386
Views
9
CrossRef citations to date
0
Altmetric
Articles

Bacterial and Archaeal Communities in Sediments from the Adjacent Waters of Rushan Bay (China) Revealed by Illumina Sequencing

, , , &
Pages 86-100 | Received 20 Jun 2018, Accepted 04 Sep 2019, Published online: 16 Sep 2019

References

  • Allen MA, Goh F, Burns BP, Neilan BA. 2009. Bacterial, archaeal and eukaryotic diversity of smooth and pustular microbial mat communities in the hypersaline lagoon of Shark Bay. Geobiology 7(1):82–96.
  • Auguet JC, Barberan A, Casamayor EO. 2010. Global ecological patterns in uncultured archaea. ISME J 4(2):182–190.
  • Baas-Becking L. 1934. Geobiologie of Inleiding Tot de Milieukunde. The Hague, the Netherlands: WP Van Srockum & Zoon (in Dutch).
  • Beijerinck MW. 1913. De infusies en de ontdekking der backteriën, Jaarboek van de Koninklijke Akademie v. Wetenschappen. Amsterdam, The Netherlands: Müller.
  • Biddle JF, Cardman Z, Mendlovitz H, Albert DB, Lloyd KG, Boetius A, Teske A. 2012. Anaerobic oxidation of methane at different temperature regimes in Guaymas Basin hydrothermal sediments. ISME J 6(5):1018–1031.
  • Biller SJ, Mosier AC, Wells GF, Francis CA. 2012. Global biodiversity of aquatic ammonia-oxidizing archaea is partitioned by habitat. Front Microbiol 3:252.
  • Boone DR, Castenholz RW, Garrity GM. 2001. Bergey’s Manual of Systematic Bacteriology (2nd ed.). New York: Springer.
  • Caffrey JM, Bano N, Kalanetra K, Hollibaugh JT. 2007. Ammonia oxidation and ammonia-oxidizing bacteria and archaea from estuaries with differing histories of hypoxia. ISME J 1(7):660–662.
  • Chen C, Zhang JA, Lu M, Qin C, Chen YH, Yang L, Huang QW, Wang JC, Shen ZG, Shen QR. 2016. Microbial communities of an arable soil treated for 8 years with organic and inorganic fertilizers. Biol Fertil Soils 52(4):455–413.
  • Cheng W, Zhang JX, Wang Z, Wang M, Xie SG. 2014. Bacterial communities in sediments of a drinking water reservoir. Ann Microbiol 64(2):875–878.
  • Coleman ML, Hedrick DB, Lovley DR, White DC, Pye K. 1993. Reduction of Fe(III) in sediments by sulfate-reducing bacteria. Nature 361(6411):436–438.
  • Coolen MJL, Abbas B, van Bleijswijk J, Hopmans EC, Kuypers MM, Wakeham SG, Sinninghe Damsté JS. 2007. Putative ammonia-oxidizing Crenarchaeota in suboxic waters of the Black Sea: a basin-wide ecological study using 16S ribosomal and functional genes and membrane lipids. Environ Microbiol 9(4):1001–1016.
  • Cretoiu MS, Kielak AM, Schluter A, van Elsas JD. 2014. Bacterial communities in chitin-amended soil as revealed by 16S rRNA gene based pyrosequencing. Soil Biol Biochem 76(1):5–11.
  • Crits-Christoph A, Robinson CK, Ma B, Ravel J, Wierzchos J, Ascaso C, Artieda O, Souza-Egipsy V, Casero MC, DiRuggiero J. 2016. Phylogenetic and functional substrate specificity for endolithic microbial communities in hyper-arid environments. Front Microbiol 7:1308–1316.
  • Cui ZS, Wang SL, Zang JY, Ran XB. 2012. Bacterial diversity in an offshore low dissolved oxygen content area contiguous to Rushan Bay. Adv Mar Sci 30(3):369–379 (in Chinese).
  • Delong EF. 1992. Archaea in coastal marine environments. Proc Natl Acad Sci USA 89(12):5685–5689.
  • Edgar RC. 2013. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods 10(10):996–998.
  • Galand PE, Casamayor EO, Kirchman DL, Lovejoy C. 2009. Ecology of the rare microbial biosphere of the Arctic Ocean. Proc Natl Acad Sci USA 106(52):22427.
  • Galand PE, Fritze H, Conrad R, Yrjälä K. 2005. Pathways for methanogenesis and diversity of methanogenic archaea in three boreal peatland ecosystems. Appl Environ Microbiol 71(4):2195–2198.
  • Ginige MP, Hugenholtz P, Daims H, Wagner M, Keller J, Blackall LL. 2004. Use of stable-isotope probing, full-cycle rRNA analysis, and fluorescence in situ hybridization-microautoradiography to study a methanol-fed denitrifying microbial community. Appl Environ Microbiol 70(1):588–596.
  • Hallam SJ, Mincer TJ, Schleper C, Preston CM, Roberts K, Richardson PM, DeLong EF. 2006. Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota. PLoS Biol 4(4):e95.
  • Horn MA, Matthies C, Küsel K, Schramm A, Drake HL. 2003. Hydrogenotrophic methanogenesis by moderately acid-tolerant methanogens of a methane-emitting acidic peat. Appl Environ Microbiol 69(1):74–83.
  • Hou J, Song CL, Cao XY, Zhou YY. 2013. Shifts between ammonia-oxidizing bacteria and archaea in relation to nitrification potential across trophic gradients in two large Chinese lakes (Lake Taihu and Lake Chaohu). Water Res 47(7):2285–2296.
  • Jaeschke A, Jørgensen SL, Bernasconi SM, Pedersen RB, Thorseth IH, Früh-Green GL. 2012. Microbial diversity of Loki’s Castle black smokers at the Arctic Mid-Ocean Ridge. Geobiology 10(6):548–561.
  • Jørgensen BB, Bak F. 1991. Pathways and microbiology of thiosulfate transformations and sulfate reduction in a marine sediment (Kattegat, Denmark). Appl Environ Microbiol 57(3):847–856.
  • Juretschko S, Loy A, Lehner A, Wagner M. 2002. The microbial community composition of a nitrifying-denitrifying activated sludge from an industrial sewage treatment plant analyzed by the full-cycle rRNA approach. Syst Appl Microbiol 25(1):84–99.
  • Kennedy SP, Ng WV, Salzberg SL, Hood L, DasSarma S. 2001. Understanding the adaptation of Halobacterium species NRC-1 to its extreme environment through computational analysis of its genome sequence. Genome Res 11(10):1641–1650.
  • Khan ST, Horiba Y, Yamamoto M, Hiraishi A. 2002. Members of the family Comamonadaceae as primary poly(3-hydroxybutyrate-co-3-hydroxyvalerate)-degrading denitrifiers in activated sludge as revealed by a polyphasic approach. Appl Environ Microbiol 68(7):3206–3214.
  • Kim BS, Kim BK, Lee JH, Kim M, Lim YW, Chun J. 2008. Rapid phylogenetic dissection of prokaryotic community structure in tidal flat using pyrosequencing. J Microbiol 46(4):357–363.
  • Kong X, Yu SY, Fang W, Liu JG, Li H. 2018. Enhancing syntrophic associations among Clostridium butyricum, Syntrophomonas and two types of methanogen by zero valent iron in an anaerobic assay with a high organic loading. Bioresour Technol 257:181–191.
  • Kormas KA, Tamaki H, Hanada S, Kamagata Y. 2009. Apparent richness and community composition of Bacteria and Archaea in geothermal springs. Aquat Microb Ecol 57(2):113–122.
  • Köster M, Wardenga R, Blume M. 2008. Microscale investigations of microbial communities in coastal surficial sediments. Mar Ecol 29(1):89–105.
  • Labrenz M, Sintes E, Toetzke F, Zumsteg A, Herndl GJ, Seidler M, Jürgens K. 2010. Relevance of a crenarchaeotal subcluster related to Candidatus Nitrosopumilus maritimus to ammonia oxidation in the suboxic zone of the central Baltic Sea. ISME J 4(12):1496–1508.
  • Lan GY, Li YW, Wu ZX, Xie GS. 2017. Impact of tropical forest conversion on soil bacterial diversity in tropical region of China. Eur J Soil Biol 83:91–97.
  • Lee CK, Barbier BA, Bottos EM, McDonald IR, Cary SC. 2012. The inter-valley soil comparative survey: the ecology of Dry Valley edaphic microbial communities. ISME J 6(5):1046–1057.
  • Li JJ, Liu F, Chen JW. 2016. The effects of various land reclamation scenarios on the succession of soil bacteria, archaea, and fungi over the short and long term. Front Ecol Evol 31(4):32.
  • Ligi T, Oopkaup K, Truu M, Preem JK, Nõlvak H, Mitsch WJ, Mander Ü, Truu J. 2014. Characterization of bacterial communities in soil and sediment of a created riverine wetland complex using high-throughput 16S rRNA amplicon sequencing. Ecol Eng 72:56–66.
  • Liu C, Li H, Zhang YY, Si DD, Chen QW. 2016. Evolution of microbial community along with increasing solid concentration during high-solids anaerobic digestion of sewage sludge. Bioresour Technol 216:87–94.
  • Liu JW, Liu XS, Wang M, Qiao YL, Zheng YF, Zhang XH. 2015. Bacterial and archaeal communities in sediments of the north Chinese marginal seas. Microb Ecol 70(1):105–117.
  • Liu ZH, Huang SB, Sun GP, Xu ZC, Xu MY. 2011. Diversity and abundance of ammonia-oxidizing archaea in the Dongjiang River, China. Microbiol Res 166(5):337–345.
  • Liu RL, Wang L, Liu QF, Wang ZX, Liu ZZ, Fang JS, Zhang L, Luo M. 2018. Depth-resolved distribution of particle-attached and free-living bacterial communities in the water column of the New Britain Trench. Front Microbiol 9:625.
  • Louca S, Parfrey LW, Doebeli M. 2016. Decoupling function and taxonomy in the global ocean microbiome. Science 353(6305):1272–1277.
  • Lozupone CA, Knight R. 2007. Global patterns in bacterial diversity. Proc Natl Acad Sci USA 104(27):11436–11440.
  • Ma Q, Qu YY, Shen WL, Zhang ZJ, Wang JW, Liu ZY, Li DX, Li HJ, Zhou JT. 2015. Bacterial community compositions of coking wastewater treatment plants in steel industry revealed by Illumina high-throughput sequencing. Bioresour Technol 179:436–443.
  • MacGregor BJ, Ravenschlag K, Amann R. 2002. Nucleic acid-based techniques for analyzing the diversity, structure, and function of microbial communities in marine waters and sediments. *Ocean Margin Syst 70(7):419–438.
  • Martins G, Terada A, Ribeiro DC, Corral AM, Brito AG, Smets BF, Nogueira R. 2011. Structure and activity of lacustrine sediment bacteria involved in nutrient and iron cycles. FEMS Microbiol Ecol 77(3):666–679.
  • Miletto M, Williams KH, N'Guessan AL, Lovley DR. 2011. Molecular analysis of the metabolic rates of discrete subsurface populations of sulfate reducers. Appl Environ Microbiol 77(18):6502–6509.
  • Munson MA, Nedwell DB, Embley TM. 1997. Phylogenetic diversity of Archaea in sediment samples from a coastal salt marsh. Appl Environ Microbiol 63(12):4729–4733.
  • Nealson KH. 1997. Sediment bacteria: who’s there, what are they doing, and what’s new? Annu Rev Earth Planet Sci 25(1):403–434.
  • Nicol GW, Schleper C. 2006. Ammonia-oxidizing Crenarchaeota: important players in the nitrogen cycle? Trends Microbiol 14(5):207–212.
  • Oren A. 2008. Microbial life at high salt concentrations: phylogenetic and metabolic diversity. Saline Syst 4:2.
  • Orphan VJ, Hinrichs KU, Ussler IIW, Paull CK, Taylor LT, Sylva SP, Hayes JM, Delong EF. 2001. Comparative analysis of methane-oxidizing archaea and sulfate-reducing bacteria in anoxic marine sediments. Appl Environ Microbiol 67(4):1922–1934.
  • Pavloudi C, Kristoffersen JB, Oulas A, de Troch M, Arvanitidis C. 2017. Sediment microbial taxonomic and functional diversity in a natural salinity gradient challenge Remane’s “species minimum” concept. PeerJ 5:e3687.
  • Perner M, Seifert R, Weber S, Koschinsky A, Schmidt K, Strauss H, Peters M, Haase K, Imhoff JF. 2007. Microbial CO2 fixation and sulfur cycling associated with low-temperature emissions at the Lilliput hydrothermal field, southern Mid-Atlantic Ridge (9°S). Environ Microbiol 9(5):1186–1201.
  • Porat I, Vishnivetskaya TA, Mosher JJ, Brandt CC, Yang ZK, Brooks SC, Liang LY, Drake MM, Podar M, Brown SD, et al. 2010. Characterization of archaeal community in contaminated and uncontaminated surface stream sediments. Microb Ecol 60(4):784–795.
  • Purkhold U, Pommerening-Roser A, Juretschko S, Schmid MC, Koops HP, Wagner M. 2000. Phylogeny of all recognized species of ammonia oxidizers based on comparative 16S rRNA and amoA sequence analysis: implications for molecular diversity surveys. Appl Environ Microbiol 66(12):5368–5382.
  • Qiu ZZ, Luo ZX, Zhao YL, Yan CZ. 2013. Effect of dissolved oxygen on the diversity of ammonia-oxidizing microorganisms in enrichment culture from estuarine wetland surface sediments and ammonia-oxidizing rate. Environ Sci 34(2):532–539 (in Chinese).
  • Ran XB, Zang JY, Wei QS, Guo JS, Yin XF, Liu W, Liu J. 2012. Hyposia and its cause of formation in the adjacent waters of Rushan Bay. Adv Mar Sci 30(3):347–356 (in Chinese).
  • Sadaie T, Sadaie A, Takada M, Hamano K, Ohnishi J, Ohta N, Matsumoto K, Sadaie Y. 2007. Reducing sludge production and the domination of Comamonadaceae by reducing the oxygen supply in the wastewater treatment procedure of a food-processing factory. Biosci Biotechnol Biochem 71(3):791–799.
  • Santoro AE, Francis CA, de Sieyes NR, Boehm AB. 2008. Shifts in the relative abundance of ammonia-oxidizing bacteria and archaea across physiochemical gradients in a subterranean estuary. Environ Microbiol 10(4):1068–1079.
  • Shehab N, Li D, Amy GL, Logan BE, Saikaly PE. 2013. Characterization of bacterial and archaeal communities in air-cathode microbial fuel cells, open circuit and sealed-off reactors. Appl Microbiol Biotechnol 97(22):9885–9895.
  • Sims A, Horton J, Gajaraj S, McIntosh S, Miles RJ, Mueller R, Reed R, Hu ZQ. 2012. Temporal and spatial distributions of ammonia-oxidizing archaea and bacteria and their ratio as an indicator of oligotrophic conditions in natural wetlands. Water Res 46(13):4121–4129.
  • Sonne-Hansen J, Ahring BK. 1999. Thermodesulfobacterium hveragerdense sp. nov., and Thermodesulfovibrio islandicus sp. nov., two thermophilic sulfate reducing bacteria isolated from a Icelandic hot spring. Syst Appl Microbiol 22(4):559–564.
  • Spang A, Hatzenpichler R, Brochier-Armanet C, Rattei T, Tischler P, Spieck E, Streit W, Stahl DA, Wagner M, Schleper C. 2010. Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota. Trends Microbiol 18(8):331–340.
  • Su ZG, Dai TJ, Tang YS, Tao YL, Huang B, Mu QL, Wen DH. 2018. Sediment bacterial community structures and their predicted functions implied the impacts from natural processes and anthropogenic activities in coastal area. Mar Pollut Bull 131:481–495.
  • Swan BK, Ehrhardt CJ, Reifel KM, Moreno LI, Valentine DL. 2010. Archaeal and bacterial communities respond differently to environmental gradients in anoxic sediments of a California hypersaline lake, the Salton Sea. Appl Environ Microbiol 76(3):757–768.
  • ter Braak C, Šmilauer P. 2002. CANOCO Reference Manual and CanoDraw for Window User’s Guide: Software for Canonical Community Ordination (Version 4.5). Ithaca, NY: Microcomputer Power.
  • Uroz S, Ioannidis P, Lengelle J, Cébron A, Morin E, Buée M, Martin F. 2013. Functional assays and metagenomic analyses reveals differences between the microbial communities inhabiting the soil horizons of a Norway spruce plantation. PLOS One 8(2):e55929.
  • Walker CB, De la Torre JR, Klotz MG, Urakawa H, Pinel N, Arp DJ, Brochier-Armanet C, Chain PSG, Chan PP, Gollabjir A, et al. 2010. Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea. Proc Natl Acad Sci USA 107(19):8818–8823.
  • Wang L, Liu L, Zheng B, Zhu Y, Wang X. 2013. Analysis of the bacterial community in the two typical intertidal sediments of Bohai Bay, China by pyrosequencing. Mar Pollut Bull 72(1):181–187.
  • Wang SY, Wang Y, Feng XJ, Zhai LM, Zhu GB. 2011. Quantitative analyses of ammonia-oxidizing archaea and bacteria in the sediments of four nitrogen-rich wetlands in China. Appl Microbiol Biotechnol 90(2):779–787.
  • Wang L, Yu M, Liu Y, Liu JW, Wu YH, Li L, Liu JH, Wang M, Zhang XH. 2018. Comparative analyses of the bacterial community of hydrothermal deposits and seafloor sediments across Okinawa Trough. J Mar Syst 180:162–172.
  • Wei GS, Li MC, Li FG, Li H, Gao Z. 2016. Distinct distribution patterns of prokaryotes between sediment and water in the Yellow River estuary. Appl Microbiol Biotechnol 100(22):9683–9697.
  • Whitman WB, Coleman DC, Wiebe WJ. 1998. Prokaryotes: the unseen majority. Proc Natl Acad Sci USA 95(12):6578–6583.
  • Yang Y, Li XG, Liu JG, Zhou ZG, Zhang TL, Wang XX. 2017. Bacterial diversity as affected by application of manure in red soils of subtropical China. Biol Fertil Soils 53(6):639–649.
  • Ye Q, Wu Y, Zhu ZY, Wang XN, Li ZQ, Zhang J. 2016. Bacterial diversity in the surface sediments of the hypoxic zone near the Changjiang Estuary and in the East China Sea. Microbiol Open 5(2):323–339.
  • Zeng YH, Li HY, Jiao NZ. 2007. Phylogenetic diversity of planktonic archaea in the estuarine region of East China Sea. Microbiol Res 162(1):26–36.
  • Zhang HG, Ma SS, Li QF, Fu XJ, Zhang Y, Qu KM. 2011. Analysis of changes of microbial community structure on bio-carrier of recirculating aquaculture systems RAS. Environ Sci 32(1):231–239. (in Chinese).
  • Zhang HX, Zheng SL, Ding JW, Wang OM, Liu FH. 2017. Spatial variation in bacterial community in natural wetland-river-sea ecosystems. J Basic Microbiol 57(6):536–546.
  • Zheng BH, Wang LP, Liu LS. 2014. Bacterial community structure and its regulating factors in the intertidal sediment along the Liaodong Bay of Bohai Sea, China. Microbiol Res 169(7–8):585–592.
  • Zhu DC, Tanabe SH, Yang C, Zhang WM, Sun JZ. 2013. Bacterial community composition of South China Sea sediments through pyrosequencing-based analysis of 16S rRNA genes. PLoS One 8(10):e78501.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.