In This Article Expand or collapse the "in this article" section Microbial (Community) Ecology

  • Introduction
  • General Overviews
  • Foundational Texts
  • Journals
  • Databases

Ecology Microbial (Community) Ecology
Sang-Hoon Lee, Ashley Shade
  • LAST REVIEWED: 12 August 2022
  • LAST MODIFIED: 28 June 2016
  • DOI: 10.1093/obo/9780199830060-0153


Microorganisms, including bacteria, archaea, fungi, and microeukaryotes, serve as the biological foundations of every ecosystem on earth. These microorganisms are largely responsible for carbon and nutrient cycling (biogeochemical cycling), help their hosts to maintain health, contribute to biotechnological advances, produce food for humans, and serve as food for invertebrates and other meiofauna. However, no microorganism exists in isolation. Rather, they form communities of co-existing populations, interacting with one another and with their local environment. Because of their importance for ecosystem functions, understanding the ecology of microbial communities is a popular subject of study. Microbial communities exhibit patterns of spatial and temporal dynamics that, in many ways, mimic the patterns exhibited by larger organisms. One challenge to identifying large-scale patterns of microbial communities is that the majority of microorganisms are yet-uncultivable in the laboratory. Therefore, the field of microbial ecology often makes large leaps forward when new technologies become available that allow for improved observation of the microbial communities, inclusive of those organisms that cannot be cultured. The molecular era of microbial ecology, beginning with fingerprinting techniques, Sanger sequencing, and taxon-specific fluorescent probes, advanced observation of spatial and temporal patterns. Recently, near-continuous advances in high-throughput sequencing permit observation of the yet-uncultivable majority of microbial communities. These advances have corresponded with decreased costs, which has democratized accessibility of sequencing technology. The improved accessibility to high-throughput sequencing has allowed researchers to extend their studies to include more comprehensive spatial and temporal series than were collected previously. Thus, our documentation and understanding of spatial and temporal microbial community patterns has expanded dramatically in the 21st century. New tools, combined with broad approaches such as field studies, laboratory manipulations, in silico modeling and in vivo experiments, are employed by microbial ecologists to address outstanding fundamental questions in microbial ecology. In this article, we will focus on the methods of observing microbial communities, their spatial and temporal patterns, and their interactions with each other and with larger organisms.

General Overviews

Microbial communities contribute as much as 550 Pg of carbon biomass to the planet and, in soils alone, an estimated 1010 cells per cubic centimeter of soil (Whitman, et al. 1998 and Torsvik, et al. 2002, both cited under Patterns in Microbial Community Ecology: Defining and Measuring Diversity). Given these tremendous microbial contributions to life on earth, microbial ecology has established itself as a broad research field. Konopka 2009 aims to define the key ecological questions in the field of microbial ecology and distinguish it from other subdisciplines. Prosser, et al. 2007 provides a framework for microbial ecologists to pursue larger questions in traditional ecology that microbial systems provide advantage or insight over “macro” ecological systems. Written in the middle of the molecular renaissance, Schmidt 2006 reminds us that traditional cultivation and other tools for assaying community functions are not only relevant but also essential for developing an insightful and comprehensive understanding of microbial communities. Complementing Schmidt’s study is Allen and Banfield 2005, which projects the importance of genomic approaches in unraveling microbial ecology. Gonzalez, et al. 2011 and Robinson, et al. 2010 provide an ecological context specific to microbiomes (host-associated microbial communities, though the term “microbiome” is sometimes used simply to describe the microbial consortia of a particularly defined habitat, e.g., the “soil microbiome” or “hospital microbiome”). Poisot, et al. 2013 discusses a toolkit for ecological insights from high-throughput sequencing, and Larsen, et al. 2012 looks toward predictive models in microbial ecology.

  • Allen, Eric E., and Jillian F. Banfield. 2005. Community genomics in microbial ecology and evolution. Nature reviews Microbiology 3:489–498.

    DOI: 10.1038/nrmicro1157

    Provides perspectives on how microbial genomics can inform interpretation of patterns in microbial ecology, written at a time when genomics was becoming an accessible and widespread approach in the field.

  • Gonzalez, A., Jose C. Clemente, Ashley Shade, et al. 2011. Our microbial selves: What ecology can teach us. EMBO 12:775–784.

    DOI: 10.1038/embor.2011.137

    Introduces patterns of microbial communities associated with human bodies, seen through the lenses of ecological principles and models.

  • Konopka, Allan. 2009. What is microbial community ecology? ISME Journal 3:1223–1230.

    DOI: 10.1038/ismej.2009.88

    Defines microbial community ecology from the perspective of active or interacting microbial community members. In addition, this reference also introduces the definitions of microbial-scale ecosystems and interactions among the species-biotic forces.

  • Larsen, Peter, Yuki Hamada, and Jack Gilbert. 2012. Modeling microbial communities: Current, developing, and future technologies for predicting microbial community interaction. Journal of Biotechnology 160:17–24.

    DOI: 10.1016/j.jbiotec.2012.03.009

    Discusses current research in modeling microbial community contributions, including elusive member interactions, to earth’s geochemical cycles.

  • Poisot, Timothee, Berangere Pequin, and Dominique Gravel. 2013. High-throughput sequencing: A roadmap toward community ecology. Ecology and Evolution 3:1125–1139.

    DOI: 10.1002/ece3.508

    Provides perspectives on how microbial community and functional ecology can be improved by high-throughput sequencing techniques. In addition, this paper also introduces various traditional ecological theories for interpreting community dynamics.

  • Prosser, James I., J. M. Brendan, Tom P. Bohannan, et al. 2007. The role of ecological theory in microbial ecology. Nature Reviews Microbiology 5:384–392.

    DOI: 10.1038/nrmicro1643

    Provides ecological theories for better understanding microbial organization, structure, mechanistic insights, and predictive power using recently accumulated sequencing data.

  • Robinson, Courtney J., J. M. Brendan, Tom P. Bohannan, and Vincent B. Young. 2010. From structure to function: The ecology of host-associated microbial communities. Microbiology and Molecular Biology Reviews 74:453–476.

    DOI: 10.1128/MMBR.00014-10

    Introduces ecological framework for microbial communities that inhabit and interact with hosts.

  • Schmidt, Thomas M. 2006. The maturing of microbial ecology. International Microbiology 9:217–223.

    Introduced many scientists to the exceptional metabolic capacity of microbes and their remarkable ability to adapt to changing environments in “The Microbe’s Contribution to Biology.” This paper also provides an overview of the physiology and adaptability of microbes according to the various basic principles for the microbial ecology.

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