How the storage effect and the number of temporal niches affect biodiversity in stochastic and seasonal environments

Temporal environmental variations affect diversity in communities of competing populations. In particular, the covariance between competition and environment is known to facilitate invasions of rare species via the storage effect. Here we present a quantitative study of the effects of temporal variations in two-species and in diverse communities. Four scenarios are compared: environmental variations may be either periodic (seasonal) or stochastic, and the dynamics may support the storage effect (global competition) or not (local competition). In two-species communities, coexistence is quantified via the mean time to absorption, and we show that stochastic variations yield shorter persistence time because they allow for rare sequences of bad years. In diverse communities, where the steady-state reflects a colonization-extinction equilibrium, the actual number of temporal niches is shown to play a crucial role. When this number is large, the same trends hold: storage effect and periodic variations increase both species richness and the evenness of the community. Surprisingly, when the number of temporal niches is small global competition acts to decrease species richness and evenness, as it focuses the competition to specific periods, thus increasing the effective fitness differences.     

Variability in Microbial Community Composition and Function Between Different Niches Within a Coral Reef

To explore how microbial community composition and function varies within a coral reef ecosystem, we performed metagenomic sequencing of seawater from four niches across Heron Island Reef, within the Great Barrier Reef. Metagenomes were sequenced from seawater samples associated with (1) the surface of the coral species Acropora palifera, (2) the surface of the coral species Acropora aspera, (3) the sandy substrate within the reef lagoon and (4) open water, outside of the reef crest. Microbial composition and metabolic function differed substantially between the four niches. The taxonomic profile showed a clear shift from an oligotroph-dominated community (e.g. SAR11, Prochlorococcus, Synechococcus) in the open water and sandy substrate niches, to a community characterised by an increased frequency of copiotrophic bacteria (e.g. Vibrio, Pseudoalteromonas, Alteromonas) in the coral seawater niches. The metabolic potential of the four microbial assemblages also displayed significant differences, with the open water and sandy substrate niches dominated by genes associated with core house-keeping processes such as amino acid, carbohydrate and protein metabolism as well as DNA and RNA synthesis and metabolism. In contrast, the coral surface seawater metagenomes had an enhanced frequency of genes associated with dynamic processes including motility and chemotaxis, regulation and cell signalling. These findings demonstrate that the composition and function of microbial communities are highly variable between niches within coral reef ecosystems and that coral reefs host heterogeneous microbial communities that are likely shaped by habitat structure, presence of animal hosts and local biogeochemical conditions.     

Association of Host and Microbial Species Diversity across Spatial Scales in Desert Rodent Communities

Relationships between host and microbial diversity have important ecological and applied implications. Theory predicts that these relationships will depend on the spatio-temporal scale of the analysis and the niche breadth of the organisms in question, but representative data on host-microbial community assemblage in nature is lacking. We employed a natural gradient of rodent species richness and quantified bacterial communities in rodent blood at several hierarchical spatial scales to test the hypothesis that associations between host and microbial species diversity will be positive in communities dominated by organisms with broad niches sampled at large scales. Following pyrosequencing of rodent blood samples, bacterial communities were found to be comprised primarily of broad niche lineages. These communities exhibited positive correlations between host diversity, microbial diversity and the likelihood for rare pathogens at the regional scale but not at finer scales. These findings demonstrate how microbial diversity is affected by host diversity at different spatial scales and suggest that the relationships between host diversity and overall disease risk are not always negative, as the dilution hypothesis predicts.     

Soil microbial diversity and soil functioning affect competition among grasses in experimental microcosms

A gradient of microbial diversity in soil was established by inoculating pasteurized soil with microbial populations of different complexity, which were obtained by a combination of soil fumigation and filtering techniques. Four different soil diversity treatments were planted with six different grass species either in monoculture or in polyculture to test how changes of general microbial functions, such as catabolic diversity and nutrient recycling efficiency would affect the performance of the plant communities. Relatively harsh soil treatments were necessary to elicit visible effects on major soil processes such as decomposition and nitrogen cycling due to the high redundancy and resilience of soil microbial communities. The strongest effects of soil diversity manipulations on plant growth occurred in polycultures where interspecific competition between plants was high. In polycultures, soil diversity reduction led to a gradual, linear decline in biomass production of one subordinate grass species (Bromus hordeaceus), which was compensated by increased growth of two intermediate competitors (Aegilops geniculata, B. madritensis). This negative covariance in growth of competing grass species smoothed the effects of soil diversity manipulations at the plant community level. As a result, total shoot biomass production remained constant. Apparently the effects of soil diversity manipulations were buffered because functional redundancy at both, the microbial and the plant community level complemented each other. The results further suggests that small trade-offs in plant fitness due to general functional shifts at the microbial level can be significant for the outcome of competition in plant communities and thus diversity at much larger scales.     

On a collision course: competition and dispersal differences create no-analogue communities and cause extinctions during climate change

Most climate change predictions omit species interactions and interspecific variation in dispersal. Here, we develop a model of multiple competing species along a warming climatic gradient that includes temperature-dependent competition, differences in niche breadth and interspecific differences in dispersal ability. Competition and dispersal differences decreased diversity and produced so-called 'no-analogue' communities, defined as a novel combination of species that does not currently co-occur. Climate change altered community richness the most when species had narrow niches, when mean community-wide dispersal rates were low and when species differed in dispersal abilities. With high interspecific dispersal variance, the best dispersers tracked climate change, out-competed slower dispersers and caused their extinction. Overall, competition slowed the advance of colonists into newly suitable habitats, creating lags in climate tracking. We predict that climate change will most threaten communities of species that have narrow niches (e.g. tropics), vary in dispersal (most communities) and compete strongly. Current forecasts probably underestimate climate change impacts on biodiversity by neglecting competition and dispersal differences.     

Spatial and resource factors influencing high microbial diversity in soil.

To begin defining the key determinants that drive microbial community structure in soil, we examined 29 soil samples from four geographically distinct locations taken from the surface, vadose zone, and saturated subsurface using a small-subunit rRNA-based cloning approach. While microbial communities in low-carbon, saturated, subsurface soils showed dominance, microbial communities in low-carbon surface soils showed remarkably uniform distributions, and all species were equally abundant. Two diversity indices, the reciprocal of Simpson's index (1/D) and the log series index, effectively distinguished between the dominant and uniform diversity patterns. For example, the uniform profiles characteristic of the surface communities had diversity index values that were 2 to 3 orders of magnitude greater than those for the high-dominance, saturated, subsurface communities. In a site richer in organic carbon, microbial communities consistently exhibited the uniform distribution pattern regardless of soil water content and depth. The uniform distribution implies that competition does not shape the structure of these microbial communities. Theoretical studies based on mathematical modeling suggested that spatial isolation could limit competition in surface soils, thereby supporting the high diversity and a uniform community structure. Carbon resource heterogeneity may explain the uniform diversity patterns observed in the high-carbon samples even in the saturated zone. Very high levels of chromium contamination (e.g., >20%) in the high-organic-matter soils did not greatly reduce the diversity. Understanding mechanisms that may control community structure, such as spatial isolation, has important implications for preservation of biodiversity, management of microbial communities for bioremediation, biocontrol of root diseases, and improved soil fertility.     

Viral control of bacterial biodiversity – evidence from a nutrient-enriched marine mesocosm experiment

We demonstrate here results showing that bottom-up and top-down control mechanisms can operate simultaneously and in concert in marine microbial food webs, controlling prokaryote diversity by a combination of viral lysis and substrate limitation. Models in microbial ecology predict that a shift in the type of bacterial growth rate limitation is expected to have a major effect on species composition within the community of bacterial hosts, with a subsequent shift in the composition of the viral community. Only moderate effects would, however, be expected in the absolute number of coexisting virus–host pairs. We investigated these relationships in nutrient-manipulated systems, under simulated in situ conditions. There was a strong correlation in the clustering of the viral and bacterial community data supporting the existence of an important link between the bacterial and viral communities. As predicted, the total number of viral populations was the same in all treatments, while the composition of the viral community varied. Our results support the theoretical prediction that there is one control mechanism for the number of niches for coexisting virus–host pairs (top-down control), and another mechanism that controls which virus–host pairs occupy these niches (bottom-up control).     

Partitioning the impact of abiotic factors and spatial patterns on species richness and community structure of ground ant assemblages in four Bornean rainforests

Contrasting theories have been proposed to explain the structure of ecological communities. Here, we studied the impact of environmental factors and spatial patterns on ground‐foraging ant communities in four different forest types of Gunung Mulu National Park in Sarawak, Borneo, Malaysia. Forest types differed in their environmental parameters and were inhabited by distinct ant communities, with various indicator species characteristic for single forest types. Three environmental parameters, soil volume, number of trees and amount of leaf litter, had the most influence on ant communities. Spatial patterns were correlated with environmental parameters and also influenced ant communities. Environmental parameters influenced community composition only moderately (r²=0.14), but had a high impact on species richness (r²=0.44). Spatial patterns explained only a small fraction of the total variance in species patterns, while much of the residual space in the ordination space of ant community patterns remained unexplained. We conclude that environmental parameters shape the number of niches within a tropical soil habitat, but identities of species that occupy those niches are accounted for by other factors like competition, traits and neutral processes that may further reduce unexplained variance in species ordination.     

Competition and species diversity: removal of dominant species increases diversity in Costa Rican butterfly communities

Biological communities are usually dominated by a few species and show characteristically skewed species abundance distributions. Although niche apportionment and resource competition are sometimes implicated in such patterns, few experimental studies have shown direct links between resource limitation, competition with dominant species and their impacts on the overall diversity and composition of large natural communities. Here I report the results of an experiment in which I first studied species diversity and composition in two Costa Rican nectar-feeding butterfly communities numerically dominated by two species of Anartia butterflies. Then I removed Anartia from these communities to study changes in resource availability, species abundance relationships, community diversity and composition as an outcome of the removal of the dominant competitors. In the face of competition with Anartia , nectar was scarce, species abundance distributions were highly skewed, and species diversity was low in both communities. Within two weeks after the removal of Anartia , there were parallel changes in both communities: competition for nectar reduced and the nectar quantity increased substantially, which facilitated increase in community diversity and resulted in significantly less skewed species abundance distributions. Higher nectar quantity also enabled the distribution of body size and proboscis length of constituent species in the communities to expand at both ends. This study thus experimentally showed that resource competition with the dominant species was excluding many species from the communities, lowering their diversity and skewing relative species abundance relationships. These findings are of fundamental importance for competition theory and community ecology because they indicate ways in which diverse communities may be affected by and recover from competition with dominant species.     

放牧干扰梯度下川西亚高山植物群落的组合机理

为了阐明放牧干扰对川西亚高山区域植物群落的组合过程以及群落结构的影响, 研究了放牧干扰梯度下的功能群均匀度和群落谱系结构的变化趋势。结果显示: 在干扰较轻的阔叶林与针叶林样地, 部分样方的功能群均匀度显著高于无效模型, 随着干扰梯度的增强, 功能群均匀度呈线性下降, 样方平均值从0.930降至0.840, 其高于无效模型的次数也逐渐降低, 干扰程度较大的草甸中出现部分样方的功能群均匀度显著低于无效模型。随着干扰程度的增强, 群落的谱系结构指数也呈逐渐上升趋势, 净关联指数平均值由-0.634逐渐增加至2.360, 邻近类群指数由-0.158上升至2.179。草甸与低矮灌丛受干扰较为严重, 其大部分样方的谱系结构指数显著高于随机群落, 表明干扰群落的谱系结构呈聚集分布。功能群均匀度与谱系结构的变化趋势一致, 表明生境筛滤效应与种间竞争作用的平衡决定着群落的组合过程。干扰降低了竞争作用, 促进了少数耐干扰功能群的优势地位, 造成功能群均匀度下降, 同时通过生境筛滤作用, 使群落的谱系结构呈现出聚集分布; 而未干扰的群落中由于竞争作用的效应, 功能群均匀度较高, 谱系结构也更加分散。研究区域植物群落的功能群均匀度与物种丰富度呈负相关, 表明物种间特别是相似物种间的竞争限制了群落的物种多样性。研究结果说明, 生态位分化和物种间的相互竞争在物种共存与群落组合中具有重要作用。     

Habitat diversity and species diversity: testing the competition hypothesis with juvenile salmonids

I experimentally tested two predictions of the hypothesis that the positive relationship between habitat diversity and species diversity arises from a reduction in the negative effects of interspecific competition. By allowing species to partition habitat and avoid competition, habitat diversity should 1) facilitate the addition of an ecologically intermediate species into an existing community, and 2) reduce the negative effects of that species on existing members of the community. I tested these predictions with juveniles of three sympatric salmonid species: coho salmon ( Oncorhynchus kisutch ), steelhead trout ( O. mykiss ), and cutthroat trout ( O. clarki ), which in natural streams occupy deep low-velocity pools, shallow high-velocity riffles, and intermediate habitats, respectively. I introduced two (coho and steelhead) and three species communities into each of three artificial stream habitats: pools, riffles, and diverse. The results provide partial support for the predictions. Cutthroat trout grew fastest in the diverse stream habitat. Though habitat diversity did not eliminate the negative effects of competition, in the three species community coho and steelhead grew as fast in the diverse habitat as in either homogeneous habitat. The results are consistent with data on species number and evenness from natural communities, where variation along other niche axes confounds the relationship between habitat diversity, interspecific competition, and species diversity.     

Ecological niches of ectoparasites

On mammals and birds communities of ectoparasites are present, which can include scores of ticks, mites and insects species. The parasitizing of arthropods terrestrial vertebrates appeared as far back a the Cretaceous period, and after 70-100 mil. years of the coevolution ectoparasites have assimilated all food resources and localities of the hosts' bodies. To the present only spatial and (to the less extent) trophic niches of parasitic insects, ticks and mites are studied completely enough. The main results these investigations are discussed in the present paper. A high abundance of the communities is reached because of their partition into the number of ecological niches. Host is complex of ecological niches for many ectoparasites species. These niches reiterate in the populations of a species closely related species of hosts and repeat from generation to generation. The each part of host (niche) being assimilated be certain parasite species is available potentially for other species. The partition of host into ecological niches is clearer than the structure of ecosystems including free-living organisms. A real extent of the ecological niches occupation by different species of ticks, mites and insects is considerably lower than a potential maximum. The degree of ecological niches saturation depends on the history of the coevolution of parasites community components, previous colonization be new ectoparasite species and many other ecological factors affecting host-parasite system. The use of the ecological niche conception in parasitology is proved to be rather promising. Ectoparasites communities because of their species diversity, different types of feeding and a number of habitats on host represent convenient models and study of them can contribute significantly to the developmeht of the general conception of ecological niche.     

Spatial and Resource Factors Influencing High Microbial Diversity in Soil

To begin defining the key determinants that drive microbial community structure in soil, we examined 29 soil samples from four geographically distinct locations taken from the surface, vadose zone, and saturated subsurface using a small-subunit rRNA-based cloning approach. While microbial communities in low-carbon, saturated, subsurface soils showed dominance, microbial communities in low-carbon surface soils showed remarkably uniform distributions, and all species were equally abundant. Two diversity indices, the reciprocal of Simpson’s index (1/D) and the log series index, effectively distinguished between the dominant and uniform diversity patterns. For example, the uniform profiles characteristic of the surface communities had diversity index values that were 2 to 3 orders of magnitude greater than those for the high-dominance, saturated, subsurface communities. In a site richer in organic carbon, microbial communities consistently exhibited the uniform distribution pattern regardless of soil water content and depth. The uniform distribution implies that competition does not shape the structure of these microbial communities. Theoretical studies based on mathematical modeling suggested that spatial isolation could limit competition in surface soils, thereby supporting the high diversity and a uniform community structure. Carbon resource heterogeneity may explain the uniform diversity patterns observed in the high-carbon samples even in the saturated zone. Very high levels of chromium contamination (e.g., >20%) in the high-organic-matter soils did not greatly reduce the diversity. Understanding mechanisms that may control community structure, such as spatial isolation, has important implications for preservation of biodiversity, management of microbial communities for bioremediation, biocontrol of root diseases, and improved soil fertility.     

Thermodynamic concepts in the study of microbial populations: age structure in Plasmodium falciparum infected red blood cells

Variability is a hallmark of microbial systems. On the one hand, microbes are subject to environmental heterogeneity and undergo changeable conditions in their immediate surroundings. On the other hand, microbial populations exhibit high cellular diversity. The relation between microbial diversity and variability of population dynamics is difficult to assess. This connection can be quantitatively studied from a perspective that combines in silico models and thermodynamic methods and interpretations. The infection process of Plasmodium falciparum parasitizing human red blood cells under laboratory cultivation conditions is used to illustrate the potential of Individual-based models in the context of predictive microbiology and parasitology. Experimental data from several in vitro cultures are compared to the outcome of an individual-based model and analysed from a thermodynamic perspective. This approach allows distinguishing between intrinsic and external constraints that give rise to the diversity in the infection forms, and it provides a criterion to quantitatively define transient and stationary regimes in the culture. Increasing the ability of models to discriminate between different states of microbial populations enhances their predictive capability which finally leads to a better the control over culture systems. The strategy here presented is of general application and it can substantially improve modelling of other types of microbial communities.     

Seed supply, recruitment, and assembly: quantifying relative seed and establishment limitation in a plant community context

There is a growing consensus that the relative constraints of seed limitation and establishment limitation in recruitment strongly influence abundance patterns in plant communities. Although these constraints have direct relevance to coexistence, most investigations utilize a seed addition approach that offers limited insight into these dynamics. Here we report the results of an assembly experiment with annual plant species from California grasslands to examine how propagule pool characteristics (dominant species abundance, functional diversity) influence establishment and seed limitation (density independence and density dependence across a gradient of seed supply) for each species, as well as how these constraints affect community diversity. Species were predominantly colimited by seed and establishment constraints, exhibiting saturating recruitment functions with increased seed supply. Consistent with competition-colonization trade-off predictions, recruitment constraints often depended on the degree of seed limitation of the competitive dominant, Brassica nigra; diversity was greatest in communities where Brassica was seed limited. Functional similarity within the propagule pool did not affect recruitment across a range of seed supply; likewise, functional diversity of the propagule pool was not related to community diversity. We conclude that seed limitation of the dominant species rather than niche similarity influences interspecific competition for safe sites and scales up to affect community-level diversity.     

When competition does not matter: grassland diversity and community composition

We examined whether the intense root competition in a rough fescue grassland plant community in central Alberta, Canada, was important in structuring plant species diversity or community composition. We measured competition intensity across gradients of species richness, evenness, and community composition, using pairs of naturally occurring plants of 12 species. One plant in each pair was isolated from neighbors to measure competition; community structure and environmental conditions were also measured at each pair. We used structural equation modeling to examine how competition influenced community structure. Competition intensity was unrelated to species richness and community composition, but increased competition intensity was associated with a slight decline in evenness. Size-symmetric root competition was probably unimportant in structuring this plant community because there are no feedback mechanisms through which size-symmetric competition can magnify small initial differences and eventually lead to competitive exclusion. In plant communities with little shoot competition, competition and community structure should be unlinked regardless of competition intensity. In more productive systems, we propose that interactions between root and shoot competition may indirectly structure communities by altering the overall asymmetry of competition.     

Influence of plant developmental stage on microbial community structure and activity in the rhizosphere of three field crops

Seasonal shifts in rhizosphere microbial populations were investigated to follow the influence of plant developmental stage. A field study of indigenous microbial rhizosphere communities was undertaken on pea (Pisum satvium var. quincy), wheat (Triticum aestivum var. pena wawa) and sugar beet (Beta vulgaris var. amythyst). Rhizosphere community diversity and substrate utilization patterns were followed throughout a growing season, by culturing, rRNA gene density gradient gel electrophoresis and BIOLOG. Culturable bacterial and fungal rhizosphere community densities were stable in pea and wheat rhizospheres, with dynamic shifts observed in the sugar beet rhizosphere. Successional shifts in bacterial and fungal diversity as plants mature demonstrated that different plants select and define their own functional rhizosphere communities. Assessment of metabolic activity and resource utilization by bacterial community-level physiological profiling demonstrated greater similarities between different plant species rhizosphere communities at the same than at different developmental stages. Marked temporal shifts in diversity and relative activity were observed in rhizosphere bacterial communities with developmental stage for all plant species studied. Shifts in the diversity of fungal and bacterial communities were more pronounced in maturing pea and sugar beet plants. This detailed study demonstrates that plant species select for specialized microbial communities that change in response to plant growth and plant inputs.     

Effects of above-ground plant species composition and diversity on the diversity of soil-borne microorganisms

A coupling of above-ground plant diversity and below-ground microbial diversity has been implied in studies dedicated to assessing the role of macrophyte diversity on the stability, resilience, and functioning of ecosystems. Indeed, above-ground plant communities have long been assumed to drive below-ground microbial diversity, but to date very little is known as to how plant species composition and diversity influence the community composition of micro-organisms in the soil. We examined this relationship in fields subjected to different above-ground biodiversity treatments and in field experiments designed to examine the influence of plant species on soil-borne microbial communities. Culture-independent strategies were applied to examine the role of wild or native plant species composition on bacterial diversity and community structure in bulk soil and in the rhizosphere. In comparing the influence of Cynoglossum officinale (hound's tongue) and Cirsium vulgare (spear thistle) on soil-borne bacterial communities, detectable differences in microbial community structure were confined to the rhizosphere. The colonisation of the rhizosphere of both plants was highly reproducible, and maintained throughout the growing season. In a separate experiment, effects of plant diversity on bacterial community profiles were also only observed for the rhizosphere. Rhizosphere soil from experimental plots with lower macrophyte diversity showed lower diversity, and bacterial diversity was generally lower in the rhizosphere than in bulk soil. These results demonstrate that the level of coupling between above-ground macrophyte communities and below-ground microbial communities is related to the tightness of the interactions involved. Although plant species composition and community structure appear to have little discernible effect on microbial communities inhabiting bulk soil, clear and reproducible changes in microbial community structure and diversity are observed in the rhizosphere. This revised version was published online in August 2006 with corrections to the Cover Date.     

New insights into relationships between active and dormant organisms,phylogenetic diversity and ecosystem productivity

Marine microbes make up a key part of ocean food webs and drive ocean chemistry through a range of metabolic processes. A fundamental question in ecology is whether the diversity of organisms in a community shapes the ecological functions of that community. While there is substantial evidence to support a positive link between diversity and ecological productivity for macro‐organisms in terrestrial environments, this relationship has not previously been verified for marine microbial communities. One factor complicating the understanding of this relationship is that many marine microbes are dormant and are easily dispersed by ocean currents, making it difficult to ensure that the organisms found in a given environmental sample accurately reflect processes occurring in that environment. Another complication is that, due to microbes great range of genotypic and phenotypic variability, communities with distantly related species may have greater range of metabolic functions than communities have the same richness and evenness, but in which the species present are more closely related to each other. In this issue of Molecular Ecology, Galand et al. (2015) provide compelling evidence that the most metabolically active communities are those in which the nondormant portion of the microbial community has the highest phylogenetic diversity. They also illustrate that focusing on the active portion of the community allows for detection of temporal patterns in community structure that would not be otherwise evident. The authors’ point out that the presence of many dormant organisms that do not contribute to ecosystem functioning is a feature that makes microbial ecosystems fundamentally different from macro‐ecosystems and that this difference needs to be accounted for in microbial ecology theory.     

A Coexisting Fungal-Bacterial Community Stabilizes Soil Decomposition Activity in a Microcosm Experiment

How diversity influences the stability of a community function is a major question in ecology. However, only limited empirical investigations of the diversity–stability relationship in soil microbial communities have been undertaken, despite the fundamental role of microbial communities in driving carbon and nutrient cycling in terrestrial ecosystems. In this study, we conducted a microcosm experiment to investigate the relationship between microbial diversity and stability of soil decomposition activities against changes in decomposition substrate quality by manipulating microbial community using selective biocides. We found that soil respiration rates and degradation enzyme activities by a coexisting fungal and bacterial community (a taxonomically diverse community) are more stable against changes in substrate quality (plant leaf materials) than those of a fungi-dominated or a bacteria-dominated community (less diverse community). Flexible changes in the microbial community composition and/or physiological state in the coexisting community against changes in substrate quality, as inferred by the soil lipid profile, may be the mechanism underlying this positive diversity–stability relationship. Our experiment demonstrated that the previously found positive diversity–stability relationship could also be valid in the soil microbial community. Our results also imply that the functional/taxonomic diversity and community ecology of soil microbes should be incorporated into the context of climate–ecosystem feedbacks. Changes in substrate quality, which could be induced by climate change, have impacts on decomposition process and carbon dioxide emission from soils, but such impacts may be attenuated by the functional diversity of soil microbial communities.