A Systematics for Discovering the Fundamental Units of Bacterial Diversity
ABSTRACT Bacterial systematists face unique challenges when trying to identify ecologically meaningful units of biological diversity. Whereas plant and animal systematists are guided by a theory-based concept of species, microbiologists have yet to agree upon a set of ecological and evolutionary properties that will serve to define a bacterial species. Advances in molecular techniques have given us a glimpse of the tremendous diversity present within the microbial world, but significant work remains to be done in order to understand the ecological and evolutionary dynamics that can account for the origin, maintenance, and distribution of that diversity. We have developed a conceptual framework that uses ecological and evolutionary theory to identify the DNA sequence clusters most likely corresponding to the fundamental units of bacterial diversity. Taking into account diverse models of bacterial evolution, we argue that bacterial systematics should seek to identify ecologically distinct groups with evidence of a history of coexistence, as based on interpretation of sequence clusters. This would establish a theory-based species unit that holds the dynamic properties broadly attributed to species outside of microbiology.
SourceAvailable from: Nobuto Takeuchi[Show abstract] [Hide abstract]
ABSTRACT: Background Fixation of beneficial genes in bacteria and archaea (collectively, prokaryotes) is often believed to erase pre-existing genomic diversity through the hitchhiking effect, a phenomenon known as genome-wide selective sweep. Recent studies, however, indicate that beneficial genes spread through a prokaryotic population via recombination without causing genome-wide selective sweeps. These gene-specific selective sweeps seem to be at odds with the existing estimates of recombination rates in prokaryotes, which appear far too low to explain such phenomena. Results We use mathematical modeling to investigate potential solutions to this apparent paradox. Most microbes in nature evolve in heterogeneous, dynamic communities, in which ecological interactions can substantially impact evolution. Here, we focus on the effect of negative frequency-dependent selection (NFDS) such as caused by viral predation (kill-the-winner dynamics). The NFDS maintains multiple genotypes within a population, so that a gene beneficial to every individual would have to spread via recombination, hence a gene-specific selective sweep. However, gene loci affected by NFDS often are located in variable regions of microbial genomes that contain genes involved in the mobility of selfish genetic elements, such as integrases or transposases. Thus, the NFDS-affected loci are likely to experience elevated rates of recombination compared with the other loci. Consequently, these loci might be effectively unlinked from the rest of the genome, so that NFDS would be unable to prevent genome-wide selective sweeps. To address this problem, we analyzed population genetic models of selective sweeps in prokaryotes under NFDS. The results indicate that NFDS can cause gene-specific selective sweeps despite the effect of locally elevated recombination rates, provided NFDS affects more than one locus and the basal rate of recombination is sufficiently low. Although these conditions might seem to contradict the intuition that gene-specific selective sweeps require high recombination rates, they actually decrease the effective rate of recombination at loci affected by NFDS relative to the per-locus basal level, so that NFDS can cause gene-specific selective sweeps. Conclusion Because many free-living prokaryotes are likely to evolve under NFDS caused by ubiquitous viruses, gene-specific selective sweeps driven by NFDS are expected to be a major, general phenomenon in prokaryotic populations. Electronic supplementary material The online version of this article (doi:10.1186/s12915-015-0131-7) contains supplementary material, which is available to authorized users.BMC Biology 04/2015; 13(1). DOI:10.1186/s12915-015-0131-7 · 7.43 Impact Factor
Article: The Prokaryotic Biology of Soil[Show abstract] [Hide abstract]
ABSTRACT: Prokaryotes ('Bacteria' and 'Archaea') are the most dominant and diverse form of life in soil and are indispensable for soil ecology and Earth system processes. This review addresses and interrelates the breadth of microbial biology in the global context of soil biology primarily for a readership less familiar with (soil) microbiology. First, the basic properties of prokaryotes and their major differences to macro-organisms are introduced. Further, technologies to study soil microbiology such as high-throughput next-generation sequencing and associated computational challenges are addressed. A brief insight into the principles of microbial systematics and taxonomy is provided. Second, the complexity and activity of microbial communities and the principles of their assembly are discussed, with a focus on the spatial distance of a few µm which is the scale at which prokaryotes perceive their environment. The interactions of prokaryotes with plant roots and soil fauna such as earthworms are addressed. Further, the role, resistance and resilience of prokaryotic soil communities in the light of anthropogenic disturbances such as global warming, elevated CO 2 and massive nitrogen and phosphorous fertilization is discussed. Finally, current discussions triggered by the above-addressed complexity of microbes in soil on whether microbial ecology needs a theory that is different from that of macroecology are viewed. Keywords spatial microbial ecology | nutrient cycling | high-throughput sequencing | OTU | ecological theory
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ABSTRACT: Recent advances in studying the dynamics of marine microbial communities have shown that the composition of these communities follows predictable patterns and involves complex network interactions, which shed light on the underlying processes regulating these globally important organisms. Such 'holistic' (or organism- and system-based) studies of these communities complement popular reductionist, often culture-based, approaches for understanding organism function one gene or protein at a time. In this Review, we summarize our current understanding of marine microbial community dynamics at various scales, from hours to decades. We also explain how the data illustrate community resilience and seasonality, and reveal interactions among microorganisms.Nature Reviews Microbiology 02/2015; 13(3). DOI:10.1038/nrmicro3417 · 23.32 Impact Factor