Microbial Ecological Theory: Current Perspectives
"thought-provoking ... a useful reference book" (Microbiol. Today)
"insightful contributions" (ASM Microbe)
Caister Academic Press
Lesley A. Ogilvie and Penny R. Hirsch
University of Brighton, UK and Rothamsted Research, Harpenden, UK (respectively)
viii + 112
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The vast explosion of high-resolution molecular data in the past few years has provided an unprecedented glimpse into the microbial world. This book synthesises current viewpoints and knowledge on microbial ecological theory. The editors have assembled a collection of essays by a diverse group of well-respected scientists who merge the boundaries of ecology and microbiology to explore some of the central tenets of macro-ecological theory with a microbial perspective. The contributors explore the mainstays of macro-ecology asking questions such as 'do microbes have biogeography?' and 'does a microbial species concept exist?', as well as showing how high-resolution molecular data is informing and underpinning the evolution of microbial ecological theory. The authors demonstrate how the application of macro-ecological theory to the microbial world is not only enhancing our understanding of microbial ecology but also providing a reference point for the development of new theories.
Written for graduate students and academic researchers, the book aims to encourage cross-disciplinary thinking and provide direction and perspective on the still fledgling field of microbial ecological theory. This volume is highly recommended for all microbiology libraries.
"well-written essays to explore a number of microbial ecological theories from population genetic and evolution theory to microbial biogeography ... The academic content of this volume is robust and the questions posted are thought-provoking ... definitely a useful reference book for scientists" from Microbiology Today (2013)
"insightful contributions from both theoretically minded "macro-ecologists" and more experimentally driven "micro-ecologists" in a volume useful to micro- and macro-ecologists ... the book does an excellent job connecting the recent proliferation of microbial genomic data with long-standing macro- ecological theories ... the six chapters of this well-written volume provide a concise review of state-of-the-art genomic and macro-ecological principles" from ASM Microbe (2013) 8, 298-299.
Table of contents
1. Genome-based and Functional Differentiation: Hallmarks of Microbial Adaptation, Divergence and Speciation?
The recent application of high-throughput molecular biology methods to natural microbial communities is profoundly changing our view on the microbial world. In particular, our understanding of microbial population-level differentiation involved in ecological adaptation that leads to microbial divergence and speciation has been profoundly altered. Numerous processes that underlie microbial differentiation have been identified but determining the relative significance of these processes remains challenging. For example, a major unresolved question is how much of observed genetic heterogeneity is due to neutral versus adaptive processes. Sequence-based and modelling analyses suggest that much of the observed variation is neutral but recent functional "meta-OMIC" data suggest that at least some of this fine-scale variation is functionally relevant and, thus, involved in adaption and divergence. From the limited amount of largely disjointed metagenomic and functional data obtained to date, extensive intra- and inter-system as well as extensive intra- and inter-population differences are apparent. Consequently, it is difficult to ascertain specific molecular patterns that define specific microbial groups that would be congruent with the definition of a microbial species. Future concomitant analysis of community genomic complements, transcriptomes, proteomes and metabolomes over relevant spatial and temporal scales will result in detailed molecular descriptions of distinct taxonomic entities. Such a system-level molecular organismal classification system will need to be solidly grounded in ecological theory, population genetic theory and evolutionary theory, and may be universally applicable to the three domains of life.
2. The Human-microbe Coevolutionary Continuum
Lesley A. Ogilvie, Andrew D.J. Overall and Brian V. Jones
Humans enter into a range of symbioses with resident and transiently colonising microbes, which span a dynamic continuum from antagonistic to mutualistic. These interactions are shaped by a complex set of selective forces, which include both host and microbially-derived selective pressures. Given the significant impact that both resident and pathogenic microbes can have on our health, there is now a move to develop a theoretical framework that may guide studies of human-microbe interactions. This should enable the deeper level of understanding required to model, predict and ultimately control human diseases related to antagonistic or aberrant host-microbe interactions. Here we explore the human-microbe coevolutionary continuum in the context of current and emerging theory, and with a focus on the opposite ends of the spectrum: mutualism and antagonism. In doing so we highlight areas in which theory is helping to enhance the understanding of this dynamic continuum and where current theory fails as well as suggesting future avenues of research.
3. Mutualism: Plant-microorganism Interactions
Penny R Hirsch and Tim H. Mauchline
Mutualism is responsible for the genesis of green plants and is implicated in their colonisation of land. Current knowledge of plant-microorganism symbioses includes a range of associations with different degrees of intimacy and mutual dependence but the mutual benefits are not always clear. Complex signalling is involved when the plant immune system recognises beneficial endosymbionts although many have also evolved mechanisms to evade or moderate plant defence pathways. A wide range of bacteria inhabit intercellular spaces but only a few are true endosymbionts able to penetrate living cells whilst remaining membrane-bound, accessing plant carbon compounds in a manner analogous to biotrophic pathogens. Unlike pathogens, they provide nutrients to the plant in exchange. The best-known examples are rhizobia, bacteria that induce root nodules on leguminous plants and fix atmospheric nitrogen; and arbuscular mycorrhizal fungi that sequester phosphate and organic N from soil and provide it to their plant hosts. Both secrete factors prior to contacting plant cells which appear to prepare the hosts for mutual rather than pathogenic interactions and suppress the defence mechanisms. The processes involved in these symbioses are compared to less intimate interactions and the nature of mutualism is discussed.
4. A Bird's Eye View of Microbial Community Dynamics
Zhanshan (Sam) Ma, Jiawei Geng, Zaid Abdo and Larry J. Forney
Microbial community dynamics is one of the most important central themes of microbial community ecology, which seems to be experiencing its first golden era thanks to the rapidly expanding datasets derived using metagenomic and other ‘-omics' methods in microbial biology. For example, much of the ongoing NIH-HMP (Human Microbiome Project) focus has been centered on the dynamics of human microbiome communities. Microbial ecologists are beginning to actively draw upon ecological theories from macro ecology to study microbial communities. In this article, we present a brief review on several selected topics of ecological theories that are most relevant to community dynamics, including the diversity-stability paradigm, intermediate disturbance hypothesis (IDH), species area/time curves (SAT), species abundance distribution (SAD), and neutral community theory. In perspective, we suggest that the study of microbial community dynamics can not only benefit from applying ecological theories originally developed in macro ecology, but also contribute to the development and testing of new ecological theories. These bidirectional interactions are of critical importance to the flourishing of theoretical microbial ecology, and studies of microbial community dynamics offers tremendous opportunities for these intellectual exchanges to occur.
5. Species-time Relationships for Bacteria
Anna Oliver, Andrew K. Lilley and Christopher J. van der Gast
The identification of spatial patterns and their relationships to ecological events is an important specialization within ecology which is now branching into the microbial world. In spatial ecology, the detection of patterns at a given spatial scale can be used to explain ecological mechanisms and processes. Furthermore, through the application of spatial statistical analyses, factors leading to ecological events can be determined and verified. One of the most commonly studied aspects of spatial ecology, recently applied in microbial ecology, is the species-area relationship (SAR). The temporal analogue of the SAR, the species-time relationship (STR), on the other hand has received far less attention, even in the science of general ecology. Like SARs, the STRs are influenced by a variety of factors including dispersal, abiotic and biotic interactions, and species-species interactions. The application of these ecological conceptual tools to microbial ecology is a rapidly developing field. This chapter proposes that the STRs are a powerful and appropriate tool for studies of microbial diversity and that they make a contribution to understanding ecological communities. From a fundamental perspective, we focus on how microbial STRs compare with those for animals and plant communities, and how they are improving our understanding of community assembly and dynamics. As we believe a key future importance of studying STRs will be for applied benefit, we also discuss how microbial STRs have been used to distinguish between anthropogenic perturbations and underlying natural dynamics and have provided ecological insights for clinical benefit in bacterial infections.
6. Microbial Biogeography: Is Everything Small Everywhere?
Diego Fontaneto and Joaquín Hortal
The distribution of microscopic organisms (that is, those smaller than 2 mm) has been historically considered non relevant for biogeography, because of the idea that due to their small size, dispersal abilities, resting stages and quick reproductive rates, the presence of microscopic organisms in any place was not limited by geographical barriers and distances. Recent studies challenge this idea, and provide theoretical and empirical evidence in support of the existence of spatial patterns at different scales, and of biogeographical processes affecting many groups of microscopic organisms. Here we review the current state of the art for microbial biogeography, summarising sources of problems and misconceptions, but also their solutions advancing the general understanding of biogeography, and conclude suggesting new avenues for future research.
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(EAN: 9781908230096 9781908230713 Subjects: [microbiology] [bacteriology] [environmental microbiology] )