Zhang, Bo. et al. The influence of slope collapse on water exchange between a pit lake and a heterogeneous aquifer. Front. Environ. Sci. Eng. 13, 20 (2019).
Google Scholar
Li, Y. et al. Distribution and ecological risk assessment of heavy metals in sediments in Chinese collapsed lakes. Pol. J. Environ. Stud. 26, 181–188 (2017).
Google Scholar
Li, J. et al. Analysis of heavy metal sources and health risk assessment of typical coal mine collapsed lakes in Huaibei Coalfield, Anhui Province, China. Polish J. Environ. Stud. 29, 3193–3202 (2020).
Google Scholar
James, I. P. & Jennifer, B. H. M. Conceptual challenges in microbial community ecology. Philos. Trans. R. Soc. B 375, 20190241 (2020).
Google Scholar
Sunagawa, S. et al. Structure and function of the global ocean microbiome. Science 348, 1261359 (2015).
Google Scholar
Falkowski Paul, G., Fenchel, T. & Delong Edward, F. The microbial engines that drive Earth’s biogeochemical cycles. Science 320, 1034–1039 (2008).
Google Scholar
Whitman, W. B., Coleman, D. C. & Wiebe, W. J. Prokaryotes: The unseen majority. Proc. Natl. Acad. Sci. USA 95, 6578 (1998).
Google Scholar
Parkes, R. J. et al. Deep sub-seafloor prokaryotes stimulated at interfaces over geological time. Nature 436, 390–394 (2005).
Google Scholar
Wurzbacher, C. et al. Shifts among Eukaryota, Bacteria, and Archaea define the vertical organization of a lake sediment. Microbiome 5, 41 (2017).
Google Scholar
Nannipieri, P. & Eldor, P. The chemical and functional characterization of soil N and its biotic components. Soil Biol. Biochem. 41, 2357–2369 (2009).
Google Scholar
Strauss, E. A., Mitchell, N. L. & Lamberti, G. A. Factors regulating nitrification in aquatic sediments: Effects of organic carbon, nitrogen availability, and pH. Can. J. Fish. Aquat. Sci. 59, 554–563 (2002).
Google Scholar
Seymour, J. R., Seuront, L. & Mitchell, J. G. Microscale gradients of planktonic microbial communities above the sediment surface in a mangrove estuary. Estuar. Coast. Shelf Sci. 73, 651–666 (2007).
Google Scholar
Aciego Pietri, J. C. & Brookes, P. C. Relationships between soil pH and microbial properties in a UK arable soil. Soil Biol. Biochem. 40, 1856–1861 (2008).
Google Scholar
Pavloudi, C., Kristoffersen, J. B., Oulas, A., De Troch, M. & Arvanitidis, C. Sediment microbial taxonomic and functional diversity in a natural salinity gradient challenge Remane’s “species minimum” concept. PeerJ 5, e3687 (2017).
Google Scholar
Wei, G., Li, M., Li, F., Li, H. & Gao, Z. Distinct distribution patterns of prokaryotes between sediment and water in the Yellow River estuary. Appl. Microbiol. Biotechnol. 100, 9683–9697 (2016).
Google Scholar
van Dijk, E. L., Auger, H., Jaszczyszyn, Y. & Thermes, C. T. Ten years of next-generation sequencing technology. Trends Genet. 30, 418–426 (2014).
Google Scholar
Sadaiappan, B., Prasannakumar, C., Subramanian, K. & Mahendran, S. Metagenomic data of vertical distribution and abundance of bacterial diversity in the hypersaline sediments of Mad Boon-mangrove ecosystem, Bay of Bengal. Data Brief 22, 716–721 (2019).
Google Scholar
Kim, K. Microbial diversity analysis of sediment from Nakdong River Estuary in the republic of Korea using 16s rRNA gene amplicon sequencing. Microbiol. Resour. Announc. 7, e01186-e11118 (2018).
Google Scholar
Deng, Y., Liu, Y., Dumont, M. & Conrad, R. Salinity affects the composition of the aerobic methanotroph community in alkaline lake sediments from the Tibetan Plateau. Microb. Ecol. 73, 101–110 (2017).
Google Scholar
Palmer, M. A., Covich, A. P., Lake, S., Biro, P. & Bund, W. JVd. Linkages between aquatic sediment biota and life above sediments as potential drivers of biodiversity. Bioscience 50, 1062–1075 (2000).
Google Scholar
Silveira, R. et al. Bacteria and archaea communities in Cerrado natural pond sediments. Microb. Ecol. 81, 563–578 (2021).
Google Scholar
Galand, P. E. et al. Disturbance increases microbial community diversity and production in marine sediments. Front. Microbiol. 7, 1950 (2016).
Google Scholar
Dai, Y. et al. Spatiotemporal variation of planktonic and sediment bacterial assemblages in two plateau freshwater lakes at different trophic status. Appl. Microbiol. Biotechnol. 100, 4161–4175 (2016).
Google Scholar
Dai, Y. et al. Macrophyte identity shapes water column and sediment bacterial community. Hydrobiologia https://doi.org/10.1007/s10750-019-3930-y (2019).
Google Scholar
Chaudhry, V., Rehman, A., Mishra, A., Chauhan, P. S. & Nautiyal, C. S. Changes in bacterial community structure of agricultural land due to long-term organic and chemical amendments. Microb. Ecol. 64, 450–460 (2012).
Google Scholar
Huang, W. et al. Comparison among the microbial communities in the lake, lake wetland, and estuary sediments of a plain river network. MicrobiologyOpen 8, e00644 (2019).
Google Scholar
Ji, B., Liang, J., Ma, Y., Zhu, L. & Liu, Y. Bacterial community and eutrophic index analysis of the East Lake. Environ. Pollut. 252, 682–688 (2019).
Google Scholar
Song, H. et al. Bacterial communities in sediments of the shallow Lake Dongping in China. J. Appl. Microbiol. 112, 79–89 (2011).
Google Scholar
Coleman, M. L., Hedrick, D. B., Lovley, D. R., White, D. C. & Pye, K. Reduction of Fe(III) in sediments by sulphate-reducing bacteria. Nature 361, 436–448 (1993).
Google Scholar
Zhang, L. et al. The molecular characteristics of dissolved organic matter in urbanized river sediments and their environmental impact under the action of microorganisms. Sci Total Environ 827, 154289 (2022).
Google Scholar
Adhikari, N. P., Adhikari, S., Liu, X., Shen, L. & Gu, Z. Bacterial diversity in alpine lakes: A review from the third pole region. J. Earth Sci. 30, 387–396 (2019).
Google Scholar
Wang, P. et al. Shift in bacterioplankton diversity and structure: Influence of anthropogenic disturbances along the Yarlung Tsangpo River on the Tibetan Plateau, China. Sci. Rep. 7, 12529 (2017).
Google Scholar
Winters, A. D., Marsh, T. L., Brenden, T. O. & Faisal, M. Molecular characterization of bacterial communities associated with sediments in the Laurentian Great Lakes. J. Great Lakes Res. 40, 640–645 (2014).
Google Scholar
Yang, J., Jiang, H., Dong, H. & Liu, Y. A comprehensive census of lake microbial diversity on a global scale. Sci. China Life Sci. 62, 1320–1331 (2019).
Google Scholar
Aida, M.-R. & Coker, J. A. The effects of extremes of pH on the growth and transcriptomic profiles of three haloarchaea. F1000Research 3, 168 (2014).
Google Scholar
Guo, H., Nasir, M., Lv, J., Dai, Y. & Gao, J. Understanding the variation of microbial community in heavy metals contaminated soil using high throughput sequencing. Ecotoxicol. Environ. Saf. 144, 300–306 (2017).
Google Scholar
Kaci, A., Petit, F., Fournier, M., Cécillon, S. & Berthe, T. Diversity of active microbial communities subjected to long-term exposure to chemical contaminants along a 40-year-old sediment core. Environ. Sci. Pollut. Res. 23, 4095–4110 (2016).
Google Scholar
Hamed, A. et al. Microbial community composition and functions are resilient to metal pollution along two forest soil gradients. FEMS Microbiol. Ecol. 91, 1–11 (2015).
Xu, M. et al. High microbial diversity stabilizes the responses of soil organic carbon decomposition to warming in the subsoil on the Tibetan Plateau. Glob. Change Biol. 27, 2061–2075 (2021).
Google Scholar
Li, Q., Zhao, X. & Hu, C. ISO10390: 2005 soil quality-determination of pH. Pollut. Control Technol. 1, 53–55 (2006).
Bremner, J. Total nitrogen. Methods of soil analysis: Part 2 chemical microbiological properties. Agron. Ser. 9, 1149–1178 (1965).
Google Scholar
O’halloran, I. & Cade-Menun, B. Total and organic phosphorus. Soil Sampling Methods Anal. 2, 265–291 (2008).
Dennis, K. L. et al. Adenomatous polyps are driven by microbe-instigated focal inflammation and are controlled by IL-10-producing T cells. Can. Res. 73, 5905–5913 (2013).
Google Scholar
Tanja, M. & Salzberg, S. L. FLASH: Fast length adjustment of short reads to improve genome assemblies. Bioinformatics 21, 2957–2963 (2011).
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).
Google Scholar
Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C. & Knight, R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27, 2194 (2011).
Google Scholar
Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460 (2010).
Google Scholar
Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335–336 (2010).
Google Scholar
Bokulich, N. A. et al. Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat. Methods 10, 57–59 (2013).
Google Scholar
Wang, Q., Garrity, G. M., Tiedje, J. M. & Cole, J. R. Nave Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73, 5261 (2007).
Google Scholar
Quast, C., Pruesse, E., Yilmaz, P., Gerken, J. & Glckner, F. O. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596 (2012).
Google Scholar
Chen, H. & Boutros, P. C. VennDiagram: A package for the generation of highly-customizable Venn and Euler diagrams in R. Bioinformatics 12, 35–30 (2011).
Google Scholar
Schloss, P. D. et al. Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75, 7537–7541 (2009).
Google Scholar
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