With the development of improved analytical tools, microbial ecologists are now able to assess microbial community structure with respect to fine-scale gradients of light, temperature, salinity, electron acceptors and donors, and relate genetically distinguishable organisms to specific environmental conditions. These studies directly address issues such as Hutchinson's 'paradox of the plankton', which questions the anomalous coexistence of species ostensibly using the same resources in apparently homogeneous environments without competitive exclusion. Communities of prochlorophytes (oxygenic photosyn-thetic bacteria) in oceanic surface waters are structured by light intensity, whereas coexisting giant sulfur-oxidizing bacteria from the genus Achromatium in freshwater sediments are structured by redox gradients (Figure 5) and their subtly different requirements for nitrate.
Although some environmental factors, or perturbations, play a role in maintaining diversity, for example, plant diversity and plant growth in soil, others engender the loss of diversity, for example, land management and environmental pollution. A high degree of ecological redundancy appears to be a feature of microbial communities; consequently, loss of diversity per se does not necessarily affect ecosystem function but diversity and functional redundancy appear to be important for the maintenance of resistance and resilience to environmental perturbation.
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20 40 60 80 Relative representation of A. oxaliferum lineages (%)
Figure 5 (a) Depth profiles of Achromatium cells, (b) redox-sensitive chemical species (Fe2+ and SO2-), and (c) the relative abundance of three Achromatium lineages identified using FISH in a sediment core from Rydal Water, UK. The trend lines show a three-point moving average of the data, and error bars represent 95% confidence intervals for counts of the Achromatium subpopulations. Reproduced from Gray ND, Howarth R, Rowan A, et al. (1999) Natural communities of Achromatium oxaliferum comprise genetically, morphologically, and ecologically distinct sub-populations. Applied and Environmental Microbiology 65: 5089-5099.
Habitat heterogeneity has long been invoked to explain the higher microbial species diversity in heterogeneous environments such as soils. Comparisons of species richness and diversity indices based on analysis of 16S rRNA sequences recovered from environmental samples have shown that spatial isolation and resource heterogeneity play an important role in maintaining bacterial diversity. Soils with low moisture content harbor bacterial communities with higher diversity than soils with a high moisture content where there is greater connectivity and opportunity for competition between coexisting bacteria.
Spatial patterns in the distribution of species have long been a staple of general ecology. However, this is an area steeped in controversy in the microbial world. This is principally a result of the assumption that small cell size, large population size, and ease of dispersal will result in microbial taxa having a cosmopolitan distribution. Accordingly, local microbial community structure is a result of selection of particular taxa on the basis of environmental fitness from the global pool of microbial species. This hypothesis was first proposed in 1934 by Bass Becking and summed up by the phrase ''everything is everywhere, the environment selects.'' It follows that functional diversity must also have a ubiquitous distribution. This view is supported by the observation that a high proportion of the global diversity of ciliates and other protozoans can be detected in any extensive survey of local diversity. These studies have been based on identification of morphospecies which are known to obscure a wealth of genetic diversity. There is good evidence for the occurrence of endemic prokaryotes in soil, hot springs, and other environments. The arguments for and against the occurrence of endemic microrganisms are clouded by classical models of allopatric speciation based on geographical isolation of two populations followed by genetic divergence and ultimately speciation. This is in reality a special case of a more general formulation where allopatric speciation can occur if the rate of genetic divergence is greater than the rate of dispersal. This general model can explain the occurrence of ende-mism in microbial species even in the absence of obvious geographical barriers to dispersal. It is likely that as with other organisms there will be globally abundant organisms that are more or less cosmopolitan and rarer organisms that are more likely to exhibit more rapid evolution than dispersal and hence exhibit endemism.
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