Costanza R, d’Arge R, de Groot R, Farber S, Grasso M, Hannon B, et al. The value of the world’s ecosystem services and natural capital. Ecol Econ. 1998;25:3–15.
Google Scholar
Grimsditch G, Alder J, Nakamura T, Kenchington R, Tamelander J. The blue carbon special edition—introduction and overview. Ocean Coast Manag. 2013;83:1–4.
Google Scholar
Duarte CM, Losada IJ, Hendriks IE, Mazarrasa I, Marbà N. The role of coastal plant communities for climate change mitigation and adaptation. Nat Clim Change. 2013;3:961–8.
Google Scholar
Mcleod E, Chmura GL, Bouillon S, Salm R, Björk M, Duarte CM, et al. A blueprint for blue carbon: toward an improved understanding of the role of vegetated coastal habitats in sequestering CO2. Front Ecol Environ. 2011;9:552–60.
Google Scholar
Neef L, Weele M van, Velthoven P van. Optimal estimation of the present-day global methane budget. Glob Biogeochem Cycles. 2010;24:GB4024.
Schlesinger WH, Bernhardt ES. Biogeochemistry: an analysis of global change. 3rd ed. Waltham, MA: Academic Press; 2013.
Lessner DJ. Methanogenesis biochemistry. eLS. John Wiley & Sons, Hoboken, NJ, USA; 2009.
Conrad R. Importance of hydrogenotrophic, aceticlastic and methylotrophic methanogenesis for methane production in terrestrial, aquatic and other anoxic environments: a mini review. Pedosphere. 2020;30:25–39.
Google Scholar
Herbert ER, Boon P, Burgin AJ, Neubauer SC, Franklin RB, Ardón M, et al. A global perspective on wetland salinization: ecological consequences of a growing threat to freshwater wetlands. Ecosphere. 2015;6:art206.
Google Scholar
Wicke B, Smeets E, Dornburg V, Vashev B, Gaiser T, Turkenburg W, et al. The global technical and economic potential of bioenergy from salt-affected soils. Energy Environ Sci. 2011;4:2669–81.
Google Scholar
Kristjansson JK, Schönheit P. Why do sulfate-reducing bacteria outcompete methanogenic bacteria for substrates? Oecologia. 1983;60:264–6.
Google Scholar
Karl DM, Beversdorf L, Björkman KM, Church MJ, Martinez A, Delong EF. Aerobic production of methane in the sea. Nat Geosci. 2008;1:473–8.
Google Scholar
Mcgenity T, Sorokin D. Methanogens and methanogenesis in hypersaline environments. Biogenesis of hydrocarbons. Springer International Publishing, New York, NY, USA; 2018. p. 1–27.
Repeta DJ, Ferrón S, Sosa OA, Johnson CG, Repeta LD, Acker M, et al. Marine methane paradox explained by bacterial degradation of dissolved organic matter. Nat Geosci. 2016;9:884–7.
Google Scholar
Oremland RS, Polcin S. Methanogenesis and sulfate reduction: competitive and noncompetitive substrates in estuarine sediments. Appl Environ Microbiol. 1982;44:1270–6.
Google Scholar
van der Gon HACD, Neue H-U. Methane emission from a wetland rice field as affected by salinity. Plant Soil. 1995;170:307–13.
Google Scholar
Gómez-Villegas P, Vigara J, León R. Characterization of the microbial population inhabiting a solar saltern pond of the Odiel Marshlands (SW Spain). Mar Drugs. 2018;16:332.
Google Scholar
Ley RE, Harris JK, Wilcox J, Spear JR, Miller SR, Bebout BM, et al. Unexpected diversity and complexity of the Guerrero Negro hypersaline microbial mat. Appl Environ Microbiol. 2006;72:3685–95.
Google Scholar
Thombre RS, Shinde VD, Oke RS, Dhar SK, Shouche YS. Biology and survival of extremely halophilic archaeon Haloarcula marismortui RR12 isolated from Mumbai salterns, India in response to salinity stress. Sci Rep. 2016;6:25642.
Google Scholar
Takekawa JY, Miles AK, Schoellhamer DH, Athearn ND, Saiki MK, Duffy WD, et al. Trophic structure and avian communities across a salinity gradient in evaporation ponds of the San Francisco Bay estuary. Hydrobiologia. 2006;567:307–27.
Google Scholar
Ver Planck WE. Salt in California. State of California Deparment of Natural Resources, Division of Mines. Mines Bull 175. San Francisco, CA, USA: 1958.
Johnck EJ. The South Bay Salt Pond Restoration Project: a cultural landscape approach for the resource management plan. Sonoma State University, Rohnert Park, CA, USA; 2008.
Ackerman JT, Marvin-DiPasquale M, Slotton D, Eagles-Smith CA, Hartman A, Agee JL, et al. The South Bay Mercury Project: using biosentinels to monitor effects of wetland restoration for the South Bay Salt Pond Restoration Project. South Bay Salt Pond Restoration Project and Resources Legacy Fund, San Francisco, CA, USA; 2013.
Valoppi L. Phase 1 studies summary of major findings of the South Bay Salt Pond Restoration Project, South San Francisco Bay, California. Phase 1 studies summary of major findings of the South Bay Salt Pond Restoration Project, South San Francisco Bay, California. Reston, VA: U.S. Geological Survey; 2018.
Callaway JC, Parker VT, Vasey MC, Schile LM, Herbert ER. Tidal wetland restoration in San Francisco Bay: history and current issues. San Franc Estuary Watershed Sci. 2011;9: Article 2.
Cargill. San Francisco Bay salt ponds. Cargill, Newark, CA, USA; 2020. https://www.cargill.com/page/sf/sf-bay-salt-ponds.
Levey JR, Vasicek P, Fricke H, Archer J, Henry RF. Salt pond SF2 restoration, wildlife, and habitat protection. American Society of Civil Engineers, Reston, VA; 2012.520−9.
Dugan HA, Summers JC, Skaff NK, Krivak-Tetley FE, Doubek JP, Burke SM, et al. Long-term chloride concentrations in North American and European freshwater lakes. Sci Data. 2017;4:170101.
Google Scholar
Tremblay J, Singh K, Fern A, Kirton ES, He S, Woyke T, et al. Primer and platform effects on 16S rRNA tag sequencing. Front Microbiol 2015;6:771.
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41:D590–96.
Google Scholar
Wang Q, Garrity GM, Tiedje JM, Cole JR. A naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 2007;73:5264−67.
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7:335–6.
Google Scholar
Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26:2460–1.
Google Scholar
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550.
Google Scholar
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19:455–77.
Google Scholar
Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013;29:1072–5.
Google Scholar
Wu Y-W, Tang Y-H, Tringe SG, Simmons BA, Singer SW. MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm. Microbiome. 2014;2:26.
Google Scholar
Kang DD, Froula J, Egan R, Wang Z. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ. 2015;3:e1165.
Google Scholar
Lin H-H, Liao Y-C. Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes. Sci Rep. 2016;6:24175.
Google Scholar
Sieber CMK, Probst AJ, Sharrar A, Thomas BC, Hess M, Tringe SG, et al. Recovery of genomes from metagenomes via a dereplication, aggregation, and scoring strategy. Nat Microbiol. 2018;3:836–43.
Google Scholar
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25:1043–55.
Google Scholar
Olm MR, Brown CT, Brooks B, Banfield JF. dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. ISME J. 2017;11:2864–8.
Google Scholar
Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, et al. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat Biotechnol. 2017;35:725–31.
Google Scholar
Yu FB, Blainey PC, Schulz F, Woyke T, Horowitz MA, Quake SR. Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples. eLife. 2017;6:e26580.
Google Scholar
von Meijenfeldt FAB, Arkhipova K, Cambuy DD, Coutinho FH, Dutilh BE. Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT. Genome Biol. 2019;20:217.
Google Scholar
Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P, McGlinn D, et al. vegan: Community Ecology Package. R package version 2.5-6. 2019. https://CRAN.R-project.org/package=vegan.
Vu VQ. ggbiplot: a ggplot2 based biplot. R package version 0.55. 2011. http://github.com/vqv/ggbiplot.
De Cáceres M, Legendre P. Associations between species and groups of sites: indices and statistical inference. Ecology. 2009;90:3566–74.
Google Scholar
Prestat E, David MM, Hultman J, Taş N, Lamendella R, Dvornik J, et al. FOAM (functional ontology assignments for metagenomes): a hidden Markov model (HMM) database with environmental focus. Nucleic Acids Res. 2014;42:e145.
Google Scholar
Liu J, Cade-Menun BJ, Yang J, Hu Y, Liu CW, Tremblay J, et al. Long-term land use affects phosphorus speciation and the composition of phosphorus cycling genes in agricultural soils. Front Microbiol. 2018;9:1643.
Manor O, Borenstein E. MUSiCC: a marker genes based framework for metagenomic normalization and accurate profiling of gene abundances in the microbiome. Genome Biol. 2015;16:53.
Google Scholar
Banerjee S, Schlaeppi K, van der Heijden MGA. Keystone taxa as drivers of microbiome structure and functioning. Nat Rev Microbiol. 2018;16:567–76.
Google Scholar
Girvan M, Newman MEJ. Community structure in social and biological networks. Proc Natl Acad Sci USA. 2002;99:7821–6.
Google Scholar
Jurasinski G, Koebsch F, Guenther A, Beetz S. flux: flux rate calculation from dynamic closed chamber measurements. R package version 0.3-0. 2014. https://CRAN.R-project.org/package=flux.
Culkin F, Smith N. Determination of the concentration of potassium chloride solution having the same electrical conductivity, at 15 °C and infinite frequency, as standard seawater of salinity 35.0000 ‰ (chlorinity 19.37394 ‰). IEEE J Ocean Eng. 1980;5:22–23.
Google Scholar
Kuever J. The Family Desulfohalobiaceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds). The Prokaryotes: Deltaproteobacteria and Epsilonproteobacteria. Berlin, Heidelberg: Springer; 2014. p. 87–95.
López-Pérez M, Rodriguez-Valera F. The Family Alteromonadaceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds). The Prokaryotes: Gammaproteobacteria. Berlin, Heidelberg: Springer; 2014. p. 69–92.
Oren A. The Order Halanaerobiales, and the Families Halanaerobiaceae and Halobacteroidaceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds). The Prokaryotes: Firmicutes and Tenericutes. Berlin, Heidelberg: Springer; 2014. p. 153−77.
Pujalte MJ, Lucena T, Ruvira MA, Arahal DR, Macián MC. The Family Rhodobacteraceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds). The Prokaryotes: Alphaproteobacteria and Betaproteobacteria. Berlin, Heidelberg: Springer; 2014. p. 439–512.
Kuever J. The Family Desulfobacteraceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds). The Prokaryotes: Deltaproteobacteria and Epsilonproteobacteria. Berlin, Heidelberg: Springer; 2014. p. 45–73.
Kuever J. The Family Desulfobulbaceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds). The Prokaryotes: Deltaproteobacteria and Epsilonproteobacteria. Berlin, Heidelberg: Springer; 2014. p. 75–86.
Kuever J. The Family Syntrophobacteraceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds). The Prokaryotes: Deltaproteobacteria and Epsilonproteobacteria. Berlin, Heidelberg: Springer; 2014. p. 289−99.
Oren A. The Family Methanosarcinaceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds). The Prokaryotes: other major lineages of bacteria and the archaea. Berlin, Heidelberg: Springer; 2014. p. 259−81.
Bonin AS, Boone DR. The Order Methanobacteriales. In: Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E (eds). The Prokaryotes: Volume 3: Archaea. Bacteria: Firmicutes, Actinomycetes. New York, NY: Springer; 2006. p. 231−43.
Kathuria S, Martiny AC. Prevalence of a calcium-based alkaline phosphatase associated with the marine cyanobacterium Prochlorococcus and other ocean bacteria. Environ Microbiol. 2011;13:74–83.
Google Scholar
Kamat SS, Williams HJ, Dangott LJ, Chakrabarti M, Raushel FM. The catalytic mechanism for aerobic formation of methane by bacteria. Nature. 2013;497:132–6.
Google Scholar
Yu X, Doroghazi JR, Janga SC, Zhang JK, Circello B, Griffin BM, et al. Diversity and abundance of phosphonate biosynthetic genes in nature. Proc Natl Acad Sci USA. 2013;110:20759–64.
Google Scholar
Fish JA, Chai B, Wang Q, Sun Y, Brown CT, Tiedje JM, et al. FunGene: the functional gene pipeline and repository. Front Microbiol. 2013;4:291.
Metcalf WW, Griffin BM, Cicchillo RM, Gao J, Janga SC, Cooke HA, et al. Synthesis of methylphosphonic acid by marine microbes: a source for methane in the aerobic ocean. Science. 2012;337:1104–7.
Google Scholar
Poffenbarger HJ, Needelman BA, Megonigal JP. Salinity influence on methane emissions from tidal marshes. Wetlands. 2011;31:831–42.
Google Scholar
Oremland RS, Boone DR. Methanolobus taylorii sp. nov., a new methylotrophic, estuarine methanogen. Int J Syst Bacteriol. 1994;44:573–5.
Google Scholar
Zhang G, Jiang N, Liu X, Dong X. Methanogenesis from methanol at low temperatures by a novel psychrophilic methanogen, “Methanolobus psychrophilus” sp. nov., prevalent in Zoige Wetland of the Tibetan Plateau. Appl Environ Microbiol. 2008;74:6114–20.
Google Scholar
Antony CP, Murrell JC, Shouche YS. Molecular diversity of methanogens and identification of Methanolobus sp. as active methylotrophic Archaea in Lonar crater lake sediments. FEMS Microbiol Ecol. 2012;81:43–51.
Google Scholar
König H, Stetter KO. Isolation and characterization of Methanolobus tindarius, sp. nov., a coccoid methanogen growing only on methanol and methylamines. Zentralblatt Für Bakteriol Mikrobiol Hyg Abt Orig C Allg Angew Ökol Mikrobiol. 1982;3:478–90.
Doerfert SN, Reichlen M, Iyer P, Wang M, Ferry JG. Methanolobus zinderi sp. nov., a methylotrophic methanogen isolated from a deep subsurface coal seam. Int J Syst Evol Microbiol. 2009;59:1064–9.
Google Scholar
Ni S, Boone DR. Isolation and characterization of a dimethyl sulfide-degrading methanogen, methanolobus siciliae HI350, from an oil well, characterization of M. siciliae T4/MT, and emendation of M. siciliae. Int J Syst Bacteriol. 1991;41:410–6.
Google Scholar
Mochimaru H, Tamaki H, Hanada S, Imachi H, Nakamura K, Sakata S, et al. Methanolobus profundi sp. nov., a methylotrophic methanogen isolated from deep subsurface sediments in a natural gas field. Int J Syst Evol Microbiol. 2009;59:714–8.
Google Scholar
Orphan VJ, Jahnke LL, Embaye T, Turk KA, Pernthaler A, Summons RE, et al. Characterization and spatial distribution of methanogens and methanogenic biosignatures in hypersaline microbial mats of Baja California. Geobiology. 2008;6:376–93.
Google Scholar
Smith JM, Green SJ, Kelley CA, Prufert‐Bebout L, Bebout BM. Shifts in methanogen community structure and function associated with long-term manipulation of sulfate and salinity in a hypersaline microbial mat. Environ Microbiol. 2008;10:386–94.
Google Scholar
Zhuang G-C, Elling FJ, Nigro LM, Samarkin V, Joye SB, Teske A, et al. Multiple evidence for methylotrophic methanogenesis as the dominant methanogenic pathway in hypersaline sediments from the Orca Basin, Gulf of Mexico. Geochim Cosmochim Acta. 2016;187:1–20.
Google Scholar
Zhuang G-C, Heuer VB, Lazar CS, Goldhammer T, Wendt J, Samarkin VA, et al. Relative importance of methylotrophic methanogenesis in sediments of the Western Mediterranean Sea. Geochim Cosmochim Acta. 2018;224:171–86.
Google Scholar
Oremland RS, Marsh LM, Polcin S. Methane production and simultaneous sulphate reduction in anoxic, salt marsh sediments. Nature. 1982;296:143–5.
Google Scholar
Wanner BL, Metcalf WW. Molecular genetic studies of a 10.9 kb operon in Escherichia coli for phosphonate uptake and biodegradation. FEMS Microbiol Lett. 1992;100:133–9.
Google Scholar
Dyhrman ST, Chappell PD, Haley ST, Moffett JW, Orchard ED, Waterbury JB, et al. Phosphonate utilization by the globally important marine diazotroph Trichodesmium. Nature. 2006;439:68–71.
Google Scholar
White AK, Metcalf WW. Microbial metabolism of reduced phosphorus compounds. Annu Rev Microbiol. 2007;61:379–400.
Google Scholar
Carini P, White AE, Campbell EO, Giovannoni SJ. Methane production by phosphate-starved SAR11 chemoheterotrophic marine bacteria. Nat Commun. 2014;5:4346.
Google Scholar
Damm E, Helmke E, Thoms S, Schauer U, Nothig E, Bakker K, et al. Methane production in aerobic oligotrophic surface water in the central Arctic Ocean. Biogeosciences. 2010;7:1099–108.
Google Scholar
Martínez A, Ventouras L-A, Wilson ST, Karl DM, Delong EF. Metatranscriptomic and functional metagenomic analysis of methylphosphonate utilization by marine bacteria. Front Microbiol. 2013;4:340.
Google Scholar
Yao M, Henny C, Maresca JA. Freshwater bacteria release methane as a by-product of phosphorus acquisition. Appl Environ Microbiol. 2016;82:6994–7003.
Google Scholar
Sosa OA, Repeta DJ, DeLong EF, Ashkezari MD, Karl DM. Phosphate-limited ocean regions select for bacterial populations enriched in the carbon–phosphorus lyase pathway for phosphonate degradation. Environ Microbiol. 2019;21:2402–14.
Google Scholar
Fisher J, Acreman MC. Wetland nutrient removal: a review of evidence. Hydrol Earth Syst Sci Discuss Eur Geosci Union. 2004;8:673–85.
Google Scholar
Kadlec RH. Constructed marshes for nitrate removal. Crit Rev Environ Sci Technol. 2012;42:934–1005.
Google Scholar
He S, Malfatti SA, McFarland JW, Anderson FE, Pati A, Huntemann M, et al. Patterns in wetland microbial community composition and functional gene repertoire associated with methane emissions. mBio. 2015;6:e00066–15.
Google Scholar
Source: Ecology - nature.com
