Spatial variance in abundance and occupancy of corals across broad geographic scales

Species assemblages vary in structure due to a wide variety of processes operating at ecological and much broader biogeographical scales. Cross-scale studies of assemblage structure are necessary to fully understand this variability. Here, we evaluate the abundance and occupancy patterns of hierarchically sampled coral assemblages in three habitats (reef flat, crest, and slope) and five regions (Indonesia, Papua New Guinea, the Solomon Islands, American Samoa, and the Society Islands) across the west-central Pacific Ocean. Specifically, we compare two alternative models that unify spatial variance and occupancy via the negative binomial distribution. The first assumes a power-law scaling between the mean and variance of abundance; the second assumes a quadratic variance-mean relationship and a constant abundance-invariant aggregation parameter. Surprisingly, the well-established power-law model performs worse than the model assuming abundance-invariant aggregation, for both variance-mean and occupancy-abundance relationships. We also find strong evidence for regional and habitat variation in these relationships and in the levels of aggregation estimated by the abundance-invariant aggregation model. Among habitats, corals on reef flats exhibited lower occupancy and higher levels of aggregation compared to reef crests and slopes. Among regions, low occupancy and high aggregation were most pronounced across all habitats in American Samoa. These patterns may be related to habitat and regional differences in disturbance and recovery processes. Our results suggest that the spatial scaling of abundance and occupancy is sensitive to processes operating among these habitats and at regional scales. However, the consistency of these relationships across species within assemblages suggests that a theoretical unification of spatial variance and occupancy patterns is indeed possible.     

Nested Subsets and the Distribution of Birds on Isolated Woodlots

Abstract. Distribution of bird species among isolated habitat patches (e.g., woodlots in an agricultural landscape) often appears to be nonrandom; species present in small, species-poor patches also are found in larger patches that support more species. Bird communities form 'nested subsets' (after Patterson & Atmar 1986) if all species found in small faunas also are found in more species-rich assemblages. Occurrence of a nested subset pattern implies an underlying, nonrandom pattern of species distributions. I used computer simulations to analyze the degree of nestedness exhibited by bird communities in east-central Illinois. Results demonstrated that the distribution of bird species breeding in isolated woodlots (1.8 to 600 ha) differed significantly from that predicted by a random distribution model; species assemblages were more "nested" than expected by chance. Most species present in small, species-poor woodlots also were found in larger, species-rich woodlots. As groups, species requiring forest interior habitat for breeding and species wintering in the tropics showed highly nested distributions. In contrast, short-distance migrants and species breeding in forest edge habitat showed more variable distribution patterns, species recorded on smaller woodlots were not always recorded on larger, more species-rich wood-lots. Apparent absences from larger woodlots may have reflected real distribution patterns or insufficient sampling of edge habitats. These results support previous conclusions that small habitat patches are insufficient for preservation of many species.     

In search of quorum effects in metacommunity structure: species co-occurrence analyses

Alternative models of community assembly emphasize regional, stochastic, dispersal-based processes or local, deterministic, niche-based processes. Community ecology's historical focus on local processes implicitly assumes that local processes surpass regional processes over time or across space to derive nonrandom metacommunity structure (i.e., a quorum effect). Quorum effects are expected late in succession among nearby sites, whereas quorum effects are not expected early in succession among distant sites. I conducted a meta-analysis of zooplankton data sets encompassing time scales of one to thousands of years and spatial scales of <1 m to thousands of kilometers. Species co-occurrence analyses statistically evaluated presence/absence patterns relative to random patterns obtained with Monte Carlo null models. A series of weighted analyses was conducted and alternative randomization algorithms and null models were evaluated. Most zooplankton metacommunities were randomly structured in unweighted analyses, and the distribution of significant structure did not follow quorum effect predictions. Weighted analyses (e.g., by habitat area) revealed significant, nonrandom structure in most zooplankton metacommunities, but the distribution of significant structure still did not adhere well to quorum effect predictions. Finally, additional weighting for study scale (number of sites) nullified most significant area-weighted structure, and again, the distribution of significant structure did not follow quorum effect predictions. Overall, a quorum effect was not supported, perhaps related to zooplankton life histories and energetics and/or the quorum effect itself. Results at the presence/absence level of resolution indicated that local processes did not generally override regional processes over time or across space to drive community structure. A full integration of dispersal- and niche-based concepts in metacommunity dynamics will be most fruitful for unraveling community assembly. Species co-occurrence analyses were scale dependent (habitat area and study size). Future analyses should use weights for important factors (e.g., habitat area), and meta-analyses should include study scale as an additional factor contributing to apparent patterns.     

Organization of Plethodon salamander communities: guild-based community assembly

A long-standing goal in evolutionary ecology is to determine whether the organization of communities is reflective of underlying deterministic processes. In this study, I examined patterns of species co-occurrence among eastern Plethodon salamanders and determined whether they were consistent with predictions from a guild model of competition-based community assembly. Using a database of 45 species and 4540 geographic sites, I found that patterns of co-occurrence were significantly nonrandom at both a regional and continental scale, and species of different size guilds were distributed more evenly in sites than was expected by chance. Sites with the highest species richness had consistent patterns of community composition, and with few exceptions, the same five species were present at all sites. Taken together, these results imply that larger Plethodon communities are assembled from simpler communities in a manner consistent with what is predicted through competitive mechanisms and suggest that stable species combinations are possible to achieve at various levels of species richness. These results also provide strong evidence consistent with the hypothesis that competitive-based community assembly is a general phenomenon in Plethodon and that interspecific competition is prevalent among the eastern species of this group.     

Microbial diversity and ecological networks as indicators of environmental quality

Evaluating the quality of ecosystems in terms of biological patrimony and functioning is of critical importance in the actual context of intensified human activities. Microbial diversity is commonly used as a bioindicator of ecosystems functioning. However, there is a lack of sensitivity of microbial diversity indicators in the case of moderate and chronic environmental degradation, such as atmospheric deposition of pollutants, agricultural practices, diffuse pollution by wastewater and climate change. As a consequence, there is a need for alternative bioindicators of soils and water quality. Here, we discuss the interest of adopting a more integrative approach based on biotic interaction networks beyond the simple diversity indicators. We review how the various biotic interactions can be integrated in the various microbial networks such as trophic, mutualistic and co-occurrence networks. Then we discuss the efficiency of microbial networks and associated metrics to detect changes in microbial communities. We conclude that the connectance, the number of links and the average degree of co-occurrence networks could vary from 10 to 50% in response to minor perturbations when microbial diversity parameters remain stable. Finally, we analyze studies that aimed at linking microbial networks and activity to evaluate the potential of such networks for providing simple and operational indicators of ecosystem quality and functioning.     

Small-scale grassland assembly patterns differ above and below the soil surface

The existence of deterministic assembly rules for plant communities remains an important and unresolved topic in ecology. Most studies examining community assembly have sampled aboveground species diversity and composition. However, plants also coexist belowground, and many coexistence theories invoke belowground competition as an explanation for aboveground patterns. We used next-generation sequencing that enables the identification of roots and rhizomes from mixed-species samples to measure coexisting species at small scales in temperate grasslands. We used comparable data from above (conventional methods) and below (molecular techniques) the soil surface (0.1 x 0.1 x 0.1 m volume). To detect evidence for nonrandom patterns in the direction of biotic or abiotic assembly processes, we used three assembly rules tests (richness variance, guild proportionality, and species co-occurrence indices) as well as pairwise association tests. We found support for biotic assembly rules aboveground, with lower variance in species richness than expected and more negative species associations. Belowground plant communities were structured more by abiotic processes, with greater variability in richness and guild proportionality than expected. Belowground assembly is largely driven by abiotic processes, with little evidence for competition-driven assembly, and this has implications for plant coexistence theories that are based on competition for soil resources.     

Large-scale biodiversity patterns in freshwater phytoplankton

Our planet shows striking gradients in the species richness of plants and animals, from high biodiversity in the tropics to low biodiversity in polar and high-mountain regions. Recently, similar patterns have been described for some groups of microorganisms, but the large-scale biogeographical distribution of freshwater phytoplankton diversity is still largely unknown. We examined the species diversity of freshwater phytoplankton sampled from 540 lakes and reservoirs distributed across the continental United States and found strong latitudinal, longitudinal, and altitudinal gradients in phytoplankton biodiversity, demonstrating that microorganisms can show substantial geographic variation in biodiversity. Detailed analysis using structural equation models indicated that these large-scale biodiversity gradients in freshwater phytoplankton diversity were mainly driven by local environmental factors, although there were residual direct effects of latitude, longitude, and altitude as well. Specifically, we found that phytoplankton species richness was an increasing saturating function of lake chlorophyll a concentration, increased with lake surface area and possibly increased with water temperature, resembling effects of productivity, habitat area, and temperature on diversity patterns commonly observed for macroorganisms. In turn, these local environmental factors varied along latitudinal, longitudinal, and altitudinal gradients. These results imply that changes in land use or climate that affect these local environmental factors are likely to have major impacts on large-scale biodiversity patterns of freshwater phytoplankton.     

Metacommunity organization of soil microorganisms depends on habitat defined by presence of Lobelia siphilitica plants

We tested regional-scale spatial patterns in soil microbial community composition for agreement with species sorting and dispersal limitation, two alternative mechanisms behind different models of metacommunity organization. Furthermore, we tested whether regional metacommunity organization depends on local habitat type. We sampled from sites across Ohio and West Virginia hosting populations of Lobelia siphilitica, and compared the metacommunity organization of soil microbial communities under L. siphilitica to those in adjacent areas at each site. In the absence of L. siphilitica, bacterial community composition across the region was consistent with species sorting. However, under L. siphilitica, bacterial community composition was consistent with dispersal limitation. Fungal community composition remained largely unexplained, although fungal communities under L. siphilitica were both significantly different in composition and less variable in composition than in adjacent areas. Our results show that communities in different local habitat types (e.g., in the presence or absence of a particular plant) may be structured on a regional scale by different processes, despite being separated by only centimeters at the local scale.     

Associations of variable coloration with niche breadth and conservation status among Australian reptiles

We evaluate predictions concerning the evolutionary and ecological consequences of color polymorphisms. Previous endeavors have aimed at identifying conditions that promote the evolution and maintenance within populations of alternative variants. But the polymorphic condition may also influence important population processes. We consider the prediction that populations that consist of alternative "ecomorphs" with coadapted gene complexes will utilize more diverse resources and display higher rates of colonization success, population persistence, and range expansions, while being less vulnerable to range contractions and extinctions, compared with monomorphic populations. We perform pairwise comparative analyses based on information for 323 species of Australian lizards and snakes. We find that species with variable color patterns have larger ranges, utilize a greater diversity of habitat types, and are underrepresented among species currently listed as threatened. These results are consistent with the proposition that the co-occurrence of multiple color variants may promote the ecological success of populations and species, but there are also alternative interpretations.     

Mapping the niche space of soil microorganisms using taxonomy and traits

The biodiversity of microbial communities has important implications for the stability and functioning of ecosystem processes. Yet, very little is known about the environmental factors that define the microbial niche and how this influences the composition and activity of microbial communities. In this study, we derived niche parameters from physiological response curves that quantified microbial respiration for a diverse collection of soil bacteria and fungi along a soil moisture gradient. On average, soil microorganisms had relatively dry optima (0.3 MPa) and were capable of respiring under low water potentials (-2.0 MPa). Within their limits of activity, microorganisms exhibited a wide range of responses, suggesting that some taxa may be able to coexist by partitioning the moisture niche axis. For example, we identified dry-adapted generalists that tolerated a broad range of water potentials, along with wet-adapted specialists with metabolism restricted to less-negative water potentials. These contrasting ecological strategies had a phylogenetic signal at a coarse taxonomic level (phylum), suggesting that the moisture niche of soil microorganisms is highly conserved. In addition, variation in microbial responses along the moisture gradient was linked to the distribution of several functional traits. In particular, strains that were capable of producing biofilms had drier moisture optima and wider niche breadths. However, biofilm production appeared to come at a cost that was reflected in a prolonged lag time prior to exponential growth, suggesting that there is a trade-off associated with traits that allow microorganisms to contend with moisture stress. Together, we have identified functional groups of microorganisms that will help predict the structure and functioning of microbial communities under contrasting soil moisture regimes.     

Biodiversity mediates productivity through different mechanisms at adjacent trophic levels

Biodiversity may enhance productivity either because diverse communities more often contain productive species (selection effects) or because they show greater complementarity in resource use. Our understanding of how these effects influence community production comes almost entirely from studies of plants. To test whether previous results apply to higher trophic levels, we first used simulations to derive expected contributions of selection and complementarity to production in competitive assemblages defined by either neutral interactions, dominance, or a trade-off between growth and competitive ability. The three types of simulated assemblages exhibited distinct interaction signatures when diversity effects were partitioned into selection and complementarity components. We then compared these signatures to those of experimental marine communities. Diversity influenced production in fundamentally different ways in assemblages of macroalgae, characterized by growth-competition trade-offs, vs. in herbivores, characterized by dominance. Forecasting the effects of changing biodiversity in multitrophic ecosystems will require recognizing that the mechanism by which diversity influences functioning can vary among trophic levels in the same food web.     

Mechanistic analysis of interspecific competition using foraging trade-offs: implications for duck assemblages

The role of interspecific competition and resource partitioning in determining the composition of species assemblages is often controversial. In many cases data on species co-occurrence or resource use (prey or habitat) have been interpreted without a clear understanding of how, or even whether, phenotypic differences constrain performance to allow resource partitioning or how these constraints and the density of resources and competitors should shape resource selection by each species. Instead, predictions have been based on assumed constraints, possibly leading to conflicting results. One such controversy involves the role of bill morphology in mediating resource partitioning among dabbling ducks (Anas spp.). To determine whether incorrect assumptions may have contributed to this controversy, I constructed mechanistic models that predict filter-feeding performance for seven species of ducks directly from bill morphology and kinetics and compared these predictions to those of earlier studies that tested the bill morphology hypothesis. The models predicted that species should share a preference for their most profitable (primary) prey while partitioning their less profitable (secondary) prey by size. Consequently, ducks should forage in the same habitats and exhibit high overlap in prey size when competitor/resource ratios are either high or low. In contrast, earlier studies expected that resource partitioning should always be evident, which implicitly assumes that species partition their primary resources. The models also predicted that the ecological similarity of species in assemblages should increase as prey abundance and size variability declines, contrary to the expectations of an earlier study. A more consistent understanding of the mechanisms regulating assemblages of dabbling ducks, and other species, might emerge if patterns of resource use and species co-occurrence were predicted directly from a mechanistic understanding of how performance trade-offs affect resource selection in the context of varying resource and competitor densities.     

Plant-soil microorganism interactions: heritable relationship between plant genotype and associated soil microorganisms

Although soil microbial communities are known to play crucial roles in the cycling of nutrients in forest ecosystems and can vary by plant species, how microorganisms respond to the subtle gradients of plant genetic variation is just beginning to be appreciated. Using a model Populus system in a common garden with replicated clones of known genotypes, we evaluated microbial biomass and community composition as quantitative traits. Two main patterns emerged. (1) Plant genotype influenced microbial biomass nitrogen in soils under replicated genotypes of Populus angustifolia, F1, and backcross hybrids, but not P. fremontii. Genotype explained up to 78% of the variation in microbial biomass as indicated by broad-sense heritability estimates (i.e., clonal repeatability). A second estimate of microbial biomass (total phospholipid fatty acid) was more conservative and showed significant genotype effects in P. angustifolia and backcross hybrids. (2) Plant genotype significantly influenced microbial community composition, explaining up to 70% of the variation in community composition within P. angustifolia genotypes alone. These findings suggest that variation in above- and belowground traits of individual plant genotypes can alter soil microbial dynamics, and suggests that further investigations of the evolutionary implications of genetic feedbacks are warranted.     

Reducing over-reporting of deterministic co-occurrence patterns in biotic communities

Null models of species co-occurrence are widely used to infer the existence of various ecological processes. Here we investigate the susceptibility of the most commonly used of these models (the C-score in conjunction with the sequential swap algorithm) to type 1 and type 2 errors. To do this we use simulated datasets with a range of numbers of sites, species and coefficients of variation (CV) in species abundance. We find that this model is particularly susceptible to type 1 errors when applied to large matrices and those with low CV in species abundance. As expected, type 2 error rates decrease with increasing numbers of sites and species, although they increase with increasing CV in species abundance. Despite this, power remains acceptable over a wide range of parameter combinations. The susceptibility of this analytical method to type 1 errors indicates that many previous studies may have incorrectly reported the existence of deterministic patterns of species co-occurrence. We demonstrate that in order to overcome the problem of high type 1 error rates, the number of swaps used to generate null distributions for smaller matrices needs to be increased to over 50,000 swaps (well beyond the 5000 commonly used in published analyses and the 30,000 suggested by Lehsten and Harmand, 2006). We also show that this approach reduces type 1 error rates in real datasets. However, even using this solution, larger datasets still suffer from high type 1 error rates. Such datasets therefore require the use of very large numbers of swaps, which calls for improvements in the most commonly used software. In general, users of this powerful analytical method must be aware that they need surprisingly large numbers of swaps to obtain unbiased estimates of structuring in biotic communities.     

A trait-based test for habitat filtering: convex hull volume

Community assembly theory suggests that two processes affect the distribution of trait values within communities: competition and habitat filtering. Within a local community, competition leads to ecological differentiation of coexisting species, while habitat filtering reduces the spread of trait values, reflecting shared ecological tolerances. Many statistical tests for the effects of competition exist in the literature, but measures of habitat filtering are less well-developed. Here, we present convex hull volume, a construct from computational geometry, which provides an n-dimensional measure of the volume of trait space occupied by species in a community. Combined with ecological null models, this measure offers a useful test for habitat filtering. We use convex hull volume and a null model to analyze California woody-plant trait and community data. Our results show that observed plant communities occupy less trait space than expected from random assembly, a result consistent with habitat filtering.     

Effects of crowding due to habitat loss on species assemblage patterns

Terrestrial animals are negatively affected by habitat loss, which is assessed on a landscape scale, whereas secondary effects of habitat loss, such as crowding, are usually disregarded. Such impacts are inherently hard to address and poorly understood, and there is a growing concern that they could have dire consequences. We sampled birds throughout a deforestation process to assess crowding stress in an adjacent habitat remnant in the southern Brazilian Atlantic Forest. Crowding is expected of highly mobile taxa, especially given the microhabitat heterogeneity of Neotropical forests, and we hypothesized that the arrival of new individuals or species in refuges shifts assemblage patterns. We used point counts to obtain bird abundances in a before-after-control-impact design sampling of a deforestation event. Temporal changes in taxonomic and functional diversity were examined with metrics used to assess alpha and beta diversity, turnover of taxonomic and functional similarity, and taxonomic and functional composition. Over time increased abundance of some species altered the Simpson index and affected the abundance-distribution of traits in the habitat remnant. Taxonomic composition and functional composition changed in the remnant, and thus bird assemblages changed over time. Taxonomic and functional metrics indicated that fugitives affected resident assemblages in refuges, and effects endured >2 years after the deforestation processes had ceased. Dissimilarity of taxonomic composition between pre- and postdeforestation assemblages increased, whereas functional composition reverted to preimpact conditions. We found that ecological disruptions resulted from crowding and escalated into disruptions of species’ assemblages and potentially compromising ecosystem functioning. It is important to consider crowding effects of highly mobile taxa during impact assessments, especially in large-scale infrastructure projects that may affect larger areas than is assumed.     

Microbial community variation and its relationship with nitrogen mineralization in historically altered forests

Past land use can impart soil legacies that have important implications for ecosystem function. Although these legacies have been linked with microbially mediated processes, little is known about the long-term influence of land use on soil microbial communities themselves. We examined whether historical land use affected soil microbial community composition (lipid profiles) and whether community composition was related to potential net nitrogen (N) mineralization rates in southern Appalachian (USA) forest stands abandoned from agriculture or logging and reforested >50 yr ago. Microbial community composition was determined by a hybrid procedure of phospholipid fatty acid (PLFA) and fatty acid methyl ester (FAME) analysis. We found that community composition varied significantly with past land use. Communities in formerly farmed stands had a higher relative abundance of markers for gram-negative bacteria and a lower abundance of markers for fungi compared with previously logged and reference (i.e., no disturbance history) stands. Potential net N mineralization rates were negatively correlated with fungal and gram-negative bacterial markers in both farmed and reference stands, and fungal abundance and soil bulk density effectively predicted mineralization rates in all stands. Our results indicate that the alteration of microbial communities by historical land use may influence the ecosystem processes they mediate. This is in contrast to typical expectations about microbial community resilience to change. Here, the decrease in fungal abundance observed from disturbance appeared to result in decreased nitrogen mineralization over the long term.     

Microbial community phylogenetic and trait diversity declines with depth in a marine oxygen minimum zone

Oxygen minimum zones (OMZs) are natural physical features of the world's oceans. They create steep physiochemical gradients in the water column, which most notably include a dramatic draw down in oxygen concentrations over small vertical distances (<100 m). Microbial communities within OMZs play central roles in ocean and global biogeochemical cycles, yet we still lack a fundamental understanding of how microbial biodiversity is distributed across OMZs. Here, we used metagenomic sequencing to investigate microbial diversity across a vertical gradient in the water column during three seasons in the Eastern Tropical South Pacific (ETSP) OMZ. Based on analysis of small subunit ribosomal RNA (SSU rRNA) gene fragments, we found that both taxonomic and phylogenetic diversity declined steeply along the transition from oxygen-rich surface water to the permanent OMZ. We observed similar declines in the diversity of protein-coding gene categories, suggesting a decrease in functional (trait) diversity with depth. Metrics of functional and trait dispersion indicated that microbial communities are phylogenetically and functionally more overdispersed in oxic waters, but clustered within the OMZ. These dispersion patterns suggest that community assembly drivers (e.g., competition, environmental filtering) vary strikingly across the oxygen gradient. To understand the generality of our findings, we compared OMZ results to two marine depth gradients in subtropical oligotrophic sites and found that the oligotrophic sites did not display similar patterns, likely reflecting unique features found in the OMZ. Finally, we discuss how our results may relate to niche theory, diversity-energy relationships and stress gradients.     

Complementary habitat use by wild bees in agro-natural landscapes

Human activity causes abrupt changes in resource availability across the landscape. In order to persist in human-altered landscapes organisms need to shift their habitat use accordingly. Little is known about the mechanisms by which whole communities persist in human-altered landscapes, including the role of complementary habitat use. We define complementary habitat use as the use of different habitats at different times by the same group of species during the course of their activity period. We hypothesize that complementary habitat use is a mechanism through which native bee species persist in human-altered landscapes. To test this idea, we studied wild bee communities in agro-natural landscapes and explored their community-level patterns of habitat and resource use over space and time. The study was conducted in six agro-natural landscapes in the eastern United States, each containing three main bee habitat types (natural habitat, agricultural fields, and old fields). Each of the three habitats exhibited a unique seasonal pattern in amount, diversity, and composition of floral resources, and together they created phenological complementarity in foraging resources for bees. Individual bee species as well as the bee community responded to these spatiotemporal patterns in floral availability and exhibited a parallel pattern of complementary habitat use. The majority of wild bee species, including all the main crop visitors, used fallow areas within crops early in the season, shifted to crops in mid-season, and used old-field habitats later in the season. The natural-forest habitat supported very limited number of bees, mostly visitors of non-crop plants. Old fields are thus an important feature in these arable landscapes for maintaining crop pollination services. Our study provides a detailed examination of how shifts in habitat and resource use may enable bees to persist in highly dynamic agro-natural landscapes, and points to the need for a broad cross-habitat perspective in managing these landscapes.