Acinas SG, Sanchez P, Salazar G et al (2021) Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities. Commun Biol 4:604
Ahasan MS, Picard J, Elliott L et al (2017) Evidence of antibiotic resistance in Enterobacteriales isolated from green sea turtles, Chelonia mydas on the Great Barrier Reef. Mar Pollut Bull 120:18–27
Albright R, Caldeira L, Hosfelt J et al (2016) Reversal of ocean acidification enhances net coral reef calcification. Nature 531:362–365
Anantharaman K, Brown CT, Hug LA et al (2016) Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. Nat Commun 7:13219
Anantharaman K, Hausmann B, Jungbluth SP et al (2018) Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle. ISME J 12:1715–1728
Arango-Argoty G, Garner E, Pruden A et al (2018) DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic data. Microbiome 6:23
Bay SK, Dong X, Bradley JA et al (2021) Trace gas oxidizers are widespread and active members of soil microbial communities. Nat Microbiol 6:246–256
Bednarz VN, van Hoytema N, Cardini U et al (2015) Dinitrogen fixation and primary productivity by carbonate and silicate reef sand communities of the Northern Red Sea. Mar Ecol Prog Ser 527:47–57
Bowers RM, Kyrpides NC, Stepanauskas R et al (2017) Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat Biotechnol 35:725–731
Boyd JA, Woodcroft BJ, Tyson GW (2018) GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes. Nucleic Acids Res 46:e59
Buongiorno J, Sipes K, Wasmund K et al (2020) Woeseiales transcriptional response to shallow burial in Arctic fjord surface sediment. PLoS One 15:e0234839
Chaumeil PA, Mussig AJ, Hugenholtz P et al (2019) GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics 36:1925–1927
Chen B, Yang Y, Liang X et al (2013) Metagenomic profiles of antibiotic resistance genes (ARGs) between human impacted estuary and deep ocean sediments. Environ Sci Technol 47:12753–12760
Chen J, Hanke A, Tegetmeyer HE et al (2017) Impacts of chemical gradients on microbial community structure. ISME J 11:920–931
Chen J, McIlroy SE, Archana A et al (2019) A pollution gradient contributes to the taxonomic, functional, and resistome diversity of microbial communities in marine sediments. Microbiome 7:104
Cordero PRF, Bayly K, Man Leung P et al (2019) Atmospheric carbon monoxide oxidation is a widespread mechanism supporting microbial survival. ISME J 13:2868–2881
Cuadrat RRC, Sorokina M, Andrade BG et al. Global ocean resistome revealed: Exploring antibiotic resistance gene abundance and distribution in TARA Oceans samples. GigaScience 2020;9
Delmont TO, Quince C, Shaiber A et al (2018) Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes. Nat Microbiol 3:804–813
Deschaseaux E, Stoltenberg L, Hrebien V et al (2019) Dimethylsulfide (DMS) fluxes from permeable coral reef carbonate sediments. Mar Chem 208:1–10
Devol AH (2015) Denitrification, anammox, and N2 production in marine sediments. Ann Rev Mar Sci 7:403–423
Dong X, Strous M (2019) An Integrated Pipeline for Annotation and Visualization of Metagenomic Contigs. Front Genet 10:999
Duprey NN, Yasuhara M, Baker DM (2016) Reefs of tomorrow: eutrophication reduces coral biodiversity in an urbanized seascape. Glob Chang Biol 22:3550–3565
Dyksma S, Bischof K, Fuchs BM et al (2016) Ubiquitous Gammaproteobacteria dominate dark carbon fixation in coastal sediments. ISME J 10:1939–1953
Edgar RC (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5:113
Engelberts JP, Robbins SJ, de Goeij JM et al (2020) Characterization of a sponge microbiome using an integrative genome-centric approach. ISME J 14:1100–1110
Eyre BD, Cyronak T, Drupp P et al (2018) Coral reefs will transition to net dissolving before end of century. Science 359:908–911
Fu L, Niu B, Zhu Z et al (2012) CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28:3150–3152
Glasl B, Bourne DG, Frade PR et al (2019) Microbial indicators of environmental perturbations in coral reef ecosystems. Microbiome 7:94
Glasl B, Robbins S, Frade PR et al (2020) Comparative genome-centric analysis reveals seasonal variation in the function of coral reef microbiomes. ISME J 14:1435–1450
Haro-Moreno JM, Lopez-Perez M, de la Torre JR et al (2018) Fine metagenomic profile of the Mediterranean stratified and mixed water columns revealed by assembly and recruitment. Microbiome 6:128
Hernandez-Zulueta J, Araya R, Vargas-Ponce O et al. First deep screening of bacterial assemblages associated with corals of the Tropical Eastern Pacific. FEMS Microbiol Ecol 2016;92
Hou L, Zheng Y, Liu M et al (2013) Anaerobic ammonium oxidation (anammox) bacterial diversity, abundance, and activity in marsh sediments of the Yangtze Estuary. J Geophys Res-Biogeo 118:1237–1246
Hou LJ, Liu M, Ou DN et al. Influences of the macrophyte (Scirpus mariqueter) on phosphorous geochemical properties in the intertidal marsh of the Yangtze Estuary. J Geophys Res-Biogeo 2008;113
Huettel M, Berg P, Kostka JE (2014) Benthic exchange and biogeochemical cycling in permeable sediments. Ann Rev Mar Sci 6:23–51
Hughes TP, Kerry JT, Alvarez-Noriega M et al (2017) Global warming and recurrent mass bleaching of corals. Nature 543:373–377
Imchen M, Kumavath R (2021) Metagenomic insights into the antibiotic resistome of mangrove sediments and their association to socioeconomic status. Environ Pollut 268:115795
Jain C, Rodriguez RL, Phillippy AM et al (2018) High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 9:5114
Janßen A, Wizemann A, Klicpera A et al. Sediment Composition and Facies of Coral Reef Islands in the Spermonde Archipelago, Indonesia. Front Mar Sci 2017;4
Kegler HF, Lukman M, Teichberg M et al (2017) Bacterial Community Composition and Potential Driving Factors in Different Reef Habitats of the Spermonde Archipelago, Indonesia. Front Microbiol 8:662
Kessler AJ, Chen YJ, Waite DW et al (2019) Bacterial fermentation and respiration processes are uncoupled in anoxic permeable sediments. Nat Microbiol 4:1014–1023
Kessler AJ, Rogers A, Cyronak T et al (2020) Pore water conditions driving calcium carbonate dissolution in reef sands. Geochim Cosmochim Ac 279:16–28
King GM (2007) Microbial carbon monoxide consumption in salt marsh sediments. FEMS Microbiol Ecol 59:2–9
Koren O, Rosenberg E (2006) Bacteria associated with mucus and tissues of the coral Oculina patagonica in summer and winter. Appl Environ Microbiol 72:5254–5259
Kumar S, Stecher G, Li M et al (2018) MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Mol Biol Evol 35:1547–1549
Li D, Luo R, Liu CM et al (2016) MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices. Methods 102:3–11
Li Y, Chen H, Song L et al (2021) Effects on microbiomes and resistomes and the source-specific ecological risks of heavy metals in the sediments of an urban river. J Hazard Mater 409:124472
Liu S, Su H, Pan YF et al (2020) Spatial and seasonal variations of antibiotics and antibiotic resistance genes and ecological risks in the coral reef regions adjacent to two typical islands in South China Sea. Mar Pollut Bull 158:111424
Matthews JL, Raina JB, Kahlke T et al (2020) Symbiodiniaceae-bacteria interactions: rethinking metabolite exchange in reef-building corals as multi-partner metabolic networks. Environ Microbiol 22:1675–1687
Ning Z, Yu K, Wang Y et al (2019) Carbon and nutrient dynamics of permeable carbonate and silicate sands adjacent to coral reefs around Weizhou Island in the northern South China Sea. Estuar Coast Shelf S 225:106229
Olm MR, Brown CT, Brooks B et al (2017) dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. ISME J 11:2864–2868
Olm MR, Crits-Christoph A, Diamond S et al (2020) Consistent Metagenome-Derived Metrics Verify and Delineate Bacterial Species Boundaries. mSystems 5:e00731–e00719
Ortiz M, Leung PM, Shelley G et al. A genome compendium reveals diverse metabolic adaptations of Antarctic soil microorganisms. bioRxiv 2020, DOI 10.1101/2020.08.06.239558
Park SJ, Andrei AS, Bulzu PA et al (2020) Expanded Diversity and Metabolic Versatility of Marine Nitrite-Oxidizing Bacteria Revealed by Cultivation- and Genomics-Based Approaches. Appl Environ Microbiol 86:e01667–e01620
Patro R, Duggal G, Love MI et al (2017) Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods 14:417–419
Pearman JK, Aylagas E, Voolstra CR et al (2019) Disentangling the complex microbial community of coral reefs using standardized Autonomous Reef Monitoring Structures (ARMS). Mol Ecol 28:3496–3507
Pernice M, Raina JB, Radecker N et al (2020) Down to the bone: the role of overlooked endolithic microbiomes in reef coral health. ISME J 14:325–334
Polonia AR, Cleary DF, Freitas R et al (2015) The putative functional ecology and distribution of archaeal communities in sponges, sediment and seawater in a coral reef environment. Mol Ecol 24:409–423
Ragsdale SW, Pierce E (2008) Acetogenesis and the Wood-Ljungdahl pathway of CO2 fixation. Biochim Biophys Acta 1784:1873–1898
Richardson LL, Goldberg WM, Kuta KG et al (1998) Florida's mystery coral-killer identified. Nature 392:557–558
Robbins SJ, Singleton CM, Chan CX et al (2019) A genomic view of the reef-building coral Porites lutea and its microbial symbionts. Nat Microbiol 4:2090–2100
Robbins SJ, Song W, Engelberts JP et al (2021) A genomic view of the microbiome of coral reef demosponges. ISME J 15:1641–1654
Roy A, Das BK, Bhattacharya J (2011) Development and Validation of a Spectrophotometric Method to Measure Sulfate Concentrations in Mine Water without Interference. Mine Water Environ 30:169–174
Rusch A, Gaidos E (2013) Nitrogen-cycling bacteria and archaea in the carbonate sediment of a coral reef. Geobiology 11:472–484
Salazar G, Paoli L, Alberti A et al (2019) Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome. Cell 179:1068–1083 e21
Sanchez-Baracaldo P, Cardona T (2020) On the origin of oxygenic photosynthesis and Cyanobacteria. New Phytol 225:1440–1446
Schottner S, Pfitzner B, Grunke S et al (2011) Drivers of bacterial diversity dynamics in permeable carbonate and silicate coral reef sands from the Red Sea. Environ Microbiol 13:1815–1826
Schuller-Levis GB, Park E (2003) Taurine: new implications for an old amino acid. FEMS Microbiol Lett 226:195–202
Shadrack RS, Pohler S, Dutra LXC et al (2020) Carbonate sediments from Maui bay (coral coast, Fiji) reflect importance of coral reef conservation. Ocean Coast Manag 198:105381
Shaffer M, Borton MA, McGivern BB et al (2020) DRAM for distilling microbial metabolism to automate the curation of microbiome function. Nucleic Acids Res 48:8883–8900
Singleton CM, Petriglieri F, Kristensen JM et al. Connecting structure to function with the recovery of over 1000 high-quality metagenome-assembled genomes from activated sludge using long-read sequencing. Nat Commun 2021;12: 2009
Uritskiy GV, DiRuggiero J, Taylor J (2018) MetaWRAP-a flexible pipeline for genome-resolved metagenomic data analysis. Microbiome 6:158
Van Goethem MW, Pierneef R, Bezuidt OKI et al (2018) A reservoir of ‘historical’ antibiotic resistance genes in remote pristine Antarctic soils. Microbiome 6:40
Vigneron A, Cruaud P, Culley AI et al (2021) Genomic evidence for sulfur intermediates as new biogeochemical hubs in a model aquatic microbial ecosystem. Microbiome 9:46
Vizcaino MI, Johnson WR, Kimes NE et al (2010) Antimicrobial resistance of the coral pathogen Vibrio coralliilyticus and Caribbean sister phylotypes isolated from a diseased octocoral. Microb Ecol 59:646–657
Wang JL, Du JZ, Baskaran M et al (2016) Mobile mud dynamics in the East China Sea elucidated using 210Pb, 137Cs, 7Be, and 234Th as tracers. J Geophys Res-Oceans 121:224–239
Woodcroft BJ, Singleton CM, Boyd JA et al (2018) Genome-centric view of carbon processing in thawing permafrost. Nature 560:49–54
Xu X, Zhu Q, Zhou Q et al (2018) An improved method for quantitatively measuring the sequences of total organic carbon and black carbon in marine sediment cores. J Oceanol Limnol 36:105–113
Zhao R, Yu K, Zhang J et al (2020) Deciphering the mobility and bacterial hosts of antibiotic resistance genes under antibiotic selection pressure by metagenomic assembly and binning approaches. Water Res 186:116318
Zhou J, Bruns MA, Tiedje JM (1996) DNA recovery from soils of diverse composition. Appl Environ Microbiol 62:316–322
Zhou Z, Tran PQ, Breister AM et al. METABOLIC: a scalable high-throughput metabolic and biogeochemical functional trait profiler based on microbial genomes. bioRxiv 2020, DOI 10.1101/761643