Jennifer B. Hughes

Counting the Uncountable: Statistical Approaches to Estimating Microbial Diversity

All biologists who sample natural communities are plagued with the problem of how well a sample reflects a communitys “true” diversity. New genetic techniques have revealed extensive microbial diversity that was previously undetected with culture-dependent methods and morphological

A taxa-area relationship for bacteria.

A positive power-law relationship between the number of species in an area and the size of that area has been observed repeatedly in plant and animal communities. This species–area relationship, thought to be one of the few laws in ecology, is fundamental to our understanding of the distribution of global biodiversity. However, such a relationship has not been reported for bacteria, and little is known regarding the spatial distribution of bacteria, relative to what is known of plants and animals. Here we describe a taxa–area relationship for bacteria over a scale of centimetres to hundreds of metres in salt marsh sediments. We found that bacterial communities located close together were more similar in composition than communities located farther apart, and we used the decay of community similarity with distance to show that bacteria can exhibit a taxa–area relationship. This relationship was driven primarily by environmental heterogeneity rather than geographic distance or plant composition.

New approaches to analyzing microbial biodiversity data.

Modern molecular techniques have revealed an extraordinary diversity of microorganisms, most of which are as yet uncharacterized. This poses a major challenge to microbial ecologists: how can one compare the microbial diversity of different environments when the vast majority of microbial taxa are usually unknown? Three statistical approaches developed by ecologists and evolutionary biologists--parametric estimation, nonparametric estimation and community phylogenetics--are proving to be promising tools to meet this challenge. The combination of these tools with molecular biology techniques allow the rigorous estimation and comparison of microbial diversity in different environments.

Trade-offs and coexistence in microbial microcosms.

Trade-offs among the abilities of organisms to respond to different environmental factors are often assumed to play a major role in the coexistence of species. There has been extensive theoretical study of the role of such trade-offs in ecological communities but it has proven difficult to study such trade-offs experimentally. Microorganisms are ideal model systems with which to experimentally study the causes and consequences of ecological trade-offs. In model communities of E. coli B and T-type bacteriophage, a trade-off in E. coli between resistance to bacteriophage and competitive ability is often observed. This trade-off can allow the coexistence of different ecological types of E. coli. The magnitude of this trade-off affects, in predictable ways, the structure, dynamics and response to environmental change of these communities. Genetic factors, environmental factors, and gene-by-environment interactions determine the magnitude of this trade-off. Environmental control of the magnitude of trade-offs represents one avenue by which environmental change can alter community properties such as invasability, stability and coexistence.

The application of rarefaction techniques to molecular inventories of microbial diversity

With the growing capacity to inventory microbial community diversity, the need for statistical methods to compare community inventories is also growing. Several approaches have been proposed for comparing the diversity of microbial communities: some adapted from traditional ecology and others designed specifically for molecular inventories of microbes. Rarefaction is one statistical method that is commonly applied in microbial studies, and this chapter discusses the procedure and its advantages and disadvantages. Rarefaction compares observed taxon richness at a standardized sampling effort using confidence intervals. Special emphasis is placed here on the need for precise, rather than unbiased, estimation methods in microbial ecology, but precision can be judged only with a very large sample or with multiple samples drawn from a single community. With low sample sizes, rarefaction curves also have the potential to lead to incorrect rankings of relative species richness, but this chapter discusses a new method with the potential to address this problem. Finally, this chapter shows how rarefaction can be applied to the comparison of the taxonomic similarity of microbial communities.

Knowledge and the environment

Some recent analyses suggest that future increases in knowledge will, more or less automatically, alleviate or even eliminate future environmental problems. Here we examine this issue. First, we discuss whether a knowledge explosion is indeed occurring, addressing some of the problems with assessing knowledge-growth. We next consider whether growth in knowledge will help the environment; we ask whether future advances in knowledge are likely to assure benign environmental outcomes, and discuss physical limitations of reducing resource consumption. Finally, we outline policy interventions that would help produce and implement environmentally helpful knowledge. Although knowledge-growth can help attenuate future environmental problems, we are skeptical as to the ability of advances in knowledge to offset fully the adverse environmental impacts of continued growth of population and per-capita consumption. The ongoing shift from a material-based to a services-based economy reduces, but does not eliminate, the significant environmental impacts associated with the increasing scale of economic output. In addition, the ability of the economy to replace certain key natural resource inputs with knowledge inputs must eventually encounter limits. Public policy has a crucial role both in discouraging environmentally damaging forms of consumption, and in promoting the generation and diffusion of environmentally beneficial knowledge.

The scale of resource specialization and the distribution and abundance of lycaenid butterflies

Abstract Numerous hypotheses have been proposed for the commonly observed, positive relationship between local abundance and geographic distribution in groups of closely related species. Here I consider how hostplant specialization and abundance affect the relative abundance and distribution of lycaenid butterflies (Lepidoptera: Lycaenidae). I first discuss three components of specialization: local specialization, turnover of specialization across a species’ range, and the minimum number of resources (or habitats) required by a species. Within this framework, I then consider one dimension of a lycaenid species’ niche, larval hostplant specialization. In a subalpine region of Colorado, I surveyed 11 lycaenid species and their hostplants at 17 sites. I compare this local information to continental hostplant use and large-scale distributions of the lycaenids and their hostplants. Local abundance of a lycaenid species is positively correlated with its local distribution (the number of sites occupied), but not with its regional or continental distribution. Neither local specialization (the number of hostplants used within one habitat) nor continental specialization (the number of hostplants used across many habitats) is correlated with local lycaenid abundance. Continental specialization is positively correlated with a species’ continental distribution, however. Finally, while generalist butterflies tend to have more hostplant available to them, differences in resource availability do not explain the differences in butterfly abundance. Although local abundance is correlated only with local distribution, I suggest that abundance-distribution relationships might emerge at regional and continental scales if local abundance were averaged across many habitat types. Consideration of the scale of a species’ resource specialization (within or among habitats) appears to be key to understanding the relationships between resource specialization, resource availability, and a species’ abundance and distribution.

Merging perspectives on biodiversity and ecosystem functioning

The Biodiversity and Ecosystem Functioning: Synthesis and Perspectives conference was held in Paris, France, from 6 to 9 December 2000.

Using the Genome to Understand Pathogenicity

Genome sequencing, the determination of the complete complement of DNA in an organism, is revolutionizing all aspects of the biological sciences. Genome sequences make available for scientific scrutiny the complete genetic capacity of an organism. With respect to microbes, this means we now have the unprecedented opportunity to investigate the molecular basis of commensal and virulence behavior. We now have genome sequences for a wide range of bacterial pathogens (obligate, facultative, and opportunistic); this has facilitated the discovery of many previously unidentified determinants of pathogenicity and has provided novel insights into what creates a pathogen. In-depth analyses of bacterial genomes are also providing new perspectives on bacterial physiology, molecular adaptation to a preferred niche, and genomic susceptibility to the uptake of foreign DNA, three key factors that can play a significant role in determining whether a species, or a strain, will have pathogenic potential.