Genetic diversity and population structure of the Bacillus cereus group bacteria from diverse marine environments

Yang Liu,Zongze Shao,Juan Du,Qiliang Lai

doi:10.1038/s41598-017-00817-1

Abstract

The phylogenetic diversity of marine bacteria belonged to the Bacillus cereus group has not been well investigated. Here, we present the genetic diversity and population structure of 71 bacteria from diverse marine environments, using a multilocus sequence typing (MLST) approach and the analyses of digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) based on some representative genomic sequences. The MLST analysis demonstrated that these isolates were highly diverse and a wide distribution in marine environments and some of them showed niche specificity to some extent. They were assigned to 27 sequence types (STs) with 23 novel STs. Phylogenetic analysis of 82 bacteria containing 11 type strains based on MLST discriminated them as 20 clusters including 10 new ones. Both the dDDH and ANI results supported the proposition that each of 20 clusters represented one independent species, including 10 putative novel species. Values of 98.3% of MLST similarity and 96.2% of ANI were proposed as the standard for the species definition of this group. In summary, the first insight into the phylogenetic diversity of the group bacteria from marine environments will contribute to better understanding of their ecological role and evolution in contrast with terrestrial environments.

Highlights

Bacillus cereus group comprises 11 closely related species, including the first described species B. anthracis, along with B. cereus, B. thuringiensis, B. mycoides, B. weihenstephanensis, B. pseudomycoides and the recently identified “B. gaemokensis”, “B. manliponensis”, B. cytotoxicus, B. toyonensis, “B. bingmayongensis” (Three species “B. gaemokensis”, “B. manliponensis” and “B. bingmayongensis” are effectively but not yet validly published and are in quotation marks throughout in this study)[1]
A considerable variation in the Ks ratios (Ka)/Ks ratio was observed in Table 2, suggesting that tpi and glpF were under higher selective pressure than gmk, ilvD, pta, purH and pycA
Bacteria of the B. cereus group are the subject of growing interest because of their considerable significance in agriculture and industry, especially in the area of food safety and health of human and animals[7]

Summary

Introduction

Bacillus cereus group comprises 11 closely related species, including the first described species B. anthracis, along with B. cereus, B. thuringiensis, B. mycoides, B. weihenstephanensis, B. pseudomycoides and the recently identified “B. gaemokensis”, “B. manliponensis”, B. cytotoxicus, B. toyonensis, “B. bingmayongensis” (Three species “B. gaemokensis”, “B. manliponensis” and “B. bingmayongensis” are effectively but not yet validly published and are in quotation marks throughout in this study)[1]. The bacteria of the B. cereus group occupy a wide range of habitats, ranging from soil to water and from plants and animals to food, probably owing to the metabolic diversity endowing them with ecological adaptation of different environments and strong survivability of spores allowing them to better withstand hostile conditions and to better disperse[19, 20] Their population structure and phylogenetic diversity in freshwater and terrestrial environments has been extensively investigated in recent years using several MLST schemes[14,15,16]. The aim of this study is to investigate the diversity and niche specificity of bacteria affiliated to the B. cereus group in marine environments by means of an MLST scheme, and to further elucidate their taxonomic position by measurements of dDDH and ANI, using 71 isolated strains together with 11 previously published type strains (Table 1)

Objectives

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Conclusion