Archaeal diversity in the seawater of Changjiang River estuary reveals its adaptability to bottom seawaters

Yan HUANG; Wu QU; Yingping FAN; Jianxin WANG

doi:10.1007/s00343-021-1035-8

Your Location：

Home >

Browse articles >

Archaeal diversity in the seawater of Changjiang River estuary reveals its adaptability to bottom seawaters

Continued from the back cover | Updated：2023-05-20

- Archaeal diversity in the seawater of Changjiang River estuary reveals its adaptability to bottom seawaters
- Journal of Oceanology and Limnology Vol. 40, Issue 3, Pages: 1051-1069(2022)
- Affiliations：
  
  Marine Microorganism Ecological & Application Lab., Zhejiang Ocean University, Zhoushan, 316022, China
- Author bio：
  
  Jianxin WANG, jxwang@zjou.edu.cn
- Funds：
- DOI：10.1007/s00343-021-1035-8
  CLC：
- Published：2022-03
- Accepted：
Scan QR Code
Yan HUANG, Wu QU, Yingping FAN, et al. Archaeal diversity in the seawater of Changjiang River estuary reveals its adaptability to bottom seawaters[J]. Journal of Oceanology and Limnology, 2022, 40(3): 1051-1069.
DOI：

Yan HUANG, Wu QU, Yingping FAN, et al. Archaeal diversity in the seawater of Changjiang River estuary reveals its adaptability to bottom seawaters[J]. Journal of Oceanology and Limnology, 2022, 40(3): 1051-1069. DOI： 10.1007/s00343-021-1035-8.

摘要

Abstract

Archaea regulate the biogeochemical processes of ocean systems. The Changjiang (Yangtze) River estuary (CRE) is a complex and dynamic area strongly affected by seawaters and ocean currents. In this study

the planktonic archaeal communities in the surface and bottom seawaters of the CRE were investigated. Significant differences in the archaeal community composition were found between the surface and bottom seawaters (

0.001). Marine Group Ⅱ (MG-Ⅱ) was dominant in the surface layers

and Nitrosopumilales was enriched in the bottom layers. Marine Group Ⅲ (MG-Ⅲ) was more abundant in the bottom layers than in the surface ones (

0.001). These results were completely different from previous findings in the CRE seawater. Instead of dissolved oxygen (DO)

temperature and salinity were the most vital environmental variations in the distribution of the archaeal communities. According to the predicted metabolic pathways

the following functional subcategories were enriched in the hypoxic condition: replication and repair

membrane transport

glycan biosynthesis and metabolism

amino acid metabolism

metabolism of cofactors and vitamins

and xenobiotics biodegradation and metabolism (

0.001)

which indicated the strong adaptability of archaea to the harsh environment in the bottom seawater. These findings expand the understanding on archaeal structure and functions in the surface and bottom seawaters

including the hypoxic zones in the CRE

and may contribute to further works of the archaeal community in the CRE.

关键词

Keywords

references

Albers S V, Koning S M, Konings W N, Driessen A J M. 2004. Insights into ABC transport in archaea. Journal of Bioenergetics and Biomembranes , 36 (1): 5–15, https://doi.org/10.1023/B:JOBB.0000019593.84933.e6..

Alves R J E, Minh B Q, Urich T, Haeseler A V, Schleper C. 2018. Unifying the global phylogeny and environmental distribution of ammonia-oxidising archaea based on amoA genes. Nature Communications , 9 (1): 1517, https://doi.org/10.1038/s41467-018-03861-1..

Amaral-Zettler L A, Rocca J D, Lamontagne M G, Dennett M R, Gast R J. 2008. Changes in microbial community structure in the wake of Hurricanes Katrina and Rita. Environmental Science & Technology , 42 (24): 9072–9078, https://doi.org/10.1021/es801904z..

Banse K. 1964. On the vertical distribution of zooplankton in the sea. Progress in Oceanography , 2 : 53–125, https://doi.org/10.1016/0079-6611(64)90003-5..

Baryshnikova A. 2016. Exploratory analysis of biological networks through visualization, clustering, and functional annotation in cytoscape. Cold Spring Harbor Protocols, 6, https://doi.org/10.1101/pdb.prot077644 https://doi.org/10.1101/pdb.prot077644 .

Battersby N S. 1990. A review of biodegradation kinetics in the aquatic environment. Chemosphere , 21 (10–11): 1243–1284, https://doi.org/10.1016/0045-6535(90)90144-I..

Belmar L, Molina V, Ulloa O. 2011. Abundance and phylogenetic identity of archaeoplankton in the permanent oxygen minimum zone of the eastern tropical South Pacific. FEMS Microbiology Ecology , 78 (2): 314–326, https://doi.org/10.1111/j.1574-6941.2011.01159.x..

Beman J M, Popp B N, Alford S E. 2012. Quantification of ammonia oxidation rates and ammonia-oxidizing archaea and bacteria at high resolution in the Gulf of California and eastern tropical North Pacific Ocean. Limnology and Oceanography , 57 (3): 711–726, https://doi.org/10.4319/lo.2012.57.3.0711..

Bolyen E, Rideout J R, Dillon M R, Bokulich N A, Abnet C C, Al-Ghalith G A, Alexander H, Alm E J, Arumugam M, Asnicar F, Bai Y, Bisanz J E, Bittinger K, Brejnrod A, Brislawn C J, Brown C T, Callahan B J, Caraballo-Rodríguez A M, Chase J, Cope E K, Da Silva R, Diener C, Dorrestein P C, Douglas G M, Durall D M, Duvallet C, Edwardson C F, Ernst M, Estaki M, Fouquier J, Gauglitz J M, Gibbons S M, Gibson D L, Gonzalez A, Gorlick K, Guo J R, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley G A, Janssen S, Jarmusch A K, Jiang L J, Kaehler B D, Kang K B, Keefe C R, Keim P, Kelley S T, Knights D, Koester I, Kosciolek T, Kreps J, Langille M G I, Lee J, Ley R, Liu Y X, Loftfield E, Lozupone C, Maher M, Marotz C, Martin B D, McDonald D, McIver L J, Melnik A V, Metcalf J L, Morgan S C, Morton J T, Naimey A T, Navas-Molina J A, Nothias L F, Orchanian S B, Pearson T, Peoples S L, Petras D, Preuss M L, Pruesse E, Rasmussen L B, Rivers A, Robeson M S II, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song S J, Spear J R, Swafford A D, Thompson L R, Torres P J, Trinh P, Tripathi A, Turnbaugh P J, Ul-Hasan S, van der Hooft J J J, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y H, Wang M X, Warren J, Weber K C, Williamson C H D, Willis A D, Xu Z Z, Zaneveld J R, Zhang Y L, Zhu Q Y, Knight R, Caporaso J G. 2019. Reproducible, interactive, scalable and extensible microbiome data science using QⅡME 2. Nature Biotechnology , 37 (8): 852–857, https://doi.org/10.1038/s41587-019-0209-9..

Bray J R, Curtis J T. 1957. An ordination of the upland forest communities of southern Wisconsin. Ecological Monographs , 27 (4): 325–349, https://doi.org/10.2307/1942268..

Brochier-Armanet C, Boussau B, Gribaldo S, Forterre P. 2008. Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota. Nature Reviews Microbiology , 6 (3): 245–252, https://doi.org/10.1038/nrmicro1852..

Cao H L, Hong Y G, Li M, Gu J D. 2011. Diversity and abundance of ammonia-oxidizing prokaryotes in sediments from the coastal Pearl River estuary to the South China Sea. Antonie Van Leeuwenhoek , 100 (4): 545–556, https://doi.org/10.1007/s10482-011-9610-1..

Caron D A. 2005. Marine microbial ecology in a molecular world: what does the future hold?. Scientia Marina , 69 (S1): 97–110..

Cavicchioli R. 2006. Cold-adapted archaea. Nature Reviews Microbiology , 4 (5): 331–343. https://doi.org/10.1038/nrmicro1390.

Dang H Y, Zhang X X, Sun J, Li T G, Zhang Z N, Yang G P. 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, https://doi.org/10.1099/mic0.2007/013581-0..

DeLong E F, Preston C M, Mincer T, Rich V, Hallam S J, Frigaard N U, Martinez A, Sullivan M B, Edwards R, Brito B R, Chisholm S W, Karl D M. 2006. Community genomics among stratified microbial assemblages in the ocean's interior. Science , 311 (5760): 496–503, https://doi.org/10.1126/science.1120250..

DeLong E F, Wu K Y, Prézelin B B, Jovine R V M. 1994. High abundance of archaea in Antarctic marine picoplankton. Nature , 371 (6499): 695–697, https://doi.org/10.1038/371695a0..

DeLong E F. 1992. Archaea in coastal marine environments. Proceedings of the National Academy of Sciences , 89 (12): 5685–5689, https://doi.org/10.1073/pnas.89.12.5685..

Deschamps P, Zivanovic Y, Moreira D, Rodriguez-Valera F, López-García P. 2014. Pangenome evidence for extensive interdomain horizontal transfer affecting lineage core and shell genes in uncultured planktonic thaumarchaeota and euryarchaeota. Genome Biology and Evolution , 6 (7): 1549–1563, https://doi.org/10.1093/gbe/evu127..

Diaz R J, Rosenberg R. 2008. Spreading dead zones and consequences for marine ecosystems. Science , 321 (5891): 926–929, https://doi.org/10.1126/science.1156401..

Doyle R J. 2002. Glycomicrobiology. Springer, Boston, MA, https://doi.org/10.1007/b113570 https://doi.org/10.1007/b113570 .

Embrandiri A, Kiyasudeen S K, Rupani P F, Ibrahim M H. 2016. Environmental xenobiotics and its effects on natural ecosystem. In: Singh A, Prasad S, Singh R eds. Plant Responses to Xenobiotics. Springer, Singapore. p. 1–18, https://doi.org/10.1007/978-981-10-2860-1_1 https://doi.org/10.1007/978-981-10-2860-1_1 ..

Francis C A, Roberts K J, Beman J M, Santoro A E, Oakley B B. 2005. Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. Proceedings of the National Academy of Sciences of the United States of America , 102 (41): 14683–14688, https://doi.org/10.1073/pnas.0506625102..

Frigaard N U, Martinez A, Mincer T J, Delong E F. 2006. Proteorhodopsin lateral gene transfer between marine planktonic Bacteria and Archaea. Nature , 439 (7078): 847–850, https://doi.org/10.1038/nature04435..

Galand P E, Casamayor E O, Kirchman D L, Potvin M, Lovejoy C. 2009. Unique archaeal assemblages in the Arctic Ocean unveiled by massively parallel tag sequencing. The ISME Journal , 3 (7): 860–869, https://doi.org/10.1038/ismej.2009.23..

Grenz C, Denis L, Pringault O, Fichez R. 2010. Spatial and seasonal variability of sediment oxygen consumption and nutrient fluxes at the sediment water interface in a subtropical lagoon (New Caledonia). Marine Pollution Bulletin , 61 (7–12): 399–412, https://doi.org/10.1016/j.marpolbul.2010.06.014..

Haro-Moreno J M, Rodriguez-Valera F, López-García P, Moreira D, Martin-Cuadrado A B. 2017. New insights into marine group Ⅲ Euryarchaeota, from dark to light. The ISME Journal , 11 (5): 1102–1117, https://doi.org/10.1038/ismej.2016.188..

Hatzenpichler R. 2012. Diversity, physiology, and niche differentiation of ammonia-oxidizing archaea. Applied and Environmental Microbiology , 78 (21): 7501–7510, https://doi.org/10.1128/AEM.01960-12..

He H, Zhen Y, Mi T Z, Yu Z G. 2016. Community composition and abundance of ammonia-oxidizing archaea in sediments from the Changjiang estuary and its adjacent area in the East China Sea. Geomicrobiology Journal , 33 (5): 416–425, https://doi.org/10.1080/01490451.2014.986695..

Herndl G J, Reinthaler T, Teira E, Van Aken H, Veth C, Pernthaler A, Pernthaler J. 2005. Contribution of Archaea to total prokaryotic production in the deep Atlantic Ocean. Applied and Environmental Microbiology , 71 (5): 2303–2309, https://doi.org/10.1128/AEM.71.5.2303-2309.2005..

Hugoni M, Taib N, Debroas D, Domaizon I, Dufournel I J, Bronner G, Salter I, Agogué H, Mary I, Galand P E. 2013. Structure of the rare archaeal biosphere and seasonal dynamics of active ecotypes in surface coastal waters. Proceedings of the National Academy of Sciences of the United States of America , 110 (15): 6004–6009, https://doi.org/10.1073/pnas.1216863110..

Ingalls A E, Shah S R, Hansman R L, Aluwihare L I, Santos G M, Druffel E R M, Pearson A. 2006. Quantifying archaeal community autotrophy in the mesopelagic ocean using natural radiocarbon. Proceedings of the National Academy of Sciences of the United States of America , 103 (17): 6442–6447, https://doi.org/10.1073/pnas.0510157103..

Iverson V, Morris R M, Frazar C D, Berthiaume C T, Morales R L, Armbrust E V. 2012. Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota. Science , 335 (6068): 587–590, https://doi.org/10.1126/science.1212665..

Jain R K, Kapur M, Labana S, Lal B, Sarma P M, Bhattacharya D, Thakur I S. 2005. Microbial diversity: application of micro-organisms for the biodegradation of xenobiotics. Current Science , 89 (1): 101–112..

Jiao N, Luo T, Zhang R, Yan W, Lin Y, Johnson Z I, Tian J, Yuan D, Yang Q, Zheng Q, Sun J, Hu D, Wang P. 2014. Presence of Prochlorococcus in the aphotic waters of the western Pacific Ocean. Biogeosciences , 11 (8): 2391–2400, https://doi.org/10.5194/bg-11-2391-2014..

Jin T, Zhang T, Ye L, Lee O O, Wong Y H, Qian P Y. 2011. Diversity and quantity of ammonia-oxidizing Archaea and Bacteria in sediment of the Pearl River Estuary, China. Applied Microbiology and Biotechnology , 90 (3): 1137–1145, https://doi.org/10.1007/s00253-011-3107-8..

Kadota H, Ishida Y. 1972. Production of volatile sulfur compounds by microorganisms. Annual Review of Microbiology , 26 (1): 127–138, https://doi.org/10.1146/annurev.mi.26.100172.001015..

Kärcher U, Schröder H, Haslinger E, Allmaier G, Schreiner R, Wieland F, Haselbeck A, König H. 1993. Primary structure of the heterosaccharide of the surface glycoprotein of Methanothermus fervidus . Journal of Biological Chemistry , 268 (36): 26821–26826, https://doi.org/10.1016/S0021-9258(19)74185-4..

Karner M B, DeLong E F, Karl D M. 2001. Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature , 409 (6819): 507–510, https://doi.org/10.1038/35054051..

Kelly J, Logan S M, Jarrell K F, VanDyke D J, Vinogradov E. 2009. A novel N-linked flagellar glycan from Methanococcus maripaludis . Carbohydrate Research , 344 (5): 648–653, https://doi.org/10.1016/j.carres.2009.01.006..

Kembel S W, Cowan P D, Helmus M R, Cornwell W K, Morlon H, Ackerly D D, Blomberg S P, Webb C O. 2010. Picante: R tools for integrating phylogenies and ecology. Bioinformatics , 26 (11): 1463–1464, https://doi.org/10.1093/bioinformatics/btq166..

Khelaifia S, Drancourt M. 2012. Susceptibility of archaea to antimicrobial agents: applications to clinical microbiology. Clinical Microbiology and Infection , 18 (9): 841–848, https://doi.org/10.1111/j.1469-0691.2012.03913.x..

Konings W N, Albers S V, Koning S, Driessen A J M. 2002. The cell membrane plays a crucial role in survival of bacteria and archaea in extreme environments. Antonie Van Leeuwenhoek , 81 (1–4): 61–72, https://doi.org/10.1023/A:1020573408652..

Könneke M, Bernhard A E, de la Torre J R, Walker C B, Waterbury J B, Stahl D A. 2005. Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature , 437 (7058): 543–546, https://doi.org/10.1038/nature03911..

Könneke M, Schubert D M, Brown P C, Hügler M, Standfest S, Schwander T, von Borzyskowski L S, Erb T J, Stahl D A, Berg I A. 2014. Ammonia-oxidizing archaea use the most energy-efficient aerobic pathway for CO 2 fixation. Proceedings of the National Academy of Sciences of the United States of America , 111 (22): 8239–8244, https://doi.org/10.1073/pnas.1402028111..

Kubo K, Lloyd K G, Biddle J F, Amann R, Teske A, Knittel K. 2012. Archaea of the Miscellaneous Crenarchaeotal Group are abundant, diverse and widespread in marine sediments. The ISME Journal , 6 (10): 1949–1965, https://doi.org/10.1038/ismej.2012.37..

Kumar S, Stecher G, Li M, Knyaz C, Tamura K. 2018. MEGA X: molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution , 35 (6): 1547–1549, https://doi.org/10.1093/molbev/msy096..

Lee S M, Chao A. 1994. Estimating population size via sample coverage for closed capture-recapture models. Biometrics , 50 (1): 88–97, https://doi.org/10.2307/2533199..

Lewalter K, Müller V. 2006. Bioenergetics of archaea: ancient energy conserving mechanisms developed in the early history of life. Biochimica et Biophysica Acta (BBA) — Bioenergetics , 1757 (5–6): 437–445, https://doi.org/10.1016/j.bbabio.2006.04.027..

Li D J, Zhang J, Huang D J, Wu Y, Liang J. 2002. Oxygen depletion off the Changjiang (Yangtze River) estuary. Science in China Series D: Earth Sciences , 45 (12): 1137–1146, https://doi.org/10.1360/02yd9110..

Li J T, Gu L Y, Bai S J, Wang J, Su L, Wei B B, Zhang L, Fang J S. 2021. Characterization of particle-associated and free-living bacterial and archaeal communities along the water columns of the South China Sea. Biogeosciences , 18 : 113–133, https://doi.org/10.5194/bg-18-113-2021..

Li X G, Yu Z M, Song X X, Cao X H, Yuan Y Q. 2011. The seasonal characteristics of dissolved oxygen distribution and hypoxia in the Changjiang Estuary. Journal of Coastal Research , 27 (6A): 52–62, https://doi.org/10.2112/JCOASTRES-D-11-00013.1..

Liu B, Ye G B, Wang F P, Bell R, Noakes J, Short T, Zhang C L. 2009. Community structure of Archaea in the water column above gas hydrates in the Gulf of Mexico. Geomicrobiology Journal , 26 (6): 363–369, https://doi.org/10.1080/01490450902929290..

Liu H D, Zhang C L, Yang C Y, Chen S Z, Cao Z W, Zhang Z W, Tian J W. 2017. Marine Group Ⅱ dominates planktonic Archaea in water column of the Northeastern South China Sea. Frontiers in Microbiology , 8 : 1098, https://doi.org/10.3389/fmicb.2017.01098..

Liu J W, Fu B B, Yang H M, Zhao M X, He B Y, Zhang X H. 2015. Phylogenetic shifts of bacterioplankton community composition along the Pearl Estuary: the potential impact of hypoxia and nutrients. Frontiers in Microbiology , 6 : 64, https://doi.org/10.3389/fmicb.2015.00064..

Liu J W, Yu S L, Zhao M X, He B Y, Zhang X H. 2014. Shifts in archaeaplankton community structure along ecological gradients of Pearl Estuary. FEMS MicrobiologyEcology , 90 (2): 424–435, https://doi.org/10.1111/1574-6941.12404..

Liu J W, Zhu S Q, Liu X Y, Yao P, Ge T T, Zhang X H. 2020. Spatiotemporal dynamics of the archaeal community in coastal sediments: assembly process and co-occurrence relationship. The ISME Journal , 14 (6): 1463–1478, https://doi.org/10.1038/s41396-020-0621-7..

Liu M, Xiao T, Wu Y, Zhou F, Zhang W C. 2011. Temporal distribution of the archaeal community in the Changjiang Estuary hypoxia area and the adjacent East China Sea as determined by denaturing gradient gel electrophoresis and multivariate analysis. Canadian Journal of Microbiology , 57 (6): 504–513, https://doi.org/10.1139/w11-037..

Lohrenz S E, Redalje D G, Cai W J, Acker J, Dagg M. 2008. A retrospective analysis of nutrients and phytoplankton productivity in the Mississippi River plume. Continental Shelf Research , 28 (12): 1466–1475, https://doi.org/10.1016/j.csr.2007.06.019 https://doi.org/10.1016/j.csr.2007.06.019 ..

López-García P, López-López A, Moreira D, Rodríguez-Valera F. 2001. Diversity of free-living prokaryotes from a deep-sea site at the Antarctic Polar Front. FEMS Microbiology Ecology , 36 (2–3): 193–202, https://doi.org/10.1016/S0168-6496(01)00133-7..

Martens-Habbena W, Berube P M, Urakawa H, de la Torre J R, Stahl D A. 2009. Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria. Nature , 461 (7266): 976–979, https://doi.org/10.1038/nature08465..

Martin-Cuadrado A B, Garcia-Heredia I, Moltó A G, López-Úbeda R, Kimes N, López-García P, Moreira D, Rodriguez-Valera F. 2015. A new class of marine Euryarchaeota group Ⅱ from the Mediterranean deep chlorophyll maximum. The ISME Journal , 9 (7): 1619–1634, https://doi.org/10.1038/ismej.2014.249..

Martín-Cuadrado A B, López-García P, Alba J C, Moreira D, Monticelli L, Strittmatter A, Gottschalk G, Rodríguez-Valera F. 2007. Metagenomics of the deep Mediterranean, a warm bathypelagic habitat. PLoS One , 2 (9): e914, https://doi.org/10.1371/journal.pone.0000914..

Martin-Cuadrado A B, Rodriguez-Valera F, Moreira D, Alba J C, Ivars-Martínez E, Henn M R, Talla E, López-García P. 2008. Hindsight in the relative abundance, metabolic potential and genome dynamics of uncultivated marine archaea from comparative metagenomic analyses of bathypelagic plankton of different oceanic regions. The ISME Journal , 2 (8): 865–886, https://doi.org/10.1038/ismej.2008.40..

Massana R, DeLong E F, Pedrós-Alió C. 2000. A few cosmopolitan phylotypes dominate planktonic archaeal assemblages in widely different oceanic provinces. Applied and Environmental Microbiology , 66 (5): 1777–1787, https://doi.org/10.1128/AEM.66.5.1777-1787.2000..

Massana R, Murray A E, Preston C M, DeLong E F. 1997. Vertical distribution and phylogenetic characterization of marine planktonic Archaea in the Santa Barbara Channel. Applied and Environmental Microbiology , 63 (1): 50–56, https://doi.org/10.1128/aem.63.1.50-56.1997..

Mescher M F, Strominger J L. 1976. Purification and characterization of a prokaryotic glycoprotein from the cell envelope of Halobacterium salinarium. Journal of Biological Chemistry , 251 (7): 2005–2014, https://doi.org/10.1016/S0021-9258(17)33647-5..

Michoud G, Ngugi D K, Barozzi A, Merlino G, Calleja M L, Delgado-Huertas A, Morán X A G, Daffonchio D. 2021. Fine-scale metabolic discontinuity in a stratified prokaryote microbiome of a Red Sea deep halocline. The ISME Journal , 15 : 2351–2365, https://doi.org/10.1038/s41396-021-00931-z..

Mirete S, de Figueras C G, González-Pastor J E. 2011. Diversity of Archaea in Icelandic hot springs based on 16S rRNA and chaperonin genes. FEMS Microbiology Ecology , 77 (1): 165–175, https://doi.org/10.1111/j.1574-6941.2011.01095.x..

Miroshnichenko M L. 2004. Thermophilic microbial communities of deep-sea hydrothermal vents. Microbiology , 73 (1): 1–13, https://doi.org/10.1023/B:MICI.0000016360.21607.83..

Molina V, Belmar L, Ulloa O. 2010. High diversity of ammonia-oxidizing archaea in permanent and seasonal oxygen-deficient waters of the eastern South Pacific. Environmental Microbiology , 12 (9): 2450–2465, https://doi.org/10.1111/j.1462-2920.2010.02218.x..

Mosier A C, Francis C A. 2008. Relative abundance and diversity of ammonia-oxidizing archaea and bacteria in the San Francisco Bay estuary. Environmental Microbiology , 10 (11): 3002–3016, https://doi.org/10.1111/j.1462-2920.2008.01764.x..

Naqvi S W A, Jayakumar D A, Narvekar P V, Naik H, Sarma V V S S, D'Souza W, Joseph S, George M D. 2000. Increased marine production of N 2 O due to intensifying anoxia on the Indian continental shelf. Nature , 408 (6810): 346–349, https://doi.org/10.1038/35042551..

Ochsenreiter T, Pfeifer F, Schleper C. 2002. Diversity of Archaea in hypersaline environments characterized by molecular-phylogenetic and cultivation studies. Extremophiles , 6 (4): 267–274, https://doi.org/10.1007/s00792-001-0253-4..

Oksanen J, Blanchet F G, Kindt R, Legendre P, O'Hara R B, Simpson G L, Solymos P, Henry M and Stevens W H. 2010. Vegan: community ecology package. R package, version 1.17–4. http://cran.R-project.org http://cran.R-project.org .

Orita R, Umehara A, Komorita T, Choi J W, Montani S, Komatsu T, Tsutsumi H. 2015. Contribution of the development of the stratification of water to the expansion of Dead Zone: a sedimentological approach. Estuarine, Coastal and Shelf Science , 164 : 204–213, https://doi.org/10.1016/j.ecss.2015.07.028..

Orsi W D, Smith J M, Wilcox H M, Swalwell J E, Carini P, Worden A Z and Santoro A E. 2015. Ecophysiology of uncultivated marine euryarchaea is linked to particulate organic matter. The ISME Journal , 9 (8): 1747–1763, https://doi.org/10.1038/ismej.2014.260..

Pereira O, Hochart C, Auguet J C, Debroas D, Galand P E. 2019. Genomic ecology of Marine Group Ⅱ, the most common marine planktonic archaea across the surface ocean. MicrobiologyOpen , 8 (9): e00852, https://doi.org/10.1002/mbo3.852..

Pester M, Schleper C, Wagner M. 2011. The Thaumarchaeota: an emerging view of their phylogeny and ecophysiology. Current Opinion in Microbiology , 14 (3): 300–306, https://doi.org/10.1016/j.mib.2011.04.007..

Pohlschroder M, Pfeiffer F, Schulze S, Halim M F A. 2018. Archaeal cell surface biogenesis. FEMS Microbiology Reviews , 42 (5): 694–717, https://doi.org/10.1093/femsre/fuy027..

Polónia A R M, Cleary D F R, da Costa Coelho F J R, Becking L E, De Voogd N J, Toha A H A, Gomes N C M. 2018. Compositional analysis of archaeal communities in high and low microbial abundance sponges in the Misool coral reef system, Indonesia. Marine Biology Research , 14 (6): 537–550, https://doi.org/10.1080/17451000.2018.1498977..

Polónia A R M, Cleary D F R, Duarte L N, de Voogd N J, Gomes N C M. 2014. Composition of Archaea in seawater, sediment, and sponges in the Kepulauan Seribu reef system, Indonesia. Microbial Ecology , 67 (3): 553–567, https://doi.org/10.1007/s00248-013-0365-2..

Qin W, Heal K R, Ramdasi R, Kobelt J N, Martens-Habbena W, Bertagnolli A D, Amin S A, Walker C B, Urakawa H, Könneke M, Devol A H, Moffett J W, Armbrust E V, Jensen G J, Ingalls A E, Stahl D A. 2017. Nitrosopumilus maritimus gen. nov., sp. nov., Nitrosopumilus cobalaminigenes sp. nov., Nitrosopumilus oxyclinae sp. nov., and Nitrosopumilus ureiphilus sp. nov., four marine ammonia-oxidizing archaea of the phylum Thaumarchaeota . International Journal of Systematic and Evolutionary Microbiology , 67 (12): 5067–5079, https://doi.org/10.1099/ijsem.0.002416..

Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner F O. 2012. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Research , 41 (D1): D590–D596, https://doi.org/10.1093/nar/gks1219..

R Core Team. 2013. R: A language and environment for statistical computing. Vienna, Austria.

Ren M L, Feng X Y, Huang Y J, Wang H, Hu Z, Clingenpeel S, Swan B K, Fonseca M M, Posada D, Stepanauskas R, Hollibaugh J T, Foster P G, Woyke T, Luo H W. 2019. Phylogenomics suggests oxygen availability as a driving force in Thaumarchaeota evolution. The ISME Journal , 13 (9): 2150–2161, https://doi.org/10.1038/s41396-019-0418-8..

Restrepo-Ortiz C X, Auguet J C, Casamayor E O. 2014. Targeting spatiotemporal dynamics of planktonic SAGMGC-1 and segregation of ammonia-oxidizing Thaumarchaeota ecotypes by newly designed primers and quantitative polymerase chain reaction. Environmental Microbiology , 16 (3): 689–700, https://doi.org/10.1111/1462-2920.12191..

Schäffer C, Messner P. 2001. Glycobiology of surface layer proteins. Biochimie , 83 (7): 591–599, https://doi.org/10.1016/S0300-9084(01)01299-8..

Schleper C, Jurgens G, Jonuscheit M. 2005. Genomic studies of uncultivated archaea. Nature Reviews Microbiology , 3 (6): 479–488, https://doi.org/10.1038/nrmicro1159..

Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett W S, Huttenhower C. 2011. Metagenomic biomarker discovery and explanation. Genome Biology , 12 (6): 1–18, https://doi.org/10.1186/gb-2011-12-6-r60..

Shen J P, Zhang L M, Zhu Y G, Zhang J B, He J Z. 2008. Abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea communities of an alkaline sandy loam. Environmental Microbiology , 10 (6): 1601–1611, https://doi.org/10.1111/j.1462-2920.2008.01578.x..

Shin D S, Pratt A J, Tainer J A. 2014. Archaeal genome guardians give insights into eukaryotic DNA replication and damage response proteins. Archaea , 2014 : 206735, https://doi.org/10.1155/2014/206735..

Sleytr U B, Schuster B, Egelseer E M, Pum D. 2014. S-layers: principles and applications. FEMS Microbiology Reviews , 38 (5): 823–864, https://doi.org/10.1111/1574-6976.12063..

Sogin M L, Morrison H G, Huber J A, Welch D M, Huse S M, Neal P R, Arrieta J M, Herndl G J. 2006. Microbial diversity in the deep sea and the underexplored "rare biosphere". Proceedings of the National Academy of Sciences of the United States of America , 103 (32): 12115–12120, https://doi.org/10.1073/pnas.0605127103..

Stahl D A, de la Torre J R. 2012. Physiology and diversity of ammonia-oxidizing Archaea. Annual Review of Microbiology , 66 (1): 83–101, https://doi.org/10.1146/annurev-micro-092611-150128..

Tarn J, Peoples L M, Hardy K, Cameron J, Bartlett D H. 2016. Identification of free-living and particle-associated microbial communities present in hadal regions of the Mariana Trench. Frontiers in Microbiology , 7 : 665, https://doi.org/10.3389/fmicb.2016.00665..

Tian J W, Yang Q X, Zhao W. 2009. Enhanced diapycnal mixing in the South China Sea. Journal of Physical Oceanography , 39 (12): 3191–3203, https://doi.org/10.1175/2009JPO3899.1..

Tolar B B, King G M, Hollibaugh J T. 2013. An analysis of Thaumarchaeota populations from the Northern Gulf of Mexico. Frontiers in Microbiology , 4 : 72, https://doi.org/10.3389/fmicb.2013.00072..

Tseng C H, Chiang P W, Lai H C, Shiah F K, Hsu T C, Chen Y L, Wen L S, Tseng C M, Shieh W Y, Saeed I, Halgamuge S, Tang S L. 2015. Prokaryotic assemblages and metagenomes in pelagic zones of the South China Sea. BMC Genomics , 16 (1): 219, https://doi.org/10.1186/s12864-015-1434-3..

Tully B J. 2019. Metabolic diversity within the globally abundant Marine Group Ⅱ Euryarchaea offers insight into ecological patterns. Nature Communications , 10 : 271. https://doi.org/10.1038/s41467-018-07840-4..

Vila-Costa M, Barberan A, Auguet J C, Sharma S, Moran M A, Casamayor E O. 2013. Bacterial and archaeal community structure in the surface microlayer of high mountain lakes examined under two atmospheric aerosol loading scenarios. FEMS Microbiology Ecology , 84 (2): 387–397, https://doi.org/10.1111/1574-6941.12068..

Voisin S, Houliston R S, Kelly J, Brisson J R, Watson D, Bardy S L, Jarrell K F, Logan S M. 2005. Identification and characterization of the unique N-linked glycan common to the flagellins and S-layer glycoprotein of Methanococcus voltae . Journal of Biological Chemistry , 280 (17): 16586–16593, https://doi.org/10.1074/jbc.M500329200..

Wang K, Ye X S, Zhang H J, Chen H P, Zhang D M, Liu L. 2016. Regional variations in the diversity and predicted metabolic potential of benthic prokaryotes in coastal northern Zhejiang, East China Sea. Scientific Reports , 6 : 38709, https://doi.org/10.1038/srep38709..

Wang L, Zhang J, Li H L, Yang H, Peng C, Peng Z S, Lu L. 2018. Shift in the microbial community composition of surface water and sediment along an urban river. Science of the Total Environment , 627 : 600–612, https://doi.org/10.1016/j.scitotenv.2018.01.203..

Weisblum B, Davies J. 1968. Antibiotic inhibitors of the bacterial ribosome. Bacteriological Reviews , 32 (4 Pt 2): 493–528..

Wickham H, Chang W. 2009. ggplot2: an implementation of the Grammar of Graphics. R package version 0.8.3.

Wu D M, Dai Q P, Liu X Z, Fan Y P, Wang J X. 2019. Comparison of bacterial community structure and potential functions in hypoxic and non-hypoxic zones of the Changjiang Estuary. PLoS One , 14 (6): e0217431, https://doi.org/10.1371/journal.pone.0217431..

Wuchter C, Abbas B, Coolen M J L, Herfort L, van Bleijswijk J, Timmers P, Strous M, Teira E, Herndl G J, Middelburg J J, Schouten S, Damsté J S S. 2006. Archaeal nitrification in the ocean. Proceedings of the National Academy of Sciences of the United States of America , 103 (33): 12317–12322, https://doi.org/10.1073/pnas.0600756103..

Yakimov M M, Cono V L, Smedile F, Deluca T H, Juárez S, Ciordia S, Fernández M, Albar J P, Ferrer M, Golyshin P N, Giuliano L. 2011. Contribution of crenarchaeal autotrophic ammonia oxidizers to the dark primary production in Tyrrhenian deep waters (Central Mediterranean Sea). The ISME Journal , 5 (6): 945–961, https://doi.org/10.1038/ismej.2010.197..

Ye Q, Wu Y, Zhu Z Y, Wang X N, Li Z Q, Zhang J. 2016. Bacterial diversity in the surface sediments of the hypoxic zone near the Changjiang Estuary and in the East China Sea. MicrobiologyOpen , 5 (2): 323–339, https://doi.org/10.1002/mbo3.330..

Ye Y Z, Doak T G. 2009. A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes. PLoS Computational Biology , 5 (8): e1000465, https://doi.org/10.1371/journal.pcbi.1000465..

Yu S L, Yao P, Liu J W, Zhao B, Zhang G L, Zhao M X, Yu Z G, Zhang X H. 2016. Diversity, abundance, and niche differentiation of ammonia-oxidizing prokaryotes in mud deposits of the eastern China marginal seas. Frontiers in Microbiology , 7 : 137, https://doi.org/10.3389/fmicb.2016.00137..

Zatopek K M, Gardner A F, Kelman Z. 2018. Archaeal DNA replication and repair: new genetic, biophysical and molecular tools for discovering and characterizing enzymes, pathways and mechanisms. FEMS Microbiology Reviews , 42 (4): 477–488, https://doi.org/10.1093/femsre/fuy017..

Zeng Y H, Li H Y, Jiao N Z. 2007. Phylogenetic diversity of planktonic archaea in the estuarine region of East China Sea. Microbiological Research , 162 (1): 26–36, https://doi.org/10.1016/j.micres.2006.03.007..

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. Frontiers in Microbiology , 6 : 1108, https://doi.org/10.3389/fmicb.2015.01108..

Zhong H H, Lehtovirta-Morley L, Liu J W, Zheng Y F, Lin H Y, Song D L, Todd J D, Tian J W, Zhang X H. 2020. Novel insights into the Thaumarchaeota in the deepest oceans: their metabolism and potential adaptation mechanisms. Microbiome , 8 (1): 78, https://doi.org/10.1186/s40168-020-00849-2..

Views

Downloads

CSCD

Alert me when the article has been cited

Submit

Tools

Publicity Resources

A physics-enhanced deep-learning model for estimating turbid shallow water depth from SAR images

High-resolution profiling observation of carbon source dynamics in a mussel farm in the Changjiang River estuary during early autumn

Evaluation of adaptability of stratified survey scheme to ichthyoplankton sampling in an integrated fishery-independent survey

Diatom-based dissolved inorganic nitrogen reconstruction in the Changjiang River estuary and its adjacent areas

Impact of estuarine reclamation projects on saltwater intrusion and freshwater resource

Related Author

Tian MA

Qing XU

Xiaobin YIN

Yan LI

Letian LÜ

Kaiguo FAN

Dawei XU

Di WU

Related Institution

National Key Laboratory of Intelligent Spatial Information

Laboratory for Regional Oceanography and Numerical Modeling, Qingdao Marine Science and Technology Center

College of Marine Technology/Sanya Oceanographic Institution, Ocean University of China

Institute of Education and Science in Chemical Technologies and Engineering, National Technical University

Ocean College, Zhejiang University

Address：Editorial Office of JOL, 88 Haijun Rd. Qingdao, 266000, China
Tel：+86-532-82898754 Email：jol@qdio.ac.cn
Technical support is provided by Beijing Founder electronics co., LTD 京ICP备09064830号-19 京公网安备11010802024621
It is recommended to read the content of this site in Chrome&IE9+. Please switch to extreme mode in browser 360.
Cookies We use cookies to help provide and enhance our service and tailor content. By continuing, you agree to the use of cookies.

⁰