Abstract
Cells of Microcystis are associated with heterotrophic bacteria and organized in colonies in natural environment, which are basic elements in the mass occurrence of cyanobacterial species. Analyzing these colonies by using metagenomics is helpful to understand species composition and relationship. Meanwhile, the difference in population abundance among Microcystis colonies could be used to recover genome bins from metagenome assemblies. Herein, we designed a pipeline to obtain high-quality genomes of mutualistic bacteria from single natural Microcystis colonies. Single colonies were lysed, and then amplified by using multiple displacement amplification to overcome the DNA quantity limit. A two-step assembly was performed after sequencing and scaffolds were grouped into putative bins based on their differential-coverage among species. We analyzed six natural colonies of three prevailing Microcystis species from Lake Taihu. Clustering results proved that colonies of the same species were similar in the microbial community composition. Eight putative population genome bins with wide bacterial diversity and different GC content were identified based on coverage difference among colonies. At the phylum level, proteobacteria was the most abundant besides cyanobacteria. Six of the population bins were further refined into nearly complete genomes (completeness > 90%).
Highlights
Cyanobacterial blooms occur as a result of massive proliferation of cyanobacteria [1], and have become a worldwide environmental problem [2]
Microcystis cells are associated with heterotrophic bacteria and organized in colonies which vary in sizes and shapes [5]
We obtained eight population genome bins of the cohabitation bacteria which differed in abundance among M. aeruginosa, M. wesenbergii and M. panniformis colonies, and six of them were further refined into high-quality genomes
Summary
Cyanobacterial blooms occur as a result of massive proliferation of cyanobacteria [1], and have become a worldwide environmental problem [2]. To improve our understanding of the relationship within Microcystis colonies, genomes of representative heterotrophic bacteria are desired to be obtained. It is challenging to disassociate and purify these heterotrophic bacteria from Microcystis colonies and only a small portion of them is representable by cultivated organisms [8]. High-quality genomes of dominant populations have been assembled from relatively low-complexity communities using metagenomics [10,11]. The genomes of individual members are still not well assembled because the microbial communities of Microcystis blooms are high complex microorganism mixtures in natural freshwater. These mixtures contain different types of Microcystis colonies and some other planktonic microbial communities
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