutritional consequences for ruminants. Anim. Feed Sci. Technol. 91, 83–93 (2001).CAS 

    Google Scholar 
    Skene, I. K. & Brooker, J. D. Characterization of tannin acylhydrolase activity in the ruminal bacterium Selenomonas ruminantium. Anaerobe 1, 321–327 (1995).CAS 

    Google Scholar 
    Khanbabaee, K. & van Ree, T. Tannins: Classification and definition. Nat. Prod. Rep. 18, 641–649 (2001).CAS 

    Google Scholar 
    Makkar, H. P. S. & Becker, K. Isolation of tannins from leaves of some trees and shrubs and their properties. J. Agric. Food Chem. 42, 731–734 (1994).CAS 

    Google Scholar 
    Bhat, T. K., Kannan, A., Singh, B. & Sharma, O. P. Value addition of feed and fodder by alleviating the antinutritional effects of tannins. Agr. Res. 2, 189–206 (2013).CAS 

    Google Scholar 
    Shimada, T. Salivary proteins as a defense against dietary tannins. J. Chem. Ecol. 32, 1149–1163 (2006).CAS 

    Google Scholar 
    Zhu, J., Filippich, L. J. & Alsalami, M. T. Tannic acid intoxication in sheep and mice. Res. Vet. Sci. 53, 280–292 (1992).CAS 

    Google Scholar 
    Kohl, K. D., Stengel, A. & Dearing, M. D. Inoculation of tannin-degrading bacteria into novel hosts increases performance on tannin-rich diets. Environ. Microbiol. 18, 1720–1729 (2016).CAS 

    Google Scholar 
    Kumar, K., Chaudhary, L. C., Agarwal, N. & Kamra, D. N. Isolation and characterization of tannin-degrading bacteria from the rumen of goats fed oak (Quercus semicarpifolia) leaves. Agr. Res. 3, 377–385 (2014).
    Google Scholar 
    Odenyo, A. A. et al. Characterization of tannin-tolerant bacterial isolates from East African ruminants. Anaerobe 7, 5–15 (2001).CAS 

    Google Scholar 
    Grilli, D. J. et al. Analysis of the rumen bacterial diversity of goats during shift from forage to concentrate diet. Anaerobe 42, 17–26 (2016).
    Google Scholar 
    Tong, J. et al. Illumina sequencing analysis of the ruminal microbiota in high-yield and low-yield lactating dairy cows. PLoS ONE 13, e0198225 (2018).
    Google Scholar 
    Pope, P. B. et al. Metagenomics of the Svalbard reindeer rumen microbiome reveals abundance of polysaccharide utilization loci. PLoS ONE 7, e38571 (2012).ADS 
    CAS 

    Google Scholar 
    Østbye, K., Wilson, R. & Rudi, K. Rumen microbiota for wild boreal cervids living in the same habitat. FEMS Microbiol. Lett. 363, fnw233 (2016).
    Google Scholar 
    Gruninger, R. J., Sensen, C. W., McAllister, T. A. & Forster, R. J. Diversity of rumen bacteria in Canadian cervids. PLoS ONE 9, e89682 (2014).ADS 

    Google Scholar 
    Henderson, G. et al. Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range. Sci. Rep. 5, 14567 (2015).CAS 

    Google Scholar 
    Reese, A. T. & Kearney, S. M. Incorporating functional trade-offs into studies of the gut microbiota. Curr. Opin. Microbiol. 50, 20–27 (2019).CAS 

    Google Scholar 
    Moeller, A. H. et al. Social behavior shapes the chimpanzee pan-microbiome. Sci. Adv. 2, e1500997 (2016).ADS 

    Google Scholar 
    Okano, T. & Matsuda, H. Biocultural diversity of Yakushima Island: Mountains, beaches, and sea. J. Mar. Isl. Cult. 2, 69–77 (2013).
    Google Scholar 
    Agetsuma, N., Agetsuma-Yanagihara, Y. & Takafumi, H. Food habits of Japanese deer in an evergreen forest: Litter-feeding deer. Mamm. Biol. 76, 201–207 (2011).
    Google Scholar 
    Higashi, Y., Hirota, S. K., Suyama, Y. & Yahara, T. Geographical and seasonal variation of plant taxa detected in faces of Cervus nippon yakushimae based on plant DNA analysis in Yakushima Island. Ecol. Res. 37, 582–597 (2022).CAS 

    Google Scholar 
    Kuroiwa, A. Nutritional ecology of the Yakushika (Cervus nippon yakushimae) population under high density Ph.D. thesis, Kyushu University, (2017).Koda, R., Agetsuma, N., Agetsuma-Yanagihara, Y., Tsujino, R. & Fujita, N. A proposal of the method of deer density estimate without fecal decomposition rate: A case study of fecal accumulation rate technique in Japan. Ecol. Res. 26, 227–231 (2011).
    Google Scholar 
    Yahara, T. in Deer eats world heritages: Ecology of deer and forets (eds T. Yumoto & H. Matsuda) 168–187 (Bunichi-Sogo-Shuppan, 2006).Onoda, Y. & Yahara, T. in Challenges for Conservation Ecology in Space and Time. (eds T. Miyashita & J. Nishihiro) 126–149 (University of Tokyo Press, 2015).Kagoshima Prefecture Nature Conservation Division. The current status of Yakusika in FY 2020, available at https://www.rinya.maff.go.jp/kyusyu/fukyu/shika/attach/pdf/yakushikaWG_R3_2-23.pdf (2020).Kuroiwa, A., Kuroe, M. & Yahara, T. Effects of density, season, and food intake on sika deer nutrition on Yakushima Island, Japan. Ecol. Res. 32, 369–378 (2017).
    Google Scholar 
    Hiura, T., Hashidoko, Y., Kobayashi, Y. & Tahara, S. Effective degradation of tannic acid by immobilized rumen microbes of a sika deer (Cervus nippon yesoensis) in winter. Anim. Feed Sci. Technol. 155, 1–8 (2010).CAS 

    Google Scholar 
    Kawarai, S. et al. Seasonal and geographical differences in the ruminal microbial and chloroplast composition of sika deer (Cervus nippon) in Japan. Sci. Rep. 12, 6356 (2022).ADS 
    CAS 

    Google Scholar 
    Li, Z. et al. Response of the rumen microbiota of sika deer Cervus nippon fed different concentrations of tannin rich plants. PLoS ONE 10, e0123481 (2015).
    Google Scholar 
    McDonald, D. et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J. 6, 610–618 (2012).CAS 

    Google Scholar 
    Kim, M., Morrison, M. & Yu, Z. Status of the phylogenetic diversity census of ruminal microbiomes. FEMS Microbiol. Ecol. 76, 49–63 (2011).CAS 

    Google Scholar 
    Weimer, P. J. Redundancy, resilience, and host specificity of the ruminal microbiota: Implications for engineering improved ruminal fermentations. Front. Microbiol. 6, 296 (2015).
    Google Scholar 
    Scott, K. P., Gratz, S. W., Sheridan, P. O., Flint, H. J. & Duncan, S. H. The influence of diet on the gut microbiota. Pharmacol. Res. 69, 52–60 (2013).CAS 

    Google Scholar 
    Tapio, I. et al. Taxon abundance, diversity, co-occurrence and network analysis of the ruminal microbiota in response to dietary changes in dairy cows. PLoS ONE 12, e0180260 (2017).
    Google Scholar 
    Ohara, M. in Agriculture in Hokkaido v2 (ed K. Iwama, Ohara, M., Araki, H., Yamada, T., Nakatsuji, H., Kataoka, T., Yamamoto, Y.) 1–18(Faculty of Agriculture, Hokkaido Univ., 2009).Igota, H., Sakuragi, M. & Uno, H. in Sika Deer: Biology and Management of Native and Introduced Populations (eds. Dale R. McCullough, Seiki Takatsuki, & Koichi Kaji) 251–272 (Springer Japan, 2009).Fernando, S. C. et al. Rumen microbial population dynamics during adaptation to a high-grain diet. Appl. Environ. Microbiol. 76, 7482–7490 (2010).ADS 
    CAS 

    Google Scholar 
    Hu, X. et al. High-throughput analysis reveals seasonal variation of the gut microbiota composition within forest musk deer (Moschus berezovskii). Front. Microbiol. 9, (2018).Artzi, L., Morag, E., Shamshoum, M. & Bayer, E. A. Cellulosomal expansion: Functionality and incorporation into the complex. Biotechnol. Biofuels 9, 61 (2016).
    Google Scholar 
    Biddle, A., Stewart, L., Blanchard, J. & Leschine, S. Untangling the genetic basis of fibrolytic specialization by Lachnospiraceae and Ruminococcaceae in diverse gut communities. Diversity 5, (2013).Eisenhauer, N., Scheu, S. & Jousset, A. Bacterial diversity stabilizes community productivity. PLoS ONE 7, e34517 (2012).ADS 
    CAS 

    Google Scholar 
    Miller, A. W., Oakeson, K. F., Dale, C. & Dearing, M. D. Effect of dietary oxalate on the gut microbiota of the mammalian herbivore Neotoma albigula. Appl. Environ. Microbiol. 82, 2669–2675 (2016).ADS 
    CAS 

    Google Scholar 
    Adams, J. M., Rehill, B., Zhang, Y. & Gower, J. A test of the latitudinal defense hypothesis: Herbivory, tannins and total phenolics in four North American tree species. Ecol. Res. 24, 697–704 (2009).CAS 

    Google Scholar 
    Nabeshima, E., Murakami, M. & Hiura, T. Effects of herbivory and light conditions on induced defense in Quercus crispula. J. Plant Res. 114, 403–409 (2001).
    Google Scholar 
    Yang, C.-M., Yang, M.-M., Hsu, J.-M. & Jane, W.-N. Herbivorous insect causes deficiency of pigment–protein complexes in an oval-pointed cecidomyiid gall of Machilus thunbergii leaf. Bot. Bull. Acad. Sin. 44, 315–321 (2003).
    Google Scholar 
    Agetsuma, N., Agetsuma-Yanagihara, Y., Takafumi, H. & Nakaji, T. Plant constituents affecting food selection by sika deer. J. Wildl. Manag. 83, 669–678 (2019).
    Google Scholar 
    Couch, C. E. et al. Diet and gut microbiome enterotype are associated at the population level in African buffalo. Nat. Commun. 12, 2267 (2021).ADS 
    CAS 

    Google Scholar 
    Goel, G., Puniya, A. K. & Singh, K. Tannic acid resistance in ruminal streptococcal isolates. J. Basic Microbiol. 45, 243–245 (2005).CAS 

    Google Scholar 
    Jiménez, N. et al. Genetic and biochemical approaches towards unravelling the degradation of gallotannins by Streptococcus gallolyticus. Microb. Cell Fact. 13, 154 (2014).
    Google Scholar 
    Nelson, K. E., Thonney, M. L., Woolston, T. K., Zinder, S. H. & Pell, A. N. Phenotypic and phylogenetic characterization of ruminal tannin-tolerant bacteria. Appl. Environ. Microbiol. 64, 3824–3830 (1998).ADS 
    CAS 

    Google Scholar 
    Selwal, M. K. et al. Optimization of cultural conditions for tannase production by Pseudomonas aeruginosa IIIB 8914 under submerged fermentation. World J. Microbiol. Biotechnol. 26, 599–605 (2010).CAS 

    Google Scholar 
    Kohl, K. D., Weiss, R. B., Cox, J., Dale, C. & Denise Dearing, M. Gut microbes of mammalian herbivores facilitate intake of plant toxins. Ecol. Lett. 17, 1238–1246 (2014).
    Google Scholar 
    Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Method 7, 335–336 (2010).CAS 

    Google Scholar 
    Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C. & Knight, R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27, 2194–2200 (2011).CAS 

    Google Scholar 
    Caporaso, J. G. et al. PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 26, 266–267 (2009).
    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 

    Google Scholar 
    R: A language and environment for statistical computing (R Foundation for Statistical Computing, Vienna, Austria, 2020).Osawa, R. Formation of a clear zone on tannin-treated brain heart infusion agar by a Streptococcus sp. isolated from feces of koalas. Appl. Environ. Microbiol. 56, 829–831 (1990).ADS 
    CAS 

    Google Scholar 
    Hamamura, N., Olson, S. H., Ward, D. M. & Inskeep, W. P. Diversity and functional analysis of bacterial communities associated with natural hydrocarbon seeps in acidic soils at Rainbow Springs, Yellowstone National Park. Appl. Environ. Microbiol. 71, 5943–5950 (2005).ADS 
    CAS 

    Google Scholar 
    Benson, D. A. et al. GenBank. Nucleic Acids Res. 41, D36–D42 (2012).ADS 

    Google Scholar 
    Chen, I.-M. A. et al. The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities. Nucleic Acids Res. 49, D751–D763 (2020)Suzuki, M. T., Taylor, L. T. & Delong, E. F. Quantitative analysis of small-subunit rRNA genes in mixed microbial populations via 5 ’-nuclease assays. Appl. Environ. Microbiol. 66, 4605–4614 (2000).ADS 
    CAS 

    Google Scholar  More

  • in

    An energetic look at the life in logged forests

    Putz, F. E. et al. Conserv. Lett. 5, 296–303 (2012).Article 

    Google Scholar 
    Blaser, J., Sarre, A., Poore, D. & Johnson, S. Status of Tropical Forest Management 2011. ITTO Tech. Ser. No. 38 (International Tropical Timber Organization, 2011); available at https://go.nature.com/3usq2an
    Google Scholar 
    Malhi, Y. et al. Nature https://doi.org/10.1038/s41586-022-05523-1 (2022).Article 

    Google Scholar 
    Zwerts, J. A. et al. Conserv. Sci. Pract. 3, e568 (2021).Article 

    Google Scholar 
    Wilkie, D. S., Bennett, E. L., Peres, C. A. & Cunningham, A. A. Ann. N. Y. Acad. Sci. 1223, 120–128 (2011).Article 
    PubMed 

    Google Scholar 
    Putz, F. E., Blate, G. M., Redford, K. H., Fimbel, R. & Robinson, J. Conserv. Biol. 15, 7–20 (2001).Article 

    Google Scholar  More

  • in

    Edaphic controls of soil organic carbon in tropical agricultural landscapes

    Study area and soil collectionTwenty NRCS map units were selected across Hawaii Commercial & Sugar Company (HC&S) in central Maui that represented seven soil orders, 10 NRCS soil series, and approximately 77% of the total plantation area (Fig. 1). Soil heterogeneity across the landscape allowed for the comparison of a continuum of soil and soil properties that have experienced the same C4 grass inputs and agricultural treatment under sugarcane production for over 100 years. Conventional sugarcane production involved 2-year growth followed by harvest burn, collection of remaining stalks by mechanical ripper, deep tillage to 40 cm, no crop rotations, and little to no residue return. The sampled soils, collected from September-August 2015, thus represent a baseline of SOC after input-intensive tropical agriculture and long-term soil disturbance. Elemental analyses from this work show consistent agricultural disturbances led to degraded SOC content ranging from 0.23 to 2.91% SOC of soil mass with an average of only 1.16% SOC across all locations and depths.Figure 1Hawaiian Commercial and Sugar in central Maui with main Hawaiian Islands inset (left). Soil series identified by NRCS across HC&S fields (right) with black dots indicating 20 locations where soils were sampled to test landscape level differences in topical soil kinetics and associated soil properties under conventional sugarcane. Maps from Ref.19 created using ESRI ArcGIS with soil series data from: Soil Survey Staff, Natural Resources Conservation Service, United States Department of Agriculture, Web Soil Survey, Available online at http://websoilsurvey.nrcs.usda.gov/. Accessed [07/30/2016]19.Full size imageThe homogenized land use history allowed focused investigation of soil property effects on SOC storage across heterogenous soils (Table 1). Though soil inputs (e.g. water, nutrients, root inputs, residue removal) and disturbance regimes (e.g. burn, rip, till, compaction, no crop rotation) were consistent across the 20 field locations, average annual surface temperatures varied from 22.9 to 25.1 °C with a mean of 24.4 °C, average annual relative humidity varied from 70.4 to 79.2% with a mean of 73.4%, and average annual rainfall varied from 306 to 1493 mm with a mean of 575 mm. Gradients of rainfall, relative humidity, and elevation across the site generally increase in an east/north-east direction towards the prevailing winds and up the western slope of Haleakalā. In contrast, surface temperatures increase in the opposite direction towards Kihei and the southern tip of the West Maui Mountains.Table 1 NRCS soil classification and environmental conditions at 20 field sites.Full size tableaSoil descriptions26.bInterpolated estimates from Ref.25.Soil sampling and analysisPit locations were identified with a handheld GPS and were sampled using NRCS Rapid Carbon Assessment methods27. A total of 75 horizons were identified from the 20 selected map units to a depth of 1 m28,29. The central depth of each horizon was sampled using volumetric bulk density cores up to 50 cm. After 50 cm, a hand auger was used to check for any further horizon changes. The bulk density of horizons past 50 cm were estimated using collected soil mass and known auger size. Collected soils were air dried, processed through a 2 mm sieve, and analyzed for total C and nitrogen percent, SOC percent, soil texture, iron (Fe) and aluminum (Al) minerals, pH, cation and anion exchange capacity, extractable cations, wet and dry size classes, aggregate stability, and soil water potential at -15 kPa. Total C and nitrogen were measured by elemental analysis (Costech, ECS 4010, Valencia, CA), with SOC content determined by elemental analysis after hydrochloric acid digestion to remove carbonates. Soil texture was measured using sedimentary separation, while a 10:1 soil slurry in water was used to test soil pH. Soil pressure plates were used to measure soil water potential at -15 kPa.Fe and Al oxides were quantified in mineral phases using selective dissolutions of collected soils, including: (1) a 20:1 sodium citrate to sodium dithionite extraction, shaken 16 h, to quantify total free minerals30, (2) 0.25 M hydroxylamine hydrochloride and hydrochloric acid extraction, shaken 16 h, to quantify amorphous minerals31, and (3) 0.1 M sodium pyrophosphate (pH 10), shaken 16 h and centrifuged at 20,000g, to quantify organo-bound metals30. Extracted Fe, Al, and Si from al extractions were measured by inductively coupled plasma analysis (PerkinElmer, Optima ICP-OES, Norwalk, CT). Exploratory ratios of Fe/Al, Fe/Si, and Al/Si for the citrate/dithionite (c), hydroxylamine (h), and pyrophosphate (p) extractions were calculated. Crystalline Fe, operationally-defined as the difference between the citrate dithionite and hydroxylamine extraction, and Al + ½ Fe32 were calculated for each extraction.Plant-available phosphorus was extracted by the Olsen method using 0.5 M sodium bicarbonate adjusted to pH 8.5 and measured by continuous flow colorimetry (Hach, Lachat Quickchem 8500, Loveland, CO). Exchangeable cations (i.e. calcium, magnesium, potassium, and sodium), effective cation exchange capacity, and anion exchange capacity were measured by compulsive exchange using barium chloride and magnesium sulfate33. Cations were quantified by continuous flow colorimetry and flame-spectroscopy (Hach, Lachat Quickchem 8500, Loveland, CO). Field soils were air dried and initially passed through a 2 mm sieve before size classes of macroaggregate (2 mm – 250 µm) and microaggregate ( More

  • in

    Biodiversity–stability relationships strengthen over time in a long-term grassland experiment

    Doak, D. F. et al. The statistical inevitability of stability‐diversity relationships in community ecology. Am. Nat. 151, 264–276 (1998).Article 
    CAS 

    Google Scholar 
    Schläpfer, F. & Schmid, B. Ecosystem effects of biodiversity: a classification hypotheses and exploration of empirical results. Ecol. Appl. 9, 893–912 (1999).Article 

    Google Scholar 
    Lehman, C. L. & Tilman, D. Biodiversity, stability, and productivity in competitive communities. Am. Nat. 156, 534–552 (2000).Article 

    Google Scholar 
    Allan, E. et al. More diverse plant communities have higher functioning over time due to turnover in complementary dominant species. Proc. Natl Acad. Sci. USA 108, 17034–17039 (2011).Article 
    ADS 
    CAS 

    Google Scholar 
    Isbell, F. et al. High plant diversity is needed to maintain ecosystem services. Nature 477, 199–202 (2011).Article 
    ADS 
    CAS 

    Google Scholar 
    Wagg, C. et al. Plant diversity maintains long-term ecosystem productivity under frequent drought by increasing short-term variation. Ecology 98, 2952–2961 (2017).Article 

    Google Scholar 
    Isbell, F. et al. Biodiversity increases the resistance of ecosystem productivity to climate extremes. Nature 526, 574–577 (2015).Article 
    ADS 
    CAS 

    Google Scholar 
    Reich, P. B. et al. Impacts of biodiversity loss escalate through time as redundancy fades. Science 336, 589–592 (2012).Article 
    ADS 
    CAS 

    Google Scholar 
    Guerrero-Ramírez, N. R. et al. Diversity-dependent temporal divergence of ecosystem functioning in experimental ecosystems. Nat. Ecol. Evol. 1, 1639–1642 (2017).Article 

    Google Scholar 
    Meyer, S. T. et al. Effects of biodiversity strengthen over time as ecosystem functioning declines at low and increases at high biodiversity. Ecosphere 7, e01619 (2016).Article 

    Google Scholar 
    Huang, Y. et al. Impacts of species richness on productivity in a large-scale subtropical forest experiment. Science 362, 80–83 (2018).Article 
    ADS 
    CAS 

    Google Scholar 
    Bongers, F. J. et al. Functional diversity effects on productivity increase with age in a forest biodiversity experiment. Nat. Ecol. Evol. 5, 1594–1603 (2021).Article 

    Google Scholar 
    Weisser, W. W. et al. Biodiversity effects on ecosystem functioning in a 15-year grassland experiment: Patterns, mechanisms, and open questions. Basic Appl. Ecol. 23, 1–73 (2017).Article 

    Google Scholar 
    Guerrero-Ramírez, N. R., Reich, P. B., Wagg, C., Ciobanu, M. & Eisenhauer, N. Diversity-dependent plant–soil feedbacks underlie long-term plant diversity effects on primary productivity. Ecosphere 10, e02704 (2019).Article 

    Google Scholar 
    Eisenhauer, N. The shape that matters: how important is biodiversity for ecosystem functioning. Sci. China Life Sci. 65, 651–653 (2022).Article 

    Google Scholar 
    Cardinale, B. J. et al. Impacts of plant diversity on biomass production increase through time because of species complementarity. Proc. Natl Acad. Sci. USA 104, 18123–18128 (2007).Article 
    ADS 
    CAS 

    Google Scholar 
    Marquard, E. et al. Plant species richness and functional composition drive overyielding in a six-year grassland experiment. Ecology 90, 3290–3302 (2009).Article 

    Google Scholar 
    Zuppinger-Dingley, D. et al. Selection for niche differentiation in plant communities increases biodiversity effects. Nature 515, 108–111 (2014).Article 
    ADS 
    CAS 

    Google Scholar 
    Loreau, M. & Hector, A. Partitioning selection and complementarity in biodiversity experiments. Nature 412, 72–76 (2001).Article 
    ADS 
    CAS 

    Google Scholar 
    Wang, S. et al. How complementarity and selection affect the relationship between ecosystem functioning and stability. Ecology 102, e03347 (2021).Article 

    Google Scholar 
    Yan, Y. et al. Mechanistic links between biodiversity effects on ecosystem functioning and stability in a multi-site grassland experiment. J. Ecol. 109, 3370–3378 (2021).Article 

    Google Scholar 
    Barry, K. E. et al. The future of complementarity: disentangling causes from consequences. Trends Ecol. Evol. 34, 167–180 (2019).Article 

    Google Scholar 
    Yachi, S. & Loreau, M. Biodiversity and ecosystem productivity in a fluctuating environment: the insurance hypothesis. Proc. Natl Acad. Sci. USA 96, 1463–1468 (1999).Article 
    ADS 
    CAS 

    Google Scholar 
    Gonzalez, A. & Loreau, M. The causes and consequences of compensatory dynamics in ecological communities. Annu. Rev. Ecol. Evol. Syst. 40, 393–414 (2009).Article 

    Google Scholar 
    Thibaut, L. M. & Connolly, S. R. Understanding diversity–stability relationships: towards a unified model of portfolio effects. Ecol. Lett. 16, 140–150 (2013).Article 

    Google Scholar 
    Craven, D. et al. Multiple facets of biodiversity drive the diversity–stability relationship. Nat. Ecol. Evol. 2, 1579–1587 (2018).Article 

    Google Scholar 
    Tilman, D., Reich, P. B. & Knops, J. M. H. Biodiversity and ecosystem stability in a decade-long grassland experiment. Nature 441, 629–632 (2006).Article 
    ADS 
    CAS 

    Google Scholar 
    Loreau, M. Biodiversity and Ecosystem Functioning (Princeton Univ. Press,2010).Loreau, M. & de Mazancourt, C. Biodiversity and ecosystem stability: a synthesis of underlying mechanisms. Ecol. Lett. 16, 106–115 (2013).Article 

    Google Scholar 
    Isbell, F. et al. Quantifying effects of biodiversity on ecosystem functioning across times and places. Ecol. Lett. 21, 763–778 (2018).Article 

    Google Scholar 
    Maron, J. L., Marler, M., Klironomos, J. N. & Cleveland, C. C. Soil fungal pathogens and the relationship between plant diversity and productivity. Ecol. Lett. 14, 36–41 (2011).Article 

    Google Scholar 
    Schnitzer, S. A. et al. Soil microbes drive the classic plant diversity–productivity pattern. Ecology 92, 296–303 (2011).Article 

    Google Scholar 
    Marquard, E. et al. Changes in the abundance of grassland species in monocultures versus mixtures and their relation to biodiversity effects. PLoS ONE 8, e75599 (2013).Article 
    ADS 
    CAS 

    Google Scholar 
    Roscher, C. et al. Identifying population- and community-level mechanisms of diversity–stability relationships in experimental grasslands. J. Ecol. 99, 1460–1469 (2011).Article 

    Google Scholar 
    Civitello, D. J. et al. Biodiversity inhibits parasites: broad evidence for the dilution effect. Proc. Natl Acad. Sci. USA 112, 8667–8671 (2015).Article 
    ADS 
    CAS 

    Google Scholar 
    Kulmatiski, A., Beard, K. H. & Heavilin, J. Plant–soil feedbacks provide an additional explanation for diversity–productivity relationships. Proc. R. Soc. B 279, 3020–3026 (2012).Article 

    Google Scholar 
    van Moorsel, S. J. et al. Co-occurrence history increases ecosystem stability and resilience in experimental plant communities. Ecology 102, e03205 (2021).Article 

    Google Scholar 
    Schöb, C., Brooker, R. W. & Zuppinger-Dingley, D. Evolution of facilitation requires diverse communities. Nat. Ecol. Evol. 2, 1381–1385 (2018).Article 

    Google Scholar 
    Temperton, V. M., Mwangi, P. N., Scherer-Lorenzen, M., Schmid, B. & Buchmann, N. Positive interactions between nitrogen-fixing legumes and four different neighbouring species in a biodiversity experiment. Oecologia 151, 190–205 (2007).Article 
    ADS 

    Google Scholar 
    Furey, G. N. & Tilman, D. Plant biodiversity and the regeneration of soil fertility. Proc. Natl Acad. Sci. USA 118, e2111321118 (2021).Article 
    CAS 

    Google Scholar 
    Gubsch, M. et al. Foliar and soil δ15N values reveal increased nitrogen partitioning among species in diverse grassland communities. Plant Cell Environ. 34, 895–908 (2011).Article 
    CAS 

    Google Scholar 
    Roscher, C., Schmid, B., Buchmann, N., Weigelt, A. & Schulze, E.-D. Legume species differ in the responses of their functional traits to plant diversity. Oecologia 165, 437–452 (2011).Article 
    ADS 

    Google Scholar 
    Eisenhauer, N. et al. Plant diversity effects on soil microorganisms support the singular hypothesis. Ecology 91, 485–496 (2010).Article 
    CAS 

    Google Scholar 
    Fornara, D. A. & Tilman, D. Plant functional composition influences rates of soil carbon and nitrogen accumulation. J. Ecol. 96, 314–322 (2008).Article 
    CAS 

    Google Scholar 
    Lange, M. et al. Plant diversity increases soil microbial activity and soil carbon storage. Nat. Commun. 6, 6707 (2015).Article 
    ADS 
    CAS 

    Google Scholar 
    Xu, S. et al. Species richness promotes ecosystem carbon storage: evidence from biodiversity-ecosystem functioning experiments. Proc. R. Soc. B 287, 20202063 (2020).Article 
    CAS 

    Google Scholar 
    Cong, W.-F. et al. Plant species richness promotes soil carbon and nitrogen stocks in grasslands without legumes. J. Ecol. 102, 1163–1170 (2014).Article 
    CAS 

    Google Scholar 
    Leimer, S. et al. Mechanisms behind plant diversity effects on inorganic and organic N leaching from temperate grassland. Biogeochemistry 131, 339–353 (2016).Article 
    CAS 

    Google Scholar 
    Xu, Q. et al. Consistently positive effect of species diversity on ecosystem, but not population, temporal stability. Ecol. Lett. 24, 2256–2266 (2021).Article 

    Google Scholar 
    Hector, A. et al. General stabilizing effects of plant diversity on grassland productivity through population asynchrony and overyielding. Ecology 91, 2213–2220 (2010).Article 
    CAS 

    Google Scholar 
    Turnbull, L. A., Levine, J. M., Loreau, M. & Hector, A. Coexistence, niches and biodiversity effects on ecosystem functioning. Ecol. Lett. 16, 116–127 (2013).Article 

    Google Scholar 
    Wright, A. J. et al. Flooding disturbances increase resource availability and productivity but reduce stability in diverse plant communities. Nat. Commun. 6, 6092 (2015).Article 
    ADS 
    CAS 

    Google Scholar 
    Fischer, F. M. et al. Plant species richness and functional traits affect community stability after a flood event. Philos. Trans. R. Soc. B 371, 20150276 (2016).Article 

    Google Scholar 
    Roscher, C. et al. A functional trait-based approach to understand community assembly and diversity–productivity relationships over 7 years in experimental grasslands. Perspect. Plant Ecol. Evol. Syst. 15, 139–149 (2013).Article 

    Google Scholar 
    Eisenhauer, N. et al. Biotic interactions, community assembly, and eco-evolutionary dynamics as drivers of long-term biodiversity–ecosystem functioning relationships. Res. Ideas Outcomes 5, e47042 (2019).Article 

    Google Scholar 
    van Moorsel, S. J., Schmid, M. W., Hahl, T., Zuppinger-Dingley, D. & Schmid, B. Selection in response to community diversity alters plant performance and functional traits. Perspect. Plant Ecol. Evol. Syst. 33, 51–61 (2018).Article 

    Google Scholar 
    van Moorsel, S. J. et al. Community evolution increases plant productivity at low diversity. Ecol. Lett. 21, 128–137 (2018).Article 

    Google Scholar 
    Roeder, A. et al. Plant diversity effects on plant longevity and their relationships to population stability in experimental grasslands. J. Ecol. 109, 2566–2579 (2021).Article 

    Google Scholar 
    Cadotte, M. W., Dinnage, R. & Tilman, D. Phylogenetic diversity promotes ecosystem stability. Ecology 93, S223–S233 (2012).Article 

    Google Scholar 
    Pu, Z., Daya, P., Tan, J. & Jiang, L. Phylogenetic diversity stabilizes community biomass. J. Plant Ecol. 7, 176–187 (2014).Article 

    Google Scholar 
    Carrara, F., Giometto, A., Seymour, M., Rinaldo, A. & Altermatt, F. Experimental evidence for strong stabilizing forces at high functional diversity of aquatic microbial communities. Ecology 96, 1340–1350 (2015).Article 

    Google Scholar 
    Hooper, D. U. et al. Effects of biodiversity on ecosystem functioning: a conceensus of current knowledge. Ecol. Monogr. 75, 3–35 (2005).Article 

    Google Scholar 
    Ruijven, J. V. & Berendse, F. Contrasting effects of diversity on the temporal stability of plant populations. Oikos 116, 1323–1330 (2007).Article 

    Google Scholar 
    Proulx, R. et al. Diversity promotes temporal stability across levels of ecosystem organization in experimental grasslands. PLoS ONE 5, e13382 (2010).Article 
    ADS 

    Google Scholar 
    Hoaglin, D. C., Iglewicz, B. & Tukey, J. W. Performance of some resistant rules for outlier labeling. JASA 81, 991–999 (1986).Article 
    MathSciNet 

    Google Scholar 
    Loreau, M. & de Mazancourt, C. Species synchrony and its drivers: neutral and nonneutral community dynamics in fluctuating environments. Am. Nat. 172, E48–E66 (2008).Article 

    Google Scholar 
    Gross, K. et al. Species richness and the temporal stability of biomass production: a new analysis of recent biodiversity experiments. Am. Nat. 183, 1–12 (2014).Article 

    Google Scholar 
    Schmid, B., Baruffol, M., Wang, Z. & Niklaus, P. A. A guide to analyzing biodiversity experiments. J. Plant Ecol. 10, 91–110 (2017).Article 

    Google Scholar 
    Rosseel, Y. lavaan: An R package for structural equation modeling. J. Stat. Softw. 48, 1–36 (2012).Article 

    Google Scholar  More

  • in

    Gapless genome assembly of East Asian finless porpoise

    Gao, A. L. & Zhou, K. Y. Growth and reproduction of three populations of finless porpoise, Neophocaena phocaenoides, in Chinese waters. Aquat Mamm 19, 3–12 (1993).
    Google Scholar 
    Jefferson, T. A. Preliminary analysis of geographic variation in cranial morphometrics of the finless porpoise (Neophocaena phocaenoides). Raffles Bull Zool 10, 3–14 (2002).
    Google Scholar 
    Pilleri, G. & Gihr, M. Contribution to the knowledge of the cetaceans of Pakistan with particular reference to the genera Neomeris, Sousa, Delphinus and Tursiops and description of a new Chinese porpoise (Neomeris asiaeorientalis). Investig Cetacea 4, 107–162 (1972).
    Google Scholar 
    Pilleri, G. & Gihr, M. On the taxonomy and ecology of the finless black porpoise, Neophocaena (Cetacea, Delphinidae). Mammalia 39, 657–673 (1975).Article 

    Google Scholar 
    Wang, P. L. The morphological characters and the problem of subspecies identifications of the finless porpoise. Fish Sci 11, 4–8 (1992).
    Google Scholar 
    Wang, P. L. On the taxonomy of the finless porpoise in China. Fish Sci 6, 10–14 (1992).
    Google Scholar 
    Gao, A. L. & Zhou, K. Y. Geographical variation of external measurements and three subspecies of Neophocaena phocaenoides in Chinese waters. Acta Theriol Sin 15, 81–92 (1995).
    Google Scholar 
    Wang, J. Y., Frasier, T. R., Yang, S. C. & White, B. N. Detecting recent speciation events: the case of the finless porpoise (genus Neophocaena). Heredity 101, 145–155 (2008).Article 

    Google Scholar 
    Jefferson, T. A. & Wang, J. Y. Revision of the taxonomy of finless porpoises (genus Neophocaena): the existence of two species. J Mar Anim Ecol 4, 3–16 (2011).
    Google Scholar 
    Zhou, X. M. et al. Population genomics of finless porpoises reveal an incipient cetacean species adapted to freshwater. Nat Commun 9, 1276 (2018).Article 
    ADS 

    Google Scholar 
    Wang, D., Turvey, S.T., Zhao, X. & Mei, Z. Neophocaena asiaeorientalis ssp. asiaeorientalis. The IUCN Red List of Threatened Species https://www.iucnredlist.org/species/43205774/45893487 (2013).Wang, J. Y. & Reeves, R. Neophocaena Asiaeorientalis. The IUCN Red List of Threatened Species https://www.iucnredlist.org/species/41754/50381766 (2017).Kasuya, T. Japanese whaling and other cetacean fisheries. Environ Sci Pollut Res Int 14, 39–48 (2007).Article 

    Google Scholar 
    Yoshida, H., Shirakihara, K., Kishino, H. & Shirakihara, M. A population size estimate of the finless porpoise, Neophocaena phocaenoides, from aerial sighting surveys in Ariake Sound and Tachibana Bay, Japan. Popul Ecol 39, 239–247 (1997).Article 

    Google Scholar 
    Amano, M., Nakahara, F., Hayano, A. & Shirakihara, K. Abundance estimate of finless porpoises off the Pacific coast of eastern Japan based on aerial surveys. Mamm Study 28, 103–110 (2003).Article 

    Google Scholar 
    Shirakihara, K., Shirakihara, M. & Yamamoto, Y. Distribution and abundance of finless porpoise in the Inland Sea of Japan. Mar Biol 150, 1025–1032 (2007).Article 

    Google Scholar 
    Zuo, T., Sun, J. Q., Shi, Y. Q. & Wang, J. Primary survey of finless porpoise population in the Bohai Sea. Acta Theriol Sin 38, 551–561 (2018).
    Google Scholar 
    Ruan, R., Guo, A. H., Hao, Y. J., Zheng, J. S. & Wang, D. De novo assembly and characterization of narrow-ridged finless porpoise renal transcriptome and identification of candidate genes involved in osmoregulation. Int J Mol Sci 16, 2220–2238 (2015).Article 

    Google Scholar 
    Li, S. H. et al. Echolocation click sounds from wild inshore finless porpoise (Neophocaena phocaenoides sunameri) with comparisons to the sonar of riverine N. p. asiaeorientalis. J Acoust Soc Am 121, 3938–3946 (2007).Article 
    ADS 

    Google Scholar 
    Dong, J. H., Wang, G. J. & Xiao, Z. Z. Migration and population difference of the finless porpoise in China. Mar Sci 5, 42–45 (1993).
    Google Scholar 
    Lu, Z. C. et al. Analysis of the diet of finless porpoise (Neophocaena asiaeorientalis sunameri) based on prey morphological characters and DNA barcoding. Conserv Genet Resour 8, 523–531 (2016).Article 

    Google Scholar 
    Chen, B. et al. Finless porpoises (Neophocaena asiaeorientalis) in the East China Sea: insights into feeding habits using morphological, molecular, and stable isotopic techniques. Can J Fish Aquat Sci 74, 1628–1645 (2017).Article 

    Google Scholar 
    Nurk, S. et al. The complete sequence of a human genome. Science 376, 44–53 (2022).Article 
    ADS 

    Google Scholar 
    Chen, Y. X. et al. SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data. Gigascience 7, 1–6 (2018).Article 
    ADS 

    Google Scholar 
    Chikhi, R. & Medvedev, P. Informed and automated k-mer size selection for genome assembly. Bioinformatics 30, 31–37 (2014).Article 

    Google Scholar 
    Chin, C. S. et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 10, 563–569 (2013).Article 

    Google Scholar 
    Cheng, H. Y., Concepcion, G. T., Feng, X. W., Zhang, H. W. & Li, H. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat Methods 18, 170–175 (2021).Article 

    Google Scholar 
    Roach, M. J., Schmidt, S. A. & Borneman, A. R. Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies. BMC Bioinformatics 19, 1–10 (2018).Article 

    Google Scholar 
    Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).Article 

    Google Scholar 
    Durand, N. C. et al. Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments. Cell Syst 3, 95–98 (2016).Article 

    Google Scholar 
    Dudchenko, O. et al. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science 356, 92–95 (2017).Article 
    ADS 

    Google Scholar 
    Xiong, Y., Brandley, M. C., Xu, S. X., Zhou, K. Y. & Yang, G. Seven new dolphin mitochondrial genomes and a time-calibrated phylogeny of whales. BMC Evol Biol 9, 1–13 (2009).Article 

    Google Scholar 
    Alonge, M. et al. RaGOO: fast and accurate reference-guided scaffolding of draft genomes. Genome Biol 20, 1–17 (2019).Article 

    Google Scholar 
    Mayer, A., Lahr, G., Swaab, D. F., Pilgrim, C. & Reisert, I. The Y-chromosomal genes SRY and ZFY are transcribed in adult human brain. Neurogenetics 1, 281–288 (1998).Article 

    Google Scholar 
    Sinclair, A. H. et al. A gene from the human sex-determining region encodes a protein with homology to a conserved DNA-binding motif. Nature 346, 240–244 (1990).Article 
    ADS 

    Google Scholar 
    Koopman, P., Gubbay, J., Vivian, N., Goodfellow, P. & Lovell-Badge, R. Male development of chromosomally female mice transgenic for Sry. Nature 351, 117–121 (1991).Article 
    ADS 

    Google Scholar 
    Salo, P. et al. Molecular mapping of the putative gonadoblastoma locus on the Y chromosome. Genes Chromosomes Cancer 14, 210–214 (1995).Article 

    Google Scholar 
    Tsuchiya, K., Reijo, R., Page, D. C. & Disteche, C. M. Gonadoblastoma: molecular definition of the susceptibility region on the Y chromosome. Am J Hum Genet 57, 1400–1407 (1995).
    Google Scholar 
    Gegenschatz-Schmid, K., Verkauskas, G., Stadler, M. B. & Hadziselimovic, F. Genes located in Y-chromosomal regions important for male fertility show altered transcript levels in cryptorchidism and respond to curative hormone treatment. Basic Clin Androl 29, 1–8 (2019).Article 

    Google Scholar 
    Chen, N. Using Repeat Masker to identify repetitive elements in genomic sequences. Curr protoc Bioinf 5, 4–10 (2004).Article 

    Google Scholar 
    Xu, Z. & Wang, H. LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Res 35, W265–W268 (2007).Article 

    Google Scholar 
    Price, A. L., Jones, N. C. & Pevzner, P. A. De novo identification of repeat families in large genomes. Bioinformatics 21, i351–i358 (2005).Article 

    Google Scholar 
    Bao, W. D., Kojima, K. K. & Kohany, O. Repbase Update, a database of repetitive elements in eukaryotic genomes. Mob DNA 6, 1–6 (2015).Article 

    Google Scholar 
    Benson, G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27, 573–580 (1999).Article 

    Google Scholar 
    Liu, W. et al. Blood Transcriptome Analysis Reveals Gene Expression Differences between Yangtze Finless Porpoises from Two Habitats: Natural and Ex Situ Protected Waters. Fishes 7, 96 (2022).Article 

    Google Scholar 
    Yin, D. H. et al. Integrated analysis of blood mRNAs and microRNAs reveals immune changes with age in the Yangtze finless porpoise (Neophocaena asiaeorientalis). Comp Biochem Physiol B Biochem Mol Biol 256, 110635 (2021).Article 

    Google Scholar 
    Kim, D., Paggi, J. M., Park, C., Bennett, C. & Salzberg, S. L. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol 37, 907–915 (2019).Article 

    Google Scholar 
    Kovaka, S. et al. Transcriptome assembly from long-read RNA-seq alignments with StringTie2. Genome Biol 20, 1–13 (2019).Article 

    Google Scholar 
    Stanke, M., Diekhans, M., Baertsch, R. & Haussler, D. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics 24, 637–644 (2008).Article 

    Google Scholar 
    Keane, M. et al. Insights into the evolution of longevity from the bowhead whale genome. Cell Rep 10, 112–122 (2015).Article 

    Google Scholar 
    Yim, H. S. et al. Minke whale genome and aquatic adaptation in cetaceans. Nat Genet 46, 88–92 (2014).Article 

    Google Scholar 
    Jones, S. J. et al. The genome of the beluga whale (Delphinapterus leucas). Genes 8, 378 (2017).Article 
    ADS 

    Google Scholar 
    Zhou, X. M. et al. Baiji genomes reveal low genetic variability and new insights into secondary aquatic adaptations. Nat Commun 4, 1–6 (2013).Article 
    ADS 

    Google Scholar 
    Foote, A. D. et al. Convergent evolution of the genomes of marine mammals. Nat Genet 47, 272–275 (2015).Article 

    Google Scholar 
    Keilwagen, J., Hartung, F. & Grau, J. GeMoMa: homology-based gene prediction utilizing intron position conservation and RNA-seq data. Methods Mol Biol 1962, 161–177 (2019).Article 

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

    Google Scholar 
    Bairoch, A. & Apweiler, R. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res 28, 45–48 (2000).Article 

    Google Scholar 
    Korf, I. Gene finding in novel genomes. BMC bioinformatics 5, 1–9 (2004).Article 

    Google Scholar 
    Finn, R. D. et al. InterPro in 2017-beyond protein family and domain annotations. Nucleic Acids Res 45, D190–D199 (2017).Article 

    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).Article 

    Google Scholar 
    Mulder, N. J. & Apweiler, R. InterPro and InterProScan: tools for protein sequence classification and comparison. Methods Mol Biol 396, 59–70 (2007).Article 

    Google Scholar 
    Ashburner, M. et al. Gene ontology: tool for the unification of biology. Nat Genet 25, 25–29 (2000).Article 

    Google Scholar 
    NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRR21047154 (2022).NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRR20760935 (2022).NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRR20760936 (2022).NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRR20997931 (2022).NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRR20997932 (2022).NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRR20997933 (2022).NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRR20997934 (2022).NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRR20997935 (2022).NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP389529 (2022).Yin, D. H. et al. Neophocaena asiaeorientalis sunameri isolate NAS202207, whole genome shotgun sequencing project. GenBank https://identifiers.org/insdc.gca:GCA_026225855.1 (2022).Yin, D. H. et al. Gapless genome assembly of East Asian finless porpoise, Neophocaena asiaeorientalis sunameri. figshare https://doi.org/10.6084/m9.figshare.20381274.v2 (2022).Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V. & Zdobnov, E. M. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31, 3210–3212 (2015).Article 

    Google Scholar 
    Marçais, G. et al. MUMmer4: A fast and versatile genome alignment system. PLoS Comput Biol 14, e1005944 (2018).Article 

    Google Scholar  More

  • in

    Adhesion of Rhodococcus bacteria to solid hydrocarbons and enhanced biodegradation of these compounds

    Semple, K. T., Morriss, A. W. J. & Paton, G. I. Bioavailability of hydrophobic organic contaminants in soils: Fundamental concepts and techniques for analysis. Eur. J. Soil Sci. 54, 809–818 (2003).Article 
    CAS 

    Google Scholar 
    Ivshina, I. et al. Removal of polycyclic aromatic hydrocarbons in soil spiked with model mixtures of petroleum hydrocarbons and heterocycles using biosurfactants from Rhodococcus ruber IEGM 231. J. Hazard. Mater. 312, 8–17 (2016).Article 
    CAS 

    Google Scholar 
    Varjani, S. J. Microbial degradation of petroleum hydrocarbons. Bioresour. Technol. 223, 277–286 (2017).Article 
    CAS 

    Google Scholar 
    Chen, J. et al. Long-chain n-alkane biodegradation coupling to methane production in an enriched culture from production water of a high-temperature oil reservoir. AMB Express 10, 63 (2020).Article 
    CAS 

    Google Scholar 
    Li, Y. & Xiong, Y. Identification and quantification of mixed sources of oil spills based on distributions and isotope profiles of long-chain n-alkanes. Mar. Pollut. Bull. 58, 1868–1873 (2009).Article 
    CAS 

    Google Scholar 
    Stout, S. A., Payne, J. R., Emsbo-Mattingly, S. D. & Baker, G. Weathering of field-collected floating and stranded Macondo oils during and shortly after the Deepwater Horizon oil spill. Mar. Pollut. Bull. 105, 7–22 (2016).Article 
    CAS 

    Google Scholar 
    Wang, X. et al. Polycyclic aromatic hydrocarbons, polychlorinated biphenyls and legacy and current pesticides in indoor environment in Australia—occurrence, sources and exposure risks. Sci. Total Environ. 693, 133588 (2019).Article 
    ADS 
    CAS 

    Google Scholar 
    Qiao, M., Qi, W., Liu, H. & Qu, J. Oxygenated polycyclic aromatic hydrocarbons in the surface water environment: Occurrence, ecotoxicity, and sources. Environ. Int. 163, 107232 (2022).Article 

    Google Scholar 
    Abbasnezhad, H., Foght, J. M. & Gray, M. R. Adhesion to the hydrocarbon phase increases phenanthrene degradation by Pseudomonas fluorescens LP6a. Biodegradation 22, 485–496 (2011).Article 
    CAS 

    Google Scholar 
    Abbasnezhad, H., Gray, M. & Foght, J. M. Influence of adhesion on aerobic biodegradation and bioremediation of liquid hydrocarbons. Appl. Microbiol. Biotechnol. 92, 653–675 (2011).Article 
    CAS 

    Google Scholar 
    Dewangan, N. K. & Conrad, J. C. Bacterial motility enhances adhesion to oil droplets. Soft Matter 16, 8237–8244 (2020).Article 
    ADS 
    CAS 

    Google Scholar 
    Rodrigues, E. M., Cesar, D. E., Santos de Oliveira, R., de Paula Siqueira, T. & Tótola, M. R. Hydrocarbonoclastic bacterial species growing on hexadecane: Implications for bioaugmentation in marine ecosystems. Environ. Pollut. 267, (2020).Wang, J. D., Qu, C. T. & Song, S. F. Temperature-induced changes in the proteome of Pseudomonas aeruginosa during petroleum hydrocarbon degradation. Arch. Microbiol. 203, 2463–2473 (2021).Article 
    CAS 

    Google Scholar 
    Bastiaens, L. et al. Isolation of adherent polycyclic aromatic hydrocarbon (PAH)-degrading bacteria using PAH-sorbing carriers. Appl. Environ. Microbiol. 66, 1834–1843 (2000).Article 
    ADS 
    CAS 

    Google Scholar 
    Tao, K., Zhao, S., Gao, P., Wang, L. & Jia, H. Impacts of Pantoea agglomerans strain and cation-modified clay minerals on the adsorption and biodegradation of phenanthrene. Ecotoxicol. Environ. Saf. 161, 237–244 (2018).Article 
    CAS 

    Google Scholar 
    Xu, X. et al. Biodegradation potential of polycyclic aromatic hydrocarbons by immobilized Klebsiella sp. in soil washing effluent. Chemosphere 223, 140–147 (2019).Wang, H. et al. Transmembrane transport of polycyclic aromatic hydrocarbons by bacteria and functional regulation of membrane proteins. Front. Environ. Sci. Eng. 14, 1–21 (2020).Article 

    Google Scholar 
    Tarasova, E. V., Grishko, V. V. & Ivshina, I. B. Cell adaptations of Rhodococcus rhodochrous IEGM 66 to betulin biotransformation. Process Biochem. 52, 1–9 (2017).Article 
    CAS 

    Google Scholar 
    Bohinc, K. et al. Available surface dictates microbial adhesion capacity. Int. J. Adhes. Adhes. 50, 265–272 (2014).Article 
    CAS 

    Google Scholar 
    Carniello, V., Peterson, B. W., van der Mei, H. C. & Busscher, H. J. Physico-chemistry from initial bacterial adhesion to surface-programmed biofilm growth. Adv. Colloid Interface Sci. 261, 1–14 (2018).Article 
    CAS 

    Google Scholar 
    Dorobantu, L. S., Bhattacharjee, S., Foght, J. M. & Gray, M. R. Analysis of force interactions between AFM tips and hydrophobic bacteria using DLVO theory. Langmuir 25, 6968–6976 (2009).Article 
    CAS 

    Google Scholar 
    Lehocký, M. et al. Adhesion of Rhodococcus sp. S3E2 and Rhodococcus sp. S3E3 to plasma prepared Teflon-like and organosilicon surfaces. J. Mater. Process. Technol. 209, 2871–2875 (2009).Hori, K. & Matsumoto, S. Bacterial adhesion: From mechanism to control. Biochem. Eng. J. 48, 424–434 (2010).Article 
    CAS 

    Google Scholar 
    Ivshina, I. B. et al. Biosurfactant-enhanced immobilization of hydrocarbon-oxidizing Rhodococcus ruber on sawdust. Appl. Microbiol. Biotechnol. 97, 5315–5327 (2013).Article 
    CAS 

    Google Scholar 
    Pen, Y. et al. Effect of extracellular polymeric substances on the mechanical properties of Rhodococcus. Biochim. Biophys. Acta – Biomembr. 1848, 518–526 (2015).Article 
    CAS 

    Google Scholar 
    De Cesare, F., Di Mattia, E., Zussman, E. & Macagnano, A. A study on the dependence of bacteria adhesion on the polymer nanofibre diameter. Environ. Sci. Nano 6, 778–797 (2019).Article 

    Google Scholar 
    Bergeau, D. et al. Unusual extracellular appendages deployed by the model strain Pseudomonas fluorescens C7R12. PLoS ONE 14, 1–20 (2019).Article 

    Google Scholar 
    Jin, X. & Marshall, J. S. Mechanics of biofilms formed of bacteria with fimbriae appendages. PLoS ONE 15, 1–22 (2020).Article 

    Google Scholar 
    Tarafdar, A., Sarkar, T. K., Chakraborty, S., Sinha, A. & Masto, R. E. Biofilm development of Bacillus thuringiensis on MWCNT buckypaper: Adsorption-synergic biodegradation of phenanthrene. Ecotoxicol. Environ. Saf. 157, 327–334 (2018).Article 
    CAS 

    Google Scholar 
    Rodrigues, A. C., Wuertz, S., Brito, A. G. & Melo, L. F. Fluorene and phenanthrene uptake by Pseudomonas putida ATCC 17514: Kinetics and physiological aspects. Biotechnol. Bioeng. 90, 281–289 (2005).Article 
    CAS 

    Google Scholar 
    Yang, H. Y., Jia, R. B., Chen, B. & Li, L. Degradation of recalcitrant aliphatic and aromatic hydrocarbons by a dioxin-degrader Rhodococcus sp. strain p52. Environ. Sci. Pollut. Res. 21, 11086–11093 (2014).Auffret, M. D., Yergeau, E., Labbé, D., Fayolle-Guichard, F. & Greer, C. W. Importance of Rhodococcus strains in a bacterial consortium degrading a mixture of hydrocarbons, gasoline, and diesel oil additives revealed by metatranscriptomic analysis. Appl. Microbiol. Biotechnol. 99, 2419–2430 (2015).Article 
    CAS 

    Google Scholar 
    Ahmed, R. Z. & Ahmed, N. Isolation of Rhodococcus sp. CMGCZ capable to degrade high concentration of fluoranthene. Water. Air. Soil Pollut. 227, 162 (2016).Ivshina, I. B., Kuyukina, M. S. & Krivoruchko, A. V. Hydrocarbon-oxidizing bacteria and their potential in eco-biotechnology and bioremediation. in Microbial Resources (ed. Kurtboke, I.) 121–148 (Elsevier Inc., 2017). https://doi.org/10.1016/B978-0-12-804765-1.00006-0.Pi, Y. et al. Microbial degradation of four crude oil by biosurfactant producing strain Rhodococcus sp. Bioresour. Technol. 232, 263–269 (2017).Article 
    CAS 

    Google Scholar 
    Cappelletti, M., Fedi, S. & Zannoni, D. Degradation of alkanes in Rhodococcus. in Biology of Rhodococcus, Microbiology Monographs 16 (ed. Alvarez, H. M.) 137–171 (Springer Nature Switzerland AG, 2019). https://doi.org/10.1007/978-3-030-11461-9_6.Kuyukina, M. S. & Ivshina, I. B. Application of Rhodococcus in bioremediation of contaminated environments. in Biology of Rhodococcus, Microbiology Monographs 16 (ed. Alvarez, H. M.) 231–262 (Springer Nature Switzerland, 2019). https://doi.org/10.1007/978-3-642-12937-7_9.Krivoruchko, A. V. et al. Adhesion of Rhodococcus ruber IEGM 342 to polystyrene studied using contact and non-contact temperature measurement techniques. Appl. Microbiol. Biotechnol. 102, 8525–8536 (2018).Article 
    CAS 

    Google Scholar 
    Rubtsova, E. V., Kuyukina, M. S. & Ivshina, I. B. Effect of cultivation conditions on the adhesive activity of Rhodococcus cells towards n-hexadecane. Appl. Biochem. Microbiol. 48, 452–459 (2012).Article 
    CAS 

    Google Scholar 
    Pearlman, R. S., Yalkowsky, S. H. & Banerjee, S. Water solubilities of polynuclear aromatic and heteroaromatic compounds. J. Phys. Chem. Ref. Data 13, 555–562 (1984).Article 
    ADS 
    CAS 

    Google Scholar 
    Wrenn, B. A. & Venosa, A. D. Selective enumeration of aromatic and aliphatic hydrocarbon degrading bacteria by a most-probable-number procedure. Can. J. Microbiol. 42, 252–258 (1996).Article 
    CAS 

    Google Scholar 
    Christofi, N., Ivshina, I. B., Kuyukina, M. S. & Philp, J. C. Biological treatment of crude oil contaminated soil in Russia. Geol. Soc. Eng. Geol. Spec. Publ. 14, 45–51 (1998).
    Google Scholar 
    Sorongon, M. L., Bloodgood, R. A. & Burchard, R. P. Hydrophobicity, adhesion, and surface-exposed proteins of gliding bacteria. Appl. Environ. Microbiol. 57, 3193–3199 (1991).Article 
    ADS 
    CAS 

    Google Scholar 
    Bellon-Fontaine, M.-N., Rault, J. & van Ossb, C. J. Microbial adhesion to solvents : a novel method to determine the electron-donor/electron-acceptor or Lewis acid-base properties of microbial cells. Colloids Surf. B Biointerfaces 7, 47–53 (1996).Article 
    CAS 

    Google Scholar 
    Mattos-Guaraldi, A. L., Formiga, L. C. D. & Andrade, A. F. B. Cell surface hydrophobicity of sucrose fermenting and nonfermenting Corynebacterium diphtheriae strains evaluated by different methods. Curr. Microbiol. 38, 37–42 (1999).Article 
    CAS 

    Google Scholar 
    Nikiyan, H., Vasilchenko, A. & Deryabin, D. Humidity-dependent bacterial cells functional morphometry investigations using atomic forcemicroscope. Int. J. Microbiol. 2010, 704170 (2010).Article 

    Google Scholar 
    Xu, J. L. et al. Rhodococcus qingshengii sp. nov., a carbendazim-degrading bacterium. Int. J. Syst. Evol. Microbiol. 57, 2754–2757 (2007).Lee, S. D. & Kim, I. S. Rhodococcus spelaei sp. nov., isolated from a cave, and proposals that Rhodococcus biphenylivorans is a later synonym of Rhodococcus pyridinivorans, Rhodococcus qingshengii and Rhodococcus baikonurensis are later synonym. Int. J. Syst. Evol. Microbiol. 71, (2021).Korshunova, I. O., Pistsova, O. N., Kuyukina, M. S. & Ivshina, I. B. The effect of organic solvents on the viability and morphofunctional properties of Rhodococcus. Appl. Biochem. Microbiol. 52, 53–61 (2016).Article 

    Google Scholar 
    de Carvalho, C. C. C. R., Wick, L. Y. & Heipieper, H. J. Cell wall adaptations of planktonic and biofilm Rhodococcus erythropolis cells to growth on C5 to C16 n-alkane hydrocarbons. Appl. Microbiol. Biotechnol. 82, 311–320 (2009).Article 
    CAS 

    Google Scholar 
    Kuyukina, M. S. et al. Oilfield wastewater biotreatment in a fluidized-bed bioreactor using co-immobilized Rhodococcus cultures. J. Environ. Chem. Eng. 5, 1252–1260 (2017).Article 
    CAS 

    Google Scholar 
    Abdel-Shafy, H. I. & Mansour, M. S. M. A review on polycyclic aromatic hydrocarbons: Source, environmental impact, effect on human health and remediation. Egypt. J. Pet. 25, 107–123 (2016).Article 

    Google Scholar 
    He, J. et al. Subchronic exposure of benzo(a)pyrene interferes with the expression of Bcl-2, Ki-67, C-myc and p53, Bax, Caspase-3 in sub-regions of cerebral cortex and hippocampus. Exp. Toxicol. Pathol. 68, 149–156 (2016).Article 
    CAS 

    Google Scholar 
    Boente, C., Baragaño, D. & Gallego, J. R. Benzo[a]pyrene sourcing and abundance in a coal region in transition reveals historical pollution, rendering soil screening levels impractical. Environ. Pollut. 266, (2020).Cao, Y. et al. Interfacial interaction between benzo[a]pyrene and pulmonary surfactant: Adverse effects on lung health. Environ. Pollut. 287, 117669 (2021).Article 
    CAS 

    Google Scholar 
    Gallardo-Moreno, A. M. et al. Thermodynamic analysis of growth temperature dependence in the adhesion of Candida parapsilosis to polystyrene. Appl. Environ. Microbiol. 68, 2610–2613 (2002).Article 
    ADS 
    CAS 

    Google Scholar 
    Kuyukina, M. S., Ivshina, I. B., Korshunova, I. O., Stukova, G. I. & Krivoruchko, A. V. Diverse effects of a biosurfactant from Rhodococcus ruber IEGM 231 on the adhesion of resting and growing bacteria to polystyrene. AMB Express 6, 1–12 (2016).Article 
    CAS 

    Google Scholar 
    Letek, M. et al. The genome of a pathogenic Rhodococcus: Cooptive virulence underpinned by key gene acquisitions. PLoS Genet. 6, 1–17 (2010).Article 

    Google Scholar 
    Dayan, A. et al. The involvement of coordinative interactions in the binding of dihydrolipoamide dehydrogenase to titanium dioxide – Localization of a putative binding site. J. Mol. Recognit. 30, 1–11 (2017).Article 
    ADS 

    Google Scholar 
    Choi, E. J. & Dimitriadis, E. K. Cytochrome c adsorption to supported, anionic lipid bilayers studied via atomic force microscopy. Biophys. J. 87, 3234–3241 (2004).Article 
    ADS 
    CAS 

    Google Scholar 
    Wright, C. J. & Armstrong, I. The application of atomic force microscopy force measurements to the characterisation of microbial surfaces. Surf. Interface Anal. 38, 1419–1428 (2006).Article 
    CAS 

    Google Scholar 
    Salerno, M., Dante, S., Patra, N. & Diaspro, A. AFM measurement of the stiffness of layers of agarose gel patterned with polylysine. Microsc. Res. Tech. 73, 982–990 (2010).CAS 

    Google Scholar 
    Campbell, J. E., Yang, J. & Day, G. M. Predicted energy-structure-function maps for the evaluation of small molecule organic semiconductors. J. Mater. Chem. C 5, 7574–7584 (2017).Article 
    CAS 

    Google Scholar 
    Wang, N. et al. Molecular elucidating of an unusual growth mechanism for polycyclic aromatic hydrocarbons in confined space. Nat. Commun. 11, 1079 (2020).Article 
    ADS 
    CAS 

    Google Scholar  More

  • in

    Root biomass and cumulative yield increase with mowing height in Festuca pratensis irrespective of Epichloë symbiosis

    Jackson, R. B. et al. The Ecology of soil carbon: Pools, vulnerabilities, and biotic and abiotic controls. Annu. Rev. Ecol. Evol. Syst. 48, 419–445. https://doi.org/10.1146/annurev-ecolsys-112414-054234 (2017).Article 

    Google Scholar 
    Sanderman, J., Hengl, T. & Fiske, G. J. Soil carbon debt of 12,000 years of human land use. PNAS 114, 9575–9580 (2017).Article 
    ADS 
    CAS 

    Google Scholar 
    Amelung, W. et al. Towards a global-scale soil climate mitigation strategy. Nat. Commun. 11, 5427. https://doi.org/10.1038/s41467-020-18887-7 (2020).Article 
    ADS 
    CAS 

    Google Scholar 
    Hopkins, A. & Holz, B. Grassland for agriculture and nature conservation: Production, quality and multi-functionality. Agron 4, 3–20 (2006).
    Google Scholar 
    van Veen, J. A., Liljeroth, E., Lekkerkerk, L. J. A. & van de Geijn, S. C. Carbon fluxes in plant-soil systems at elevated atmospheric CO2 levels. Ecol. Appl. 1, 175–181. https://doi.org/10.2307/1941810 (1991).Article 

    Google Scholar 
    Jones, M. B. & Donnelly, A. Carbon sequestration in temperate grassland ecosystems and the influence of management, climate and elevated CO2. New Phytol. 164, 423–439. https://doi.org/10.1111/j.1469-8137.2004.01201.x (2004).Article 

    Google Scholar 
    Ward, S. E. et al. Legacy effects of grassland management on soil carbon to depth. Glob. Change Biol. 22, 2929–2938. https://doi.org/10.1111/gcb.13246 (2016).Article 
    ADS 

    Google Scholar 
    Hungate, B. A. et al. The fate of carbon in grasslands under carbon dioxide enrichment. Nature 388, 576–579. https://doi.org/10.1038/41550 (1997).Article 
    ADS 
    CAS 

    Google Scholar 
    Six, J., Conant, R. T., Paul, E. A. & Paustian, K. Stabilization mechanisms of soil organic matter: Implications for C-saturation of soils. Plant Soil 241, 155–176. https://doi.org/10.1023/A:1016125726789 (2002).Article 
    CAS 

    Google Scholar 
    Chang, J. et al. Climate warming from managed grasslands cancels the cooling effect of carbon sinks in sparsely grazed and natural grasslands. Nat. Commun. 12, 118. https://doi.org/10.1038/s41467-020-20406-7 (2021).Article 
    ADS 
    CAS 

    Google Scholar 
    IPCC. 2001. Climate change 2001: The scientific basis contribution of working group 1 to the third assessment report of the intergovernmental panel on climate change In (eds Houghton, J. T., Ding, Y., Griggs, D. J., Noguer, M., Van Der Linden, P. J., Dai, X., Maskell, K. & Johnson, C. A.) (Cambridge University Press).Gwin, L. Scaling-up sustainable livestock production: Innovation and challenges for grass-fed beef in the U.S. J. Sustain. Agric. 33, 189–209. https://doi.org/10.1080/10440040802660095 (2009).Article 

    Google Scholar 
    Iqbal, J., Siegrist, J. A., Nelson, J. A. & McCulley, R. L. Fungal endophyte infection increases carbon sequestration potential of southeastern USA tall fescue stands. Soil Biol. Biochem. 44, 81–92. https://doi.org/10.1016/j.soilbio.2011.09.010 (2012).Article 
    CAS 

    Google Scholar 
    Robinson, R. A. & Sutherland, W. J. Post-war changes in arable farming and biodiversity in Great Britain. J. Appl. Ecol. 39, 157–176. https://doi.org/10.1046/j.1365-2664.2002.00695.x (2002).Article 

    Google Scholar 
    Law, Q. D., Bigelow, C. A. & Patton, A. J. Selecting turfgrasses and mowing practices that reduce mowing requirements. Crop Sci. 56, 3318–3327. https://doi.org/10.2135/cropsci2015.09.0595 (2016).Article 

    Google Scholar 
    White, L. M. Carbohydrate reserves of grasses: A review. Rangel Ecol. Manag. 26(1), 13–18 (1973).Article 
    CAS 

    Google Scholar 
    Virkajarvi, P. Effects of defoliation height on regrowth of timothy and meadow fescue in the generative and vegetative phases of growth. Agric. Food Sci. 12, 177–193 (2003).Article 

    Google Scholar 
    Reicher, Z., Patton, A. J., Bigelow, C. A. & Voigt, T. Mowing, Thatching, Aerifying, and Rolling Turf (Turf Grass Sci. Purdue Univ, 2006).
    Google Scholar 
    Kaatz, P. Cutting management for cool-season forage grasses. Michigan State University Extension, https://www.canr.msu.edu/news/cutting_management_for_cool_season_forage_grasses (2011).Briske, D. D. Strategies of plant survival in grazed systems: A functional interpretation. Ecol. Manag. Graz. Syst. 37–67 (1996).Crider, F. J. Root-growth stoppage resulting from defoliation of grass (No. 156759). United States Department of Agriculture, Economic Research Service (1995).Lal, R., Negassa, W. & Lorenz, K. Carbon sequestration in soil. Curr. Opin. Environ. Sustain. 15, 79–86. https://doi.org/10.1016/j.cosust.2015.09.002 (2015).Article 

    Google Scholar 
    Coughenour, M. B., McNaughton, S. J. & Wallace, L. L. Modelling primary production of perennial graminoids – uniting physiological processes and morphometric traits. Ecol. Modell. 23, 101–134. https://doi.org/10.1016/0304-3800(84)90121-2 (1984).Article 
    CAS 

    Google Scholar 
    Whipps, J. M. & Lynch, J. M. Energy losses by the plant in rhizodeposition. Plant products and the new technology / edited by K.W. Fuller and J.R. Gallon (1985).Johansson, G. Release of organic C from growing roots of meadow fescue (Festuca pratensis L.). Soil Biol. Biochem. 24, 427–433. https://doi.org/10.1016/0038-0717(92)90205-C (1992).Article 

    Google Scholar 
    Woodburn, A. T. Glyphosate: Production, pricing and use worldwide. Pest Manag. Sci. 56, 309–312. https://doi.org/10.1002/(SICI)1526-4998(200004)56:4%3c309::AID-PS143%3e3.0.CO;2-C (2000).Article 
    CAS 

    Google Scholar 
    Duke, S. O. & Powles, S. B. Glyphosate: A once-in-a-century herbicide. Pest Manag. Sci. 64, 319–325. https://doi.org/10.1002/ps.1518 (2008).Article 
    CAS 

    Google Scholar 
    Helander, M., Saloniemi, I. & Saikkonen, K. Glyphosate in northern ecosystems. Trends Plant Sci. 17, 569–574. https://doi.org/10.1016/j.tplants.2012.05.008 (2012).Article 
    CAS 

    Google Scholar 
    Benbrook, C. M. Trends in glyphosate herbicide use in the United States and globally. Environ. Sci. Eur. 28, 3. https://doi.org/10.1186/s12302-016-0070-0 (2016).Article 
    CAS 

    Google Scholar 
    Helander, M. et al. Glyphosate decreases mycorrhizal colonization and affects plant-soil feedback. Sci. Total Environ. 642, 285–291. https://doi.org/10.1016/j.scitotenv.2018.05.377 (2018).Article 
    ADS 
    CAS 

    Google Scholar 
    Helander, M., Pauna, A., Saikkonen, K. & Saloniemi, I. Glyphosate residues in soil affect crop plant germination and growth. Sci. Rep. 9, 19653. https://doi.org/10.1038/s41598-019-56195-3 (2019).Article 
    ADS 
    CAS 

    Google Scholar 
    Zaller, J. G. & Brühl, C. A. Editorial: Non-target effects of pesticides on organisms inhabiting agroecosystems. Front Environ. Sci. 7, 75. https://doi.org/10.3389/fenvs.2019.00075 (2019).Article 

    Google Scholar 
    Muola, A. et al. Risk in the circular food economy: Glyphosate-based herbicide residues in manure fertilizers decrease crop yield. Sci. Total Environ. 750, 141422. https://doi.org/10.1016/j.scitotenv.2020.141422 (2021).Article 
    ADS 
    CAS 

    Google Scholar 
    Fuchs, B., Saikkonen, K. & Helander, M. Glyphosate-modulated biosynthesis driving plant defense and species interactions. Trends Plant Sci. 26, 312–323. https://doi.org/10.1016/j.tplants.2020.11.004 (2021).Article 
    CAS 

    Google Scholar 
    Fuchs, B. et al. A Glyphosate-based herbicide in soil differentially affects hormonal homeostasis and performance of non-target crop plants. Front Plant Sci. 12, 787958 (2022).Article 

    Google Scholar 
    Borggaard, O. K. & Gimsing, A. L. Fate of glyphosate in soil and the possibility of leaching to ground and surface waters: A review. Pest Manag. Sci. 64, 441–456. https://doi.org/10.1002/ps.1512 (2008).Article 
    CAS 

    Google Scholar 
    Rueppel, M. L., Brightwell, B. B., Schaefer, J. & Marvel, J. T. Metabolism and degradation of glyphosate in soil and water. J. Agric. Food Chem. 25, 517–528. https://doi.org/10.1021/jf60211a018 (1977).Article 
    CAS 

    Google Scholar 
    Carlisle, S. M. & Trevors, J. T. Glyphosate in the environment. Wat Air Soil Poll 39, 409–420 (1988).Article 
    ADS 
    CAS 

    Google Scholar 
    Torstensson, N. T. L., Lundgren, L. N. & Stenström, J. Influence of climatic and edaphic factors on persistence of glyphosate and 2,4-D in forest soils. Ecotoxicol. Environ. Saf. 18, 230–239. https://doi.org/10.1016/0147-6513(89)90084-5 (1989).Article 
    CAS 

    Google Scholar 
    Stenrød, M., Eklo, O. M., Charnay, M.-P. & Benoit, P. Effect of freezing and thawing on microbial activity and glyphosate degradation in two Norwegian soils. Pest Manag. Sci. 61, 887–898. https://doi.org/10.1002/ps.1107 (2005).Article 
    CAS 

    Google Scholar 
    Antier, C. et al. Glyphosate use in the European agricultural sector and a framework for its further monitoring. Sustainability 12, 5682. https://doi.org/10.3390/su12145682 (2020).Article 
    CAS 

    Google Scholar 
    Jones, R. J. Effect of an associate grass, cutting interval, and cutting height on yield and botanical composition of Siratro pastures in a sub-tropical environment. Aust. J. Exp. Agric. 14, 334–342. https://doi.org/10.1071/ea9740334 (1974).Article 

    Google Scholar 
    Volenec, J. J. & Nelson, C. J. Responses of Tall Fescue leaf meristems to N fertilization and harvest frequency. Crop Sci. 23(4), 720–724. https://doi.org/10.2135/cropsci1983.0011183X002300040028x (1983).Article 

    Google Scholar 
    Saikkonen, K. et al. Fungal endophytes help prevent weed invasions. Agric. Ecosyst. Environ. 165, 1–5. https://doi.org/10.1016/j.agee.2012.12.002 (2013).Article 

    Google Scholar 
    Scavo, A. & Mauromicale, G. Integrated weed management in herbaceous field crops. Agronomy 10, 466. https://doi.org/10.3390/agronomy10040466 (2020).Article 

    Google Scholar 
    Clay, K. & Holah, J. Fungal endophyte symbiosis and plant diversity in successional fields. Science 285, 1742–1744. https://doi.org/10.1126/science.285.5434.1742 (1999).Article 
    CAS 

    Google Scholar 
    Gundel, P. E., Pérez, L. I., Helander, M. & Saikkonen, K. Symbiotically modified organisms: Nontoxic fungal endophytes in grasses. Trends Plant Sci. 18, 420–427. https://doi.org/10.1016/j.tplants.2013.03.003 (2013).Article 
    CAS 

    Google Scholar 
    Kauppinen, M., Saikkonen, K., Helander, M., Pirttilä, A. M. & Wäli, P. R. Epichloë grass endophytes in sustainable agriculture. Nat. Plants 2, 15224 (2016).Article 

    Google Scholar 
    Clay, K. Fungal endophytes of grasses. Annu. Rev. Ecol. Syst. 21, 275–297 (1990).Article 

    Google Scholar 
    Saikkonen, K., Young, C. A., Helander, M. & Schardl, C. L. Endophytic Epichloë species and their grass hosts: From evolution to applications. Plant Mol. Biol. 90, 665–675. https://doi.org/10.1007/s11103-015-0399-6 (2016).Article 
    CAS 

    Google Scholar 
    Ahlholm, J. U., Helander, M., Lehtimäki, S., Wäli, P. & Saikkonen, K. Vertically transmitted fungal endophytes: Different responses of host-parasite systems to environmental conditions. Oikos 99, 173–183. https://doi.org/10.1034/j.1600-0706.2002.990118.x (2002).Article 

    Google Scholar 
    Easton, H. S. & Fletcher, L. R. in Proc. 6th International Symposium Fungal Endophytes of Grasses (eds Popay, A. J. & Thom, E. R.) 11–18 (New Zealand Grassland Association, 2007).Saari, S., Lehtonen, P., Helander, M. & Saikkonen, K. High variation in frequency of infection by endophytes in cultivars of meadow fescue in Finland. Grass Forage Sci. 64, 169–176. https://doi.org/10.1111/j.1365-2494.2009.00680.x (2009).Article 

    Google Scholar 
    König, J., Fuchs, B., Krischke, M., Mueller, M. J. & Krauss, J. Hide and seek: Infection rates and alkaloid concentrations of Epichloë festucae var. lolii in Lolium perenne along a land-use gradient in Germany. Grass Forage Sci. 73, 510–516. https://doi.org/10.1111/gfs.12330 (2018).Article 
    CAS 

    Google Scholar 
    Krauss, J. et al. Epichloë endophyte infection rates and alkaloid content in commercially available grass seed mixtures in Europe. Microorganisms 8, 498. https://doi.org/10.3390/microorganisms8040498 (2020).Article 
    CAS 

    Google Scholar 
    Brink, G. E., Casler, M. D. & Martin, N. P. Meadow Fescue, Tall Fescue, and Orchardgrass response to defoliation management. Agronomy J 102, 667–674. https://doi.org/10.2134/agronj2009.0376 (2010).Article 

    Google Scholar 
    Conant, R. T., Cerri, C. E. P., Osborne, B. B. & Paustian, K. Grassland management impacts on soil carbon stocks: A new synthesis. Ecol. Appl. 27, 662–668. https://doi.org/10.1002/eap.1473 (2017).Article 

    Google Scholar 
    Trlica, M. J. Distribution and utilization of carbohydrate reserves in range plants. In (ed Sosebee, R. E.) 73–96 (Rangeland Plant Physiology, 1977).Faeth, S. H. & Sullivan, T. J. Mutualistic asexual endophytes in a native grass are usually parasitic. Am. Nat. 161, 310–325. https://doi.org/10.1086/345937 (2003).Article 

    Google Scholar 
    Saikkonen, K., Saari, S. & Helander, M. Defensive mutualism between plants and endophytic fungi?. Fungal Divers. 41, 101–113. https://doi.org/10.1007/s13225-010-0023-7 (2010).Article 

    Google Scholar 
    Clay, K. & Schardl, C. Evolutionary origins and ecological consequences of endophyte symbiosis with grasses. Am. Nat. 160, 99–127. https://doi.org/10.1086/342161 (2002).Article 

    Google Scholar 
    Rozpądek, P. et al. The fungal endophyte Epichloë typhina improves photosynthesis efficiency of its host orchard grass (Dactylis glomerata). Planta 242, 1025–1035. https://doi.org/10.1007/s00425-015-2337-x (2015).Article 
    CAS 

    Google Scholar 
    Xia, C. et al. An Epichloë endophyte improves photosynthetic ability and dry matter production of its host Achnatherum inebrians infected by Blumeria graminis under various soil water conditions. Fungal Ecol. 22, 26–34. https://doi.org/10.1016/j.funeco.2016.04.002 (2016).Article 

    Google Scholar 
    Malinowski, D., Leuchtmann, A., Schmidt, D. & Nosberger, J. Symbiosis with Neotyphodium uncinatum endophyte may increase the competitive ability of meadow fescue. Agron. J. 89, 833–839 (1997).Article 

    Google Scholar 
    Schardl, C. L., Leuchtmann, A. & Spiering, M. J. Symbioses of grasses with seedborne fungal endophytes. Ann. Rev. Plant Biol. 55, 315–340. https://doi.org/10.1146/annurev.arplant.55.031903.141735 (2004).Article 
    CAS 

    Google Scholar 
    Chen, Z. et al. Fungal endophyte improves survival of Lolium perenne in low fertility soils by increasing root growth, metabolic activity and absorption of nutrients. Plant Soil 452, 185–206. https://doi.org/10.1007/s11104-020-04556-7 (2020).Article 
    CAS 

    Google Scholar 
    Franz, J. E., Mao, M.K. and Sikorski, J.A. (1997). Uptake, transport and metabolism of glyphosate in plants, in Glyphosate: A unique global herbicide, ed by Franz JE, ACS Monograph No 189, American Chemical Society, Washington, DC, pp 143–181.Pline, W. A., Wilcut, J. W., Edmisten, K. L. & Wells, R. Physiological and morphological response of glyphosate-resistant and non-glyphosate-resistant cotton seedlings to root-absorbed glyphosate. Pestic. Biochem. Phys. 73, 48–58. https://doi.org/10.1016/S0048-3575(02)00014-7 (2002).Article 
    CAS 

    Google Scholar 
    Johansson, G. Carbon distribution in grass (Festuca pratensis L.) during regrowth after cutting—utilization of stored and newly assimilated carbon. Plant Soil 151, 11–20. https://doi.org/10.1007/BF00010781 (1993).Article 
    ADS 
    CAS 

    Google Scholar 
    Ergon, Å. et al. How can forage production in Nordic and Mediterranean Europe adapt to the challenges and opportunities arising from climate change?. Euro J. Agron. 92, 97–106. https://doi.org/10.1016/j.eja.2017.09.016 (2018).Article 

    Google Scholar 
    Niemelainen, O. et al. Increase in perennial forage yields driven by climate change, at Apukka Research Station, Rovaniemi, 1980–2017. Agric. Food Sci. 29, 139–153 (2020).Article 

    Google Scholar 
    Anwar, M. R., Liu, D. L., Macadam, I. & Kelly, G. Adapting agriculture to climate change: A review. Theor. Appl. Climatol. 113, 225–245. https://doi.org/10.1007/s00704-012-0780-1 (2013).Article 
    ADS 

    Google Scholar 
    Farmit. Nurmea yli kymppitonni hehtaarilta. Farmit.net. (accessed 28 June 2022); https://www.farmit.net/nurmikasvit-lypsylehma/2016/05/24/nurmea-yli-kymppitonni-hehtaarilta (2016).Peltonen, S., Aalto, K., Hennola, I. & Anttila, S. (Eds.). Peltojen kunnostus. (Tieto Tuottamaan; No. 145), (ProAgria Keskusten Liiton julkaisuja; No. 1163). ProAgria maaseutukeskusten liitto (2019).Laihonen, M., Saikkonen, K., Helander, M. & Tammaru, T. Insect oviposition preference between Epichloë-symbiotic and Epichloë-free grasses does not necessarily reflect larval performance. Ecol. Evol. 10, 7242–7249. https://doi.org/10.1002/ece3.6450 (2020).Article 

    Google Scholar  More

  • in

    Half-millennium evidence suggests that extinction debts of global vertebrates started in the Second Industrial Revolution

    Tilman, D., May, R. M., Lehman, C. L. & Nowak, M. A. Habitat destruction and the extinction debt. Nature 371, 65–66 (1994).Article 

    Google Scholar 
    Newbold, T. et al. Global effects of land use on local terrestrial biodiversity. Nature 520, 45–50 (2015).Article 
    CAS 
    PubMed 

    Google Scholar 
    Urban, M. C. Accelerating extinction risk from climate change. Science 348, 571–573 (2015).Article 
    CAS 
    PubMed 

    Google Scholar 
    Fonseca, C. R. et al. Conservation biology: four decades of problem- and solution-based research. Perspect. Ecol. Conserv. 19, 121–130 (2021).
    Google Scholar 
    Smits, P. & Finnegan, S. How predictable is extinction? Forecasting species survival at million-year timescales. Philos. Trans. R. Soc. B Biol. Sci. 374, 20190392 (2019).Article 

    Google Scholar 
    Hanski, I. & Ovaskainen, O. Extinction debt at extinction threshold. Conserv. Biol. 16, 666–673 (2002).Article 

    Google Scholar 
    Kuussaari, M. et al. Extinction debt: a challenge for biodiversity conservation. Trends Ecol. Evol. 24, 564–571 (2009).Article 
    PubMed 

    Google Scholar 
    Ridding, L. E. et al. Inconsistent detection of extinction debts using different methods. Ecography 44, 33–43 (2021).Article 

    Google Scholar 
    Berglund, H. & Jonsson, B. G. Verifying an extinction debt among lichens and fungi in northern Swedish boreal forests. Conserv. Biol. 19, 338–348 (2005).Article 

    Google Scholar 
    Jones, I. L., Bunnefeld, N., Jump, A. S., Peres, C. A. & Dent, D. H. Extinction debt on reservoir land-bridge islands. Biol. Conserv. 199, 75–83 (2016).Article 

    Google Scholar 
    Triantis, K. et al. Extinction debt on oceanic islands. Ecography 33, 285–294 (2010).
    Google Scholar 
    Wearn, O. R., Reuman, D. C. & Ewers, R. M. Extinction debt and windows of conservation opportunity in the Brazilian Amazon. Science 337, 228–232 (2012).Article 
    CAS 
    PubMed 

    Google Scholar 
    Pan, Y. et al. Spatial and temporal scales of landscape structure affect the biodiversity-landscape relationship across ecologically distinct species groups. Landsc. Ecol. 37, 2311–2325 (2022).Article 

    Google Scholar 
    Soga, M. & Koike, S. Mapping the potential extinction debt of butterflies in a modern city: Implications for conservation priorities in urban landscapes. Anim. Conserv. 16, 1–11 (2013).Article 

    Google Scholar 
    Knapp, S., Winter, M. & Klotz, S. Increasing species richness but decreasing phylogenetic richness and divergence over a 320-year period of urbanization. J. Appl. Ecol. 54, 1152–1160 (2017).Article 

    Google Scholar 
    McGill, B. J., Dornelas, M., Gotelli, N. J. & Magurran, A. E. Fifteen forms of biodiversity trend in the anthropocene. Trends Ecol. Evol. 30, 104–113 (2015).Article 
    PubMed 

    Google Scholar 
    Chen, Y. & Peng, S. Evidence and mapping of extinction debts for global forest-dwelling reptiles, amphibians and mammals. Sci. Rep. 7, 1–10 (2017).
    Google Scholar 
    Krauss, J. et al. Habitat fragmentation causes immediate and time-delayed biodiversity loss at different trophic levels. Ecol. Lett. 13, 597–605 (2010).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Cowlishaw, G. Predicting the pattern of decline of African primate diversity: An extinction debt from historical deforestation. Conserv. Biol. 13, 1183–1193 (1999).Article 

    Google Scholar 
    Figueiredo, L., Krauss, J., Steffan-Dewenter, I. & Sarmento Cabral, J. Understanding extinction debts: spatio–temporal scales, mechanisms and a roadmap for future research. Ecography 42, 1973–1990 (2019).Article 

    Google Scholar 
    Aerts, R. & Honnay, O. Forest restoration, biodiversity and ecosystem functioning. BMC Ecol. 11, 1–21 (2011).Article 

    Google Scholar 
    Haddad, N. M. et al. Habitat fragmentation and its lasting impact on Earth’s ecosystems. Sci. Adv. 1, e1500052 (2015).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Maxwell, S. L. et al. Area-based conservation in the twenty-first century. Nature 586, 217–227 (2020).Article 
    CAS 
    PubMed 

    Google Scholar 
    IUCN. The IUCN Red List of Threatened Species, Version 2019-1. https://www.iucnredlist.org. Downloaded on 23 February 2022. (2019).Brown, J. L. et al. Spatial biodiversity patterns of Madagascar’s amphibians and reptiles. PLoS ONE 11, e0144076 (2016).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Powney, G. D., Grenyer, R., Orme, C. D. L., Owens, I. P. F. & Meiri, S. Hot, dry and different: Australian lizard richness is unlike that of mammals, amphibians and birds. Glob. Ecol. Biogeogr. 19, 386–396 (2010).Article 

    Google Scholar 
    Pianka, E. R. Desert lizard diversity: additional comments and some data. Am. Nat. 134, 344–364 (1989).Article 

    Google Scholar 
    Chen, Y. H. Combining the species-area-habitat relationship and environmental cluster analysis to set conservation priorities: A study in the Zhoushan Archipelago, China. Conserv. Biol. 23, 537–545 (2009).Article 
    PubMed 

    Google Scholar 
    Ricklefs, R. E. & Lovette, I. J. The roles of island area per se and habitat diversity in the species-area relationships of four Lesser Antillean faunal groups. J. Anim. Ecol. 68, 1142–1160 (1999).Article 

    Google Scholar 
    Souza, F. L., Martins, F. I. & Raizer, J. Habitat heterogeneity and anuran community of an agroecosystem in the Pantanal of Brazil. Phyllomedusa 13, 41–50 (2014).Article 

    Google Scholar 
    Kelt, D. A. & Van Vuren, D. H. The ecology and macroecology of mammalian home range area. Am. Nat. 157, 637–645 (2001).Article 
    CAS 
    PubMed 

    Google Scholar 
    McNab, B. K. Bioenergetics and the determination of home range size. Am. Nat. 97, 133–140 (1963).Article 

    Google Scholar 
    Powell, R. A. & Mitchell, M. S. What is a home range? J. Mammal. 93, 948–958 (2012).Article 

    Google Scholar 
    Hoffmann, S., Irl, S. D. H. & Beierkuhnlein, C. Predicted climate shifts within terrestrial protected areas worldwide. Nat. Commun. 10, 1–10 (2019).Article 

    Google Scholar 
    Giam, X. et al. Reservoirs of richness: least disturbed tropical forests are centres of undescribed species diversity. Proc. R. Soc. B 279, 67–76 (2012).Article 
    PubMed 

    Google Scholar 
    Pillay, R. et al. Tropical forests are home to over half of the world’s vertebrate species. Front. Ecol. Environ. 20, 10–15 (2022).Article 
    PubMed 

    Google Scholar 
    Li, H. et al. Large numbers of vertebrates began rapid population decline in the late 19th century. Proc. Natl Acad. Sci. USA 113, 14079–14084 (2016).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Pringle, R. M. Upgrading protected areas to conserve wild biodiversity. Nature 546, 91–99 (2017).Article 
    CAS 
    PubMed 

    Google Scholar 
    Forzieri, G., Dakos, V., McDowell, N. G., Ramdane, A. & Cescatti, A. Emerging signals of declining forest resilience under climate change. Nature 608, 534–539 (2022).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Diamond, J. M. Biogeographic kinetics: estimation of relaxation times for Avifaunas of southwest Pacific islands. Proc. Natl Acad. Sci. USA 69, 3199–3203 (1972).Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Jackson, S. T. & Sax, D. F. Balancing biodiversity in a changing environment: extinction debt, immigration credit and species turnover. Trends Ecol. Evol. 25, 153–160 (2010).Article 
    PubMed 

    Google Scholar 
    Foley, J. A. et al. Amazonia revealed: forest degradation and loss of ecosystem goods and services in the Amazon Basin. Front. Ecol. Environ. 5, 25–32 (2007).Article 

    Google Scholar 
    Asamoah, E. F., Beaumont, L. J. & Maina, J. M. Climate and land-use changes reduce the benefits of terrestrial protected areas. Nat. Clim. Chang. 11, 1105–1110 (2021).Article 

    Google Scholar 
    Hurtt, G. C. et al. Harmonization of land-use scenarios for the period 1500–2100: 600 years of global gridded annual land-use transitions, wood harvest, and resulting secondary lands. Clim. Change 109, 117–161 (2011).Article 

    Google Scholar 
    Peng, S. et al. Sensitivity of land use change emission estimates to historical land use and land cover mapping. Glob. Biogeochem. Cycles 31, 626–643 (2017).Article 
    CAS 

    Google Scholar 
    Jain, A. K., Meiyappan, P., Song, Y. & House, J. I. CO2 emissions from land-use change affected more by nitrogen cycle, than by the choice of land-cover data. Glob. Chang. Biol. 19, 2893–2906 (2013).Article 
    PubMed 

    Google Scholar 
    Poulter, B. et al. Plant functional type classification for earth system models: results from the European Space Agency’s Land Cover Climate Change Initiative. Geosci. Model Dev. 8, 2315–2328 (2015).Article 

    Google Scholar 
    Pongratz, J., Reick, C., Raddatz, T. & Claussen, M. A reconstruction of global agricultural areas and land cover for the last millennium. Global Biogeochem. Cycles 22, (2008).Dietz, F. C. The industrial revolution. In the Hands of a Child (1970).Gütschow, J., Jeffery, L. & Gieseke, R. The PRIMAP-hist national historical emissions time series (1850-2016). V. 2.0. GFZ Data Services (2019).Dinerstein, E. et al. An ecoregion-based approach to protecting half the terrestrial realm. Bioscience 67, 534–545 (2017).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Protected Planet: The World Database on Protected Areas (UNEP-WCMC and IUCN, accessed 9 January 2022); www.protectedplanet.net.Butchart, S. H. M. et al. Shortfalls and solutions for meeting national and global conservation area targets. Conserv. Lett. 8, 329–337 (2015).Article 

    Google Scholar 
    R Core Team. R: A Language and Environment for Statistical Computing Version 4.0.2 (2020). More