{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T08:30:09Z","timestamp":1772181009479,"version":"3.50.1"},"reference-count":150,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,1,16]],"date-time":"2025-01-16T00:00:00Z","timestamp":1736985600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2025,1,16]],"date-time":"2025-01-16T00:00:00Z","timestamp":1736985600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Microbiome"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Seawater microbes (bacteria and archaea) play essential roles in coral reefs by facilitating nutrient cycling, energy transfer, and overall reef ecosystem functioning. However, environmental disturbances such as degraded water quality and marine heatwaves, can impact these vital functions as seawater microbial communities experience notable shifts in composition and function when exposed to stressors. This sensitivity highlights the potential of seawater microbes to be used as indicators of reef health. Microbial indicator analysis has centered around measuring the taxonomic composition of seawater microbial communities, but this can obscure heterogeneity of gene content between taxonomically similar microbes, and thus, microbial functional genes have been hypothesized to have more scope for predictive potential, though empirical validation for this hypothesis is still pending. Using a metagenomics study framework, we establish a functional baseline of seawater microbiomes across offshore Great Barrier Reef (GBR) sites to compare the diagnostic value between taxonomic and functional information in inferring continuous physico-chemical metrics in the surrounding reef.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Integrating gene-centric metagenomics analyses with 17 physico-chemical variables (temperature, salinity, and particulate and dissolved nutrients) across 48 reefs revealed that associations between microbial functions and environmental parameters were twice as stable compared to taxonomy-environment associations. Distinct seasonal variations in surface water chemistry were observed, with nutrient concentrations up to threefold higher during austral summer, explained by enhanced production of particulate organic matter (POM) by photoautotrophic picocyanobacteria, primarily\n                      <jats:italic>Synechococcus<\/jats:italic>\n                      . In contrast, nutrient levels were lower in winter, and POM production was also attributed to\n                      <jats:italic>Prochlorococcus<\/jats:italic>\n                      . Additionally, heterotrophic microbes (e.g.,\n                      <jats:italic>Rhodospirillaceae<\/jats:italic>\n                      ,\n                      <jats:italic>Burkholderiaceae<\/jats:italic>\n                      ,\n                      <jats:italic>Flavobacteriaceae<\/jats:italic>\n                      , and\n                      <jats:italic>Rhodobacteraceae<\/jats:italic>\n                      ) were enriched in reefs with elevated dissolved organic carbon (DOC) and phytoplankton-derived POM, encoding functional genes related to membrane transport, sugar utilization, and energy metabolism. These microbes likely contribute to the coral reef microbial loop by capturing and recycling nutrients derived from\n                      <jats:italic>Synechococcus<\/jats:italic>\n                      and\n                      <jats:italic>Prochlorococcus<\/jats:italic>\n                      , ultimately transferring nutrients from picocyanobacterial primary producers to higher trophic levels.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>This study reveals that functional information in reef-associated seawater microbes more\u00a0robustly associates with physico-chemical variables than taxonomic data, highlighting the importance of incorporating microbial function in reef monitoring initiatives. Our integrative approach to mine for stable seawater microbial biomarkers can be expanded to include additional continuous metrics of reef health (e.g., benthic cover of corals and macroalgae, fish counts\/biomass) and may be applicable to other large-scale reef metagenomics datasets beyond the GBR.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s40168-024-01972-0","type":"journal-article","created":{"date-parts":[[2025,1,16]],"date-time":"2025-01-16T00:19:41Z","timestamp":1736986781000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Gene content of seawater microbes is a strong predictor of water chemistry across the Great Barrier Reef"],"prefix":"10.1186","volume":"13","author":[{"given":"Marko","family":"Terzin","sequence":"first","affiliation":[]},{"given":"Steven J.","family":"Robbins","sequence":"additional","affiliation":[]},{"given":"Sara C.","family":"Bell","sequence":"additional","affiliation":[]},{"given":"Kim-Anh","family":"L\u00ea Cao","sequence":"additional","affiliation":[]},{"given":"Renee K.","family":"Gruber","sequence":"additional","affiliation":[]},{"given":"Pedro R.","family":"Frade","sequence":"additional","affiliation":[]},{"given":"Nicole S.","family":"Webster","sequence":"additional","affiliation":[]},{"given":"Yun Kit","family":"Yeoh","sequence":"additional","affiliation":[]},{"given":"David G.","family":"Bourne","sequence":"additional","affiliation":[]},{"given":"Patrick W.","family":"Laffy","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2025,1,16]]},"reference":[{"key":"1972_CR1","doi-asserted-by":"publisher","first-page":"17995","DOI":"10.1073\/pnas.1208909109","volume":"109","author":"G De\u2019ath","year":"2012","unstructured":"De\u2019ath G, Fabricius KE, Sweatman H, Puotinen M. The 27-year decline of coral cover on the Great Barrier Reef and its causes. Proc Natl Acad Sci U S A. 2012;109:17995\u20139.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"1972_CR2","doi-asserted-by":"crossref","unstructured":"Hoegh-Guldberg O, Poloczanska ES, Skirving W, Dove S. Coral reef ecosystems under climate change and ocean acidification. Front Marine Sci. 2017;4 [Cited 2023 May 30]. Available from: https:\/\/www.frontiersin.org\/articles\/10.3389\/fmars..","DOI":"10.3389\/fmars.2017.00158"},{"key":"1972_CR3","doi-asserted-by":"publisher","first-page":"82","DOI":"10.1038\/nature22901","volume":"546","author":"TP Hughes","year":"2017","unstructured":"Hughes TP, Barnes ML, Bellwood DR, Cinner JE, Cumming GS, Jackson JBC, et al. Coral reefs in the Anthropocene. Nature. 2017;546:82\u201390.","journal-title":"Nature"},{"key":"1972_CR4","doi-asserted-by":"crossref","unstructured":"Souter D, Planes S, Wicquart J, Logan M, Obura D, Staub F, editors. Status of coral reefs of the world: 2020 report.\u00a02021. https:\/\/gcrmn.net\/wpcontent\/uploads\/2023\/04\/GCRMN_Souter_et_al_2021_Status_of_Coral_Reefs_of_the_World_2020_V1.pdf.","DOI":"10.59387\/WOTJ9184"},{"key":"1972_CR5","doi-asserted-by":"publisher","first-page":"1278","DOI":"10.1016\/j.oneear.2021.08.016","volume":"4","author":"TD Eddy","year":"2021","unstructured":"Eddy TD, Lam VWY, Reygondeau G, Cisneros-Montemayor AM, Greer K, Palomares MLD, et al. Global decline in capacity of coral reefs to provide ecosystem services. One Earth. 2021;4:1278\u201385.","journal-title":"One Earth"},{"key":"1972_CR6","doi-asserted-by":"publisher","first-page":"589","DOI":"10.1007\/s00338-009-0512-x","volume":"28","author":"TF Cooper","year":"2009","unstructured":"Cooper TF, Gilmour JP, Fabricius KE. Bioindicators of changes in water quality on coral reefs: review and recommendations for monitoring programmes. Coral Reefs. 2009;28:589\u2013606.","journal-title":"Coral Reefs"},{"key":"1972_CR7","doi-asserted-by":"publisher","first-page":"320","DOI":"10.1016\/j.marpolbul.2011.09.004","volume":"65","author":"KE Fabricius","year":"2012","unstructured":"Fabricius KE, Cooper TF, Humphrey C, Uthicke S, De\u2019ath G, Davidson J, et al. A bioindicator system for water quality on inshore coral reefs of the Great Barrier Reef. Marine Pollution Bulletin. 2012;65:320\u201332.","journal-title":"Marine Pollution Bulletin"},{"key":"1972_CR8","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1007\/s00227-017-3097-x","volume":"164","author":"B Glasl","year":"2017","unstructured":"Glasl B, Webster NS, Bourne DG. Microbial indicators as a diagnostic tool for assessing water quality and climate stress in coral reef ecosystems. Mar Biol. 2017;164:91.","journal-title":"Mar Biol"},{"key":"1972_CR9","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1007\/13836_2018_29","volume-title":"Population Genomics: Marine Organisms","author":"S Roitman","year":"2018","unstructured":"Roitman S, Joseph Pollock F, Medina M. Coral microbiomes as bioindicators of reef health. In: Oleksiak MF, Rajora OP, editors. Population Genomics: Marine Organisms. Cham: Springer International Publishing; 2018. p. 39\u201357. https:\/\/doi.org\/10.1007\/13836_2018_29."},{"key":"1972_CR10","doi-asserted-by":"publisher","first-page":"5117","DOI":"10.1021\/acs.est.2c05369","volume":"57","author":"A Apprill","year":"2023","unstructured":"Apprill A, Girdhar Y, Mooney TA, Hansel CM, Long MH, Liu Y, et al. Toward a new era of coral reef monitoring. Environ Sci Technol. 2023;57:5117.","journal-title":"Environ Sci Technol"},{"key":"1972_CR11","doi-asserted-by":"publisher","first-page":"94","DOI":"10.1186\/s40168-019-0705-7","volume":"7","author":"B Glasl","year":"2019","unstructured":"Glasl B, Bourne DG, Frade PR, Thomas T, Schaffelke B, Webster NS. Microbial indicators of environmental perturbations in coral reef ecosystems. Microbiome. 2019;7:94.","journal-title":"Microbiome"},{"key":"1972_CR12","doi-asserted-by":"publisher","first-page":"100972","DOI":"10.1016\/j.isci.2020.100972","volume":"23","author":"I Vanwonterghem","year":"2020","unstructured":"Vanwonterghem I, Webster NS. Coral reef microorganisms in a changing climate. iScience. 2020;23:100972.","journal-title":"iScience"},{"key":"1972_CR13","doi-asserted-by":"publisher","DOI":"10.1111\/1462-2920.16610","volume":"26","author":"CC Becker","year":"2024","unstructured":"Becker CC, Weber L, Llopiz JK, Mooney TA, Apprill A. Microorganisms uniquely capture and predict stony coral tissue loss disease and hurricane disturbance impacts on US Virgin Island reefs. Environ Microbiol. 2024;26: e16610.","journal-title":"Environ Microbiol"},{"key":"1972_CR14","doi-asserted-by":"publisher","first-page":"431","DOI":"10.1146\/annurev-marine-042121-080917","volume":"15","author":"CE Nelson","year":"2023","unstructured":"Nelson CE, Wegley Kelly L, Haas AF. Microbial interactions with dissolved organic matter are central to coral reef ecosystem function and resilience. Annu Rev Mar Sci. 2023;15:431\u201360.","journal-title":"Annu Rev Mar Sci"},{"key":"1972_CR15","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1186\/s40793-023-00543-4","volume":"19","author":"M Terzin","year":"2024","unstructured":"Terzin M, Laffy PW, Robbins S, Yeoh YK, Frade PR, Glasl B, et al. The road forward to incorporate seawater microbes in predictive reef monitoring. Environmental Microbiome. 2024;19:5.","journal-title":"Environmental Microbiome"},{"key":"1972_CR16","doi-asserted-by":"crossref","unstructured":"Amin AKMR, Feng G, Al-saari N, Meirelles PM, Yamazaki Y, Mino S, et al. The first temporal and spatial assessment of Vibrio diversity of the surrounding seawater of coral reefs in Ishigaki, Japan. Front Microbiol. 2016;7. Available from: https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2016.01185.\u00a0[Cited 2023 Mar 7].","DOI":"10.3389\/fmicb.2016.01185"},{"key":"1972_CR17","doi-asserted-by":"publisher","first-page":"789","DOI":"10.1038\/s41467-017-00912-x","volume":"8","author":"T Bush","year":"2017","unstructured":"Bush T, Diao M, Allen RJ, Sinnige R, Muyzer G, Huisman J. Oxic-anoxic regime shifts mediated by feedbacks between biogeochemical processes and microbial community dynamics. Nat Commun. 2017;8:789.","journal-title":"Nat Commun"},{"key":"1972_CR18","doi-asserted-by":"publisher","first-page":"104","DOI":"10.1186\/s40168-019-0714-6","volume":"7","author":"J Chen","year":"2019","unstructured":"Chen J, McIlroy SE, Archana A, Baker DM, Panagiotou G. A pollution gradient contributes to the taxonomic, functional, and resistome diversity of microbial communities in marine sediments. Microbiome. 2019;7:104.","journal-title":"Microbiome"},{"key":"1972_CR19","doi-asserted-by":"publisher","first-page":"442","DOI":"10.1038\/s42003-020-01166-y","volume":"3","author":"PR Frade","year":"2020","unstructured":"Frade PR, Glasl B, Matthews SA, Mellin C, Serr\u00e3o EA, Wolfe K, et al. Spatial patterns of microbial communities across surface waters of the Great Barrier Reef. Commun Biol. 2020;3:442.","journal-title":"Commun Biol"},{"key":"1972_CR20","doi-asserted-by":"publisher","first-page":"22133","DOI":"10.1038\/s41598-020-79152-x","volume":"10","author":"KD Raj","year":"2020","unstructured":"Raj KD, Mathews G, Obura DO, Laju RL, Bharath MS, Kumar PD, et al. Low oxygen levels caused by Noctiluca scintillans bloom kills corals in Gulf of Mannar, India. Sci Rep. 2020;10:22133.","journal-title":"Sci Rep"},{"key":"1972_CR21","doi-asserted-by":"crossref","unstructured":"Wambua S, Gourl\u00e9 H, de Villiers EP, Karlsson-Lindsj\u00f6 O, Wambiji N, Macdonald A, et al. Cross-sectional variations in structure and function of coral reef microbiome with local anthropogenic impacts on the Kenyan Coast of the Indian Ocean. Front Microbiol. 2021;12. Available from: https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2021.673128.","DOI":"10.3389\/fmicb.2021.673128"},{"key":"1972_CR22","doi-asserted-by":"publisher","first-page":"3039","DOI":"10.1038\/s41467-023-38500-x","volume":"14","author":"PE Galand","year":"2023","unstructured":"Galand PE, Ruscheweyh H-J, Salazar G, Hochart C, Henry N, Hume BCC, et al. Diversity of the Pacific Ocean coral reef microbiome. Nat Commun. 2023;14:3039.","journal-title":"Nat Commun"},{"key":"1972_CR23","doi-asserted-by":"publisher","first-page":"1272","DOI":"10.1126\/science.aaf4507","volume":"353","author":"S Louca","year":"2016","unstructured":"Louca S, Parfrey LW, Doebeli M. Decoupling function and taxonomy in the global ocean microbiome. Science. 2016;353:1272\u20137.","journal-title":"Science"},{"key":"1972_CR24","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s42003-020-0856-x","volume":"3","author":"J Alneberg","year":"2020","unstructured":"Alneberg J, Bennke C, Beier S, Bunse C, Quince C, Ininbergs K, et al. Ecosystem-wide metagenomic binning enables prediction of ecological niches from genomes. Commun Biol. 2020;3:1\u201310.","journal-title":"Commun Biol"},{"key":"1972_CR25","doi-asserted-by":"publisher","first-page":"e03832","DOI":"10.1128\/mbio.03832-21","volume":"13","author":"W Song","year":"2022","unstructured":"Song W, Liu J, Qin W, Huang J, Yu X, Xu M, et al. Functional traits resolve mechanisms governing the assembly and distribution of nitrogen-cycling microbial communities in the global ocean. mBio. 2022;13:e03832\u201321.","journal-title":"mBio"},{"key":"1972_CR26","doi-asserted-by":"publisher","first-page":"299","DOI":"10.1038\/35012500","volume":"405","author":"H Ochman","year":"2000","unstructured":"Ochman H, Lawrence JG, Groisman EA. Lateral gene transfer and the nature of bacterial innovation. Nature. 2000;405:299\u2013304.","journal-title":"Nature"},{"key":"1972_CR27","doi-asserted-by":"publisher","first-page":"11512","DOI":"10.1073\/pnas.0801925105","volume":"105","author":"SD Allison","year":"2008","unstructured":"Allison SD, Martiny JBH. Resistance, resilience, and redundancy in microbial communities. Proc Natl Acad Sci. 2008;105:11512\u20139.","journal-title":"Proc Natl Acad Sci"},{"key":"1972_CR28","doi-asserted-by":"publisher","first-page":"14288","DOI":"10.1073\/pnas.1101591108","volume":"108","author":"C Burke","year":"2011","unstructured":"Burke C, Steinberg P, Rusch D, Kjelleberg S, Thomas T. Bacterial community assembly based on functional genes rather than species. Proc Natl Acad Sci. 2011;108:14288\u201393.","journal-title":"Proc Natl Acad Sci"},{"key":"1972_CR29","doi-asserted-by":"publisher","first-page":"188","DOI":"10.1016\/j.soilbio.2016.03.017","volume":"97","author":"S Banerjee","year":"2016","unstructured":"Banerjee S, Kirkby CA, Schmutter D, Bissett A, Kirkegaard JA, Richardson AE. Network analysis reveals functional redundancy and keystone taxa amongst bacterial and fungal communities during organic matter decomposition in an arable soil. Soil Biol Biochem. 2016;97:188\u201398.","journal-title":"Soil Biol Biochem"},{"key":"1972_CR30","doi-asserted-by":"publisher","first-page":"4361","DOI":"10.1038\/s41467-021-24547-1","volume":"12","author":"E Faure","year":"2021","unstructured":"Faure E, Ayata S-D, Bittner L. Towards omics-based predictions of planktonic functional composition from environmental data. Nat Commun. 2021;12:4361.","journal-title":"Nat Commun"},{"key":"1972_CR31","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41559-016-0015","volume":"1","author":"S Louca","year":"2016","unstructured":"Louca S, Jacques SMS, Pires APF, Leal JS, Srivastava DS, Parfrey LW, et al. High taxonomic variability despite stable functional structure across microbial communities. Nat Ecol Evol. 2016;1:1\u201312.","journal-title":"Nat Ecol Evol"},{"key":"1972_CR32","doi-asserted-by":"publisher","first-page":"936","DOI":"10.1038\/s41559-018-0519-1","volume":"2","author":"S Louca","year":"2018","unstructured":"Louca S, Polz MF, Mazel F, Albright MBN, Huber JA, O\u2019Connor MI, et al. Function and functional redundancy in microbial systems. Nat Ecol Evol. 2018;2:936\u201343.","journal-title":"Nat Ecol Evol"},{"key":"1972_CR33","doi-asserted-by":"crossref","unstructured":"Jurburg SD, Salles JF, Jurburg SD, Salles JF. Functional redundancy and ecosystem function \u2014 the soil microbiota as a case study. In: Biodiversity in ecosystems - linking structure and function. IntechOpen; 2015 [Cited 2024 Jul 30]. Available from: https:\/\/www.intechopen.com\/chapters\/47598.","DOI":"10.5772\/58981"},{"key":"1972_CR34","doi-asserted-by":"publisher","first-page":"402","DOI":"10.1016\/j.tim.2016.02.002","volume":"24","author":"A Moya","year":"2016","unstructured":"Moya A, Ferrer M. Functional redundancy-induced stability of gut microbiota subjected to disturbance. Trends Microbiol. 2016;24:402\u201313.","journal-title":"Trends Microbiol"},{"key":"1972_CR35","doi-asserted-by":"publisher","first-page":"595","DOI":"10.1136\/gutjnl-2020-321747","volume":"70","author":"M Fassarella","year":"2021","unstructured":"Fassarella M, Blaak EE, Penders J, Nauta A, Smidt H, Zoetendal EG. Gut microbiome stability and resilience: elucidating the response to perturbations in order to modulate gut health. Gut. 2021;70:595\u2013605.","journal-title":"Gut"},{"key":"1972_CR36","doi-asserted-by":"publisher","first-page":"177","DOI":"10.1111\/geb.12528","volume":"26","author":"JM Haggerty","year":"2017","unstructured":"Haggerty JM, Dinsdale EA. Distinct biogeographical patterns of marine bacterial taxonomy and functional genes. Glob Ecol Biogeogr. 2017;26:177\u201390.","journal-title":"Glob Ecol Biogeogr"},{"key":"1972_CR37","doi-asserted-by":"publisher","first-page":"pgad287","DOI":"10.1093\/pnasnexus\/pgad287","volume":"2","author":"CC Becker","year":"2023","unstructured":"Becker CC, Weber L, Zgliczynski B, Sullivan C, Sandin S, Muller E, et al. Microorganisms and dissolved metabolites distinguish Florida\u2019s Coral Reef habitats. PNAS Nexus. 2023;2:pgad287.","journal-title":"PNAS Nexus."},{"key":"1972_CR38","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.1511","volume":"4","author":"FE Angly","year":"2016","unstructured":"Angly FE, Heath C, Morgan TC, Tonin H, Rich V, Schaffelke B, et al. Marine microbial communities of the Great Barrier Reef lagoon are influenced by riverine floodwaters and seasonal weather events. PeerJ. 2016;4: e1511.","journal-title":"PeerJ"},{"key":"1972_CR39","doi-asserted-by":"publisher","first-page":"1435","DOI":"10.1038\/s41396-020-0622-6","volume":"14","author":"B Glasl","year":"2020","unstructured":"Glasl B, Robbins S, Frade PR, Marangon E, Laffy PW, Bourne DG, et al. Comparative genome-centric analysis reveals seasonal variation in the function of coral reef microbiomes. ISME J. 2020;14:1435\u201350.","journal-title":"ISME J"},{"key":"1972_CR40","doi-asserted-by":"publisher","first-page":"Article 35","DOI":"10.2202\/1544-6115.1390","volume":"7","author":"KA L\u00ea Cao","year":"2008","unstructured":"L\u00ea Cao KA, Rossouw D, Robert-Grani\u00e9 C, Besse P. A sparse PLS for variable selection when integrating omics data. Stat Appl Genet Mol Biol. 2008;7:Article 35.","journal-title":"Stat Appl Genet Mol Biol"},{"key":"1972_CR41","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-10-34","volume":"10","author":"K-A L\u00ea Cao","year":"2009","unstructured":"L\u00ea Cao K-A, Martin PG, Robert-Grani\u00e9 C, Besse P. Sparse canonical methods for biological data integration: application to a cross-platform study. BMC Bioinformatics. 2009;10: 34.","journal-title":"BMC Bioinformatics"},{"key":"1972_CR42","doi-asserted-by":"publisher","first-page":"465","DOI":"10.1038\/nature16942","volume":"532","author":"L Guidi","year":"2016","unstructured":"Guidi L, Chaffron S, Bittner L, Eveillard D, Larhlimi A, Roux S, et al. Plankton networks driving carbon export in the oligotrophic ocean. Nature. 2016;532:465\u201370.","journal-title":"Nature"},{"key":"1972_CR43","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s42003-023-04597-5","volume":"6","author":"BD Jameson","year":"2023","unstructured":"Jameson BD, Murdock SA, Ji Q, Stevens CJ, Grundle DS, Kim JS. Network analysis of 16S rRNA sequences suggests microbial keystone taxa contribute to marine N2O cycling. Commun Biol. 2023;6:1\u201314.","journal-title":"Commun Biol"},{"key":"1972_CR44","doi-asserted-by":"publisher","first-page":"1612","DOI":"10.1038\/s41396-023-01461-6","volume":"17","author":"T Priest","year":"2023","unstructured":"Priest T, von Appen W-J, Oldenburg E, Popa O, Torres-Vald\u00e9s S, Bienhold C, et al. Atlantic water influx and sea-ice cover drive taxonomic and functional shifts in Arctic marine bacterial communities. ISME J. 2023;17:1612\u201325.","journal-title":"ISME J"},{"key":"1972_CR45","doi-asserted-by":"publisher","first-page":"128","DOI":"10.1186\/s12859-017-1553-8","volume":"18","author":"F Rohart","year":"2017","unstructured":"Rohart F, Eslami A, Matigian N, Bougeard S, L\u00ea Cao K-A. MINT: a Multivariate INTegrative method to identify reproducible molecular signatures across independent experiments and platforms. BMC Bioinformatics. 2017;18:128.","journal-title":"BMC Bioinformatics"},{"key":"1972_CR46","unstructured":"R Core Team. RStudio Desktop. RStudio; 2023. Available from: https:\/\/www.rstudio.com\/products\/rstudio\/download\/."},{"key":"1972_CR47","unstructured":"Hijmans RJ, Etten J van, Sumner M, Cheng J, Baston D, Bevan A, et al. raster: Geographic data analysis and modeling. 2023 [Cited 2024 Jul 30]. Available from: https:\/\/cran.r-project.org\/web\/packages\/raster\/index.html."},{"key":"1972_CR48","doi-asserted-by":"publisher","first-page":"1686","DOI":"10.21105\/joss.01686","volume":"4","author":"H Wickham","year":"2019","unstructured":"Wickham H, Averick M, Bryan J, Chang W, McGowan LD, Fran\u00e7ois R, et al. Welcome to the tidyverse. Journal of Open Source Software. 2019;4:1686.","journal-title":"Journal of Open Source Software"},{"key":"1972_CR49","unstructured":"Dunnington D, Thorne B, Hernang\u00f3mez D. ggspatial: Spatial data framework for ggplot2. 2023 [Cited 2024 Jul 30]. Available from: https:\/\/cran.r-project.org\/web\/packages\/ggspatial\/index.html."},{"key":"1972_CR50","doi-asserted-by":"publisher","first-page":"439","DOI":"10.32614\/RJ-2018-009","volume":"10","author":"E Pebesma","year":"2018","unstructured":"Pebesma E. Simple features for R: standardized support for spatial vector data. The R Journal. 2018;10:439.","journal-title":"The R Journal"},{"key":"1972_CR51","doi-asserted-by":"publisher","DOI":"10.1201\/9780429459016","volume-title":"Spatial Data Science: With Applications in R","author":"E Pebesma","year":"2023","unstructured":"Pebesma E, Bivand R. Spatial Data Science: With Applications in R. 1st ed. New York: Chapman and Hall\/CRC; 2023 [Cited 2024 Jul 30]. Available from: https:\/\/www.taylorfrancis.com\/books\/9780429459016.","edition":"1"},{"key":"1972_CR52","doi-asserted-by":"publisher","first-page":"3282","DOI":"10.21105\/joss.03282","volume":"6","author":"DR Barneche","year":"2021","unstructured":"Barneche DR, Coleman G, Fermor D, Klein E, Robinson T, Smith J, et al. dataaimsr: an R client for the Australian Institute of Marine Science Data Platform API which provides easy access to AIMS Data Platform. Journal of Open Source Software. 2021;6:3282.","journal-title":"Journal of Open Source Software"},{"key":"1972_CR53","unstructured":"Slowikowski K, Schep A, Hughes S, Dang TK, Lukauskas S, Irisson JO, et al. ggrepel: automatically position non-overlapping text labels with \u201cggplot2\u201d. 2024 [Cited 2024 Jul 30]. Available from: https:\/\/cran.r-project.org\/web\/packages\/ggrepel\/index.html."},{"key":"1972_CR54","unstructured":"Great Barrier Reef Marine Park Authority. Marine monitoring program annual report quality assurance and quality control manual 2020-21. Great Barrier Reef Marine Park Authority; 2022. Available from: https:\/\/elibrary.gbrmpa.gov.au\/jspui\/handle\/11017\/3932."},{"key":"1972_CR55","unstructured":"IMOS. Underway sensors: enhanced measurements from Ships of Opportunity (SOOP): RV Cape Ferguson | AIMS data repository | aims.gov.au. 2015 [Cited 2024 Mar 8]. Available from: https:\/\/apps.aims.gov.au\/metadata\/view\/da560e78-1a4e-43dc-aa4b-c99c3c4ab700."},{"key":"1972_CR56","first-page":"24","volume-title":"Automated analysis of nutrients in tropical sea waters","author":"VD Ryle","year":"1981","unstructured":"Ryle VD, Mueller HR, Gentien P. Automated analysis of nutrients in tropical sea waters. Townsville: Australian Institute of Marine Science; 1981. p. 24."},{"key":"1972_CR57","unstructured":"Parsons TR, Maita Y, Lalli CM. A manual of chemical and biological methods for seawater analysis. Pergamon Press; 1984 [Cited 2024 May 9]. Available from: https:\/\/repository.oceanbestpractices.org\/handle\/11329\/2043."},{"key":"1972_CR58","unstructured":"Bran & Luebbe. Directory of Autoanalyser Methods, Bran and Luebbe GmbH, Norderstedt, Germany.\u00a01997. https:\/\/apps.aims.gov.au\/metadata\/view\/0828edb9-b7b9-47f8-b4b6-43fa73a58867."},{"key":"1972_CR59","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1016\/0304-4203(81)90027-X","volume":"10","author":"JC Valderrama","year":"1981","unstructured":"Valderrama JC. The simultaneous analysis of total nitrogen and total phosphorus in natural waters. Mar Chem. 1981;10:109\u201322.","journal-title":"Mar Chem"},{"key":"1972_CR60","doi-asserted-by":"publisher","first-page":"280","DOI":"10.4319\/lo.1965.10.2.0280","volume":"10","author":"DW Menzel","year":"1965","unstructured":"Menzel DW, Corwin N. The measurement of total phosphorus in seawater based on the liberation of organically bound fractions by persulfate OXIDATION1. Limnol Oceanogr. 1965;10:280\u20132.","journal-title":"Limnol Oceanogr"},{"key":"1972_CR61","unstructured":"Strickland JDH, Parsons TR. A Practical Handbook of Seawater Analysis, 2nd edition. 1972 [cited 2024 May 9]. Available from:\u00a0https:\/\/repository.oceanbestpractices.org\/handle\/11329\/1994."},{"key":"1972_CR62","doi-asserted-by":"publisher","first-page":"4134","DOI":"10.1038\/s41467-019-12156-y","volume":"10","author":"ES Bott\u00e9","year":"2019","unstructured":"Bott\u00e9 ES, Nielsen S, Abdul Wahab MA, Webster J, Robbins S, Thomas T, et al. Changes in the metabolic potential of the sponge microbiome under ocean acidification. Nat Commun. 2019;10:4134.","journal-title":"Nat Commun"},{"key":"1972_CR63","unstructured":"Andrews. Babraham Bioinformatics - FastQC a quality control tool for high throughput sequence data. 2010 [Cited 2023 May 30]. Available from: https:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/."},{"key":"1972_CR64","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","volume":"30","author":"AM Bolger","year":"2014","unstructured":"Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114\u201320.","journal-title":"Bioinformatics"},{"key":"1972_CR65","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1038\/nmeth.3176","volume":"12","author":"B Buchfink","year":"2015","unstructured":"Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2015;12:59\u201360.","journal-title":"Nat Methods"},{"key":"1972_CR66","doi-asserted-by":"publisher","first-page":"e1004957","DOI":"10.1371\/journal.pcbi.1004957","volume":"12","author":"DH Huson","year":"2016","unstructured":"Huson DH, Beier S, Flade I, G\u00f3rska A, El-Hadidi M, Mitra S, et al. MEGAN community edition - interactive exploration and analysis of large-scale microbiome sequencing data. PLOS Computational Biology. 2016;12:e1004957.","journal-title":"PLOS Computational Biology"},{"key":"1972_CR67","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0061217","volume":"8","author":"PJ McMurdie","year":"2013","unstructured":"McMurdie PJ, Holmes S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE. 2013;8: e61217.","journal-title":"PLoS ONE"},{"key":"1972_CR68","unstructured":"Lahti L, Shetty\u00a0S, et al. Tools for microbiome analysis in R. Version. 2017. http:\/\/microbiome.github.com\/microbiome."},{"key":"1972_CR69","doi-asserted-by":"publisher","first-page":"e1005752","DOI":"10.1371\/journal.pcbi.1005752","volume":"13","author":"F Rohart","year":"2017","unstructured":"Rohart F, Gautier B, Singh A, L\u00ea Cao K-A. mixOmics: an R package for \u2018omics feature selection and multiple data integration. PLoS Comput Biol. 2017;13: e1005752.","journal-title":"PLoS Comput Biol"},{"key":"1972_CR70","unstructured":"Martinez Arbizu P. pairwiseAdonis: Pairwise multilevel comparison using adonis. R package version 0.4.\u00a02020.\u00a0https:\/\/github.com\/pmartinezarbizu\/pairwiseAdonis."},{"key":"1972_CR71","doi-asserted-by":"publisher","first-page":"1068","DOI":"10.1016\/j.cell.2019.10.014","volume":"179","author":"G Salazar","year":"2019","unstructured":"Salazar G, Paoli L, Alberti A, Huerta-Cepas J, Ruscheweyh H-J, Cuenca M, et al. Gene expression changes and community turnover differentially shape the global ocean metatranscriptome. Cell. 2019;179:1068\u20131083.e21.","journal-title":"Cell"},{"key":"1972_CR72","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-319-24277-4","volume-title":"ggplot2","author":"H Wickham","year":"2016","unstructured":"Wickham H. ggplot2. Cham: Springer International Publishing; 2016 [Cited 2024 Jul 31]. Available from: http:\/\/link.springer.com\/10.1007\/978-3-319-24277-4."},{"key":"1972_CR73","first-page":"719","volume":"10","author":"J Oksanen","year":"2007","unstructured":"Oksanen J, Kindt R, Legendre P, O\u2019Hara B, Stevens MHH, Oksanen MJ, et al. The vegan package Community ecology package. 2007;10:719.","journal-title":"The vegan package Community ecology package"},{"key":"1972_CR74","doi-asserted-by":"publisher","first-page":"417","DOI":"10.1111\/j.1467-9868.2010.00740.x","volume":"72","author":"N Meinshausen","year":"2010","unstructured":"Meinshausen N, B\u00fchlmann P. Stability selection. J Royal Statistical Soc Series B (Statistical Methodology). 2010;72:417\u201373.","journal-title":"J Royal Statistical Soc Series B (Statistical Methodology)"},{"key":"1972_CR75","doi-asserted-by":"publisher","DOI":"10.1201\/9781003026860","volume-title":"Multivariate data integration using R: methods and applications with the mixOmics package","author":"KAL L\u00ea Cao","year":"2021","unstructured":"L\u00ea Cao KAL, Welham ZM. Multivariate data integration using R: methods and applications with the mixOmics package. New York: Chapman and Hall\/CRC; 2021."},{"key":"1972_CR76","doi-asserted-by":"publisher","first-page":"1261359","DOI":"10.1126\/science.1261359","volume":"348","author":"S Sunagawa","year":"2015","unstructured":"Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K, Salazar G, et al. Ocean plankton. Structure and function of the global ocean microbiome. Science. 2015;348:1261359.","journal-title":"Science"},{"key":"1972_CR77","doi-asserted-by":"crossref","unstructured":"Loreau M. Does functional redundancy exist? 2004 [Cited 2024 Jul 31]. Available from: https:\/\/nsojournals.onlinelibrary.wiley.com\/doi\/10.1111\/j.0030-1299.2004.12685.x.","DOI":"10.1111\/j.0030-1299.2004.12685.x"},{"key":"1972_CR78","doi-asserted-by":"publisher","first-page":"e03184","DOI":"10.1002\/ecs2.3184","volume":"11","author":"C Biggs","year":"2020","unstructured":"Biggs C, Yeager L, Bolser D, Bonsell C, Dichiera A, Hou Z, et al. Does functional redundancy affect ecological stability and resilience? A review and meta-analysis. Ecosphere. 2020;11:e03184.","journal-title":"Ecosphere"},{"key":"1972_CR79","doi-asserted-by":"publisher","DOI":"10.1016\/j.mib.2022.102263","volume":"72","author":"A Shade","year":"2023","unstructured":"Shade A. Microbiome rescue: directing resilience of environmental microbial communities. Curr Opin Microbiol. 2023;72: 102263.","journal-title":"Curr Opin Microbiol"},{"key":"1972_CR80","doi-asserted-by":"publisher","first-page":"1487","DOI":"10.1093\/icesjms\/fsad077","volume":"80","author":"LC Flensborg","year":"2023","unstructured":"Flensborg LC, Maureaud AA, Bravo DN, Lindegren M. An indicator-based approach for assessing marine ecosystem resilience. ICES J Mar Sci. 2023;80:1487\u201399.","journal-title":"ICES J Mar Sci"},{"key":"1972_CR81","doi-asserted-by":"crossref","unstructured":"Chambers JC, Allen CR, Cushman SA. Operationalizing ecological resilience concepts for managing species and ecosystems at risk. Front Ecol Evol. 2019;7 [ Cited 2024 Apr 24]. Available from: https:\/\/www.frontiersin.org\/articles\/10.3389\/fevo..","DOI":"10.3389\/fevo.2019.00241"},{"key":"1972_CR82","doi-asserted-by":"publisher","first-page":"342","DOI":"10.1071\/MF06236","volume":"58","author":"J Brodie","year":"2007","unstructured":"Brodie J, De\u2019ath G, Devlin M, Furnas M, Wright M. Spatial and temporal patterns of near-surface chlorophyll a in the Great Barrier Reef lagoon. Marine and Freshwater Research. 2007;58:342\u201353.","journal-title":"Marine and Freshwater Research"},{"key":"1972_CR83","unstructured":"De\u2019ath G, Fabricius KE. Water quality of the Great Barrier Reef\u202f: distributions, effects on reef biota and trigger values for the protection of ecosystem health. Great Barrier Reef Marine Park Authority; 2008. Available from: https:\/\/elibrary.gbrmpa.gov.au\/jspui\/handle\/11017\/416."},{"key":"1972_CR84","doi-asserted-by":"publisher","first-page":"363","DOI":"10.1016\/0278-4343(86)90078-6","volume":"6","author":"MJ Furnas","year":"1986","unstructured":"Furnas MJ, Mitchell AW. Phytoplankton dynamics in the central Great Barrier Reef\u2014I. Seasonal changes in biomass and community structure and their relation to intrusive activity. Continental Shelf Research. 1986;6:363\u201384.","journal-title":"Continental Shelf Research."},{"key":"1972_CR85","doi-asserted-by":"publisher","first-page":"8395","DOI":"10.1002\/2016JC012294","volume":"121","author":"JA Benthuysen","year":"2016","unstructured":"Benthuysen JA, Tonin H, Brinkman R, Herzfeld M, Steinberg C. Intrusive upwelling in the Central Great Barrier Reef. J Geophys Res Oceans. 2016;121:8395\u2013416. https:\/\/doi.org\/10.1002\/2016JC012294.","journal-title":"J Geophys Res Oceans"},{"key":"1972_CR86","doi-asserted-by":"publisher","first-page":"253","DOI":"10.1016\/j.marpolbul.2004.11.010","volume":"51","author":"M Furnas","year":"2005","unstructured":"Furnas M, Mitchell A, Skuza M, Brodie J. In the other 90%: phytoplankton responses to enhanced nutrient availability in the Great Barrier Reef Lagoon. Mar Pollut Bull. 2005;51:253\u201365.","journal-title":"Mar Pollut Bull"},{"key":"1972_CR87","volume":"2012","author":"L Charpy","year":"2012","unstructured":"Charpy L, Casareto BE, Langlade MJ, Suzuki Y. Cyanobacteria in coral reef ecosystems: a review. Journal of Marine Sciences. 2012;2012: e259571.","journal-title":"Journal of Marine Sciences"},{"key":"1972_CR88","doi-asserted-by":"publisher","first-page":"5629","DOI":"10.1038\/s41467-023-41183-z","volume":"14","author":"M Bahadori","year":"2023","unstructured":"Bahadori M, Chen C, Lewis S, Wang J, Shen J, Hou E, et al. The origin of suspended particulate matter in the Great Barrier Reef. Nat Commun. 2023;14:5629.","journal-title":"Nat Commun"},{"key":"1972_CR89","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1002\/lno.10389","volume":"62","author":"SP McNally","year":"2017","unstructured":"McNally SP, Parsons RJ, Santoro AE, Apprill A. Multifaceted impacts of the stony coral Porites astreoides on picoplankton abundance and community composition. Limnol Oceanogr. 2017;62:217\u201334.","journal-title":"Limnol Oceanogr"},{"key":"1972_CR90","doi-asserted-by":"publisher","first-page":"2882","DOI":"10.1038\/s41396-019-0456-2","volume":"13","author":"V Meunier","year":"2019","unstructured":"Meunier V, Bonnet S, Pernice M, Benavides M, Lorrain A, Grosso O, et al. Bleaching forces coral\u2019s heterotrophy on diazotrophs and Synechococcus. ISME J. 2019;13:2882\u20136.","journal-title":"ISME J"},{"key":"1972_CR91","doi-asserted-by":"publisher","first-page":"809","DOI":"10.1093\/plankt\/23.8.809","volume":"23","author":"N Crosbie","year":"2001","unstructured":"Crosbie N, Furnas M. Abundance, distribution and flow-cytometric characterization of picophytoprokaryote populations in central (17degreesS) and southern (20degreesS) shelf waters of the Great Barrier Reef. Journal of Plankton Research - J PLANKTON RES. 2001;23:809\u201328.","journal-title":"Journal of Plankton Research - J PLANKTON RES"},{"key":"1972_CR92","doi-asserted-by":"publisher","first-page":"125","DOI":"10.1016\/j.marpolbul.2004.11.028","volume":"50","author":"KE Fabricius","year":"2005","unstructured":"Fabricius KE. Effects of terrestrial runoff on the ecology of corals and coral reefs: review and synthesis. Mar Pollut Bull. 2005;50:125\u201346.","journal-title":"Mar Pollut Bull"},{"key":"1972_CR93","doi-asserted-by":"publisher","first-page":"648","DOI":"10.1080\/07388551.2019.1594153","volume":"39","author":"UC Dave","year":"2019","unstructured":"Dave UC, Kadeppagari R-K. Alanine dehydrogenase and its applications \u2013 a review. Crit Rev Biotechnol. 2019;39:648\u201364.","journal-title":"Crit Rev Biotechnol"},{"key":"1972_CR94","doi-asserted-by":"publisher","first-page":"6344","DOI":"10.1128\/AEM.01336-16","volume":"82","author":"L Hudek","year":"2016","unstructured":"Hudek L, Premachandra D, Webster WAJ, Br\u00e4u L. Role of phosphate transport system component PstB1 in phosphate internalization by Nostoc punctiforme. Appl Environ Microbiol. 2016;82:6344\u201356.","journal-title":"Appl Environ Microbiol"},{"key":"1972_CR95","doi-asserted-by":"publisher","first-page":"1299","DOI":"10.1128\/AEM.69.2.1299-1304.2003","volume":"69","author":"MV Zubkov","year":"2003","unstructured":"Zubkov MV, Fuchs BM, Tarran GA, Burkill PH, Amann R. High rate of uptake of organic nitrogen compounds by Prochlorococcus cyanobacteria as a key to their dominance in oligotrophic oceanic waters. Appl Environ Microbiol. 2003;69:1299\u2013304.","journal-title":"Appl Environ Microbiol"},{"key":"1972_CR96","doi-asserted-by":"publisher","first-page":"12552","DOI":"10.1073\/pnas.0601301103","volume":"103","author":"A Martiny","year":"2006","unstructured":"Martiny A, Coleman M, Chisholm S. Phosphate acquisition genes in Prochlorococcus ecotypes. Proc Natl Acad Sci U S A. 2006;103:12552\u20137.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"1972_CR97","doi-asserted-by":"publisher","first-page":"918","DOI":"10.1126\/science.1122692","volume":"312","author":"HA Bouman","year":"2006","unstructured":"Bouman HA, Ulloa O, Scanlan DJ, Zwirglmaier K, Li WKW, Platt T, et al. Oceanographic basis of the global surface distribution of Prochlorococcus ecotypes. Science. 2006;312:918\u201321.","journal-title":"Science"},{"key":"1972_CR98","doi-asserted-by":"publisher","first-page":"1042","DOI":"10.1038\/nature01947","volume":"424","author":"G Rocap","year":"2003","unstructured":"Rocap G, Larimer FW, Lamerdin J, Malfatti S, Chain P, Ahlgren NA, et al. Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature. 2003;424:1042\u20137.","journal-title":"Nature"},{"key":"1972_CR99","doi-asserted-by":"publisher","first-page":"333","DOI":"10.1038\/ismej.2015.115","volume":"10","author":"JA Sohm","year":"2016","unstructured":"Sohm JA, Ahlgren NA, Thomson ZJ, Williams C, Moffett JW, Saito MA, et al. Co-occurring Synechococcus ecotypes occupy four major oceanic regimes defined by temperature, macronutrients and iron. ISME J. 2016;10:333\u201345.","journal-title":"ISME J"},{"key":"1972_CR100","doi-asserted-by":"crossref","unstructured":"Fogg GE. The ecological significance of extracellular products of phytoplankton photosynthesis. 1983 [Cited 2024 Jul 31]. Available from: https:\/\/www.degruyter.com\/document\/doi\/10.1515\/botm.1983.26.1.3\/html?lang=en.","DOI":"10.1515\/botm.1983.26.1.3"},{"key":"1972_CR101","doi-asserted-by":"publisher","first-page":"1007","DOI":"10.1002\/lno.12053","volume":"67","author":"MA Moran","year":"2022","unstructured":"Moran MA, Ferrer-Gonz\u00e1lez FX, Fu H, Nowinski B, Olofsson M, Powers MA, et al. The Ocean\u2019s labile DOC supply chain. Limnol Oceanogr. 2022;67:1007\u201321.","journal-title":"Limnol Oceanogr"},{"key":"1972_CR102","doi-asserted-by":"publisher","first-page":"508","DOI":"10.1038\/s41564-022-01090-3","volume":"7","author":"MA Moran","year":"2022","unstructured":"Moran MA, Kujawinski EB, Schroer WF, Amin SA, Bates NR, Bertrand EM, et al. Microbial metabolites in the marine carbon cycle. Nat Microbiol. 2022;7:508\u201323.","journal-title":"Nat Microbiol"},{"key":"1972_CR103","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1016\/j.scitotenv.2016.02.031","volume":"551\u2013552","author":"W He","year":"2016","unstructured":"He W, Chen M, Schlautman MA, Hur J. Dynamic exchanges between DOM and POM pools in coastal and inland aquatic ecosystems: a review. Sci Total Environ. 2016;551\u2013552:415\u201328.","journal-title":"Sci Total Environ"},{"key":"1972_CR104","doi-asserted-by":"publisher","first-page":"19327","DOI":"10.1073\/pnas.1208895109","volume":"109","author":"A Vardi","year":"2012","unstructured":"Vardi A, Haramaty L, Van Mooy BAS, Fredricks HF, Kimmance SA, Larsen A, et al. Host\u2013virus dynamics and subcellular controls of cell fate in a natural coccolithophore population. Proc Natl Acad Sci. 2012;109:19327\u201332.","journal-title":"Proc Natl Acad Sci"},{"key":"1972_CR105","doi-asserted-by":"publisher","first-page":"341","DOI":"10.1146\/annurev-marine-010213-135014","volume":"7","author":"KD Bidle","year":"2015","unstructured":"Bidle KD. The molecular ecophysiology of programmed cell death in marine phytoplankton. Ann Rev Mar Sci. 2015;7:341\u201375.","journal-title":"Ann Rev Mar Sci"},{"key":"1972_CR106","doi-asserted-by":"publisher","first-page":"413","DOI":"10.1146\/annurev-marine-010814-015924","volume":"9","author":"DK Steinberg","year":"2017","unstructured":"Steinberg DK, Landry MR. Zooplankton and the ocean carbon cycle. Ann Rev Mar Sci. 2017;9:413\u201344.","journal-title":"Ann Rev Mar Sci"},{"key":"1972_CR107","doi-asserted-by":"publisher","first-page":"336","DOI":"10.1002\/lno.12272","volume":"68","author":"D De Corte","year":"2023","unstructured":"De Corte D, Varela MM, Louro AM, Bercovici SK, Valencia-Vila J, Sintes E, et al. Zooplankton-derived dissolved organic matter composition and its bioavailability to natural prokaryotic communities. Limnol Oceanogr. 2023;68:336\u201347.","journal-title":"Limnol Oceanogr"},{"key":"1972_CR108","doi-asserted-by":"crossref","unstructured":"Carlson CA, Hansell DA. Chapter 3 - DOM sources, sinks, reactivity, and budgets. In: Hansell DA, Carlson CA, editors. Biogeochemistry of marine dissolved organic matter (Second Edition). Boston: Academic Press; 2015. p. 65\u2013126 [Cited 2024 Aug 1]. Available from: https:\/\/www.sciencedirect.com\/science\/article\/pii\/B9780124059405000030.","DOI":"10.1016\/B978-0-12-405940-5.00003-0"},{"key":"1972_CR109","doi-asserted-by":"publisher","first-page":"1528","DOI":"10.1016\/j.cub.2019.03.047","volume":"29","author":"TN Enke","year":"2019","unstructured":"Enke TN, Datta MS, Schwartzman J, Cermak N, Schmitz D, Barrere J, et al. Modular assembly of polysaccharide-degrading marine microbial communities. Curr Biol. 2019;29:1528\u20131535.e6.","journal-title":"Curr Biol"},{"key":"1972_CR110","doi-asserted-by":"publisher","first-page":"17780","DOI":"10.1038\/s41598-019-54290-z","volume":"9","author":"A Mentges","year":"2019","unstructured":"Mentges A, Feenders C, Deutsch C, Blasius B, Dittmar T. Long-term stability of marine dissolved organic carbon emerges from a neutral network of compounds and microbes. Sci Rep. 2019;9:17780.","journal-title":"Sci Rep"},{"key":"1972_CR111","doi-asserted-by":"publisher","first-page":"257","DOI":"10.3354\/meps010257","volume":"10","author":"F Azam","year":"1983","unstructured":"Azam F, Fenchel T, Field J, Gray J, Meyer-Reil L, Thingstad F. The ecological role of water-column microbes in the sea. Mar Ecol Prog Ser. 1983;10:257\u201363.","journal-title":"Mar Ecol Prog Ser"},{"key":"1972_CR112","doi-asserted-by":"publisher","first-page":"782","DOI":"10.1038\/nrmicro1747","volume":"5","author":"F Azam","year":"2007","unstructured":"Azam F, Malfatti F. Microbial structuring of marine ecosystems. Nat Rev Microbiol. 2007;5:782\u201391.","journal-title":"Nat Rev Microbiol"},{"key":"1972_CR113","doi-asserted-by":"publisher","unstructured":"Kirchman DL. Carbon pumps in the oceans. In: Kirchman DL, editor. Microbes: the unseen agents of climate change. Oxford University Press; 2024. p. 0. [Cited 2024 Aug 1]. Available from:\u00a0https:\/\/doi.org\/10.1093\/oso\/9780197688564.003.0004.","DOI":"10.1093\/oso\/9780197688564.003.0004"},{"key":"1972_CR114","doi-asserted-by":"publisher","first-page":"66","DOI":"10.1038\/nature02344","volume":"428","author":"C Wild","year":"2004","unstructured":"Wild C, Huettel M, Klueter A, Kremb SG, Rasheed MYM, J\u00f8rgensen BB. Coral mucus functions as an energy carrier and particle trap in the reef ecosystem. Nature. 2004;428:66\u201370.","journal-title":"Nature"},{"key":"1972_CR115","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1002\/ece3.1050","volume":"4","author":"U Cardini","year":"2014","unstructured":"Cardini U, Bednarz V, Foster R, Wild C. Benthic N2 fixation in coral reefs and the potential effects of human-induced environmental change. Ecol Evol. 2014;4:4.","journal-title":"Ecology and Evolution."},{"key":"1972_CR116","doi-asserted-by":"publisher","unstructured":"Pujalte MJ, Lucena T, Ruvira MA, Arahal DR, Maci\u00e1n MC. The family Rhodobacteraceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F, editors. The Prokaryotes: Alphaproteobacteria and Betaproteobacteria. Berlin, Heidelberg: Springer; 2014. p. 439\u2013512 [Cited 2024 May 13]. Available from:\u00a0https:\/\/doi.org\/10.1007\/978-3-642-30197-1_377.","DOI":"10.1007\/978-3-642-30197-1_377"},{"key":"1972_CR117","doi-asserted-by":"publisher","unstructured":"Baldani JI, Videira SS, dos Santos Teixeira KR, Reis VM, de Oliveira ALM, Schwab S, et al. The family Rhodospirillaceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F, editors. The Prokaryotes: Alphaproteobacteria and Betaproteobacteria. Berlin, Heidelberg: Springer; 2014. p. 533\u2013618 [Cited 2024 May 13]. Available from:\u00a0https:\/\/doi.org\/10.1007\/978-3-642-30197-1_300.","DOI":"10.1007\/978-3-642-30197-1_300"},{"key":"1972_CR118","doi-asserted-by":"publisher","first-page":"569","DOI":"10.1186\/s12864-020-06971-7","volume":"21","author":"A Gavriilidou","year":"2020","unstructured":"Gavriilidou A, Gutleben J, Versluis D, Forgiarini F, van Passel MWJ, Ingham CJ, et al. Comparative genomic analysis of Flavobacteriaceae: insights into carbohydrate metabolism, gliding motility and secondary metabolite biosynthesis. BMC Genomics. 2020;21:569.","journal-title":"BMC Genomics"},{"key":"1972_CR119","doi-asserted-by":"crossref","unstructured":"Je W. The NADH: ubiquinone oxidoreductase (complex I) of respiratory chains. Q Rev Biophys. 1992;25 [Cited 2024 Jun 19]. Available from: https:\/\/pubmed.ncbi.nlm.nih.gov\/1470679\/.\u00a0","DOI":"10.1017\/S003358350000425X"},{"key":"1972_CR120","doi-asserted-by":"publisher","first-page":"186","DOI":"10.1016\/S0005-2728(98)00027-9","volume":"1364","author":"T Ohnishi","year":"1998","unstructured":"Ohnishi T. Iron\u2013sulfur clusters\/semiquinones in complex I. Biochimica et Biophysica Acta (BBA) - Bioenergetics. 1998;1364:186\u2013206.","journal-title":"Biochimica et Biophysica Acta (BBA) - Bioenergetics"},{"key":"1972_CR121","doi-asserted-by":"publisher","first-page":"2266","DOI":"10.1021\/bi027158b","volume":"42","author":"T Yagi","year":"2003","unstructured":"Yagi T, Matsuno-Yagi A. The proton-translocating NADH-quinone oxidoreductase in the respiratory chain: the secret unlocked. Biochemistry. 2003;42:2266\u201374.","journal-title":"Biochemistry"},{"key":"1972_CR122","doi-asserted-by":"publisher","DOI":"10.3390\/microorganisms10050926","volume":"10","author":"L Hederstedt","year":"2022","unstructured":"Hederstedt L. Diversity of cytochrome c oxidase assembly proteins in bacteria. Microorganisms. 2022;10: 926.","journal-title":"Microorganisms"},{"key":"1972_CR123","doi-asserted-by":"publisher","first-page":"228","DOI":"10.1111\/j.1462-2920.2011.02602.x","volume":"14","author":"JM Rinta-Kanto","year":"2012","unstructured":"Rinta-Kanto JM, Sun S, Sharma S, Kiene RP, Moran MA. Bacterial community transcription patterns during a marine phytoplankton bloom. Environ Microbiol. 2012;14:228\u201339.","journal-title":"Environ Microbiol"},{"key":"1972_CR124","doi-asserted-by":"publisher","first-page":"608","DOI":"10.1126\/science.1218344","volume":"336","author":"H Teeling","year":"2012","unstructured":"Teeling H, Fuchs BM, Becher D, Klockow C, Gardebrecht A, Bennke CM, et al. Substrate-controlled succession of marine bacterioplankton populations induced by a phytoplankton bloom. Science. 2012;336:608\u201311.","journal-title":"Science"},{"key":"1972_CR125","unstructured":"Gregor R, Szabo RE, Vercelli GT, Gralka M, Reynolds R, Qu EB, et al. Widespread B-vitamin auxotrophy in marine particle-associated bacteria. bioRxiv. 2023. p. 2023.10.16.562604 [Cited 2024 Jul 17]. Available from: https:\/\/www.biorxiv.org\/content\/10.1101\/2023.10.16.562604v1."},{"key":"1972_CR126","doi-asserted-by":"publisher","first-page":"43682","DOI":"10.1074\/jbc.M306344200","volume":"278","author":"J Sivaraman","year":"2003","unstructured":"Sivaraman J, Li Y, Banks J, Cane DE, Matte A, Cygler M. Crystal structure of Escherichia coli PdxA, an enzyme involved in the pyridoxal phosphate biosynthesis pathway. J Biol Chem. 2003;278:43682\u201390.","journal-title":"J Biol Chem"},{"key":"1972_CR127","doi-asserted-by":"publisher","first-page":"81","DOI":"10.1016\/0167-4838(95)00025-P","volume":"1248","author":"RA John","year":"1995","unstructured":"John RA. Pyridoxal phosphate-dependent enzymes. Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology. 1995;1248:81\u201396.","journal-title":"Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology"},{"key":"1972_CR128","doi-asserted-by":"publisher","first-page":"463","DOI":"10.1093\/oxfordjournals.jbchem.a124931","volume":"118","author":"H Hayashi","year":"1995","unstructured":"Hayashi H. Pyridoxal enzymes: mechanistic diversity and uniformity. The Journal of Biochemistry. 1995;118:463\u201373.","journal-title":"The Journal of Biochemistry"},{"key":"1972_CR129","doi-asserted-by":"publisher","first-page":"383","DOI":"10.1146\/annurev.biochem.73.011303.074021","volume":"73","author":"AC Eliot","year":"2004","unstructured":"Eliot AC, Kirsch JF. Pyridoxal phosphate enzymes: mechanistic, structural, and evolutionary considerations. Annu Rev Biochem. 2004;73:383\u2013415.","journal-title":"Annu Rev Biochem"},{"key":"1972_CR130","doi-asserted-by":"publisher","first-page":"6003","DOI":"10.1021\/bi00018a001","volume":"34","author":"H J\u00f6rnvall","year":"1995","unstructured":"J\u00f6rnvall H, Persson B, Krook M, Atrian S, Gonzalez-Duarte R, Jeffery J, et al. Short-chain dehydrogenases\/reductases (SDR). Biochemistry. 1995;34:6003\u201313.","journal-title":"Biochemistry"},{"key":"1972_CR131","doi-asserted-by":"publisher","first-page":"247","DOI":"10.1016\/S0009-2797(02)00164-3","volume":"143\u2013144","author":"U Oppermann","year":"2003","unstructured":"Oppermann U, Filling C, Hult M, Shafqat N, Wu X, Lindh M, et al. Short-chain dehydrogenases\/reductases (SDR): the 2002 update. Chem Biol Interact. 2003;143\u2013144:247\u201353.","journal-title":"Chem Biol Interact"},{"key":"1972_CR132","doi-asserted-by":"publisher","first-page":"473","DOI":"10.1146\/annurev.arplant.50.1.473","volume":"50","author":"KM Herrmann","year":"1999","unstructured":"Herrmann KM, Weaver LM. The shikimate pathway. Annu Rev Plant Physiol Plant Mol Biol. 1999;50:473\u2013503.","journal-title":"Annu Rev Plant Physiol Plant Mol Biol"},{"key":"1972_CR133","doi-asserted-by":"publisher","first-page":"557","DOI":"10.1016\/S0092-8674(02)00619-0","volume":"108","author":"V Ramakrishnan","year":"2002","unstructured":"Ramakrishnan V. Ribosome structure and the mechanism of translation. Cell. 2002;108:557\u201372.","journal-title":"Cell"},{"key":"1972_CR134","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1111\/j.1574-6976.2007.00094.x","volume":"32","author":"W Vollmer","year":"2008","unstructured":"Vollmer W, Blanot D, De Pedro MA. Peptidoglycan structure and architecture. FEMS Microbiol Rev. 2008;32:149\u201367.","journal-title":"FEMS Microbiol Rev"},{"key":"1972_CR135","doi-asserted-by":"publisher","DOI":"10.1101\/cshperspect.a000414","volume":"2","author":"TJ Silhavy","year":"2010","unstructured":"Silhavy TJ, Kahne D, Walker S. The bacterial cell envelope. Cold Spring Harb Perspect Biol. 2010;2: a000414.","journal-title":"Cold Spring Harb Perspect Biol"},{"key":"1972_CR136","doi-asserted-by":"publisher","first-page":"3842","DOI":"10.1128\/JB.183.13.3842-3847.2001","volume":"183","author":"JT Park","year":"2001","unstructured":"Park JT. Identification of a Dedicated recycling pathway for anhydro-N-acetylmuramic acid andN-acetylglucosamine derived from Escherichia coli cell wall murein. J Bacteriol. 2001;183:3842\u20137.","journal-title":"J Bacteriol"},{"key":"1972_CR137","unstructured":"Riemann L, Azam F. Widespread N-acetyl-d-glucosamine uptake among pelagic marine bacteria and its ecological implications. 2002 [Cited 2024 Aug 8]. Available from: https:\/\/journals.asm.org\/doi\/10.1128\/aem.68.11.5554-5562.2002."},{"key":"1972_CR138","doi-asserted-by":"publisher","first-page":"3643","DOI":"10.1128\/JB.187.11.3643-3649.2005","volume":"187","author":"T Uehara","year":"2005","unstructured":"Uehara T, Suefuji K, Valbuena N, Meehan B, Donegan M, Park JT. Recycling of the anhydro-N-acetylmuramic acid derived from cell wall murein involves a two-step conversion to N-acetylglucosamine-phosphate. J Bacteriol. 2005;187:3643\u20139.","journal-title":"J Bacteriol"},{"key":"1972_CR139","doi-asserted-by":"publisher","first-page":"1660","DOI":"10.1128\/JB.188.4.1660-1662.2006","volume":"188","author":"T Uehara","year":"2006","unstructured":"Uehara T, Suefuji K, Jaeger T, Mayer C, Park JT. MurQ Etherase Is Required by Escherichia coli in order to metabolize anhydro-N-acetylmuramic acid obtained either from the environment or from its own cell wall. J Bacteriol. 2006;188:1660\u20132.","journal-title":"J Bacteriol"},{"key":"1972_CR140","doi-asserted-by":"crossref","unstructured":"Viegas CA. Chapter Four - Microbial bioassays in environmental toxicity testing. In: Gadd GM, Sariaslani S, editors. Advances in Applied Microbiology. Academic Press; 2021. p. 115\u201358 [Cited 2024 May 10]. Available from: https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0065216421000046.","DOI":"10.1016\/bs.aambs.2021.03.002"},{"key":"1972_CR141","doi-asserted-by":"publisher","first-page":"206","DOI":"10.1006\/eesa.2001.2140","volume":"51","author":"C Durrieu","year":"2002","unstructured":"Durrieu C, Tran-Minh C. Optical algal biosensor using alkaline phosphatase for determination of heavy metals. Ecotoxicol Environ Saf. 2002;51:206\u20139.","journal-title":"Ecotoxicol Environ Saf"},{"key":"1972_CR142","doi-asserted-by":"publisher","DOI":"10.3390\/microorganisms8050744","volume":"8","author":"K Knapik","year":"2020","unstructured":"Knapik K, Bagi A, Krolicka A, Baussant T. Metatranscriptomic analysis of oil-exposed seawater bacterial communities archived by an environmental sample processor (ESP). Microorganisms. 2020;8: 744.","journal-title":"Microorganisms"},{"key":"1972_CR143","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.3000483","volume":"17","author":"S Planes","year":"2019","unstructured":"Planes S, Allemand D, Agostini S, Banaigs B, Boissin E, Boss E, et al. The Tara Pacific expedition\u2014a pan-ecosystemic approach of the \u201c-omics\u201d complexity of coral reef holobionts across the Pacific Ocean. PLoS Biol. 2019;17: e3000483.","journal-title":"PLoS Biol"},{"key":"1972_CR144","doi-asserted-by":"publisher","first-page":"428","DOI":"10.1038\/s41579-020-0364-5","volume":"18","author":"S Sunagawa","year":"2020","unstructured":"Sunagawa S, Acinas SG, Bork P, Bowler C, Tara Oceans Coordinators, Acinas SG, et al. Tara Oceans: towards global ocean ecosystems biology. Nat Rev Microbiol. 2020;18:428\u201345.","journal-title":"Nat Rev Microbiol"},{"key":"1972_CR145","doi-asserted-by":"publisher","DOI":"10.1002\/lol2.10422","author":"EJ Raes","year":"2024","unstructured":"Raes EJ, Myles S, MacNeil L, Wietz M, Bienhold C, Tait K, et al. Seasonal patterns of microbial diversity across the world oceans. Limnol Oceanogr Lett. 2024. https:\/\/doi.org\/10.1002\/lol2.10422.","journal-title":"Limnol Oceanogr Lett"},{"key":"1972_CR146","doi-asserted-by":"publisher","first-page":"169","DOI":"10.1016\/j.mib.2018.01.015","volume":"43","author":"PL Buttigieg","year":"2018","unstructured":"Buttigieg PL, Fadeev E, Bienhold C, Hehemann L, Offre P, Boetius A. Marine microbes in 4D-using time series observation to assess the dynamics of the ocean microbiome and its links to ocean health. Curr Opin Microbiol. 2018;43:169\u201385.","journal-title":"Curr Opin Microbiol"},{"key":"1972_CR147","doi-asserted-by":"publisher","first-page":"266","DOI":"10.1038\/s41467-017-02571-4","volume":"9","author":"AM Martin-Platero","year":"2018","unstructured":"Martin-Platero AM, Cleary B, Kauffman K, Preheim SP, McGillicuddy DJ, Alm EJ, et al. High resolution time series reveals cohesive but short-lived communities in coastal plankton. Nat Commun. 2018;9:266.","journal-title":"Nat Commun"},{"key":"1972_CR148","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0229442","volume":"15","author":"L Weber","year":"2020","unstructured":"Weber L, Apprill A. Diel, daily, and spatial variation of coral reef seawater microbial communities. PLoS ONE. 2020;15: e0229442.","journal-title":"PLoS ONE"},{"key":"1972_CR149","doi-asserted-by":"publisher","first-page":"537","DOI":"10.1038\/s41564-018-0128-4","volume":"3","author":"C Laber","year":"2018","unstructured":"Laber C, Hunter J, Carvalho F, Collins J, Hunter E, Schieler B, et al. Coccolithovirus facilitation of carbon export in the North Atlantic. Nature Microbiology. 2018;3:537.","journal-title":"Nature Microbiology"},{"key":"1972_CR150","doi-asserted-by":"publisher","first-page":"569","DOI":"10.1038\/s41579-019-0222-5","volume":"17","author":"R Cavicchioli","year":"2019","unstructured":"Cavicchioli R, Ripple WJ, Timmis KN, Azam F, Bakken LR, Baylis M, et al. Scientists\u2019 warning to humanity: microorganisms and climate change. Nat Rev Microbiol. 2019;17:569\u201386.","journal-title":"Nat Rev Microbiol"}],"container-title":["Microbiome"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s40168-024-01972-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s40168-024-01972-0\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s40168-024-01972-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,2,12]],"date-time":"2025-02-12T20:12:53Z","timestamp":1739391173000},"score":1,"resource":{"primary":{"URL":"https:\/\/microbiomejournal.biomedcentral.com\/articles\/10.1186\/s40168-024-01972-0"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,1,16]]},"references-count":150,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["1972"],"URL":"https:\/\/doi.org\/10.1186\/s40168-024-01972-0","relation":{"has-preprint":[{"id-type":"doi","id":"10.21203\/rs.3.rs-4900069\/v1","asserted-by":"object"}]},"ISSN":["2049-2618"],"issn-type":[{"value":"2049-2618","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,1,16]]},"assertion":[{"value":"12 August 2024","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 November 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"16 January 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Samples were collected under the permit G12\/35236\u20131 issued by the Great Barrier Reef Marine Park Authority.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"11"}}