A comparison of bacterial communities from OMZ sediments in the Arabian Sea and the Bay of Bengal reveals major differences in nitrogen turnover and carbon recycling potential

References

• Arango CP, Tank JL, Schaller JL, Royer TV, Bernot MJ, David MB. 2007. Benthic organic carbon influences denitrification in streams with high nitrate concentration. Freshwater Biology. 52(7):1210–1222. doi:10.1111/j.1365-2427.2007.01758.x.
   Web of Science ®Google Scholar
• Azam F, Sajjad M. 2005. Colorimetric determination of organic carbon in soil by dichromate digestion in a microwave oven. Pakistan Journal of Biological Sciences. 8(4):596–598. doi:10.3923/pjbs.2005.596.598.
   Google Scholar
• Bernard BB, Bernard H, Brooks JM. 1995. Determination of total carbon, total organic carbon and inorganic carbon in sediments TDI-Brooks International/B&B Labratories Inc. College Station (pp. 1–5).
   Google Scholar
• Bertics VJ, Löscher CR, Salonen I, Dale AW, Gier J, Schmitz RA, Treude T. 2013. Occurrence of benthic microbial nitrogen fixation coupled to sulfate reduction in the seasonally hypoxic Eckernförde Bay, Baltic Sea. Biogeosciences. 10:1243–1258. doi:10.5194/bg-10-1243-2013.
   Web of Science ®Google Scholar
• Bhushan R, Dutta K, Somayajulu B. 2001. Concentrations and burial fluxes of organic and inorganic carbon on the eastern margins of the Arabian Sea. Marine Geology. 178(1):95–113. doi:10.1016/S0025-3227(01)00179-7.
   Web of Science ®Google Scholar
• Bohlen L, Dale AW, Sommer S, Mosch T, Hensen C, Noffke A, Scholz F, Wallmann K. 2011. Benthic nitrogen cycling traversing the Peruvian oxygen minimum zone. Geochimica et Cosmochimica Acta. 75(20):6094–6111. doi:10.1016/j.gca.2011.08.010.
   Web of Science ®Google Scholar
• Bristow LA, Callbeck CM, Larsen M, Altabet MA, Dekaezemacker J, Forth M, Gauns M, Glud RN, Kuypers MM, Lavik G. 2017. N2 production rates limited by nitrite availability in the Bay of Bengal oxygen minimum zone. Nature Geoscience. 10(1):24–29. doi:10.1038/ngeo2847.
   Web of Science ®Google Scholar
• Callbeck CM, Lavik G, Ferdelman TG, Fuchs B, Gruber-Vodicka HR, Hach PF, Littmann S, Schoffelen NJ, Kalvelage T, Thomsen S. 2018. Oxygen minimum zone cryptic sulfur cycling sustained by offshore transport of key sulfur oxidizing bacteria. Nature Communications. 9(1):1729–1740. doi:10.1038/s41467-018-04041-x.
   PubMedGoogle Scholar
• Canfield DE, Stewart FJ, Thamdrup B, De Brabandere L, Dalsgaard T, Delong EF, Revsbech NP, Ulloa O. 2010. A cryptic sulfur cycle in oxygen-minimum-zone waters off the Chilean coast. Science. 330(6009):1375–1378. doi:10.1126/science.1196889.
   PubMed Web of Science ®Google Scholar
• Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI. 2010. QIIME allows analysis of high-throughput community sequencing data. Nature Methods. 7(5):335–336. doi:10.1038/nmeth.f.303.
   PubMed Web of Science ®Google Scholar
• Choi H, Koh H-W, Kim H, Chae J-C, Park S-J. 2016. Microbial community composition in the marine sediments of Jeju Island: next-generation sequencing surveys. Journal of Microbiology and Biotechnology. 26(5):883–890. doi:10.4014/jmb.1512.12036.
   PubMed Web of Science ®Google Scholar
• Chun J, Lee J-H, Jung Y, Kim M, Kim S, Kim BK, Lim Y-W. 2007. EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. International Journal of Systematic and Evolutionary Microbiology. 57(10):2259–2261. doi:10.1099/ijs.0.64915-0.
   PubMed Web of Science ®Google Scholar
• Claesson MJ, Wang Q, O'Sullivan O, Greene-Diniz R, Cole JR, Ross RP, O'Toole PW. 2010. Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions. Nucleic Acids Research. 38(22):e200. doi:10.1093/nar/gkq873.
   PubMed Web of Science ®Google Scholar
• Cowie G, Mowbray S, Kurian S, Sarkar A, White C, Anderson A, Vergnaud B, Johnstone G, Brear S, Woulds C. 2014. Comparative organic geochemistry of Indian margin (Arabian Sea) sediments: estuary to continental slope. Biogeosciences. 11(23):6683–6696. doi:10.5194/bg-11-6683-2014.
   Web of Science ®Google Scholar
• Dale AW, Sommer S, Bohlen L, Treude T, Bertics VJ, Bange HW, Pfannkuche O, Schorp T, Mattsdotter M, Wallmann K. 2011. Rates and regulation of nitrogen cycling in seasonally hypoxic sediments during winter (Boknis Eck, SW Baltic Sea): sensitivity to environmental variables. Estuarine, Coastal and Shelf Science. 95(1):14–28. doi:10.1016/j.ecss.2011.05.016.
   Web of Science ®Google Scholar
• Dang H, Zhang X, Sun J, Li T, Zhang Z, Yang G. 2008. Diversity and spatial distribution of sediment ammonia-oxidizing crenarchaeota in response to estuarine and environmental gradients in the Changjiang Estuary and East China Sea. Microbiology. 154(7):2084–2095. doi:10.1099/mic.0.2007/013581-0.
   PubMed Web of Science ®Google Scholar
• de Voogd NJ, Cleary DF, Polónia AR, Gomes NC. 2015. Bacterial community composition and predicted functional ecology of sponges, sediment and seawater from the thousand islands reef complex, West Java, Indonesia. FEMS Microbiology Ecology. 91(4):fiv019. doi:10.1093/femsec/fiv019.
   PubMed Web of Science ®Google Scholar
• Devol AH. 2015. Denitrification, anammox, and N2 production in marine sediments. Annual Review of Marine Science. 7:403–423. doi:10.1146/annurev-marine-010213-135040.
   PubMed Web of Science ®Google Scholar
• Diaz RJ, Rosenberg R. 2008. Spreading dead zones and consequences for marine ecosystems. Science. 321(5891):926–929. doi:10.1126/science.1156401.
   PubMed Web of Science ®Google Scholar
• Divya B, Parvathi A, Bharathi PL, Nair S. 2011. 16S rRNA-based bacterial diversity in the organic-rich sediments underlying oxygen-deficient waters of the eastern Arabian Sea. World Journal of Microbiology and Biotechnology. 27(12):2821–2833. doi:10.1007/s11274-011-0760-0.
   Web of Science ®Google Scholar
• Dyksma S, Lenk S, Sawicka JE, Mußmann M. 2018. Uncultured gammaproteobacteria and desulfobacteraceae account for major acetate assimilation in a coastal marine sediment. Frontiers in Microbiology. 9:3124–3124. doi:10.3389/fmicb.2018.03124.
   PubMed Web of Science ®Google Scholar
• Edgar RC. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 26(19):2460–2461. doi:10.1093/bioinformatics/btq461.
   PubMed Web of Science ®Google Scholar
• Eschbach M, Schreiber K, Trunk K, Buer J, Jahn D, Schobert M. 2004. Long-term anaerobic survival of the opportunistic pathogen Pseudomonas aeruginosa via pyruvate fermentation. Journal of Bacteriology. 186(14):4596–4604. doi:10.1128/JB.186.14.4596-4604.2004.
   PubMed Web of Science ®Google Scholar
• Fernandes GL, Shenoy BD, Menezes LD, Meena RM, Damare SR. 2019. Prokaryotic diversity in oxygen depleted waters of the Bay of Bengal inferred using culture-dependent and-independent methods. Indian Journal of Microbiology. 59(2):193–199. doi:10.1007/s12088-019-00786-1.
   PubMed Web of Science ®Google Scholar
• Fernandes S, Mazumdar A, Bhattacharya S, Peketi A, Mapder T, Roy R, Carvalho MA, Roy C, Mahalakshmi P, Da Silva R. 2018. Enhanced carbon-sulfur cycling in the sediments of Arabian Sea oxygen minimum zone center. Scientific Reports. 8(1):8665–8680. doi:10.1038/s41598-018-27002-2.
   PubMedGoogle Scholar
• Fierer N, Jackson RB. 2006. The diversity and biogeography of soil bacterial communities. Proceedings of the National Academy of Sciences of the United States of America. 103(3):626–631. doi:10.1073/pnas.0507535103.
   PubMed Web of Science ®Google Scholar
• Froelich PN, Klinkhammer G, Bender Maa, Luedtke N, Heath GR, Cullen D, Dauphin P, Hammond D, Hartman B, Maynard V. 1979. Early oxidation of organic matter in pelagic sediments of the eastern equatorial Atlantic: suboxic diagenesis. Geochimica et Cosmochimica Acta. 43(7):1075–1090. doi:10.1016/0016-7037(79)90095-4.
   Web of Science ®Google Scholar
• Fuchs BM, Woebken D, Zubkov MV, Burkill P, Amann R. 2005. Molecular identification of picoplankton populations in contrasting waters of the Arabian Sea. Aquatic Microbial Ecology. 39(2):145–157. doi:10.3354/ame039145.
   Web of Science ®Google Scholar
• Fulweiler RW, Nixon SW, Buckley BA, Granger SL. 2007. Reversal of the net dinitrogen gas flux in coastal marine sediments. Nature. 448:180–182. doi:10.1038/nature05963.
   PubMed Web of Science ®Google Scholar
• Ganesh S, Parris DJ, DeLong EF, Stewart FJ. 2014. Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone. The ISME Journal. 8(1):187–211. doi:10.1038/ismej.2013.144.
   PubMed Web of Science ®Google Scholar
• Gerdes G, Klenke T, Noffke N. 2000. Microbial signatures in peritidal siliciclastic sediments: a catalogue. Sedimentology. 47(2):279–308. doi:10.1046/j.1365-3091.2000.00284.x.
   Web of Science ®Google Scholar
• Gier J, Löscher CR, Dale AW, Sommer S, Lomnitz U, Treude T. 2017. Benthic dinitrogen fixation traversing the oxygen minimum zone off Mauritania (NW Africa). Frontiers in Marine Science. 4(390):Article 390. doi:10.3389/fmars.2017.00390.
   Google Scholar
• Gier J, Sommer S, Löscher CR, Dale AW, Schmitz RA, Treude T. 2016. Nitrogen fixation in sediments along a depth transect through the Peruvian oxygen minimum zone. Biogeosciences. 13(14):4065–4080. doi:10.5194/bg-13-4065-2016.
   Web of Science ®Google Scholar
• Glöckner FO, Fuchs BM, Amann R. 1999. Bacterioplankton compositions of lakes and oceans: a first comparison based on fluorescence in situ hybridization. Environmental Microbiology. 65:3721–3726. doi:10.1128/aem.65.8.3721-3726.
   Web of Science ®Google Scholar
• Heaton L, Fullen MA, Bhattacharyya R. 2016. Critical analysis of the van Bemmelen conversion factor used to convert soil organic matter data to soil organic carbon data: comparative analyses in a UK loamy sand soil. Espaço Aberto. 6(1):35–44. doi:10.36403/espacoaberto.2016.5244.
   Google Scholar
• Hodkinson BP, Grice EA. 2015. Next-generation sequencing: a review of technologies and tools for wound microbiome research. Advances in Wound Care. 4(1):50–58. doi:10.1089/wound.2014.0542.
   PubMed Web of Science ®Google Scholar
• Horn MA, Ihssen J, Matthies C, Schramm A, Acker G, Drake HL. 2005. Dechloromonas denitrificans sp. nov., Flavobacterium denitrificans sp. nov., Paenibacillus anaericanus sp. nov. and Paenibacillus terrae strain MH72, N2O-producing bacteria isolated from the gut of the earthworm Aporrectodea caliginosa. International Journal of Systematic and Evolutionary Microbiology 55(3):1255–1265. doi:10.1099/ijs.0.63484-0.
   PubMedGoogle Scholar
• Im W-T, Hu Z-Y, Kim K-H, Rhee S-K, Meng H, Lee S-T, Quan Z-X. 2012. Description of Fimbriimonas ginsengisoli gen. nov., sp. nov. within the Fimbriimonadia class nov., of the phylum Armatimonadetes. Antonie van Leeuwenhoek. 102(2):307–317. doi:10.1007/s10482-012-9739-6.
   PubMed Web of Science ®Google Scholar
• Iwai S, Weinmaier T, Schmidt BL, Albertson DG, Poloso NJ, Dabbagh K, DeSantis TZ. 2016. Piphillin: improved prediction of metagenomic content by direct inference from human microbiomes. PLoS One. 11(11):e0166104. doi:10.1371/journal.pone.0166104.
   PubMed Web of Science ®Google Scholar
• Janssen PH. 2006. Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Applied and Environmental Microbiology. 72(3):1719–1728. doi:10.1128/AEM.72.3.1719-1728.2006.
   PubMed Web of Science ®Google Scholar
• Jensen MM, Lam P, Revsbech NP, Nagel B, Gaye B, Jetten MS, Kuypers MM. 2011. Intensive nitrogen loss over the Omani Shelf due to anammox coupled with dissimilatory nitrite reduction to ammonium. The ISME Journal. 5(10):1660–1670. doi:10.1038/ismej.2011.44.
   PubMed Web of Science ®Google Scholar
• Krause S, Liebetrau V, Löscher CR, Böhm F, Gorb S, Eisenhauer A, Treude T. 2018. Marine ammonification and carbonic anhydrase activity induce rapid calcium carbonate precipitation. Geochimica et Cosmochimica Acta. 243:116–132. doi:10.1016/j.gca.2018.09.018.
   Web of Science ®Google Scholar
• Kümmel S, Herbst F-A, Bahr A, Duarte M, Pieper DH, Jehmlich N, Seifert J, von Bergen M, Bombach P, Richnow HH, Vogt C. 2015. Anaerobic naphthalene degradation by sulfate-reducing Desulfobacteraceae from various anoxic aquifers. FEMS Microbiology Ecology. 91(3):13. doi:10.1093/femsec/fiv006.
   Web of Science ®Google Scholar
• Langille MG, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Thurber RLV, Knight R. 2013. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nature Biotechnology. 31(9):814–821. doi:10.1038/nbt.2676.
   PubMed Web of Science ®Google Scholar
• Leloup J, Loy A, Knab NJ, Borowski C, Wagner M, Jørgensen BB. 2007. Diversity and abundance of sulfate-reducing microorganisms in the sulfate and methane zones of a marine sediment, Black Sea. Environmental Microbiology. 9(1):131–142. doi:10.1111/j.1462-2920.2006.01122.x.
   PubMed Web of Science ®Google Scholar
• Liu J, Sun F, Wang L, Ju X, Wu W, Chen Y. 2014. Molecular characterization of a microbial consortium involved in methane oxidation coupled to denitrification under micro-aerobic conditions. Microbial Biotechnology. 7(1):64–76. doi:10.1111/1751-7915.12097.
   PubMed Web of Science ®Google Scholar
• Long C, Lu X-L, Gao Y, Jiao B-H, Liu X-Y. 2011. Description of a Sulfitobacter strain and its extracellular cyclodipeptides. Evidence-Based Complementary and Alternative Medicine. 2011:24–29. doi:10.1155/2011/393752.
   Web of Science ®Google Scholar
• Löscher CR, Mohr W, Bange HW, Canfield DE. 2020. No nitrogen fixation in the Bay of Bengal? Biogeosciences. 17(4):851–864. doi:10.5194/bg-17-851-2020.
   Web of Science ®Google Scholar
• Luo H, Moran MA. 2015. How do divergent ecological strategies emerge among marine bacterioplankton lineages? Trends in Microbiology. 23(9):577–584. doi:10.1016/j.tim.2015.05.004.
   PubMed Web of Science ®Google Scholar
• Lv X, Yu J, Fu Y, Ma B, Qu F, Ning K, Wu H. 2014. A meta-analysis of the bacterial and archaeal diversity observed in wetland soils. The Scientific World Journal. 2014:1–12. doi:10.1155/2014/437684.
   Google Scholar
• Madigan M, Cox SS, Stegeman RA. 1984. Nitrogen fixation and nitrogenase activities in members of the family Rhodospirillaceae. Journal of Bacteriology. 157(1):73–78. doi:10.1128/JB.157.1.73-78.1984.
   PubMed Web of Science ®Google Scholar
• Maltby J, Sommer S, Dale AW, Treude T. 2016. Microbial methanogenesis in the sulfate-reducing zone of surface sediments traversing the Peruvian margin. Biogeosciences. 13(1):283–299. doi:10.5194/bg-13-283-2016.
   Web of Science ®Google Scholar
• Manske AK, Glaeser J, Kuypers MM, Overmann J. 2005. Physiology and phylogeny of green sulfur bacteria forming a monospecific phototrophic assemblage at a depth of 100 meters in the Black Sea. Applied and Environmental Microbiology. 71(12):8049–8060. doi:10.1128/AEM.71.12.8049-8060.2005.
   PubMed Web of Science ®Google Scholar
• McCreary Jr JP, Yu Z, Hood RR, Vinaychandran P, Furue R, Ishida A, Richards KJ. 2013. Dynamics of the Indian-Ocean oxygen minimum zones. Progress in Oceanography. 112-113:15–37. doi:10.1016/j.pocean.2013.03.002.
   Web of Science ®Google Scholar
• Meyers PA. 1994. Preservation of elemental and isotopic source identification of sedimentary organic matter. Chemical Geology. 114:289–302. doi:10.1016/0009-2541(94)90059-0.
   Web of Science ®Google Scholar
• Mußmann M, Pjevac P, Krüger K, Dyksma S. 2017. Genomic repertoire of the Woeseiaceae/JTB255, cosmopolitan and abundant core members of microbial communities in marine sediments. The ISME Journal. 11(5):1276–1281. doi:10.1038/ismej.2016.185.
   PubMed Web of Science ®Google Scholar
• Naqvi SWA, Lam P, Narvenkar G, Sarkar A, Naik H, Pratihary A, Shenoy DM, Gauns M, Kurian S, Damare S. 2018. Methane stimulates massive nitrogen loss from freshwater reservoirs in India. Nature Communications. 9(1):1265–1274. doi:10.1038/s41467-018-03607-z.
   PubMedGoogle Scholar
• Naqvi SWA, Naik H, Pratihary A, D'Souza W, Narvekar P, Jayakumar D, Devol A, Yoshinari T, Saino T. 2006. Coastal versus open-ocean denitrification in the Arabian Sea. Biogeosciences. 3(4):621–633. doi:10.5194/bg-3-621-2006.
   Web of Science ®Google Scholar
• Narayan NR, Weinmaier T, Laserna-Mendieta EJ, Claesson MJ, Shanahan F, Dabbagh K, Iwai S, DeSantis TZ. 2020. Piphillin predicts metagenomic composition and dynamics from DADA2-corrected 16S rDNA sequences. BMC Genomics. 21(1):1–12. doi:10.1186/s12864-020-6537-9.
   Web of Science ®Google Scholar
• Nelson D, Sommers L. 1982. Total carbon, organic carbon, and organic matter. In: Page AL, editor. Methods of soil analysis Part 2. Chemical and microbiological properties. Vol. 2. Madison (WI): American Society of Agronomy, Soil Science Society of America; p. 539–579. doi:10.2134/agronmonogr9.2.c38.
   Google Scholar
• Okubo T, Ikeda S, Yamashita A, Terasawa K, Minamisawa K. 2009. Pyrosequence read length of 16S rRNA gene affects phylogenetic assignment of plant-associated bacteria. Microbes and Environments. 27(2):204–208. doi:10.1264/jsme2.ME11258.
   Google Scholar
• Orsi WD, Coolen MJL, Wuchter C, He L, More KD, Irigoien X, Chust G, Johnson C, Hemingway JD, Lee M, et al. 2017. Climate oscillations reflected within the microbiome of Arabian Sea sediments. Scientific Reports. 7(1):6040. doi:10.1038/s41598-017-05590-9.
   PubMedGoogle Scholar
• Padilla CC, Bristow LA, Sarode N, Garcia-Robledo E, Ramírez EG, Benson CR, Bourbonnais A, Altabet MA, Girguis PR, Thamdrup B. 2016. NC10 bacteria in marine oxygen minimum zones. The ISME Journal. 10(8):2067. doi:10.1038/ismej.2015.262.
   PubMed Web of Science ®Google Scholar
• Pattan J, Mir IA, Parthiban G, Karapurkar SG, Matta V, Naidu P, Naqvi S. 2013. Coupling between suboxic condition in sediments of the western Bay of Bengal and southwest monsoon intensification: a geochemical study. Chemical Geology. 343:55–66. doi:10.1016/j.chemgeo.2013.02.011.
   Web of Science ®Google Scholar
• Paulmier ADR-P. 2009. Oxygen minimum zones (OMZs) in the modern ocean. Progress in Oceanography. 80:113–128. doi:10.1016/j.pocean.2008.08.001.
   Web of Science ®Google Scholar
• Penton CR, Devol AH, Tiedje JM. 2006. Molecular evidence for the broad distribution of anaerobic ammonium-oxidizing bacteria in freshwater and marine sediments. Applied and Environmental Microbiology. 72(10):6829–6832. doi:10.1128/AEM.01254-06.
   PubMed Web of Science ®Google Scholar
• Pitcher A, Villanueva L, Hopmans EC, Schouten S, Reichart G-J, Damsté JSS. 2011. Niche segregation of ammonia-oxidizing archaea and anammox bacteria in the Arabian Sea oxygen minimum zone. The ISME Journal. 5(12):1896. doi:10.1038/ismej.2011.60.
   PubMed Web of Science ®Google Scholar
• Pramanik A, Basak P, Banerjee S, Sengupta S, Chattopadhyay D, Bhattacharyya M. 2016. Metagenomic exploration of the bacterial community structure at Paradip Port, Odisha, India. Genomics Data. 7:94–96. doi:10.1016/j.gdata.2015.12.005.
   PubMedGoogle Scholar
• Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO. 2012. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Research. 41(D1):D590–D596. doi:10.1093/nar/gks1219.
   PubMed Web of Science ®Google Scholar
• Quince C, Lanzen A, Davenport RJ, Turnbaugh PJ. 2011. Removing noise from pyrosequenced amplicons. BMC Bioinformatics. 12(1):38. doi:10.1186/1471-2105-12-38.
   PubMedGoogle Scholar
• Rajpathak SN, Banerjee R, Mishra PG, Khedkar AM, Patil YM, Joshi SR, Deobagkar DD. 2018. An exploration of microbial and associated functional diversity in the OMZ and non-OMZ areas in the Bay of Bengal. Journal of Biosciences. 43(4):635–648. doi:10.1007/s12038-018-9781-2.
   PubMed Web of Science ®Google Scholar
• Ramaswamy V, Gaye B. 2006. Regional variations in the fluxes of foraminifera carbonate, coccolithophorid carbonate and biogenic opal in the northern Indian Ocean. Deep Sea Research Part I: Oceanographic Research Papers. 53(2):271–293. doi:10.1016/j.dsr.2005.11.003.
   Web of Science ®Google Scholar
• Ramos HC, Hoffmann T, Marino M, Nedjari H, Presecan-Siedel E, Dreesen O, Glaser P, Jahn D. 2000. Fermentative metabolism of Bacillus subtilis: physiology and regulation of gene expression. Journal of Bacteriology. 182(11):3072–3080. doi:10.1128/JB.182.11.3072-3080.2000.
   PubMed Web of Science ®Google Scholar
• Robinson RS, Kienast M, Luiza Albuquerque A, Altabet M, Contreras S, De Pol Holz R, Dubois N, Francois R, Galbraith E, Hsu TC. 2012. A review of nitrogen isotopic alteration in marine sediments. Paleoceanography. 27(4). doi:10.1029/2012PA002321.
   Google Scholar
• Sarkar A, Naqvi SWA, Lavik G, Pratihary A, Naik H, Shirodkar G, Kuypers MM. 2020. Massive nitrogen loss over the western Indian continental shelf during seasonal anoxia: evidence from isotope pairing technique. Frontiers in Marine Science. 7(678):1–14. doi:10.3389/fmars.2020.00678.
   PubMedGoogle Scholar
• Sarma V, Krishna M, Viswanadham R, Rao G, Rao V, Sridevi B, Kumar B, Prasad V, Subbaiah CV, Acharyya T. 2013. Intensified oxygen minimum zone on the western shelf of Bay of Bengal during summer monsoon: influence of river discharge. Journal of Oceanography. 69(1):45–55. doi:10.1007/s10872-012-0156-2.
   Web of Science ®Google Scholar
• Sarma V, Kumar MD, Saino T. 2007. Impact of sinking carbon flux on accumulation of deep-ocean carbon in the Northern Indian Ocean. Biogeochemistry. 82(1):89–100. doi:10.1007/s10533-006-9055-1.
   Web of Science ®Google Scholar
• Schimel JP, Schaeffer SM. 2015. Microbial control over carbon cycling in soil. Frontiers in Microbiology. 3:348–358. doi:10.3389/fmicb.2012.00348.
   Google Scholar
• Schlitzer R. 2015. Data analysis and visualization with Ocean Data View. Canadian Meteorological and Oceanographic Society Bulletin SCMO. 43(1):9–13. hdl:10013/epic.45187.d001
   Google Scholar
• Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ. 2009. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology. 75(23):7537–7541. doi:10.1128/AEM.01541-09.
   PubMed Web of Science ®Google Scholar
• Schunck H, Lavik G, Desai DK, Großkopf T, Kalvelage T, Löscher CR, Paulmier A, Contreras S, Siegel H, Holtappels M. 2013. Giant hydrogen sulfide plume in the oxygen minimum zone off Peru supports chemolithoautotrophy. PLoS One. 8(8):e68661. doi:10.1371/journal.pone.0068661.
   PubMed Web of Science ®Google Scholar
• Shao M-F, Zhang T, Fang HH-P. 2010. Sulfur-driven autotrophic denitrification: diversity, biochemistry, and engineering applications. Applied Microbiology and Biotechnology. 88(5):1027–1042. doi:10.1007/s00253-010-2847-1.
   PubMed Web of Science ®Google Scholar
• Shirodkar G, Naqvi SWA, Naik H, Pratihary AK, Kurian S, Shenoy DM. 2018. Methane dynamics in the shelf waters of the West coast of India during seasonal anoxia. Marine Chemistry. 203:55–63. doi:10.1016/j.marchem.2018.05.001.
   Web of Science ®Google Scholar
• Sorokin DY. 1995. Sulfitobacter pontiacus gen. nov., sp. nov. – a new heterotrophic bacterium from the Black Sea, specialized on sulfite oxidation. Microbiology. 64(3):295. doi:10.1007/s12275-019-9150-3.
   Web of Science ®Google Scholar
• Stewart FJ, Ulloa O, DeLong EF. 2012. Microbial metatranscriptomics in a permanent marine oxygen minimum zone. Environmental Microbiology. 14(1):23–40. doi:10.1111/j.1462-2920.2010.02400.x.
   PubMed Web of Science ®Google Scholar
• Suh S-S, Park M, Hwang J, Lee S, Moh SH, Park KH, Lee T-K. 2014. Characterization of bacterial communities associated with seasonal water masses from Tongyoung in South Sea of Korea. Ocean Science Journal. 49(3):193–200. doi:10.1007/s12601-014-0019-4.
   Web of Science ®Google Scholar
• Ulloa O, Wright JJ, Belmar L, Hallam SJ. 2013. Pelagic oxygen minimum zone microbial communities. In: Rosenberg E., DeLong E.F., Lory S., Stackebrandt E., Thompson F., editors. The Prokaryotes. Berlin: Springer; p. 113–122. doi:10.1007/978-3-642-30123-0_45.
   Google Scholar
• van der Weijden CH, Reichart GJ, Visser HJ. 1999. Enhanced preservation of organic matter in sediments deposited within the oxygen minimum zone in the northeastern Arabian Sea. Deep Sea Research Part I: Oceanographic Research Papers. 46(5):807–830. doi:10.1016/S0967-0637(98)00093-4.
   Web of Science ®Google Scholar
• Van Goethem MW, Makhalanyane TP, Cowan DA, Valverde A. 2017. Cyanobacteria and Alphaproteobacteria may facilitate cooperative interactions in niche communities. Frontiers in Microbiology. 8:2099. doi:10.3389/fmicb.2017.02099.
   PubMed Web of Science ®Google Scholar
• Varki A, Gagneux P. 2017. Biological functions of glycans (Essentials of glycobiology) [Internet]. 3rd ed. New York: Cold Spring Harbor Laboratory Press.
   Google Scholar
• Wang Y, Sheng H-F, He Y, Wu J-Y, Jiang Y-X, Tam NF-Y, Zhou H-W. 2012. Comparison of the levels of bacterial diversity in freshwater, intertidal wetland, and marine sediments by using millions of illumina tags. Applied and Environmental Microbiology. 78(23):8264–8271. doi:10.1128/AEM.01821-12.
   PubMed Web of Science ®Google Scholar
• Ward B, Devol A, Rich J, Chang B, Bulow S, Naik H, Pratihary A, Jayakumar A. 2009. Denitrification as the dominant nitrogen loss process in the Arabian Sea. Nature. 461(7260):78–81. doi:10.1038/nature08276.
   PubMed Web of Science ®Google Scholar
• Wegner C-E, Richter-Heitmann T, Klindworth A, Klockow C, Richter M, Achstetter T, Glöckner FO, Harder J. 2013. Expression of sulfatases in Rhodopirellula baltica and the diversity of sulfatases in the genus Rhodopirellula. Marine Genomics. 9:51–61. doi:10.1016/j.margen.2012.12.001.
   PubMed Web of Science ®Google Scholar
• West NJ, Schönhuber WA, Fuller NJ, Amann RI, Rippka R, Post AF, Scanlan DJ. 2001. Closely related Prochlorococcus genotypes show remarkably different depth distributions in two oceanic regions as revealed by in situ hybridization using 16S rRNA-targeted oligonucleotides. Microbiology. 147(7):1731–1744. doi:10.1099/00221287-147-7-1731.
   PubMedGoogle Scholar
• Yakimov MM, Giuliano L, Gentile G, Crisafi E, Chernikova TN, Abraham W-R, Lünsdorf H, Timmis KN, Golyshin PN. 2003. Oleispira antarctica gen. nov., sp. nov., a novel hydrocarbonoclastic marine bacterium isolated from Antarctic coastal sea water. International Journal of Systematic and Evolutionary Microbiology. 53(3):779–785. doi:10.1099/ijs.0.02366-0.
   PubMedGoogle Scholar
• Yanagibayashi M, Nogi Y, Li L, Kato C. 1999. Changes in the microbial community in Japan Trench sediment from a depth of 6292 m during cultivation without decompression. FEMS Microbiology Letters. 170(1):271–279. doi:10.1111/j.1574-6968.1999.tb13384.x.
   PubMed Web of Science ®Google Scholar
• Yu Z, Wang X, Han G, Liu X, Zhang E. 2018. Organic and inorganic carbon and their stable isotopes in surface sediments of the Yellow River Estuary. Scientific Reports. 8(1):1–10. doi:10.1038/s41598-018-29200-4.
   PubMedGoogle Scholar
• Zhu D, Tanabe S-H, Yang C, Zhang W, Sun J. 2013. Bacterial community composition of South China Sea sediments through pyrosequencing-based analysis of 16S rRNA genes. PLoS One. 8(10):e78501. doi:10.1371/journal.pone.0078501.
   PubMed Web of Science ®Google Scholar