Bacterial competition: surviving and thriving in the microbial jungle
TL;DR: A growing body of theoretical and experimental population studies indicates that the interactions within and between bacterial species can have a profound impact on the outcome of competition in nature.
Abstract: Most natural environments harbour a stunningly diverse collection of microbial species. In these communities, bacteria compete with their neighbours for space and resources. Laboratory experiments with pure and mixed cultures have revealed many active mechanisms by which bacteria can impair or kill other microorganisms. In addition, a growing body of theoretical and experimental population studies indicates that the interactions within and between bacterial species can have a profound impact on the outcome of competition in nature. The next challenge is to integrate the findings of these laboratory and theoretical studies and to evaluate the predictions that they generate in more natural settings.
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TL;DR: Insights into the underlying structural principles of indigenous microbial phyllosphere populations will help to develop a deeper understanding of the phyllospheric microbiota and will have applications in the promotion of plant growth and plant protection.
Abstract: Our knowledge of the microbiology of the phyllosphere, or the aerial parts of plants, has historically lagged behind our knowledge of the microbiology of the rhizosphere, or the below-ground habitat of plants, particularly with respect to fundamental questions such as which microorganisms are present and what they do there. In recent years, however, this has begun to change. Cultivation-independent studies have revealed that a few bacterial phyla predominate in the phyllosphere of different plants and that plant factors are involved in shaping these phyllosphere communities, which feature specific adaptations and exhibit multipartite relationships both with host plants and among community members. Insights into the underlying structural principles of indigenous microbial phyllosphere populations will help us to develop a deeper understanding of the phyllosphere microbiota and will have applications in the promotion of plant growth and plant protection.
1,450 citations
TL;DR: This Review highlights mechanisms that have evolved in microorganisms to allow them to successfully enter and exit a dormant state, and discusses the implications of microbial seed banks for evolutionary dynamics, population persistence, maintenance of biodiversity, and the stability of ecosystem processes.
Abstract: Dormancy is a bet-hedging strategy used by a wide range of taxa, including microorganisms. It refers to an organism's ability to enter a reversible state of low metabolic activity when faced with unfavourable environmental conditions. Dormant microorganisms generate a seed bank, which comprises individuals that are capable of being resuscitated following environmental change. In this Review, we highlight mechanisms that have evolved in microorganisms to allow them to successfully enter and exit a dormant state, and discuss the implications of microbial seed banks for evolutionary dynamics, population persistence, maintenance of biodiversity, and the stability of ecosystem processes.
1,399 citations
Cites background from "Bacterial competition: surviving an..."
...Microbial growth in these habitats is characterized by boom and bust population cycles owing to fluctuations in environmental variables, rapid depletion of growth-limiting resources, and interspecific interactions such as competition and predatio...
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TL;DR: A new freshwater lake phylogeny constructed from all published 16S rRNA gene sequences from lake epilimnia is presented and a unifying vocabulary to discuss freshwater taxa is proposed, providing a coherent framework for future studies.
Abstract: Freshwater bacteria are at the hub of biogeochemical cycles and control water quality in lakes. Despite this, little is known about the identity and ecology of functionally significant lake bacteria. Molecular studies have identified many abundant lake bacteria, but there is a large variation in the taxonomic or phylogenetic breadths among the methods used for this exploration. Because of this, an inconsistent and overlapping naming structure has developed for freshwater bacteria, creating a significant obstacle to identifying coherent ecological traits among these groups. A discourse that unites the field is sorely needed. Here we present a new freshwater lake phylogeny constructed from all published 16S rRNA gene sequences from lake epilimnia and propose a unifying vocabulary to discuss freshwater taxa. With this new vocabulary in place, we review the current information on the ecology, ecophysiology, and distribution of lake bacteria and highlight newly identified phylotypes. In the second part of our review, we conduct meta-analyses on the compiled data, identifying distribution patterns for bacterial phylotypes among biomes and across environmental gradients in lakes. We conclude by emphasizing the role that this review can play in providing a coherent framework for future studies.
1,230 citations
TL;DR: Both patterns are unlikely to be the result of ecological drift, but are inevitable emergent properties of open microbial systems resulting mainly from biotic interactions and environmental and spatial processes.
Abstract: Microbial communities often exhibit incredible taxonomic diversity, raising questions regarding the mechanisms enabling species coexistence and the role of this diversity in community functioning. On the one hand, many coexisting but taxonomically distinct microorganisms can encode the same energy-yielding metabolic functions, and this functional redundancy contrasts with the expectation that species should occupy distinct metabolic niches. On the other hand, the identity of taxa encoding each function can vary substantially across space or time with little effect on the function, and this taxonomic variability is frequently thought to result from ecological drift between equivalent organisms. Here, we synthesize the powerful paradigm emerging from these two patterns, connecting the roles of function, functional redundancy and taxonomy in microbial systems. We conclude that both patterns are unlikely to be the result of ecological drift, but are inevitable emergent properties of open microbial systems resulting mainly from biotic interactions and environmental and spatial processes.
790 citations
TL;DR: How the spatial arrangement of genotypes within a community influences the cooperative and competitive cell–cell interactions that define biofilm form and function is discussed.
Abstract: Bacteria often live within matrix-embedded communities, termed biofilms, which are now understood to be a major mode of microbial life. The study of biofilms has revealed their vast complexity both in terms of resident species composition and phenotypic diversity. Despite this complexity, theoretical and experimental work in the past decade has identified common principles for understanding microbial biofilms. In this Review, we discuss how the spatial arrangement of genotypes within a community influences the cooperative and competitive cell-cell interactions that define biofilm form and function. Furthermore, we argue that a perspective rooted in ecology and evolution is fundamental to progress in microbiology.
699 citations
References
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01 Jan 1975TL;DR: Ressenya de l'obra d'E. O. Wilson apareguda el 1975, Sociobiology. The New Synthesis.The Belknap Press of Harvard University Press.
Abstract: Ressenya de l'obra d'E. O. Wilson apareguda el 1975, Sociobiology. The New Synthesis .The Belknap Press of Harvard University Press.
6,126 citations
TL;DR: Bacterial growth is considered as a method for the study of bacterial physiology and biochemistry, with the interpretation of quantitative data referring to bacterial growth limited to populations considered genetically homogeneous.
Abstract: The study of the growth of bacterial cultures does not constitute a specialized subject or branch of research: it is the basic method of Microbiology. It would be a foolish enterprise, and doomed to failure, to attempt reviewing briefly a \"subject\" which covers actually our whole discipline. Unless, of course, we considered the formal laws of growth for their own sake, an approach which has repeatedly proved sterile. In the present review we shall consider bacterial growth as a method for the study of bacterial physiology and biochemistry. More precisely, we shall concern ourselves with the quantitative aspects of the method, with the interpretation of quantitative data referring to bacterial growth. Furthermore, we shall considerz exclusively the positive phases of growth, since the study of bacterial \"death,\" i.e., of the negative phases of growth, involves distinct problems and methods. The discussion will be limited to populations considered genetically homogeneous. The problems of mutation and selection in growing cultures have been excellently dealt with in recent review articles by Delbriick (1) and Luria (2). No attempt is made at reviewing the literature on a subject which, as we have just seen, is not really a subject at all. The papers and results quoted have been selected as illustrations of the points discussed.
4,104 citations
TL;DR: It is shown that bacterial communities of deep water masses of the North Atlantic and diffuse flow hydrothermal vents are one to two orders of magnitude more complex than previously reported for any microbial environment.
Abstract: The evolution of marine microbes over billions of years predicts that the composition of microbial communities should be much greater than the published estimates of a few thousand distinct kinds of microbes per liter of seawater. By adopting a massively parallel tag sequencing strategy, we show that bacterial communities of deep water masses of the North Atlantic and diffuse flow hydrothermal vents are one to two orders of magnitude more complex than previously reported for any microbial environment. A relatively small number of different populations dominate all samples, but thousands of low-abundance populations account for most of the observed phylogenetic diversity. This "rare biosphere" is very ancient and may represent a nearly inexhaustible source of genomic innovation. Members of the rare biosphere are highly divergent from each other and, at different times in earth's history, may have had a profound impact on shaping planetary processes.
3,535 citations
TL;DR: In this review, taking an evolutionary perspective, important discoveries over the last decade about the plant immune response are highlighted.
2,668 citations
2,598 citations