Abstract
Interactions between chemodiverse dissolved organic matter (DOM) and biodiverse microbes are governed by a myriad of intrinsic and extrinsic factors which are not well understood. Here, we update and bridge the gap of this interdisciplinary theme comprehensively. At an ecosystem level, aquatic ecosystems dominated by algae-sourced DOM (e.g., eutrophic lake or coastal upwelling areas) harbor more biolabile DOM, such as directly assimilable monomers and readily hydrolysable biopolymers. However, other ecosystems prevailed by DOM supply from soil and vascular plants (e.g., river or wetland) have more biorefractory DOM, such as low molecular weight (LMW) residue of aliphatic C skeletons and geopolymers. A variety of heterotrophic bacteria, archaea, fungi, phagotrophic protists, and even photoautotrophic phytoplankton shows genomic and/or culturing experimental evidence of being able to process a diverse type of organics. The various biodegradable organics have different chemical structures and chemical bonds such as carbohydrates, amino acids, proteins, lignins, lipids, carboxylic acids, humic acids, hydrocarbons, and nanoplastics. Meanwhile, bio-production of metabolism intermediates and/or biorefractory organics (e.g., carboxyl-rich alicyclic molecules, CRAM) is observed despite general decay of bulk dissolved organic carbon (DOC) during bioassay experiments. In particular, emerging evidence shows that archaea contribute significantly to biomass in the marine mesopelagic zone and subsurface environments and their abundance often increases with depth in sediments. Furthermore, not only intrinsic factors (e.g., DOM composition and structure), but also extrinsic ones (e.g., sunlight and dissolved oxygen) play important roles in interplays between DOM and microbes.
Similar content being viewed by others
References
Ali P, Shah A A, Hasan F, Hertkorn N, Gonsior M, Sajjad W, Chen F. 2020. A glacier bacterium produces high yield of cryoprotective exopolysaccharide. Front Microbiol, 10, https://doi.org/10.3389/fmicb.2019.03096
Al-Nasrawi H. 2012. Biodegradation of crude oil by fungi isolated from Gulf of Mexico. J Bioremed Biodegrad, 3: 147
Aluwihare L I, Repeta D J. 1999. A comparison of the chemical characteristics of oceanic DOM and extracellular DOM produced by marine algae. Mar Ecol Prog Ser, 186: 105–117
Aluwihare L I, Repeta D J, Pantoja S, Johnson C G. 2005. Two chemically distinct pools of organic nitrogen accumulate in the ocean. Science, 308: 1007–1010
Amaral V, Graeber D, Calliari D, Alonso C. 2016. Strong linkages between DOM optical properties and main clades of aquatic bacteria. Limnol Oceanogr, 61: 906–918
Amon R M W, Benner R. 1994. Rapid cycling of high-molecular-weight dissolved organic matter in the ocean. Nature, 369: 549–552
Amon R M W, Benner R. 1996. Bacterial utilization of different size classes of dissolved organic matter. Limnol Oceanogr, 41: 41–51
Ankrah N Y D, May A L, Middleton J L, Jones D R, Hadden M K, Gooding J R, LeCleir G R, Wilhelm S W, Campagna S R, Buchan A. 2014. Phage infection of an environmentally relevant marine bacterium alters host metabolism and lysate composition. ISME J, 8: 1089–1100
Antony R, Willoughby A S, Grannas A M, Catanzano V, Sleighter R L, Thamban M, Hatcher P G. 2018. Photo-biochemical transformation of dissolved organic matter on the surface of the coastal East Antarctic ice sheet. Biogeochemistry, 141: 229–247
Arístegui J, Agustí S, Middelburg J J, Duarte C M. 2006. Respiration in the Mesopelagic and Bathypelagic Zones of the Oceans. Oxford: Oxford University Press. 181–205
Arnosti C. 2003. 13-microbial extracellular enzymes and their role in dissolved organic matter cycling. In: Findlay S E G, Sinsabaugh R L, eds. Aquatic Ecosystems. Burlington: Academic Press. 315–342
Arnosti C, Wietz M, Brinkhoff T, Hehemann J H, Probandt D, Zeugner L, Amann R. 2021. The biogeochemistry of marine polysaccharides: Sources, inventories, and bacterial drivers of the carbohydrate cycle. Annu Rev Mar Sci, 13: 81–108
Azam F. 1998. Microbial control of oceanic carbon flux: The plot thickens. Science, 280: 694–696
Azam F, Fenchel T, Field J G, Gray J S, Meyer-Reil L A, Thingstad F. 1983. The ecological role of water-column microbes in the sea. Mar Ecol Prog Ser, 10: 257–263
Azam F, Smith D C, Steward G F, Hagström A. 1994. Bacteria-organic matter coupling and its significance for oceanic carbon cycling. Microb Ecol, 28: 167–179
Baltar F, Alvarez-Salgado X A, Arístegui J, Benner R, Hansell D A, Herndl G J, Lønborg C. 2021. What is refractory organic matter in the ocean? Front Mar Sci, 8, https://doi.org/10.3389/fmars.2021.642637
Battin T J, Kaplan L A, Findlay S, Hopkinson C S, Marti E, Packman A I, Newbold J D, Sabater F. 2008. Biophysical controls on organic carbon fluxes in fluvial networks. Nat Geosci, 1: 95–100
Bayer B, Hansman R L, Bittner M J, Noriega-Ortega B E, Niggemann J, Dittmar T, Herndl G J. 2019. Ammonia-oxidizing archaea release a suite of organic compounds potentially fueling prokaryotic heterotrophy in the ocean. Environ Microbiol, 21: 4062–4075
Benner R, Amon R M W. 2015. The size-reactivity continuum of major bioelements in the ocean. Annu Rev Mar Sci, 7: 185–205
Benner R, Biddanda B. 1998. Photochemical transformations of surface and deep marine dissolved organic matter: Effects on bacterial growth. Limnol Oceanogr, 43: 1373–1378
Benner R, Kaiser K. 2011. Biological and photochemical transformations of amino acids and lignin phenols in riverine dissolved organic matter. Biogeochemistry, 102: 209–222
Benner R, Pakulski J D, McCarthy M, Hedges J I, Hatcher P G. 1992. Bulk chemical characteristics of dissolved organic matter in the ocean. Science, 255: 1561–1564
Berg G, Rybakova D, Fischer D, Cernava T, Vergès M C C, Charles T, Chen X, Cocolin L, Eversole K, Corral G H, Kazou M, Kinkel L, Lange L, Lima N, Loy A, Macklin J A, Maguin E, Mauchline T, McClure R, Mitter B, Ryan M, Sarand I, Smidt H, Schelkle B, Roume H, Kiran G S, Selvin J, Souza R S C, van Overbeek L, Singh B K, Wagner M, Walsh A, Sessitsch A, Schloter M. 2020. Microbiome definition re-visited: Old concepts and new challenges. Microbiome, 8: 103
Bergauer K, Fernandez-Guerra A, Garcia J A L, Sprenger R R, Stepanauskas R, Pachiadaki M G, Jensen O N, Herndl G J. 2018. Organic matter processing by microbial communities throughout the Atlantic water column as revealed by metaproteomics. Proc Natl Acad Sci USA, 115: E400
Bertrand E M, McCrow J P, Moustafa A, Zheng H, McQuaid J B, Delmont T O, Post A F, Sipler R E, Spackeen J L, Xu K, Bronk D A, Hutchins D A, Allen A E. 2015. Phytoplankton bacterial interactions mediate micronutrient colimitation at the coastal Antarctic sea ice edge. Proc Natl Acad Sci USA, 112: 9938–9943
Biddanda B, Benner R. 1997. Carbon, nitrogen, and carbohydrate fluxes during the production of particulate and dissolved organic matter by marine phytoplankton. Limnol Oceanogr, 42: 506–518
Biddanda B, Ogdahl M, Cotner J. 2001. Dominance of bacterial metabolism in oligotrophic relative to eutrophic waters. Limnol Oceanogr, 46: 730–739
Biersmith A, Benner R. 1998. Carbohydrates in phytoplankton and freshly produced dissolved organic matter. Mar Chem, 63: 131–144
Blough N V, Zepp R G. 1995. Reactive oxygen species in natural waters. In: Foote C S, Valentine J S, Greenberg A, Liebman J F, eds. Active Oxygen in Chemistry. Dordrecht: Springer Netherlands. 280–333
Bochdansky A B, Clouse M A, Herndl G J. 2017. Eukaryotic microbes, principally fungi and labyrinthulomycetes, dominate biomass on bathypelagic marine snow. ISME J, 11: 362–373
Broman E, Asmala E, Carstensen J, Pinhassi J, Dopson M. 2019. Distinct coastal microbiome populations associated with autochthonous- and allochthonous-like dissolved organic matter. Front Microbiol, 10, https://doi.org/10.3389/fmicb.2019.02579
Bronk D A. 2002. Chapter 5-Dynamics of DON. In: Hansell D A, Carlson C A, eds. Biogeochemistry of Marine Dissolved Organic Matter. San Diego: Academic Press. 153–247
Bugg T D H, Ahmad M, Hardiman E M, Rahmanpour R. 2011. Pathways for degradation of lignin in bacteria and fungi. Nat Prod Rep, 28: 1883–1896
Cai M, Liu Y, Yin X, Zhou Z, Friedrich M W, Richter-Heitmann T, Nimzyk R, Kulkarni A, Wang X, Li W, Pan J, Yang Y, Gu J D, Li M. 2020. Diverse Asgard archaea including the novel phylum Gerdarchaeota participate in organic matter degradation. Sci China Life Sci, 63: 886–897
Carlson C A. 2002. Chapter 4-production and removal processes. In: Hansell D A, Carlson C A, eds. Biogeochemistry of Marine Dissolved Organic Matter. San Diego: Academic Press. 91–151
Carini P, White A E, Campbell E O, Giovannoni S J. 2014. Methane production by phosphate-starved SAR11 chemoheterotrophic marine bacteria. Nat Commun, 5: 4346
Cavicchioli R, Ripple W J, Timmis K N, Azam F, Bakken L R, Baylis M, Behrenfeld M J, Boetius A, Boyd P W, Classen A T, Crowther T W, Danovaro R, Foreman C M, Huisman J, Hutchins D A, Jansson J K, Karl D M, Koskella B, Mark Welch D B, Martiny J B H, Moran M A, Orphan V J, Reay D S, Remais J V, Rich V I, Singh B K, Stein L Y, Stewart F J, Sullivan M B, van Oppen M J H, Weaver S C, Webb E A, Webster N S. 2019. Scientists’ warning to humanity: Microorganisms and climate change. Nat Rev Microbiol, 17: 569–586
Chen J, Li H, Zhang Z, He C, Shi Q, Jiao N, Zhang Y. 2020. DOC dynamics and bacterial community succession during long-term degradation of Ulva prolifera and their implications for the legacy effect of green tides on refractory DOC pool in seawater. Water Res, 185: 116268
Chen M, Hur J. 2015. Pre-treatments, characteristics, and biogeochemical dynamics of dissolved organic matter in sediments: A review. Water Res, 79: 10–25
Chen M, Jaffé R. 2014. Photo- and bio-reactivity patterns of dissolved organic matter from biomass and soil leachates and surface waters in a subtropical wetland. Water Res, 61: 181–190
Chen M, Jaffé R. 2016. Quantitative assessment of photo- and bio-reactivity of chromophoric and fluorescent dissolved organic matter from biomass and soil leachates and from surface waters in a subtropical wetland. Biogeochemistry, 129: 273–289
Chen M, Kim J H, Lee Y K, Lee D H, Jin Y K, Hur J. 2021. Subsea permafrost as a potential major source of dissolved organic matter to the East Siberian Arctic Shelf. Sci Total Environ, 777: 146100
Chen M, Kim J H, Nam S I, Niessen F, Hong W L, Kang M H, Hur J. 2016. Production of fluorescent dissolved organic matter in Arctic Ocean sediments. Sci Rep, 6: 39213
Chin Y P, Aiken G, O’Loughlin E. 1994. Molecular weight, polydispersity, and spectroscopic properties of aquatic humic substances. Environ Sci Technol, 28: 1853–1858
Churchill S A, Harper J P, Churchill P F. 1999. Isolation and characterization of a Mycobacterium species capable of degrading three- and four-ring aromatic and aliphatic hydrocarbons. Appl Environ Microbiol, 65: 549–552
Clark L L, Ingall E D, Benner R. 1998. Marine phosphorus is selectively remineralized. Nature, 393: 426
Colatriano D, Tran P Q, Guéguen C, Williams W J, Lovejoy C, Walsh D A. 2018. Genomic evidence for the degradation of terrestrial organic matter by pelagic Arctic Ocean Chloroflexi bacteria. Commun Biol, 1: 90
Cole J J, Findlay S, Pace M L. 1988. Bacterial production in fresh and saltwater ecosystems: A cross-system overview. Mar Ecol Prog Ser, 43: 1–10
Cory R M, Ward C P, Crump B C, Kling G W. 2014. Sunlight controls water column processing of carbon in arctic fresh waters. Science, 345: 925–928
Cory R M, Kling G W. 2018. Interactions between sunlight and microorganisms influence dissolved organic matter degradation along the aquatic continuum. Limnol Oceanogr Lett, 3: 102–116
Cottrell M T, Kirchman D L. 2000. Natural assemblages of marine proteobacteria and members of the Cytophaga-Flavobacter cluster consuming low- and high-molecular-weight dissolved organic matter. Appl Environ Microbiol, 66: 1692–1697
Covert J S, Moran M A. 2001. Molecular characterization of estuarine bacterial communities that use high- and low-molecular weight fractions of dissolved organic carbon. Aquat Microb Ecol, 25: 127–139
Cunliffe M, Hollingsworth A, Bain C, Sharma V, Taylor J D. 2017. Algal polysaccharide utilisation by saprotrophic planktonic marine fungi. Fungal Ecol, 30: 135–138
Dang H, Jiao N. 2014. Perspectives on the microbial carbon pump with special reference to microbial respiration and ecosystem efficiency in large estuarine systems. Biogeosciences, 11: 3887–3898
Dashtban M, Schraft H, Syed T A, Qin W. 2010. Fungal biodegradation and enzymatic modification of lignin. Int J Biochem Mol Biol, 1: 36–50
de Haan H. 1977. Effect of benzoate on microbial decomposition of fulvic acids in Tjeukemeer (the Netherlands). Limnol Oceanogr, 22: 38–44
del Giorgio P A, Davis J. 2003. Chapter 17-patterns in dissolved organic matter lability and consumption across aquatic ecosystems. In: Findlay S E G, Sinsabaugh R L, eds. Aquatic Ecosystems. Burlington: Academic Press. 399–424
de Melo M L, Kothawala D N, Bertilsson S, Amaral J H, Forsberg B, Sarmento H. 2020. Linking dissolved organic matter composition and bacterioplankton communities in an Amazon floodplain system. Limnol Oceanogr, 65: 63–76
Detmers J, Strauss H, Schulte U, Bergmann A, Knittel K, Kuever J. 2004. FISH shows that Desulfotomaculum spp. are the dominating sulfate-reducing bacteria in a pristine aquifer. Microb Ecol, 47: 236–242
Dittmar T, Lennartz S T, Buck-Wiese H, Hansell D A, Santinelli C, Vanni C, Blasius B, Hehemann J H. 2021. Enigmatic persistence of dissolved organic matter in the ocean. Nat Rev Earth Environ, 2: 570–583
Dittmar T, Paeng J. 2009. A heat-induced molecular signature in marine dissolved organic matter. Nat Geosci, 2: 175–179
Dittmar T, Stubbins A. 2014. Dissolved organic matter in aquatic systems. In: Holland H D, Turekian K K, eds. Treatise on Geochemistry. 2nd ed. Oxford: Elsevier. 125–156
Dong X, Greening C, Rattray J E, Chakraborty A, Chuvochina M, Mayumi D, Dolfing J, Li C, Brooks J M, Bernard B B, Groves R A, Lewis I A, Hubert C R J. 2019. Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments. Nat Commun, 10: 1816
Dong X, Rattray J E, Campbell D C, Webb J, Chakraborty A, Adebayo O, Matthews S, Li C, Fowler M, Morrison N M, MacDonald A, Groves R A, Lewis I A, Wang S H, Mayumi D, Greening C, Hubert C R J. 2020. Thermogenic hydrocarbon biodegradation by diverse depth-stratified microbial populations at a Scotian Basin cold seep. Nat Commun, 11: 5825
Dyhrman S T, Benitez-Nelson C R, Orchard E D, Haley S T, Pellechia P J. 2009. A microbial source of phosphonates in oligotrophic marine systems. Nat Geosci, 2: 696–699
Ebrahimi A, Schwartzman J, Cordero O X. 2019. Cooperation and spatial self-organization determine rate and efficiency of particulate organic matter degradation in marine bacteria. Proc Natl Acad Sci USA, 116: 23309–23316
Farag I F, Biddle J F, Zhao R, Martino A J, House C H, León-Zayas R I. 2020. Metabolic potentials of archaeal lineages resolved from metagenomes of deep Costa Rica sediments. ISME J, 14: 1345–1358
Field C B, Behrenfeld M J, Randerson J T, Falkowski P. 1998. Primary production of the biosphere: Integrating terrestrial and oceanic components. Science, 281: 237–240
Findlay S, Sinsabaugh R L. 1999. Unravelling the sources and bioavailability of dissolved organic matter in lotic aquatic ecosystems. Mar Freshwater Res, 50: 781–790
Findlay S, Tank J, Dye S, Valett H M, Mulholland P J, McDowell W H, Johnson S L, Hamilton S K, Edmonds J, Dodds W K, Bowden W B. 2002. A cross-system comparison of bacterial and fungal biomass in detritus pools of headwater streams. Microb Ecol, 43: 55–66
Flemming H C, Wuertz S. 2019. Bacteria and archaea on Earth and their abundance in biofilms. Nat Rev Microbiol, 17: 247–260
Follett C L, Repeta D J, Rothman D H, Xu L, Santinelli C. 2014. Hidden cycle of dissolved organic carbon in the deep ocean. Proc Natl Acad Sci USA, 111: 16706–16711
Foreman C M, Covert J S. 2003. Chapter 14-linkages between dissolved organic matter composition and bacterial community structure. In: Findlay S E G, Sinsabaugh R L, eds. Aquatic Ecosystems. Burlington: Academic Press. 343–362
Fouilland E, Mostajir B. 2010. Revisited phytoplanktonic carbon dependency of heterotrophic bacteria in freshwaters, transitional, coastal and oceanic waters. FEMS Microbiol Ecol, 73: 419–429
Gao L, Gu J D. 2021. A new unified conceptual framework involving maintenance energy, metabolism and toxicity for research on degradation of organic pollutants. Int Biodeter Biodegr, 162: 105253
Gao H, Zepp R G. 1998. Factors influencing photoreactions of dissolved organic matter in a coastal river of the southeastern United States. Environ Sci Technol, 32: 2940–2946
Gattuso J P, Frankignoulle M, Wollast R. 1998. Carbon and carbonate metabolism in coastal aquatic ecosystems. Annu Rev Ecol Syst, 29: 405–434
Ghosal D, Ghosh S, Dutta T K, Ahn Y. 2016. Current state of knowledge in microbial degradation of polycyclic aromatic hydrocarbons (PAHs): A review. Front Microbiol, 7, https://doi.org/10.3389/fmicb.2016.01369
Giovannoni S J. 2017. SAR11 bacteria: The most abundant plankton in the oceans. Annu Rev Mar Sci, 9: 231–255
Glockner F O, Fuchs B M, Amann R. 1999. Bacterioplankton compositions of lakes and oceans: A first comparison based on fluorescence in situ hybridization. Appl Environ Microbiol, 65: 3721–3726
Golyshin P N, Chernikova T N, Abraham W R, Lünsdorf H, Timmis K N, Yakimov M M. 2002. Oleiphilaceae fam. nov., to include Oleiphilus messinensis gen. nov., sp. nov., a novel marine bacterium that obligately utilizes hydrocarbons.. Int J Systatic Evolary Microbiol, 52: 901–911
Gómez-Consarnau L, González J M, Coll-Lladó M, Gourdon P, Pascher T, Neutze R, Pedrós-Alió C, Pinhassi J. 2007. Light stimulates growth of proteorhodopsin-containing marine Flavobacteria. Nature, 445: 210–213
Gonsior M, Peake B M, Cooper W T, Podgorski D C, D’Andrilli J, Dittmar T, Cooper W J. 2011. Characterization of dissolved organic matter across the subtropical convergence off the South Island, New Zealand. Mar Chem, 123: 99–110
Gu J D. 2021. Biodegradability of plastics: The issues, recent advances, and future perspectives. Environ Sci Pollut Res, 28: 1278–1282
Hammel K E. 1997. Fungal degradation of lignin. In: Cadisch G and Giller K E, eds. Driven by Nature: Plant Litter Quality and Decomposition. Wallingford: CAB International. 33–45
Hansell D A. 2013. Recalcitrant dissolved organic carbon fractions. Annu Rev Mar Sci, 5: 421–445
Hansell D A, Carlson C A, Repeta D J, Schlitzer R. 2009. Dissolved organic matter in the ocean: A controversy stimulates new insights. Oceanography, 22: 202–211
Harvey G R, Boran D A, Chesal L A, Tokar J M. 1983. The structure of marine fulvic and humic acids. Mar Chem, 12: 119–132
Hawkes J A, Rossel P E, Stubbins A, Butterfield D, Connelly D P, Achterberg E P, Koschinsky A, Chavagnac V, Hansen C T, Bach W, Dittmar T. 2015. Efficient removal of recalcitrant deep-ocean dissolved organic matter during hydrothermal circulation. Nat Geosci, 8: 856–860
Hedges J I. 1992. Global biogeochemical cycles: Progress and problems. Mar Chem, 39: 67–93
Hedges J I, Keil R G. 1995. Sedimentary organic matter preservation: An assessment and speculative synthesis. Mar Chem, 49: 81–115
Hernes P J, Benner R. 2006. Terrigenous organic matter sources and reactivity in the North Atlantic Ocean and a comparison to the Arctic and Pacific oceans. Mar Chem, 100: 66–79
Hertkorn N, Benner R, Frommberger M, Schmitt-Kopplin P, Witt M, Kaiser K, Kettrup A, Hedges J I. 2006. Characterization of a major refractory component of marine dissolved organic matter. Geochim Cosmochim Acta, 70: 2990–3010
Hertkorn N, Harir M, Koch B P, Michalke B, Schmitt-Kopplin P. 2013. High-field NMR spectroscopy and FTICR mass spectrometry: Powerful discovery tools for the molecular level characterization of marine dissolved organic matter. Biogeosciences, 10: 1583–1624
Herzsprung P, Hertkorn N, Friese K, Schmitt-Kopplin P. 2010. Photochemical degradation of natural organic sulfur compounds (CHOS) from iron-rich mine pit lake pore waters-an initial understanding from evaluation of single-elemental formulae using ultra-high-resolution mass spectrometry. Rapid Commun Mass Spectrom, 24: 2909–2924
Holmer M. 2019. Chapter 13-productivity and biogeochemical cycling in seagrass ecosystems. In: Perillo G M E, Wolanski E, Cahoon D R, Hopkinson C S, eds. Coastal Wetlands. Amsterdam: Elsevier. 443–477
Horvath R S. 1972. Microbial co-metabolism and the degradation of organic compounds in nature. Bacteriol Rev, 36: 146–155
Hou J, Sievert S M, Wang Y, Seewald J S, Natarajan V P, Wang F, Xiao X. 2020. Microbial succession during the transition from active to inactive stages of deep-sea hydrothermal vent sulfide chimneys. Microbiome, 8: 102
Hur J. 2011. Microbial changes in selected operational descriptors of dissolved organic matter from various sources in a watershed. Water Air Soil Pollut, 215: 465–476
Hur J, Park M H, Schlautman M A. 2009. Microbial transformation of dissolved leaf litter organic matter and its effects on selected organic matter operational descriptors. Environ Sci Technol, 43: 2315–2321
Imachi H, Nobu M K, Nakahara N, Morono Y, Ogawara M, Takaki Y, Takano Y, Uematsu K, Ikuta T, Ito M, Matsui Y, Miyazaki M, Murata K, Saito Y, Sakai S, Song C, Tasumi E, Yamanaka Y, Yamaguchi T, Kamagata Y, Tamaki H, Takai K. 2020. Isolation of an archaeon at the prokaryote-eukaryote interface. Nature, 577: 519–525
Inagaki F, Hinrichs K U, Kubo Y, Bowles M W, Heuer V B, Hong W L, Hoshino T, Ijiri A, Imachi H, Ito M, Kaneko M, Lever M A, Lin Y S, Methé B A, Morita S, Morono Y, Tanikawa W, Bihan M, Bowden S A, Elvert M, Glombitza C, Gross D, Harrington G J, Hori T, Li K, Limmer D, Liu C H, Murayama M, Ohkouchi N, Ono S, Park Y S, Phillips S C, Prieto-Mollar X, Purkey M, Riedinger N, Sanada Y, Sauvage J, Snyder G, Susilawati R, Takano Y, Tasumi E, Terada T, Tomaru H, Trembath-Reichert E, Wang D T, Yamada Y. 2015. Exploring deep microbial life in coal-bearing sediment down to ∼2.5 km below the ocean floor. Science, 349: 420–424
Ivanovsky R N, Lebedeva N V, Keppen O I, Chudnovskaya A V. 2020. Release of photosynthetically fixed carbon as dissolved organic matter by anoxygenic phototrophic bacteria. Microbiology, 89: 28–34
Jiao N, Cai R, Zheng Q, Tang K, Liu J, Jiao F, Wallace D, Chen F, Li C, Amann R, Benner R, Azam F. 2018. Unveiling the enigma of refractory carbon in the ocean. Natl Sci Rev, 5: 459–463
Jiao N, Herndl G J, Hansell D A, Benner R, Kattner G, Wilhelm S W, Kirchman D L, Weinbauer M G, Luo T, Chen F, Azam F. 2010. Microbial production of recalcitrant dissolved organic matter: Long-term carbon storage in the global ocean. Nat Rev Microbiol, 8: 593–599
Jiao N, Robinson C, Azam F, Thomas H, Baltar F, Dang H, Hardman-Mountford N J, Johnson M, Kirchman D L, Koch B P, Legendre L, Li C, Liu J, Luo T, Luo Y W, Mitra A, Romanou A, Tang K, Wang X, Zhang C, Zhang R. 2014. Mechanisms of microbial carbon sequestration in the ocean—Future research directions. Biogeosciences, 11: 5285–5306
Jiao N, Zheng Q. 2011. The microbial carbon pump: From genes to ecosystems. Appl Environ Microbiol, 77: 7439–7444
Johnson W M, Kido Soule M C, Kujawinski E B. 2016. Evidence for quorum sensing and differential metabolite production by a marine bacterium in response to DMSP. ISME J, 10: 2304–2316
Kaiser K, Benner R. 2008. Erratum: Major bacterial contribution to the ocean reservoir of detrital organic carbon and nitrogen. Limnol Oceanogr, 53: 1192
Kaiser K, Benner R. 2009. Biochemical composition and size distribution of organic matter at the Pacific and Atlantic time-series stations. Mar Chem, 113: 63–77
Kaiser K, Benner R. 2012. Organic matter transformations in the upper mesopelagic zone of the North Pacific: Chemical composition and linkages to microbial community structure. J Geophys Res, 117: C01023
Karner M B, DeLong E F, Karl D M. 2001. Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature, 409: 507–510
Kawasaki N, Benner R. 2006. Bacterial release of dissolved organic matter during cell growth and decline: Molecular origin and composition. Limnol Oceanogr, 51: 2170–2180
Kepkay P E, Johnson B D. 1989. Coagulation on bubbles allows microbial respiration of oceanic dissolved organic carbon. Nature, 338: 63–65
Kirchman D. 2002. The ecology of Cytophaga-Flavobacteria in aquatic environments. FEMS Microbiol Ecol, 39: 91–100
Kirchman D L. 2003. Chapter 9-the contribution of monomers and other low-molecular weight compounds to the flux of dissolved organic material in aquatic ecosystems. In: Findlay S E G, Sinsabaugh R L, eds. Aquatic Ecosystems. Burlington: Academic Press. 217–241
Kirchman D L. 2018. Microbial proteins for organic material degradation in the deep ocean. Proc Natl Acad Sci USA, 115: 445–447
Kirchman D L, Suzuki Y, Garside C, Ducklow H W. 1991. High turnover rates of dissolved organic carbon during a spring phytoplankton bloom. Nature, 352: 612–614
Kleber M, Bourg I C, Coward E K, Hansel C M, Myneni S C B, Nunan N. 2021. Dynamic interactions at the mineral-organic matter interface. Nat Rev Earth Environ, 2: 402–421
Koch H, Dürwald A, Schweder T, Noriega-Ortega B, Vidal-Melgosa S, Hehemann J H, Dittmar T, Freese H M, Becher D, Simon M, Wietz M. 2019. Biphasic cellular adaptations and ecological implications of Alteromonasmacleodii degrading a mixture of algal polysaccharides. ISME J, 13: 92–103
Koch B P, Kattner G, Witt M, Passow U. 2014. Molecular insights into the microbial formation of marine dissolved organic matter: Recalcitrant or labile? Biogeosciences, 11: 4173–4190
Koehler B, Landelius T, Weyhenmeyer G A, Machida N, Tranvik L J. 2014. Sunlight-induced carbon dioxide emissions from inland waters. Glob Biogeochem Cycle, 28: 696–711
Koh E Y, Atamna-Ismaeel N, Martin A, Cowie R O M, Beja O, Davy S K, Maas E W, Ryan K G. 2010. Proteorhodopsin-bearing bacteria in Antarctic sea ice. Appl Environ Microbiol, 76: 5918–5925
Krause-Jensen D, Duarte C M. 2016. Substantial role of macroalgae in marine carbon sequestration. Nat Geosci, 9: 737–742
Kubo K, Lloyd K G F Biddle J, Amann R, Teske A, Knittel K. 2012. Archaea of the Miscellaneous Crenarchaeotal Group are abundant, diverse and widespread in marine sediments. ISME J, 6: 1949–1965
Kujawinski E B. 2011. The impact of microbial metabolism on marine dissolved organic matter. In: Carlson C A, Giovannoni S J, eds. Annual Review of Marine Science. 567–599
Laane R W P M, Koole L. 1982. The relation between fluorescence and dissolved organic carbon in the Ems-Dollart estuary and the Western Wadden Sea. Netherlands J Sea Res, 15: 217–227
Lauro F M, McDougald D, Thomas T, Williams T J, Egan S, Rice S, DeMaere M Z, Ting L, Ertan H, Johnson J, Ferriera S, Lapidus A, Anderson I, Kyrpides N, Munk A C, Detter C, Han C S, Brown M V, Robb F T, Kjelleberg S, Cavicchioli R. 2009. The genomic basis of trophic strategy in marine bacteria. Proc Natl Acad Sci USA, 106: 15527–15533
Iavorivska L, Boyer E W, DeWalle D R. 2016. Atmospheric deposition of organic carbon via precipitation. Atmos Environ, 146: 153–163
Lazar C S, Baker B J, Seitz K, Hyde A S, Dick G J, Hinrichs K U, Teske A P. 2016. Genomic evidence for distinct carbon substrate preferences and ecological niches of Bathyarchaeota in estuarine sediments. Environ Microbiol, 18: 1200–1211
Lechtenfeld O J, Hertkorn N, Shen Y, Witt M, Benner R. 2015. Marine sequestration of carbon in bacterial metabolites. Nat Commun, 6: 6711
Lechtenfeld O J, Kattner G, Flerus R, McCallister S L, Schmitt-Kopplin P, Koch B P. 2014. Molecular transformation and degradation of refractory dissolved organic matter in the Atlantic and Southern Ocean. Geochim Cosmochim Acta, 126: 321–337
Li M, Baker B J, Anantharaman K, Jain S, Breier J A, Dick G J. 2015. Genomic and transcriptomic evidence for scavenging of diverse organic compounds by widespread deep-sea archaea. Nat Commun, 6: 8933
Li Y, Shahbaz M, Zhu Z, Deng Y, Tong Y, Chen L, Wu J, Ge T. 2021. Oxygen availability determines key regulators in soil organic carbon mineralisation in paddy soils. Soil Biol Biochem, 153: 108106
Lian J, Zheng X, Zhuo X, Chen Y L, He C, Zheng Q, Lin T H, Sun J, Guo W, Shi Q, Jiao N, Cai R. 2021. Microbial transformation of distinct exogenous substrates into analogous composition of recalcitrant dissolved organic matter. Environ Microbiol, 23: 2389–2403
Liang B, Wang L Y, Mbadinga S M, Liu J F, Yang S Z, Gu J D, Mu B Z. 2015. Anaerolineaceae and Methanosaeta turned to be the dominant microorganisms in alkanes-dependent methanogenic culture after long-term of incubation. AMB Expr, 5: 117
Lin X, Handley K M, Gilbert J A, Kostka J E. 2015. Metabolic potential of fatty acid oxidation and anaerobic respiration by abundant members of Thaumarchaeota and Thermoplasmata in deep anoxic peat. ISME J, 9: 2740–2744
Lipp J S, Morono Y, Inagaki F, Hinrichs K U. 2008. Significant contribution of Archaea to extant biomass in marine subsurface sediments. Nature, 454: 991–994
Liu Y, Makarova K S, Huang W C, Wolf Y I, Nikolskaya A N, Zhang X, Cai M, Zhang C J, Xu W, Luo Z, Cheng L, Koonin E V, Li M. 2021. Expanded diversity of Asgard archaea and their relationships with eukaryotes. Nature, 593: 553–557
Liu Q, Li W, Liu D, Li L, Li J, Lv N, Liu F, Zhu B, Zhou Y, Xin Y, Dong X. 2021. Light stimulates anoxic and oligotrophic growth of glacial Flavobacterium strains that produce zeaxanthin. ISME J, 15: 1844–1857
Lloyd K G, Schreiber L, Petersen D G, Kjeldsen K U, Lever M A, Steen A D, Stepanauskas R, Richter M, Kleindienst S, Lenk S, Schramm A, Jørgensen B B. 2013. Predominant archaea in marine sediments degrade detrital proteins. Nature, 496: 215–218
Lloyd K G, Steen A D, Ladau J, Yin J, Crosby L. 2018. Phylogenetically novel uncultured microbial cells dominate earth microbiomes. mSystems, 3: E00055–00018
Logares R, Bråte J, Bertilsson S, Clasen J L, Shalchian-Tabrizi K, Rengefors K. 2009. Infrequent marine-freshwater transitions in the microbial world. Trends Microbiol, 17: 414–422
Lombard J, López-García P, Moreira D. 2012. The early evolution of lipid membranes and the three domains of life. Nat Rev Microbiol, 10: 507–515
Lønborg C, Álvarez-Salgado X A, Davidson K, Martínez-García S, Teira E. 2010. Assessing the microbial bioavailability and degradation rate constants of dissolved organic matter by fluorescence spectroscopy in the coastal upwelling system of the Ría de Vigo. Mar Chem, 119: 121–129
Lønborg C, Álvarez-Salgado X A, Letscher R T, Hansell D A. 2018. Large stimulation of recalcitrant dissolved organic carbon degradation by increasing ocean temperatures. Front Mar Sci, 4, https://doi.org/10.3389/fmars.2017.00436
Lønborg C, Carreira C, Jickells T, Álvarez-Salgado X A. 2020. Impacts of global change on ocean dissolved organic carbon (DOC) cycling. Front Mar Sci, 7, https://doi.org/10.3389/fmars.2020.00466
Lønborg C, Cuevas L A, Reinthaler T, Herndl G J, Gasol J M, Morán X A G, Bates N R, Álvarez-Salgado X A. 2016. Depth dependent relationships between temperature and ocean heterotrophic prokaryotic production. Front Mar Sci, 3, https://doi.org/10.3389/fmars.2016.00090
Lønborg C, Davidson K, Álvarez-Salgado X A, Miller A E J. 2009. Bioavailability and bacterial degradation rates of dissolved organic matter in a temperate coastal area during an annual cycle. Mar Chem, 113: 219–226
Lønborg C, Søndergaard M. 2009. Microbial availability and degradation of dissolved organic carbon and nitrogen in two coastal areas. Estuar Coast Shelf Sci, 81: 513–520
Mahmoudi N, Beaupré S R, Steen A D, Pearson A. 2017. Sequential bioavailability of sedimentary organic matter to heterotrophic bacteria. Environ Microbiol, 19: 2629–2644
Margesin R, Collins T. 2019. Microbial ecology of the cryosphere (glacial and permafrost habitats): Current knowledge. Appl Microbiol Biotechnol, 103: 2537–2549
Martinez-Varela A, Casas G, Piña B, Dachs J, Vila-Costa M. 2020. Large enrichment of anthropogenic organic matter degrading bacteria in the sea-surface microlayer at Coastal Livingston Island (Antarctica). Front Microbiol, 11, https://doi.org/10.3389/fmicb.2020.571983
McCarren J, Becker J W, Repeta D J, Shi Y, Young C R, Malmstrom R R, Chisholm S W, DeLong E F. 2010. Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea. Proc Natl Acad Sci USA, 107: 16420–16427
McCarthy M D, Hedges J I, Benner R. 1998. Major bacterial contribution to marine dissolved organic nitrogen. Science, 281: 231–234
McDonald N, Achterberg E P, Carlson C A, Gledhill M, Liu S, Matheson-Barker J R, Nelson N B, Parsons R J. 2019. The role of heterotrophic bacteria and archaea in the transformation of lignin in the open ocean. Front Mar Sci, 6, https://doi.org/10.3389/fmars.2019.00743
McGenity T J, Folwell B D, McKew B A, Sanni G O. 2012. Marine crude-oil biodegradation: A central role for interspecies interactions. Aquat Biosyst, 8: 10
Medeiros P M, Seidel M, Gifford S M, Ballantyne F, Dittmar T, Whitman W B, Moran M A. 2017. Microbially-Mediated Transformations of Estuarine Dissolved Organic Matter. Front Mar Sci, 4, https://doi.org/10.3389/fmars.2017.00069
Miles C J, Brezonik P L. 1981. Oxygen consumption in humic-colored waters by a photochemical ferrous-ferric catalytic cycle. Environ Sci Technol, 15: 1089–1095
Miller W L, Moran M A. 1997. Interaction of photochemical and microbial processes in the degradation of refractory dissolved organic matter from a coastal marine environment. Limnol Oceanogr, 42: 1317–1324
Moran M A, Kujawinski E B, Stubbins A, Fatland R, Aluwihare L I, Buchan A, Crump B C, Dorrestein P C, Dyhrman S T, Hess N J, Howe B, Longnecker K, Medeiros P M, Niggemann J, Obernosterer I, Repeta D J, Waldbauer J R. 2016. Deciphering ocean carbon in a changing world. Proc Natl Acad Sci USA, 113: 3143–3151
Moran M A, Covert J S. 2003. Chapter 10-photochemically mediated linkages between dissolved organic matter and bacterioplankton. In: Findlay S E G, Sinsabaugh R L, eds. Aquatic Ecosystems. Burlington: Academic Press. 243–262
Nagata T. 2008. Organic matter-bacteria interactions in seawater. In: Kirchman D L, ed. Microbial Ecology of the Oceans. Hoboken: John Wiley & Sons, Inc. 207–241
Nagata T, Kirchman D L. 1996. Bacterial degradation of protein adsorbed to model submicron particles in seawater. Mar Ecol Prog Ser, 132: 241–248
Nelson N B, Siegel D A, Carlson C A, Swan C M. 2010. Tracing global biogeochemical cycles and meridional overturning circulation using chromophoric dissolved organic matter. Geophys Res Lett, 37: L03610
Noriega-Ortega B E, Wienhausen G, Mentges A, Dittmar T, Simon M, Niggemann J. 2019. Does the chemodiversity of bacterial exometabolomes sustain the chemodiversity of marine dissolved organic matter? Front Microbiol, 10, https://doi.org/10.3389/fmicb.2019.00215
Ogawa H, Amagai Y, Koike I, Kaiser K, Benner R. 2001. Production of refractory dissolved organic matter by bacteria. Science, 292: 917–920
Oni O E, Schmidt F, Miyatake T, Kasten S, Witt M, Hinrichs K U, Friedrich M W. 2015. Microbial communities and organic matter composition in surface and subsurface sediments of the Helgoland Mud Area, North Sea. Front Microbiol, 6, https://doi.org/10.3389/fmicb.2015.01290
Ouverney C C, Fuhrman J A. 1999. Combined microautoradiography-16S rRNA probe technique for determination of radioisotope uptake by specific microbial cell types in situ. Appl Environ Microbiol, 65: 1746–1752
Paço A, Duarte K, da Costa J P, Santos P S M, Pereira R, Pereira M E, Freitas A C, Duarte A C, Rocha-Santos T A P. 2017. Biodegradation of polyethylene microplastics by the marine fungus Zalerion maritimum. Sci Total Environ, 586: 10–15
Penniston J T. 1971. High hydrostatic pressure and enzymic activity: Inhibition of multimeric enzymes by dissociation. Arch Biochem Biophys, 142: 322–332
Pomeroy L R. 1974. The ocean’s food web, a changing paradigm. Bioscience, 24: 499–504
Porter A W, Young L Y. 2014. Chapter 5-benzoyl-CoA, a universal biomarker for anaerobic degradation of aromatic compounds. In: Sariaslani S, Gadd G M, eds. Advances in Applied Microbiology. London: Academic Press. 167–203
Pütter A. 1907. Der Stoffhaushalt des Meeres. Zeitschriftfür Allgemeine Physiologie, 7: 321–368
Quinn J P, Kulakova A N, Cooley N A, McGrath J W. 2007. New ways to break an old bond: the bacterial carbon-phosphorus hydrolases and their role in biogeochemical phosphorus cycling. Environ Microbiol, 9: 2392–2400
Raymond P A, Hartmann J, Lauerwald R, Sobek S, McDonald C, Hoover M, Butman D, Striegl R, Mayorga E, Humborg C, Kortelainen P, Dürr H, Meybeck M, Ciais P, Guth P. 2013. Global carbon dioxide emissions from inland waters. Nature, 503: 355–359
Rivkin R B, Legendre L. 2001. Biogenic carbon cycling in the upper ocean: Effects of microbial respiration. Science, 291: 2398–2400
Rocker D, Brinkhoff T, Grüner N, Dogs M, Simon M. 2012. Composition of humic acid-degrading estuarine and marine bacterial communities. FEMS Microbiol Ecol, 80: 45–63
Ruff S E. 2020. Microbial communities and metabolisms at hydrocarbon seeps. In: Teske A, Carvalho V, eds. Marine Hydrocarbon Seeps: Microbiology and Biogeochemistry of a Global Marine Habitat. Cham: Springer International Publishing. 1–19
Salazar G, Paoli L, Alberti A, Huerta-Cepas J, Ruscheweyh H J, Cuenca M, Field C M, Coelho L P, Cruaud C, Engelen S, Gregory A C, Labadie K, Marec C, Pelletier E, Royo-Llonch M, Roux S, Sánchez P, Uehara H, Zayed A A, Zeller G, Carmichael M, Dimier C, Ferland J, Kandels S, Picheral M, Pisarev S, Poulain J, Acinas S G, Babin M, Bork P, Bowler C, de Vargas C, Guidi L, Hingamp P, Iudicone D, Karp-Boss L, Karsenti E, Ogata H, Pesant S, Speich S, Sullivan M B, Wincker P, Sunagawa S, Acinas S G, Babin M, Bork P, Boss E, Bowler C, Cochrane G, de Vargas C, Follows M, Gorsky G, Grimsley N, Guidi L, Hingamp P, Iudicone D, Jaillon O, Kandels-Lewis S, Karp-Boss L, Karsenti E, Not F, Ogata H, Pesant S, Poulton N, Raes J, Sardet C, Speich S, Stemmann L, Sullivan M B, Sunagawa S, Wincker P. 2019. Gene expression changes and community turnover differentially shape the global ocean metatranscriptome. Cell, 179: 1068–1083.e21
Santos-Júnior C D, Sarmento H, de Miranda F P, Henrique-Silva F, Logares R. 2020. Uncovering the genomic potential of the Amazon River microbiome to degrade rainforest organic matter. Microbiome, 8: 151
Schindler D W, Vallentyne J R. 2008. The Algal Bowl: overfertilization of the World’s Freshwaters and Estuaries. Edmonton: University of Alberta Press
Schopf J W. 1983. Earth’s Earliest Biosphere: Its Origin and Evolution. Princeton: Princeton University Press
Seidel M, Yager P L, Ward N D, Carpenter E J, Gomes H R, Krusche AV, Richey J E, Dittmar T, Medeiros P M. 2015. Molecular-level changes of dissolved organic matter along the Amazon River-to-ocean continuum. Mar Chem, 177: 218–231
Seitz K W, Dombrowski N, Eme L, Spang A, Lombard J, Sieber J R, Teske A P, Ettema T J G, Baker B J. 2019. Asgard archaea capable of anaerobic hydrocarbon cycling. Nat Commun, 10: 1822
Shah A A, Hasan F, Hameed A, Ahmed S. 2008. Biological degradation of plastics: A comprehensive review. Biotechnol Adv, 26: 246–265
Sherr B F, Sherr E B, Hopkinson C S. 1988. Trophic interactions within pelagic microbial communities: Indications of feedback regulation of carbon flow. Hydrobiologia, 159: 19–26
Sichert A, Corzett C H, Schechter M S, Unfried F, Markert S, Becher D, Fernandez-Guerra A, Liebeke M, Schweder T, Polz M F, Hehemann J H. 2020. Verrucomicrobia use hundreds of enzymes to digest the algal polysaccharide fucoidan. Nat Microbiol, 5: 1026–1039
Sinsabaugh R L, Findlay S. 2003. Chapter 20-dissolved organic matter: Out of the black box into the mainstream. In: Findlay S E G, Sinsabaugh R L, eds. Aquatic Ecosystems. Burlington: Academic Press. 479–498
Sipler R E, Bronk D A, Seitzinger S P, Lauck R J, McGuinness L R, Kirkpatrick G J, Heil C A, Kerkhof L J, Schofield O M. 2013. Trichodesmium-derived dissolved organic matter is a source of nitrogen capable of supporting the growth of toxic red tide Karenia brevis. Mar Ecol Prog Ser, 483: 31–45
Sipler R E, Kellogg C T E, Connelly T L, Roberts Q N, Yager P L, Bronk D A. 2017. Microbial community response to terrestrially derived dissolved organic matter in the coastal arctic. Front Microbiol, 8, https://doi.org/10.3389/fmicb.2017.01018
Smith H J, Dieser M, McKnight D M, SanClements M D, Foreman C M. 2018. Relationship between dissolved organic matter quality and microbial community composition across polar glacial environments. FEMS Microbiol Ecol, 94, https://doi.org/10.1093/femsec/fiy090
Song X, Xu Y, Li G, Zhang Y, Huang T, Hu Z. 2011. Isolation, characterization of Rhodococcus sp. P14 capable of degrading high-molecular-weight polycyclic aromatic hydrocarbons and aliphatic hydrocarbons. Mar Pollut Bull, 62: 2122–2128
Sosa O A, Repeta D J, Ferrón S, Bryant J A, Mende D R, Karl D M, DeLong E F. 2017. Isolation and characterization of bacteria that degrade phosphonates in marine dissolved organic matter. Front Microbiol, 8, https://doi.org/10.3389/fmicb.2017.01786
Spencer R G M, Guo W, Raymond P A, Dittmar T, Hood E, Fellman J, Stubbins A. 2014. Source and biolability of ancient dissolved organic matter in glacier and lake ecosystems on the Tibetan Plateau. Geochim Cosmochim Acta, 142: 64–74
Strome D J, Miller M C. 2010. Photolytic changes in dissolved humic substances. SIL Proc 1922–2010, 20: 1248–1254
Stubbins A, Niggemann J, Dittmar T. 2012. Photo-lability of deep ocean dissolved black carbon. Biogeosciences, 9: 1661–1670
Stubbins A, Spencer R G M, Chen H, Hatcher P G, Mopper K, Hernes P J, Mwamba V L, Mangangu A M, Wabakanghanzi J N, Six J. 2010. Illuminated darkness: Molecular signatures of Congo River dissolved organic matter and its photochemical alteration as revealed by ultrahigh precision mass spectrometry. Limnol Oceanogr, 55: 1467–1477
Suttle C A. 2005. Viruses in the sea. Nature, 437: 356–361
Tang K, Jiao N, Liu K, Zhang Y, Li S. 2012. Distribution and functions of TonB-dependent transporters in marine bacteria and environments: Implications for dissolved organic matter utilization. PLoS ONE, 7: e41204
Tanoue E, Nishiyama S, Kamo M, Tsugita A. 1995. Bacterial membranes: Possible source of a major dissolved protein in seawater. Geochim Cosmochim Acta, 59: 2643–2648
Tao X, Feng J, Yang Y, Wang G, Tian R, Fan F, Ning D, Bates C T, Hale L, Yuan M M, Wu L, Gao Q, Lei J, Schuur E A G, Yu J, Bracho R, Luo Y, Konstantinidis K T, Johnston E R, Cole J R, Penton C R, Tiedje J M, Zhou J. 2020. Winter warming in Alaska accelerates lignin decomposition contributed by Proteobacteria. Microbiome, 8: 84
Taube R, Ganzert L, Grossart H P, Gleixner G, Premke K. 2018. Organic matter quality structures benthic fatty acid patterns and the abundance of fungi and bacteria in temperate lakes. Sci Total Environ, 610–611: 469–481
Taylor C R, Hardiman E M, Ahmad M, Sainsbury P D, Norris P R, Bugg T D H. 2012. Isolation of bacterial strains able to metabolize lignin from screening of environmental samples. J Appl Microbiol, 113: 521–530
Teeling H, Fuchs B M, Becher D, Klockow C, Gardebrecht A, Bennke C M, Kassabgy M, Huang S, Mann A J, Waldmann J, Weber M, Klind-worth A, Otto A, Lange J, Bernhardt J, Reinsch C, Hecker M, Peplies J, Bockelmann F D, Callies U, Gerdts G, Wichels A, Wiltshire K H, Glöckner F O, Schweder T, Amann R. 2012. Substrate-controlled succession of marine bacterioplankton populations induced by a phytoplankton bloom. Science, 336: 608–611
Tripp H J, Kitner J B, Schwalbach M S, Dacey J W H, Wilhelm L J, Giovannoni S J. 2008. SAR11 marine bacteria require exogenous reduced sulphur for growth. Nature, 452: 741–744
Valentine D L, Kessler J D, Redmond M C, Mendes S D, Heintz M B, Farwell C, Hu L, Kinnaman F S, Yvon-Lewis S, Du M, Chan E W, Garcia Tigreros F, Villanueva C J. 2010. Propane respiration jumpstarts microbial response to a deep oil spill. Science, 330: 208–211
Vanwonterghem I, Evans P N, Parks D H, Jensen P D, Woodcroft B J, Hugenholtz P, Tyson G W. 2016. Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota. Nat Microbiol, 1: 16170
Vetter Y A, Deming J W, Jumars P A, Krieger-Brockett B B. 1998. A predictive model of bacterial foraging by means of freely released extracellular enzymes. Microb Ecol, 36: 75–92
Vorobev A, Sharma S, Yu M, Lee J, Washington B J, Whitman W B, Ballantyne Iv F, Medeiros P M, Moran M A. 2018. Identifying labile DOM components in a coastal ocean through depleted bacterial transcripts and chemical signals. Environ Microbiol, 20: 3012–3030
Wang W, Tao J, Liu H, Li P, Chen S, Wang P, Zhang C. 2020. Contrasting bacterial and archaeal distributions reflecting different geochemical processes in a sediment core from the Pearl River Estuary. AMB Expr, 10: 16
Wang Y, Wegener G, Ruff S E, Wang F. 2021. Methyl/alkyl-coenzyme M reductase-based anaerobic alkane oxidation in Archaea. Environ Microbiol, 23: 530–541
Ward N D, Bianchi T S, Sawakuchi H O, Gagne-Maynard W, Cunha A C, Brito D C, Neu V, de Matos Valerio A, da Silva R, Krusche AV, Richey J E, Keil R G. 2016. The reactivity of plant-derived organic matter and the potential importance of priming effects along the lower Amazon River. J Geophys Res-Biogeosci, 121: 1522–1539
Warren R A J. 1996. Microbial hydrolysis of polysaccharides. Annu Rev Microbiol, 50: 183–212
Weiner R M, Taylor L E, Henrissat B, Hauser L, Land M, Coutinho P M, Rancurel C, Saunders E H, Longmire A G, Zhang H, Bayer E A, Gilbert H J, Larimer F, Zhulin I B, Ekborg N A, Lamed R, Richardson P M, Borovok I, Hutcheson S. 2008. Complete genome sequence of the complex carbohydrate-degrading marine bacterium, saccharophagusdegradans strain 2–40T. PLoS Genet, 4: e1000087
Weiss M S, Abele U, Weckesser J, Welte W, Schiltz E, Schulz G E. 1991. Molecular architecture and electrostatic properties of a bacterial porin. Science, 254: 1627–1630
Wetzel R G. 1993. Humic compounds from wetlands: Complexation, inactivation, and reactivation of surface-bound and extracellular enzymes. SIL Proc 1922–2010, 25: 122–128
Wetzel R G. 2003. Chapter 19-dissolved organic carbon: detrital energetics, metabolic regulators, and drivers of ecosystem stability of aquatic ecosystems. In: Findlay S E G, Sinsabaugh R L, eds. Aquatic Ecosystems. Burlington: Academic Press. 455–477
White E M, Vaughan P P, Zepp R G. 2003. Role of the photo-Fenton reaction in the production of hydroxyl radicals and photobleaching of colored dissolved organic matter in a coastal river of the southeastern United States. Aquat Sci-Res Across Boundaries, 65: 402–414
Whitman W B, Coleman D C, Wiebe W J. 1998. Prokaryotes: The unseen majority. Proc Natl Acad Sci USA, 95: 6578–6583
Williams P. 2000. Heterotrophic bacteria and the dynamics of dissolved organic material. In: Kirchman D L, ed. Microbial Ecology of the Oceans. New York: Wiley-Blackwell
Woese C R, Fox G E. 1977. Phylogenetic structure of the prokaryotic domain: The primary kingdoms. Proc Natl Acad Sci USA, 74: 5088–5090
Xiao X, Zhang Y, Wang F. 2021. Hydrostatic pressure is the universal key driver of microbial evolution in the deep ocean and beyond. Environ Microbiol Rep, 13: 68–72
Yamada-Onodera K, Mukumoto H, Katsuyaya Y, Saiganji A, Tani Y. 2001. Degradation of polyethylene by a fungus, Penicillium simplicissimum YK. Polym Degrad Stab, 72: 323–327
Yamashita Y, Tanoue E. 2003. Distribution and alteration of amino acids in bulk DOM along a transect from bay to oceanic waters. Mar Chem, 82: 145–160
Yamashita Y, Tanoue E. 2008. Production of bio-refractory fluorescent dissolved organic matter in the ocean interior. Nat Geosci, 1: 579–582
Young C L, Ingall E D. 2010. Marine dissolved organic phosphorus composition: Insights from samples recovered using combined electrodialysis/reverse osmosis. Aquat Geochem, 16: 563–574
Yu T, Wu W, Liang W, Lever M A, Hinrichs K U, Wang F. 2018. Growth of sedimentary Bathyarchaeota on lignin as an energy source. Proc Natl Acad Sci USA, 115: 6022–6027
Zhang J W, Dong H P, Hou L J, Liu Y, Ou Y F, Zheng Y L, Han P, Liang X, Yin G Y, Wu D M, Liu M, Li M. 2021. Newly discovered Asgard archaea Hermodarchaeota potentially degrade alkanes and aromatics via alkyl/benzyl-succinate synthase and benzoyl-CoA pathway. ISME J, 15: 1826–1843
Zhang C, Dang H, Azam F, Benner R, Legendre L, Passow U, Polimene L, Robinson C, Suttle C A, Jiao N. 2018. Evolving paradigms in biological carbon cycling in the ocean. Natl Sci Rev, 5:481–499
Zhang C L, Xie W, Martin-Cuadrado A B, Rodriguez-Valera F. 2015. Marine Group II Archaea, potentially important players in the global ocean carbon cycle. Front Microbiol, 6, https://doi.org/10.3389/fmicb.2015.01108
Zhang C J, Pan J, Duan C H, Wang Y M, Liu Y, Sun J, Zhou H C, Song X, Li M. 2019. Prokaryotic diversity in mangrove sediments across Southeastern China fundamentally differs from that in other biomes. mSystems, 4, https://doi.org/10.1128/mSystems.00442-19
Zhao Z, Gonsior M, Schmitt-Kopplin P, Zhan Y, Zhang R, Jiao N, Chen F. 2019. Microbial transformation of virus-induced dissolved organic matter from picocyanobacteria: Coupling of bacterial diversity and DOM chemodiversity. ISME J, 13: 2551–2565
Zhou Z, Liu Y, Lloyd K G, Pan J, Yang Y, Gu J D, Li M. 2019. Genomic and transcriptomic insights into the ecology and metabolism of benthic archaeal cosmopolitan, Thermoprofundales (MBG-D archaea). ISME J, 13: 885–901
Zhou Z, Pan J, Wang F, Gu J D, Li M. 2018. Bathyarchaeota: Globally distributed metabolic generalists in anoxic environments. FEMS Microbiol Rev, 42: 639–655
Zinger L, Gobet A, Pommier T. 2012. Two decades of describing the unseen majority of aquatic microbial diversity. Mol Ecol, 21: 1878–1896
Acknowledgements
Thanks extend to the scientific editor and two anonymous reviewers for constructive suggestions to improve this manuscript. The authors appreciate David Michael Esserman for language editing. This work was supported by the Special Fund for Science and Technology and the Key Discipline Fund in Environmental Science and Engineering from Guangdong Province of China.
Author information
Authors and Affiliations
Corresponding authors
Electronic supplementary material
Rights and permissions
About this article
Cite this article
Chen, M., Hur, J., Gu, JD. et al. Microbial degradation of various types of dissolved organic matter in aquatic ecosystems and its influencing factors. Sci. China Earth Sci. 66, 169–189 (2023). https://doi.org/10.1007/s11430-021-9996-1
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11430-021-9996-1