A metacommunity framework for enhancing the effectiveness of biological monitoring strategies

The use of genus-level determinations and biovolume classes as surrogates to indicate environmental drivers of stream diatom communities in the Brazilian Pampa

The demand for low-cost and time-efficient biomonitoring and ecological assessment strategies has increased due to threats to biodiversity. We evaluated the ability of surrogates (genera and biovolume classes) to access information provided by diatom species. Moreover, we investigated whether the relative importance of spatial and environment on diatom communities identified at the genus or classified at biovolume classes reflects the ecological responses at the species. We used biotic, environmental, and spatial data from Pampa streams. We employed Procrustes analysis to detect whether the spatial variation of communities at the species level was represented by the surrogates and variation partitioning to evaluate the relative importance of spatial and environment. We found high congruence between the surrogates and diatom species communities. Furthermore, whilst both spatial and environment were important to explain species composition, only the environment was important for both surrogates. We suggest that the use of genus-level determinations can provide information about the environmental relationships of species, whereas biovolume classes may be useful to detect changes in diatom communities. These results are a first step to seek for strategies aiming to simplify biological monitoring and assessments at pampean streams, especially considering the demand for the identification of organisms at the species.

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.

Indictors of wetland health improve following small-scale ecological restoration on private land

Globally wetlands are imperilled and restoring these highly productive and biodiverse ecosystems is key to regaining their lost function and health. Much of the fertile, low-lying land that was historically wetland is now farmed, so privately-owned locations play critical roles in regaining space for wetlands. However, wetland restoration on private property is often small-scale and supported by minimal funding and expertise. Little is known about what these efforts achieve, and what contexts facilitate the greatest gains in wetland health. Using a paired plot design for 18 restored and 18 unrestored wetlands, we aimed to understand changes in wetland health following restoration on private property. We characterised plant and microbial communities and soil characteristics following wetland restoration and explored how environmental settings of restored wetlands related to the clustering of wetland health indicators. We found that all indicators of wetland health significantly increased following restoration except for the ratio of Gram negative to Gram positive bacteria. Restoration enhanced plant alpha and beta diversity, adding ~13 native plant species per plot. Soils in restored wetlands contained 20% more organic matter, and 25% more microbial biomass, which was driven by an increased abundance of fungi. Restoration reduced soil bulk density by 0.19 g^-1 cm³ and Olsen Phosphorus by 23%. These effects on soil physical characteristics and microbial communities were strongest in the wettest locations. Restored wetlands clustered into three main groups based on indicators of wetland health. Hydrological flow explained the clustering of wetlands, with riverine wetlands exhibiting greater indicators of recovery than depressional wetlands, suggesting that hydrological flow may influence post-restoration recovery. Overall, this study shows that small-scale wetland restoration on private land improved wetland health, providing evidence that it can be an effective use of marginal agricultural land.

Concordância entre plantas regenerantes, formigas e outros artrópodes na Mata Atlântica: a importância da identidade das árvores no dossel

RESUMO O monitoramento das práticas de restauração é um processo caro, mas essencial para verificar o seu sucesso. Uma forma de reduzir os custos amostrais é por meio da utilização de indicadores de biodiversidade, termo utilizado para um grupo funcional ou taxonômico que é concordante com outro grupo. O objetivo deste trabalho foi avaliar a concordância entre a riqueza e a composição de plantas regenerantes, formigas e outros artrópodes sob o dossel de quatro espécies arbóreas em uma área de restauração na Mata Atlântica, Brasil, bem como determinar a relação das comunidades biológicas com parâmetros ambientais e espaciais. Foi encontrado que as variáveis ambientais, muitas vezes ligadas a identidade da árvore, são preponderantes para determinar a relação entre formigas, outros artrópodes e plantas regenerantes. Além disso, as formigas demonstraram ser indicadores fracos da diversidade e composição de plantas regenerantes e outros artrópodes e essa relação não foi guiada pelas variáveis ambientais e espaciais. Assim, os resultados aqui encontrados recomendam cautela ao utilizar formigas como indicadores de biodiversidade de plantas e outros artrópodes em programas de monitoramento na Mata Atlântica.

Shortcuts for biomonitoring programs of stream ecosystems: Evaluating the taxonomic, numeric, and cross-taxa congruence in phytoplankton, periphyton, zooplankton, and fish assemblages

Different biological groups can be used for monitoring aquatic ecosystems because they can respond to variations in the environment. However, the evaluation of different bioindicators may demand multiple financial resources and time, especially when abundance quantification and species-level identification are required. In this study, we evaluated whether taxonomic, numerical resolution and cross-taxa can be used to optimize costs and time for stream biomonitoring in Central Brazil (Cerrado biome). For this, we sampled different biological groups (fish, zooplankton, phytoplankton, and periphyton) in stream stretches distributed in a gradient of land conversion dominated by agriculture and livestock. We used the Mantel and Procrustes analyses to test the association among different taxonomic levels (species to class), the association between incidence and abundance data (numerical resolution), and biological groups. We also assessed the relative effect of local environmental and spatial predictors on different groups. The taxonomic levels and numerical resolutions were strongly correlated in all taxonomic groups (r > 0.70). We found no correlations among biological groups. Different sets of environmental variables were the most important to explain the variability in species composition of distinct biological groups. Thus, we conclude that monitoring the streams in this region using bioindicators is more informative through higher taxonomic levels with occurrence data than abundance. However, different biological groups provide complementary information, reinforcing the need for a multi-taxa approach in biomonitoring.

River network connectivity and fish diversity

Frequent and severe disruptions of natural river flows associated with human activities significantly alter hydrological connectivity in large river networks, with deleterious effects on fish diversity. Understanding the relationship between fish diversity and river network connectivity is fundamental to ensuring species persistence, ecosystem integrity, and human well-being. Here, we provide a review of the mechanisms by which river network connectivity (RNC) affects fish diversity. We review the relationships between forms, systems and types of RNC and fish diversity, based on more than 100 previous studies. In summary, sustaining RNC promotes fish diversity in longitudinal and lateral axes, and species sorting, dispersal dynamics, and habitat availability are the main factors driving the distribution of fish diversity, followed by nutrition and trophic dynamics. Our work highlights the effects of RNC on fish diversity, and provides a mechanistic understanding of how RNC affects fish diversity across river basins, thus providing scientific guidance for protecting fish biodiversity and improving the health of river network ecosystems.

Environmental factors and river network position allow prediction of benthic community assemblies: A model of nematode metacommunities

The field of metacommunity studies is growing rapidly, including recent applications to river networks. Most of these studies have targeted a single river network but whether their findings are relevant to other river systems is unknown. This study investigated the influence of environmental, spatial and temporal parameters on the community structure of nematodes in the river networks of the Elbe and Rhine. We asked whether the variance in community structure was better explained by spatial variables representing the watercourse than by overland distances. After determining the patterns in the Elbe river network, we tested whether they also explained the Rhine data. The Elbe data were evaluated using a boosted regression tree analysis. The predictive ability of the model was then assessed using the Rhine data. In addition to strong temporal dynamics, environmental factors were more important than spatial factors in structuring riverine nematode communities. Community structure was more strongly influenced by watercourse than by Euclidean distances. Application of the model's predictions to the Rhine data correlated significantly with field observations. Our model shows that the consequences of changes in environmental factors or habitat connectivity for aquatic communities across different river networks are quantifiable.

Patterns of litter inputs, hyphomycetes and invertebrates in a Brazilian savanna stream: a process of degradative succession

Litter breakdown is an important ecological process at the bottom of food webs in streams. Previous studies have been based only on a temporal interval of a single season, thus ignoring seasonal variation in litter input and community structure. We investigated organic matter input in a Brazilian savanna stream and the influence of its associated hyphomycetes on the invertebrate community. Organic matter input was sampled monthly and the leaves submitted to decomposition experiments. There were lower breakdown rates and higher invertebrate species richness and abundance during the dry season, which reached their maximum in July due to low stream discharge. Invertebrate composition was best explained by hyphomycetes (mainly byFlagellospora curvulaandAnguillospora filiformis). Hyphomycetes have the capacity to degrade complex compounds of litter and to rapidly absorb nutrients by growing branched filaments, thus making the leaves more favourable for consumption by invertebrates. Shredder abundance was negatively related to litter richness, indicating possible species-specific relationships. We observed a sequential process with increased leaf litter input promoting an increase in hyphomycetes biomass, which in turn favoured invertebrate density.

Do latitudinal gradients exist in New Zealand stream invertebrate metacommunities?

That biodiversity declines with latitude is well known, but whether a metacommunity process is behind this gradient has received limited attention. We tested the hypothesis that dispersal limitation is progressively replaced by mass effects with increasing latitude, along with a series of related hypotheses. We explored these hypotheses by examining metacommunity structure in stream invertebrate metacommunities spanning the length of New Zealand’s two largest islands (∼1,300 km), further disentangling the role of dispersal by deconstructing assemblages into strong and weak dispersers. Given the highly dynamic nature of New Zealand streams, our alternative hypothesis was that these systems are so unpredictable (at different stages of post-flood succession) that metacommunity structure is highly context dependent from region to region. We rejected our primary hypotheses, pinning this lack of fit on the strong unpredictability of New Zealand’s dynamic stream ecosystems and fauna that has evolved to cope with these conditions. While local community structure turned over along this latitudinal gradient, metacommunity structure was highly context dependent and dispersal traits did not elucidate patterns. Moreover, the emergent metacommunity types exhibited no trends, nor did the important environmental variables. These results provide a cautionary tale for examining singular metacommunities. The considerable level of unexplained contingency suggests that any inferences drawn from one-off snapshot sampling may be misleading and further points to the need for more studies on temporal dynamics of metacommunity processes.

Species complexes within epiphytic diatoms and their relevance for the bioindication of trophic status

The popularity of aquatic bioassessments has increased in Europe and worldwide, with a considerable number of methods being based on benthic diatoms. Recent evidence from molecular data and mating experiments has shown that some traditional diatom morphospecies represent species complexes, containing several to many cryptic species. This case study is based on epiphytic diatom and environmental data from shallow fishponds, investigating whether the recognition and use of fine taxonomic resolution (cryptic species) can improve assessment of community response to environmental drivers and increase sharpness of classification, compared to coarse taxonomic resolution (genus level and species level with unresolved species complexes). Secondly, trophy bioindication based on a species matrix divided into two compartments (species complexes and remaining species) was evaluated against the expectation that species complexes would be poor trophy indicators, due to their expected wide ecological amplitude. Finally, the response of species complexes and their members (cryptic species) to a trophic gradient (phosphorus) were compared. Multivariate analyses showed similar efficiency of all three taxonomic resolutions in depicting community patterns and their environmental correlates, suggesting that even genus level resolution is sufficient for routine bioassessment of shallow fishponds with a wide trophic range. However, after controlling for coarse taxonomic matrices, fine taxonomic resolution (with resolved cryptic species) still showed sufficient variance related to the environmental variable (habitat groups), and increased the sharpness of classification, number of indicator species for habitat categories, and gave better separation of habitat categories in the ordination space. Regression analysis of trophic bioindication and phosphorus concentration showed a weak relationship for species complexes but a close relationship for the remaining taxa. GLM models also showed that no species complex responded to phosphorus concentration. It follows that the studied species complexes have wide tolerances to, and no apparent optima for, phosphorus concentrations. In contrast, various responses (linear, unimodal, or no response) of cryptic species within species complexes were found to total phosphorus concentration. In some cases, fine taxonomic resolution to species level including cryptic species has the potential to improve data interpretation and extrapolation, supporting recent views of species surrogacy.

Drivers of metacommunity structure diverge for common and rare Amazonian tree species

We analysed the flora of 46 forest inventory plots (25 m x 100 m) in old growth forests from the Amazonian region to identify the role of environmental (topographic) and spatial variables (obtained using PCNM, Principal Coordinates of Neighbourhood Matrix analysis) for common and rare species. For the analyses, we used multiple partial regression to partition the specific effects of the topographic and spatial variables on the univariate data (standardised richness, total abundance and total biomass) and partial RDA (Redundancy Analysis) to partition these effects on composition (multivariate data) based on incidence, abundance and biomass. The different attributes (richness, abundance, biomass and composition based on incidence, abundance and biomass) used to study this metacommunity responded differently to environmental and spatial processes. Considering standardised richness, total abundance (univariate) and composition based on biomass, the results for common species differed from those obtained for all species. On the other hand, for total biomass (univariate) and for compositions based on incidence and abundance, there was a correspondence between the data obtained for the total community and for common species. Our data also show that in general, environmental and/or spatial components are important to explain the variability in tree communities for total and common species. However, with the exception of the total abundance, the environmental and spatial variables measured were insufficient to explain the attributes of the communities of rare species. These results indicate that predicting the attributes of rare tree species communities based on environmental and spatial variables is a substantial challenge. As the spatial component was relevant for several community attributes, our results demonstrate the importance of using a metacommunities approach when attempting to understand the main ecological processes underlying the diversity of tropical forest communities.

Environment and Spatial Influences on Aquatic Insect Communities in Cerrado Streams: the Relative Importance of Conductivity, Altitude, and Conservation Areas

The aquatic insect community is an important element for stream functionality and diversity, but the effects of altitude and conservation areas on the aquatic insect community have been poorly explored in neotropical ecozone. The lack of studies about the relative importance of space and environment on community structure is another obstacle within aquatic insect ecology, which precludes the inclusion of these studies in more current frameworks, like the metacommunity dynamics. We evaluated the relationship between the aquatic insect community structure at 19 streams in the Brazilian Cerrado and spatial and environmental variables, namely geographical distance among sites, stream altitude, chemical variables, and environmental protection areas. We partitioned the variance explained by spatial and environmental components using a partial redundancy analysis. The environment exhibited a strong spatial structure for abundance and number of genera, increasing these community parameters with elevated water conductivity. Only community composition had a large unexplained portion of variance, with a small portion constrained by environmental (altitude and conductivity) and spatial factors. A relevant point in the result was the streams with high conductivity were located outside of the conservation areas. These results suggest that the relationship between number of genera and abundance with environmental conditions is always associated with spatial configuration of streams. Our study shows that altitude is an important determinant of community structure, as it exerts indirect influences, and electrical conductivity directly determines community composition, and that some national parks may be inefficient in maintaining the diversity of aquatic insects in the Cerrado region.

Enhancing sampling design in mist-net bat surveys by accounting for sample size optimization

The advantages of mist-netting, the main technique used in Neotropical bat community studies to date, include logistical implementation, standardization and sampling representativeness. Nonetheless, study designs still have to deal with issues of detectability related to how different species behave and use the environment. Yet there is considerable sampling heterogeneity across available studies in the literature. Here, we approach the problem of sample size optimization. We evaluated the common sense hypothesis that the first six hours comprise the period of peak night activity for several species, thereby resulting in a representative sample for the whole night. To this end, we combined re-sampling techniques, species accumulation curves, threshold analysis, and community concordance of species compositional data, and applied them to datasets of three different Neotropical biomes (Amazonia, Atlantic Forest and Cerrado). We show that the strategy of restricting sampling to only six hours of the night frequently results in incomplete sampling representation of the entire bat community investigated. From a quantitative standpoint, results corroborated the existence of a major Sample Area effect in all datasets, although for the Amazonia dataset the six-hour strategy was significantly less species-rich after extrapolation, and for the Cerrado dataset it was more efficient. From the qualitative standpoint, however, results demonstrated that, for all three datasets, the identity of species that are effectively sampled will be inherently impacted by choices of sub-sampling schedule. We also propose an alternative six-hour sampling strategy (at the beginning and the end of a sample night) which performed better when resampling Amazonian and Atlantic Forest datasets on bat assemblages. Given the observed magnitude of our results, we propose that sample representativeness has to be carefully weighed against study objectives, and recommend that the trade-off between logistical constraints and additional sampling performance should be carefully evaluated.

The taxonomic distinctness of macroinvertebrate communities of Atlantic Forest streams cannot be predicted by landscape and climate variables, but traditional biodiversity indices can

Predicting how anthropogenic activities may influence the various components of biodiversity is essential for finding ways to reduce diversity loss. This challenge involves: a) understanding how environmental factors influence diversity across different spatial scales, and b) developing ways to measure these relationships in a way that is fast, economical, and easy to communicate. In this study, we investigate whether landscape and bioclimatic variables could explain variation in biodiversity indices in macroinvertebrate communities from 39 Atlantic Forest streams. In addition to traditional diversity measures, i.e., species richness, abundance and Shannon index, we used a taxonomic distinctness index that measures the degree of phylogenetic relationship among taxa. The amount of variation in the diversity measures that was explained by environmental and spatial variables was estimated using variation partitioning based on multiple regression. Our study demonstrates that taxonomic distinctness does not respond in the same way as the traditional used in biodiversity studies. We found no evidence that taxonomic distinctness responds predictably to variation in landscape metrics, indicating the need for the incorporation of predictors at multiple scales in this type of study. The lack of congruence between taxonomic distinctness and other indices and its low predictability may be related to the fact that this measure expresses long-term evolutionary adaptation to ecosystem conditions, while the other traditional biodiversity metrics respond to short-term environmental changes.

Much beyond Mantel: bringing Procrustes association metric to the plant and soil ecologist's toolbox

The correlation of multivariate data is a common task in investigations of soil biology and in ecology in general. Procrustes analysis and the Mantel test are two approaches that often meet this objective and are considered analogous in many situations especially when used as a statistical test to assess the statistical significance between multivariate data tables. Here we call the attention of ecologists to the advantages of a less familiar application of the Procrustean framework, namely the Procrustean association metric (a vector of Procrustean residuals). These residuals represent differences in fit between multivariate data tables regarding homologous observations (e.g., sampling sites) that can be used to estimate local levels of association (e.g., some groups of sites are more similar in their association between biotic and environmental features than other groups of sites). Given that in the Mantel framework, multivariate information is translated into a pairwise distance matrix, we lose the ability to contrast homologous data points across dimensions and data matrices after their fit. In this paper, we attempt to familiarize ecologists with the benefits of using these Procrustean residual differences to further gain insights about the processes underlying the association among multivariate data tables using real and hypothetical examples.

Best Practicable Aggregation of Species: a step forward for species surrogacy in environmental assessment and monitoring

The available taxonomic expertise and knowledge of species is still inadequate to cope with the urgent need for cost-effective methods to quantifying community response to natural and anthropogenic drivers of change. So far, the mainstream approach to overcome these impediments has focused on using higher taxa as surrogates for species. However, the use of such taxonomic surrogates often limits inferences about the causality of community patterns, which in turn is essential for effective environmental management strategies. Here, we propose an alternative approach to species surrogacy, the “Best Practicable Aggregation of Species” (BestAgg), in which surrogates exulate from fixed taxonomic schemes. The approach uses null models from random aggregations of species to minimizing the number of surrogates without causing significant losses of information on community patterns. Surrogate types are then selected in order to maximize ecological information. We applied the approach to real case studies on natural and human-driven gradients from marine benthic communities. Outcomes from BestAgg were also compared with those obtained using classic taxonomic surrogates. Results showed that BestAgg surrogates are effective in detecting community changes. In contrast to classic taxonomic surrogates, BestAgg surrogates allow retaining significantly higher information on species-level community patterns than what is expected to occur by chance and a potential time saving during sample processing up to 25% higher. Our findings showed that BestAgg surrogates from a pilot study could be used successfully in similar environmental investigations in the same area, or for subsequent long-term monitoring programs. BestAgg is virtually applicable to any environmental context, allowing exploiting multiple surrogacy schemes beyond stagnant perspectives strictly relying on taxonomic relatedness among species. This prerogative is crucial to extend the concept of species surrogacy to ecological traits of species, thus leading to ecologically meaningful surrogates that, while cost effective in reflecting community patterns, may also contribute to unveil underlying processes. A specific R code for BestAgg is provided.