Vertical distribution of bacterial community structure in the sediments of two eutrophic lakes revealed by denaturing gradient gel electrophoresis (DGGE) and multivariate analysis techniques
01 Feb 2009-World Journal of Microbiology & Biotechnology (Springer Netherlands)-Vol. 25, Iss: 2, pp 225-233
TL;DR: Wang et al. as discussed by the authors investigated the vertical distribution of bacterial community structure in two eutrophic lakes of China, Lake Taihu and Lake Xuanwu, using a molecular fingerprinting technique, denaturing gradient gel electrophoresis (DGGE) followed by DNA sequence analysis, and the results were interpreted with multivariate statistical analysis.
Abstract: Vertical distribution of bacterial community structure was investigated in the sediments of two eutrophic lakes of China, Lake Taihu and Lake Xuanwu. Profiles of bacterial communities were generated using a molecular fingerprinting technique, denaturing gradient gel electrophoresis (DGGE) followed by DNA sequence analysis, and the results were interpreted with multivariate statistical analysis. To assess changes in the genetic diversity of bacterial communities with changing depth, DGGE banding patterns were analysed by cluster analysis. Distinct clusters were recognized in different sampling stations of Lake Taihu. Canonical correspondence analysis (CCA) was carried out to infer the relationship between environmental variables and bacterial community structure. DGGE samples collected at the same sampling site clustered together in both lakes. Total phosphorus, organic matter and pH were considered to be the key factors driving the changes in bacterial community composition.
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TL;DR: Investigation of sediment bacterial and archaeal communities in 13 freshwater lakes on the Yunnan Plateau showed a large variation in bacterial andArchaeal abundances, and Quantitative PCR assay showed high bacterial and Archaeal diversities.
Abstract: Both Bacteria and Archaea might be involved in various biogeochemical processes in lacustrine sediment ecosystems. However, the factors governing the intra-lake distribution of sediment bacterial and archaeal communities in various freshwater lakes remain unclear. The present study investigated the sediment bacterial and archaeal communities in 13 freshwater lakes on the Yunnan Plateau. Quantitative PCR assay showed a large variation in bacterial and archaeal abundances. Illumina MiSeq sequencing illustrated high bacterial and archaeal diversities. Bacterial abundance was regulated by sediment total organic carbon and total nitrogen, and water depth, while nitrate nitrogen was an important determinant of bacterial diversity. Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, Chlorobi, Chloroflexi, Cyanobacteria, Firmicutes, Gemmatimonadetes, Nitrospirae, Planctomycetes, and Verrucomicrobia were the major components of sediment bacterial communities. Proteobacteria was the largest phylum, but its major classes and their proportions varied greatly among different lakes, affected by sediment nitrate nitrogen. In addition, both Euryarchaeota and Crenarchaeota were important members in sediment archaeal communities, while unclassified Archaea usually showed the dominance.
200 citations
TL;DR: Results from this study suggest that agricultural fertilization practices have a great impact on soil bacterial community size and structure.
167 citations
Cites background from "Vertical distribution of bacterial ..."
...CCA has been proven more effective in illustrating the relationship between bacterial community composition and environmental parameters than univariate methods (Salles et al., 2006; Zeng et al., 2009)....
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TL;DR: The results revealed that the bacterial communities in different layers of sediment sample were very similar, and were related to Alpha-, Beta-, Gamma- and Deltaproteobacteria, Nitrospira, Bacteroids, Firmicutes, Gemmatimonadetes, Verrucomicrobia, Chlorobi, Actinobacteria and Acidobacteria.
162 citations
Cites background from "Vertical distribution of bacterial ..."
...Zeng et al. (2009) also indicated that the concentration of oxygen decreased with depth in the upper sediment layers of Lake Taihu....
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TL;DR: Either planktonic or sediment bacterial community structure showed a distinct difference between in Dianchi Lake and in Erhai Lake, and an evident structure difference was also found between planktonics and sediment bacterial communities in either of these two lakes.
Abstract: Both planktonic and sediment bacterial assemblages are the important components of freshwater lake ecosystems. However, their spatiotemporal shift and the driving forces remain still elusive. Eutrotrophic Dianchi Lake and mesotrophic Erhai Lake are the largest two freshwater lakes on the Yunnan Plateau (southwestern China). The present study investigated the spatiotemporal shift in both planktonic and sediment bacterial populations in these two plateau freshwater lakes at different trophic status. For either lake, both water and sediment samples were collected from six sampling locations in spring and summer. Bacterioplankton community abundance in Dianchi Lake generally far outnumbered that in Erhai Lake. Sediment bacterial communities in Erhai Lake were found to have higher richness and diversity than those in Dianchi Lake. Sediments had higher bacterial community richness and diversity than waters. The change patterns for both planktonic and sediment bacterial communities were lake-specific and season-specific. Either planktonic or sediment bacterial community structure showed a distinct difference between in Dianchi Lake and in Erhai Lake, and an evident structure difference was also found between planktonic and sediment bacterial communities in either of these two lakes. Planktonic bacterial communities in both Dianchi Lake and Erhai Lake mainly included Proteobacteria (mainly Alpha-, Beta-, and Gammaproteobacteria), Bacteroidetes, Actinobacteria, Cyanobacteria, and Firmicutes, while sediment bacterial communities were mainly represented by Proteobacteria (mainly Beta- and Deltaproteobacteria), Bacteroidetes, Chlorobi, Nitrospirae, Acidobacteria, and Chloroflexi. Trophic status could play important roles in shaping both planktonic and sediment bacterial communities in freshwater lakes.
92 citations
Cites background from "Vertical distribution of bacterial ..."
...…structure remain largely unclear, although previous studies suggested that it might be affected by one or two sediment parameters, including pH (Zeng et al. 2008, 2009; Zhao et al. 2011), ORP (Zeng et al. 2008), organic matter (Liu et al. 2015), nitrogen (Chen et al. 2015; Liu et al. 2015),…...
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...…factors have been proposed to be the potential determinants to sediment bacterial community structure in freshwater lake, including organic matter, phosphorus, pH, nitrogen, and heavy metal (Bai et al. 2012; Song et al. 2012; Yu et al. 2015; Zeng et al. 2009; Zhang et al. 2015a; Zhao et al. 2011)....
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...…by one or two sediment parameters, including pH (Zeng et al. 2008, 2009; Zhao et al. 2011), ORP (Zeng et al. 2008), organic matter (Liu et al. 2015), nitrogen (Chen et al. 2015; Liu et al. 2015), phosphorus (Song et al. 2012; Yu et al. 2015; Zeng et al. 2009), and heavy metal (Yu et al. 2015)....
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04 Sep 2017
TL;DR: The results indicated that the sediments from moderately eUTrophic and trophic lake had the higher bacterial diversity than lightly eutrophic lake, and temperature was the main factor influencing the bacterial community in the three lakes.
Abstract: Sediment microbial communities play an important role in lake trophic status. This study determined millions of Illumina reads (16S rRNA gene amplicons) to compare the bacterial communities in moderately eutrophic, lightly eutrophic, and moderately trophic regions using a technically consistent approach. The results indicated that the sediments from moderately eutrophic and trophic lake had the higher bacterial diversity than lightly eutrophic lake. Proteobacteria was the most abundant phylum (22.7%-86.2%) across samples from three regions. The sediments from moderately eutrophic region were enriched with Chloroflexi and Nitrospirae. Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes were enriched in the sediments from lightly eutrophic lake. The sediments from moderately trophic lake contained a high abundance of Acidobacteria and Deltaproteobacteria because of the low pH of the sediments in this lake. In moderately eutrophic region, Nitrospira held an absolute predominance, while Lysobacter and Flavobacterium were the most predominant genera in lightly eutrophic region. Temperature was the main factor influencing the bacterial community in the three lakes. The bacterial communities in the sediment samples obtained from moderately eutrophic lake were associated with nutrient concentration, whereas organic matter and total nitrogen contents mainly influenced the bacterial communities in sediments obtained from lightly eutrophic lake and moderately trophic lake, respectively.
66 citations
References
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TL;DR: A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original.
Abstract: The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSIBLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.
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Monograph•
01 May 2003TL;DR: In this article, a simple introduction to ordination methods and guidance on the correct interpretation of ordination diagrams is given for students and researchers dealing with complex ecological problems, such as the variation of biotic communities with environmental conditions or the response of Biotic communities to experimental manipulation.
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