Odonata (Insecta) as a tool for the biomonitoring of environmental quality

Despite the fundamental dependence of human populations on water resources, a range of anthropogenic impacts, in particular the removal of riparian vegetation, threaten freshwater environments. One of the most effective means of evaluating the effects of anthropogenic disturbance in aquatic ecosystems is the use of bioindicators, and the insects of the order Odonata are among the most efficient indicators, due to their enormous sensitivity to environmental changes. In this context, the present study aimed to verify which parameters of the odonate community (species richness, abundance/biomass, composition, taxonomic diversity and taxonomic/phylogenetic distinctness) are most effective for the evaluation of the loss of environmental integrity. The study focused on 50 streams in the northeast of the Brazilian state of Pará. The streams were sampled during the dry season, between June and August 2011. The physical characteristics of each stream were evaluated using a Habitat Integrity Index (HII). The species composition provided the best parameter for the evaluation of ecological integrity, providing a relatively accurate assessment at a lower mean research cost than other parameters. Taxonomic diversity and distinctness also provided relatively reliable results, contributed additional information on the evolutionary relationships among the odonate taxa, and also provided a low-cost approach. Deconstructing communities is necessary to detect impacts, considering the considerable variation in the environmental requirements of the different species. Overall, the parameter that best responded to gradients of disturbance was species composition, followed by diversity and taxonomic distinctness. Given these findings, odonate-based biomonitoring should focus on these parameters to guarantee the optimal detection and evaluation of habitat alterations.     

Large-Scale Biomonitoring of Remote and Threatened Ecosystems via High-Throughput Sequencing

Biodiversity metrics are critical for assessment and monitoring of ecosystems threatened by anthropogenic stressors. Existing sorting and identification methods are too expensive and labour-intensive to be scaled up to meet management needs. Alternately, a high-throughput DNA sequencing approach could be used to determine biodiversity metrics from bulk environmental samples collected as part of a large-scale biomonitoring program. Here we show that both morphological and DNA sequence-based analyses are suitable for recovery of individual taxonomic richness, estimation of proportional abundance, and calculation of biodiversity metrics using a set of 24 benthic samples collected in the Peace-Athabasca Delta region of Canada. The high-throughput sequencing approach was able to recover all metrics with a higher degree of taxonomic resolution than morphological analysis. The reduced cost and increased capacity of DNA sequence-based approaches will finally allow environmental monitoring programs to operate at the geographical and temporal scale required by industrial and regulatory end-users.     

Data synthesis and bioindicator development for nontidal streams in the interstate Potomac River basin, USA

Water resource agencies are increasingly confronted with issues of methods and data comparability when assessing inter-jurisdictional waters. The Interstate Commission on the Potomac River Basin (ICPRB) is developing an assessment framework for the diverse nontidal monitoring data collected by Potomac basin jurisdictions. The ICPRB's goal is to augment the jurisdictions’ water quality assessments with uniform, basin-wide evaluations of habitat and biological integrity. Disparate datasets were integrated and used to select and calibrate a common suite of biological indicators of human disturbance. Aggregated physiographic regions were most effective at grouping streams into site classes with similar attributes. Common elements from states’ habitat and water quality assessments were used to define regional reference and impairment criteria. Seven macroinvertebrate metrics distinguished reference from impaired sites in most regions: EPT richness, Hilsenhoff Family Biotic Index, percent clingers, percent collectors, percent dominance, percent EPT, and taxonomic richness. Reference communities in the Piedmont region of the basin were dissimilar from those in Highland and Valley regions, suggesting a need for different reference conditions and metric thresholds in these regions. Results confirm that useful bioindicators of aquatic health can be generated from multiple datasets if the synthesis is done with care.     

Phylogenetic signal of sub‐arctic beetle communities

Postglacial dispersal and colonization processes have shaped community patterns in sub‐Arctic regions such as Churchill, Manitoba, and Canada. This study investigates evolutionary community structure within the beetle (Coleoptera) families of Churchill and tests whether biological traits have played a role in governing colonization patterns from refugial and southerly geographic regions. This study quantifies sub‐Arctic beetle phylogenetic community structure for each family using the net relatedness index (NRI) and nearest taxon index (NTI), calculated using publicly available data from the Barcode of Life Data Systems (BOLD); compares patterns across families with different traits (habitat, diet) using standard statistical analysis (ANOVA) as well as phylogenetic generalized least squares (PGLS) using a family‐level beetle phylogeny obtained from the literature; and compares community structure in Churchill with a region in southern Canada (Guelph, Ontario). These analyses were also repeated at a genus level. The dominant pattern detected in our study was that aquatic families were much better represented in Churchill compared to terrestrial families, when compared against richness sampled from across Canada and Alaska. Individually, most families showed significant phylogenetic clustering in Churchill, likely due to the strong environmental filtering present in Arctic environments. There was no significant difference in phylogenetic structure between Churchill and Guelph but with a trend toward stronger clustering in the North. Fungivores were significantly more overdispersed than other feeding modes, predators were significantly more clustered, and aquatic families showed significantly stronger clustering compared to terrestrial. This study contributes to our understanding of the traits and processes structuring insect biodiversity and macroecological trends in the sub‐Arctic.     

Can taxonomic distinctness assess anthropogenic impacts in inland waters? A case study from a Mediterranean river basin

1. It is increasingly recognised that adequate measures of biodiversity should include information on the ‘relatedness’ of species within ecological assemblages, or the phylogenetic levels at which diversity is expressed. Taxonomic distinctness measures provide a series of indices to achieve this, which are independent of sample size. Taxonomic distinctness has been employed widely in marine systems, where it has been suggested that this index can provide a reliable measure of anthropogenic impact. 2. We tested the behaviour of three related taxonomic distinctiveness indices (Average Taxonomic Distinctness, Δ⁺; Variation in Taxonomic Distinctness, Λ⁺; and Total Taxonomic Distinctness, sΔ⁺) in relation to putative levels of anthropogenic impact in inland waters and their potential utility in environmental monitoring, using an extensive data set for aquatic beetles from the south‐east of the Iberian Peninsula. 3. Taxonomic distinctness measures were not able to identify human disturbance effects and there were no clear relationships between these new biodiversity measures and the disturbance level recorded at individual localities. Furthermore, the taxonomic distinctness measures used were apparently less sensitive to the effects of anthropogenic impact than other diversity metrics, such as species richness and rarity. 4. We conclude that taxonomic distinctness indices may not always perform as well as other metrics in the assessment of environmental quality. In addition, taxonomic distinctness measure should be interpreted with caution, as their performance and ability to detect anthropogenic disturbance may depend on the phylogenetic structure of sampled taxa within a region, and their evolutionary and ecological history.     

Multidecadal changes in functional diversity lag behind the recovery of taxonomic diversity

While there has been increasing interest in how taxonomic diversity is changing over time, less is known about how long‐term taxonomic changes may affect ecosystem functioning and resilience. Exploring long‐term patterns of functional diversity can provide key insights into the capacity of a community to carry out ecological processes and the redundancy of species’ roles. We focus on a protected freshwater system located in a national park in southeast Germany. We use a high‐resolution benthic macroinvertebrate dataset spanning 32 years (1983–2014) and test whether changes in functional diversity are reflected in taxonomic diversity using a multidimensional trait‐based approach and regression analyses. Specifically, we asked: (i) How has functional diversity changed over time? (ii) How functionally distinct are the community''s taxa? (iii) Are changes in functional diversity concurrent with taxonomic diversity? And (iv) what is the extent of community functional redundancy? Resultant from acidification mitigation, macroinvertebrate taxonomic diversity increased over the study period. Recovery of functional diversity was less pronounced, lagging behind responses of taxonomic diversity. Over multidecadal timescales, the macroinvertebrate community has become more homogenous with a high degree of functional redundancy, despite being isolated from direct anthropogenic activity. While taxonomic diversity increased over time, functional diversity has yet to catch up. These results demonstrate that anthropogenic pressures can remain a threat to biotic communities even in protected areas. The differences in taxonomic and functional recovery processes highlight the need to incorporate functional traits in assessments of biodiversity responses to global change.     

Development of a macroinvertebrate multimetric index for the assessment of low-land streams in the neotropics

The water and habitat quality in Panamanian streams and rivers are being degraded by agriculture, urbanization, industrial activities, mining, and other forms of development. Thus, the need for standards, especially those examining the biological attributes of lotic systems, are urgently required. We describe the development of a multimetric index based on macroinvertebrates collected in low-land streams in the Panama Canal Watershed (PCW), which differed in their levels of human impacts. The index was developed using 12 streams and validated using a further three, all of which were sampled on four occasions, in the dry and wet seasons of 2007 and 2008. We examined 42 metrics related to macroinvertebrate community structure, composition, and function. Based on their ability to distinguish reference from moderately or severely impacted streams, and on their independence, we selected seven metrics (Margalef's index (taxa), Shannon's evenness index (taxa), number of EPT (taxa), % of Trichoptera, ratio of Chironomidae/Diptera individuals, % of scrapers, and % of shredders). These metrics were then standardized and developed into the Neotropical Low-land Stream Multimetric Index (NLSMI). Overall, the NLSMI distinguished well among the different levels of impairment (Reference, Moderate impact, and Severe impact) and showed a strong, significant correlation with principal component analysis (PCA) axis one values, with the PCA based on a set of physico-chemical variables indicative of stream quality. The wet season generally resulted in lower NLSMI values, leading us to suggest that sampling for biomonitoring be carried out in the dry season. Overall, this preliminary macroinvertebrate NLSMI shows promise for developing a biomonitoring programme to assess the ecological integrity of streams, to aid with management, restoration, and conservation, and to serve as a basis to develop a more geographically extensive multimetric index.     

Elements of metacommunity structure in Amazonian Zygoptera among streams under different spatial scales and environmental conditions

An important aspect of conservation is to understand the founding elements and characteristics of metacommunities in natural environments, and the consequences of anthropogenic disturbance on these patterns. In natural Amazonian environments, the interfluves of the major rivers play an important role in the formation of areas of endemism through the historical isolation of species and the speciation process. We evaluated elements of metacommunity structure for Zygoptera (Insecta: Odonata) sampled in 93 Amazonian streams distributed in two distinct biogeographic regions (areas of endemism). Of sampled streams, 43 were considered to have experienced negligible anthropogenic impacts, and 50 were considered impacted by anthropogenic activities. Our hypothesis was that preserved (“negligible impact”) streams would present a Clementsian pattern, forming clusters of distinct species, reflecting the biogeographic pattern of the two regions, and that anthropogenic streams would present random patterns of metacommunity, due to the loss of more sensitive species and dominance of more tolerant species, which have higher dispersal ability and environmental tolerance. In negligible impact streams, the Clementsian pattern reflected a strong biogeographic pattern, which we discuss considering the areas of endemism of Amazonian rivers. As for communities in human‐impacted streams, a biotic homogenization was evident, in which rare species were suppressed and the most common species had become hyper‐dominant. Understanding the mechanisms that trigger changes in metacommunities is an important issue for conservation, because they can help create mitigation measures for the impacts of anthropogenic activities on biological communities, and so should be expanded to studies using other taxonomic groups in both tropical and temperate systems, and, wherever possible, at multiple spatial scales.     

From compositional to functional biodiversity metrics in bioassessment: A case study using stream macroinvertebrate communities

While compositional diversity is a common metric for assessing human impacts on aquatic communities, functional diversity is scarcely employed, though highly desirable from the perspective of the European Water Framework Directive. Using abundance data from 99 minimally disturbed sites (i.e., no or very weak anthropogenic impact) from a national survey, we studied the spatial variability of compositional and functional biodiversity metrics across a predefined ecoregional classification. Metrics of compositional diversity comprised taxonomic and EPT richness and Simpson diversity. Functional diversity metrics were based on Rao's Quadratic Entropy (RQE), which described the differences among benthic invertebrate genera in eleven biological traits (e.g., size, life cycle, reproduction types, feeding habits). Using generalized linear models we show that taxonomic richness may vary greatly across ecoregions, contrasting with Simpson diversity and functional metrics that varied weakly in response to natural environmental variability. Functional diversity metrics, because of their stability in response to natural environmental variability, may be useful tools for assessing human impairment to ecosystem function. We further tested the response of functional diversity metrics to a specific human impact (sewage) and demonstrated significant modifications of functional diversity downstream of sewage pollution. Further investigations are required to test the ability of functional diversity metrics to precisely and accurately indicate different types of human impacts.     

Modelling Stream-Fish Functional Traits in Reference Conditions: Regional and Local Environmental Correlates

Identifying the environmental gradients that control the functional structure of biological assemblages in reference conditions is fundamental to help river management and predict the consequences of anthropogenic stressors. Fish metrics (density of ecological guilds, and species richness) from 117 least disturbed stream reaches in several western Iberia river basins were modelled with generalized linear models in order to investigate the importance of regional- and local-scale abiotic gradients to variation in functional structure of fish assemblages. Functional patterns were primarily associated with regional features, such as catchment elevation and slope, rainfall, and drainage area. Spatial variations of fish guilds were thus associated with broad geographic gradients, showing (1) pronounced latitudinal patterns, affected mainly by climatic factors and topography, or (2) at the basin level, strong upstream-downstream patterns related to stream position in the longitudinal gradient. Maximum native species richness was observed in midsize streams in accordance with the river continuum concept. The findings of our study emphasized the need to use a multi-scale approach in order to fully assess the factors that govern the functional organization of biotic assemblages in ‘natural’ streams, as well as to improve biomonitoring and restoration of fluvial ecosystems.     

Development of a benthic macroinvertebrate multimetric index (MMI) for Neotropical Savanna headwater streams

Assessing the ecological impacts of anthropogenic pressures is a key task in environmental management. Multimetric indices (MMIs), based on aquatic assemblage responses to anthropogenic pressures, have been used increasingly throughout the world. The MMI approach is a low-cost, rapid field method that produces an aquatic condition index that responds precisely to anthropogenic pressures, making it useful for conservation and environmental management. We developed four candidate MMIs based on benthic macroinvertebrate assemblages sampled at 40 randomly selected sites to assess the environmental condition of streams upstream of a hydroelectric power plant in the Brazilian Neotropical Savanna biome. Those MMIs were built from landscape-adjusted and unadjusted biological metrics as well as two alternative ways of choosing metrics. The alternative MMIs performances were tested by comparing their precision to distinguish least-disturbed areas, responsiveness to discriminate least- and most-disturbed areas, and sensitivity to anthropogenic pressures at catchment and local scales. The best performing MMI had landscape-adjusted metrics and was produced through use of principal component analysis for metric selection. It included 4 metrics: Ephemeroptera richness, average tolerance score per taxon, percentage of predator individuals, and percentage of Odonata individuals adjusted by elevation. This index discriminated well the anthropogenic pressures at local- and catchment-scales, and at both scales simultaneously, as indicated by an integrated disturbance index. Our methodological development included statistical criteria for identifying least- and most-disturbed sites, calibrating for natural landscape variability, and use of non-redundant metrics. Therefore, we expect it will provide a model for environmental assessment of water resources elsewhere in Brazil and in other nations.     

Taxonomy‐free molecular diatom index for high‐throughput eDNA biomonitoring

Current biodiversity assessment and biomonitoring are largely based on the morphological identification of selected bioindicator taxa. Recently, several attempts have been made to use eDNA metabarcoding as an alternative tool. However, until now, most applied metabarcoding studies have been based on the taxonomic assignment of sequences that provides reference to morphospecies ecology. Usually, only a small portion of metabarcoding data can be used due to a limited reference database and a lack of phylogenetic resolution. Here, we investigate the possibility to overcome these limitations using a taxonomy‐free approach that allows the computing of a molecular index directly from eDNA data without any reference to morphotaxonomy. As a case study, we use the benthic diatoms index, commonly used for monitoring the biological quality of rivers and streams. We analysed 87 epilithic samples from Swiss rivers, the ecological status of which was established based on the microscopic identification of diatom species. We compared the diatom index derived from eDNA data obtained with or without taxonomic assignment. Our taxonomy‐free approach yields promising results by providing a correct assessment for 77% of examined sites. The main advantage of this method is that almost 95% of OTUs could be used for index calculation, compared to 35% in the case of the taxonomic assignment approach. Its main limitations are under‐sampling and the need to calibrate the index based on the microscopic assessment of diatoms communities. However, once calibrated, the taxonomy‐free molecular index can be easily standardized and applied in routine biomonitoring, as a complementary tool allowing fast and cost‐effective assessment of the biological quality of watercourses.     

Among-habitat and Temporal Variability of Selected Macroinvertebrate Based Metrics in a Mediterranean Shallow Lake (NW Spain)

According to the European Water Framework Directive, waterbodies have to be classified on the basis of their ecological status using biological quality elements, such as macroinvertebrates. This needs to take into consideration the influence of natural variation (both spatial and temporal) of reference biological communities as this may obscure the effects caused by anthropogenic disturbance. We studied the influence of among-habitat and temporal (seasonal and interannual) changes on the macroinvertebrate communities of an Iberian shallow lake and the variability of 21 measures potentially useful for bioindication purposes. Two series of data were examined: (a) macroinvertebrate samples taken on four occasions over an annual cycle were used to assess the effects of seasonality and among-habitat variability; (b) macroinvertebrate samples collected in three consecutive summers were used to assess interannual variability. Coefficients of variation, expressed as percentage, were used to quantify the effect of among-habitat and temporal variability on the selected metrics. According to our results, % Insecta, Shannon–Wiener diversity index and the qualitative taxonomic metrics (measures based on number of taxa) were robust in terms of temporal (seasonal and interannual) and among-habitat variability. Abundance ratio and some metrics based on functional feeding groups were highly variable. Therefore, qualitative taxonomic metrics may be promising tools in biomonitoring programs of Mediterranean shallow lakes due to their comparatively low variability.     

Biomarker/bioindicator response profiles of organisms can help differentiate between sources of anthropogenic stressors in aquatic ecosystems

Aquatic ecosystems can be chronically stressed by multiple environmental factors which originate from a variety of point and non-point sources. In addition, these stressors may vary both spatially and temporally, and, combined with synergestic and cumulative interactions of these stressors, complicate the interpretation and evaluation of stress responses in organisms. To help identify and differentiate between sources of anthropogenic stressors in aquatic systems, a diagnostic approach based on exposure-response profiles in sentinel organisms was developed from the known effects of various anthropogenic activities on biological systems. To generate these exposure-effects profiles, biomarkers of exposure were plotted against bioindicators of corresponding effects for several major anthropogenic activities including petrochemical, pulp and paper, domestic sewage, mining operations, land-development, and agricultural activities. Biomarkers of exposure to environmental stressors varied widely depending on the type of anthropogenic activity involved. Bioindicator effects, however, including histopathological lesions, bioenergetic status, growth, reproductive impairment, and community-level endpoints were similar among several of the major anthropogenic activities because responses at these higher levels are less specific to stressors than are biomarkers. This approach appears useful for helping to identify and diagnose sources of stress in environments impacted by multiple stressors. By identifying the types and sources of environmental stressors impacting key components of biological systems, aquatic ecosystems can be more effectively protected, regulated, and managed to help improve and maintain environmental quality and ecosystem fitness.     

Macroinvertebrate-based multimetric predictive models for evaluating the human impact on biotic condition of Bolivian streams

We developed and validated a single multimetric index based on predictive models that could evaluate anthropogenic disturbances in streams of three disparate ecoregions of Bolivia. To do so, we examined 45 candidate metrics reflecting different aspects of macroinvertebrate assemblage structure and function gleaned from available literature and for their potential to indicate degradation. More importantly, we integrated functional trait metrics to improve the sensitivity of our index. To quantify possible deviation from reference conditions, we first established and validated statistical models describing metric responses to natural environmental differences in the absence of any significant anthropogenic disturbance. We considered that the residual distributions of these models described the response range of each metric, independently of natural environmental influence. After testing the sensitivity of these residuals to a gradient of anthropogenic disturbance, we retained eight metrics that were used in the final assemblage index, four metrics based on richness and composition and four metrics based on biological traits. Our index performed well in discriminating between reference and disturbed sites, giving a significant negative linear response to a gradient of physical and chemical anthropogenic disturbances. After employing a probability survey design and sampling a relatively small number of sites throughout all major ecoregions of Bolivia, we believe our methodology can be used to develop a monitoring tool to evaluate status and trends in biological condition for streams of the entire country despite its complex and heterogeneous geology and climate.     

Applying conservation reserve design strategies to define ecosystem monitoring priorities

In an era of unprecedented ecological upheaval, monitoring ecosystem change at large spatial scales and over long‐time frames is an essential endeavor of effective environmental management and conservation. However, economic limitations often preclude revisiting entire monitoring networks at high frequency. We aimed here to develop a prioritization strategy for monitoring networks to select a subset of existing sites that meets the principles of complementarity and representativeness of the whole ecological reality, and maximizes ecological complementarity (species accumulation) and the spatial and environmental representativeness. We applied two well‐known approaches for conservation design, the “minimum set” and the “maximal coverage” problems, using a suite of alpha and beta biodiversity metrics. We created a novel function for the R environment that performs biodiversity metric comparisons and site prioritization on a plot‐by‐plot basis. We tested our procedures using plot data provided by the Terrestrial Ecosystem Research Network (TERN) AusPlots, an Australian long‐term monitoring network of 774 vegetation and soil monitoring plots. We selected 250 plots and 80% of the total species recorded as targets for the maximal coverage and minimum set problems, respectively. We compared the subsets selected by the different biodiversity metrics in terms of complementarity and spatial and environmental representativeness. We found that prioritization based on species turnover (i.e., iterative selection of the most dissimilar plot to a cumulative sample in terms of species replacement) maximized ecological complementarity and spatial representativeness, while also providing high environmental coverage. Species richness was an unreliable metric for spatial representation. Selection based on range‐rarity‐richness was balanced in terms of complementarity and representativeness, whereas its richness‐corrected implementation failed to capture ecological and environmental variation. Prioritization based on species turnover is desirable to cover the maximum variability of the whole network. Synthesis and applications: Our results inform monitoring design and conservation priorities, which can benefit by considering the turnover component of beta diversity in addition to univariate metrics. Our tool is computationally efficient, free, and can be readily applied to any species versus sites dataset, facilitating rapid decision‐making.     

Biogeography of curimatid fishes reveals multiple lowland–upland river transitions and differential diversification in the Neotropics (Teleostei,Curimatidae)

The Neotropics harbors a megadiverse ichthyofauna comprising over 6300 species with approximately 80% in just three taxonomic orders within the clade Characiphysi. This highly diverse group has evolved in tropical South America over tens to hundreds of millions of years influenced mostly by re‐arrangements of river drainages in lowland and upland systems. In this study, we investigate patterns of spatial diversification in Neotropical freshwater fishes in the family Curimatidae, a species‐rich clade of the order Characiformes. Specifically, we examined ancestral areas, dispersal events, and shifts in species richness using spatially explicit biogeographic and macroevolutionary models to determine whether lowlands–uplands serve as museums or cradles of diversification for curimatids. We used fossil information to estimate divergence times in BEAST, multiple time‐stratified models of geographic range evolution in BioGeoBEARS, and alternative models of geographic state‐dependent speciation and extinction in GeoHiSSE. Our results suggest that the most recent common ancestor of curimatids originated in the Late Cretaceous likely in lowland paleodrainages of northwestern South America. Dispersals from lowland to upland river basins of the Brazilian and Guiana shields occurred repeatedly across independently evolving lineages in the Cenozoic. Colonization of upland drainages was often coupled with increased rates of net diversification in species‐rich genera such as Cyphocharax and Steindachnerina. Our findings demonstrate that colonization of novel aquatic environments at higher elevations is associated with an increased rate of diversification, although this pattern is clade‐dependent and driven mostly by allopatric speciation. Curimatids reinforce an emerging perspective that Amazonian lowlands act as a museum by accumulating species along time, whereas the transitions to uplands stimulate higher net diversification rates and lineage diversification.     

Taxonomic and functional diversity covary in rock pool microalgal communities despite their different drivers

Local biodiversity has traditionally been estimated with taxonomic diversity metrics such as species richness. Recently, the concept of biodiversity has been extended beyond species identity by ecological traits determining the functional role of a species in a community. This interspecific functional diversity typically responds more strongly to local environmental variation compared with taxonomic diversity, while taxonomic diversity may mirror more strongly dispersal processes compared with functional metrics. Several trait‐based indices have been developed to measure functional diversity for various organisms and habitat types, but studies of their applicability on aquatic microbial communities have been underrepresented. We examined the drivers and covariance of taxonomic and functional diversity among diatom rock pool communities on the Baltic Sea coast. We quantified three taxonomic (species richness, Shannon''s diversity, and Pielou''s evenness) and three functional (functional richness, evenness, and divergence) diversity indices and determined abiotic factors best explaining variation in these indices by generalized linear mixed models. The six diversity indices were highly collinear except functional evenness, which merely correlated significantly with taxonomic evenness. All diversity indices were always explained by water conductivity and temperature–sampling month interaction. Taxonomic diversity was further consistently explained by pool distance to the sea, and functional richness and divergence by pool location. The explained variance in regression models did not markedly differ between taxonomic and functional metrics. Our findings do not clearly support the superiority of neither set of diversity indices in explaining coastal microbial diversity, but rather highlight the general overlap among the indices. However, as individual metrics may be driven by different factors, the greatest advantage in assessing biodiversity is nevertheless probably achieved with a simultaneous application of the taxonomic and functional diversity metrics.