Ecologists have long studied the relationship between biotic composition and ecosystem functioning in larger organisms; however, only recently has this relationship been investigated widely in microorganisms. Recent studies are reviewed within a framework of three experimental approaches that are often used to study larger organisms: environmental treatment, common garden, and reciprocal transplant experiments. Although the composition of microorganisms cannot be easily manipulated in the field, applying these approaches to intact microbial communities can begin to tease apart the effects of microbial composition from environmental parameters on ecosystem functioning. The challenges in applying these approaches to microorganisms are highlighted and it is discussed how the experimental approach and duration affects a study's interpretation. In general, long-term environmental treatment experiments identify correlative relationships between microbial composition and ecosystem functioning, whereas short-term common garden experiments demonstrate that microbial composition influences ecosystem functioning. Finally, reciprocal transplants simultaneously test for interactive effects of the environment and composition on functioning. The studies reviewed provide evidence that, at least in some cases, microbial composition influences ecosystem functioning. It is concluded that whole-community experiments offer a way to test whether information about microbial composition will help predict ecosystem responses to global change.

Although microorganisms largely drive many ecosystem processes, the relationship between microbial composition and their functioning remains unclear. To tease apart the effects of composition and the environment directly, microbial composition must be manipulated and maintained, ideally in a natural ecosystem. In this study, we aimed to test whether variability in microbial composition affects functional processes in a field setting, by reciprocally transplanting riverbed sediments between low-and high-salinity locations along the Nonesuch River (Maine, USA). We placed the sediments into microbial 'cages' to prevent the migration of microorganisms, while allowing the sediments to experience the abiotic conditions of the surroundings. We performed two experiments, short-(1 week) and long-term (7 weeks) reciprocal transplants, after which we assayed a variety of functional processes in the cages. In both experiments, we examined the composition of bacteria generally (targeting the 16S rDNA gene) and sulfate-reducing bacteria (SRB) specifically (targeting the dsrAB gene) using terminal restriction fragment length polymorphism (T-RFLP). In the short-term experiment, sediment processes (CO 2 production, CH 4 flux, nitrification and enzyme activities) depended on both the sediment's origin (reflecting differences in microbial composition between salt and freshwater sediments) and the surrounding environment. In the long-term experiment, general bacterial composition (but not SRB composition) shifted in response to their new environment, and this composition was significantly correlated with sediment functioning. Further, sediment origin had a diminished effect, relative to the short-term experiment, on sediment processes. Overall, this study provides direct evidence that microbial composition directly affects functional processes in these sediments.

Many successful exotic invasive species are functionally distinct from the dominant native species they displace. Occasionally invasion occurs where the exotic species possesses functional traits relatively similar to those of the dominant native. We examined the ecological consequences of such an invasion within a mesic, temperate grassland at the Konza Prairie Long‐Term Ecological Research site. We assessed potential changes in carbon (C) and nitrogen (N) cycling and plant diversity following the invasion of a C4 bunch grass species, Andropogon bladhii, into a tallgrass prairie dominated by the native C4 grass species, A. gerardii. In these prairies burning is an important management tool used to maintain native‐species dominance. We determined how frequent spring fires affected the impacts of A. bladhii in this system. Over a two‐year study our results show that burning regulated the effects that the invasive species has on the native prairie. Compared to the native species, A. bladhii exhibited significantly greater plant biomass, significantly lower pools of soil N, significantly lower rates of decay and C cycling, and higher foliar and root tissue C:N ratio in response to burning. Notable spatial heterogeneity in C and N cycling was evident in areas dominated by the invasive bunch grass. In addition to altered ecosystem processes, areas dominated by the invasive, A. bladhii, had significantly lower plant species diversity. In a grassland ecosystem where burning is an important management tool for controlling exotic‐species establishment, maintaining native‐species dominance, and increasing productivity, A. bladhii may be able to successfully out‐compete the native C4 grass species by using traits typically used to explain the dominance of the native species. With frequent fire, the invasive species has the potential to decrease long‐term fertility by lowering N inputs in litter and increasing erosion in non‐vegetated soil between bunches, while also having a negative effect on plant diversity. By using fire to promote native C4 grasses and maintain these tallgrass prairies, the threat of invasion by nonnative C4 species may raise a dilemma for future management of these C4 grasslands.

Ammonia oxidation is a central process in the nitrogen cycle. Particularly in marine and estuarine environments, few experiments have been conducted to tease apart the factors influencing their abundance and composition. To investigate the effect of nitrogen and phosphorus availability on ammonia-oxidizing bacteria (AOB), we conducted a nutrient enrichment experiment in a Maine salt marsh and sampled sediment communities in three seasons over 2 years. We assessed community composition using terminal restriction fragment length polymorphism analysis and sequencing of cloned fragments of the ammonia monooxygenase (amoA) gene. Almost all of the amoA sequences fell within the marine and estuarine-specific Nitrosospira-like clade. Applied separately, nitrogen and phosphorus significantly altered AOB composition; however, together the nutrients had an interactive effect, and composition did not change. In contrast, nutrient enrichment did not alter AOB abundance. Furthermore, the response of AOB composition to nutrient enrichment varied over time. We conclude that closely related taxa within the marine/estuarine-specific Nitrosospira-like clade vary in their preference for nutrient concentrations, and this preference may depend on other temporally variable abiotic factors. Finally, AOB composition was highly variable within and across years even in untreated plots. Further studies are needed to test how these different aspects of compositional variability in AOB communities influence nitrogen cycling.

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