Lake regionalization and diatom metacommunity structuring in tropical South America

Community metabarcoding reveals the relative role of environmental filtering and spatial processes in metacommunity dynamics of soil microarthropods across a mosaic of montane forests

Disentangling the relative role of environmental filtering and spatial processes in driving metacommunity structure across mountainous regions remains challenging, as the way we quantify spatial connectivity in topographically and environmentally heterogeneous landscapes can influence our perception of which process predominates. More empirical data sets are required to account for taxon- and context-dependency, but relevant research in understudied areas is often compromised by the taxonomic impediment. Here we used haplotype-level community DNA metabarcoding, enabled by stringent filtering of amplicon sequence variants (ASVs), to characterize metacommunity structure of soil microarthropod assemblages across a mosaic of five forest habitats on the Troodos mountain range in Cyprus. We found similar β diversity patterns at ASV and species (OTU, operational taxonomic unit) levels, which pointed to a primary role of habitat filtering resulting in the existence of largely distinct metacommunities linked to different forest types. Within-habitat turnover was correlated to topoclimatic heterogeneity, again emphasizing the role of environmental filtering. However, when integrating landscape matrix information for the highly fragmented Quercus alnifolia habitat, we also detected a major role of spatial isolation determined by patch connectivity, indicating that stochastic and niche-based processes synergistically govern community assembly. Alpha diversity patterns varied between ASV and OTU levels, with OTU richness decreasing with elevation and ASV richness following a longitudinal gradient, potentially reflecting a decline of genetic diversity eastwards due to historical pressures. Our study demonstrates the utility of haplotype-level community metabarcoding for characterizing metacommunity structure of complex assemblages and improving our understanding of biodiversity dynamics across mountainous landscapes worldwide.

Community composition exceeds area as a predictor of long-term conservation value

Conserving biodiversity often requires deciding which sites to prioritise for protection. Predicting the impact of habitat loss is a major challenge, however, since impacts can be distant from the perturbation in both space and time. Here we study the long-term impacts of habitat loss in a mechanistic metacommunity model. We find that site area is a poor predictor of long-term, regional-scale extinctions following localised perturbation. Knowledge of the compositional distinctness (average between-site Bray-Curtis dissimilarity) of the removed community can markedly improve the prediction of impacts on regional assemblages, even when biotic responses play out at substantial spatial or temporal distance from the initial perturbation. Fitting the model to two empirical datasets, we show that this conclusions holds in the empirically relevant parameter range. Our results robustly demonstrate that site area alone is not sufficient to gauge conservation priorities; analysis of compositional distinctness permits improved prioritisation at low cost.

Environmental filtering and mass effect are two important processes driving lake benthic diatoms: Results of a DNA metabarcoding study in a large lake

Environmental filtering is often found to dominate assembly rules in diatoms. These microalgae are diverse, especially at subspecies level, and tend to exhibit a niche phylogenetic conservatism. Therefore, other rules, such as competition or mass effects, should be detectable when environmental gradients and dispersal barriers are limited. We used metabarcoding to analyse benthic littoral diatom communities in 153 sites in a large lake (Geneva) exhibiting weak geographical barriers and weak environmental gradients outside river estuaries. We assessed assembly rules using variance partitioning, phylogenetic and source tracking analyses. No phylogenetic over-dispersion of communities, indicative of exclusive competition, was detected. Instead, we found these communities to be phylogenetically over-clustered, indicating environmental filtering, which was even stronger near river estuaries where environmental gradients are stronger. Finally, using a Bayesian method (SourceTracker), we found that rivers flowing into the lake bring communities that settle, especially in sites close to estuaries. Rivers with the highest discharges are primarily responsible for immigration, explaining 27% of lake composition. Therefore, despite favourable conditions to observe other rules, our results support that diatom communities are prominently assembled by environmental filtering and immigration processes, in particular from rivers. However, this does not exclude that other assembly rules may be at play at a finer spatial, temporal and/or phylogenetic scale.

Contrasting influences of two dominant plants, Dasiphora fruticosa and Ligularia virguarea, on aboveground and belowground communities in an alpine meadow

Soil organisms are abundant, phylogenetically and functionally diverse, and interact to catalyse and regulate critical soil processes. Understanding what structures belowground communities is therefore fundamental to gaining insight into ecosystem functioning. Dominant plants have been shown to influence belowground communities both directly and indirectly through changes in abiotic and biotic factors. In a field study, we used piecewise structural equation modelling to disentangle and compare the effects of a dominant allelopathic plant, Ligularia virgaurea, and a dominant facilitative plant, Dasiphora fruticosa, on understory plant, soil microbial and nematode community composition in an alpine meadow on the Tibetan plateau. Dasiphora fruticosa was associated with changes in edaphic variables (total nitrogen, soil organic carbon, pH and ammonium), understory plant and soil bacterial communities, whereas Ligularia virguarea was associated with increased soil ammonium content and soil fungal richness relative to dominant plant-free control plots. Moreover, nematode richness was significantly greater under D. fruticosa, with no change in nematode community composition. By contrast, nematode richness under Ligularia virgaurea was similar to that of dominant plant-free control plots, but nematode community composition differed from the control. The effects of both plants were predominantly direct rather than mediated by indirect pathways despite the observed effects on understory plant communities, soil properties and microbial assemblages. Our results highlight the importance of plants in determining soil communities and provide new insight to disentangle the complex above- and belowground linkages.

Rhizosphere Diazotrophs and Other Bacteria Associated with Native and Encroaching Legumes in the Succulent Karoo Biome in South Africa

Total and diazotrophic bacteria were assessed in the rhizosphere soils of native and encroaching legumes growing in the Succulent Karoo Biome (SKB), South Africa. These were Calobota sericea, Lessertia diffusa, Vachellia karroo, and Wiborgia monoptera, of Fabaceae family near Springbok (Northern Cape Province) and neighboring refugia of the Fynbos biome for C. sericea for comparison purposes. Metabarcoding approach using 16S rRNA gene revealed Actinobacteria (26.7%), Proteobacteria (23.6%), Planctomycetes, and Acidobacteria (10%), while the nifH gene revealed Proteobacteria (70.3%) and Cyanobacteria (29.5%) of the total sequences recovered as the dominant phyla. Some of the diazotrophs measured were assigned to families; Phyllobacteriaceae (39%) and Nostocaceae (24.4%) (all legumes), Rhodospirillaceae (7.9%), Bradyrhizobiaceae (4.6%) and Methylobacteriaceae (3%) (C. sericea, V. karroo, W. monoptera), Rhizobiaceae (4.2%; C. sericea, L. diffusa, V. Karroo), Microchaetaceae (4%; W. monoptera, V. karroo), Scytonemataceae (3.1%; L. diffusa, W. monoptera), and Pseudomonadaceae (2.7%; V. karroo) of the total sequences recovered. These families have the potential to fix the atmospheric nitrogen. While some diazotrophs were specific or shared across several legumes, a member of Mesorhizobium species was common in all rhizosphere soils considered. V. karroo had statistically significantly higher Alpha and distinct Beta-diversity values, than other legumes, supporting its influence on soil microbes. Overall, this work showed diverse bacteria that support plant life in harsh environments such as the SKB, and shows how they are influenced by legumes.

Contrasting effects of Western vs Mediterranean diets on monocyte inflammatory gene expression and social behavior in a primate model

Dietary changes associated with industrialization increase the prevalence of chronic diseases, such as obesity, type II diabetes, and cardiovascular disease. This relationship is often attributed to an 'evolutionary mismatch' between human physiology and modern nutritional environments. Western diets enriched with foods that were scarce throughout human evolutionary history (e.g. simple sugars and saturated fats) promote inflammation and disease relative to diets more akin to ancestral human hunter-gatherer diets, such as a Mediterranean diet. Peripheral blood monocytes, precursors to macrophages and important mediators of innate immunity and inflammation, are sensitive to the environment and may represent a critical intermediate in the pathway linking diet to disease. We evaluated the effects of 15 months of whole diet manipulations mimicking Western or Mediterranean diet patterns on monocyte polarization in a well-established model of human health, the cynomolgus macaque (Macaca fascicularis). Monocyte transcriptional profiles differed markedly between diets, with 40% of transcripts showing differential expression (FDR < 0.05). Monocytes from Western diet consumers were polarized toward a more proinflammatory phenotype. The Western diet shifted the co-expression of 445 gene pairs, including small RNAs and transcription factors associated with metabolism and adiposity in humans, and dramatically altered behavior. For example, Western-fed individuals were more anxious and less socially integrated. These behavioral changes were also associated with some of the effects of diet on gene expression, suggesting an interaction between diet, central nervous system activity, and monocyte gene expression. This study provides new molecular insights into an evolutionary mismatch and uncovers new pathways through which Western diets alter monocyte polarization toward a proinflammatory phenotype.

Ecoregional Characteristics Drive the Distribution Patterns of Neotropical Stream Diatoms

We assessed the relative influence of ecoregional features in explaining diatom distribution in the Orinoco river basin. Ecoregions in the Colombian Orinoco can be seen as imprints of the evolutionary history of the basin, for their current biodiversity and physiographic features are the result of the geological and climatic shifts that have occurred since the Tertiary. Thus, they represent an ideal testing ground for studying the interplay between ecological and evolutionary processes shaping diversity patterns of microorganisms, such as diatoms, in the present day. To study this interplay, we compared diatom community composition variance within and among seven ecoregions and assessed the explanatory power of environmental, spatial and historical drivers. This was done by a combination of correlation analyses, multivariate methods and constrained ordinations. We also deconstructed the whole community data set into ecological guilds (low- and high-profile, and motile) to explore their individual response to the contemporary and historical drivers. Taken together, these analyses indicated that contemporary constraints to species occurrence and dispersal, as well as the legacies of historical events, can provide an explanation for the contemporary distribution of diatoms in the Colombian Orinoco. Specifically, we provided evidence showing that both historical legacies and contemporary environmental conditions (temperature, pH, and phosphorus concentration) are interacting to determine diatoms' distribution. Our results suggest the need to consider ecoregional gradients for unraveling the mechanisms shaping tropical diversity as well as for designing conservation plans.

Freshwater phytoplankton diversity: models, drivers and implications for ecosystem properties

Our understanding on phytoplankton diversity has largely been progressing since the publication of Hutchinson on the paradox of the plankton. In this paper, we summarise some major steps in phytoplankton ecology in the context of mechanisms underlying phytoplankton diversity. Here, we provide a framework for phytoplankton community assembly and an overview of measures on taxonomic and functional diversity. We show how ecological theories on species competition together with modelling approaches and laboratory experiments helped understand species coexistence and maintenance of diversity in phytoplankton. The non-equilibrium nature of phytoplankton and the role of disturbances in shaping diversity are also discussed. Furthermore, we discuss the role of water body size, productivity of habitats and temperature on phytoplankton species richness, and how diversity may affect the functioning of lake ecosystems. At last, we give an insight into molecular tools that have emerged in the last decades and argue how it has broadened our perspective on microbial diversity. Besides historical backgrounds, some critical comments have also been made.

Consistent metacommunity structure despite inconsistent drivers of assembly at the continental scale

A fundamental goal of community ecology is to understand the drivers of community assembly and diversity. Local factors acting on community assembly are typically related to environmental conditions while regional factors are typically related to dispersal. Previous research has not consistently demonstrated the importance of local or regional factors, but this is likely because these factors act in concert and not in isolation. Studies that simultaneously integrate local and regional factors into analyses of community assembly can be a useful avenue to further our understanding of this core concept in community ecology. Here, we aimed to identify metacommunity structure and diversity and the local and regional drivers of community assembly at the continental scale. We evaluated metacommunity structure and drivers of assembly of macroinvertebrate communities in 941 rivers and streams nested within nine ecoregions distributed across the conterminous United States. Pattern-based metacommunity analyses and boosted regression tree techniques were used to (a) assign metacommunity structures and (b) identify the environmental, landscape and network drivers of assembly. We also evaluated how biodiversity scaled across hierarchical levels and varied among ecoregions. Metacommunity structures were consistent for the conterminous United States and each of the nine ecoregion subsets, with each ecoregional metacommunity displaying a Clementsian structure. Environmental variables were the predominant drivers of assembly, suggesting the importance of species sorting and environmental filtering on community structure; however, the identity of the most influential environmental variables differed among ecoregions and suggested hierarchical filtering on assembly. Partitioned diversity was found to be lower at the local and ecoregional levels, but turnover in diversity among ecoregions was higher than expected. Our results demonstrate contingencies in community assembly, notwithstanding consistency in metacommunity structure and support the importance of environmental control over community assembly and biodiversity. Moreover, biodiversity at the continental scale is likely maintained through this inherent variation in the drivers of assembly and concomitant changes in community composition among ecoregions. We suggest that further work should evaluate the assembly of other facets of community structure and the underlying mechanisms of the contingency in assembly drivers.

Diatoms as indicators of the multivariate environment of mountain lakes

Diatom assemblages are used widely as indicators of environmental conditions. They have been particularly useful in the assessment of some acute environmental problems such as water acidification, eutrophication and salinisation. High mountain lakes are currently a research focus as sentinels of global change, predominantly of long-distance atmospheric pollution and climate warming. The diatom assemblages in these lakes are extremely rich, and the sediment record provides short and long historical perspectives of the changes. We investigated the relative sensitivity of diatoms to the main environmental gradients found in mountain lakes and evaluated the strength and uncertainties for predicting simultaneously several environmental variables associated with these gradients based on a survey of 83 lakes in the Pyrenees. Variables related to the ionic composition and acid-base balance (calcium*, acid neutralizing capacity*, magnesium, sodium, and sulphates), trophic conditions (total phosphorus* and dissolved organic carbon) and physical factors (water temperature*, irradiance at the lake bottom*, and macrophyte cover) explained independently the variation in the diatom assemblages. However, the assemblage predictive capacity of these variables- tested by developing transfer functions (Weighted Averaging- Partial Least Squares) - was only acceptable for a subset of the variables (*). The spatial autocorrelation of the environmental variables had no influence on the performance of the transfer functions except for water temperature, which is highly dependent on altitude. Our results indicate that diatom assemblages have great potential for assessments of multiple environmental variables in mountain lakes and, consequently, in applications of global change surveillance.

Modeling Water Yield: Assessing the Role of Site and Region-Specific Attributes in Determining Model Performance of the InVEST Seasonal Water Yield Model

Simple hydrological models, such as the Seasonal Water Yield Model developed by the Natural Capital Project (InVEST SWYM), are attractive as data requirements are relatively easy to satisfy. However, simple models may produce unrealistic results when the underlying hydrological processes are inadequately described. We used the variation in performance of the InVEST SWYM across watersheds to identify correlates of poorly modeled outcomes of InVEST SWYM. We grouped 749 watersheds from across North America into five bioclimatic regions using nine environmental variables. For each region, we compared the predicted flow patterns to actual flow conditions over a 15-year period. The correlation between the modeled and actual flows was highly dispersed and relatively poor, with 92% of r2 values less than 0.5 and 42% less than 0.1. We linked cryospheric variables to model performance in the bioclimatic region with the poorest model performance (the Low elevation Boreal Sub-humid region—LeBSh). After incorporating cryospheric conditions into the InVEST SWYM, predictions improved significantly in 30% of the LeBSh watersheds. We provide a relatively straightforward approach for identifying processes that simple hydrological models may not consider or which need further attention or refinement.