The Bacteria and Archaea are the most genetically diverse superkingdoms of life, and techniques for exploring that diversity are only just becoming widespread. Taxonomists classify these organisms into species in much the same way as they classify eukaryotes, but differences in their biology-including horizontal gene transfer between distantly related taxa and variable rates of homologous recombination-mean that we still do not understand what a bacterial species is. This is not merely a semantic question; evolutionary theory should be able to explain why species exist at all levels of the tree of life, and we need to be able to define species for practical applications in industry, agriculture, and medicine. Recent studies have emphasized the need to combine genetic diversity and distinct ecology in an attempt to define species in a coherent and convincing fashion. The resulting data may help to discriminate among the many theories of prokaryotic species that have been produced to date.
"The urgency of this issue has been highlighted over the last decade, as advances in sequencing technology prompted a boom in the study of microbial diversity in natural environments       . In the microbial world, the partitioning problem is intensified by the prevalence of asexual reproduction and horizontal gene transfer  . Nevertheless, the currently dominant view in the field is that the partitioned community assumption, while conceptually problematic, is operationally necessary    . "
[Show abstract][Hide abstract] ABSTRACT: Most of classical theoretical ecology is based on the assumption that
organisms in a community can be naturally partitioned into groups of
individuals that can be treated as identical. At the same time, mounting
experimental evidence from studies of microbial communities raises the
intriguing question whether this intuition is an accurate description of the
microbial world. This work builds on Mac Arthur's model of competitive
coexistence on multiple resources to construct a framework that does not rely
on postulated existence of species as fundamental ecological variables. In one
parameter regime, effective "species" with a core and accessory genome
naturally appear in this model as emergent concepts. However, the same model
allows a smooth transition to a highly diverse regime where the species
formalism becomes inadequate. An alternative description is proposed based on
the dynamical modes of population fluctuations. This approach provides a
naturally hierarchical description of community dynamics which is well-defined
even when the species description breaks down. The relevance of this framework
for understanding the complexity of naturally observed microbial communities is
"Also, the genomes would be altered greatly while microbiota survive at various niches in rhizosphere. The environmental gradients in rhizosphere could maintain complex niches, where the accessory genomes of microbial strains have been altered greatly (Fraser et al. 2009). "
[Show abstract][Hide abstract] ABSTRACT: AimsThe response of microbial metagenome to polycyclic aromatic hydrocarbons (PAHs) degradation in the rice rhizosphere remains poorly understood. We investigated the spatial and temporal variations of microbial communities and reconstructed metagenomes along the rice rhizosphere gradient during PAHs degradation.Methods and ResultsThe experiment was performed in rhizoboxes, in which the rhizosphere region was divided into five 1-mm thick layers. Based on denaturant gradient gel electrophoresis profiling and sequencing of bacterial and archaeal 16S rRNA genes, predicted metagenomes were reconstructed. The microbial communities in the rice rhizosphere were influenced by the PAHs concentration and distance from the root surface during PAHs degradation. Correlation network analysis showed that archaea played an important role in PAHs degradation. Predicted metagenomes can be clustered into two groups with high and low PAHs degrading potential, respectively. The relative abundance of genes for defense mechanisms, replication, recombination and reparation was significantly higher in samples with high PAHs degrading potentials. The relative abundance of the dioxygenase gene was greater near the root surface of the rice. However, the abundance of aldolase and dehydrogenase was constant in rhizosphere soils at different distances from the root surface.Conclusions
Distance from root surface and PAH concentrations affected the microbial communities and metagenomes in rice rhizosphere. The abundance of dioxygenase genes relating to PAH degradation in metagenomes mirrored the PAH degradation potential in rice rhizosphere.Significance and Impact of the StudyOur findings suggested that the predicted metagenomes reconstructed from 16S rRNA marker gene sequences provide further insights into the spatial variation and dynamics of microbial functioning that occur during bioremediation.
"Even more, it is noteworthy that at least one population of each genus presented evidence of expansion that was statistically supported. In clonal and free-living populations of bacteria, evolutionary models predict that populations experience strong fluctuations, either by selective sweeps or by metapopulation dynamics (Fraser et al., 2009; Kopac & Cohan, 2011; Shapiro & Polz, 2014). The results obtained in this study can be explained by these models since the analyzed lineages come from a natural setting and present no evidence of recombination (Table S2; Roberts & Cohan, 1995; Spiers, Buckling & Rainey, 2000; Rebollar et al., 2012). "
[Show abstract][Hide abstract] ABSTRACT: Comparative population studies can help elucidate the influence of historical events upon current patterns of biodiversity among taxa that coexist in a given geographic area. In particular, comparative assessments derived from population genetics and coalescent theory have been used to investigate population dynamics of bacterial pathogens in order to understand disease epidemics. In contrast, and despite the ecological relevance of non-host associated and naturally occurring bacteria, there is little understanding of the processes determining their diversity. Here we analyzed the patterns of genetic diversity in coexisting populations of three genera of bacteria (Bacillus, Exiguobacterium, and Pseudomonas) that are abundant in the aquatic systems of the Cuatro Cienegas Basin, Mexico. We tested the hypothesis that a common habitat leaves a signature upon the genetic variation present in bacterial populations, independent of phylogenetic relationships. We used multilocus markers to assess genetic diversity and (1) performed comparative phylogenetic analyses, (2) described the genetic structure of bacterial populations, (3) calculated descriptive parameters of genetic diversity, (4) performed neutrality tests, and (5) conducted coalescent-based historical reconstructions. Our results show a trend of synchronic expansions across most populations independent of both lineage and sampling site. Thus, we provide empirical evidence supporting the analysis of coexisting bacterial lineages in natural environments to advance our understanding of bacterial evolution beyond medical or health-related microbes.
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