Ecology

Teale, S. A. & Castello, J. D. The past as key to the future: a new perspective on forest health. In Forest Health: An Integrated Perspective (eds Castello, J. D. & Teale, S. A.) 3–16 (Cambridge University Press, 2011). https://doi.org/10.1017/CBO9780511974977.002.Chapter 

Google Scholar 
Jactel, H., Koricheva, J. & Castagneyrol, B. Responses of forest insect pests to climate change: Not so simple. Curr. Opin. Insect Sci. 35, 103–108 (2019).Article 
PubMed 

Google Scholar 
Trumbore, S., Brando, P. & Hartmann, H. Forest health and global change. Science 349, 814–818 (2015).Article 
ADS 
CAS 
PubMed 

Google Scholar 
North, M. P. et al. Operational resilience in western US frequent-fire forests. For. Ecol. Manag. 507, 120004 (2022).Article 

Google Scholar 
Raffa, K. F. et al. A literal use of “forest health” safeguards against misuse and misapplication. J. For. 107, 276–277 (2009).
Google Scholar 
Kolb, T. E., Wagner, M. R. & Covington, W. W. Concepts of forest health: Utilitarian and ecosystem perspectives. J. For. 92, 10–15 (1994).
Google Scholar 
Cale, J. A. et al. A quantitative index of forest structural sustainability. Forests 5, 1618–1634 (2014).Article 

Google Scholar 
Lintz, H. E. et al. Quantifying density-independent mortality of temperate tree species. Ecol. Indic. 66, 1–9 (2016).Article 

Google Scholar 
Stanke, H., Finley, A. O., Domke, G. M., Weed, A. S. & MacFarlane, D. W. Over half of western United States’ most abundant tree species in decline. Nat. Commun. 12, 451 (2021).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Bettinger, P., Boston, K., Siry, J. P. & Grebner, D. L. Chapter 2—Valuing and Characterizing Forest Conditions. In Forest Management and Planning (eds Bettinger, P. et al.) 21–63 (Academic Press, 2017). https://doi.org/10.1016/B978-0-12-809476-1.00002-3.Chapter 

Google Scholar 
Crowther, T. W. et al. Mapping tree density at a global scale. Nature 525, 201–205 (2015).Article 
ADS 
CAS 
PubMed 

Google Scholar 
Fettig, C. J. et al. The effectiveness of vegetation management practices for prevention and control of bark beetle infestations in coniferous forests of the western and southern United States. For. Ecol. Manag. 238, 24–53 (2007).Article 

Google Scholar 
Morin, R. S. & Liebhold, A. M. Invasions by two non-native insects alter regional forest species composition and successional trajectories. For. Ecol. Manag. 341, 67–74 (2015).Article 

Google Scholar 
Nowak, J. T., Meeker, J. R., Coyle, D. R., Steiner, C. A. & Brownie, C. Southern pine beetle infestations in relation to forest stand conditions, previous thinning, and prescribed burning: Evaluation of the southern pine beetle prevention program. J. For. 113, 454–462 (2015).
Google Scholar 
Asaro, C. & Chamberlin, L. A. Outbreak history (1953–2014) of spring defoliators impacting oak-dominated forests in Virginia, with emphasis on gypsy moth (Lymantria dispar L.) and fall cankerworm (Alsophila pometaria Harris). Am. Entomol. 61, 174–185 (2015).Article 

Google Scholar 
Negrón, J. F. Probability of infestation and extent of mortality associated with the Douglas-fir beetle in the Colorado Front Range. For. Ecol. Manag. 107, 71–85 (1998).Article 

Google Scholar 
Negrón, J. F. & Popp, J. B. Probability of ponderosa pine infestation by mountain pine beetle in the Colorado Front Range. For. Ecol. Manag. 191, 17–27 (2004).Article 

Google Scholar 
Schmid, J. M. & Frye, R. H. Spruce Beetle in the Rockies. Gen. Tech. Rep. RM-49 (US Department of Agriculture, Forest Service, Rocky Mountain Forest and Range Experiment Station, 1977).
Google Scholar 
Krivak-Tetley, F. E. et al. Aggressive tree killer or natural thinning agent? Assessing the impacts of a globally important forest insect. For. Ecol. Manag. 483, 118728 (2021).Article 

Google Scholar 
Bradford, J. B. et al. Tree mortality response to drought-density interactions suggests opportunities to enhance drought resistance. J. Appl. Ecol. 59, 549–559 (2022).Article 

Google Scholar 
Young, D. J. N. et al. Long-term climate and competition explain forest mortality patterns under extreme drought. Ecol. Lett. 20, 78–86 (2017).Article 
PubMed 

Google Scholar 
Furniss, T. J., Das, A. J., van Mantgem, P. J., Stephenson, N. L. & Lutz, J. A. Crowding, climate, and the case for social distancing among trees. Ecol. Appl. 32, e2507 (2022).Article 
PubMed 

Google Scholar 
Woodall, C. W. & Weiskittel, A. R. Relative density of United States forests has shifted to higher levels over last two decades with important implications for future dynamics. Sci. Rep. 11, 1–12 (2021).Article 

Google Scholar 
Gandhi, K. J. K., Campbell, F. & Abrams, J. Current status of forest health policy in the United States. Insects 10, 1–14 (2019).Article 

Google Scholar 
Ciesla, W. M. The role of human activities on forest insect outbreaks worldwide. Int. For. Rev. 17, 269–281 (2015).
Google Scholar 
Jactel, H. & Brockerhoff, E. G. Tree diversity reduces herbivory by forest insects. Ecol. Lett. 10, 835–848 (2007).Article 
PubMed 

Google Scholar 
Marini, L., Ayres, M. P. & Jactel, H. Impact of stand and landscape management on forest pest damage. Annu. Rev. Entomol. 67, 181–199 (2022).Article 
PubMed 

Google Scholar 
Guyot, V., Castagneyrol, B., Vialatte, A., Deconchat, M. & Jactel, H. Tree diversity reduces pest damage in mature forests across Europe. Biol. Lett. 12, 20151037 (2016).Article 
PubMed 
PubMed Central 

Google Scholar 
Kneeshaw, D. D. et al. The vision of managing for pest-resistant landscapes: Realistic or utopic? Curr. For. Rep. 7, 97–113 (2021).PubMed 
PubMed Central 

Google Scholar 
Chisholm, P. J., Stevens-Rumann, C. S. & Davis, T. S. Interactions between climate and stand conditions predict pine mortality during a bark beetle outbreak. Forests 12, 360 (2021).Article 

Google Scholar 
Ferrell, G. T., Otrosina, W. J. & Demars, C. J. Predicting susceptibility of white fir during a drought-associated outbreak of the fir engraver, Scolytus ventralis in California. Can. J. For. Res. 24, 302–305 (1994).Article 

Google Scholar 
Asaro, C., Nowak, J. T. & Elledge, A. Why have southern pine beetle outbreaks declined in the southeastern U.S. with the expansion of intensive pine silviculture? A brief review of hypotheses. For. Ecol. Manag. 391, 338–348 (2017).Article 

Google Scholar 
Nowak, J. T., Klepzig, K. D., Coyle, D. R., Carothers, W. A. & Gandhi, K. J. K. Southern pine beetles in central hardwood forests: Frequency, spatial extent, and changes to forest structure. In Managing Forest Ecosystems Volume 32: Natural Disturbances and Historic Range of Variation (eds Greenberg, C. H. & Collins, B. S.) 73–88 (Springer International Publishing, 2016). https://doi.org/10.1007/978-3-319-21527-3_4.Chapter 

Google Scholar 
Crocker, S. J., Liknes, G. C., McKee, F. R., Albers, J. S. & Aukema, B. H. Stand-level factors associated with resurging mortality from eastern larch beetle (Dendroctonus simplex LeConte). For. Ecol. Manag. 375, 27–34 (2016).Article 

Google Scholar 
Mattson, W. J. & Addy, N. D. Phytophagous insects as regulators of forest primary production. Science 190, 515–522 (1975).Article 
ADS 

Google Scholar 
Thom, D. & Seidl, R. Natural disturbance impacts on ecosystem services and biodiversity in temperate and boreal forests. Biol. Rev. 91, 760–781 (2016).Article 
PubMed 

Google Scholar 
Grégoire, J. C., Raffa, K. F. & Lindgren, B. S. Economics and politics of bark beetles. In Bark Beetles: Biology and Ecology of Native and Invasive Species (eds Vega, F. E. & Hofstetter, R. W.) 585–613 (Academic Press, 2015). https://doi.org/10.1016/B978-0-12-417156-5.00015-0.Chapter 

Google Scholar 
Kolb, T. E. et al. Observed and anticipated impacts of drought on forest insects and diseases in the United States. For. Ecol. Manag. 380, 321–334 (2016).Article 

Google Scholar 
Fettig, C. J. et al. Changing climates, changing forests: A western North American perspective. J. For. 111, 214–228 (2013).
Google Scholar 
Liebhold, A. M. et al. A highly aggregated geographical distribution of forest pest invasions in the USA. Divers. Distrib. 19, 1208–1216 (2013).Article 

Google Scholar 
Siegert, N. W., Mccullough, D. G., Liebhold, A. M. & Telewski, F. W. Dendrochronological reconstruction of the epicentre and early spread of emerald ash borer in North America. Divers. Distrib. 20, 847–858 (2014).Article 

Google Scholar 
Smith, A., Herms, D. A., Long, R. P. & Gandhi, K. J. K. Community composition and structure had no effect on forest susceptibility to invasion by the emerald ash borer (Coleoptera: Buprestidae). Can. Entomol. 147, 318–328 (2015).Article 

Google Scholar 
Aukema, J. E. et al. Historical accumulation of nonindigenous forest pests in the continental United States. Bioscience 60, 886–897 (2010).Article 

Google Scholar 
Hicke, J. A. et al. Effects of biotic disturbances on forest carbon cycling in the United States and Canada. Glob. Chang. Biol. 18, 7–34 (2012).Article 
ADS 

Google Scholar 
Feeny, P. Seasonal changes in oak leaf tannins and nutrients as a cause of spring feeding by winter moth caterpillars. Ecology 51, 565–581 (1970).Article 

Google Scholar 
Schowalter, T. D., Hargrove, W. W. & Crossley, D. A. Herbivory in forested ecosystems. Annu. Rev. Entomol. 31, 177–196 (1986).Article 

Google Scholar 
Seidl, R. et al. Forest disturbances under climate change. Nat. Clim. Chang. 7, 395–402 (2017).Article 
ADS 
PubMed 
PubMed Central 

Google Scholar 
Colautti, R. I., Ricciardi, A., Grigorovich, I. A. & MacIsaac, H. J. Is invasion success explained by the enemy release hypothesis? Ecol. Lett. 7, 721–733 (2004).Article 

Google Scholar 
Catford, J. A., Jansson, R. & Nilsson, C. Reducing redundancy in invasion ecology by integrating hypotheses into a single theoretical framework. Divers. Distrib. 15, 22–40 (2009).Article 

Google Scholar 
Guyot, V. et al. Tree diversity limits the impact of an invasive forest pest. PLoS One 10, 1–16 (2015).Article 

Google Scholar 
Root, R. B. Organization of a plant-arthropod association in simple and diverse habitats: The fauna of collards (Brassica oleracea). Ecol. Monogr. 43, 95–124 (1973).Article 

Google Scholar 
Acker, S. A., Boetsch, J. R., Fallon, B. & Denn, M. Stable background tree mortality in mature and old-growth forests in western Washington (NW USA). For. Ecol. Manag. 532, 120817 (2023).Article 

Google Scholar 
Shive, K. L. et al. Ancient trees and modern wildfires: Declining resilience to wildfire in the highly fire-adapted giant sequoia. For. Ecol. Manag. 511, 120110 (2022).Article 

Google Scholar 
Searle, E. B., Chen, H. Y. H. & Paquette, A. Higher tree diversity is linked to higher tree mortality. Proc. Natl. Acad. Sci. U.S.A. 119, 1–7 (2022).Article 

Google Scholar 
Hart, S. J., Veblen, T. T., Eisenhart, K. S., Jarvis, D. & Kulakowski, D. Drought induces spruce beetle (Dendroctonus rufipennis) outbreaks across northwestern Colorado. Ecology 95, 930–939 (2014).Article 
PubMed 

Google Scholar 
Hart, S. J., Veblen, T. T. & Kulakowski, D. Do tree and stand-level attributes determine susceptibility of spruce-fir forests to spruce beetle outbreaks in the early 21st century? For. Ecol. Manag. 318, 44–53 (2014).Article 

Google Scholar 
Temperli, C. et al. Are density reduction treatments effective at managing for resistance or resilience to spruce beetle disturbance in the southern Rocky Mountains? For. Ecol. Manag. 334, 53–63 (2014).Article 

Google Scholar 
Six, D. L., Biber, E. & Long, E. Management for mountain pine beetle outbreak suppression: Does relevant science support current policy? Forests 5, 103–133 (2014).Article 

Google Scholar 
Black, S. H., Kulakowski, D., Noon, B. R. & Dellasala, D. A. Do bark beetle outbreaks increase wildfire risks in the central U.S. rocky mountains? Implications from recent research. Nat. Areas J. 33, 59–65 (2013).Article 

Google Scholar 
Oswalt, S. N., Smith, W. B., Miles, P. D. & Pugh, S. A. Forest Resources of the United States, 2017: A Technical Document Supporting the Forest Service 2020 RPA Assessment. Gen. Tech. Rep. WO-97 (US Department of Agriculture, Forest Service, 2019). https://doi.org/10.2737/WO-GTR-97.Book 

Google Scholar 
Cleland, D. et al. Terrestrial condition assessment for national forests of the USDA Forest Service in the continental US. Sustainability 9, 1–19 (2017).Article 

Google Scholar 
USDA Forest Service Forest Health Protection. Insect and Disease Detection Survey (IDS) data downloads. https://www.fs.usda.gov/foresthealth/applied-sciences/mapping-reporting/detection-surveys.shtml (2021). Accessed on 9 October 2021.Spruce, J. P. et al. Assessment of MODIS NDVI time series data products for detecting forest defoliation by gypsy moth outbreaks. Remote Sens. Environ. 115, 427–437 (2011).Article 
ADS 

Google Scholar 
Gomez, D. F., Ritger, H. M. W., Pearce, C., Eickwort, J. & Hulcr, J. Ability of remote sensing systems to detect bark beetle spots in the southeastern US. Forests 11, 1–10 (2020).Article 

Google Scholar 
Hanavan, R. P. et al. Supplementing the forest health national aerial survey program with remote sensing during the COVID-19 pandemic: Lessons learned from a collaborative approach. J. For. 120, 125–132 (2021).
Google Scholar 
Johnson, E. W. & Wittwer, D. Aerial detection surveys in the United States. Aust. For. 71, 212–215 (2008).Article 

Google Scholar 
Bright, B. C. et al. Using satellite imagery to evaluate bark beetle-caused tree mortality reported in aerial surveys in a mixed conifer forest in Northern Idaho, USA. Forests 11, 1–19 (2020).Article 

Google Scholar 
Coleman, T. W. et al. Accuracy of aerial detection surveys for mapping insect and disease disturbances in the United States. For. Ecol. Manag. 430, 321–336 (2018).Article 

Google Scholar 
Hicke, J. A., Xu, B., Meddens, A. J. H. & Egan, J. M. Characterizing recent bark beetle-caused tree mortality in the western United States from aerial surveys. For. Ecol. Manag. 475, 118402 (2020).Article 

Google Scholar 
Kosiba, A. M. et al. Spatiotemporal patterns of forest damage and disturbance in the northeastern United States: 2000–2016. For. Ecol. Manag. 430, 94–104 (2018).Article 

Google Scholar 
Meigs, G. W., Kennedy, R. E., Gray, A. N. & Gregory, M. J. Spatiotemporal dynamics of recent mountain pine beetle and western spruce budworm outbreaks across the Pacific Northwest Region USA. For. Ecol. Manag. 339, 71–86 (2015).Article 

Google Scholar 
Bechtold, W. A. & Patterson, P. L. The Enhanced Forest Inventory and Analysis Program—National Sampling Design and Estimation Procedures. Gen. Tech. Rep. SRS-80 (US Department of Agriculture, Forest Service, Southern Research Station, 2005). https://doi.org/10.2737/SRS-GTR-80.Book 

Google Scholar 
Randolph, K. D. C. et al. Past and present individual-tree damage assessments of the US national forest inventory. Environ. Monit. Assess. 193, 116 (2021).Article 
PubMed 

Google Scholar 
Kromroy, K. W., Juzwik, J., Castillo, P. & Hansen, M. H. Using forest service forest inventory and analysis data to estimate regional oak decline and oak mortality. North. J. Appl. For. 25, 17–24 (2008).Article 

Google Scholar 
Coulston, J. W., Edgar, C. B., Westfall, J. A. & Taylor, M. E. Estimation of forest disturbance from retrospective observations in a broad-scale inventory. Forests 11, 1298 (2020).Article 

Google Scholar 
Wilson, B. T., Lister, A. J. & Riemann, R. I. A nearest-neighbor imputation approach to mapping tree species over large areas using forest inventory plots and moderate resolution raster data. For. Ecol. Manag. 271, 182–198 (2012).Article 

Google Scholar 
Blackard, J. A. et al. Mapping U.S. forest biomass using nationwide forest inventory data and moderate resolution information. Remote Sens. Environ. 112, 1658–1677 (2008).Article 
ADS 

Google Scholar 
Brosofske, K. D., Froese, R. E., Falkowski, M. J. & Banskota, A. A review of methods for mapping and prediction of inventory attributes for operational forest management. For. Sci. 60, 733–756 (2014).Article 

Google Scholar 
Lister, A. J. et al. Use of remote sensing data to improve the efficiency of national forest inventories: A case study from the United States national forest inventory. Forests 11, 1–41 (2020).Article 

Google Scholar 
USDA Forest Service Forest Health Protection. Individual Tree Species Parameter (ITSP) maps – GIS data downloads. https://www.fs.usda.gov/foresthealth/applied-sciences/mapping-reporting/indiv-tree-parameter-maps.shtml (2021). Accessed on 9 October 2021.Ellenwood, J. R., Krist, F. J. & Romero, S. A. National Individual Tree Species Atlas. FHTET-15-01 (US Department of Agriculture, Forest Service, Forest Health Technology Enterprise Team, 2015).
Google Scholar 
Krist, F. J. et al. National Insect and Disease Forest Risk Assessment. FHTET-14-01 (US Department of Agriculture, Forest Service, Forest Health Technology Enterprise Team, 2014).
Google Scholar 
Rulequest Inc. Cubist, release 2.07. https://www.rulequest.com/cubist-info.html (2011). Accessed on 15 July 2022.R Core Team. R: A language and environment for statistical computing. https://www.r-project.org (2021). Accessed on 4 March 2022.Esri Inc. ArcGIS Pro 2.8.0. https://www.esri.com/en-us/arcgis/products/arcgis-pro/overview (2021). Accessed on 4 March 2022. More

Cohan FM. Bacterial species and speciation. Syst Biol. 2001;50:513–24.Article 
CAS 
PubMed 

Google Scholar 
Delmont TO, Kiefl E, Kilinc O, Esen OC, Uysal I, Rappe MS, et al. Single-amino acid variants reveal evolutionary processes that shape the biogeography of a global SAR11 subclade. eLife 2019;8:e46497.Article 
PubMed 
PubMed Central 

Google Scholar 
Hunt DE, David LA, Gevers D, Preheim SP, Alm EJ, Polz MF. Resource partitioning and sympatric differentiation among closely related bacterioplankton. Science 2008;320:1081–5.Article 
CAS 
PubMed 

Google Scholar 
Moore LR, Rocap G, Chisholm SW. Physiology and molecular phylogeny of coexisting Prochlorococcus ecotypes. Nature 1998;393:464–7.Article 
CAS 
PubMed 

Google Scholar 
Rivas LR. A reinterpretation of the concepts “sympatric” and “allopatric” with proposal for the additional terms “syntopic” and “allotopic”. Syst Zool. 1964;13:42–3.Article 

Google Scholar 
Friedman J, Alm EJ, Shapiro BJ. Sympatric speciation: when is it possible in bacteria? PLoS One. 2013;8:e53539.Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Kiene RP, Nowinski B, Esson K, Preston C, Marin R III, Birch J, et al. Unprecedented DMSP concentrations in a massive dinoflagellate bloom in Monterey Bay. Ca Geophys Res Lett. 2019;46:12279–88.Article 

Google Scholar 
Scholin CA, Birch J, Jensen S, Marin R, Massion E, Pargett D, et al. The quest to develop ecogenomic sensors a 25-year history of the environmental sample processor (ESP) as a case study. Oceanography. 2017;30:100–13.Article 

Google Scholar 
Nowinski B, Smith CB, Thomas CM, Esson K, Marin R, Preston CM, et al. Microbial metagenomes and metatranscriptomes during a coastal phytoplankton bloom. Sci Data. 2019;6:1–7.Article 
CAS 

Google Scholar 
Luo H, Löytynoja A, Moran MA. Genome content of uncultivated marine Roseobacters in the surface ocean. Environ Microbiol. 2012;14:41–51.Article 
CAS 
PubMed 

Google Scholar 
Connon SA, Giovannoni SJ. High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates. Appl Environ Microbiol. 2002;68:3878–85.Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Feng X, Chu X, Qian Y, Henson MW, Lanclos VC, Qin F, et al. Mechanisms driving genome reduction of a novel Roseobacter lineage. ISME J. 2021;15:3576–86.Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Moran MA, Belas R, Schell M, González J, Sun F, Sun S, et al. Ecological genomics of marine roseobacters. Appl Environ Microbiol. 2007;73:4559–69.Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Newton RJ, Griffin LE, Bowles KM, Meile C, Gifford S, Givens CE, et al. Genome characteristics of a generalist marine bacterial lineage. ISME J. 2010;4:784–98.Article 
CAS 
PubMed 

Google Scholar 
Suzuki MT, Preston CM, Béjà O, De La Torre J, Steward G, DeLong EF. Phylogenetic screening of ribosomal RNA gene-containing clones in bacterial artificial chromosome (BAC) libraries from different depths in Monterey Bay. Micro Ecol. 2004;48:473–88.Article 
CAS 

Google Scholar 
Buchan A, González JM, Moran MA. Overview of the marine Roseobacter lineage. Appl Environ Microbiol. 2005;71:5665–77.Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Giebel H-A, Kalhoefer D, Lemke A, Thole S, Gahl-Janssen R, Simon M, et al. Distribution of Roseobacter RCA and SAR11 lineages in the North Sea and characteristics of an abundant RCA isolate. ISME J. 2011;5:8–19.Article 
PubMed 

Google Scholar 
Ottesen EA, Marin R, Preston CM, Young CR, Ryan JP, Scholin CA, et al. Metatranscriptomic analysis of autonomously collected and preserved marine bacterioplankton. ISME J. 2011;5:1881–95.Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Zhang Y, Sun Y, Jiao N, Stepanauskas R, Luo H. Ecological genomics of the uncultivated marine Roseobacter lineage CHAB-I-5. Appl Environ Microbiol. 2016;82:2100–11.Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Aylward FO, Eppley JM, Smith JM, Chavez FP, Scholin CA, DeLong EF. Microbial community transcriptional networks are conserved in three domains at ocean basin scales. Proc Nat Acad Sci. 2015;112:5443–8.Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Ottesen EA, Young CR, Eppley JM, Ryan JP, Chavez FP, Scholin CA, et al. Pattern and synchrony of gene expression among sympatric marine microbial populations. Proc Nat Acad Sci. 2013;110:E488–E97.Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Nowinski B, Motard‐Côté J, Landa M, Preston CM, Scholin CA, Birch JM, et al. Microdiversity and temporal dynamics of marine bacterial dimethylsulfoniopropionate genes. Environ Microbiol. 2019;21:1687–701.Article 
CAS 
PubMed 

Google Scholar 
Mukherjee S, Stamatis D, Bertsch J, Ovchinnikova G, Sundaramurthi JC, Lee J, et al. Genomes OnLine Database (GOLD) v. 8: overview and updates. Nucleic Acids Res. 2021;49:D723–D33.Article 
CAS 
PubMed 

Google Scholar 
Chen I-MA, Chu K, Palaniappan K, Pillay M, Ratner A, Huang J, et al. IMG/M v. 5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes. Nucleic Acids Res. 2019;47:D666–D77.Article 
CAS 
PubMed 

Google Scholar 
Satinsky BM, Gifford SM, Crump BC, Moran MA. Use of internal standards for quantitative metatranscriptome and metagenome analysis. In: DeLong EF, editor. Methods in Enzymology 531: Elsevier; 2013. p. 237–50.Satinsky BM, Gifford SM, Crump BC, Smith C.Moran MA, Internal genomic DNA standard for quantitative metagenome analysis V3. protocols io 2017; https://doi.org/10.17504/protocols.io.jxdcpi6p.Satinsky BM, Gifford SM, Crump BC, Smith C.Moran MA, Preparation of custom synthesized RNAtranscript standard V3. protocols io. 2017; https://doi.org/10.17504/protocols.io.jxccpiwp.Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357.Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Kang DD, Froula J, Egan R, Wang Z. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ 2015;3:e1165.Article 
PubMed 
PubMed Central 

Google Scholar 
Olm MR, Brown CT, Brooks B, Banfield JF. dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. ISME J. 2017;11:2864–8.Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25:1043–55.Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Rodriguez-R LM, Konstantinidis KT. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ Prepr. 2016. Report No.: 2167–9843Lee K, Choo Y-J, Giovannoni SJ, Cho J-C. Maritimibacter alkaliphilus gen. nov., sp. nov., a genome-sequenced marine bacterium of the Roseobacter clade in the order Rhodobacterales. Int J Syst Evol Microbiol. 2007;57:1653–8.Article 
PubMed 

Google Scholar 
Eren AM, Esen ÖC, Quince C, Vineis JH, Morrison HG, Sogin ML, et al. Anvi’o: an advanced analysis and visualization platform for ‘omics data. PeerJ 2015;3:e1319.Article 
PubMed 
PubMed Central 

Google Scholar 
Tatusov RL, Galperin MY, Natale DA, Koonin EV. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 2000;28:33–6.Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Huerta-Cepas J, Forslund K, Coelho LP, Szklarczyk D, Jensen LJ, Von Mering C, et al. Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper. Mol Biol Evol. 2017;34:2115–22.Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Aramaki T, Blanc-Mathieu R, Endo H, Ohkubo K, Kanehisa M, Goto S, et al. KofamKOALA: KEGG ortholog assignment based on profile HMM and adaptive score threshold. Bioinformatics 2020;36:2251–2.Article 
CAS 
PubMed 

Google Scholar 
Bushnell B. BBMap: a fast, accurate, splice-aware aligner. No. LBNL-7065E. Lawrence Berkeley National Laboratory, Berkeley, CA (United States); 2014.Markowitz VM, Chen I-MA, Palaniappan K, Chu K, Szeto E, Grechkin Y, et al. The integrated microbial genomes system: an expanding comparative analysis resource. Nucleic Acids Res. 2010;38:D382–D90.Article 
CAS 
PubMed 

Google Scholar 
Sun Y, Luo H. Homologous recombination in core genomes facilitates marine bacterial adaptation. Appl Environ Microbiol. 2018;84:e02545–17.Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Pfaffel O. ClustImpute: An R package for K-means clustering with build-in missing data imputation. https://www.researchgate.net/publication/341881683.Moran MA, Satinsky B, Gifford SM, Luo H, Rivers A, Chan L-K, et al. Sizing up metatranscriptomics. ISME J 2013;7:237–43.Article 
CAS 
PubMed 

Google Scholar 
Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K, Salazar G, et al. Structure and function of the global ocean microbiome. Science. 2015;348:1261359.Article 
PubMed 

Google Scholar 
Gifford SM, Zhao L, Stemple B, DeLong K, Medeiros PM, Seim H, et al. Microbial niche diversification in the Galápagos Archipelago and its response to El Niño. Front Microbiol. 2020;11:575194.Article 
PubMed 
PubMed Central 

Google Scholar 
Rich VI, Pham VD, Eppley J, Shi Y, DeLong EF. Time‐series analyses of Monterey Bay coastal microbial picoplankton using a ‘genome proxy’microarray. Environ Microbiol. 2011;13:116–34.Article 
CAS 
PubMed 

Google Scholar 
Riedel T, Tomasch J, Buchholz I, Jacobs J, Kollenberg M, Gerdts G, et al. Constitutive expression of the proteorhodopsin gene by a flavobacterium strain representative of the proteorhodopsin-producing microbial community in the North Sea. Appl Environ Microbiol. 2010;76:3187–97.Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Iverson V, Morris RM, Frazar CD, Berthiaume CT, Morales RL, Armbrust EV. Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota. Science 2012;335:587–90.Article 
CAS 
PubMed 

Google Scholar 
Yooseph S, Nealson KH, Rusch DB, McCrow JP, Dupont CL, Kim M, et al. Genomic and functional adaptation in surface ocean planktonic prokaryotes. Nature 2010;468:60–6.Article 
CAS 
PubMed 

Google Scholar 
Wagner-Döbler I, Biebl H. Environmental biology of the marine Roseobacter lineage. Annu Rev Microbiol. 2006;60:255–80.Article 
PubMed 

Google Scholar 
West NJ, Obernosterer I, Zemb O, Lebaron P. Major differences of bacterial diversity and activity inside and outside of a natural iron‐fertilized phytoplankton bloom in the Southern Ocean. Environ Microbiol. 2008;10:738–56.Article 
CAS 
PubMed 

Google Scholar 
Luo H, Moran MA. Evolutionary ecology of the marine Roseobacter clade. Microbiol Mol Biol Rev. 2014;78:573–87.Article 
PubMed 
PubMed Central 

Google Scholar 
Simon M, Scheuner C, Meier-Kolthoff JP, Brinkhoff T, Wagner-Döbler I, Ulbrich M, et al. Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats. ISME J 2017;11:1483–99.Article 
PubMed 
PubMed Central 

Google Scholar 
Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Comm. 2018;9:1–8.Article 

Google Scholar 
Caro‐Quintero A, Konstantinidis KT. Bacterial species may exist, metagenomics reveal. Environ Microbiol. 2012;14:347–55.Article 
PubMed 

Google Scholar 
Tindall BJ, Rosselló-Móra R, Busse H-J, Ludwig W, Kämpfer P. Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol. 2010;60:249–66.Article 
CAS 
PubMed 

Google Scholar 
Cohan FM. What are bacterial species? Ann Rev Microbiol. 2002;56:457–87.Article 
CAS 

Google Scholar 
Mende DR, Sunagawa S, Zeller G, Bork P. Accurate and universal delineation of prokaryotic species. Nat Meth. 2013;10:881–4.Article 
CAS 

Google Scholar 
Olm MR, Crits-Christoph A, Diamond S, Lavy A, Matheus Carnevali PB, Banfield JF. Consistent metagenome-derived metrics verify and delineate bacterial species boundaries. mSystems 2020;5:e00731–19.Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Konstantinidis KT, Tiedje JM. Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead. Curr Opin Microbiol. 2007;10:504–9.Article 
CAS 
PubMed 

Google Scholar 
Delmont TO, Eren EM. Linking pangenomes and metagenomes: The Prochlorococcus metapangenome. PeerJ 2018;2018:e4320–e.Article 

Google Scholar 
Neidhardt F, Umbarger H Chemical composition of Escherichia coli. In: FC N, Curtiss R III, JL I, ECC L, KB L, B M, et al., editors. Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology. Washington DC: ASM Press; 1996. p. 13-6.Taniguchi Y, Choi PJ, Li G-W, Chen H, Babu M, Hearn J, et al. Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science. 2010;329:533–8.Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Rodríguez-Gijón A, Nuy JK, Mehrshad M, Buck M, Schulz F, Woyke T, et al. A genomic perspective across Earth’s microbiomes reveals that genome size in Archaea and Bacteria is linked to ecosystem type and trophic strategy. Front Microbiol. 2022;12:761869.Article 
PubMed 
PubMed Central 

Google Scholar 
Ryu K-S, Kim C, Kim I, Yoo S, Choi B-S, Park C. NMR application probes a novel and ubiquitous family of enzymes that alter monosaccharide configuration. J Biol Chem. 2004;279:25544–8.Article 
CAS 
PubMed 

Google Scholar 
Giachino A, Waldron KJ. Copper tolerance in bacteria requires the activation of multiple accessory pathways. Mol Microbiol. 2020;114:377–90.Article 
CAS 
PubMed 

Google Scholar 
Wang X, Zhang Y, Ren M, Xia T, Chu X, Liu C, et al. Cryptic speciation of a pelagic Roseobacter population varying at a few thousand nucleotide sites. ISME J. 2020;14:3106–19.Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Uchimiya M, Schroer W, Olofsson M, Edison AS, Moran MA. Diel investments in metabolite production and consumption in a model microbial system. ISME J. 2022;16:1306–17.Article 
CAS 
PubMed 

Google Scholar 
Cordero OX, Wildschutte H, Kirkup B, Proehl S, Ngo L, Hussain F, et al. Ecological populations of bacteria act as socially cohesive units of antibiotic production and resistance. Science 2012;337:1228–31.Article 
CAS 
PubMed 

Google Scholar 
Morris JJ, Lenski RE, Zinser ER. The Black Queen Hypothesis: evolution of dependencies through adaptive gene loss. mBio 2012;3:e00036–12.Article 
PubMed 
PubMed Central 

Google Scholar 
Environmental data from CTD during the Fall 2016 ESP deployment in Monterey Bay, CA. Biological and Chemical Oceanography Data Management Office (BCO-DMO). 2019. Available from: https://doi.org/10.1575/1912/bco-dmo.756376.1.Environmental data from Niskin bottle sampling during the Fall 2016 ESP deployment in Monterey Bay. Biological and Chemical Oceanography Data Management Office (BCO-DMO). 2019. Available from: https://doi.org/10.1575/1912/bco-dmo.756413.1. More

McFall-Ngai, M. et al. Animals in a bacterial world, a new imperative for the life sciences. Proc. Natl. Acad. Sci. U.S.A. 110, 3229–3236 (2013).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Hammer, T. J., Sanders, J. G. & Fierer, N. Not all animals need a microbiome. FEMS Microbiol. Lett. 366, fnz117 (2019).Article 
CAS 
PubMed 

Google Scholar 
Griffiths, S. M. et al. Host genetics and geography influence microbiome composition in the sponge Ircinia campana. J. Anim. Ecol. 88, 1684–1695 (2019).Article 
PubMed 
PubMed Central 

Google Scholar 
Coleman-Derr, D. et al. Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species. New Phytol. 209, 798–811 (2016).Article 
CAS 
PubMed 

Google Scholar 
Marzinelli, E. M. et al. Continental-scale variation in seaweed host-associated bacterial communities is a function of host condition, not geography. Environ. Microbiol. 17, 4078–4088 (2015).Article 
PubMed 

Google Scholar 
Wang, L., English, M. K., Tomas, F. & Mueller, R. S. Recovery and community succession of the Zostera marina Rhizobiome after transplantation. bioRxiv https://doi.org/10.1101/2020.04.20.052357 (2020).Article 
PubMed 
PubMed Central 

Google Scholar 
Copeland, J. K., Yuan, L., Layeghifard, M., Wang, P. W. & Guttman, D. S. Seasonal community succession of the phyllosphere microbiome. Mol. Plant. Microbe. Interact. 28, 274–285 (2015).Article 
CAS 
PubMed 

Google Scholar 
Shi, S. et al. Successional trajectories of rhizosphere bacterial communities over consecutive seasons. MBio 6, e00746 (2015).Article 
PubMed 
PubMed Central 

Google Scholar 
Shade, A., McManus, P. S. & Handelsman, J. Unexpected diversity during community succession in the apple flower microbiome. MBio 4, e00602 (2013).Article 
PubMed 
PubMed Central 

Google Scholar 
Avena, C. V. et al. Deconstructing the bat skin microbiome: Influences of the host and the environment. Front. Microbiol. 7, 1753 (2016).Article 
PubMed 
PubMed Central 

Google Scholar 
Rothschild, D. et al. Environment dominates over host genetics in shaping human gut microbiota. Nature 555, 210–215 (2018).Article 
ADS 
CAS 
PubMed 

Google Scholar 
Glasl, B., Smith, C. E., Bourne, D. G. & Webster, N. S. Disentangling the effect of host-genotype and environment on the microbiome of the coral Acropora tenuis. PeerJ 7, e6377 (2019).Article 
PubMed 
PubMed Central 

Google Scholar 
Weigel, B. L. & Erwin, P. M. Effects of reciprocal transplantation on the microbiome and putative nitrogen cycling functions of the intertidal sponge, Hymeniacidon heliophila. Sci. Rep. 7, 43247 (2017).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Fuhrman, J. A., Cram, J. A. & Needham, D. M. Marine microbial community dynamics and their ecological interpretation. Nat. Rev. Microbiol. 13, 133–146 (2015).Article 
CAS 
PubMed 

Google Scholar 
Ziegler, M. et al. Coral bacterial community structure responds to environmental change in a host-specific manner. Nat. Commun. 10, 3092 (2019).Article 
ADS 
PubMed 
PubMed Central 

Google Scholar 
Wagner, M. R. et al. Host genotype and age shape the leaf and root microbiomes of a wild perennial plant. Nat. Commun. 7, 12151 (2016).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Kraft, N. J. B. et al. Community assembly, coexistence and the environmental filtering metaphor. Funct. Ecol. 29, 592–599 (2015).Article 

Google Scholar 
Weiher, E. & Keddy, P. A. The assembly of experimental wetland plant communities. Oikos 73, 323–335 (1995).Article 

Google Scholar 
Cavender-Bares, J., Kitajima, K. & Bazzaz, F. A. Multiple trait associations in relation to habitat differentiation among 17 Floridian oak species. Ecol. Monogr. 74, 635–662 (2004).Article 

Google Scholar 
Cavender-Bares, J., Ackerly, D. D., Baum, D. A. & Bazzaz, F. A. Phylogenetic overdispersion in Floridian oak communities. Am. Nat. 163, 823–843 (2004).Article 
CAS 
PubMed 

Google Scholar 
Webb, C. O. Exploring the Phylogenetic structure of ecological communities: An example for rain forest trees. Am. Nat. 156, 145–155 (2000).Article 
PubMed 

Google Scholar 
Webb, C. O., Ackerly, D. D., McPeek, M. A. & Donoghue, M. J. Phylogenies and community ecology. Annu. Rev. Ecol. Syst. 33, 475–505 (2002).Article 

Google Scholar 
Kembel, S. W. et al. Relationships between phyllosphere bacterial communities and plant functional traits in a neotropical forest. Proc. Natl. Acad. Sci. U.S.A. 111, 13715–13720 (2014).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Burke, C., Steinberg, P., Rusch, D., Kjelleberg, S. & Thomas, T. Bacterial community assembly based on functional genes rather than species. Proc. Natl. Acad. Sci. U.S.A. 108, 14288–14293 (2011).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Martiny, J. B. H., Jones, S. E., Lennon, J. T. & Martiny, A. C. Microbiomes in light of traits: A phylogenetic perspective. Science https://doi.org/10.1126/science.aac9323 (2015).Article 
PubMed 

Google Scholar 
Goberna, M. & Verdú, M. Predicting microbial traits with phylogenies. ISME J. 10, 959–967 (2016).Article 
PubMed 

Google Scholar 
Duarte, C. M. The future of seagrass meadows. Environ. Conserv. 29, 192–206 (2002).Article 

Google Scholar 
Fonseca, M. S., Fisher, J. S., Zieman, J. C. & Thayer, G. W. Influence of the seagrass, Zostera marina L., on current flow. Estuar. Coast. Shelf Sci. 15, 351–364 (1982).Article 
ADS 

Google Scholar 
Fonseca, M. S., Kenworthy, W. J. & Thayer, G. W. A low cost transplanting procedure for sediment stabilization and habitat development using eelgrass (Zostera marina). Wetlands 2, 138–151 (1982).Article 

Google Scholar 
Moore, K. A. & Short, F. T. Zostera: Biology, ecology, and management. In Seagrasses: Biology, ecology and conservation (eds Larkum, A. W. D. et al.) 361–386 (Springer, 2006).
Google Scholar 
Fahimipour, A. K. et al. Global-scale structure of the eelgrass microbiome. Appl. Environ. Microbiol. 83, e03391-16 (2017).Article 
PubMed 
PubMed Central 

Google Scholar 
Bengtsson, M. M. et al. Eelgrass leaf surface microbiomes are locally variable and highly correlated with epibiotic eukaryotes. Front. Microbiol. 8, 1312 (2017).Article 
PubMed 
PubMed Central 

Google Scholar 
Cúcio, C., Engelen, A. H., Costa, R. & Muyzer, G. Rhizosphere microbiomes of European + seagrasses are selected by the plant, but are not species specific. Front. Microbiol. 7, 440 (2016).Article 
PubMed 
PubMed Central 

Google Scholar 
Schenck, F. R., DuBois, K., Kardish, M. R., Stachowicz, J. J. & Hughes, A. R. The effect of warming on seagrass wasting disease depends on host genotypic identity and diversity. Ecology e3959 (2022).Beatty, D. S. et al. Predictable changes in eelgrass microbiomes with increasing wasting disease prevalence across 23° latitude in the Northeastern Pacific. mSystems 7, e0022422 (2022).Article 
PubMed 

Google Scholar 
Hughes, A. R., Stachowicz, J. J. & Williams, S. L. Morphological and physiological variation among seagrass (Zostera marina) genotypes. Oecologia 159, 725–733 (2009).Article 
ADS 
PubMed 

Google Scholar 
Randall Hughes, A. & Stachowicz, J. J. Seagrass genotypic diversity increases disturbance response via complementarity and dominance. J. Ecol. 99, 445–453 (2010).
Google Scholar 
Kamel, S. J., Hughes, A. R., Grosberg, R. K. & Stachowicz, J. J. Fine-scale genetic structure and relatedness in the eelgrass Zostera marina. Mar. Ecol. Prog. Ser. 447, 127–137 (2012).Article 
ADS 

Google Scholar 
Abbott, J. M., DuBois, K., Grosberg, R. K., Williams, S. L. & Stachowicz, J. J. Genetic distance predicts trait differentiation at the subpopulation but not the individual level in eelgrass Zostera marina. Ecol. Evol. 8, 7476–7489 (2018).Article 
PubMed 
PubMed Central 

Google Scholar 
Sand-Jensen, K. Biomass, net production and growth dynamics in an eelgrass (Zostera marina L.) population in Vellerup Vig, Denmark. Ophelia 14, 185–201 (1975).Article 

Google Scholar 
Vacher, C. et al. The phyllosphere: Microbial jungle at the plant-climate interface. Annu. Rev. Ecol. Evol. Syst. 47, 1–24 (2016).Article 

Google Scholar 
Miazaki, A. S., Gastauer, M. & Meira-Neto, J. A. A. Environmental severity promotes phylogenetic clustering in campo rupestre vegetation. Acta Bot. Brasilica 29, 561–566 (2015).Article 

Google Scholar 
DuBois, K., Williams, S. L. & Stachowicz, J. J. Previous exposure mediates the response of eelgrass to future warming via clonal transgenerational plasticity. Ecology 101, e03169 (2020).Article 
PubMed 

Google Scholar 
Rüger, L. et al. Assembly patterns of the rhizosphere microbiome along the longitudinal root axis of maize (Zea mays L.). Front. Microbiol. 12, 614501 (2021).Article 
PubMed 
PubMed Central 

Google Scholar 
Fitzpatrick, C. R. et al. Assembly and ecological function of the root microbiome across angiosperm plant species. Proc. Natl. Acad. Sci. U.S.A. 115, E1157–E1165 (2018).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Fitzgerald, D. B., Winemiller, K. O., Sabaj Pérez, M. H. & Sousa, L. M. Seasonal changes in the assembly mechanisms structuring tropical fish communities. Ecology 98, 21–31 (2017).Article 
PubMed 

Google Scholar 
Campbell, A. H., Marzinelli, E. M., Gelber, J. & Steinberg, P. D. Spatial variability of microbial assemblages associated with a dominant habitat-forming seaweed. Front. Microbiol. 6, 230 (2015).Article 
PubMed 
PubMed Central 

Google Scholar 
Eriander, L., Infantes, E., Olofsson, M., Olsen, J. L. & Moksnes, P.-O. Assessing methods for restoration of eelgrass (Zostera marina L.) in a cold temperate region. J. Exp. Mar. Bio. Ecol. 479, 76–88 (2016).Article 

Google Scholar 
Zhou, Y. et al. Restoring eelgrass (Zostera marina L.) habitats using a simple and effective transplanting technique. PLoS ONE 9, e92982 (2014).Article 
ADS 
PubMed 
PubMed Central 

Google Scholar 
Galushko, A. & Kuever, J. Desulfocapsaceae. Bergey’s Manual of Systematics of Archaea and Bacteria 1–6 Preprint at https://doi.org/10.1002/9781118960608.fbm00332 (2021).Waite, D. W. et al. Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities. Int. J. Syst. Evol. Microbiol. 70, 5972–6016 (2020).Article 
CAS 
PubMed 

Google Scholar 
Knoblauch, C., Sahm, K. & Jørgensen, B. B. Psychrophilic sulfate-reducing bacteria isolated from permanently cold arctic marine sediments: description of Desulfofrigus oceanense gen. nov., sp. nov., Desulfofrigus fragile sp. nov., Desulfofaba gelida gen. nov., sp. nov., Desulfotalea psychrophila gen. nov., sp. nov. and Desulfotalea arctica sp. nov.. Int. J. Syst. Bacteriol. 49 Pt 4, 1631–1643 (1999).Article 
CAS 
PubMed 

Google Scholar 
Isaksen, M. F. & Teske, A. Desulforhopalus vacuolatus gen. nov., sp. nov., a new moderately psychrophilic sulfate-reducing bacterium with gas vacuoles isolated from a temperate estuary. Arch. Microbiol. 166, 160–168 (1996).Article 
CAS 

Google Scholar 
Song, J., Hwang, J., Kang, I. & Cho, J.-C. A sulfate-reducing bacterial genus, Desulfosediminicola gen. nov., comprising two novel species cultivated from tidal-flat sediments. Sci. Rep. 11, 19978 (2021).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Trevelline, B. K., Fontaine, S. S., Hartup, B. K. & Kohl, K. D. Conservation biology needs a microbial renaissance: a call for the consideration of host-associated microbiota in wildlife management practices. Proc. Biol. Sci. 286, 20182448 (2019).PubMed 
PubMed Central 

Google Scholar 
Christian, N., Whitaker, B. K. & Clay, K. Microbiomes: Unifying animal and plant systems through the lens of community ecology theory. Front. Microbiol. 6, 869 (2015).Article 
PubMed 
PubMed Central 

Google Scholar 
Zieman, J. C. Productivity in seagrasses: Methods and rates. In Handbook of Seagrass Biology: An ecosystem perspective (eds Phillips, R. C. & McRoy, C. P.) 87–116 (Garland STPM Press, 1980).
Google Scholar 
Dennison, W. C. Leaf production. Seagrass research methods, UNESCO, Paris 77–79 (1990).Walters, W. et al. Improved bacterial 16S rRNA gene (V4 and V4–5) and fungal internal transcribed spacer marker gene primers for microbial community surveys. mSystems 1, e00009-15 (2016).Article 
PubMed 

Google Scholar 
Comeau, A. M., Douglas, G. M. & Langille, M. G. I. Microbiome Helper: A custom and streamlined workflow for microbiome research. mSystems 2, e00127-16 (2017).Article 
PubMed 
PubMed Central 

Google Scholar 
Callahan, B. J. et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
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).Article 
CAS 
PubMed 

Google Scholar 
Wright, E. S. DECIPHER: Harnessing local sequence context to improve protein multiple sequence alignment. BMC Bioinform. 16, 322 (2015).Article 

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).Article 
ADS 
PubMed 
PubMed Central 

Google Scholar 
Britton, T., Anderson, C. L., Jacquet, D., Lundqvist, S. & Bremer, K. Estimating divergence times in large phylogenetic trees. Syst. Biol. 56, 741–752 (2007).Article 
PubMed 

Google Scholar 
McMurdie, P. J. & Holmes, S. phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 8, e61217 (2013).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Paradis, E. & Schliep, K. ape 50: An environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 35, 526–528 (2019).Article 
CAS 
PubMed 

Google Scholar 
Silverman, J. D., Washburne, A. D., Mukherjee, S. & David, L. A. A phylogenetic transform enhances analysis of compositional microbiota data. Elife 6, 1–20 (2017).Article 

Google Scholar 
McMurdie, P. J. & Holmes, S. Waste not, want not: Why rarefying microbiome data is inadmissible. PLoS Comput. Biol. 10, e1003531 (2014).Article 
ADS 
PubMed 
PubMed Central 

Google Scholar 
Webb, C. O., Ackerly, D. D. & Kembel, S. W. Phylocom: Software for the analysis of phylogenetic community structure and trait evolution. Bioinformatics 24, 2098–2100 (2008).Article 
CAS 
PubMed 

Google Scholar 
Russel, J. Russel88/MicEco: v0.9.15. (2021). 10.5281/zenodo.4733747.Kembel, S. W. et al. Picante: R tools for integrating phylogenies and ecology. Bioinformatics 26, 1463–1464 (2010).Article 
CAS 
PubMed 

Google Scholar 
Friedman, J., Hastie, T. & Tibshirani, R. Regularization paths for generalized linear models via coordinate descent. J. Stat. Softw. 33, 1–22 (2010).Article 
PubMed 
PubMed Central 

Google Scholar 
Kahle, D. & Wickham, H. Ggmap: Spatial visualization with ggplot2. R J. 5, 144 (2013).Article 

Google Scholar  More

Jayathilake PG, Jana S, Rushton S, Swailes D, Bridgens B, Curtis T, et al. Extracellular polymeric substance production and aggregated bacteria colonization influence the competition of microbes in biofilms. Front Microbiol. 2017;8:1865.Article 
PubMed 
PubMed Central 

Google Scholar 
Flemming H-C, Neu TR, Wingender J (eds). The Perfect Slime: Microbial Extracellular Polymeric Substances (EPS). IWA Publishing, London, 2016.Morales-García AL, Bailey RG, Jana S, Burgess JG. The role of polymers in cross-kingdom bioadhesion. Philos Trans R Soc Lond B Biol Sci. 2019;374:20190192.Article 
PubMed 
PubMed Central 

Google Scholar 
Davey ME, O’Toole GA. Microbial biofilms: From ecology to molecular genetics. Microbiol Mol. 2000;64:847–67.Article 
CAS 

Google Scholar 
Peters BM, Jabra-Rizk MA, O’May GA, Costerton JW, Shirtliff ME. Polymicrobial interactions: Impact on pathogenesis and human disease. Clin Microbiol Rev. 2012;25:193–213.Article 
PubMed 
PubMed Central 

Google Scholar 
Karygianni L, Ren Z, Koo H, Thurnheer T. Biofilm matrixome: Extracellular components in structured microbial communities. Trends Microbiol. 2020;28:668–81.Article 
CAS 
PubMed 

Google Scholar 
Morris BEL, Henneberger R, Huber H, Moissl-Eichinger C. Microbial syntrophy: Interaction for the common good. FEMS Microbiol Rev. 2013;37:384–406.Article 
CAS 
PubMed 

Google Scholar 
Decho AW, Gutierrez T. Microbial extracellular polymeric substances (EPSs) in ocean systems. Front Microbiol. 2017;8:922.Article 
PubMed 
PubMed Central 

Google Scholar 
Boleij M, Seviour T, Wong LL, van Loosdrecht MCM, Lin Y. Solubilization and characterization of extracellular proteins from anammox granular sludge. Water Res. 2019;164:114952.Article 
CAS 
PubMed 

Google Scholar 
Kim D, Barraza JP, Arthur RA, Hara A, Lewis K, Liu Y, et al. Spatial mapping of polymicrobial communities reveals a precise biogeography associated with human dental caries. Proc Natl Acad Sci USA. 2020;117:12375–86.Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Sadiq FA, Burmølle M, Heyndrickx M, Flint S, Lu W, Chen W, et al. Community-wide changes reflecting bacterial interspecific interactions in multispecies biofilms. Crit Rev Microbiol. 2021;47:338–58.Article 
PubMed 

Google Scholar 
Liu W, Jacquiod S, Brejnrod A, Russel J, Burmølle M, Sørensen SJ. Deciphering links between bacterial interactions and spatial organization in multispecies biofilms. ISME J. 2019;13:3054–66.Article 
PubMed 
PubMed Central 

Google Scholar 
Bridier A, Le Coq D, Dubois-Brissonnet F, Thomas V, Aymerich S, Briandet R. The spatial architecture of Bacillus subtilis biofilms deciphered using a surface-associated model and in situ imaging. PLOS One. 2011;6:e16177.Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Lee KWK, Periasamy S, Mukherjee M, Xie C, Kjelleberg S, Rice SA. Biofilm development and enhanced stress resistance of a model, mixed-species community biofilm. ISME J. 2014;8:894–907.Article 
CAS 
PubMed 

Google Scholar 
Myszka K, Czaczyk K. Characterization of adhesive exopolysaccharide (EPS) produced by Pseudomonas aeruginosa under starvation conditions. Curr Microbiol. 2009;58:541–6.Article 
CAS 
PubMed 

Google Scholar 
Harimawan A, Ting YP. Investigation of extracellular polymeric substances (EPS) properties of P. aeruginosa and B. subtilis and their role in bacterial adhesion. Colloids Surf B. 2016;146:459–67.Article 
CAS 

Google Scholar 
Yang X-R, Li H, Nie S-A, Su J-Q, Weng B-S, Zhu G-B, et al. Potential contribution of anammox to nitrogen loss from paddy soils in Southern China. Appl Environ Microbiol. 2015;81:938–47.Article 
PubMed 
PubMed Central 

Google Scholar 
Kartal B, van Niftrik L, Keltjens JT, Op den Camp HJM, Jetten MSM Chapter 3 – Anammox—Growth physiology, cell biology, and metabolism. In: Poole RK, editor. Adv Microb Physiol. 60: Academic Press; 2012. p. 211–62.Lu Y, Natarajan G, Nguyen TQN, Thi SS, Arumugam K, Seviour TW, et al. Species level enrichment of AnAOB and associated growth morphology under the effect of key metabolites. bioRxiv. 2020. 2020.02.04.934877Gonzalez-Gil G, Sougrat R, Behzad AR, Lens PN, Saikaly PE. Microbial community composition and ultrastructure of granules from a full-scale anammox reactor. Micro Ecol. 2015;70:118–31.Article 
CAS 

Google Scholar 
Kindaichi T, Yuri S, Ozaki N, Ohashi A. Ecophysiological role and function of uncultured Chloroflexi in an anammox reactor. Water Sci Technol. 2012;66:2556–61.Article 
CAS 
PubMed 

Google Scholar 
Qin Y, Han B, Cao Y, Wang T. Impact of substrate concentration on anammox-UBF reactors start-up. Bioresour Technol. 2017;239:422–9.Article 
CAS 
PubMed 

Google Scholar 
Chen Z, Meng Y, Sheng B, Zhou Z, Jin C, Meng F. Linking exoproteome function and structure to anammox biofilm development. Environ Sci Technol. 2019;53:1490–500.Article 
CAS 
PubMed 

Google Scholar 
Ali M, Shaw DR, Albertsen M, Saikaly PE. Comparative genome-centric analysis of freshwater and marine ANAMMOX cultures suggests functional redundancy in nitrogen removal processes. Front Microbiol. 2020;11:1637.Article 
PubMed 
PubMed Central 

Google Scholar 
Jia F, Yang Q, Liu X, Li X, Li B, Zhang L, et al. Stratification of extracellular polymeric substances (EPS) for aggregated anammox microorganisms. Environ Sci Technol. 2017;51:3260–8.Article 
CAS 
PubMed 

Google Scholar 
Hou X, Liu S, Zhang Z. Role of extracellular polymeric substance in determining the high aggregation ability of anammox sludge. Water Res. 2015;75:51–62.Article 
CAS 
PubMed 

Google Scholar 
Feng C, Lotti T, Lin Y, Malpei F. Extracellular polymeric substances extraction and recovery from anammox granules: Evaluation of methods and protocol development. Chem Eng J. 2019;374:112–22.Article 
CAS 

Google Scholar 
Lotti T, Carretti E, Berti D, Montis C, Del Buffa S, Lubello C, et al. Hydrogels formed by anammox extracellular polymeric substances: Structural and mechanical insights. Sci Rep. 2019;9:11633.Article 
PubMed 
PubMed Central 

Google Scholar 
Jakubovics NS, Goodman SD, Mashburn-Warren L, Stafford GP, Cieplik F. The dental plaque biofilm matrix. Periodontology 2000. 2021;86:32–56.Article 
PubMed 
PubMed Central 

Google Scholar 
Ðapa T, Leuzzi R, Ng YK, Baban ST, Adamo R, Kuehne SA, et al. Multiple factors modulate biofilm formation by the anaerobic pathogen Clostridium difficile. J Bacteriol. 2013;195:545–55.Article 
PubMed 
PubMed Central 

Google Scholar 
Honma K, Inagaki S, Okuda K, Kuramitsu HK, Sharma A. Role of a Tannerella forsythia exopolysaccharide synthesis operon in biofilm development. Micro Pathog. 2007;42:156–66.Article 
CAS 

Google Scholar 
Li X-R, Du B, Fu H-X, Wang R-F, Shi J-H, Wang Y, et al. The bacterial diversity in an anaerobic ammonium-oxidizing (anammox) reactor community. Syst Appl Microbiol. 2009;32:278–89.Article 
CAS 
PubMed 

Google Scholar 
Cho S, Takahashi Y, Fujii N, Yamada Y, Satoh H, Okabe S. Nitrogen removal performance and microbial community analysis of an anaerobic up-flow granular bed anammox reactor. Chemosphere 2010;78:1129–35.Article 
CAS 
PubMed 

Google Scholar 
Morgenroth E, Sherden T, Van Loosdrecht MCM, Heijnen JJ, Wilderer PA. Aerobic granular sludge in a sequencing batch reactor. Water Res. 1997;31:3191–4.Article 
CAS 

Google Scholar 
Wong LL, Natarajan G, Boleij M, Thi SS, Winnerdy FR, Mugunthan S, et al. Extracellular protein isolation from the matrix of anammox biofilm using ionic liquid extraction. Appl Microbiol Biotechnol. 2020;104:3643–54.Article 
CAS 
PubMed 

Google Scholar 
Law Y, Kirkegaard RH, Cokro AA, Liu X, Arumugam K, Xie C, et al. Integrative microbial community analysis reveals full-scale enhanced biological phosphorus removal under tropical conditions. Sci Rep. 2016;6:25719.Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Ondov BD, Bergman NH, Phillippy AM. Interactive metagenomic visualization in a Web browser. BMC Bioinform. 2011;12:385.Article 

Google Scholar 
Liu X, Arumugam K, Natarajan G, Seviour TW, Drautz-Moses DI, Wuertz S, et al. Draft genome sequence of a Candidatus brocadia bacterium enriched from activated sludge collected in a tropical climate. Genome Announc. 2018;6:e00406–18.Article 
PubMed 
PubMed Central 

Google Scholar 
Price MN, Dehal PS, Arkin AP. FastTree 2-approximately maximum-likelihood trees for large alignments. PloS One. 2010;5:e9490–e.Article 
PubMed 
PubMed Central 

Google Scholar 
Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, et al. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nat Biotechnol. 2018;36:566–9.Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25:1043–55.Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Buchfink B, Reuter K, Drost H-G. Sensitive protein alignments at tree-of-life scale using DIAMOND. Nat Methods. 2021;18:366–8.Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2015;12:59–60.Article 
CAS 
PubMed 

Google Scholar 
Daims H, Nielsen JL, Nielsen PH, Schleifer K-H, Wagner M. In situ characterization of Nitrospira-like nitrite-oxidizing bacteria active in wastewater treatment plants. Appl Environ Microbiol. 2001;67:5273–84.Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Seviour T, Wong LL, Lu Y, Mugunthan S, Yang Q, Shankari UDOCS, et al. Phase transitions by an abundant protein in the anammox extracellular matrix mediate cell-to-cell aggregation and biofilm formation. mBio 2020;11:e02052–20.Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Protter DSW, Rao BS, Van Treeck B, Lin Y, Mizoue L, Rosen MK, et al. Intrinsically disordered regions can contribute promiscuous interactions to RNP granule assembly. Cell Rep. 2018;22:1401–12.Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Fulton KM, Smith JC, Twine SM. Clinical applications of bacterial glycoproteins. Expert Rev Proteom. 2016;13:345–53.Article 
CAS 

Google Scholar 
Upreti RK, Kumar M, Shankar V. Bacterial glycoproteins: Functions, biosynthesis and applications. Proteomics 2003;3:363–79.Article 
CAS 
PubMed 

Google Scholar 
van Teeseling MCF, Maresch D, Rath CB, Figl R, Altmann F, Jetten MSM, et al. The S-layer protein of the anammox bacterium Kuenenia stuttgartiensiss is heavily O-glycosylated. Front Microbiol. 2016;7:1721.PubMed 
PubMed Central 

Google Scholar 
McGonigle JM, Lang SQ, Brazelton WJ, Parales RE. Genomic evidence for formate metabolism by Chloroflexi as the key to unlocking deep carbon in lost city microbial ecosystems. Appl Environ Microbiol. 2020;86:e02583–19.Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Vuillemin A, Kerrigan Z, D’Hondt S, Orsi WD. Exploring the abundance, metabolic potential and gene expression of subseafloor Chloroflexi in million-year-old oxic and anoxic abyssal clay. FEMS Microbiol Ecol. 2020;96:fiaa223.Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Kartal B, de Almeida NM, Maalcke WJ, Op den Camp HJ, Jetten MS, Keltjens JT. How to make a living from anaerobic ammonium oxidation. FEMS Microbiol Rev. 2013;37:428–61.Article 
CAS 
PubMed 

Google Scholar 
Loera-Muro A, Guerrero-Barrera A, Tremblay DNY, Hathroubi S, Angulo C. Bacterial biofilm-derived antigens: A new strategy for vaccine development against infectious diseases. Expert Rev Vaccines. 2021;20:385–96.Article 
CAS 
PubMed 

Google Scholar 
Hobley L, Harkins C, MacPhee CE, Stanley-Wall NR. Giving structure to the biofilm matrix: An overview of individual strategies and emerging common themes. FEMS Microbiol Rev. 2015;39:649–69.Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Elias S, Banin E. Multi-species biofilms: Living with friendly neighbors. FEMS Microbiol Rev. 2012;36:990–1004.Article 
CAS 
PubMed 

Google Scholar 
Teeseling MCFV, Almeida NMD, Klingl A, Speth DR, Camp HJMOD, Rachel R, et al. A new addition to the cell plan of anammox bacteria: Candidatus Kuenenia stuttgartiensis has a protein surface layer as the outermost layer of the cell. J Bacteriol. 2014;196:80–9.Article 
PubMed 
PubMed Central 

Google Scholar 
Paula AJ, Hwang G, Koo H. Dynamics of bacterial population growth in biofilms resemble spatial and structural aspects of urbanization. Nat Commun. 2020;11:1354.Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Kragelund C, Caterina L, Borger A, Thelen K, Eikelboom D, Tandoi V, et al. Identity, abundance and ecophysiology of filamentous Chloroflexi species present in activated sludge treatment plants. FEMS Microbiol Ecol. 2007;59:671–82.Article 
CAS 
PubMed 

Google Scholar 
Nierychlo M, Miłobędzka A, Petriglieri F, McIlroy B, Nielsen PH, McIlroy SJ. The morphology and metabolic potential of the Chloroflexi in full-scale activated sludge wastewater treatment plants. FEMS Microbiol Ecol. 2018;95.Kragelund C, Thomsen TR, Mielczarek AT, Nielsen PH. Eikelboom’s morphotype 0803 in activated sludge belongs to the genus Caldilinea in the phylum Chloroflexi. FEMS Microbiol Ecol. 2011;76:451–62.Article 
CAS 
PubMed 

Google Scholar 
Zhang J, Miao Y, Zhang Q, Sun Y, Wu L, Peng Y. Mechanism of stable sewage nitrogen removal in a partial nitrification-anammox biofilm system at low temperatures: Microbial community and EPS analysis. Bioresour Technol. 2020;297:122459.Article 
CAS 
PubMed 

Google Scholar 
Björnsson L, Hugenholtz P, Tyson GW, Blackall LL. Filamentous Chloroflexi (green non-sulfur bacteria) are abundant in wastewater treatment processes with biological nutrient removal. Microbiology 2002;148:2309–18.Article 
PubMed 

Google Scholar 
Boleij M, Pabst M, Neu TR, van Loosdrecht MCM, Lin Y. Identification of glycoproteins isolated from extracellular polymeric substances of full-scale anammox granular sludge. Environ Sci Technol. 2018;52:13127–35.Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Pabst M, Grouzdev DS, Lawson CE, Kleikamp HBC, de Ram C, Louwen R, et al. A general approach to explore prokaryotic protein glycosylation reveals the unique surface layer modulation of an anammox bacterium. ISME J. 2022;16:346–57.Article 
CAS 
PubMed 

Google Scholar 
Berlanga M, Guerrero R. Living together in biofilms: The microbial cell factory and its biotechnological implications. Micro Cell Fact. 2016;15:165.Article 

Google Scholar 
Liu T, Tian R, Li Q, Wu N, Quan X. Strengthened attachment of anammox bacteria on iron-based modified carrier and its effects on anammox performance in integrated floating-film activated sludge (IFFAS) process. Sci Total Environ. 2021;787:147679.Article 
CAS 
PubMed 

Google Scholar  More

Zhe, W. et al. Probing the nature of soil organic matter. Crit. Rev. Environ. Sci. Technol. 52, 4072–4093 (2022).Article 

Google Scholar 
Blanco-Canqui, H. & Lal, R. Mechanisms of carbon sequestration in soil aggregates. Crit. Rev. Plant Sci. 23, 481–504 (2004).Article 
CAS 

Google Scholar 
Six, J., Paustian, K., Elliott, E. T. & Combrink, C. Soil structure and organic matter: I. Distribution of aggregate–size classes and aggregate–associated carbon. Soil Sci. Soc. Am. J. 64, 681–689 (2000).Article 
ADS 
CAS 

Google Scholar 
Lehmann, J. & Kleber, M. The contentious nature of soil organic matter. Nature 528, 60–68 (2015).Article 
ADS 
CAS 
PubMed 

Google Scholar 
Six, J., Bossuyt, H., Degryze, S. & Denef, K. A history of research on the link between (micro)aggregates, soil biota, and soil organic matter dynamics. Soil Tillage Res. 79, 7–31 (2004).Article 

Google Scholar 
Tisdall, J. M. & Oades, J. M. Organic matter and water-stable aggregates in soils. Eur. J. Soil Sci. 33, 141–163 (1982).Article 
CAS 

Google Scholar 
Luo, Y. et al. Rice rhizodeposition promotes the build-up of organic carbon in soil via fungal necromass. Soil Biol. Biochem. 160, 108345 (2021).Article 
CAS 

Google Scholar 
Wang, X. et al. Organic amendments drive shifts in microbial community structure and keystone taxa which increase C mineralization across aggregate size classes. Soil Biol. Biochem. 153, 108062 (2021).Article 
CAS 

Google Scholar 
Duan, Y. et al. Long–term fertilisation reveals close associations between soil organic carbon composition and microbial traits at aggregate scales. Agric. Ecosyst. Environ. 306, 107169 (2021).Article 
CAS 

Google Scholar 
Christensen, B. T. Physical fractionation of soil and structural and functional complexity in organic matter turnover. Eur. J. Soil Sci. 52, 345–353 (2001).Article 
CAS 

Google Scholar 
Olk, D. C. & Gregorich, E. G. Overview of the symposium proceedings, “meaningful pools in determining soil carbon and nitrogen dynamics”. Soil Sci. Soc. Am. J. 70, 967–974 (2006).Article 
ADS 
CAS 

Google Scholar 
Courtier-Murias, D. et al. Unraveling the long–term stabilization mechanisms of organic materials in soils by physical fractionation and NMR spectroscopy. Agric. Ecosyst. Environ. 171, 9–18 (2013).Article 
CAS 

Google Scholar 
Rodrigues, L. A. T. et al. Short– and long–term effects of animal manures and mineral fertilizer on carbon stocks in subtropical soil under no–tillage. Geoderma 386, 114913 (2021).Article 
ADS 
CAS 

Google Scholar 
Mao, J., Dan, C. O., Fang, X., He, Z. & Schmidt-Rohr, K. Influence of animal manure application on the chemical structures of soil organic matter as investigated by advanced solid–state NMR and FT–IR spectroscopy. Geoderma 146, 353–362 (2008).Article 
ADS 
CAS 

Google Scholar 
Simonetti, G. et al. Characterization of humic carbon in soil aggregates in a long–term experiment with manure and mineral fertilization. Soil Sci. Soc. Am. J. 25, 880–890 (2012).Article 

Google Scholar 
Cambardella, C. A. & Elliott, E. T. Particulate soil organic-matter changes across a grassland cultivation sequence. Soil Sci. Soc. Am. J. 56, 777–783 (1992).Article 
ADS 

Google Scholar 
Conant, R. T., Six, J. & Paustian, K. Land use effects on soil carbon fractions in the southeastern United States. I. Management-intensive versus extensive grazing. Biol. Fertil. Soils 38, 386–392 (2003).Article 
CAS 

Google Scholar 
Blanco-Moure, N., Gracia, R., Bielsa, A. C. & López, M. V. Soil organic matter fractions as affected by tillage and soil texture under semiarid Mediterranean conditions. Soil Tillage Res. 155, 381–389 (2016).Article 

Google Scholar 
Yu, H. et al. Accumulation of organic C components in soil and aggregates. Sci. Rep. 5, 13804 (2015).Article 
ADS 
PubMed 
PubMed Central 

Google Scholar 
Schöning, I., Morgenroth, G. & Kögel-Knabner, I. O/N–alkyl and alkyl C are stabilised in fine particle size fractions of forest soils. Biogeochemistry 73, 475–497 (2005).Article 

Google Scholar 
Solomon, D., Lehmann, J., Kinyangi, J., Liang, B. & Schäfer, T. Carbon K-edge NEXAFS and FTIR–ATR spectroscopic investigation of organic carbon speciation in soils. Soil Sci. Soc. Am. J. 13, 107–119 (2005).Article 

Google Scholar 
Yan, H., Chen, C., Xu, Z., Williams, D. & Xu, J. Assessing management impacts on soil organic matter quality in subtropical Australian forests using physical and chemical fractionation as well as 13C NMR spectroscopy. Soil Biol. Biochem. 41, 640–650 (2009).Article 

Google Scholar 
Masoom, H. et al. Soil organic matter in its native state: Unravelling the most complex biomaterial on earth. Environ. Sci. Technol. 50, 1670–1680 (2016).Article 
ADS 
CAS 
PubMed 

Google Scholar 
Vogel, C. et al. Clay mineral composition modifies decomposition and sequestration of organic carbon and nitrogen in fine soil fractions. Biol. Fertil. Soils 51, 427–442 (2015).Article 
CAS 

Google Scholar 
Sharma, S., Singh, P., Angmo, P. & Satpute, S. Total and labile pools of organic carbon in relation to soil biological properties under contrasting land-use systems in a dry mountainous region. Carbon Manage. 13, 352–371 (2022).Article 
CAS 

Google Scholar 
Six, J., Elliott, E., Paustian, K. & Doran, J. Aggregation and soil organic matter accumulation in cultivated and native grassland soils. Soil Sci. Soc. Am. J. 62, 1367–1377 (1998).Article 
ADS 
CAS 

Google Scholar 
Elliott, E. T. Aggregate structure and carbon, nitrogen, and phosphorus in native and cultivated soils. Soil Sci. Soc. Am. J. 50, 627–633 (1986).Article 
ADS 

Google Scholar 
Yu, H., Ding, W., Luo, J., Geng, R. & Cai, Z. Long-term application of organic manure and mineral fertilizers on aggregation and aggregate-associated carbon in a sandy loam soil. Soil Tillage Res. 124, 170–177 (2012).Article 

Google Scholar 
Carter, M. R. & Gregorich, E. G. (eds) Soil Sampling and Methods of Analysis 2nd edn, 230–233 (Taylor & Francis Group, CRC, 2007).
Google Scholar 
Lu, R. (ed.) Soil and Agro-chemistry Analytical Methods 146–149 (China Agricultural Science and Technology Press, 1999).
Google Scholar 
Wu, J., Joergensen, R. G., Pommerening, B., Chaussod, R. & Brookes, P. C. Measurement of soil microbial biomass C by fumigation extraction: An automated procedure. Soil Biol. Biochem. 22, 1167–1169 (1990).Article 
CAS 

Google Scholar 
Zhang, X., Zhu, A., Yang, W. & Zhang, J. Accumulation of organic components and its association with macroaggregation in a sandy loam soil following conservation tillage. Plant Soil. 416, 1–15 (2017).Article 
CAS 

Google Scholar 
Skjemstad, J. O., Clarke, P., Taylor, J. A., Oades, J. M. & Newman, R. H. The removal of magnetic materials from surface soils—a solid state 13C CP/MAS NMR study. Soil Res. 32, 1215–1229 (1994).Article 
CAS 

Google Scholar 
Ringle, C. M., Wende, S. & Becker, J. M. SmartPLS 3.” Boenningstedt: SmartPLS GmbH. Preprint at http://www.smartpls.com (2015).Jerbi, M., Labidi, S., Lounès-Hadj Sahraoui, A., Chaar, H. & Ben Jeddi, F. Higher temperatures and lower annual rainfall do not restrict, directly or indirectly, the mycorrhizal colonization of barley (Hordeum vulgare L.) under rainfed conditions. PLoS ONE 15, e0241794 (2020).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Cohen, J. Statistical power analysis for the behavioral sciences 2nd edn, 407–530 (Erlbaum Associates, Berlin, 1988).MATH 

Google Scholar 
Singh, P. & Benbi, D. K. Physical and chemical stabilization of soil organic matter in cropland ecosystems under rice–wheat, maize–wheat and cotton–wheat cropping systems in northwestern India. Carbon Manag. 12, 603–621 (2021).Article 
CAS 

Google Scholar 
Kiem, R. & Kögel-Knabner, I. Contribution of lignin and polysaccharides to the refractory carbon pool in C–depleted arable soils. Soil Biol. Biochem. 35, 101–118 (2003).Article 
CAS 

Google Scholar 
Lutzow, M. V. et al. Stabilization of organic matter in temperate soils: mechanisms and their relevance under different soil conditions: a review. Eur. J. Soil Sci. 57, 426–445 (2006).Article 

Google Scholar 
Yudina, A. V., Klyueva, V. V., Romanenko, K. A. & Fomin, D. S. Micro- within macro: How micro-aggregation shapes the soil pore space and water-stability. Geoderma 415, 115771 (2022).Article 
ADS 
CAS 

Google Scholar 
Tisdall, J. M., Smith, S. E. & Rengasamy, P. Aggregation of soil by fungal hyphae. Soil Res. 35, 55–60 (1997).Article 

Google Scholar 
Li, T. et al. Contrasting impacts of manure and inorganic fertilizer applications for nine years on soil organic carbon and its labile fractions in bulk soil and soil aggregates. CATENA 194, 104739 (2020).Article 
CAS 

Google Scholar 
Liang, Y. et al. Effect of chemical fertilizer and straw-derived organic amendments on continuous maize yield, soil carbon sequestration and soil quality in a Chinese Mollisol. Agric. Ecosyst. Environ. 314, 107403 (2021).Article 
CAS 

Google Scholar 
Liang, C., Kästner, M. & Joergensen, R. G. Microbial necromass on the rise: The growing focus on its role in soil organic matter development. Soil Biol. Biochem. 150, 108000 (2020).Article 
CAS 

Google Scholar 
Sharma, S., Singh, P. & Kumar, S. Responses of soil carbon pools, enzymatic activity, and crop yields to nitrogen and straw incorporation in a rice-wheat cropping system in North-Western India. Front. Sustain. Food Syst. 4, 532704 (2020).Article 

Google Scholar 
Puget, P., Chenu, C. & Balesdent, J. Dynamics of soil organic matter associated with particle–size fractions of water–stable aggregates. Eur. J. Soil Sci. 51, 595–605 (2000).Article 

Google Scholar  More

Finkelman, S., Navarro, S., Rindner, M. & Dias, R. Effect of low pressure on the survival of Trogoderma granarium Everts, Lasioderma serricorne (F.) and Oryzaephilus surinamensis (L.) at 30°C. J. Stored. Prod. Res. 42, 23–30 (2006).Article 

Google Scholar 
Hosseininaveh, V. A., Bandani, A. P., Azmayeshfard, P. S., Hosseinkhani, S. & Kazzazi, M. Digestive proteolytic and amylolytic activities in Trogoderma granarium Everts (Dermestidae: Coleoptera). J. Stored. Prod. Res. 43, 515–522 (2007).Article 
CAS 

Google Scholar 
Burges, H. D. Development of the khapra beetle, Trogoderma granarium, in the lower part of its temperature range. J. Stored. Prod. Res. 44, 32–35 (2008).Article 

Google Scholar 
Hagstrum D. W & Subramanyam, B. Stored-Product Insect Resource (AACC International, 2009).Beal, R. S. Synopsis of the economic species of Trogoderma occurring in the United States with description of a new species (Coleoptera: Dermestidae). Ann. Entomol. Soc. Am. 49, 559–566 (1956).Article 

Google Scholar 
Kerr, J. A. Khapra beetle returns. Pest Control 49(12), 24–25 (1984).
Google Scholar 
Sinha, R. N. & Utida, S. Climatic areas potentially vulnerable to stored product insects in Japan. Appl. Entomol. Zool. 2, 124–132 (1967).Article 

Google Scholar 
Banks, H. J. Distribution and establishment of Trogoderma granarium Everts (Coleoptera: Dermestidae): Climatic and other influences. J. Stored. Prod. Res. 13, 183–202 (1977).Article 

Google Scholar 
Kavallieratos, N. G., Athanassiou, C. G., Guedes, R. N. C., Drempela, J. D. & Boukouvala, M. C. Invader competition with local competitors: Displacement or coexistence among the invasive khapra beetle, Trogoderma granarium Everts (Coleoptera: Dermestidae), and two other major stored-grain beetles?. Front. Plant. Sci. 8, 1837 (2017).Article 
PubMed 
PubMed Central 

Google Scholar 
Lampiri, E., Baliota, G. V., Morrison, W. M., Domingue, M. J. & Athanassiou, C. Comparative population growth of the khapra beetle (Coleoptera: Dermestidae) and the warehouse beetle (Coleoptera: Dermestidae) on wheat and rice. J. Econ. Entomol. 115, 344–352 (2021).Article 

Google Scholar 
Athanassiou, C. G., Phillips, T. W. & Wakil, W. Biology and control of the khapra beetle, Trogoderma granarium, a major quarantine threat to global food security. Ann. Rev. Entomol. 64, 131–148 (2019).Article 
CAS 

Google Scholar 
Stibick, J. New pest response guidelines: khapra beetle. APHIS– PPQ–Emergency and Domestic Programs. (U.S Department of Agriculture, 2009).Myers, S. W. & Hagstrum, D. W. Quarantine, In Stored stored product protection, (ed. Hagstrum D.W. Phillips T.W. & Cuperus G.) 297–304 (Kansas State University, 2012).Day, C. & White, B. Khapra beetle, Trogoderma granarium interceptions and eradications in Australia and around the world. In SARE working papers 1609. (Crawley: School of Agricul. Res. Econ. 2016).Burges, H. D. Diapause, pest status and control of the Khapra beetle. Trogoderma Granar. Everts Ann. Appl. Biol. 50, 614–617 (1962).Article 

Google Scholar 
Nair, K. & Desai, A. The termination of diapause in Trogoderma granarium Everts (Coleoptera, Dermestidae). J. Stored. Prod. Res. 8, 275–290 (1973).Article 

Google Scholar 
Burges, H. D. Studies on the Dermestid beetle Trogoderma granarium Everts—IV. Feeding, growth, and respiration with particular reference to diapause larvae. J. Insect. Physiol. 5, 317–334 (1960).Article 
CAS 

Google Scholar 
Wilches, D., Laird, R. A., Floate, K. & Fields, P. G. A review of diapause and tolerance to extreme temperatures in dermestids (Coleoptera). J. Stored Prod. Res. 68, 50–62 (2016).Article 

Google Scholar 
Vick, K. W., Drummond, P. C. & Coffelt, J. A. Trogoderma inclusum and T. glabrum: Effects of time of day on production of female pheromone, male responsiveness and mating. Ann. Entomol. Soc. Am. 66, 1001–1004 (1973).Article 

Google Scholar 
Partida, G. J. & Strong, R. G. Distribution and relative abundance of Trogoderma spp. in relation to climate zones of California. J. Econ. Entomol. 63, 1553–1560 (1970).Article 

Google Scholar 
Hagstrum, D. W. Seasonal variation of stored wheat environment and insect populations. J. Econ. Entomol. 16, 77–83 (1987).
Google Scholar 
Mullen, M. A. & Arbogast, R. T. Insect succession in a stored-corn ecosystem in southeast Georgia. J. Econ. Entomol. 81, 899–912 (1988).
Google Scholar 
Partida, G. J. & Strong, R. G. Comparative studies on the biologies of six species of Trogoderma: T. inclusum. Ann. Entomol. Soc. Am. 68, 91–103 (1975).Article 

Google Scholar 
Beal, R. S. Biology and taxonomy of the nearctic species of Trogoderma. Univ. Calif. Misc. Publ. Entomol. 10, 35–102 (1954).
Google Scholar 
Castañé, C., Agustí, N., del Estal, P. & Riudavets, J. Survey of Trogoderma spp in Spanish mills and warehouses. J. Stored. Prod. Res. 88, 1061 (2020).Article 

Google Scholar 
Levinson, H. Z. & Mori, K. The pheromone activity of chiral isomers of trogodermal for male khapra beetles. Naturwissenschaften 67, 148–149 (1980).Article 
CAS 

Google Scholar 
Silverstein, R. M. et al. Perception by Trogoderma species of chirality and methyl branching at a site far removed from a functional group in a pheromone component. J. Chem. Ecol. 6, 911–917 (1980).Article 
CAS 

Google Scholar 
Vick, K. W. Effects of interspecific matings of Trogoderma glabrum and T. inclusum on oviposition and re-mating. Ann. Entomol. Soc. Am. 66, 237–239 (1973).Article 
MathSciNet 

Google Scholar 
Drijfhout, S. et al. Catalogue of abrupt shifts in intergovernmental panel on climate change climate models. Proc. Natl. Acad. Sci. USA 112, E5777–E5786 (2015).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Phillips, T. W., Pfannenstiel, L. & Hagstrum, D. Survey of Trogoderma species (Coleoptera: Dermestidae) associated with international trade of dried distiller’s grains and solubles in the USA. Julius-Kühn-Archiv 1, 233–238 (2018).
Google Scholar 
Hadaway, A. The biology of the beetles, Trogoderma granarium Everts and Trogoderma versicolor (Creutz). Bull. Entomol. Res. 46, 781–796 (1956).Article 
CAS 

Google Scholar 
Gorham, J. R. Insect and Mite Pests in Food: An Illustrated Key. Vols. 1 and 2, (U.S Department of Agriculture, 1991).Furui, S., Miyanoshita, A., Imamura, T., Minegishi, Y. & Kokutani, R. Qualitative real-time PCR identification of the khapra beetle, Trogoderma granarium (Coleoptera: Dermestidae). Appl. Entomol. Zool. 54, 101–107 (2019).Article 
CAS 

Google Scholar 
Olson, R. L., Farris, R. E., Barr, N. B. & Cognato, A. I. Molecular identification of Trogoderma granarium (Coleoptera: Dermestidae) using the 16s gene. J Pest Sci 87, 701–710 (2014).Article 

Google Scholar 
Wu, Y. et al. Development of an array of molecular tools for the identification of khapra beetle (Trogoderma granarium), a destructive beetle of stored food products. Sci. Rep. 13, 3327 (2023).Article 
PubMed 
PubMed Central 

Google Scholar 
Lampiri, E., Athanassiou, C. & Arthur, F. H. Population growth and development of the khapra beetle (Coleoptera: Dermestidae), on different sorghum fractions. J. Econ. Entomol. 114, 424–429 (2021).Article 
CAS 
PubMed 

Google Scholar 
Athanassiou, C. G., Kavallieratos, N. G. & Boukouvala, M. C. Population growth of the khapra beetle, Trogoderma granarium Everts (Coleoptera: Dermestidae) on different commodities. J. Stored. Prod. Res. 69, 72–77 (2016).Article 

Google Scholar 
Karnavar, G. K. Mating behaviour and fecundity in Trogoderma granarium (Coleoptera: Dermestidae). J. Stored. Prod. Res. 8, 65–69 (1972).Article 

Google Scholar 
Pray, L. A. & Goodnight, C. J. Genetic variation in inbreeding depression in the red flour beetle Tribolium castaneum. Evolution 49, 176–188 (1995).Article 
PubMed 

Google Scholar 
Barzin, S., Naseri, B., Fathi, S. A. A., Razmjou, J. & Aeinehchi, P. Feeding efficiency and digestive physiology of Trogoderma granarium Everts (Coleoptera: Dermestidae) on different rice cultivars. J. Stored. Prod. Res. 84, 101511 (2019).Article 

Google Scholar 
Naseri, B., Aeinehchi, P. & Ashjerdi, A. R. Nutritional responses and digestive enzymatic profile of Trogoderma granarium Everts (Coleoptera: Dermestidae) on 10 commercial rice cultivars. J. Stored. Prod. Res. 87, 101591 (2020).Article 

Google Scholar 
Sarwar, M. & Sattar, M. Varietals assessment of different wheat varieties for their resistance response to Khapra beetle Trogoderma granarium. Pak. J. Seed. Technol. 1(10), 1–7 (2007).
Google Scholar 
Wilches, D., Laird, R., Floate, K. & Fields, P. Effects of acclimation and diapause on the cold tolerance of Trogoderma granarium. Entomol. Exp. Appl. 165, 169–178 (2017).Article 
CAS 

Google Scholar 
Paini, D. R. & Yemshanov, D. Modelling the arrival of invasive organisms via the international marine shipping network: a Khapra beetle study. PLoS ONE 7(9), e44589 (2012).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Morrison, W. R., Grosdidier, R. F., Arthur, F. H., Myers, S. W. & Domingue, M. J. Attraction, arrestment, and preference by immature Trogoderma variabile and Trogoderma granarium to food and pheromonal stimuli. J. Pest Sci. 93, 135–147 (2020).Article 

Google Scholar 
Arthur, F. H. & Morrison, W. M. Methodology for assessing progeny production and grain damage on commodities treated with insecticides. Agronomy 10(6), 804 (2020).Article 
CAS 

Google Scholar  More

Acropora Biological Review Team. Atlantic Acropora Status Review: Report to National Marine Fisheries Service (Acropora Biological Review Team, 2005).
Google Scholar 
Gardner, T. A., Côté, I. M., Gill, J. A., Grant, A. & Watkinson, A. R. Long-term region-wide declines in Caribbean Corals. Science 301, 958–960 (2003).ADS 
CAS 
PubMed 

Google Scholar 
Jackson, E. J., Donovan, M., Cramer, K. & Lam, V. Status and Trends of Caribbean Coral Reefs: 1970–2012 306 (International Union for the Conservation of Nature, 2012).
Google Scholar 
Schopmeyer, S. A. et al. Regional restoration benchmarks for Acropora cervicornis. Coral Reefs 36, 1047–1057 (2017).ADS 

Google Scholar 
Lirman, D. et al. Propagation of the threatened staghorn coral Acropora cervicornis: Methods to minimize the impacts of fragment collection and maximize production. Coral Reefs 29, 729–735 (2010).ADS 

Google Scholar 
Mercado-Molina, A. E., Ruiz-Diaz, C. P. & Sabat, A. M. Demographics and dynamics of two restored populations of the threatened reef-building coral Acropora cervicornis. J. Nat. Conserv. 24, 17–23 (2015).
Google Scholar 
Young, C., Schopmeyer, S. & Lirman, D. A review of reef restoration and coral propagation using the threatened genus Acropora in the Caribbean and Western Atlantic. Bull. Mar. Sci. 88, 1075–1098 (2012).
Google Scholar 
Carne, L., Kaufman, L. & Scavo, K. Measuring success for Caribbean acroporid restoration: key results from ten years of work in southern Belize. In Proc. 13th International Coral Reef Symposium, Honolulu (Abstract No. 27909) (2016).Ware, M. et al. Survivorship and growth in staghorn coral (Acropora cervicornis) outplanting projects in the Florida Keys National Marine Sanctuary. PLoS ONE 15, e0231817 (2020).CAS 
PubMed 
PubMed Central 

Google Scholar 
Shaver, E. C. et al. A roadmap to integrating resilience into the practice of coral reef restoration. Glob. Change Biol. 28, 4751–4764 (2022).CAS 

Google Scholar 
DeFilippo, L. B. et al. Assessing the potential for demographic restoration and assisted evolution to build climate resilience in coral reefs. Ecol. Appl. 32, e2650 (2022).PubMed 
PubMed Central 

Google Scholar 
Lapointe, B. E., Brewton, R. A., Herren, L. W., Porter, J. W. & Hu, C. Nitrogen enrichment, altered stoichiometry, and coral reef decline at Looe Key, Florida Keys, USA: A 3-decade study. Mar. Biol. 166, 108 (2019).
Google Scholar 
Montenero, K. A. Florida Keys Integrated Ecosystem Assessment Ecosystem Status Report. https://doi.org/10.25923/F7CE-ST38.Palacio-Castro, A. M., Dennison, C. E., Rosales, S. M. & Baker, A. C. Variation in susceptibility among three Caribbean coral species and their algal symbionts indicates the threatened staghorn coral, Acropora cervicornis, is particularly susceptible to elevated nutrients and heat stress. Coral Reefs 40, 1601–1613 (2021).
Google Scholar 
Vega Thurber, R. L. et al. Chronic nutrient enrichment increases prevalence and severity of coral disease and bleaching. Glob. Change Biol. 20, 544–554 (2014).ADS 

Google Scholar 
Zaneveld, J. R. et al. Overfishing and nutrient pollution interact with temperature to disrupt coral reefs down to microbial scales. Nat. Commun. 7, 11833 (2016).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Bruno, J. F. et al. Thermal stress and coral cover as drivers of coral disease outbreaks. PLoS Biol. 5, e124 (2007).PubMed 
PubMed Central 

Google Scholar 
Wiedenmann, J. et al. Nutrient enrichment can increase the susceptibility of reef corals to bleaching. Nat. Clim. Change 3, 160–164 (2012).ADS 

Google Scholar 
Rädecker, N., Pogoreutz, C., Voolstra, C. R., Wiedenmann, J. & Wild, C. Nitrogen cycling in corals: The key to understanding holobiont functioning? Trends Microbiol. 23, 490–497 (2015).PubMed 

Google Scholar 
Shantz, A. A. & Burkepile, D. E. Context-dependent effects of nutrient loading on the coral–algal mutualism. Ecology 95, 1995–2005 (2014).PubMed 

Google Scholar 
Burkepile, D. E. et al. Nitrogen identity drives differential impacts of nutrients on coral bleaching and mortality. Ecosystems 23, 798–811 (2020).CAS 

Google Scholar 
Fabricius, K. E. Effects of terrestrial runoff on the ecology of corals and coral reefs: Review and synthesis. Mar. Pollut. Bull. 50, 125–146 (2005).CAS 
PubMed 

Google Scholar 
Ferrier-Pagès, C., Gattuso, J.-P., Dallot, S. & Jaubert, J. Effect of nutrient enrichment on growth and photosynthesis of the zooxanthellate coral Stylophora pistillata. Coral Reefs 19, 103–113 (2000).
Google Scholar 
Bourne, D. G., Morrow, K. M. & Webster, N. S. Insights into the coral microbiome: Underpinning the health and resilience of reef ecosystems. Annu. Rev. Microbiol. 70, 317–340 (2016).CAS 
PubMed 

Google Scholar 
Krediet, C. J., Ritchie, K. B., Paul, V. J. & Teplitski, M. Coral-associated micro-organisms and their roles in promoting coral health and thwarting diseases. Proc. R. Soc. B Biol. Sci. 280, 20122328 (2013).
Google Scholar 
Mao-Jones, J., Ritchie, K. B., Jones, L. E. & Ellner, S. P. How microbial community composition regulates coral disease development. PLoS Biol. 8, e1000345 (2010).PubMed 
PubMed Central 

Google Scholar 
Zilber-Rosenberg, I. & Rosenberg, E. Role of microorganisms in the evolution of animals and plants: The hologenome theory of evolution. FEMS Microbiol. Rev. 32, 723–735 (2008).CAS 
PubMed 

Google Scholar 
West, A. G. et al. The microbiome in threatened species conservation. Biol. Conserv. 229, 85–98 (2019).
Google Scholar 
Ritchie, K. Regulation of microbial populations by coral surface mucus and mucus-associated bacteria. Mar. Ecol. Prog. Ser. 322, 1–14 (2006).ADS 
CAS 

Google Scholar 
Rohwer, F., Seguritan, V., Azam, F. & Knowlton, N. Diversity and distribution of coral-associated bacteria. Mar. Ecol. Prog. Ser. 243, 1–10 (2002).ADS 

Google Scholar 
Klinges, G., Maher, R. L., Thurber, R. L. V. & Muller, E. M. Parasitic ‘Candidatus aquarickettsia rohweri’ is a marker of disease susceptibility in Acropora cervicornis but is lost during thermal stress. Environ. Microbiol. 22, 5341–5355 (2020).CAS 
PubMed 
PubMed Central 

Google Scholar 
Williams, S. D. et al. Geographically driven differences in microbiomes of Acropora cervicornis originating from different regions of Florida’s Coral Reef. PeerJ 10, e13574 (2022).PubMed 
PubMed Central 

Google Scholar 
Klinges, J. G., Patel, S. H., Duke, W. C., Muller, E. M. & Vega Thurber, R. L. Phosphate enrichment induces increased dominance of the parasite Aquarickettsia in the coral Acropora cervicornis. FEMS Microbiol. Ecol. 98, 013 (2022).
Google Scholar 
Rosales, S. M. et al. Microbiome differences in disease-resistant vs susceptible Acropora corals subjected to disease challenge assays. Sci. Rep. 9, 18279 (2019).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Gignoux-Wolfsohn, S., Precht, W., Peters, E., Gintert, B. & Kaufman, L. Ecology, histopathology, and microbial ecology of a white-band disease outbreak in the threatened staghorn coral Acropora cervicornis. Dis. Aquat. Org. 137, 217–237 (2020).
Google Scholar 
Miller, N., Maneval, P., Manfrino, C., Frazer, T. K. & Meyer, J. L. Spatial distribution of microbial communities among colonies and genotypes in nursery-reared Acropora cervicornis. PeerJ 8, e9635 (2020).PubMed 
PubMed Central 

Google Scholar 
Aguirre, E. G., Million, W. C., Bartels, E., Krediet, C. J. & Kenkel, C. D. Host-specific epibiomes of distinct Acropora cervicornis genotypes persist after field transplantation. Coral Reefs. https://doi.org/10.1007/s00338-022-02218-x (2022).Article 

Google Scholar 
Shaver, E. C. et al. Effects of predation and nutrient enrichment on the success and microbiome of a foundational coral. Ecology 98, 830–839 (2017).PubMed 

Google Scholar 
Muller, E. M., Bartels, E. & Baums, I. B. Bleaching causes loss of disease resistance within the threatened coral species Acropora cervicornis. eLife 7, e35066 (2018).PubMed 
PubMed Central 

Google Scholar 
Miller, M. W. et al. Genotypic variation in disease susceptibility among cultured stocks of Elkhorn and Staghorn corals. PeerJ 7, e6751 (2019).PubMed 
PubMed Central 

Google Scholar 
Sunagawa, S., Woodley, C. M. & Medina, M. Threatened corals provide underexplored microbial habitats. PLoS ONE 5, e9554 (2010).ADS 
PubMed 
PubMed Central 

Google Scholar 
Pantos, O. et al. The bacterial ecology of a plague-like disease affecting the Caribbean coral Montastrea annularis. Environ. Microbiol. 5, 370–382 (2003).CAS 
PubMed 

Google Scholar 
Sheu, S.-Y., Liu, L.-P., Tang, S.-L. & Chen, W.-M. Thalassotalea euphylliae sp. nov., isolated from the torch coral Euphyllia glabrescens. Int. J. Syst. Evol. Microbiol. 66, 5039–5045 (2016).CAS 
PubMed 

Google Scholar 
Nakagawa, T., Iino, T., Suzuki, K.-I. & Harayama, S. Ferrimonas futtsuensis sp. nov. and Ferrimonas kyonanensis sp. nov., selenate-reducing bacteria belonging to the Gammaproteobacteria isolated from Tokyo Bay. Int. J. Syst. Evol. Microbiol. 56, 2639–2645 (2006).CAS 
PubMed 

Google Scholar 
Maher, R. L. et al. Coral microbiomes demonstrate flexibility and resilience through a reduction in community diversity following a thermal stress event. Front. Ecol. Evol. 8, 1 (2020).ADS 

Google Scholar 
Bourne, D., Iida, Y., Uthicke, S. & Smith-Keune, C. Changes in coral-associated microbial communities during a bleaching event. ISME J. 2, 350–363 (2008).CAS 
PubMed 

Google Scholar 
Ziegler, M. et al. Coral bacterial community structure responds to environmental change in a host-specific manner. Nat. Commun. 10, 3092 (2019).ADS 
PubMed 
PubMed Central 

Google Scholar 
McDevitt-Irwin, J. M. et al. Responses of coral-associated bacterial communities to local and global stressors. Front. Mar. Sci. 4, 262 (2017).
Google Scholar 
Klinges, J. G. et al. Phylogenetic, genomic, and biogeographic characterization of a novel and ubiquitous marine invertebrate-associated Rickettsiales parasite, Candidatus aquarickettsia rohweri, gen. nov., sp. nov. ISME J. 13, 2938–2953 (2019).PubMed 
PubMed Central 

Google Scholar 
Muscatine, L., Falkowski, P. G., Dubinsky, Z., Cook, P. A. & McCloskey, L. R. The effect of external nutrient resources on the population dynamics of zooxanthellae in a reef coral. Proc. R. Soc. Lond. B 236, 311–324 (1989).ADS 

Google Scholar 
Waite, D. W. et al. Comparative genomic analysis of the class Epsilonproteobacteria and proposed reclassification to Epsilonbacteraeota (phyl. Nov.). Front. Microbiol. 8, 682 (2017).PubMed 
PubMed Central 

Google Scholar 
Waite, D. W. et al. Addendum: Comparative genomic analysis of the class Epsilonproteobacteria and proposed reclassification to Epsilonbacteraeota (phyl. Nov.). Front. Microbiol. 9, 772 (2018).PubMed 
PubMed Central 

Google Scholar 
Rosales, S. M. et al. Bacterial metabolic potential and micro-eukaryotes enriched in stony coral tissue loss disease lesions. Front. Mar. Sci. 8, 776859 (2022).
Google Scholar 
Ricci, F. et al. Beneath the surface: Community assembly and functions of the coral skeleton microbiome. Microbiome 7, 159 (2019).PubMed 
PubMed Central 

Google Scholar 
Yang, S.-H. et al. Metagenomic, phylogenetic, and functional characterization of predominant endolithic green sulfur bacteria in the coral Isopora palifera. Microbiome 7, 3 (2019).PubMed 
PubMed Central 

Google Scholar 
Cai, L. et al. Metagenomic analysis reveals a green sulfur bacterium as a potential coral symbiont. Sci. Rep. 7, 9320 (2017).ADS 
PubMed 
PubMed Central 

Google Scholar 
Allgeier, J. E., Burkepile, D. E. & Layman, C. A. Animal pee in the sea: Consumer-mediated nutrient dynamics in the world’s changing oceans. Glob. Change Biol. 23, 2166–2178 (2017).ADS 

Google Scholar 
Hughes, D. J. et al. Coral reef survival under accelerating ocean deoxygenation. Nat. Clim. Change 10, 296–307 (2020).ADS 
CAS 

Google Scholar 
Miura, N. et al. Ruegeria sp. strains isolated from the reef-building coral Galaxea fascicularis inhibit growth of the temperature-dependent pathogen Vibrio coralliilyticus. Mar. Biotechnol. 21, 1–8 (2019).CAS 

Google Scholar 
Bruno, J. F., Petes, L. E., Harvell, C. D. & Hettinger, A. Nutrient enrichment can increase the severity of coral diseases. Ecol. Lett. 6, 1056–1061 (2003).
Google Scholar 
Ezzat, L. et al. Thermal stress interacts with surgeonfish feces to increase coral susceptibility to dysbiosis and reduce tissue regeneration. Front. Microbiol. 12, 620458 (2021).PubMed 
PubMed Central 

Google Scholar 
Gajigan, A. P., Diaz, L. A. & Conaco, C. Resilience of the prokaryotic microbial community of Acropora digitifera to elevated temperature. Microbiol. Open 6, e00478 (2017).
Google Scholar 
MacKnight, N. J. et al. Microbial dysbiosis reflects disease resistance in diverse coral species. Commun. Biol. 4, 679 (2021).PubMed 
PubMed Central 

Google Scholar 
Palacio-Castro, A. M., Rosales, S. M., Dennison, C. E. & Baker, A. C. Microbiome signatures in Acropora cervicornis are associated with genotypic resistance to elevated nutrients and heat stress. Coral Reefs 41, 1389–1403 (2022).
Google Scholar 
Vollmer, S. V. & Kline, D. I. Natural disease resistance in threatened staghorn corals. PLoS ONE 3, e3718 (2008).ADS 
PubMed 
PubMed Central 

Google Scholar 
Hughes, T. P. et al. Spatial and temporal patterns of mass bleaching of corals in the Anthropocene. Science 359, 80–83 (2018).ADS 
CAS 
PubMed 

Google Scholar 
Parkinson, J. E. et al. Extensive transcriptional variation poses a challenge to thermal stress biomarker development for endangered corals. Mol. Ecol. 27, 1103–1119 (2018).CAS 
PubMed 

Google Scholar 
Siebeck, U. E., Logan, D. & Marshall, N. J. CoralWatch—A flexible coral bleaching monitoring tool for you and your group. In Proc. 11th Int. Coral Reef Symp. Ft Lauderdale, Florida, 7–11 July, Vol. 1392, 5 (2008).Parada, A. E., Needham, D. M. & Fuhrman, J. A. Every base matters: Assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. Environ. Microbiol. 18, 1403–1414 (2016).CAS 
PubMed 

Google Scholar 
Apprill, A., McNally, S., Parsons, R. & Weber, L. Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton. Aquat. Microb. Ecol. 75, 129–137 (2015).
Google Scholar 
Messyasz, A., Maher, R. L., Meiling, S. S. & Thurber, R. V. Nutrient enrichment predominantly affects low diversity microbiomes in a marine trophic symbiosis between algal farming fish and corals. Microorganisms 9, 1873 (2021).CAS 
PubMed 
PubMed Central 

Google Scholar 
Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. J. 17, 10–12 (2011).
Google Scholar 
Callahan, B. J. et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).CAS 
PubMed 
PubMed Central 

Google Scholar 
McMurdie, P. J. & Holmes, S. phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 8, e61217 (2013).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Magurran, A. E. Ecological Diversity and Its Measurement (Princeton University Press, 1988).
Google Scholar 
Lahti, L. & Shetty, S. Microbiome R Package.Gloor, G. B., Macklaim, J. M., Pawlowsky-Glahn, V. & Egozcue, J. J. Microbiome datasets are compositional: And this is not optional. Front. Microbiol. 8, 2224 (2017).PubMed 
PubMed Central 

Google Scholar 
Anderson, M. J. A new method for non-parametric multivariate analysis of variance. Austral Ecol. 26, 32–46 (2001).
Google Scholar 
Oksanen, J. et al. vegan: Community Ecology Package (2019).Martinez Arbizu, P. pairwiseAdonis: Pairwise multilevel comparison using adonis. R Package Version 0.0.1 (2017).Anderson, M. J. Distance-based tests for homogeneity of multivariate dispersions. Biometrics 62, 245–253 (2006).MathSciNet 
PubMed 
MATH 

Google Scholar 
Kaul, A., Mandal, S., Davidov, O. & Peddada, S. D. Analysis of microbiome data in the presence of excess zeros. Front. Microbiol. 8, 2114 (2017).PubMed 
PubMed Central 

Google Scholar  More

Mounier, A. et al. Deciphering African late middle Pleistocene hominin diversity and the origin of our species. Nat. Commun. https://doi.org/10.1038/s41467-019-11213-w (2019).Schlebusch, C. M. et al. Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago. Science 358, 652–655 (2017).CAS 
PubMed 

Google Scholar 
Lombard, M. et al. Ancient human DNA: how sequencing the genome of a boy from Ballito Bay changed human history. S Afr. J. Sci. 114, 1–3 (2018).
Google Scholar 
Grün, R. et al. Direct dating of Florisbad hominid. Nature 382, 500–501 (1996).PubMed 

Google Scholar 
Grine, F. et al. The Middle Stone Age human fossil record from Klasies River Main Site. J. Hum. Evol. 103, 53–78 (2017).PubMed 

Google Scholar 
Henshilwood, C. S. et al. A 100,000-year-old ochre-processing workshop at Blombos Cave, South Africa. Science 33, 219–222 (2011).
Google Scholar 
Lombard, M. et al. Four-field co-evolutionary model for human cognition: variation in the Middle Stone Age/Middle Palaeolithic. J. Archeol. Method Theory 28, 142–177 (2021).
Google Scholar 
Wadley, L. What stimulated rapid, cumulative innovation after 100,000 years ago? J. Archeol. Method Theory 28, 120–141 (2021).
Google Scholar 
Tylen, K. et al. The evolution of early symbolic behavior in Homo sapiens. Proc. Natl Acad. Sci. USA 117, 4578–4584 (2020).CAS 
PubMed 
PubMed Central 

Google Scholar 
Rifkin, R. F. et al. Ancient oncogenesis, infection, and human evolution. Evol. Appl. https://doi.org/10.1111/eva.12497 (2017).Pittman, K. J. et al. The legacy of past pandemics: common human mutations that protect against infectious disease. PLoS Pathog. 12, e1005680 (2016).PubMed 
PubMed Central 

Google Scholar 
Andam, C. P. et al. Microbial genomics of ancient plagues and outbreaks. Trends Microbiol. 24, 978–990 (2016).CAS 
PubMed 

Google Scholar 
Houldcroft, C. J. et al. Migrating microbes: what pathogens can tell us about population movements and human evolution. Ann. Hum. Biol. 44, 397–407 (2017).PubMed 

Google Scholar 
Reyes-Centeno, H. et al. Testing modern human out-of-Africa dispersal models using dental nonmetric data. Curr. Anthropol. 58, 406–417 (2017).
Google Scholar 
Pimenoff, V. N. et al. The role of aDNA in understanding the co-evolutionary patterns of human sexually transmitted infections. Genes https://doi.org/10.3390/genes9070317 (2018).Ferwerda, B. et al. Functional consequences of Toll-like Receptor 4 polymorphisms. Mol. Med. 14, 346–352 (2008).CAS 
PubMed 
PubMed Central 

Google Scholar 
Tanabe, K. et al. Plasmodium falciparum accompanied the human expansion out of Africa. Curr. Biol. 20, 1283–1289 (2010).CAS 
PubMed 

Google Scholar 
Linz, B. et al. An African origin for the intimate association between humans and Helicobacter pylori. Nature 445, 915–918 (2007).PubMed 
PubMed Central 

Google Scholar 
Nédélec, Y. et al. Genetic ancestry and natural selection drive population differences in immune responses to pathogens. Cell 167, 657–669 (2016).PubMed 

Google Scholar 
Owers, K. A. et al. Adaptation to infectious disease exposure in indigenous Southern African populations. Proc. Biol. Sci. https://doi.org/10.1098/rspb.2017.0226 (2017).Schlebusch, C. M. et al. Khoe-San genomes reveal unique variation and confirm the deepest population divergence in Homo sapiens. Mol. Biol. Evol. https://doi.org/10.1093/molbev/msaa140 (2020).Kessler, S. E. et al. Selection to outsmart the germs: the evolution of disease recognition and social cognition. J. Hum. Evol. 108, 92–109 (2017).PubMed 

Google Scholar 
Thornhill, R. et al. The parasite-stress theory of sociality, the behavioral immune system, and human social and cognitive uniqueness. Evol. Behav. Sci. 8, 257–264 (2014).
Google Scholar 
Gurven, M. et al. Longevity among hunter‐gatherers: a cross‐cultural examination. Popul Dev. Rev. 33, 321–365 (2007).
Google Scholar 
Pfeiffer, S. et al. The people behind the samples: biographical features of past hunter-gatherers from KwaZulu-Natal who yielded aDNA. Int. J. Paleopathol. 24, 158–164 (2019).PubMed 

Google Scholar 
Schriefer, M. E. et al. Identification of a novel rickettsial infection in a patient diagnosed with murine typhus. J. Clin. Microbiol. 32, 949–954 (1994).CAS 
PubMed 
PubMed Central 

Google Scholar 
Pages, F. et al. The past and present threat of vector-borne diseases in deployed troops. Clin. Microbiol. Infect. 16, 209–224 (2010).CAS 
PubMed 

Google Scholar 
Wood, D. E. et al. Improved metagenomic analysis with Kraken 2. Genome Biol. https://doi.org/10.1186/s13059-019-1891-0 (2019).Jónsson, H. et al. mapDamage 2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics 29, 1682–1684 (2013).PubMed 
PubMed Central 

Google Scholar 
Gillespie, J. J. et al. Genomic diversification in strains of Rickettsia felis isolated from different arthropods. Genome Biol. Evol. 7, 35–56 (2015).CAS 

Google Scholar 
Cardwell, M. M. et al. The Sca2 autotransporter protein from Rickettsia conorii is sufficient to mediate adherence to and invasion of cultured mammalian cells. Infect. Immun. 77, 5272–5280 (2009).CAS 
PubMed 
PubMed Central 

Google Scholar 
Kay, G. L. et al. Recovery of a Medieval Brucella melitensis genome using shotgun metagenomics. mBio. https://doi.org/10.1128/mBio.01337-14 (2014).Schuenemann, V. J. et al. Genome-wide comparison of medieval and modern Mycobacterium leprae. Science 341, 179–183 (2013).CAS 
PubMed 

Google Scholar 
Müller, R. et al. Genotyping of ancient Mycobacterium tuberculosis strains reveals historic genetic diversity. Proc. Biol. Sci. https://doi.org/10.1098/rspb.2013.3236 (2014).Rasmussen, S. et al. Early divergent strains of Yersinia pestis in Eurasia 5,000 years ago. Cell 163, 571–582 (2015).CAS 
PubMed 
PubMed Central 

Google Scholar 
Vågene, A. J. et al. Salmonella enterica genomes from victims of a major sixteenth-century epidemic in Mexico. Nat. Ecol. Evol. 2, 520–528 (2018).PubMed 

Google Scholar 
Guellil, M. et al. Genomic blueprint of a relapsing fever pathogen in 15th century Scandinavia. Proc. Natl Acad. Sci. USA 115, 10422–10427 (2018).CAS 
PubMed 
PubMed Central 

Google Scholar 
Patterson Ross, Z. et al. The paradox of HBV evolution as revealed from a 16th century mummy. PLoS Pathog. https://doi.org/10.1371/journal.ppat.1006750 (2015).Marciniak, S. et al. Plasmodium falciparum malaria in 1st-2nd century CE southern Italy. Curr. Biol. 26, 1220–1222 (2016).
Google Scholar 
Margaryan, A. et al. Ancient pathogen DNA in human teeth and petrous bones. Ecol. Evol. https://doi.org/10.1002/ece3.3924 (2018).Zhou, Z. et al. Pan-genome analysis of ancient and modern Salmonella enterica demonstrates genomic stability of the invasive Para C lineage for millennia. Curr. Biol. 28, 2420–2428 (2018).CAS 
PubMed 
PubMed Central 

Google Scholar 
Williams, K. M. Update on bone health in paediatric chronic disease. Endocrinol. Metab. Clin. North Am. https://doi.org/10.1016/j.ecl.2016.01.009 (2016).Latham, K.E. et al. DNA recovery and analysis from skeletal material in modern forensic contexts. Forensic Sci. Res. https://doi.org/10.1080/20961790.2018.1515594 (2019).Briggs, H. M. et al. Diagnosis and management of tickborne Rickettsial diseases: rocky mountain spotted fever and other spotted fever group Rickettsioses, Ehrlichioses, and Anaplasmosis – United States. MMWR Recomm. Rep. 65, 1–44 (2016).
Google Scholar 
Jonker, F. A. M. et al. Anaemia, iron deficiency and susceptibility to infection in children in sub‐Saharan Africa, guideline dilemmas. Br. J. Haematol. https://doi.org/10.1111/bjh.14593. (2017).Key, F. M. et al. Emergence of human-adapted Salmonella enterica is linked to the Neolithization process. Nat. Ecol. Evol. 4, 324–333 (2020).
Google Scholar 
Angelakis, E. et al. Rickettsia felis: the complex journey of an emergent human pathogen. Trends Parasitol. https://doi.org/10.1016/j.pt.2016.04.009 (2016).Legendre, K. P. et al. Rickettsia felis: A review of transmission mechanisms of an emerging pathogen. Trop. Med. Infect. Dis. https://doi.org/10.3390/tropicalmed2040064 (2017).Mediannikov, O. et al. Common epidemiology of Rickettsia felis infection and malaria, Africa. Emerg. Infect. Dis. https://doi.org/10.3201/eid1911.130361 (2014).Gonçalves, B. P. et al. Examining the human infectious reservoir for Plasmodium falciparum malaria in areas of differing transmission intensity. Nat. Commun. https://doi.org/10.1038/s41467-017-01270-4 (2017).Snowden, J. et al. Rickettsia rickettsiae (Rocky Mountain Spotted Fever). StatPearls Publishing, available from https://www.ncbi.nlm.nih.gov/books/NBK430881/ (2017).Azad, A. A. Pathogenic Rickettsiae as bioterrorism agents. Ann. N. Y Acad. Sci. 990, 734–738 (2007).
Google Scholar 
Oliveira, R. P. et al. Rickettsia felis in Ctenocephalides spp. fleas, Brazil. Emerg. Infect. Dis. https://doi.org/10.3201/eid0803.010301 (2002).Parola, P. et al. Rickettsia felis: The next mosquito-borne outbreak? Lancet Infect. Dis. https://doi.org/10.1016/S1473-3099(16)30331-0 (2016).Wadley, L. Legacies from the Later Stone Age. S Afr Archaeol Bull. Goodwin Ser. 6, 42–53 (1989).
Google Scholar 
Henn, B. M. et al. The great human expansion. Proc. Natl Acad. Sci. USA 109, 17758–17764 (2012).CAS 
PubMed 
PubMed Central 

Google Scholar 
Yang, D. Y. et al. Technical note: improved DNA extraction from ancient bones using silica-based spin columns. Am. J. Phys. Anthropol. 105, 539–543 (1998).CAS 
PubMed 

Google Scholar 
Malmström, E. M. et al. More on contamination: the use of asymmetric molecular behavior to identify authentic ancient human DNA. Mol. Biol. Evol. 24, 998–1004 (2007).PubMed 

Google Scholar 
Dabney, J. et al. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc. Natl Acad. Sci. USA 110, 15758–15763 (2013).CAS 
PubMed 
PubMed Central 

Google Scholar 
Meyer, M. et al. Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harbor Protoc. https://doi.org/10.1101/pdb.prot5448 (2010).Li, H. et al. Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics 26, 589–595 (2010).PubMed 
PubMed Central 

Google Scholar 
Briggs, A. W. et al. Patterns of damage in genomic DNA sequences from a Neandertal. Proc. Natl Acad. Sci. USA 104, 14616–14621 (2007).CAS 
PubMed 
PubMed Central 

Google Scholar 
Borry, M. et al. PyDamage: automated ancient damage identification and estimation for contigs in ancient DNA de novo assembly. PeerJ. https://doi.org/10.7717/peerj.11845 (2021).Schubert, M. et al. AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Res. https://doi.org/10.1186/s13104-016-1900-2 (2016).Langmead, B. et al. Fast gapped-read alignment with Bowtie 2. Nat. Methods. https://doi.org/10.1038/nmeth.1923 (2012).Bankevich, A. et al. SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. https://doi.org/10.1089/cmb.2012.0021 (2012).Jain, C. et al. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun. https://doi.org/10.1038/s41467-018-07641-9 (2018).Gardner, S. H. et al. kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome. Bioinformatics. https://doi.org/10.1093/bioinformatics/btv271 (2015).Contreras-Moreira, B. et al. GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis. Appl. Environ. Microbiol. https://doi.org/10.1128/AEM.02411-13 (2013).Krzywinski, M. et al. Circos: an information aesthetic for comparative genomics. Genome Res. https://doi.org/10.1101/gr.092759.109 (2009).Parks, D. H. et al. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes Genome Res. https://doi.org/10.1101/gr.186072.114 (2015).Suyama, M. et al. PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res. 34, W609–W612 (2006).CAS 
PubMed 
PubMed Central 

Google Scholar 
Dereeper, A. et al. Phylogeny. fr: Robust phylogenetic analysis for the non-specialist. Nucleic Acids Res. https://doi.org/10.1093/nar/gkn180 (2008).Nguyen, L. T. et al. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. https://doi.org/10.1093/molbev/msu300 (2015).Hoang, D. T. et al. UFBoot2: improving the ultrafast bootstrap approximation. Mol. Biol. Evol. https://doi.org/10.1093/molbev/msx281 (2018).Kalyaanamoorthy, S. et al. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat. Methods. https://doi.org/10.1038/nmeth.4285 (2017).Price, M. N. et al. FastTree 2–approximately maximum-likelihood trees for large alignments. PLoS One. https://doi.org/10.1371/journal.pone.0009490 (2010).Stamatakis, A. RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. https://doi.org/10.1093/bioinformatics/btl446 (2006).Kumar, S. et al. MEGA-CC: Computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis. Bioinformatics. https://doi.org/10.1093/bioinformatics/bts507 (2012).Shimodaira, H. An approximately unbiased test of phylogenetic tree selection. Syst. Biol. https://doi.org/10.1080/10635150290069913 (2002).Olm, M. R. et al. dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. ISME J. https://doi.org/10.1038/ismej.2017.126 (2017).Posada, D. jModelTest: phylogenetic model averaging. Mol. Biol. Evol. 7, 1253–1256 (2008).
Google Scholar 
Letunic, I. et al. Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 23, 127–128 (2007).CAS 
PubMed 

Google Scholar  More