Relative roles of niche and neutral processes on turnover of plant,fungal and bacterial communities in arid and semi-arid areas at the regional scale

The mechanisms that determine the spatial structure of macroscopic and microbial communities and how they respond to environmental changes are central themes that have been explored in ecological research. However, little is known about the relative roles and importance of neutral and niche-related factors in the assemblage of bacterial, fungal, and plant communities. Here partial Mantel, null model, and variation partitioning analysis were used to compare mechanisms driving the beta diversity of bacteria, fungi and plant communities at the regional scale in arid and semi-arid areas. Denaturing gradient gel electrophoresis (PCR-DGGE) was used to evaluate the distribution pattern of microbial communities, and vegetation survey were conducted to evaluate the characteristics of plant communities. We found that bacterial, fungal, and plant communities were strongly influenced by niche processes at the regional scale in arid and semi-arid areas. Bacteria had a stronger habitat association, indicating community assembly is strongly affected by niche processes. Fungi, with their body size between plants and bacteria, had moderate environment correlation, and plants had less environment association than fungi or bacteria, which suggests that body size may determine the association between organism and environment. We concluded that the pivotal niche process, environmental filtering, weakened with increasing body size, and it should be considered when we evaluate the relative roles of deterministic and stochastic processes in community assemblage.     

Upstream trophic structure modulates downstream community dynamics via resource subsidies

In many natural systems, the physical structure of the landscape dictates the flow of resources. Despite mounting evidence that communities’ dynamics can be indirectly coupled by reciprocal among ecosystem resource flows, our understanding of how directional resource flows might indirectly link biological communities is limited. We here propose that differences in community structure upstream should lead to different downstream dynamics, even in the absence of dispersal of organisms. We report an experimental test of the effect of upstream community structure on downstream community dynamics in a simplified but highly controlled setting, using protist microcosms. We implemented directional flows of resources, without dispersal, from a standard resource pool into upstream communities of contrasting interaction structure and then to further downstream communities of either one or two trophic levels. Our results demonstrate that different types of species interactions in upstream habitats may lead to different population sizes and levels of biomass in these upstream habitats. This, in turn, leads to varying levels of detritus transfer (dead biomass) to the downstream communities, thus influencing their population densities and trophic interactions in predictable ways. Our results suggest that the structure of species interactions in directionally structured ecosystems can be a key mediator of alterations to downstream habitats. Alterations to upstream habitats can thus cascade down to downstream communities, even without dispersal.     

Temporal variability in detritus resource maintains diversity of bacterial communities

Competition theory generally predicts that diversity is maintained by temporal environmental fluctuations. One of the many suggested mechanisms for maintaining diversity in fluctuating environments is the gleaner-opportunist trade-off, whereby gleaner species have low threshold resource levels and low maximum growth rates in high resource concentration while opportunist species show opposite characteristics. We measured the growth rates of eight heterotrophic aquatic bacteria under different concentrations of chemically complex plant detritus resource. The growth rates revealed gleaner-opportunist trade-offs. The role of environmental variability in maintaining diversity was tested in a 28-day experiment with three different resource fluctuation regimes imposed on two four-species bacterial communities in microcosms. We recorded population densities with serial dilution plating and total biomass as turbidity. Changes in resource availability were measured from filter-sterilised medium by re-introducing the consumer species and recording short-term growth rates. The type of environmental variation had no effect on resource availability, which declined slowly during the experiment and differed in level between the communities. However, the slowly fluctuating environment had the highest Shannon diversity index, biomass, and coefficient of variation of biomass in both communities. We did not find a clear link between the gleaner-opportunist trade-off and diversity in fluctuating environments. Nevertheless, our results do not exclude this explanation and support the general view that temporal environmental variation maintains species diversity also in communities feeding chemically complex resource.     

The Impact of Resource Availability on Bacterial Resistance to Phages in Soil

Resource availability can affect the coevolutionary dynamics between host and parasites, shaping communities and hence ecosystem function. A key finding from theoretical and in vitro studies is that host resistance evolves to greater levels with increased resources, but the relevance to natural communities is less clear. We took two complementary approaches to investigate the effect of resource availability on the evolution of bacterial resistance to phages in soil. First, we measured the resistance and infectivity of natural communities of soil bacteria and phage in the presence and absence of nutrient-providing plants. Second, we followed the real-time coevolution between defined bacteria and phage populations with resource availability manipulated by the addition or not of an artificial plant root exudate. Increased resource availability resulted in increases in bacterial resistance to phages, but without a concomitant increase in phage infectivity. These results suggest that phages may have a reduced impact on the control of bacterial densities and community composition in stable, high resource environments.     

Environmental Impacts and Scarcity Perception Influence Local Institutions in Indigenous Amazonian Kichwa Communities

Much of the literature on common-pool resources has focused on elucidating the social mechanisms and local institutions that lead to the regulation of common-pool resources. There is much less information about how management regimes translate into environmental impacts or how environmental impacts influence the emergence of management decisions. We use quantitative and qualitative methods to investigate the link between forest condition, agricultural change and the emergence of common-pool resource management regimes in two indigenous Kichwa communities in the Ecuadorian Amazon. We show that forest condition is linked to agricultural production and that the perception of common-pool resource scarcity influences the emergence of management regimes. We argue that population pressure, market forces and resource scarcity, which are usually associated with measures of agricultural change can also promote the emergence of common-pool resource management regimes.     

Resource specialization determines whether history influences community structure

History, specifically the sequence of species arrival, can affect community composition. Tests for a locally operating mechanism that can produce this result remain rare. Here we show how interspecific competition for resources combined with history can produce different communities. Specifically, history should influence community structure much less when all competitors use the same resource base than when some resources are unavailable to some competitors. We manipulated the resources available to competing ciliates in aquatic microcosms to test this hypothesis. We created communities that had only bacteria, or both bacteria and algae as consumable resources. When only bacteria were available, the best competitor, Colpidium striatum , always dominated regardless of differences in colonization history. History did affect the densities of competitively equivalent subordinate species, Paramecium tetraurelia and P. caudatum . The least effective competitor, Tetrahymena thermophila , went extinct in almost every community. P. tetraurelia and P. caudatum can also consume algae in addition to bacteria. History had a much larger effect in communities where both bacteria and algae were available as resources. In these communities, the initially dominant species always maintained dominance throughout the experiment, with the exception of T. thermophila which still went extinct. The experiment lasted for over 30 generations of the dominant species, so all effects of history persisted over ecologically important time scales.     

Soil bacterial diversity in degraded and restored lands of Northeast Brazil

Land degradation deteriorates biological productivity and affects environmental, social, and economic sustainability, particularly so in the semi-arid region of Northeast Brazil. Although some studies exist reporting gross measures of soil microbial parameters and processes, limited information is available on how land degradation and restoration strategies influence the diversity and composition of soil microbial communities. In this study we compare the structure and diversity of bacterial communities in degraded and restored lands in Northeast Brazil and determine the soil biological and chemical properties influencing bacterial communities. We found that land degradation decreased the diversity of soil bacteria as indicated by both reduced operational taxonomic unit (OTU) richness and Shannon index. Soils under native vegetation and restoration had significantly higher bacterial richness and diversity than degraded soils. Redundancy analysis revealed that low soil bacterial diversity correlated with a high respiratory quotient, indicating stressed microbial communities. By contrast, soil bacterial communities in restored land positively correlated with high soil P levels. Importantly, however, we found significant differences in the soil bacterial community composition under native vegetation and in restored land, which may indicate differences in their functioning despite equal levels of bacterial diversity.     

Resources Alter the Structure and Increase Stochasticity in Bromeliad Microfauna Communities

Although stochastic and deterministic processes have been found to jointly shape structure of natural communities, the relative importance of both forces may vary across different environmental conditions and across levels of biological organization. We tested the effects of abiotic environmental conditions, altered trophic interactions and dispersal limitation on the structure of aquatic microfauna communities in Costa Rican tank bromeliads. Our approach combined natural gradients in environmental conditions with experimental manipulations of bottom-up interactions (resources), top-down interactions (predators) and dispersal at two spatial scales in the field. We found that resource addition strongly increased the abundance and reduced the richness of microfauna communities. Community composition shifted in a predictable way towards assemblages dominated by flagellates and ciliates but with lower abundance and richness of algae and amoebae. While all functional groups responded strongly and predictably to resource addition, similarity among communities at the species level decreased, suggesting a role of stochasticity in species-level assembly processes. Dispersal limitation did not affect the communities. Since our design excluded potential priority effects we can attribute the differences in community similarity to increased demographic stochasticity of resource-enriched communities related to erratic changes in population sizes of some species. In contrast to resources, predators and environmental conditions had negligible effects on community structure. Our results demonstrate that bromeliad microfauna communities are strongly controlled by bottom-up forces. They further suggest that the relative importance of stochasticity may change with productivity and with the organizational level at which communities are examined.     

Long-Term Characterization of Free-Living and Particle-Associated Bacterial Communities in Lake Tiefwaren Reveals Distinct Seasonal Patterns

Seasonal changes in environmental conditions have a strong impact on microbial community structure and dynamics in aquatic habitats. To better elucidate the response of bacterial communities to environmental changes, we have measured a large variety of limnetic variables and investigated bacterial community composition (BCC) and dynamics over seven consecutive years between 2003 and 2009 in mesotrophic Lake Tiefwaren (NE Germany). We separated between free-living (FL, >0.2, <5.0?μm) and particle-associated (PA, >5.0?μm) bacteria to account for different bacterial lifestyles and to obtain a higher resolution of the microbial diversity. Changes in BCC were studied by DGGE based on PCR-amplified 16S rRNA gene fragments. Sequencing of DGGE bands revealed that ca. 70?% of all FL bacteria belonged to the Actinobacteria, whereas PA bacteria were dominated by Cyanobacteria (43?%). FL communities were generally less diverse and rather stable over time compared to their PA counterpart. Annual changes in reoccurring seasonal patterns of dominant freshwater bacteria were supported by statistical analyses, which revealed several significant correlations between DGGE profiles and various environmental variables, e.g. temperature and nutrients. Overall, FL bacteria were generally less affected by environmental changes than members of the PA fraction. Close association of PA bacteria with phytoplankton and zooplankton suggests a tight coupling of PA bacteria to organisms of higher trophic levels. Our results indicate substantial differences in bacterial lifestyle of pelagic freshwater bacteria, which are reflected by contrasting seasonal dynamics and relationships to a number of environmental variables.     

Environmental degradation results in contrasting changes in the assembly processes of stream bacterial and fungal communities

Environmental degradation may have strong effects on community assembly processes. We examined the assembly of bacterial and fungal communities in anthropogenically altered and near‐pristine streams. Using pyrosequencing of bacterial and fungal DNA from decomposed alder Alnus incana leaves, we specifically examined if environmental degradation deterministically decreases or increases the compositional turnover of bacterial and fungal communities. Our results showed that near‐pristine streams and anthropogenically altered streams supported distinct fungal and bacterial communities. The mechanisms assembling these communities were different in near‐pristine and altered environments. Environmental disturbance homogenized bacterial communities, whereas fungal communities were more dissimilar in disturbed sites than in near‐pristine sites. Compositional variation of both bacteria and fungi was related to water chemistry variables in disturbed sites, further implying the influence of environmental degradation on community assembly. Bacterial and fungal communities in near‐pristine streams were weakly controlled by environmental factors, suggesting that the relative importance of niche‐based versus neutral processes in assembling microbial communities may strongly depend on the spatial scale and local environmental context. Our results thus suggest that environmental degradation may strongly affect the composition and β‐diversity of stream microbial communities colonizing leaf litter, and that the direction of the change can be different between bacteria and fungi. A better understanding of the environmental tolerances of microbes and the mechanisms assembling microbial communities in natural environmental settings is needed to predict how environmental alteration is likely to affect microbial communities.     

Predicting spatial patterns of soil bacteria under current and future environmental conditions

Soil bacteria are largely missing from future biodiversity assessments hindering comprehensive forecasts of ecosystem changes. Soil bacterial communities are expected to be more strongly driven by pH and less by other edaphic and climatic factors. Thus, alkalinisation or acidification along with climate change may influence soil bacteria, with subsequent influences for example on nutrient cycling and vegetation. Future forecasts of soil bacteria are therefore needed. We applied species distribution modelling (SDM) to quantify the roles of environmental factors in governing spatial abundance distribution of soil bacterial OTUs and to predict how future changes in these factors may change bacterial communities in a temperate mountain area. Models indicated that factors related to soil (especially pH), climate and/or topography explain and predict part of the abundance distribution of most OTUs. This supports the expectations that microorganisms have specific environmental requirements (i.e., niches/envelopes) and that they should accordingly respond to environmental changes. Our predictions indicate a stronger role of pH over other predictors (e.g. climate) in governing distributions of bacteria, yet the predicted future changes in bacteria communities are smaller than their current variation across space. The extent of bacterial community change predictions varies as a function of elevation, but in general, deviations from neutral soil pH are expected to decrease abundances and diversity of bacteria. Our findings highlight the need to account for edaphic changes, along with climate changes, in future forecasts of soil bacteria.Subject terms: Microbial ecology, Metagenomics, Climate-change ecology     

Indigenous Cultural and Natural Resources Management and Mobility in Arnhem Land,Northern Australia

Many programmes formally engage Australian Indigenous people in land and sea management to provide environmental services. There are also many Indigenous people who ‘look after country’ without rewards or payment because of cultural obligations. We investigated how Indigenous peoples’ mobility in and around two communities (Maningrida and Ngukurr) is affected by their formal or informal engagement in cultural and natural resource management (CNRM). Understanding factors that influence peoples’ mobility is important if essential services are to be provided to communities efficiently. We found that those providing formal CNRM were significantly less likely to stay away from settlements than those ‘looking after their country’ without payment or reward. Paying Indigenous people to engage with markets for CNRM through carbon farming or payments for environmental services (PES) schemes may alter traditional activities and reduce mobility, particularly movements away from communities that extend the time spent overnight on country. This could have both environmental and social consequences that could be managed through greater opportunities for people to engage in formal CNRM while living away from communities and greater recognition of the centrality of culture to all Indigenous CNRM, formal or otherwise.     

Consequences of varying regional heterogeneity in source–sink metacommunities

Although the influence of dispersal on coexistence mechanisms in metacommunities has received great emphasis, few studies have addressed how such influence is affected varying regional heterogeneity. We present a mechanistic model of resource competition in a metacommunity based on classical models of plant competition for limiting resources. We defined regional heterogeneity as the differences in resource supply rates (or resource availabilities) across local communities. As suggested by previous work, the highest diversify occurred at intermediate levels of dispersal among local communities. However our model shows how the effects of dispersal depend on the amount of heterogeneity among local communities and vice versa. Both regional and local species richness were the highest when heterogeneity was intermediate. We suggest that empirical studies that found no evidence for source–sink or mass effects at the community level may have examined communities with limited ranges of dispersal and regional heterogeneity. This model of species coexistence contributes to a broader understanding of patterns in real communities.     

Responses of Biofilm-Dwelling Ciliate Communities to Planktonic and Benthic Resource Enrichment

Four experiments covering different seasons were performed to test the impact of increased benthic and planktonic resource availability on the structure of biofilm-dwelling ciliate communities which were cultivated in river bypass systems. The growth of benthic bacteria was stimulated by the addition of dissolved organic carbon. The enrichment of the planktonic resource was achieved by supplementation with suspended bacteria. It was shown that both resource enrichments can differentially influence abundance and taxonomic structure of ciliate communities. Furthermore, both resources can influence different stages during biofilm colonization. Increased benthic bacterial growth mainly resulted in both an accumulation of primarily grazing-resistant bacterial filaments and in an increase in the number of vagile heterotrophic flagellates. This can stimulate nanophagous ciliates (feeding on flagellates) in addition to the direct stimulation of bacteriovorous ciliates. The effects of the planktonic bacteria enrichments were twofold: They could have been utilized either directly by suspension-feeding ciliates or indirectly through an enhanced growth of suspension-feeding attached heterotrophic flagellates, which were then in turn grazed upon by ciliates. The magnitude of responses of the total ciliate abundance to the two resource enrichments further depended on the background conditions, thereby showing temporarily variable limitations of these resources. Furthermore, the particular taxonomic groups stimulated by one resource type sometimes differed between the experiments, an observation which demonstrates that the response depends on different environmental factors and is not easily predictable based simply on resource type. Taken together, our results emphasize the need of a differentiated view on the effects of resources on complex biofilm-dwelling consumer communities with respect to both the origin of carbon source as well as the particular environmental conditions.     

The structure and stability of model ecosystems assembled in a variable environment

To explore how environmental variability may create non‐random community structure, we simulated the assembly of model communities under varying levels of environmental variability. We assembled communities by creating a large pool of randomly constructed species, and then added species from this pool sequentially, allowing extinctions of invading and resident species to occur until the community became saturated. Because much current research on community structure focuses on single trophic levels, we constructed species pools consisting only of competitors. To compare with more realistic communities, we also created species pools with multiple trophic levels. For both types of communities, following assembly we calculated a variety of metrics of community structure, and five measures of community stability. Communities assembled under high environmental variability had fewer species, fewer and weaker interactions among species, and greater evenness in abundance of persisting species. For single trophic‐level communities, community size was dictated primarily by competitive exclusion. In contrast, for multiple trophic‐level communities, community size was increasingly limited by dynamical instabilities as environmental variability increased. Differences in community structure resulting from assembly under high environmental variability led to differences in community stability. According to two measures of stability related to population variability – the characteristic return rate to equilibrium and the coefficient of variation in individual species densities – stability increased for communities assembled under high environmental variability. In contrast, three additional measures of stability that are not directly related to population variability showed a variety of patterns, either increasing, decreasing, or remaining constant. Thus, communities assembled in highly variable environments are not necessarily generically more stable. Our results demonstrate that environmental variability can structure communities and affect their stability properties in non‐trivial ways. Thus, when making predictions about the response of communities to future extinctions or environmental degradation, account should be given to the forces responsible for community structure.     

Contrasting resource limitations of marine primary producers: implications for competitive interactions under enriched CO2 and nutrient regimes

Primary producers rarely exist under their ideal conditions, with key processes often limited by resource availability. As human activities modify environmental conditions, and therefore resource availability, some species may be released from these limitations while others are not, potentially disrupting community structure. In order to examine the limitations experienced by algal functional groups that characterise alternate community structures (i.e. turf-forming algae and canopy-forming kelp), we exposed these groups to contemporary and enriched levels of carbon dioxide (CO₂) and nutrients. Turfs responded to the individual enrichment of both CO₂ and nutrients, with the greatest shift in the biomass and carbon:nitrogen (C:N) ratios observed under their combined enrichment. In contrast, kelp responded to enriched nutrients, but not enriched CO₂. We hypothesise that the differing limitations reflect the contrasting physiologies of these functional groups, specifically their methods of C acquisition, such as the possession and/or efficiency of a carbon concentrating mechanism (CCM). Importantly, our results reveal that these functional groups, whose interactions structure entire communities, experience distinct resource limitations, with some potentially limited by a single type of resource (i.e. kelp by nutrients), while others may be co-limited (i.e. turf by CO₂ and nutrients). Consequently, the identification of how alternate conditions modify resource availability and limitations may facilitate anticipation of the future sustainability of major ecosystem components and the communities they support.     

Effect of Leaf Type and Pesticide Exposure on Abundance of Bacterial Taxa in Mosquito Larval Habitats

Lentic freshwater systems including those inhabited by aquatic stages of mosquitoes derive most of their carbon inputs from terrestrial organic matter mainly leaf litter. The leaf litter is colonized by microbial communities that provide the resource base for mosquito larvae. While the microbial biomass associated with different leaf species in container aquatic habitats is well documented, the taxonomic composition of these microbes and their response to common environmental stressors is poorly understood. We used indoor aquatic microcosms to determine the abundances of major taxonomic groups of bacteria in leaf litters from seven plant species and their responses to low concentrations of four pesticides with different modes of action on the target organisms; permethrin, malathion, atrazine and glyphosate. We tested the hypotheses that leaf species support different quantities of major taxonomic groups of bacteria and that exposure to pesticides at environmentally relevant concentrations alters bacterial abundance and community structure in mosquito larval habitats. We found support for both hypotheses suggesting that leaf litter identity and chemical contamination may alter the quality and quantity of mosquito food base (microbial communities) in larval habitats. The effect of pesticides on microbial communities varied significantly among leaf types, suggesting that the impact of pesticides on natural microbial communities may be highly complex and difficult to predict. Collectively, these findings demonstrate the potential for detritus composition within mosquito larval habitats and exposure to pesticides to influence the quality of mosquito larval habitats.     

Size‐based interactions across trophic levels in food webs of shallow Mediterranean lakes

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Individual‐based modelling of resource competition to predict density‐dependent population dynamics: a case study with white storks

Density regulation influences population dynamics through its effects on demographic rates and consequently constitutes a key mechanism explaining the response of organisms to environmental changes. Yet, it is difficult to establish the exact form of density dependence from empirical data. Here, we developed an individual‐based model to explore how resource limitation and behavioural processes determine the spatial structure of white stork Ciconia ciconia populations and regulate reproductive rates. We found that the form of density dependence differed considerably between landscapes with the same overall resource availability and between home range selection strategies, highlighting the importance of fine‐scale resource distribution in interaction with behaviour. In accordance with theories of density dependence, breeding output generally decreased with density but this effect was highly variable and strongly affected by optimal foraging strategy, resource detection probability and colonial behaviour. Moreover, our results uncovered an overlooked consequence of density dependence by showing that high early nestling mortality in storks, assumed to be the outcome of harsh weather, may actually result from density dependent effects on food provision. Our findings emphasize that accounting for interactive effects of individual behaviour and local environmental factors is crucial for understanding density‐dependent processes within spatially structured populations. Enhanced understanding of the ways animal populations are regulated in general, and how habitat conditions and behaviour may dictate spatial population structure and demographic rates is critically needed for predicting the dynamics of populations, communities and ecosystems under changing environmental conditions.