Are natural microcosms useful model systems for ecology?

Several recent, high-impact ecological studies feature natural microcosms as tools for testing effects of fragmentation, metacommunity theory or links between biodiversity and ecosystem processes. These studies combine the microcosm advantages of small size, short generation times, contained structure and hierarchical spatial arrangement with advantages of field studies: natural environmental variance, 'openness' and realistic species combinations with shared evolutionary histories. This enables tests of theory pertaining to spatial and temporal dynamics, for example, the effects of neighboring communities on local diversity, or the effects of biodiversity on ecosystem function. Using examples, we comment on the position of natural microcosms in the roster of ecological research strategies and tools. We conclude that natural microcosms are as versatile as artificial microcosms, but as complex and biologically realistic as other natural systems. Research to date combined with inherent attributes of natural microcosms make them strong candidate model systems for ecology.     

On the reproducibility of microcosm experiments - different community composition in parallel phototrophic biofilm microcosms

Phototrophic biofilms were cultivated simultaneously using the same inoculum in three identical flow-lane microcosms located in different laboratories. The growth rates of the biofilms were similar in the different microcosms, but denaturing gradient gel electrophoresis (DGGE) analysis of both 16S and 18S rRNA gene fragments showed that the communities developed differently in terms of species richness and community composition. One microcosm was dominated by Microcoleus and Phormidium species, the second microcosm was dominated by Synechocystis and Phormidium species, and the third microcosm was dominated by Microcoleus- and Planktothrix- affiliated species. No clear effect of light intensity on the cyanobacterial community composition was observed. In addition, DGGE profiles obtained from the cultivated biofilms showed a low resemblance with the profiles derived from the inoculum. These findings demonstrate that validation of reproducibility is essential for the use of microcosm systems in microbial ecology studies.     

Evolutionary community ecology of plant-associated arthropods in terrestrial ecosystems

In the 21st century, researchers have attempted a synthesis between community ecology and evolutionary biology. This emerging research area, which aims to synthesize community ecology and evolutionary biology, is evolutionary community ecology. Evolutionary community ecology addresses how intraspecific trait variation in community members is essential for predicting community properties and, how community properties are a key component of the selective forces that determine genetic and phenotypic variation in a community member. In this paper, I review recent findings in evolutionary community ecology in plant-associated arthropods in terrestrial ecosystems. I discuss roles of both genetic variation and phenotypic plasticity as a source of trait variation in plants in shaping plant-associated arthropod communities. Also, I discuss effects of genetic variation in herbivores on plant-associated arthropod communities. Furthermore, I highlight community context evolution in which multiple species interactions and community composition affect trait evolution of a community member. Finally, I argue that future studies should investigate a feedback loop between community and evolutionary dynamics beyond unidirectional studies on effects of evolution on a community or vice versa. This approach will provide major insights into mechanistic principles for making predictions of community ecology.     

Patterns in Species Persistence and Biomass Production in Soil Microcosms Recovering from a Disturbance Reject a Neutral Hypothesis for Bacterial Community Assembly

The neutral theory of biodiversity has emerged as a major null hypothesis in community ecology. The neutral theory may sufficiently well explain the structuring of microbial communities as the extremely high microbial diversity has led to an expectation of high ecological equivalence among species. To address this possibility, we worked with microcosms of two soils; the microcosms were either exposed, or not, to a dilution disturbance which reduces community sizes and removes some very rare species. After incubation for recovery, changes in bacterial species composition in microcosms compared with the source soils were assessed by pyrosequencing of bacterial 16S rRNA genes. Our assays could detect species with a proportional abundance ≥ 0.0001 in each community, and changes in the abundances of these species should have occurred during the recovery growth, but not be caused by the disturbance per se. The undisturbed microcosms showed slight changes in bacterial species diversity and composition, with a small number of initially low-abundance species going extinct. In microcosms recovering from the disturbance, however, species diversity decreased dramatically (by > 50%); and in most cases there was not a positive relationship between species initial abundance and their chance of persistence. Furthermore, a positive relationship between species richness and community biomass was observed in microcosms of one soil, but not in those of the other soil. The results are not consistent with a neutral hypothesis that predicts a positive abundance-persistence relationship and a null effect of diversity on ecosystem functioning. Adaptation mechanisms, in particular those associated with species interactions including facilitation and predation, may provide better explanations.     

The distribution and activity of sulphate reducing bacteria in estuarine and coastal marine sediments

Sulphate-reducing bacteria (SRB) play a vital role both the carbon and sulphur cycles and thus are extremely important components of the global microbial community. However, it is clear that the ecology, the distribution and activity of different SRB groups is poorly understood. Probing of rRNA suggests that different sediments have distinctly different patterns of SRB with complex factors controlling the activity of these organisms. The linking of community structure and function using sediment slurry microcosms suggests that certain groups of SRB, e.g., Desulfobacter and Desulfobulbus, can be linked to the use of specific substrates in situ. However, it is still unclear what environmental substrates are utilised by the majority of known SRBs. The work to date has greatly enhanced our understanding of the ecology of these organisms and is beginning to suggest patterns in their distribution and activity that may be relevant to understanding microbial ecology in general. This revised version was published online in August 2006 with corrections to the Cover Date.     

Microbial ecology of chlorinated solvent biodegradation

This study focused on the microbial ecology of tetrachloroethene (PCE) degradation to trichloroethene, cis‐1,2‐dichloroethene and vinyl chloride to evaluate the relationship between the microbial community and the potential accumulation or degradation of these toxic metabolites. Multiple soil microcosms supplied with different organic substrates were artificially contaminated with PCE. A thymidine analogue, bromodeoxyuridine (BrdU), was added to the microcosms and incorporated into the DNA of actively replicating cells. We compared the total and active bacterial communities during the 50‐day incubations by using phylogenic microarrays and 454 pyrosequencing to identify microorganisms and functional genes associated with PCE degradation to ethene. By use of this integrative approach, both the key community members and the ecological functions concomitant with complete PCE degradation could be determined, including the presence and activity of microbial community members responsible for producing hydrogen and acetate, which are critical for Dehalococcoides‐mediated PCE degradation. In addition, by correlation of chemical data and phylogenic microarray data, we identified several bacteria that could potentially oxidize hydrogen. These results demonstrate that PCE degradation is dependent on some microbial community members for production of appropriate metabolites, while other members of the community compete for hydrogen in soil at low redox potentials.     

Soil community composition drives aboveground plant–herbivore–parasitoid interactions

Soil organisms can influence higher trophic level aboveground organisms, but only very few studies have considered such effects. We manipulated soil community composition of model grassland ecosystems by introducing nematode communities, microorganisms, neither or both groups. Above ground, aphids ( Rhopalosiphum padi ) and parasitoids ( Aphidius colemani ) were introduced, and we measured individual performance and population dynamics of plants, aphids and parasitoids. In microcosms with nematode inoculations either with or without microorganism inoculation, aphids offspring production was significantly reduced by 31%. Aphid populations on both host plants Agrostis capillaris and Anthoxanthum odoratum were lowest in microcosms with combined nematode and microorganism inoculations. Opposite results were found for parasitoids. While the number of emerged parasitoids did not differ between treatments, parasitoid mortality and the proportion of males were significantly lower in microcosms with nematode and microorganism inoculations. Parasitized aphids were significantly larger in microcosms with nematodes inoculated. Plant biomass did not differ, but in the preferred host plant A. odoratum , foliar phenolic content was reduced in the presence of nematodes, and also the concentration of amino acids in the phloem. This study shows that the composition of the soil community matters for aboveground multitrophic interactions.     

Soil Communities Promote Temporal Stability and Species Asynchrony in Experimental Grassland Communities

Background

Over the past two decades many studies have demonstrated that plant species diversity promotes primary productivity and stability in grassland ecosystems. Additionally, soil community characteristics have also been shown to influence the productivity and composition of plant communities, yet little is known about whether soil communities also play a role in stabilizing the productivity of an ecosystem.

Methodology/Principal Findings

Here we use microcosms to assess the effects of the presence of soil communities on plant community dynamics and stability over a one-year time span. Microcosms were filled with sterilized soil and inoculated with either unaltered field soil or field soil sterilized to eliminate the naturally occurring soil biota. Eliminating the naturally occurring soil biota not only resulted in lower plant productivity, and reduced plant species diversity, and evenness, but also destabilized the net aboveground productivity of the plant communities over time, which was largely driven by changes in abundance of the dominant grass Lolium perenne. In contrast, the grass and legumes contributed more to net aboveground productivity of the plant communities in microcosms where soil biota had been inoculated. Additionally, the forbs exhibited compensatory dynamics with grasses and legumes, thus lowering temporal variation in productivity in microcosms that received the unaltered soil inocula. Overall, asynchrony among plant species was higher in microcosms where an unaltered soil community had been inoculated, which lead to higher temporal stability in community productivity.

Conclusions/Significance

Our results suggest that soil communities increase plant species asynchrony and stabilize plant community productivity by equalizing the performance among competing plant species through potential antagonistic and facilitative effects on individual plant species.     

Effect of salinity on temporal and spatial dynamics of ammonia-oxidising bacteria from intertidal freshwater sediment

Temporal and spatial dynamics within an ammonia-oxidising community from intertidal, freshwater sediments were studied in microcosms simulating flooding twice a day with fresh, brackish and marine waters. The microcosms had been filled with the upper 5 cm of intertidal freshwater sediment from the river Scheldt. Changes in community composition were examined by denaturing gradient gel electrophoresis of amplified DNA from the community. In the first week of incubation the initially present members of the Nitrosomonas oligotropha lineage were replaced by other members of the same lineage in the top layer of the sediment subjected to flooding with freshwater. Prolonged incubation extended niche differentiation to a depth of 5 cm. In the microcosms flooded with saline media, the initially present members of the N. oligotropha lineage were replaced by strains belonging to the Nitrosomonas marina lineage, but only in the top 1cm. Shift in community composition occurred earlier in the marine microcosms than in the brackish microcosms and was slower than the change in the freshwater microcosms. Irrespective of the nature of the flooding medium, shifts in community composition were always consistent among replicate microcosms. We conclude that salinity is an important steering factor in niche differentiation among ammonia-oxidising bacteria and also that changes within the community of this functional group of bacteria may occur at different rates.     

集合群落(metacommunity)研究动态

由于人类活动等原因,自然生境在日益丧失和破碎化。因此,集合种群结构作为空间生态学的一个重要的研究途径越来越受到人们的重视,而斑块化环境中的生物群落即集合群落也成为生态学的一个研究热点。文中综述了集合群落动态,群落物种丰富度和物种分布,生境的丧失和破坏对集合群落的影响等的最新研究成果。     

Decline of soil microbial diversity does not influence the resistance and resilience of key soil microbial functional groups following a model disturbance

Analysing the consequences of the decrease in biodiversity for ecosystem functioning and stability has been a major concern in ecology. However, the impact of decline in soil microbial diversity on ecosystem sustainability remains largely unknown. This has been assessed for decomposition, which is insured by a large proportion of the soil microbial community, but not for more specialized and less diverse microbial groups. We determined the impact of a decrease in soil microbial diversity on the stability (i.e. resistance and resilience following disturbance) of two more specialized bacterial functional groups: denitrifiers and nitrite oxidizers. Soil microbial diversity was reduced using serial dilutions of a suspension obtained from a non-sterile soil that led to loss of species with low cell abundance, inoculation of microcosms of the same sterile soil with these serial dilutions, and subsequent incubation to enable establishment of similar cell abundances between treatments. The structure, cell abundance and activity of denitrifying and nitrite-oxidizing communities were characterized after incubation. Increasing dilution led to a progressive decrease in community diversity as assessed by the number of denaturating gradient gel electrophoresis (DGGE) bands, while community functioning was not impaired when cell abundance recovered after incubation. The microcosms were then subjected to a model disturbance: heating to 42 degrees C for 24 h. Abundance, structure and activity of each community were measured 3 h after completion of the disturbance to assess resistance, and after incubation of microcosms for 1 month to assess resilience. Resistance and resilience to the disturbance differed between the two communities, nitrite oxidizers being more affected. However, reducing the diversity of the two microbial functional groups did not impair either their resistance or their resilience following the disturbance. These results demonstrate the low sensitivity of the resistance and resilience of both microbial groups to diversity decline provided that cell abundance is similar between treatments.     

Effect of different root endophytic fungi on plant community structure in experimental microcosms

Understanding the effects of root‐associated microbes in explaining plant community patterns represents a challenge in community ecology. Although typically overlooked, several lines of evidence point out that nonmycorrhizal, root endophytic fungi in the Ascomycota may have the potential to drive changes in plant community ecology given their ubiquitous presence, wide host ranges, and plant species‐specific fitness effects. Thus, we experimentally manipulated the presence of root endophytic fungal species in microcosms and measured its effects on plant communities. Specifically, we tested whether (1) three different root endophyte species can modify plant community structure; (2) those changes can also modified the way plant respond to different soil types; and (3) the effects are modified when all the fungi are present. As a model system, we used plant and fungal species that naturally co‐occur in a temperate grassland. Further, the soil types used in our experiment reflected a strong gradient in soil texture that has been shown to drive changes in plant and fungal community structure in the field. Results showed that each plant species responded differently to infection, resulting in distinct patterns of plant community structure depending on the identity of the fungus present. Those effects depended on the soil type. For example, large positive effects due to presence of the fungi were able to compensate for less nutrients levels in one soil type. Further, host responses when all three fungi were present were different from the ones observed in single fungal inoculations, suggesting that endophyte–endophyte interactions may be important in structuring plant communities. Overall, these results indicate that plant responses to changes in the species identity of nonmycorrhizal fungal community species and their interactions can modify plant community structure.     

Phylogenetic diversity stabilizes community biomass

Aims The relationship between biodiversity and ecological stability is a long-standing issue in ecology. Current diversity–stability studies, which have largely focused on species diversity, often report an increase in the stability of aggregate community properties with increasing species diversity. Few studies have examined the linkage between phylogenetic diversity, another important dimension of biodiversity, and stability. By taking species evolutionary history into account, phylogenetic diversity may better capture the diversity of traits and niches of species in a community than species diversity and better relate to temporal stability. In this study, we investigated whether phylogenetic diversity could affect temporal stability of community biomass independent of species diversity.Methods We performed an experiment in laboratory microcosms with a pool of 12 bacterivorous ciliated protist species. To eliminate the possibility of species diversity effects confounding with phylogenetic diversity effects, we assembled communities that had the same number of species but varied in the level of phylogenetic diversity. Weekly disturbance, in the form of short-term temperature shock, was imposed on each microcosm and species abundances were monitored over time. We examined the relationship between temporal stability of community biomass and phylogenetic diversity and evaluated the role of several stabilizing mechanisms for explaining the influence of phylogenetic diversity on temporal stability.Important findings Our results showed that increasing phylogenetic diversity promoted temporal stability of community biomass. Both total community biomass and summed variances showed a U-shaped relationship with phylogenetic diversity, driven by the presence of large, competitively superior species that attained large biomass and high temporal variation in their biomass in both low and high phylogenetic diversity communities. Communities without these species showed patterns consistent with the reduced strength of competition and increasingly asynchronous species responses to environmental changes under higher phylogenetic diversity, two mechanisms that can drive positive diversity–stability relationships. These results support the utility of species phylogenetic knowledge for predicting ecosystem functions and their stability.     

Mutualistic Interactions Drive Ecological Niche Convergence in a Diverse Butterfly Community

Ecological communities are structured in part by evolutionary interactions among their members. A number of recent studies incorporating phylogenetics into community ecology have upheld the paradigm that competition drives ecological divergence among species of the same guild. However, the role of other interspecific interactions, in particular positive interactions such as mutualism, remains poorly explored. We characterized the ecological niche and inferred phylogenetic relationships among members of a diverse community of neotropical Müllerian mimetic butterflies. Müllerian mimicry is one of the best studied examples of mutualism, in which unpalatable species converge in wing pattern locally to advertize their toxicity to predators. We provide evidence that mutualistic interactions can drive convergence along multiple ecological axes, outweighing both phylogeny and competition in shaping community structure. Our findings imply that ecological communities are adaptively assembled to a much greater degree than commonly suspected. In addition, our results show that phenotype and ecology are strongly linked and support the idea that mimicry can cause ecological speciation through multiple cascading effects on species' biology.     

Microbial Diversity and Structure Are Drivers of the Biological Barrier Effect against Listeria monocytogenes in Soil

Understanding the ecology of pathogenic organisms is important in order to monitor their transmission in the environment and the related health hazards. We investigated the relationship between soil microbial diversity and the barrier effect against Listeria monocytogenes invasion. By using a dilution-to-extinction approach, we analysed the consequence of eroding microbial diversity on L. monocytogenes population dynamics under standardised conditions of abiotic parameters and microbial abundance in soil microcosms. We demonstrated that highly diverse soil microbial communities act as a biological barrier against L. monocytogenes invasion and that phylogenetic composition of the community also has to be considered. This suggests that erosion of diversity may have damaging effects regarding circulation of pathogenic microorganisms in the environment.     

Microbial community assessment in oil-impacted salt marsh sediment microcosms by traditional and nucleic acid-based indices.

The effect of oil amendment in salt marsh sediment microcosms was examined by most probable number (MPN), DNA-hybridization with domain-specific oligonucleotide probes and whole community 16S rDNA-hybridizations. Gas chromatography (GC/MS) analysis of oil residues in sediments from microcosms after 3 months of operation showed that the quantity of petroleum hydrocarbons was lower in microcosms amended with oil compared to microcosms amended with oil+plant detritus. Bacterial numbers (total-MPN) increased in all experimental microcosms (amended with plant detritus, oil, and oil+plant detritus). In comparison to the intact sediment, the proportions of oil-degrading bacteria increased >100-fold in the oil amended microcosm and >10-fold in the plant detritus and the oil+plant detritus amended microcosms. DNA-hybridizations with Bacteria, Archaea and Eukarya oligonucleotide probes indicated few changes in the petroleum contaminated sediment community profile. In contrast, rDNA-hybridizations indicated that the bacterial community profile of the oil-impacted sediments, after 1 month of exposure, was significantly different from the control sediment.     

Plant–animal interactions in seagrass beds: ongoing and future challenges for understanding population and community dynamics

Seagrass beds are some of the most productive parts of coastal ecosystems, hosting a wide variety of associated fauna. This paper reviews recent studies of animal–plant interactions in seagrass beds, focusing particularly on studies conducted in Japan and Thailand. Although the positive effect of seagrass habitat structure on animals has been widely acknowledged, the magnitude of this effect varies greatly among studies. A comparative study on epifaunal communities and a manipulative experiment using an infaunal bivalve revealed that behavioral and life-history traits of component species and their interactions influence the observed variation. Some recent studies have challenged the previously accepted view that direct herbivory on seagrasses is rare, and has a minor effect on the seagrass community. A series of studies of dugong herbivory revealed that the marine mammal has great impacts not only on seagrass productivity but also on the infaunal community. Furthermore, it has been found that seed predators have a negative influence on seed production and the subsequent recruitment of seagrass. Recent studies have also demonstrated significant effects of fine-scale landscape patterns in seagrass vegetation on productivity, species interactions and community structure in seagrass beds. Future research integrating new concepts and theories in ecology, such as metapopulation and hierarchy theories, with new research tools, such as molecular-genetic analyses and remote-sensing techniques, may aid in developing a more comprehensive understanding of population and community dynamics in seagrass beds.This article is an invited review contributed by the winner of the 2003 Population Ecology Young Scientist Award.     

The merging of community ecology and phylogenetic biology

The increasing availability of phylogenetic data, computing power and informatics tools has facilitated a rapid expansion of studies that apply phylogenetic data and methods to community ecology. Several key areas are reviewed in which phylogenetic information helps to resolve long-standing controversies in community ecology, challenges previous assumptions, and opens new areas of investigation. In particular, studies in phylogenetic community ecology have helped to reveal the multitude of processes driving community assembly and have demonstrated the importance of evolution in the assembly process. Phylogenetic approaches have also increased understanding of the consequences of community interactions for speciation, adaptation and extinction. Finally, phylogenetic community structure and composition holds promise for predicting ecosystem processes and impacts of global change. Major challenges to advancing these areas remain. In particular, determining the extent to which ecologically relevant traits are phylogenetically conserved or convergent, and over what temporal scale, is critical to understanding the causes of community phylogenetic structure and its evolutionary and ecosystem consequences. Harnessing phylogenetic information to understand and forecast changes in diversity and dynamics of communities is a critical step in managing and restoring the Earth's biota in a time of rapid global change.     

Successional dynamics of the bee community in a tropical dry forest: Insights from taxonomy and functional ecology

Despite the recent rapid growth of tropical dry forest succession ecology, most studies on this topic have focused on plant community attribute recovery, whereas animal community successional dynamics has been largely overlooked, and the few existing studies have used taxonomic approaches. Here, we analyze the successional changes in the bee community in a Mexican tropical dry forest, by integrating taxonomic (species, genus, and family diversity) and functional (sociability, nesting strategy, and body size) information for bees. Over one year, in a successional chronosequence (2–67 years after abandonment) we collected 469 individual bees, representing five families, 36 genera, and 69 species. Linear modeling showed decreases in taxonomic diversity with succession, more strongly so for species. Bee species turnover along succession ranged from moderate to high, decreasing slightly at intermediate stages. An RLQ analysis (ordination method that allows relating environmental variables with functional attributes) revealed clear relations between bee functional traits and the plant community. RLQ axis 1 was positively related to vegetation structural and diversity variables, and to eusociality, while solitary, parasociality, and ground nesting was negatively associated with it. Early successional fallows attract mostly solitary and parasocial bees; older fallows tend to attract eusocial bees with aerial nesting. The continuous taxonomic turnover observed by us and the functional analysis suggest that the disappearance of old fallows from agricultural landscapes would likely result in significant reductions and even local extinctions of particular bee guilds. Considering the low viability of preserving large mature tropical dry forest tracts, the conservation of older successional stands emerges as a crucial component of landscape management.Abstract in Spanish is available with online material.