Abstract
River-bay systems are transitional areas that hold important roles in biogeochemical processes between continents and oceans. However, composition and structure of microbial communities shaped by such environments have not been clear yet. In this study, we used high-throughput sequencing of 16S rRNA genes to analyze the diversity and composition of sediment bacterial communities from the Shenzhen river-bay system during dry and wet seasons. The results showed that sediment bacterial community structure was varied according to habitats (river vs. estuary) and seasons (wet season vs. dry season). The alpha diversity of sediment bacterial community was significantly higher in the dry season than in the wet season, while no significant difference of alpha diversity was found between river and estuary. Neutral community model revealed a significant influence of stochastic processes on sediment bacterial community assembly, especially in the wet season. However, the beta nearest-taxon index indicated that deterministic processes were more responsible for the assembly of sediment bacterial community. Additionally, redundancy analysis suggested strong links between sediment bacterial communities and environmental factors in Shenzhen river-bay system, with the environmental factors explaining 63.5% of the bacterial community variation. Specifically, NH4+, pH, and salinity were the three most important contributing factors that shaped the sediment bacterial communities. Overall, this study provides a valuable reference to get insights into the spatiotemporal pattern of sediment bacterial communities in a typical river-bay system.
Key Points
• Stochastic processes contribute sediment bacterial community assembly.
• Deterministic processes dominate sediment bacterial community assembly.
• Environmental factors shape sediment bacterial communities.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Data availability
All the raw reads in the current study have been deposited at the Sequence Read Archive of the National Center for Biotechnology Information under the accession number PRJNA673162.
References
Bastian M, Heymann S (2009) Jacomy M (2009) Gephi: an open source software for exploring and manipulating networks. Icwsm 8:361–362
Boer SI, Hedtkamp SI, van Beusekom JE, Fuhrman JA, Boetius A, Ramette A (2009) Time- and sediment depth-related variations in bacterial diversity and community structure in subtidal sands. ISME J 3(7):780–791. https://doi.org/10.1038/ismej.2009.29
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. https://doi.org/10.1038/nmeth.2276
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7(5):335–336. https://doi.org/10.1038/nmeth.f.303
Carpenter EJ, Romans K (1991) Major role of the cyanobacterium trichodesmium in nutrient cycling in the north atlantic ocean. Science 254(5036):1356–1358. https://doi.org/10.1126/science.254.5036.1356
Chafee M, Fernandez-Guerra A, Buttigieg PL, Gerdts G, Eren AM, Teeling H, Amann RI (2018) Recurrent patterns of microdiversity in a temperate coastal marine environment. ISME J 12(1):237–252. https://doi.org/10.1038/ismej.2017.165
Chen W, Ren K, Isabwe A, Chen H, Liu M, Yang J (2019) Stochastic processes shape microeukaryotic community assembly in a subtropical river across wet and dry seasons. Microbiome 7(1):138. https://doi.org/10.1186/s40168-019-0749-8
de Oliveira LFV, Margis R (2015) The source of the river as a nursery for microbial diversity. PLoS One 10(3):e0120608. https://doi.org/10.1371/journal.pone.0120608
Fang H, Lai H, Cheng W, Huang L, He G (2017) Modeling sediment transport with an integrated view of the biofilm effects. Water Resour Res 53(9):7536–7557. https://doi.org/10.1002/2017WR020628
Fortunato CS, Herfort L, Zuber P, Baptista AM, Crump BC (2012) Spatial variability overwhelms seasonal patterns in bacterioplankton communities across a river to ocean gradient. ISME J 6(3):554–563. https://doi.org/10.1038/ismej.2011.135
Gibbons SM, Jones E, Bearquiver A, Blackwolf F, Roundstone W, Scott N, Hooker J, Madsen R, Coleman ML, Gilbert JA (2014) Human and environmental impacts on river sediment microbial communities. PLoS One 9(5):e97435. https://doi.org/10.1371/journal.pone.0097435
Inoue J-I, Oshima K, Suda W, Sakamoto M, Iino T, Noda S, Hongoh Y, Hattori M, Ohkuma M (2015) Distribution and evolution of nitrogen fixation genes in the phylum Bacteroidetes. Microbes Environ 30:44–50. https://doi.org/10.1264/jsme2.ME14142
Kent M (2011) Vegetation description and data analysis: a practical approach. Wiley, Hoboken
Li M, Cao H, Hong Y, Gu J-D (2013) Using the variation of anammox bacteria community structures as a bio-indicator for anthropogenic/terrestrial nitrogen inputs in the Pearl River Delta (PRD). Appl Microbiol Biotechnol 97(22):9875–9883
Liao J, Cao X, Wang J, Zhao L, Sun J, Jiang D, Huang Y (2017) Similar community assembly mechanisms underlie similar biogeography of rare and abundant bacteria in lakes on Yungui Plateau, China. Limnol Oceanogr 62(2):723–735. https://doi.org/10.1007/s00253-013-4990-y
Liao H, Yen JY, Guan Y, Ke D, Liu C (2020) Differential responses of stream water and bed sediment microbial communities to watershed degradation. Environ Int 134:105198. https://doi.org/10.1016/j.envint.2019.105198
Liu S, Ren H, Shen L, Lou L, Tian G, Zheng P, Hu B (2015) pH levels drive bacterial community structure in sediments of the Qiantang River as determined by 454 pyrosequencing. Front Microbiol 6:285. https://doi.org/10.3389/fmicb.2015.00285
Liu J, Chen X, Shu HY, Lin XR, Zhou QX, Bramryd T, Shu WS, Huang LN (2018) Microbial community structure and function in sediments from e-waste contaminated rivers at Guiyu area of China. Environ Pollut 235:171–179. https://doi.org/10.1016/j.envpol.2017.12.008
Liu J, Zhu S, Liu X, Yao P, Ge T, Zhang XH (2020) Spatiotemporal dynamics of the archaeal community in coastal sediments: assembly process and co-occurrence relationship. ISME J 14(6):1463–1478. https://doi.org/10.1038/s41396-020-0621-7
Logares R, Lindström ES, Langenheder S, Logue JB, Paterson H, Laybourn-Parry J, Rengefors K, Tranvik L, Bertilsson S (2013) Biogeography of bacterial communities exposed to progressive long-term environmental change. ISME J 7(5):937–948. https://doi.org/10.1038/ismej.2012.168
Magoc T, Salzberg SL (2011) FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27(21):2957–2963. https://doi.org/10.1093/bioinformatics/btr507
McCoy DL, Jones JM, Anderson JW, Harmon M, Hartwell I, Hameedi J (2002) Distribution of cytochrome P4501A1–inducing chemicals in sediments of the Delaware River-Bay system, USA. Environ Toxicol Chem 21(8):1618–1627
Muylaert K, Sabbe K, Vyverman W (2009) Changes in phytoplankton diversity and community composition along the salinity gradient of the Schelde estuary (Belgium/The Netherlands). Estuar Coast Shelf Sci 82(2):335–340. https://doi.org/10.1016/j.ecss.2009.01.024
Nemergut DR, Costello EK, Hamady M, Lozupone C, Jiang L, Schmidt SK, Fierer N, Townsend AR, Cleveland CC, Stanish L, Knight R (2011) Global patterns in the biogeography of bacterial taxa. Environ Microbiol 13(1):135–144. https://doi.org/10.1111/j.1462-2920.2010.02315.x
Ostman O, Drakare S, Kritzberg ES, Langenheder S, Logue JB, Lindstrom ES (2010) Regional invariance among microbial communities. Ecol Lett 13(1):118–127. https://doi.org/10.1111/j.1461-0248.2009.01413.x
Parkes RJ, Cragg B, Roussel E, Webster G, Weightman A, Sass H (2014) A review of prokaryotic populations and processes in sub-seafloor sediments, including biosphere: geosphere interactions. Mar Geol 352:409–425. https://doi.org/10.1016/j.margeo.2014.02.009
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glockner FO (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41(Database issue):D590–D596. https://doi.org/10.1093/nar/gks1219
Ren Z, Qu X, Zhang M, Yu Y, Peng W (2019) Distinct Bacterial Communities in Wet and Dry Seasons During a Seasonal Water Level Fluctuation in the Largest Freshwater Lake (Poyang Lake) in China. Front Microbiol 10:1167. https://doi.org/10.3389/fmicb.2019.01167
Riemann L, Farnelid H, Steward GF (2010) Nitrogenase genes in non-cyanobacterial plankton: prevalence, diversity and regulation in marine waters. Aquat Microb Ecol 61(3):235–247. https://doi.org/10.3354/ame01431
Roguet A, Laigle GS, Therial C, Bressy A, Soulignac F, Catherine A, Lacroix G, Jardillier L, Bonhomme C, Lerch TZ, Lucas FS (2015) Neutral community model explains the bacterial community assembly in freshwater lakes. FEMS Microbiol Ecol 91(11). https://doi.org/10.1093/femsec/fiv125
Satinsky BM, Crump BC, Smith CB, Sharma S, Zielinski BL, Doherty M, Meng J, Sun S, Medeiros PM, Paul JH (2014) Microspatial gene expression patterns in the Amazon River Plume. Proc Natl Acad Sci U S A 111(30):11085–11090. https://doi.org/10.1073/pnas.1402782111
Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75(23):7537–7541. https://doi.org/10.1128/AEM.01541-09
Sieburth JM (1967) Seasonal selection of estuarine bacteria by water temperature. J Exp Mar Biol Ecol 1(1):98–121. https://doi.org/10.1016/0022-0981(67)90009-3
Sloan WT, Lunn M, Woodcock S, Head IM, Nee S, Curtis TP (2006) Quantifying the roles of immigration and chance in shaping prokaryote community structure. Environ Microbiol 8(4):732–740. https://doi.org/10.1111/j.1462-2920.2005.00956.x
Song H, Li Z, Du B, Wang G, Ding Y (2012) Bacterial communities in sediments of the shallow Lake Dongping in China. J Appl Microbiol 112(1):79–89. https://doi.org/10.1111/j.1365-2672.2011.05187.x
Sorokin DY, Lucker S, Vejmelkova D, Kostrikina NA, Kleerebezem R, Rijpstra WI, Damste JS, Le Paslier D, Muyzer G, Wagner M, van Loosdrecht MC, Daims H (2012) Nitrification expanded: discovery, physiology and genomics of a nitrite-oxidizing bacterium from the phylum Chloroflexi. ISME J 6(12):2245–2256. https://doi.org/10.1038/ismej.2012.70
Stoichev T, Amouroux D, Wasserman J, Point D, De Diego A, Bareille G, Donard O (2004) Dynamics of mercury species in surface sediments of a macrotidal estuarine–coastal system (Adour River, Bay of Biscay). Estuar Coast Shelf Sci 59(3):511–521. https://doi.org/10.1016/j.ecss.2003.10.007
Wang Y, Pan J, Yang J, Zhou Z, Pan Y, Li M (2020) Patterns and processes of free-living and particle-associated bacterioplankton and archaeaplankton communities in a subtropical river-bay system in South China. Limnol Oceanogr 65:S161–S179. https://doi.org/10.1002/lno.11314
Wu J, Xiong J, Hu C, Shi Y, Wang K, Zhang D (2015) Temperature sensitivity of soil bacterial community along contrasting warming gradient. Appl Soil Ecol 94:40–48. https://doi.org/10.1016/j.apsoil.2015.04.018
Xie W, Luo H, Murugapiran SK, Dodsworth JA, Chen S, Sun Y, Hedlund BP, Wang P, Fang H, Deng M (2018) Localized high abundance of Marine Group II archaea in the subtropical Pearl River Estuary: implications for their niche adaptation. Environ Microbiol 20(2):734–754. https://doi.org/10.1111/1462-2920.14004
Yang J, Ma L, Jiang H, Wu G, Dong H (2016) Salinity shapes microbial diversity and community structure in surface sediments of the Qinghai-Tibetan Lakes. Sci Rep 6:25078. https://doi.org/10.1038/srep25078
Yu Y, Lee C, Kim J, Hwang S (2005) Group-specific primer and probe sets to detect methanogenic communities using quantitative real-time polymerase chain reaction. Biotechnol Bioeng 89(6):670–679. https://doi.org/10.1002/bit.20347
Zehr JP, Mellon MT, Zani S (1998) New Nitrogen-Fixing Microorganisms Detected in Oligotrophic Oceans by Amplification of Nitrogenase (nifH) Genes. Appl Environ Microbiol 64(12):5067. https://doi.org/10.1128/AEM.64.12.5067-5067.1998
Zehr JP, Jenkins BD, Short SM, Steward GF (2003) Nitrogenase gene diversity and microbial community structure: a cross-system comparison. Environ Microbiol 5(7):539–554. https://doi.org/10.1046/j.1462-2920.2003.00451.x
Zhang M, Wu Z, Sun Q, Ding Y, Ding Z, Sun L (2019) The spatial and seasonal variations of bacterial community structure and influencing factors in river sediments. J Environ Manag 248:109293. https://doi.org/10.1016/j.jenvman.2019.109293
Zhang B, Li Y, Xiang SZ, Yan Y, Yang R, Lin MP, Wang XM, Xue YL, Guan XY (2020a) Sediment Microbial Communities and Their Potential Role as Environmental Pollution Indicators in Xuande Atoll, South China Sea. Front Microbiol 11:1011. https://doi.org/10.3389/fmicb.2020.01011
Zhang CJ, Chen YL, Pan J, Wang YM, Li M (2020b) Spatial and seasonal variation of methanogenic community in a river-bay system in South China. Appl Microbiol Biotechnol 104(10):4593–4603. https://doi.org/10.1007/s00253-020-10613-z
Funding
This work was funded by the National Natural Science Foundation of China (Grant Nos. 31970105, 32000002), the Basic and Applied Basic Research of Guangdong Province (Grant No. 2019A1515110089), the Natural Science Foundation of Guangdong Province (Grant No. 2018A030310486), the Innovation Team Project of Universities in Guangdong Province (Grant no. 2020KCXTD023), the Shenzhen Science and Technology Program (Grant no. JCYJ20200109105010363), the China Postdoctoral Science Foundation (Grant No. 2018 M643153), and the CAS Interdisciplinary Innovation Team (Grant No. JCTD-2018-16).
Author information
Authors and Affiliations
Contributions
ZL, BL, and ML conceived and designed the experiments. BL, QW, and CZ performed the experiments. BL and ZL analyzed the data. SZ contributed reagents/materials/analysis tools. ZL, BL, and ML wrote and all authors edited and approved the paper.
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that they have no conflict of interest.
Ethical statement
This article does not contain any studies with human participants performed by any of the authors.
Additional information
Publisher’s note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
ESM 1
(PDF 1312 kb)
Rights and permissions
About this article
Cite this article
Lu, Z., Liu, Z., Zhang, C. et al. Spatial and seasonal variations of sediment bacterial communities in a river-bay system in South China. Appl Microbiol Biotechnol 105, 1979–1989 (2021). https://doi.org/10.1007/s00253-021-11142-z
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00253-021-11142-z