Microbial communities in the deep-sea sediments of the South São Paulo Plateau, Southwestern Atlantic Ocean.
Asphalt seep; Atlantic Ocean
Deep-sea sediment
Microbial diversity
Journal
International microbiology : the official journal of the Spanish Society for Microbiology
ISSN: 1618-1905
Titre abrégé: Int Microbiol
Pays: Switzerland
ID NLM: 9816585
Informations de publication
Date de publication:
Nov 2023
Nov 2023
Historique:
received:
14
02
2023
accepted:
06
04
2023
revised:
30
03
2023
medline:
3
11
2023
pubmed:
24
4
2023
entrez:
24
04
2023
Statut:
ppublish
Résumé
Microbial communities play a key role in the ocean, acting as primary producers, nutrient recyclers, and energy providers. The São Paulo Plateau is a region located on the southeastern coast of Brazil within economic importance, due to its oil and gas reservoirs. With this focus, this study examined the diversity and composition of microbial communities in marine sediments located at three oceanographic stations in the southern region of São Paulo Plateau using the HOV Shinkai 6500 in 2013. The 16S rRNA gene was sequenced using the universal primers (515F and 926R) by the Illumina Miseq platform. The taxonomic compositions of samples recovered from SP3 station were markedly distinct from those obtained from SP1 and SP2. Although all three stations exhibited a high abundance of Gammaproteobacteria (> 15%), this taxon dominated more than 90% of composition of the A and C sediment layers at SP3. The highest abundance of the archaeal class Nitrososphaeria was presented at SP1, mainly at layer C (~ 21%), being absent at SP3 station. The prediction of chemoheterotrophy and fermentation as important microbial functions was supported by the data. Additionally, other metabolic pathways related to the cycles of nitrogen, carbon and sulfur were also predicted. The core microbiome analysis comprised only two ASVs. Our study contributes to a better understanding of microbial communities in an economically important little-explored region. This is the third microbiological survey in plateau sediments and the first focused on the southern region.
Identifiants
pubmed: 37093322
doi: 10.1007/s10123-023-00358-w
pii: 10.1007/s10123-023-00358-w
doi:
Substances chimiques
RNA, Ribosomal, 16S
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
1041-1051Subventions
Organisme : Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
ID : 88887.370353/2019-00
Organisme : Japan Agency for Marine-Earth Science and Technology
ID : provision of equipment, drugs or supplements
Informations de copyright
© 2023. The Author(s), under exclusive licence to Springer Nature Switzerland AG.
Références
Aguiar JE, de Lacerda LD, Miguens FC, Marins RV (2014) The geostatistics of the metal concentrations in sediments from the eastern Brazilian continental shelf in areas of gas and oil production. J South Amer Earth Sci 51:91–104. https://doi.org/10.1016/j.jsames.2013.12.005
doi: 10.1016/j.jsames.2013.12.005
Almeida AG, Kowsmann RO (2015) Geomorfologia do talude Continental e do Platô de São Paulo na Bacia de Campos. Geologia e Geomorfologia 1:33–66. https://doi.org/10.1016/B978-85-352-6937-6.50010-0
doi: 10.1016/B978-85-352-6937-6.50010-0
Anantharaman K, Hausmann B, Jungbluth SP et al (2018) Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle. ISME J 12:1715–1728. https://doi.org/10.1038/s41396-018-0078-0
doi: 10.1038/s41396-018-0078-0
pubmed: 29467397
pmcid: 6018805
Arnosti C (2014) Patterns of Microbially Driven Carbon Cycling in the Ocean: Links between Extracellular Enzymes and Microbial Communities. Adv Oceanogr 1–12. https://doi.org/10.1155/2014/706082
Azam F, Malfatti F (2007) Microbial structuring of marine ecosystems. Nat Rev Microbiol 5:782–791. https://doi.org/10.1038/nrmicro1747
doi: 10.1038/nrmicro1747
pubmed: 17853906
Bernardino AF, Berenguer V, Ribeiro-Ferreira VP (2016) Bathymetric and regional changes in benthic macrofaunal assemblages on the deep Eastern Brazilian margin, SW Atlantic. Deep Sea Res Part i: Oceanogr Res Papers 111:110–120. https://doi.org/10.1016/j.dsr.2016.02.016
doi: 10.1016/j.dsr.2016.02.016
Biddle JF, Lipp JS, Lever MA, Lloyd KG, Sorensen KB, Anderson R et al (2006) Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru. Proc Natl Acad Sci 103:3846–3851. https://doi.org/10.1073/pnas.0600035103
doi: 10.1073/pnas.0600035103
pubmed: 16505362
pmcid: 1533785
Bienhold C, Zinger L, Boetius A, Ramette A (2016) Diversity and Biogeography of Bathyal and Abyssal Seafloor Bacteria. PLoS ONE 11:1–20. https://doi.org/10.1371/journal.pone.0148016
doi: 10.1371/journal.pone.0148016
Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA et al (2019) Reproducible, interactive, scalable, and extensible microbiome data science using QIIME 2. Nat Biotechnol 37:852–857. https://doi.org/10.1038/s41587-019-0209-9
doi: 10.1038/s41587-019-0209-9
pubmed: 31341288
pmcid: 7015180
Bowles MW, Mogollon JM, Kasten S, Zabel M, Hinrichs KU (2014) Global rates of marine sulfate reduction and implications for sub-sea-floor metabolic activities. Science 344:889–891. https://doi.org/10.1126/science.1249213
doi: 10.1126/science.1249213
pubmed: 24812207
Burdige DJ (2007) Preservation of organic matter in marine sediments: controls, mechanisms, and an imbalance in sediment organic carbon budgets? Chem Rev 107:467–485. https://doi.org/10.1021/cr050347q
doi: 10.1021/cr050347q
pubmed: 17249736
Callahan BJ, McMurdie PJ, Rosen MJ et al (2016) DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods 13:581–583. https://doi.org/10.1038/nmeth.3869
doi: 10.1038/nmeth.3869
pubmed: 27214047
pmcid: 4927377
Chen W-M, Xie P-B, Young C-C, Sheu S-Y (2017) Formosimonas limnophila gen. nov., sp. nov., a new member of the family Burkholderiaceae isolated from a freshwater lake. Int J Syst Evol Microbiol. 67:17–24. https://doi.org/10.1099/ijsem.0.001561
doi: 10.1099/ijsem.0.001561
pubmed: 27902193
Cordes EE, Jones DOB, Schlacher TA, Amon DJ, Bernardino AF, Brooke S, Carney R, DeLeo DM, Dunlop KM, Escobar-Briones EG, Gates AR, Génio L, Gobin J, Henry L-A, Herrera S, Hoyt S, Joye M, Kark S, Mestre NC, Metaxas A, Pfeifer S, Sink K, Sweetman AK, Witte U (2016) Environmental Impacts of the Deep-Water Oil and Gas Industry: A Review to Guide Management Strategies. Front Environ Sci 4:58. https://doi.org/10.3389/fenvs.2016.00058
doi: 10.3389/fenvs.2016.00058
Corinaldesi C (2015) New perspectives in benthic deep-sea microbial ecology. Front Mar Sci 2:1–12. https://doi.org/10.3389/fmars.2015.00017
doi: 10.3389/fmars.2015.00017
Danovaro R, Company JB, Corinaldesi C, D’Onghia G, Galil B et al (2010) Deep-Sea Biodiversity in the Mediterranean Sea: The Known, the Unknown, and the Unknowable. PLoS ONE 5(8):e11832. https://doi.org/10.1371/journal.pone.0011832
doi: 10.1371/journal.pone.0011832
pubmed: 20689848
pmcid: 2914020
Francis CA, Roberts KJ, Beman JM, Santoro AE, Oakley BB (2005) Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. Proc Natl Acad Sci 102(41):14683–14688. https://doi.org/10.1073/pnas.0506625102
doi: 10.1073/pnas.0506625102
pubmed: 16186488
pmcid: 1253578
Francis C, Beman J, Kuypers M (2007) New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation. ISME J 1:19–27. https://doi.org/10.1038/ismej.2007.8
doi: 10.1038/ismej.2007.8
pubmed: 18043610
Franco NR, Giraldo MÁ, López-Alvarez D, Gallo-Franco JJ, Dueñas LF, Puentes V, Castillo A (2021) Bacterial Composition and Diversity in Deep-Sea Sediments from the Southern Colombian Caribbean Sea. Diversity 13:10. https://doi.org/10.3390/d13010010
doi: 10.3390/d13010010
Fujikura K, Yamanaka T, Sumida PYG, Bernardino AF, Pereira OS, Kanehara T, Nagano Y, Nakayama CR, Nobrega M, Pellizari VH, Shigeno S, Yoshida T, Zhang J, Kitazato H (2017) Discovery of asphalt seeps in the deep Southwest Atlantic off Brazil. Deep Sea Res II 146:35–44. https://doi.org/10.1016/j.dsr2.2017.04.002
doi: 10.1016/j.dsr2.2017.04.002
Gilbert JA, Neufeld JD (2014) Life in a World without Microbes. PLoS Biol 12 (12). https://doi.org/10.1371/journal.pbio.1002020
Giongo A, Haag T, Simão TL, Medina-Silva R, Utz LRP, Bogo MR, Bonatto SL, Zamberlan PM, Augustin AH, Lourega RV et al (2016) Discovery of a chemosynthesis-based community in the western South Atlantic Ocean. Deep Sea Res i 112:45–56. https://doi.org/10.1016/j.dsr.2015.10.010
doi: 10.1016/j.dsr.2015.10.010
Gutierrez T (2018) Marine, aerobic hydrocarbon-degrading Gammaproteobacteria – overview. In: Taxonomy, genomics and ecophysiology of hydrocarbon-degrading microbes; Handbook of Hydrocarbon and Lipid Microbiology. (Eds: McGenity TJ and Prince R); Springer, Berlin; volume 6, section 6.10. https://doi.org/10.1007/978-3-319-60053-6_22-1
Gutierrez T, Kleindienst S (2020) Uncovering Microbial Hydrocarbon Degradation Processes: The Promise of Stable Isotope Probing. In: Teske A, Carvalho V (eds) Marine Hydrocarbon Seeps. Springer Oceanography. Springer, Cham. https://doi.org/10.1007/978-3-030-34827-4_10
Hallam SJ, Mincer TJ, Schleper C, Preston CM, Roberts K et al (2006) Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota. PLoS Biol 4:95. https://doi.org/10.1371/journal.pbio.0040095
doi: 10.1371/journal.pbio.0040095
Hongxiang X, Min W, Xiaogu W, Junyi Y, Chunsheng W (2008) Bacterial diversity in deep-sea sediment from the northeastern Pacific Ocean. Acta Ecol Sin 28(2):479–485. https://doi.org/10.1016/S1872-2032(08)60026-8
doi: 10.1016/S1872-2032(08)60026-8
Hoshino T, Doi H, Uramoto G-I, Wörmer L, Adhikari RR, Xiao N, Morono Y, D’Hondt S, Hinrichs K-U, Inagaki F (2020) Global diversity of microbial communities in marine sediment. Proc Natl Acad Sci USA 117:27587–27597. https://doi.org/10.1073/pnas.1919139117
doi: 10.1073/pnas.1919139117
pubmed: 33077589
pmcid: 7959581
Hubalek et al (2016) Connectivity to the surface determines diversity patterns in subsurface aquifers of the Fennoscandian shield. ISME J 10:2447–2458. https://www.nature.com/articles/ismej201636
Jiang K, Zhang J, Sakatoru A, Kambayashi S, Yamanaka T, Kanehara T, Fujikura K, Pellizari VH (2018) Discovery and biogeochemistry of asphalt seeps in the North São Paulo Plateau, Brazilian Margin. Sci Rep 8:12619. https://doi.org/10.1038/s41598-018-30928-2
doi: 10.1038/s41598-018-30928-2
pubmed: 30135574
pmcid: 6105600
Jørgensen BB (1990) A Thiosulfate Shunt in the Sulfur Cycle of Marine Sediments. Science 249:152–154. https://doi.org/10.1126/science.249.4965.152
doi: 10.1126/science.249.4965.152
pubmed: 17836966
Jørgensen BB, Boetius A (2007) Feast and famine – microbial life in the deep-sea bed. Nat Rev Microbiol 5:770–781. https://doi.org/10.1038/nrmicro1745
doi: 10.1038/nrmicro1745
pubmed: 17828281
Karner MB, DeLong EF, Karl DM (2001) Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature 409:507–510. https://doi.org/10.1038/35054051
doi: 10.1038/35054051
pubmed: 11206545
Kitazato H, Fujikura K, Sumida PGY, Pellizari VH, Perez JA (2017) Editorial: Rich geo- and bio-diversities exist in the South West Atlantic deep-sea: The first human-occupied submersible Shinkai 6500 dive cruise (Iatá-piúna). Deep Sea Res II 146:1–3. https://doi.org/10.1016/j.dsr2.2017.11.007
doi: 10.1016/j.dsr2.2017.11.007
Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, Glöckner FO (2013) Evaluation of general 16S ribosomal RNA gene PCR 545 primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res 7:41. https://doi.org/10.1093/nar/gks808
doi: 10.1093/nar/gks808
Knittel K, Boetius A (2009) Anaerobic oxidation of methane: progress with an unknown process. Annu Rev Microbiol 63:311–334. https://doi.org/10.1146/annurev.micro.61.080706.093130
doi: 10.1146/annurev.micro.61.080706.093130
pubmed: 19575572
Kubo K, Lloyd K, 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. https://doi.org/10.1038/ismej.2012.37
doi: 10.1038/ismej.2012.37
pubmed: 22551871
pmcid: 3449235
Kumar N, Gambôa LAP (1979) Evolution of the São Paulo Plateau (southeastern Brazilian margin) and implications for the early history of the South Atlantic. GSA Bull 90(3):281–293. https://doi.org/10.1130/0016-7606(1979)90%3c281:EOTSPP%3e2.0.CO;2
doi: 10.1130/0016-7606(1979)90<281:EOTSPP>2.0.CO;2
Li H, Yu Y, Luo W, Zeng Y, Chen B (2009) Bacterial diversity in surface sediments from the Pacific Arctic Ocean. Extremophiles 13(2):233–246. https://doi.org/10.1007/s00792-009-0225-7
doi: 10.1007/s00792-009-0225-7
pubmed: 19153801
Lindh MV, Maillot BM, Shulse CN, Gooday AJ, Amon DJ, Smith CR, Church MJ (2017) From the Surface to the Deep-Sea: Bacterial Distributions across Polymetallic Nodule Fields in the Clarion-Clipperton Zone of the Pacific Ocean. Front Microbiol 8:1696. https://doi.org/10.3389/fmicb.2017.01696
doi: 10.3389/fmicb.2017.01696
pubmed: 28943866
pmcid: 5596108
Louca S, Parfrey LW, Doebeli M (2016) Decoupling function and taxonomy in the global ocean microbiome. Science 353:1272–1277. https://doi.org/10.1126/science.aaf4507
doi: 10.1126/science.aaf4507
pubmed: 27634532
Mariano J, La Rovere E (2007) Oil and gas exploration and production activities in Brazil: The consideration of environmental issues in the bidding rounds promoted by the National Petroleum Agency. Energy Policy 35(5):2899–2911. https://doi.org/10.1016/j.enpol.2006.10.005
doi: 10.1016/j.enpol.2006.10.005
McMurdie PJ, Holmes S (2013) Phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. Plos One 8(4). https://doi.org/10.1371/journal.pone.0061217 .
Medina-Silva R, Oliveira RR, Trindade FJ, Borges LGA, Simão TLL, Augustin AH, Valdez FP, Constant MJ, Simundi CL, Eizirik E, Groposo C, Miller DJ, Silva PR, Viana AR, Ketzer JMM, Giongo A (2018) Microbiota associated with tubes of Escarpia sp. from cold seeps in the southwestern Atlantic Ocean constitutes a community distinct from that of surrounding marine sediment and water. Antonie Van Leeuwenhoek 11:533–550. https://doi.org/10.1007/s10482-017-0975-7
doi: 10.1007/s10482-017-0975-7
Miller DJ, Ketzer JM, Viana AR, Kowsmann RO, Freire AFM, Oreiro SG et al (2015) Natural gas hydrates in the Rio Grande cone (Brazil): a new province in the western South Atlantic. Mar Geol Petrol 67:187–196. https://doi.org/10.1016/j.marpetgeo.2015.05.012
doi: 10.1016/j.marpetgeo.2015.05.012
Nealson KH (2006) The Manganese-Oxidizing Bacteria. In: Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E (eds) The Prokaryotes. Springer, New York, NY. https://doi.org/10.1007/0-387-30745-1_11
doi: 10.1007/0-387-30745-1_11
Nicol GW, Schleper C (2006) Ammonia-oxidising Crenarchaeota: important players in the nitrogen cycle? Trends Microbiol 14(5):207–212. https://doi.org/10.1016/j.tim.2006.03.004
doi: 10.1016/j.tim.2006.03.004
pubmed: 16603359
Okrasińska A, Bokus A, Duk K, Gesiorska A, Sokolowska B, Milobedzka A, Wrzosek M, Pawlowska J (2021) New Endohyphal Relationships between Mucoromycota and Burkholderiaceae Representatives. Appl Environ Microbiol 87. https://doi.org/10.1128/AEM.02707-20
Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P, McGlinn D, Minchin PR, O´Hara RB, Simpson GL, Solymos P, Stevens MHH, Szoecs E, Wagner H (2020) Vegan: Community Ecology Package. R Package Version 2.5–7. https://CRAN.R-project.org/package=vegan . Accessed 12 June 2021.
Pannekens M, Kroll L, Müller H, Mbow FT, Meckenstock RU (2019) Oil reservoirs, an exceptional habitat for microorganisms. New Biotechnol 49:1–9. https://doi.org/10.1016/j.nbt.2018.11.006
doi: 10.1016/j.nbt.2018.11.006
Parada AE, Needham DM, Fuhrman JA (2016) Every base matters: Assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. Environ Microbiol 18(5):1403–1414. https://doi.org/10.1111/1462-2920.13023
doi: 10.1111/1462-2920.13023
pubmed: 26271760
Pedregosa F, Varoquaux G, Gramfort A, Michel V, Thirion B, Grisel O, Blondel M, Prettenhofer P, Weiss R, Dubourg V, Vanderplas J, Passos A, Cournapeau D, Brucher M, Perrot M, Duchesnay É (2011) Scikit-learn: Machine learning in Python. J Mach Learn Res 12(85): 2825–2830. http://jmlr.org/papers/v12/pedregosa11a.html Accessed 10 September 2021
Petro C, Starnawski P, Schramm A, Kjeldsen KU (2017) Microbial community assembly in marine sediments. AME Special 79:177–195. https://doi.org/10.3354/ame01826
doi: 10.3354/ame01826
Pfannkuche O, Lochte K (1993) Open ocean pelago-benthic coupling: cyanobacteria as tracers of sedimenting salp faeces. Deep Sea Res Part I 40(4):727–737. https://doi.org/10.1016/0967-0637(93)90068-E
doi: 10.1016/0967-0637(93)90068-E
Philippot L, Andersson SGE, Battin TJ, Prosser JI, Schimel JP, Whitman WB, Hallin S (2010) The ecological coherence of high bacterial taxonomic ranks. Nat Rev Microbiol (8):523–529. https://www.nature.com/articles/nrmicro2367
Prince RC, Gramain A, McGenity TJ (2010) Prokaryotic Hydrocarbon Degraders In: Timmis, K.N. (eds) Handbook of Hydrocarbon and Lipid Microbiology. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-77587-4_118
Puente-Sánchez F, et al (2018) Viable cyanobacteria in the deep continental subsurface. Proc Natl Acad Sci U.S.A. 115 (42):10702–10707. https://doi.org/10.1073/pnas.1808176115
Queiroz LL, Bendia AG, Duarte RTD, das Graças DA, da Costa da Silva AL, Nakayama CR, Sumida PY, Lima AOS, Nagano Y, Fujikura K, Kitazato H, Pellizari VH (2020) Bacterial diversity in deep-sea sediments under influence of asphalt seep at the São Paulo Plateau. Antonie van Leeuwenhoeck 113:707–717. https://doi.org/10.1007/s10482-020-01384-8
doi: 10.1007/s10482-020-01384-8
Quince C, Lanzen A, Davenport RJ, Turnbaugh PJ (2011) Removing Noise From Pyrosequenced Amplicons. BMC Bioinformatics 12:834–839. https://doi.org/10.1186/1471-2105-12-38
doi: 10.1186/1471-2105-12-38
R Core Team (2021) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL: https://www.R-project.org/
Ruff SE, Biddle JF, Teske AP, Knittel K, Boetius A, Ramette A (2015) Global dispersion and local diversification of the methane seep microbiome. P Natl Acad Sci USA 112:4015–4020. https://doi.org/10.1073/pnas.1421865112
doi: 10.1073/pnas.1421865112
Ruff SE (2020) Microbial Communities and Metabolisms at Hydrocarbon Seeps. Teske A, Carvalho V (eds.) Marine Hydrocarbon Seeps. Springer Oceanography. Springer, Cham. https://doi.org/10.1007/978-3-030-34827-4_1
Schauer R, Bienhold C, Ramette A, Harder J (2010) Bacterial diversity and biogeography in deep-sea surface sediments of the South Atlantic Ocean. ISME J 4:159–170. https://doi.org/10.1038/ismej.2009.106
doi: 10.1038/ismej.2009.106
pubmed: 19829317
Schubotz F, Lipp JS, Elvert M, Hinrichs K-U (2011a) Stable carbon isotopic compositions of intact polar lipids reveal complex carbon flow patterns among degrading hydrocarbon-degrading microbial communities at the Chapopote asphalt volcano. Geochim Cosmochim Acta 75(16):4399–4415. https://doi.org/10.1016/j.gca.2011.05.018(A)
doi: 10.1016/j.gca.2011.05.018(A)
Schubotz F, Lipp JS, Elvert M, Kasten S, Mollar XP, Zabel M et al (2011b) Petroleum degradation and associated microbial signatures at the Chapopote asphalt volcano, Southern Gulf of Mexico. Geochim Cosmochim Acta 75(16):4377–4398. https://doi.org/10.1016/j.gca.2011.05.025(B)
doi: 10.1016/j.gca.2011.05.025(B)
Shlimon AG, Mansurbeg H, Othman RS, Gittel A, Aitken CM, Head IM, Finster KW, Kjeldsen KU (2020) Microbial community composition in crude oils and asphalts from the Kurdistan Region of Iraq. Geomicrobiology J 37:1–18. https://doi.org/10.1080/01490451.2020.1753131
doi: 10.1080/01490451.2020.1753131
Stal LJ (2012) Cyanobacterial mats and stromatolites. In: Whitton BA (eds.) Ecology of Cyanobacteria II. Springer, Dordrecht. 65–125. https://doi.org/10.1007/978-94-007-3855-3_4
Suess E (2014) Marine cold seeps and their manifestations: geological control, biogeochemical criteria, and environmental conditions. Int J Earth Sci 103:1889–1916. https://doi.org/10.1007/s00531-014-1010-0
doi: 10.1007/s00531-014-1010-0
Tang T, Kisslinger K, Lee C (2014) Silicate deposition during decomposition of cyanobacteria may promote the export of picophytoplankton to the deep ocean. Nat Commun 5:4143. https://doi.org/10.1038/ncomms5143
doi: 10.1038/ncomms5143
pubmed: 24920300
Tavormina PL, Ussler W, Orphan VJ (2008) Planktonic and sediment-associated aerobic methanotrophs in two seep systems along the North American Margin. Appl Environ Microbiol 74:3985–3995. https://doi.org/10.1128/AEM.00069-08
doi: 10.1128/AEM.00069-08
pubmed: 18487407
pmcid: 2446507
Teske A, Brinkhoff T, Muyzer G, Moser DP, Rethmeier J, Jannasch HW (2000) Diversity of thiosulfate-oxidizing bacteria from marine sediments and hydrothermal vents. Appl Environ Microbiol 66(8):3125–33. https://doi.org/10.1128/AEM.66.8.3125-3133.2000
doi: 10.1128/AEM.66.8.3125-3133.2000
pubmed: 10919760
pmcid: 92124
Thiel H, Pfannkuche O, Schriever G, Lochte K, Gooday AJ, Hemleben CH et al (1990) Phytodetritus on the deep-sea floor in a central oceanic region of the north-east Atlantic. Biol Oceanogr 6:203–239. https://doi.org/10.1080/01965581.1988.10749527
doi: 10.1080/01965581.1988.10749527
Wang P, Xiao X, Wang F (2005) Phylogenetic analysis of Archaea in the deep-sea sediments of West Pacific Warm Pool. Extremophiles 9:209–217. https://doi.org/10.1007/s00792-005-0436-5
doi: 10.1007/s00792-005-0436-5
pubmed: 15761691
Wasmund K, Mußmann M, Loy A (2017) The life sulfuric: the microbial ecology of sulfur cycling in marine sediments. Env Micro Reports 9(4):323–344. https://doi.org/10.1111/1758-2229.12538
doi: 10.1111/1758-2229.12538
Whitton BA, Potts M (2012) Introduction to the cyanobacteria. In: Whitton BA (eds.) Ecology of Cyanobacteria II. Springer, Dordrecht. 1–11. https://doi.org/10.1007/978-94-007-3855-3_1
Wuchter C, Schouten S, Boschker HTS, Damsté JSS (2003) Bicarbonate uptake by marine Crenarchaeota. FEMS Microbiol Lett 219:203–207. https://doi.org/10.1016/S0378-1097(03)00060-0
doi: 10.1016/S0378-1097(03)00060-0
pubmed: 12620621
Wuchter C, Abbas B, Coolen MJL, Herfort L, van Bleijswijk J, Timmers P, Strous M, Teira E, Herndl GJ, Middelburg JJ, Schouten S, Damste JSS (2006) Archaeal nitrification in the ocean. Proc Natl Acad Sci 103(33):12317–12322. https://doi.org/10.1073/pnas.0600756103
doi: 10.1073/pnas.0600756103
pubmed: 16894176
pmcid: 1533803
Xie H, Xue YF, Zhao AM et al (2005) (2005) Preliminary research on bacterial diversity of Parece Vela Basin Pacific Ocean by culture-independent method. Acta Microbiol Sin 45:1–5
Zhang J, Liu R, Xi S, Cai R, Zhang X, Sun C (2020) A novel bacterial thiosulfate oxidation pathway provides a new clue about the formation of zero-valent sulfur in the deep sea. ISME J 14:2261–2274. https://doi.org/10.1038/s41396-020-0684-5
doi: 10.1038/s41396-020-0684-5
pubmed: 32457501
pmcid: 7608252
Zinger L, Amaral-Zetter LA, Fuhrman JA, Horner-Devine MC, Huse SM, Mark Welch DB et al (2011) Global Patterns of Bacterial Beta-Diversity in Seafloor and Seawater Ecosystems. PLoS ONE 6(9):1–11. https://doi.org/10.1371/journal.pone.0024570
doi: 10.1371/journal.pone.0024570