Perspective

Microbial Ecology: Searching for Principles

The extraordinary diversity of microbial ecosystems complicates efforts to develop principles encompassing microbial ecology
Allan Konopka

odern microbial ecology spans approximately 50 years. Although Martinus Beijerinck and Sergei Winogradsky both thought about ecological niches in the early part of the 20th century, they approached the challenge by trying to cultivate microbes under simulated natural conditions. Hence, I consider Robert Hungate the rst truly modern microbial ecologist. Focusing on rumen microbes, he and his colleagues dealt directly with the ecosystem of these microorganisms. Instead of limiting their efforts to isolating and identifying microorganisms of the rumen, Hungate and his collaborators also measured their activities in situ. In 1966, Hungate published The Rumen and its Microbes, synthesizing years of research to better understand that ecosystem. Microbial ecology has grown substantially since then. For instance, more than 2,200 mem-

bers of ASM consider the microbial ecology division their primary or secondary afliation. Interest on the international scale is also striking. This growth in interest continues to spur a great deal of research, expanding our breadth of detailed knowledge about many different microbial ecosystems. However, this growth in interest has not led to a synthesis of the eld as a whole. The last overarching view of microbial ecology was published 40 years ago by Thomas Brock in the inuential book, Principles of Microbial Ecology. Thus, it is time to reexamine the key principles of microbial ecology. Analytic Tools Expand Knowledge, Necessitating a Review of Principles As in other elds of science, new technologies stimulate ecology research, and ecologists have proved adept at adopting analytic tools from other elds. For instance, radioisotopes came into use during the early 1950s for use in determining in situ ux rates in a wide variety of ecosystems. Microbial ecologists during the 1980s learned through microelectrode-based analyses that microbes deal with gradients on very small distance scales. Meanwhile beginning in the mid-1980s, Norman Pace and his many collaborators began applying molecular biology techniques to study microbial ecosystems. Those efforts continue to build momentum, providing a wealth of insights into the distribution and natural history of microbes. These and other powerful analytic techniques are being applied to the extraordinary diversity of habitats occupied by microbes. Faced with the wealth of specic information gained from these studies, there are solid reasons for reviewing the principles underlying microbial ecology.

Summary Amid recent growth in knowledge about microbial ecology, it is time to reexamine key principles and to identify new ones.

Identifying the principles of microbial ecology

will benet students entering this eld, and could lead to better cooperation with ecologists working in related elds.

To understand the interactions of a microbe

with its environment, one should consider the immediate microenvironment before assessing its wider dynamic effects.

Developing an ecotype concept would benet

microbial systematics and microbial ecology, and will depend on cooperation among physiologists, ecologists, and bioinformaticists.

Allan Konopka is Professor of Biological Sciences in the Department of Biological Sciences, Purdue University, West Lafayette, Ind. akonopka@purdue .edu

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Spatial Scales of Microbial Ecology

Global and landscape scale Aquatic and terrestrial biomes Macroscopic scalePhysical/chemical/biological interactions within ecosystems. Aquatic systems: planktonic vs. benthic habitats Terrestrial systems: saturated vs. unsaturated soils Macroorganism-associated ecosystems: tissue-specic habitats Microscopic scaleSystem dynamics near and within a microbial cell

For one thing, such a review will provide a better framework for young scientists when they begin to evaluate the idiosyncrasies of particular systems that they may be studying. This effort will benet not only those who are considered card-carrying microbial ecologists, but also scientists in allied elds. Communicating the principles of microbial ecology to colleagues who study macrobiota also could have an impact on general ecological theory, and could help to better identify areas where microbial ecology should develop independently. Further, a statement of principles provides a framework for evaluating what may be novel in an exceptional system and can lead to a deeper understanding of a eld. In the case of microbial ecology, developing a statement of principles is perhaps more difcult than in other areas of microbiology because of the extraordinary diversity of microbial ecosystems. In other elds, a critical mass of scientists focuses on a model system. The synergy among them can lead to rapid developments and the evolution of fundamental principles. For example, many fundamental principles of molecular genetics and transcriptional regulation arose from an intense focus on studying Escherichia coli. Because microbial ecology research programs are being supported by several funding agencies with different missions, that sharp focus on a single entity is not likely to be repeated. Hence, microbial ecologists will need to consider how best to synthesize phenomena and to search for fundamental principles among disparate ecosystems. Dening the Boundaries of Microbial Ecology The 19th-century German biologist Ernst Haeckel coined the term oekologie, based in part on

the Greek word for house, to describe the study of organisms in the context of their households in nature. Because microbial ecologists study interactions of microbes with their abiotic and biotic environments, their focus differs somewhat from those who study environmental microbiology or pure microbial diversity. Although the study of microbial diversity has important implications for evolution, systematics, biotechnology, and ecology, it is distinct from microbial ecology. Ecological studies examine not only the natural history of a microbe, including its distribution and abundance in relationship to its environment, but also investigate the mechanisms underlying its distribution. One very important implication of Haeckels denition is that the authentic ecology of microbes occurs on spatial scales of nanometers to micrometers. Nonetheless, microbial activities can affect the environment on a much larger scale because ecological systems operate on so many different scales. Microbial ecology can be viewed as a study of these different (yet interconnected) systems (see box, above). In the last decade, the term systems biology has been applied to the study of complex processes at the organism level; however, those studying ecology analyze complex systems that similarly embody emergent properties. Living and abiotic processes affect one another at the global and landscape scales. For example, arid conditions in the African desert can stimulate iron-limited photosynthesis when iron-containing dust particles are transported over thousands of kilometers to distant oceanic sites. At the ecosystem level, there are complex and complementary interactions among physical, chemical, and biological components. However, to understand the interactions of a microbe with its environment, one should rst consider the immediate microenvironment (Fig. 1). By focusing on this scale, we can describe the important physical and chemical characteristics of a minimum set of microbial ecosystems (see table). However, it is apparent that some characteristics overlap. For example, a planktonic microbe in the metalimnion, or mid-layer, of a thermally stratied lake may exploit vertical gradients of nutrients however, the gradients have a spatial scale of meters rather than the millimeters typical of a microbial mat. Importantly, one should not lose sight of the dynamic

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impact of microbial activity, even if it appears to be conned to a microscopic system. Those dynamics often produce effects at the macroscopic and landscape levels.

FIGURE 1

Overarching Principles for Microbial Ecology One means for uncovering the principles of microbial ecology entails envisioning how microorganisms interact with their environments at the microscopic scale. The principles then can be divided into three groups overarching themes, population ecology, and physiological ecology. Microbes comprise nearly half of all biomass on earth. All habitats suitable for plants and animals also harbor microbial populations. In addition, some microbes are adapted to grow under physical and chemical conditions that are too extreme for plant and animal growth. The primary role of microbes in the biosphere is as catalysts of biogeochemical cycles. That is, microbes mediate kinetically inhibited but therProcesses at the microenvironment scale. modynamically favorable reactions. Some microbes may also have strong effects on the ecology of specic micro- or macro-organisms, via metabolize broad ranges of substrates. Complex their roles as pathogens or symbionts. microbial communities contain metabolically difThe effects of microbial catalysis on the rates of ferent populations, whose diversity provides resilchemical and energy ow through an ecosystem ience in the face of environmental perturbations, depend upon the population size of microbes reducing the chance that extreme conditions will the number of catalystsand the physiological kill all the species performing a particular ecoactivity of those microbes (as determined by logical function. Microbial populations are caextant physical and chemical conditions). In stable ecosystems, small numbers of microbes can still produce signicant effects Microbial-scale ecosystems over geological time spans. Ecosystem type Examples Characteristics The results of microbial catalysis can have Planktonic Open ocean, lakes Oligotroph lifestyle; highprofound effects on the physical and chemiafnity uptake of multiple cal characteristics of the macroenvironment. nutrients However, microbial activity is determined by the physical and chemical characteristics Surface associated Freshwater and ocean Gradient lifestyle; (saturated water) sediments, hydrodynamic processes and of the microenvironment, which is measured subsurface uid ow determine nutrient on a micrometer scale. sediments, microbial uxes; biomass density Microbes exhibit greater metabolic versamats, biolms affects gradient steepness tility than do macroorganisms. This versatilSurface associated Surface and vadose Water availability limits ity is expressed in at least four different (unsaturated water) zone soils activity and dispersal; ways. Microbes can use essentially all redormancy; patchy nutrient distribution duced chemicals on earth as an energy source provided that the oxidation of a specic chemMacroorganism associated Gastrointestinal tract, Co-evolution; specic ical can be coupled to reduction of a terminal rhizosphere, epiphytes molecular interactions with surface associated molecules electron acceptor in a thermodynamically favorable reaction. Some microorganisms

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pable of rapid evolutionary responses to environmental perturbations as a result of mechanisms that generate relatively high mutation frequencies as well as horizontal gene transfers across large phylogenetic boundaries. Population Ecology The types and numbers of different microbes present in a habitat are a function of the diversity and amounts of nutrient resources available, modulated by the organisms ability to withstand forces that eliminate it from the habitat. Loss forces may be biotic, involving predators or parasites; physical, such as ushing or scouring actions; or physiological, such as a lack of nutrients. Microbial populations may exhibit larger dynamics in biomass, composition, and activity than do plant and animal populations. These complex, nonequilibrium dynamics are consequences of several factors, including the temporal frequency of changes in important environmental factors, the rapid pace of physiological adaptation by microbes to changing environmental conditions, positive and negative interactions between different microbes, and the capacity for rapid genetic change. An important consequence of these population-based principles is that neither environmental nor biological factors by themselves determine the observed temporal changes in microbial populations. Instead, those changes typically depend on intricate interactions among these factors. Physiological Ecology Shortages of a single essential resource are sufcient to limit the microbial biomass that accumulates in a particular ecosystem. This principle restates the law of the minimum, which German scientist Justus von Liebig formulated during the 19th century. Any nutrient resource that microbes take up may be conserved as part of the biomass, used as an energy source and terminal electron acceptor, or can function as both a component of biomass and a source for energy. In the ecology of macroorganisms, the case in which nutrient resources determine the level of biomass is termed bottom-up control. Nutrient resources are not limiting in top-down controlled systems because a predator or parasite maintains the biomass level below the carrying capacity of the system.

Growth of microbes on the limiting nutrient (or a set of nutrients) will depress its concentration to a value that limits microbial growth rate. The real limitation is upon the rate of nutrient transport into the cytoplasm. Hydrodynamics or mass transport may limit the nutrient ux rate in an ecosystem. Competition among microbes for low concentrations of a limiting nutrient and temporal variability in its availability both serve as strong selective forces in natural habitats. Physiological and morphological characteristics can have adaptive value under specic conditions. Those variants may include the number, diversity, and afnity of transporters in cell membranes; regulation of the capacity to take up nutrients; cell size, due to the change in surface area to volume that impacts capacities for substrate uptake versus assimilation; types of storage polymers; metabolic versatility; motility and chemotaxis; and capacity to survive during nutrient shortages. The cell surface interacts critically with the external environment. This interaction affects nutrient uptake and metabolite excretion, signaling between cells, and both specic or nonspecic interactions with biotic and abiotic surfaces. The Relationship of Macroorganismal Ecology to Microbial Ecology Many principles that were developed with the ecology of plants and animals in mind also apply to microbes. Microbial ecosystems can provide advantages for researchers who are testing ecological theories that would be difcult to address through experiments involving plants or animals. Both microbial and macro-scale ecologists have recognized that professional interactions have not been as effective as possible; therefore, renewed efforts to develop mutual awareness would benet both areas of ecology. However, in at least two areas, the principles of macroorganism ecology do not readily apply to microbial ecology. One such area is community ecology, in which the analysis of interactions of organisms at different trophic levels via food-web analysis is an important component. With the exception of the microbial loop in aquatic ecosystems, microbial ecologists have not focused on trophic-level interactions. However, microbial ecologists are becoming increasingly aware of the impact of viruses as predators on microbes.

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The other area, which focuses on the effects of the environment on evolutionary developmental biology, is still a relatively new one for ecologists who study plants and animalsin part, accounting for why it is not yet a subject for microbial ecologists. However, because some populations of microbessuch as those in biolmsare multicellular, they could be examined from this perspective. Missing Principles, Implications for the Future of Microbial Ecology Some areas of research in microbial ecology do not lend themselves to the framing of general principles either because there is no consensus regarding experimental observations or because no fundamental concept has emerged. In particular, it is problematic to formulate concepts regarding species diversity and the effects of time, space, and environmental heterogeneities upon diversity patterns. These difculties reect a continuing ambivalence as to what constitutes a bacterial species. In an ecological context, this ambivalence revolves around the difculty in dening an ecotypea genetically cohesive population whose functional ecology is distinct from others. Analysis of genome sequences illuminates the nature of the problemsequences of multiple strains from one bacterial species may differ substantially from one another. Strains appear to gain or lose genetic modules, and those changes can substantially alter their respective physiological
ACKNOWLEDGMENTS

properties. How then does a microbial ecologist assess functional diversity in a habitat? During the 1970s and 1980s, microbial ecologists made signicant progress in determining rates of microbial activities in natural habitats. Despite that progress, they found it difcult to determine which particular microorganisms were most important in catalyzing reactions within those habitats. Over the past 15 years, however, microbial ecologists have made enormous progress determining the breadth of microbial diversity in nature, albeit without simultaneously analyzing physiological processes. These two separate lines of inquiry need to fuse, and there are new experimental strategies for doing so. For instance, physiological and nucleic acid-based techniques can be combined to identify the microbes in natural habitats that catalyze biogeochemical processes. The most pressing concerns come from those areas where principles are missing because we lack fundamental concepts. For instance, we cannot understand functional diversity without rst agreeing on what biological units to study. Ecological insights might be combined with multilocus nucleotide sequence analyses to provide a path towards dening ecotypes. Developing an ecotype concept would benet microbial systematics and microbial ecology, and will depend on a partnership developing between physiological ecologists and bioinformaticists. Genome sequences arrive at a breathtaking rate. Can our understanding of the physiological responses of microbes to their environments keep pace?

I thank Jim Fredrickson, Mike Madigan, Brian Oakley, Jim Staley, and Dave Ward for their comments and discussion. SUGGESTED READING Andrews, J. H. 1991. Comparative ecology of microorganisms and macroorganisms. Springer, New York. Andrews, J. H. 1998. Bacteria as modular organisms. Annu. Rev. Microbiol. 52:105126. Brock, T. D. 1966. Principles of microbial ecology. Prentice-Hall, Englewood Cliffs, N.J. Gevers, D., F. M. Cohan, J. G. Lawrence, B. G. Spratt, T. Coenye, E. J. Feil, E. Stackebrandt, Y. Van de Peer, P. Vandamme, F. L. Thompson, and J. Swings. 2005. Re-evaluating prokaryotic species. Nature Rev. Microbiol. 3:733739. Madsen, E. L. 2005. Identifying microorganisms responsible for ecologically signicant biogeochemical processes. Nature Rev. Microbiol. 3:439 446. Olsen, G. J., D. J. Lane, S. J. Giovannoni, N. R. Pace, and D. A. Stahl. 1986. Microbial ecology and evolution: a ribosomal RNA approach. Annu. Rev. Microbiol. 40:337365. Rossello-Mora, R., and R. Amann. 2001. The species concept for prokaryotes. FEMS Microbiol. Rev. 25:39 67. Weinbauer, M. G. 2004. Ecology of prokaryotic viruses. FEMS Microbiol. Rev. 28:127181. Whitman, W. B., D. C. Coleman, and W. J. Wiebe. 1998. Prokaryotes: the unseen majority. Proc. Natl. Acad. Sci. USA 95:6578 6583.

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