Bacterial Diversity In The Sediment Of Chenghai Lake Of Yunnan Plateau

Sediments of lakes are important habitats, in which, there are many kinds of microorganism’s participation and substances frequently exchanged. Microbial communities play important roles in nutrient recycling and decomposition of chemical compounds in freshwater sediments. Sediment biogeochemical properties provide niches for metabolically diversity microorganisms. Changes of the environmental factors, can influence microbial community structure in the sediment environments。 Therefore, investigations of bacterial communities and their diversity in freshwater sediments will greatly enhance our understanding of the aquatic ecosystem.The objective of this research was to study the bacterial community composition and diversity in Chenghai Lake sediments. An integrated approach was employed cultivation-independent approachs including DGGE fingerprint and16S rDNA clone sequencing and cultivation-dependent method. The abundant bacterial communities of six Chenghai Lake sediments were compared and discussed; at the same time, the relationships between bacterial community compositions and environmental factors were to be investigated. The results of this study expand our current understanding of microbial ecology in Yunnan Plateau Lakes.The result of bacterial DGGE fingerprint shows that, there are high bacterial abundance and diversity in Chenghai Lake sediments. Cluster analysis based on abundances and diversity revealed that bacterial communities in the14sediment samples from Chenghai Lake could be clustered into three groups. Then, we selected6representative sediment samples to carry out further study on the bacteria diversity using an integrated approach including16S rDNA clone sequencing and cultivation method.RDP classifier analysis based on16S rDNA clone sequences indicated that2715clone sequences from6sediment samples collected from Chenghai Lake could be classified as nineteen bacterial phyla:Actinobacteria, Chloroflexi, Firmicutes, Cyanobacteria, Acidobacteria, Verrucomcrobia, Planctomycetes, Bacteroidetes, Proteobacteria, Armatimonadetes, Caldiserica, Deferribacteres, Gemmatimonadetes, Spirochaetes, Chlorobi, Nitrospira, Elusimicrobia, and two Candidates WS3and TM7Chloroflexi, Betaproteobacteria, Deltaproteobacteria, Gammaproteobacteria and Firmicutes are dominant groups and present in all Chenghai Lake sediments. There are only24OTU of666OTU were present in all six sediment samples. the Cluster analysis and PCoA analysis based on abundances at the species-level revealed that bacterial communities differences in the6sediment samples from Chenghai Lake, the number six sediment samples has the highest bacteria abundance and diversity. The relative abundances of Actinobacteria Planctomycetes, Alphaproteobacteria and Chlorobi in Chenghai Lake sediments were significantly correlated with total phosphorus. RDA result demonstrated that the changes of TP could have significant effect on members of bacteria in Chenghai Lake.The bacterial diversity and correlated with abiotic factors in the sediments of Chenghai Lake were also researched by using454pyrosequencing.The pyrosequencing analysis of16S rRNA gene amplicons from six sediment samples produced38977reads, leaving30506reads after quality filtering and removal of chimeric sequences. The average sequence length was of433nucleotides, excluding the adaptor and barcode primer sequences. The sequences could be assigned to4802operational taxonomic units. Of our filtered sequences, we found24different bacterial phyla across all sediment samples with the Silva alignment. Proteobacteria and Chloroflexi were the most abundant phylum across all samples.The highest diversity was found in No.6sediment samples and the lowest diversity in No.5sediment sample by using species richness, coverage and diversity estimations. Pearson correlation and RDA result demonstrated that the changes of TP could have significant effect on bacterial communities in sediments of Chenghai Lake.Despite our454pyrosequencing reads being an order of magnitude larger than their corresponding clone sequences, similar dominant bacterial community and similar correlations with environmental abiotic factors were obtained.Based on the analysis results of cultivation-independent approach and environmental factors, we selected or designed four media to isolate the bacterial strains from the6sediment samples of Chenghai Lake. Phylogenetic analysis based on16S rRNA gene sequence indicated that the isolates could be classified into one hundred and forty-eight genomic species, including eleven potential novel species, the16S rRNA gene sequence of most isolates are different from their phylogenetic neighbours. These isolates belong to sixty genera of thirty-four families(Aerococcaceae, Alcaligenaceae, Bacillaceae, Caulobacteraceae, Cellulomonadaceae, Corynebacteraceae, Rhodobacteriaceae, Cyclobacteriaceae, Dermabacteraceae, Dermacoccaceae, Dietziaceae, Enterobacteriaceae, Flavobacteraceae, Intrasporangiaceae, Jiangellaceae, Methylobacteraceae, Microbacteriaceae, Micrococcaceae, Micromonosporaceae, Moraxellaceae, Mycobacteraceae, Nocardiaceae, Nocardioidaceae, Paenibacillaceae, Promicromonosporaceae, Pseudomonadaceae, Pseudonocardiaceae, Rhodobacteriaceae, Sphingobacteriaceae, Sphingomonadaceae, Staphylococcaceae, Streptomycetaceae, Streptosporangiaceae and Xanthomonadaceae) in four bacteria phyla(Actinobacteria, Proteobacteria, Firmicutes and Bacteriodetes). The results presented above shown that there are abundant bacterial diversity and potential novel taxa in sediments of Chenghai Lake.We detected24bacteria phyla using cultivation-independent approach and isolated4bacterial phyla strains using cultivation-dependent method. However, some isolates is not found using cultivation-independent method. The result proves that the strategies we selected were suitable for the cultivation of these microorganisms, but also reveals the sequencing depth our selected can not reflect the entire microorganism in the environment. In all, cultivation-independent method cannot replace cultivation-dependent method. Only using an integrated approach including cultivation-indpendent and cultivation-dependent methods, we can comprehensive and systematic understand the bacterial diversity in the sediments of Chenghai Lake.