Genomic Heterogeneity and Ecological Speciation within One Subspecies of Bacillus subtilis

Abstract

bClosely related bacterial genomes usually differ in gene content, suggesting that nearly every strain in nature may be ecologically unique. We have tested this hypothesis by sequencing the genomes of extremely close relatives within a recognized taxon and analyzing the genomes for evidence of ecological distinctness. We compared the genomes of four Death Valley isolates plus the laboratory strain W23, all previously classified as Bacillus subtilis subsp. spizizenii and hypothesized through multilocus analysis to be members of the same ecotype (an ecologically homogeneous population), named putative ecotype 15 (PE15). These strains showed a history of positive selection on amino acid sequences in 38 genes. Each of the strains was under a different regimen of positive selection, suggesting that each strain is ecologically unique and represents a distinct ecological speciation event. The rate of speciation appears to be much faster than can be resolved with multilocus sequencing. Each PE15 strain contained unique genes known to confer a function for bacteria. Remarkably, no unique gene conferred a metabolic system or subsystem function that was not already present in all the PE15 strains sampled. Thus, the origin of ecotypes within this clade shows no evidence of qualitative divergence in the set of resources utilized. Ecotype formation within this clade is consistent with the nanoniche model of bacterial speciation, in which ecotypes use the same set of resources but in different proportions, and genetic cohesion extends beyond a single ecotype to the set of ecotypes utilizing the same resources.

Species concepts and speciation factors in cyanobacteria, with connection to the problems of diversity and classification

“…Hanage et al 2005;Konstantinidis and Tiedje 2005;Hanage 2013), because they lack ecologically or genetically coherent groups. Such ''fuzziness'' might be apparent in ambiguous ecological boundaries among species, which was suggested by Cohan and Perry (2007) and Kopac et al (2014). For cyanobacteria, the most obvious phenotypic features (i.e.…”

“…Cohesion might not necessarily be the key factor for the existence of species delimitations, and Kopac et al (2014) proposed ecological differences among ecotypes as key features. They suggest that ecotypes exist indefinitely, but lineages within ecotypes are changing.…”

“…Similar considerations may be obtained from the investigations on the marine planktic genera Synechococcus and Prochlorococcus (Johnson et al 2006) or fine-scale distribution of marine Vibrionaceae (Preheim et al 2011). On the other hand, Kopac et al (2014) analyzed all orthologous genes within Bacillus subtilis and showed that MLSA was insufficient to distinguish ecotypes, which are considered as species in this paper.…”

“…It often contains genes specific to some environment with a large portion of unannotated gene families without any known function (e.g. Shi and Falkowski 2008), which putatively plays an important role in rapidly changing environments (Rodriguez-Valera et al 2009) and niche partitioning among close relatives (Kopac et al 2014). The shell genome genes do not seem to be randomly dispersed over the chromosome, but rather concentrated within genomic islands with frequent HGT and HR events (Hacker and Carniel 2001;RodriguezValera et al 2009).…”

Isolation, screening and growth optimization of antagonistic Bacillus subtilis MS21 from Thengapattanam estuary against plant fungal pathogens

“…High genetic heterogeneity of different Bacillus species (Choudhary andJohri, 2009 andKopac et al, 2014) particularly B. subtilis allows to suggest that search and identification of new strains from different sources may expand the number of practically important strains and to improve our understanding of mechanisms involved in antagonistic interactions. Antifungal action of Bacillus metabolites may be due to disruption of fungal cell wall and inhibition of normal conidia development (Fujiwara et al, 2013).…”