Volume 42 Issue 9
Sep.  2023
Turn off MathJax
Article Contents
Changfeng Qu, Xixi Wang, Liping Zhang, Huamao Yuan, Xuegang Li, Ning Li, Fushan Chen, Jinlai Miao. Prokaryotic diversity and community composition in the surface sediments of the Changjiang River Estuary in summer[J]. Acta Oceanologica Sinica, 2023, 42(9): 113-124. doi: 10.1007/s13131-023-2153-2
Citation: Changfeng Qu, Xixi Wang, Liping Zhang, Huamao Yuan, Xuegang Li, Ning Li, Fushan Chen, Jinlai Miao. Prokaryotic diversity and community composition in the surface sediments of the Changjiang River Estuary in summer[J]. Acta Oceanologica Sinica, 2023, 42(9): 113-124. doi: 10.1007/s13131-023-2153-2

Prokaryotic diversity and community composition in the surface sediments of the Changjiang River Estuary in summer

doi: 10.1007/s13131-023-2153-2
Funds:  The National Natural Science Foundation of China under contract Nos 32000074 and 42176130; the Science and Technology Planning Project of Guangxi under contract No. AA21196002; the Natural Science Foundation of Shandong Province under contract No. ZR2021MD044; the Tai Mountain Industry Leading Talent of Shandong under contract No. 2019TSCYCX-06; the Key Research and Development Program of Shandong Province under contract No. 2021TZXD008; the Biosafety Research Program under contract No. 20SWAQX04; the Shandong Program of Pilot National Laboratory for Marine Science and Technology (Qingdao) under contract No. 2022QNLM030003-1.
More Information
  • Microorganisms are fundamental for the functioning of marine ecosystems and are involved in the decomposition of organic matter, transformation of nutrients and circulation of biologically-important chemicals. Based on the complexity of the natural geographic characteristics of the Changjiang River Estuary, the geographic distribution of sedimentary microorganisms and the causes of this distribution are largely unexplored. In this work, the surface sediment samples from the adjacent sea area of the Changjiang River Estuary were collected. Their prokaryotic diversity was examined by high-throughput sequencing technology, and the environmental factors of the bacterial community were investigated. The results indicated that the distribution of prokaryotic communities in the sediments of the study areas showed obvious spatial heterogeneity. The sampling sequences divided the sample regions into three distinct clusters. Each geographic region had a unique community structure, although Proteobacteria, Bacteroidota, Desulfobacterota, Acidobacteriota, and Actinobacteriota all existed in these three branches. Canonical correspondence analysis demonstrated that prokaryotic diversity and community distribution were significantly correlated with the geographic location of sediment, seawater depth, and in particular, nutrient content (e.g., total phosphorus, total organic carbon and dissolved oxygen). Moreover, it was found for the first time that the metal ions obviously affected the composition and distribution of the prokaryotic community in this area. In general, this work provides new insights into the structural characteristics and driving factors of prokaryotic communities under the background of the ever-changing Changjiang River Estuary.
  • loading
  • Aldunate M, De La Iglesia R, Bertagnolli A D, et al. 2018. Oxygen modulates bacterial community composition in the coastal upwelling waters off central Chile. Deep-Sea Research Part II: Topical Studies in Oceanography, 156: 68–79. doi: 10.1016/j.dsr2.2018.02.001
    Aponte H, Meli P, Butler B, et al. 2020. Meta-analysis of heavy metal effects on soil enzyme activities. Science of the Total Environment, 737: 139744. doi: 10.1016/j.scitotenv.2020.139744
    Baldock J A, Skjemstad J O. 2000. Role of the soil matrix and minerals in protecting natural organic materials against biological attack. Organic Geochemistry, 31(7−8): 697–710. doi: 10.1016/S0146-6380(00)00049-8
    Beardsley R C, Limeburner R, Yu H, et al. 1985. Discharge of the Changjiang (Yangtze River) into the East China Sea. Continental Shelf Research, 4(1−2): 57–76. doi: 10.1016/0278-4343(85)90022-6
    Bell T H, Yergeau E, Maynard C, et al. 2013. Predictable bacterial composition and hydrocarbon degradation in Arctic soils following diesel and nutrient disturbance. The ISME Journal, 7(6): 1200–1210. doi: 10.1038/ismej.2013.1
    Biddle J F, Lipp J S, Lever M A, et al. 2006. Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru. Proceedings of the National Academy of Sciences of the United States of America, 103(10): 3846–3851
    Caporaso J G, Kuczynski J, Stombaugh J, et al. 2010. QIIME allows analysis of high-throughput community sequencing data. Nature Methods, 7(5): 335–336. doi: 10.1038/nmeth.f.303
    Chai Chao, Yu Zhiming, Shen Zhiliang, et al. 2009. Nutrient characteristics in the Yangtze River Estuary and the adjacent East China Sea before and after impoundment of the Three Gorges Dam. Science of the Total Environment, 407(16): 4687–4695. doi: 10.1016/j.scitotenv.2009.05.011
    Chen Quanrui, Fan Jingfeng, Su Jie, et al. 2020. Spatial distribution characteristics of bacterial community structure and gene abundance in sediments of the Bohai Sea. Acta Oceanologica Sinica, 39(2): 69–78. doi: 10.1007/s13131-020-1554-8
    Chen Chung-Chi, Gong Gwo-Ching, Shiah Fuh-Kwo. 2007. Hypoxia in the East China Sea: one of the largest coastal low-oxygen areas in the world. Marine Environmental Research, 64(4): 399–408. doi: 10.1016/j.marenvres.2007.01.007
    Chen Shifu, Zhou Yanqing, Chen Yaru, et al. 2018. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics, 34(17): i884–i890. doi: 10.1093/bioinformatics/bty560
    D’Hondt S, Jørgensen B B, Miller D J, et al. 2004. Distributions of microbial activities in deep subseafloor sediments. Science, 306(5705): 2216–2221. doi: 10.1126/science.1101155
    Dong Chunming, Sheng Huafang, Wang Weiguo, et al. 2017. Bacterial distribution pattern in the surface sediments distinctive among shelf, slope and basin across the western Arctic Ocean. Polar Biology, 40(2): 423–436. doi: 10.1007/s00300-016-1970-6
    Edgar R C. 2013. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nature Methods, 10(10): 996–998. doi: 10.1038/nmeth.2604
    Ehrlich H L. 1997. Microbes and metals. Applied Microbiology and Biotechnology, 48(6): 687–692. doi: 10.1007/s002530051116
    Fuerst J A, Sagulenko E. 2011. Beyond the bacterium: planctomycetes challenge our concepts of microbial structure and function. Nature Reviews Microbiology, 9(6): 403–413. doi: 10.1038/nrmicro2578
    Green J, Bohannan B J M. 2006. Spatial scaling of microbial biodiversity. Trends in Ecology & Evolution, 21(9): 501–507
    Hinrichs K U, Inagaki F. 2012. Downsizing the deep biosphere. Science, 338(6104): 204–205. doi: 10.1126/science.1229296
    Hollingsworth A L, Jones D O B, Young C R. 2021. Spatial variability of abyssal nitrifying microbes in the North-Eastern Clarion-Clipperton zone. Frontiers in Marine Science, 8: 663420. doi: 10.3389/fmars.2021.663420
    Horner-Devine M C, Carney K M, Bohannan B J M. 2004. An ecological perspective on bacterial biodiversity. Proceedings of the Royal Society B: Biological Sciences, 271(1535): 113–122. doi: 10.1098/rspb.2003.2549
    Hoshino T, Doi H, Uramoto G I, et al. 2020. Global diversity of microbial communities in marine sediment. Proceedings of the National Academy of Sciences of the United States of America, 117(44): 27587–27597
    Hoshino T, Inagaki F. 2019. Abundance and distribution of Archaea in the subseafloor sedimentary biosphere. The ISME Journal, 13(1): 227–231. doi: 10.1038/s41396-018-0253-3
    Jeandel C, Tachikawa K, Bory A, et al. 2000. Biogenic barium in suspended and trapped material as a tracer of export production in the tropical NE Atlantic (EUMELI sites). Marine Chemistry, 71(1−2): 125–142. doi: 10.1016/S0304-4203(00)00045-1
    Jetten M S M, Sliekers O, Kuypers M, et al. 2003. Anaerobic ammonium oxidation by marine and freshwater planctomycete-like bacteria. Applied Microbiology and Biotechnology, 63(2): 107–114. doi: 10.1007/s00253-003-1422-4
    Ji M K, van Dorst J, Bissett A, et al. 2016. Microbial diversity at Mitchell Peninsula, Eastern Antarctica: a potential biodiversity “hotspot”. Polar Biology, 39(2): 237–249. doi: 10.1007/s00300-015-1776-y
    Kallmeyer J, Pockalny R, Adhikari R R, et al. 2012. Global distribution of microbial abundance and biomass in subseafloor sediment. Proceedings of the National Academy of Sciences of the United States of America, 109(40): 16213–16216
    Li Jiang, Gu Xiaoqian, Gui Yuanyuan. 2020. Prokaryotic diversity and composition of sediments from Prydz Bay, the Antarctic peninsula region, and the Ross Sea, Southern Ocean. Frontiers in Microbiology, 11: 783. doi: 10.3389/fmicb.2020.00783
    Li Daoji, Zhang Jing, Huang Daji, et al. 2002. Oxygen depletion off the Changjiang (Yangtze River) Estuary. Science in China Series D: Earth Sciences, 45(12): 1137–1146. doi: 10.1360/02yd9110
    Lozupone C, Knight R. 2005. UniFrac: a new phylogenetic method for comparing microbial communities. Applied and Environmental Microbiology, 71(12): 8228–8235. doi: 10.1128/AEM.71.12.8228-8235.2005
    Lozupone C, Lladser M E, Knights D, et al. 2011. UniFrac: an effective distance metric for microbial community comparison. The ISME Journal, 5(2): 169–172. doi: 10.1038/ismej.2010.133
    Ludwig W, Probst J L, Kempe S. 1996. Predicting the oceanic input of organic carbon by continental erosion. Global Biogeochemical Cycles, 10(1): 23–41. doi: 10.1029/95GB02925
    Magoč T, Salzberg S L. 2011. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics, 27(21): 2957–2963. doi: 10.1093/bioinformatics/btr507
    Martin J M, Meybeck M. 1979. Elemental mass-balance of material carried by major world rivers. Marine Chemistry, 7(3): 173–206. doi: 10.1016/0304-4203(79)90039-2
    Martiny J B H, Bohannan B J M, Brown J H, et al. 2006. Microbial biogeography: putting microorganisms on the map. Nature Reviews Microbiology, 4(2): 102–112. doi: 10.1038/nrmicro1341
    Milliman J D, Syvitski J P M. 1992. Geomorphic/tectonic control of sediment discharge to the ocean: the importance of small mountainous rivers. The Journal of Geology, 100(5): 525–544. doi: 10.1086/629606
    Muyzer G, Stams A J M. 2008. The ecology and biotechnology of sulphate-reducing bacteria. Nature Reviews Microbiology, 6(6): 441–454. doi: 10.1038/nrmicro1892
    Orcutt B N, Sylvan J B, Knab N J, et al. 2011. Microbial ecology of the dark ocean above, at, and below the seafloor. Microbiology and Molecular Biology Reviews, 75(2): 361–422. doi: 10.1128/MMBR.00039-10
    Pfeifer K, Kasten S, Hensen C, et al. 2001. Reconstruction of primary productivity from the barium contents in surface sediments of the South Atlantic Ocean. Marine Geology, 177(1−2): 13–24. doi: 10.1016/S0025-3227(01)00121-9
    Segata N, Izard J, Waldron L, et al. 2011. Metagenomic biomarker discovery and explanation. Genome Biology, 12(6): R60. doi: 10.1186/gb-2011-12-6-r60
    Smit E, Leeflang P, Gommans S, et al. 2001. Diversity and seasonal fluctuations of the dominant members of the bacterial soil community in a wheat field as determined by cultivation and molecular methods. Applied and Environmental Microbiology, 67(5): 2284–2291. doi: 10.1128/AEM.67.5.2284-2291.2001
    Smith S V, Renwick W H, Buddemeier R W, et al. 2001. Budgets of soil erosion and deposition for sediments and sedimentary organic carbon across the conterminous United States. Global Biogeochemical Cycles, 15(3): 697–707. doi: 10.1029/2000GB001341
    Smouse P E, Long J C, Sokal R R. 1986. Multiple regression and correlation extensions of the mantel test of matrix correspondence. Systematic Biology, 35(4): 627–632
    Stackebrandt E, Goebel B M. 1994. Taxonomic Note: A place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. International Journal of Systematic and Evolutionary Microbiology, 44(4): 846–849. doi: 10.1099/00207713-44-4-846
    Sun Qiqi, Song Jinming, Li Xuegang, et al. 2021. The bacterial diversity and community composition altered in the oxygen minimum zone of the Tropical Western Pacific Ocean. Journal of Oceanology and Limnology, 39(5): 1690–1704. doi: 10.1007/s00343-021-0370-0
    Takebayashi S, Narihiro T, Fujii Y, et al. 2007. Water availability is a critical determinant of a population shift from Proteobacteria to Actinobacteria during start-up operation of mesophilic fed-batch composting. Microbes and Environments, 22(3): 279–289. doi: 10.1264/jsme2.22.279
    Thamdrup B, Rosselló-Mora R, Amann R. 2000. Microbial manganese and sulfate reduction in Black Sea shelf sediments. Applied and Environmental Microbiology, 66(7): 2888–2897. doi: 10.1128/AEM.66.7.2888-2897.2000
    Thomson B C, Ostle N, McNamara N, et al. 2010. Vegetation affects the relative abundances of dominant soil bacterial taxa and soil respiration rates in an upland grassland soil. Microbial Ecology, 59(2): 335–343. doi: 10.1007/s00248-009-9575-z
    Wang Houjie, Yang Zuosheng, Wang Yan, et al. 2008. Reconstruction of sediment flux from the Changjiang (Yangtze River) to the sea since the 1860s. Journal of Hydrology, 349(3−4): 318–332. doi: 10.1016/j.jhydrol.2007.11.005
    Wang Qiong Garrity G M, Tiedje J M, et al. 2007. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and Environmental Microbiology, 73(16): 5261–5267. doi: 10.1128/AEM.00062-07
    Yergeau E, Bokhorst S, Kang S, et al. 2012. Shifts in soil microorganisms in response to warming are consistent across a range of Antarctic environments. The ISME Journal, 6(3): 692–702. doi: 10.1038/ismej.2011.124
    Zhang Dongsheng. 2011. Diversity and distribution of microorganism in Changjiang Estuary and adjacent areas (in Chinese)[dissertation]. Hangzhou: Zhejiang University
    Zhang Jing, Liu Sumei, Ren Jingling, et al. 2007. Nutrient gradients from the eutrophic Changjiang (Yangtze River) Estuary to the oligotrophic Kuroshio waters and re-evaluation of budgets for the East China Sea Shelf. Progress in Oceanography, 74(4): 449–478. doi: 10.1016/j.pocean.2007.04.019
    Zhang Guiling, Zhang Jiezhang, Liu Sumei, et al. 2010. Nitrous oxide in the Changjiang (Yangtze River) Estuary and its adjacent marine area: riverine input, sediment release and atmospheric fluxes. Biogeosciences, 7(11): 3505–3516. doi: 10.5194/bg-7-3505-2010
    Zhu Jianrong, Zhu Zhuoyi, Lin Jun, et al. 2016. Distribution of hypoxia and pycnocline off the Changjiang Estuary, China. Journal of Marine Systems, 154: 28–4. doi: 10.1016/j.jmarsys.2015.05.002
  • 加载中

Catalog

    通讯作者: 陈斌, bchen63@163.com
    • 1. 

      沈阳化工大学材料科学与工程学院 沈阳 110142

    1. 本站搜索
    2. 百度学术搜索
    3. 万方数据库搜索
    4. CNKI搜索

    Figures(6)  / Tables(3)

    Article Metrics

    Article views (112) PDF downloads(5) Cited by()
    Proportional views
    Related

    /

    DownLoad:  Full-Size Img  PowerPoint
    Return
    Return