Metacommunity Structure Analysis Research Articles

Skin bacterial metacommunities of San Francisco Bay Area salamanders are structured by host genus and habitat quality.

Host-associated microbial communities can influence physiological processes of macroorganisms, including contributing to infectious disease resistance. For instance, some bacteria that live on amphibian skin produce antifungal compounds that inhibit two lethal fungal pathogens, Batrachochytrium dendrobatidis (Bd) and Batrachochytrium salamandrivorans (Bsal). Therefore, differences in microbiome composition among host species or populations within a species can contribute to variation in susceptibility to Bd/Bsal. This study applies 16S rRNA sequencing to characterize the skin bacterial microbiomes of three widespread terrestrial salamander genera native to the western United States. Using a metacommunity structure analysis, we identified dispersal barriers for these influential bacteria between salamander families and localities. We also analysed the effects of habitat characteristics such as percent natural cover and temperature seasonality on the microbiome. We found that certain environmental variables may influence the skin microbial communities of some salamander genera more strongly than others. Each salamander family had a somewhat distinct community of putative anti-Bd skin bacteria, suggesting that salamanders may select for a functional assembly of cutaneous symbionts that could differ in its ability to protect these amphibians from disease. Our observations raise the need to consider host identity and environmental heterogeneity during the selection of probiotics to treat wildlife diseases.

Variation in processes structuring fish assemblages as inferred from metacommunity analyses: Differences between headwater and adventitious streams within a river network

Community assembly is generally affected by the spatial position of local patches. Examining metacommunity processes and structures in small streams with different river network positions (e.g., headwater streams in the periphery of river networks vs adventitious streams in relatively central positions) may help us better understand how spatial position influences metacommunity structuring. In this study, based on data collected from sampling 24 headwater and 15 adventitious stream sites in the Xin’an Basin, China, we examined whether and how fish metacommunity processes and structures differed between the 2 stream types. We used distanced-based redundancy analysis coupled with forward selection to assess the relative roles of environmental and spatial factors in metacommunity processes, and we applied the elements of metacommunity structure analysis, extended by using different ordinations, to identify metacommunity structures. We found that the 2 types of streams were similar in environmental heterogeneity, but fish assemblages in adventitious streams were more dissimilar to one another than were assemblages in headwater streams and had more riverine immigrants. The amount of among-stream variation in species composition was low in both stream types. In headwater streams, assemblage–environment relationships were stronger than assemblage–space relationships, but we found the opposite pattern in adventitious streams. Species turnover was strong in both headwater and adventitious streams. However, assemblages in headwater streams showed both nested and quasi-nested structures, whereas the assemblages in adventitious streams were more consistent with Clementsian structure. Our results suggest that different metacommunity processes may occur in small streams with distinct river network positions and that extended elements of metacommunity structure analysis can help identify the underlying mechanisms that produce metacommunity structure. The effect of spatial position within river networks on stream fish metacommunity structuring appears to be weak, but our analyses do imply that river immigrants can influence species composition in adventitious streams to some extent.

Metacommunity Structures of Macroinvertebrates and Diatoms in High Mountain Streams, Yunnan, China

The metacommunity concept has received increasing interest in the past two decades. However, there has been limited research examining metacommunity structure of communities in high mountain streams. These ecosystems are often physically constrained and can display large environmental gradients within a relatively small spatial extent. Here, we examined metacommunity structures of stream organisms in a high mountain region, which is part of the Hengduan Mountains region in the Southwest China. Macroinvertebrates and diatoms were collected from six streams in two opposite aspects of the same mountain with different connectivity between streams. On the west aspect, streams are tributaries of a river (i.e. river-connected) while streams flow into a lake (i.e. lake-connected) on the east aspect. We used Elements of Metacommunity Structure analysis to explore the metacommunity structuring of these two biological models. We also compared the contribution of dispersal and environmental filtering in structuring metacommunities by looking at Euclidean, network, topographic, and environmental distances. Communities of diatoms and macroinvertebrates were structured with clear turnover on both aspects. Further, diatom communities exhibited Clementsian structure on both aspects. Macroinvertebrates exhibited different metacommunity structures on the river-connected aspect (Quasi-Clementsian) and lake-connected aspect (Clementsian). Our results indicated that on the lake-connected aspect, environmental filtering had a stronger association with community dissimilarity than on the river-connected aspect for both macroinvertebrate and diatom communities. Diatom communities were more influenced by environmental filtering on the east aspect with weakened network connectivity compared with those on the west aspect. Our results also emphasized the potential effects of biotic interactions between macroinvertebrates and diatoms on shaping community structures of one other. Given that high mountain streams are scarcely examined, our study provides substantial elements to further understand metacommunity structure and highlights the necessity of future research to reveal the underlying mechanisms of community structuring in these remote ecosystems.

Metacommunity structure analysis reveals nested patterns in deconstructed macroinvertebrates assemblages

Understanding processes driving patterns of species distribution and diversity is one of the main objectives of community ecology. The aim of our study was to evaluate the spatial variation in assemblage composition of stream‐dwelling macroinvertebrates and identify which factors (e.g. water quality, land cover) are the most important drivers. We applied the elements of the metacommunity structure approach on a dataset of 38 communities from the Futaleufú basin in northwestern Patagonia. To better understand assemblage variation, we deconstructed our macroinvertebrate dataset into different taxonomic and trait groups. We then identified the most influential factors driving community composition using random forests. We found that half of our datasets (i.e. macroinvertebrate groups) exhibited a nested structure with clumped species loss, while the other half showed a quasi‐nested pattern with either clumped or stochastic species loss. Overall, water quality was the most important driver of community variation, although climate, geography, and land cover were more or less relevant in particular cases. We found differences in the relative importance of the selected explanatory variables among datasets. This would suggest that different components of the macroinvertebrate community respond differently to environmental factors. Our findings could be of value for conservation planning, as they suggest that preserving the most species‐rich streams would, to some extent, guarantee the conservation of the entire species pool.

Metacommunity Structure of Helminths of Necromys Lasiurus (Rodentia: Sigmodontinae) in Different Land Use Areas in the Brazilian Cerrado

The ecology of host-parasite interactions can be studied in the infracommunity and component community scales, which may show different patterns in species distributions, interacting and affecting each other on a regional scale. Few studies have been carried out concerning the structure and variation of the helminth communities of wild rodents in Brazil. The rodent Necromys lasiurus is typical from the mammalian fauna of the Cerrado biome; however, the environmental disturbances are making this species occur in rural areas and in other biomes where it may act as host/reservoir of many diseases. This study aimed to describe the composition and structure of the helminth metacommunity in the rodent N. lasiurus in the Brazilian Cerrado, Uberlândia, State of Minas Gerais, using the analysis of metacommunity structure. Rodents were sampled in 3 habitat types: borders of soybean and corn plantations, pasturelands, and preserved areas of Cerrado borders. Adult helminths of 8 species were found in the gastrointestinal tract: Protospirura numidica criceticola, Physaloptera sp., Pterygodermatites ( Paucipectines) zygodontomis (Spirurida), Stilestrongylus freitasi (Rhabditida), Trichuris navonae (Trichurida) and Syphacia ( Syphacia) alata (Oxiurida) of the Phylum Nematoda; Rodentolepis akodontis (Cyclophyllidea) of the Phylum Platyhelminthes; and Moniliformis sp. (Moniliformida) of the Phylum Acanthocephala. Season and the kind of land use favored some helminths species in this rodent, especially in the plantation area, although diversity was not largely influenced by the land use. Plantation areas could provide an increase in the host abundance and the occurrence of other rodent species, favoring a higher rate of parasite exchange among different hosts. A checkerboard structure of metacommunity was found on the infracommunity scale, which suggests the existence of interspecific competition. A quasi-nested structure of metacommunity was observed on the component community scale showing that most species were influenced by the same environmental gradient and that the species-poor communities were subsets of species-rich communities. Syphacia alata, P. zygodontomis, S. freitasi, and R. akodontis were dominant species in all habitats and represented the core-species in the metacommunity.

Metacommunity structure of the helminths of the black-eared opossum Didelphis aurita in peri-urban, sylvatic and rural environments in south-eastern Brazil.

Among the Brazilian marsupials, the species of the genus Didelphis are the most parasitized by helminths. This study aimed to describe the species composition and to analyse the helminth communities of the Atlantic Forest common opossum Didelphis aurita at infracommunity and component community levels using the Elements of Metacommunity Structure Analysis, considering peri-urban, sylvatic and rural environments in the state of Rio de Janeiro, Brazil. Seventy-three specimens of D. aurita were captured during the study. Fourteen species of helminths were collected: nine of the phylum Nematoda (Trichuris minuta, Trichuris didelphis, Globocephalus marsupialis, Heterostrongylus heterostrongylus, Travassostrongylus orloffi, Viannaia hamata, Aspidodera raillieti, Cruzia tentaculata and Turgida turgida); four of the phylum Platyhelminthes (three species of Trematoda, Duboisiella proloba, Brachylaima advena and Rhopalias coronatus, and one species of the class Cestoda); and one species of the phylum Acanthocephala (Oligacanthorhynchus microcephalus). More than 95% of the animals were infected with parasites. The most abundant parasite species were V. hamata, T. turgida, C. tentaculata and T. orloffi. The nematodes T. turgida, C. tentaculata and A. raillieti were the most dominant species in the three environments. The analysis of the metacommunity structure indicated a structured pattern as a function of the environmental gradient, but only when all localities were considered together. At the infracommunity and component community levels, quasi-nested and nested structures with stochastic species loss were observed, respectively. The results indicate that the settlement of helminth species in the opossums can be attributed to the heterogeneity among individual hosts in relation to their exposure to parasites and to extrinsic factors, which vary among habitats, considering a regional scale. On a local scale, the characteristics of this host species may promote homogenization among individual hosts in terms of their exposure to the helminths. This study constitutes a new host record for the species G. marsupialis and T. didelphis and represents a pioneering investigation of the helminth metacommunity of a Neotropical marsupial.

Substantial changes in the depth distributions of benthic invertebrates in the eastern Kattegat since the 1880s.

Bottom trawling and eutrophication are well known for their impacts on the marine benthic environment in the last decades. Evaluating the effects of these pressures is often restricted to contemporary benthic data, limiting the potential to observe change from an earlier (preimpact) state. In this study, we compared benthic species records from 1884 to 1886 by CGJ Petersen with recent data to investigate how benthic invertebrate species in the eastern Kattegat have changed since preimpact time. The study shows that species turnover between old and recent times was high, ca. 50%, and the species richness in the investigation area was either unchanged or higher in recent times, suggesting no net loss of species. Elements of metacommunity structure analysis of datasets from the 1880s, 1990s, and 2000s revealed a clear change in the depth distribution structure since the 1880s. The system changed from a Quasi‐nested/Random pattern unrelated to depth in the 1880s with many species depth ranges over a major part of the studied depth interval, to a Clementsian pattern in recent times strongly positively correlated with depth. Around 30% of the 117 species recorded both in old and in recent times, including most trawling‐sensitive species, that is large, semiemergent species, showed a decrease in maximal depth of occurrence from the deeper zone fished today to the shallower unfished zone, with on average 20 m. Concurrently, the species category remaining in the fished zone was dominated by species less sensitive to bottom trawling like infauna polychaetes and small‐sized Peracarida crustaceans, most likely with short longevity. The depth interval and magnitude of the changes in depth distribution and the changes in species composition indicate impacts from bottom trawling rather than eutrophication. Furthermore, the high similarity of results from the recent datasets 10 years apart suggests chronic impact keeping the system in an altered state.

Strong spatial turnover in cichlid fish assemblages in the upper río Madera (Amazon basin) despite the absence of hydrological barriers

In freshwater ecosystems, spatial turnover in fish assemblages is often attributed to dispersal limitation imposed by fragmentation of water bodies. Other factors like environmental properties or biotic interactions have often been assumed to be minute relative to dispersal limitation when hydrogeological barriers are abundant. This study aims to describe the spatial differentiation of cichlid fish assemblages in the upper rio Madera in Bolivia, Brazil and Peru, a large drainage system characterized by the absence of significant hydrogeological barriers. We assessed the relative importance of spatial, climatic and geological predictors in the observed biogeographic structure using an integrative combination of cluster analyses, elements of metacommunity structure analysis, variation partitioning, and network analysis. Our results show that distinct assemblages of cichlid fish species replace each other across the landscape and that this turnover is partially determined by climate and geological gradients. A considerable fraction of the cichlid assembly structure could not be assigned to either space, climate or geology and might be explained by unmeasured parameters such as habitat structure or biotic interactions. Incorporating knowledge on spatial turnover of species assemblages into conservation strategies will be essential for the biodiversity management of the diverse aquatic fauna of the upper rio Madera.

Inferring implications of climate change in south Florida hardwood hammocks through analysis of metacommunity structure

AbstractAimIn order to explore how variation in regional biogeography would affect forest responses to climate change, we analysed metacommunity structure of trees in natural forest fragments across a boundary between tropical and sub‐tropical temperature regimes. We wished to determine whether species assemblages were constrained by periodic cold temperatures, dispersal limitation and/or local processes associated with fragment size, and consider how these influences might affect future species migration and community reassembly.LocationSoutheastern Florida, USA.MethodsWe collected complete tree species lists for 144 forest fragments, from our own surveys supplemented by publicly available sources. The resulting species‐by‐site data matrix was re‐ordered based on an ordination that identified the latent environmental axis most responsible for variation in composition, and metacommunity structure was analysed for coherence, turnover and range boundary clumping. Matrix structure was tested for associations with site variables, and with community‐aggregated functional traits related to cold tolerance, dispersal limitation and fragment size.ResultsForest patch size was the strongest single correlate with composition and species richness, but mean January temperature and a neighbourhood index denoting degree of isolation from other patches contributed significantly to regression models. The species‐by‐site matrix was highly nested, with trees common to small upland fragments in the Everglades interior representing a distinct subset of the richer assemblages found in sites closer to the coast. Interior forests were smaller, more isolated, and subject to cooler minimum temperatures than more coastal forests, and were comprised primarily of early‐successional, animal dispersed species.Main conclusionsWhile warming winter temperatures may relax some constraints on the northward migration of tropical species through the region, sea level rise will raise ground water levels, decreasing the size and number of suitable mesic patches, and increasing their isolation. The result will be a loss in tree species diversity, especially among late‐successional, edge‐sensitive species.

Metacom: an R package for the analysis of metacommunity structure

Metacommunity theory is an extension of metapopulation theory with the goal of understanding how ecological communities vary through space and time. One off‐shoot of metacommunity theory deals with understanding how community structure varies along biotic or environmental gradients. The Elements of Metacommunity Structure framework is a three‐tiered analysis of metacommunity structure that enables the user to identify metacommunity properties that arise in site‐by‐species incidence matrices. These properties can then be related to underlying variables that influence species distributions. The EMS framework is now implemented in metacom, an open source R package that allows for the analysis and plotting of metacommunities.

Evaluating the role of biotic interactions in structuring communities using a gradient analysis of multiple interacting guilds

The extent to which ecological communities are coherent entities as opposed to mere intersections of individual species distributions has long been one of the fundamental questions of ecology. Gradient analysis is one commonly used tool for addressing this question; however, all such studies have used organisms from a single taxon or guild. This risks missing important connections due to non‐competitive interactions, which should be more likely to occur between members of different guilds. Such organisms are unlikely to compete for resources and can have complementary niches that promote non‐competitive interactions. We examined the abundances of taxa in four interacting guilds along an elevation gradient in a forest in the southern Appalachian mountains. A causal discovery algorithm was used to investigate the relative frequencies of interguild and intraguild interactions. These were approximately equally common once taxonomic richness was taken into account. We used elements of metacommunity structure analysis to study the extent to which species distributions are non‐independent and tested the hypothesis that combinations of two or more interacting guilds exhibit more coherence than single guilds. In this analysis, all guilds other than collembola were classified as Clementsian or quasi‐Clementsian. (Collembola were classified as random.) When sets of multiple guilds were examined, Clementsian and quasi‐Clementsian structures predominated. We also compared boundary conjunction, measured as Morisita’s index (MI) for these sets of guilds to the weighted average of the guilds’ MI values. Only sets of directly interacting guilds had higher‐than‐baseline boundary conjunction values, and such boundary conjunction values are found in all but one set of directly interacting guilds. Our results highlight the importance of inter‐guild interactions in structuring patterns of cooccurrence. Trophic interactions and plant–fungus symbioses (mutualistic and/or pathogen–host) appear particularly important.

Disentangling the drivers of metacommunity structure across spatial scales.

Metacommunity theories attribute different relative degrees of importance to dispersal, environmental filtering, biotic interactions and stochastic processes in community assembly, but the role of spatial scale remains uncertain. Here we used two complementary statistical tools to test: (1) whether or not the patterns of community structure and environmental influences are consistent across resolutions; and (2) whether and how the joint use of two fundamentally different statistical approaches provides a complementary interpretation of results. Grassland plants in the French Alps. We used two approaches across five spatial resolutions (ranging from 1 km × 1 km to 30 km × 30 km): variance partitioning, and analysis of metacommunity structure on the site-by-species incidence matrices. Both methods allow the testing of expected patterns resulting from environmental filtering, but variance partitioning allows the role of dispersal and environmental gradients to be studied, while analysis of the site-by-species metacommunity structure informs an understanding of how environmental filtering occurs and whether or not patterns differ from chance expectation. We also used spatial regressions on species richness to identify relevant environmental factors at each scale and to link results from the two approaches. Major environmental drivers of richness included growing degree-days, temperature, moisture and spatial or temporal heterogeneity. Variance partitioning pointed to an increase in the role of dispersal at coarser resolutions, while metacommunity structure analysis pointed to environmental filtering having an important role at all resolutions through a Clementsian assembly process (i.e. groups of species having similar range boundaries and co-occurring in similar environments). The combination of methods used here allows a better understanding of the forces structuring ecological communities than either one of them used separately. A key aspect in this complementarity is that variance partitioning can detect effects of dispersal whereas metacommunity structure analysis cannot. Moreover, the latter can distinguish between different forms of environmental filtering (e.g. individualistic versus group species responses to environmental gradients).

Compositional patterns in Holarctic peat bog inhabiting oribatid mite (Acari: Oribatida) communities

Abstract Soil inhabiting oribatid mites (Acari: Oribatida) are one of the most interesting groups of animals because of their ecological characteristics at the community level. However, existing knowledge does not provide comprehensive explanations of the mechanisms underlying their community or metacommunity structure. The aim of this study is to investigate peat bog inhabiting oribatid mite metacommunity distribution throughout the Holarctic region. Species incidence data was collected (mainly from published sources) for 46 peat bog localities, comprising a total of 410 species. Characteristics of species composition (coherence, turnover and boundary clumping) were analyzed to reveal patterns of peat bog oribatid metacommunity for different ecological guilds. We also applied correlation and regression analysis to detect whether peat bog oribatid communities show latitudinal gradient and distance decay in compositional similarity. Analysis of metacommunity structure showed non-random structure for all ecological guilds studied with dominating nested and Clementsian patterns. No significant evidence was found for latitudinal gradients in species composition whereas non-linear distance decay in compositional similarity is a common phenomenon for peat bog oribatid communities. We discuss these metacommunity patterns within the framework of existing hypotheses and conclude that the community level structure for peat bog oribatid species is largely determined by interspecific interactions and common biogeographical history, whereas metacommunity patterns are the result of postglacial colonization processes.

Structure, composition and dynamics of a calcareous grassland metacommunity over a 70‐year interval

Summary1. Calcareous grasslands are communities of high conservation value, often characterized by high plant species richness. These grasslands have experienced a major decline in area throughout Europe, principally resulting from agricultural intensification. Although they have been the focus of extensive previous research, few attempts have been made to examine the long‐term dynamics of multiple communities at the landscape scale.2. To assess long‐term change in the structure and composition of a calcareous grassland metacommunity, 88 extant sites first surveyed by R. Good in the 1930s were resurveyed in 2009. Values of α‐, β‐ and γ‐diversity were compared between the two surveys, using a one‐way analysis of similarity (ANOSIM) and non‐metric multidimensional scaling. Elements of metacommunity structure (EMS) analysis was used to identify metacommunity structure, and changes in metacommunity composition were related to plant traits.3. Analyses indicated that α‐diversity increased over time, with mean (±SD) species richness per site increasing from 29.31 ± 7.65 in the 1930s to 40.18 ± 16.41 in 2009. No change in β‐diversity was recorded. However, γ‐diversity increased, with the total number of species rising from 219 in the 1930s to 280 in 2009. Species composition shifted over time, associated with a decline in ‘stress‐tolerant’ species typical of species‐rich calcareous grasslands, and an increase in species typical of mesotrophic grasslands. This was associated with an increase in mean Ellenberg N value, suggesting that eutrophication has been a driver of floristic change.4. Elements of metacommunity structure analysis indicated that the structure of this grassland plant metacommunity was Clementsian at both survey times, indicating species sorting. Metacommunity structure was stable over time, despite changes in α‐ and γ‐diversity. Analysis of potential structuring mechanisms revealed a significant influence of elevation.5. Synthesis. This investigation provides a rare example of the long‐term dynamics of a plant metacommunity. Results indicate that substantial change has occurred in the composition of calcareous grasslands during this time, both at local and regional scales. The investigation provides evidence of the impact of environmental change on immigration and extinction processes operating in calcareous grasslands at different scales, and highlights challenges for their future conservation.