Unifying ecology to include all creatures great and small

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    was a science in which field observations of organisms had from community ecology with tools from molecular micro-

    Editorial TRENDS in Ecology and Evolution Vol.21 No.9a central role. Microbial ecology, however, developed initi-ally from interests in agriculture, industry and medicine,with the principle approach being laboratory experimenta-tion on pure cultures. Ecological research with microbeshad to overcome substantial methodological obstacles(such as small size and lack of morphological detail) thatecological research with plants and animals did not.

    A significant communication barrier still exists todaybetween the disciplines, with different literatures andlanguages. Individuals truly bilingual in both microbialand general ecology are rare. The separation between thedisciplines is reinforced by the technical challenges thatmicrobial ecologists face. Most microorganisms cannot be

    bial ecology, our understanding of human health and dis-ease can be greatly improved. Finally, Whitaker andBanfield[3] describe the use of new genomic approaches toexplore microbial populations and to identify general pro-cesses that generate, structure and maintain genetic diver-sity. Together, these three articles describe a promisingapproach to the study of ecology, one that seeks to includeall creatures great and small.

    References1 Green, J. and Bohannan, B.J.M. (2006) Spatial scaling of microbialbiodiversity. Trends Ecol. Evol. 21, 501507

    2 Dethlefsen, L. et al. (2006) Assembly of the human intestinal microbiota.Trends Ecol. Evol. 21, 517523

    3 Whitaker, R.J. and Banfield, J.F. (2006) Population genomics in naturalmicrobial communities. Trends Ecol. Evol. 21, 508516

    Corresponding author: Bohannan, B.J.M. (bohannan@stanford.edu)Available online 21 July 2006.

    www.sciencedirect.com 0169-5347/$ see front matter 2006 Elsevier Ltd. All rights reserved. doi:10.1016/j.tree.2006.07.008Microbial ecology

    Unifying ecology tocreatures great andM. Claire Horner-Devine1 and Brendan J.M1School of Aquatic and Fishery Sciences, University of Washin2Department of Biological Sciences, Stanford University, Stanf

    Two ecologiesOne way in which researchers confront the complexity ofthe natural world is by dividing the study of nature amonga variety of different disciplines, each with its ownperspective, traditions and history. This can be a verypowerful approach, providing multiple, overlappingwindows on the natural world. However, disciplinessometimes become isolated from one another, which canact as an impediment to understanding as barriers tocommunication grow. The fields of microbial ecology andgeneral ecology (i.e. the traditional discipline of ecology)are an example of such a process. These fields have naturalcomplementary strengths that have become overshadowedby their separation over time. This has come at a cost toboth disciplines, denying microbial ecologists access to thetheoretical, conceptual and analytical tools developed bygeneral ecologists, and preventing general ecologists fromstudying the ecology of the dominant form of life on Earth,microorganisms. This themed issue of TREE featuresthree examples of microbial biodiversity research that isbridging the gap between these disciplines.

    Obstacles to unifying ecologyThere are both historical and technical reasons why thestudy of microbial ecology has become separated from thegeneral science of ecology. Although these disciplineshave a common beginning, rooted in the desire to under-stand the diversity of life, they diverged early in theirdevelopment. The science of general ecology developedas a subdiscipline of botany and zoology, heavily influencedby the naturalist tradition in these disciplines. As such, itinclude allsmallBohannan2

    n, Seattle, WA 98195, USA, CA 94305, USA

    distinguishedmorphologically in the field; neither can theybe studied in captivity. Determining the distribution andabundance of most microbes requires the use of molecularmarkers that range in their degree of taxonomic specificity.Because of the small size and short generation times ofmicroorganisms, it is more technically challenging(although not impossible) to study microbial ecology atthe scale of interacting individuals, and most microbialecology studies are of aggregate properties of communitiesat large relative spatial and temporal scales. The use ofsuch fundamentally different approaches in the two dis-ciplines can make it challenging to directly apply generalecological theories to microorganisms.

    Opportunities for unifying ecologyDespite these challenges, the separation betweenmicrobialand general ecology has narrowed in recent years. This isespecially true for the study ofmicrobial biodiversity, whererecent advances provide a unique opportunity to unify thescience of ecology by identifying ecological patterns andprocesses common to all forms of life. This themed issueofTREE highlights three of these new advances. Green andBohannan[1] discuss spatial patterns of biodiversity, a cen-tral issue in ecology, and highlight spatial scaling rules thatmightbe common toall formsof life.Althoughhumanhealthand disease have been at the forefront of microbiologyresearch sinceearly in itshistory, theapplicationof conceptsfrom general ecology is now opening new avenues forresearch in human health. Dethlefsen et al.[2] review thecurrent state of knowledge regarding themicrobial diversityof the human body and show that, by combining approaches