Bacterial community composition in aquatic and sediment samples with spatiotemporal dynamics in large, shallow, eutrophic Lake Chaohu, China

References

• Bokulich NA, Subramanian S, Faith JJ, Gevers D, Gordon JI, Knight R, Mills DA, Caporaso JG. 2013. Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat Methods. 10(1):57–59.
   PubMed Web of Science ®Google Scholar
• Cai YJ, Gong ZJ, Xie P. 2012. Community structure and spatiotemporal patterns of macrozoobenthos in Lake Chaohu (China). Aquat Biol. 17(1):35–46.
   Web of Science ®Google Scholar
• Chao A. 1984. Nonparametric-estimation of the number of classes in a population. Scand J Stat. 11:265–270.
   Web of Science ®Google Scholar
• Chao A, Yang MCK. 1993. Stopping rules and estimation for recapture debugging with unequal failure rates. Biometrika. 80(1):193–201.
   Web of Science ®Google Scholar
• Chen J, Wang PF, Wang C, Wang X, Miao LZ, Liu S, Yuan QS. 2018. Bacterial communities in riparian sediments: A large-scale longitudinal distribution pattern and response to dam construction. Front Microbiol. 9:999.
   PubMed Web of Science ®Google Scholar
• Dai Y, Yang YY, Wu Z, Feng QY, Xie SG, Liu Y. 2016. Spatiotemporal variation of planktonic and sediment bacterial assemblages in two plateau freshwater lakes at different trophic status. Appl Microbiol Biotechnol. 100(9):4161–4175.
   PubMed Web of Science ®Google Scholar
• DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL. 2006. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microb. 72(7):5069–5072.
   PubMed Web of Science ®Google Scholar
• Dykhuizen DE. 1998. Santa Rosalia revisited: why are there so many species of bacteria? Anton Leeuw Inter J G. 73(1):25–33.
   PubMed Web of Science ®Google Scholar
• Edgar RC. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 26(19):2460–2461.
   PubMed Web of Science ®Google Scholar
• Freitag TE, Chang L, Prosser JI. 2006. Changes in the community structure and activity of betaproteobacterial ammonia-oxidizing sediment bacteria along a freshwater-marine gradient. Environ Microbiol. 8(4):684–696.
   PubMed Web of Science ®Google Scholar
• Ganzert L, Bajerski F, Wagner D. 2014. Bacterial community composition and diversity of five different permafrost-affected soils of Northeast Greenland. FEMS Microbiol Ecol. 89(2):426–441.
   PubMed Web of Science ®Google Scholar
• Griffiths RI, Thomson BC, James P, Bell T, Bailey MJ, Whiteley AS. 2011. The bacterial biogeography of British soils. Environ Microbiol. 13(6):1642–1654.
   PubMed Web of Science ®Google Scholar
• Huang W, Jiang X. 2016. Profiling of sediment microbial community in Dongting Lake before and after impoundment of the three gorges dam. Int J Environ Res Public Health. 13(6):617.
   PubMed Web of Science ®Google Scholar
• Ip CCM, Li XD, Zhang GS, Farmer JG, Wai OWH, Li YS. 2004. Over one hundred years of trace metal fluxes in the sediments of the Pearl River Estuary, South China. Environ Pollut. 132(1):157–172.
   PubMed Web of Science ®Google Scholar
• Ji B, Qin H, Guo SD, Chen W, Zhang XC, Liang JC. 2018. Bacterial communities of four adjacent fresh lakes at different trophic status. Ecotoxicol Environ Saf. 157:388–394.
   PubMed Web of Science ®Google Scholar
• Jiang Y-J, He W, Liu W-X, Qin N, Ouyang H-L, Wang Q-M, Kong X-Z, He Q-S, Yang C, Yang B, et al. 2014. The seasonal and spatial variations of phytoplankton community and their correlation with environmental factors in a large eutrophic Chinese lake (Lake Chaohu). Ecol Indic. 40:58–67.
   Web of Science ®Google Scholar
• Jin XC, Tu QY. 1990. The standard methods for observation and analysis in lake eutrophication. Beijing: Chinese Environmental Science Press; p. 240.
   Google Scholar
• Keshri J, Ram AS, P, Sime-Ngando T. 2018. Distinctive patterns in the taxonomical resolution of bacterioplankton in the sediment and pore waters of contrasted freshwater lakes. Microb Ecol. 75(3):662–673.
   PubMed Web of Science ®Google Scholar
• Kong FX, Gao G. 2005. Hypothesis on cyanobacteria bloom-forming mechanism in large shallow eutrophic lakes. Acta Ecol Sin. 25:589–595.
   Google Scholar
• Kurilkina MI, Zakharova YR, Galachyants YP, Petrova DP, Bukin YS, Domysheva VM, Blinov VV, Likhoshway YV. 2016. Bacterial community composition in the water column of the deepest freshwater Lake Baikal as determined by next-generation sequencing. FEMS Microbiol Ecol. 92:fiw094.
   PubMed Web of Science ®Google Scholar
• Laing GD, Vos RD, Vandecasteele B, Lesage E, Tack F, Verloo M. 2008. Effect of salinity on heavy metal mobility and availability in intertidal sediments of the Scheldt estuary. Estuar Coast Shelf S. 77:589–602.
   Web of Science ®Google Scholar
• Li JF, Zhang JY, Liu LY, Fan YC, Li LS, Yang YF, Lu ZH, Zhang XD. 2015. Annual periodicity in planktonic bacterial and archaeal community composition of eutrophic Lake Taihu. Sci Rep. 5(1):15488.
   PubMed Web of Science ®Google Scholar
• Liu LX, Xu M, Qiu S, Shen RC. 2015. Spatial patterns of benthic bacterial communities in a large lake. Internat Rev Hydrobiol. 100(3–4):97–105.
   Web of Science ®Google Scholar
• Ma YT, Li JQ, Wu J, Kong ZY, Feinstein LM, Ding X, Ge G, Wu L. 2018. Bacterial and fungal community composition and functional activity associated with lake wetland water level gradients. Sci Rep. 8(1):760.
   PubMed Web of Science ®Google Scholar
• Magoc T, Salzberg SL. 2011. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics. 27(21):2957–2963.
   PubMed Web of Science ®Google Scholar
• Nelson D. 1982. Dry combustion method using medium temperature resistance furnace. Chemical and Microbial Properties, 2nd edn. Soil Science Society of America and American Society of Agronomy Book Series No.9: 539–579.
   Google Scholar
• Paerl HW. 2014. Mitigating harmful cyanobacterial blooms in a human- and climatically-impacted world. Life (Basel). 4(4):988–1012.
   PubMedGoogle Scholar
• Paerl HW, Otten TG. 2013. Harmful cyanobacterial blooms: causes, consequences, and controls. Microb Ecol. 65(4):995–1010.
   PubMed Web of Science ®Google Scholar
• Psenner R, Alfreider A, Schwarz A. 2008. Aquatic microbial ecology: water desert, microcosm, ecosystem. What's Next?. Internat Rev Hydrobiol. 93(4–5):606–623.
   Web of Science ®Google Scholar
• Roske K, Sachse R, Scheerer C, Roske I. 2012. Microbial diversity and composition of the sediment in the drinking water reservoir Saidenbach (Saxonia, Germany). Syst Appl Microbiol. 35:35–44.
   PubMed Web of Science ®Google Scholar
• Shannon CE. 1948. A mathematical theory of communication. Bell Syst Tech J. 27(3):379–423.
   Google Scholar
• Sheng P, Yu YZ, Zhang GH, Huang JL, He L, Ding JN. 2016. Bacterial diversity and distribution in seven different estuarine sediments of Poyang Lake, China. Environ Earth Sci. 75(6):479.
   Web of Science ®Google Scholar
• Simpson EH. 1949. Measurement of diversity. Nature. 163(4148):688.
   Web of Science ®Google Scholar
• Spring S, Schulze R, Overmann J, Schleifer K-H. 2000. Identification and characterization of ecologically significant prokaryotes in the sediment of freshwater lakes molecular and cultivation studies. Fems Microbiol Rev. 24(5):573–590.
   PubMed Web of Science ®Google Scholar
• Staley C, Unno T, Gould TJ, Jarvis B, Phillips J, Cotner JB, Sadowsky MJ. 2013. Application of –generation sequencing to characterize the bacterial community of the Upper Mississippi River. J Appl Microbiol. 115(5):1147–1158.
   PubMed Web of Science ®Google Scholar
• 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 Microb. 76(3):757–768.
   PubMed Web of Science ®Google Scholar
• Ter Braak CJF, Smilauer P. 2002. CANOCO reference manual and CanoDraw for Windows user’s guide: software for canonical community ordination (version 4.5). Microcomputer Power (Ithaca NYUSA).
   Google Scholar
• Wan Y, Bai Y, He J, Zhang YP, Li RF, Ruan XH. 2017. Temporal and spatial variations of aquatic environmental characteristics and sediment bacterial community in five regions of Lake Taihu. Aquat Ecol. 51(3):343–358.
   Web of Science ®Google Scholar
• Wang J, Li Y, Wang P, Niu L, Zhang W, Wang C. 2016. Response of bacterial community compositions to different sources of pollutants in sediments of a tributary of Taihu Lake, China. Environ Sci Pollut Res Int. 23(14):13886–13894.
   PubMed Web of Science ®Google Scholar
• Ward NL, Challacombe JF, Janssen PH, Henrissat B, Coutinho PM, Wu M, Xie G, Haft DH, Sait M, Badger J, et al. 2009. Three genomes from the Phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils. Appl and Environ Microb. 75(7):2046–2056.
   PubMed Web of Science ®Google Scholar
• Wei CL, Bao S, Zhu XY, Huang XX. 2008. Spatio-temporal variations of the bacterioplankton community composition in Chaohu Lake, China. Prog Nat Sci. 18(9):1115–1122.
   Web of Science ®Google Scholar
• Wei GS, Li J, Wang NX, Gao Z. 2014. Spatial abundance and diversity of bacterioplankton in a typical stream-forming ecosystem, Huangqian Reservoir, China. J Microbiol Biotechnol. 24(10):1308–1318.
   PubMed Web of Science ®Google Scholar
• Williamson CE, Saros JE, Vincent WF, Smol JP. 2009. Lakes and reservoirs as sentinels, integrators, and regulators of climate change. Limnol Oceanogr. 54(6):2273–2282.
   Web of Science ®Google Scholar
• Woodhouse JN, Kinsela AS, Collins RN, Bowling LC, Honeyman GL, Holliday J, Neilan BA. 2016. Microbial communities reflect temporal changes in cyanobacterial composition in a shallow ephemeral freshwater lake. ISME J. 10(6):1337–1351.
   PubMed Web of Science ®Google Scholar
• Wu H, Li Y, Zhang J, Niu L, Zhang W, Cai W, Zhu X. 2017. Sediment bacterial communities in a eutrophic lake influenced by multiple inflow-rivers. Environ Sci Pollut Res Int. 24:19795–19806.
   PubMed Web of Science ®Google Scholar
• Xing P, Kong FX. 2007. Intra-habitat heterogeneity of environmental factors regulating bacterioplankton community composition in Lake Taihu, China. Aquat Microb Ecol. 48:113–122.
   Web of Science ®Google Scholar
• Xu MQ, Cao H, Xie P, Deng DG, Feng WS, Xu J. 2005. The temporal and spatial distribution, composition and abundance of Protozoa in Chaohu Lake, China: relationship with eutrophication. Eur J Protistol. 41(3):183–192.
   Web of Science ®Google Scholar
• Yang J, Jiang H C, W, G, Liu W, Zhang GJ. 2016. Distinct factors shape aquatic and sedimentary microbial community structures in the lakes of Western China. Front Microbiol. 7:1782.
   PubMed Web of Science ®Google Scholar
• Yang LB, Lei K, Meng W, Fu G, Yan WJ. 2013. Temporal and spatial changes in nutrients and chlorophyll-α in a shallow lake, Lake Chaohu, China: an 11-year investigation. J Environ Sci (China). 25(6):1117–1123.
   PubMed Web of Science ®Google Scholar
• Yu C, Zhang J, Wu L, Liu YZ, Ge G. 2015. Effects of heavy metal and nutrients on benthic microbial communities in freshwater sediment of Poyang Lake (China). JRST. 12(2):105–111.
   Web of Science ®Google Scholar
• Zan FY, Huo SL, Xi BD, Li QQ, Liao HQ, Zhang JT. 2011. Phosphorus distribution in the sediments of a shallow eutrophic lake, Lake Chaohu, China. Environ Earth Sci. 62(8):1643–1653.
   Web of Science ®Google Scholar
• Zhang L, Wang SR, Li YP, Zhao HC, Qian WB. 2015. Spatial and temporal distributions of microorganisms and their role in the evolution of Erhai Lake eutrophication. Environ Earth Sci. 74(5):3887–3896.
   Web of Science ®Google Scholar
• Zhong AP, Guo SH, Li FM, Li G, Jiang KX. 2006. Impact of anions on the heavy metals release from marine sediments. J Environ Sci (China). 18(6):1216–1220.
   PubMed Web of Science ®Google Scholar
• Zinger L, Gobet A, Pommier T. 2012. Two decades of describing the unseen majority of aquatic microbial diversity. Mol Ecol. 21(8):1878–1896.
   PubMed Web of Science ®Google Scholar