Search

Termites (Isoptera) constitute a considerable fraction of the global animal biomass. Conventionally, termite dry biomass estimates (g) range between 1:3 and 1:6 of fresh biomass (g). But estimates are often based on a few species or coarse taxonomic resolution. In this study, we (1) calculated the fresh and dry mass of 15 widely distributed Neotropical termite species (three families) and (2) established the conversion ratio for dry mass, which is indispensable for biomass estimates. Workers and soldiers were sampled in their colonies and quickly weighed in the laboratory to obtain the fresh mass. Then, the individuals were placed in 80% alcohol for 5 days and weighed. Finally, the samples were dried at 60°C for 24 h and weighed again. Our results suggest an average ratio of 1:4.2 (dry‐to‐fresh mass), with a mean (±SE) conversion ratio of 0.24 ± 0.06, for estimating termite biomass at local, regional, and global scales. Moreover, our results demonstrate that values from termites preserved in alcohol could still be used to estimate biomass. Specifically, after insertion in alcohol, the termites lost 16.9%–56% of their water content, with an average of 26.5%. While this represents a source of bias in estimates using samples from biological collections, dry mass was significantly related to fresh mass (Radj2 = 0.99; dry mass = 0.000055 + 0.22 × fresh mass), and to the mass of termites in alcohol (Radj2 = 0.97; dry mass = 0.00014 + 0.26 × mass in alcohol). Applying our results to data from the literature indicates that global termite dry biomass ranges from 89 to 106 Mt. [ABSTRACT FROM AUTHOR]

Microscopic epibionts on molluscan shells are a component of the biodiversity of intertidal coastal areas. Because molluscan shells are discrete habitats for the epibiont community, and the molluscan basibionts belong to the local community, epibiont diversity can be evaluated hierarchically by basibiont categories including species. To evaluate the structure of epibiont diversity and effects of taxonomic resolution on the evaluation, epibionts on molluscan shells and inert surfaces were investigated at three geographically distant sites in Japan. In total, 94 species-level taxonomic units of epibionts were obtained from 31 basibiont molluscan species and inert surfaces (plastics and rock chips). The density and the species richness at the site of the lowest latitude were significantly lower than those at the other sites. The epibiont community differed between the three sites, although the major portion of the epibionts were diatoms. Between-site diversity contributed most of the total diversity of the species richness and Simpson diversity in the five levels of the hierarchical partitioning: sample (individual basibiont), basibiont species (molluscan species), surface group (bivalves, chitons + limpets, and globose gastropods), site, and the total. The taxonomic resolution did not markedly affect the variability of communities between the three sites, although the taxon richness was reduced to 51 in the genus-level analysis. The lower taxonomic resolution (genus level); however, increased the contribution of the within-sample and decreased the contribution of β diversities at the higher hierarchies, leading to a possible overestimation of biotic homogenization between the communities. [ABSTRACT FROM AUTHOR]

Multimetric indices (MMIs) are used worldwide to assess the ecological conditions of aquatic and terrestrial ecosystems. Different criteria and approaches are used to construct MMIs, resulting in widely different indices. Therefore, scientists, managers, and policymakers sometimes question whether such MMIs are useful for biomonitoring and bioassessment programs. Crucial design issues for biomonitoring programs include MMI responsiveness, the bioindicator group used, survey design, field sampling methods, level of taxonomic resolution, metric selection and scoring, and reference condition identification. We performed a meta-analysis on MMI development and applications worldwide to analyze the response of MMIs to different disturbance factors and to determine the degree to which MMI construction features influence their responsiveness to anthropogenic disturbances. We used the Web of Science database to find articles that applied an MMI and related MMI values to an environmental stressor, and we extracted data from 157 articles. We performed random-effects modeling to estimate the overall effect of MMI responses to disturbance and used subgroup analysis to analyze the extent to which the effect sizes varied as a function of different MMI construction features. We found that reference condition criteria had the major effect on MMI responses to disturbance. The environmental disturbance type, the number of metrics, and the ecosystem type to which MMIs were applied contributed more weakly to the effect size variance. The general response of MMIs to disturbance was little affected by the bioindicator group, taxonomic resolution, metric selection criteria, or scoring method. These findings have important implications for designing biomonitoring programs, including developing and improving cost-effective biological indices, because they could enhance MMI development and application protocols. [ABSTRACT FROM AUTHOR]

Abstract The present study was carried out to investigate the palynoflora of Murree formation using microscopic techniques to understand the climatic changes and vegetation’s evolution. In this palynological study, 31 samples were collected, analyzed, and then identified as palynomorphs using different previous published literature. The results of this study will be described in terms of the evolutionary history of plants and the depositional environment of the reported taxa in the study area. The botanical affinities and systematic description of the taxa were examined using light and scanning electron microscopy. The floral record identified Asteraceae as the dominant family and Pinus as a genus. Most of angiosperms i.e Fabaceae and Poaceae, have a poor fossil record but have an abundant palynological record in the study area. The highest polar diameter (75.75 μm), colpus length (34.5 μm) and colpus width (31 μm) were examined for the Convolvulus. Most of the taxa explained here had a wide geographical occurrence in Southeast Asia and show the abundance of angiosperms in the Miocene epoch. The palynological record of Holocene samples is important to know about the vegetation’s origin and environmental fluctuations in the study area.

Resolution of systematic associations and species boundaries is vital for developing conservation priorities for threatened taxa. A complex of Fontainea (Euphorbiaceae) populations, endemic to rainforest communities in central-eastern Australia, comprises several taxonomically challenging species. Fontainea oraria is Critically Endangered, with only one natural population of 10 mature individuals, with the closely related species F. australis being listed as Vulnerable. A recently discovered Fontainea population (currently nominated as F. sp. Coffs Harbour) with taxonomic similarities to F. oraria has been provisionally listed as Critically Endangered, with fewer than 40 individuals. This study employed an integrative approach, combining genetic data and morphometrics to determine species boundaries for three threatened Fontainea population groups as a model system for an integrative approach to delimiting cryptic species. Although our results suggest the potential subdivision of the population groups into three taxa, caution is warranted because this hypothesis remains inconclusive. Taxonomic challenges demand a careful approach, acknowledging the possibility of alternative interpretations. Contrary to supporting distinct species, our morphological and genetic data may also be interpreted as indicative of a single species with geographic variation, a phenomenon observed in genetically linked populations experiencing isolation by distance. Overall, we highlight the need for further research to establish species limits to guide conservation actions. [ABSTRACT FROM AUTHOR]

ABSTRACT Insects of the Ephemeroptera order have been used as bioindicators of water quality as they respond to countless anthropic impacts. In this study, we assessed the use of Ephemeroptera as bioindicators of streams impacted by agricultural activities. We collected Ephemeroptera nymphs in six streams with different uses and soil cover in their drainage areas located in the northern region of the Brazilian state of Rio Grande do Sul. Based on soil use and cover analysis, we categorized the streams as ‘natural’ (drainage area with >42% native arboreal vegetation) and ‘agricultural’ (drainage area with >72% agricultural use). We collected a total of 2,767 organisms, distributed into four families and eleven genera. We observed greater abundance (68%) and taxonomic richness (11 genera) of Ephemeroptera in the agricultural streams. The natural streams comprise 32% of the fauna collected, with eight genera. That pattern was especially determined by the Baetidae and Leptohyphidae families. The genera Caenis, Cloeodes, and Tricorythopsis were abundant in the agricultural streams. In this study, we observed that genera of Ephemeroptera are tolerant to environmental changes, particularly those caused by agricultural activities. Therefore, the use of the order in studies to assess water quality must be carried out with caution.

Spiders are the most abundant naturally occurring predators in vineyards and play a crucial role in natural pest control. However, vineyards are frequently sprayed with fungicides, which can harm spider communities. Fungus-resistant grape varieties can drastically reduce this fungicide input. The spiders on grape vines that were sprayed with a variable number of fungicide applications in 32 vineyards in different landscapes in Southwestern Germany were recorded. Vineyards received between 0 and 14 fungicidal sprays of varying toxicity (cumulated hazard quotients for honeybee up to 6). The majority of spiders benefited from a reduction in the number fungicide sprays, particularly Dictynidae, Philodromidae, Theridiidae and Thomisidae. Overall, space web weavers, orb web weavers and ambush hunters were most strongly affected by the frequency and toxicity of fungicide applications. The response of spiders to the landscape were highly variable and included both positive and negative effects of the percentage cover of woodland. In conclusion, reducing the cumulative hazard of fungicides by reducing the number of fungicide applications is a key element in fostering spiders in vineyards.

Spiders are the most abundant naturally occurring predators in vineyards and play a crucial role in natural pest control. However, vineyards are frequently sprayed with fungicides, which can harm spider communities. Fungus-resistant grape varieties can drastically reduce this fungicide input. The spiders on grape vines that were sprayed with a variable number of fungicide applications in 32 vineyards in different landscapes in Southwestern Germany were recorded. Vineyards received between 0 and 14 fungicidal sprays of varying toxicity (cumulated hazard quotients for honeybee up to 6). The majority of spiders benefited from a reduction in the number fungicide sprays, particularly Dictynidae, Philodromidae, Theridiidae and Thomisidae. Overall, space web weavers, orb web weavers and ambush hunters were most strongly affected by the frequency and toxicity of fungicide applications. The response of spiders to the landscape were highly variable and included both positive and negative effects of the percentage cover of woodland. In conclusion, reducing the cumulative hazard of fungicides by reducing the number of fungicide applications is a key element in fostering spiders in vineyards. [ABSTRACT FROM AUTHOR]

Tardigrades are rarely included in large biodiversity surveys, mainly because of the impracticalities that follow larger sampling and identification of these microscopic animals. Consequently, there is a lack of data on their biogeographical distribution. Here, we analyse environmental DNA sequences of eutardigrades obtained with a metabarcoding protocol on Danish soil samples collected during a national biodiversity project (Biowide). Specifically, we aimed to investigate the applicability of the V4 region (~400 bp) of the 18S rRNA marker gene to assign taxonomy to 96 eutardigrade molecular operational taxonomic units (MOTUs), using three different methods (alignment-, tree- and phylogeny-based methods). Tardigrade reference libraries are currently suffering from insufficient taxon coverage, in some cases challenging the interpretation of data based on similarity searches. This can, to some extent, be accounted for by supplementing identification with algorithms that incorporate a backbone phylogeny and infer models of evolution. Together, the present findings suggest that the V4 region of the 18S rRNA gene offers a promising tool to identify unknown MOTUs of eutardigrades to genus or family level and can, in some cases, be used to assign to species level. [ABSTRACT FROM AUTHOR]

DNA barcoding is a crucial method for assessing and monitoring species diversity amidst escalating threats to global biodiversity. I explore DNA barcoding's potential as a robust and reliable tool for biodiversity assessment. It begins with a comprehensive review of existing literature, delving into the theoretical foundations, methodologies and applications of DNA barcoding. The suitability of various DNA regions, like the COI gene, as universal barcodes are extensively investigated. Additionally, the advantages and limitations of different DNA sequencing technologies and bioinformatics tools are evaluated within the context of DNA barcoding. To evaluate the efficacy of DNA barcoding, diverse ecosystems, including terrestrial, freshwater and marine habitats, are sampled. Extracted DNA from collected specimens undergoes amplification and sequencing of the target barcode region. Comparison of the obtained DNA sequences with reference databases allows for the identification and classification of the sampled organisms. Findings demonstrate that DNA barcoding accurately identifies species, even in cases where morphological identification proves challenging. Moreover, it sheds light on cryptic and endangered species, aiding conservation efforts. I also investigate patterns of genetic diversity and evolutionary relationships among different taxa through the analysis of genetic data. This research contributes to the growing knowledge on DNA barcoding and its applicability for biodiversity assessment. The advantages of this approach, such as speed, accuracy and cost-effectiveness, are highlighted, along with areas for improvement. By unlocking the genetic code, DNA barcoding enhances our understanding of biodiversity, supports conservation initiatives and informs evidence-based decision-making for the sustainable management of ecosystems.

DNA barcoding is a crucial method for assessing and monitoring species diversity amidst escalating threats to global biodiversity. I explore DNA barcoding's potential as a robust and reliable tool for biodiversity assessment. It begins with a comprehensive review of existing literature, delving into the theoretical foundations, methodologies and applications of DNA barcoding. The suitability of various DNA regions, like the COI gene, as universal barcodes are extensively investigated. Additionally, the advantages and limitations of different DNA sequencing technologies and bioinformatics tools are evaluated within the context of DNA barcoding. To evaluate the efficacy of DNA barcoding, diverse ecosystems, including terrestrial, freshwater and marine habitats, are sampled. Extracted DNA from collected specimens undergoes amplification and sequencing of the target barcode region. Comparison of the obtained DNA sequences with reference databases allows for the identification and classification of the sampled organisms. Findings demonstrate that DNA barcoding accurately identifies species, even in cases where morphological identification proves challenging. Moreover, it sheds light on cryptic and endangered species, aiding conservation efforts. I also investigate patterns of genetic diversity and evolutionary relationships among different taxa through the analysis of genetic data. This research contributes to the growing knowledge on DNA barcoding and its applicability for biodiversity assessment. The advantages of this approach, such as speed, accuracy and cost-effectiveness, are highlighted, along with areas for improvement. By unlocking the genetic code, DNA barcoding enhances our understanding of biodiversity, supports conservation initiatives and informs evidence-based decision-making for the sustainable management of ecosystems. [ABSTRACT FROM AUTHOR]

Simple Summary: Urban ecosystems provide habitat to many species, including invasive species such as the cane toad (Rhinella marina) that is particularly successful in human-altered landscapes. There have been numerous investigations of the cane toad diet, but most of these studies identified prey items at lower taxonomic resolutions (i.e., order or family). We used higher resolution for prey identification and multiple dietary measures of prey consumption to assess the ecological role of cane toads in the urban landscape of southwest Florida. Prey taxa commonly considered urban pests dominated the diet of cane toads inhabiting golf course communities, and there were differences in prey consumed during the wet and dry seasons of this region. We provided a better understanding of the potential relationships between cane toads and their prey in the urban environment. We investigated the diet of cane toads (Rhinella marina) inhabiting urbanized areas in southwest Florida to provide high taxonomic resolution of prey items, contrast toad diets between sampling seasons and sexes, and assess this invasive species' ecological role in the urban landscape. A pest control agency collected cane toads from two golf course communities in Naples, Florida, USA during November–December 2018 (early dry season) and June–July 2019 (early wet season), and faunal stomach contents were quantified from a random subsample of 240 adult toads (30 males and 30 females from each community and season). Yellow-banded millipedes (Anadenobolus monilicornis), big-headed ants (Pheidole spp.), and hunting billbugs (Sphenophorus venatus vestitus) were the most frequently consumed prey items and had the highest total numbers and/or volume with corresponding highest indices of relative importance. There was considerable overlap in the seasonal prey importance values for each golf course community and little if any difference in the importance values between toad sexes in each community. Nonetheless, big-headed ants were the most important prey in both communities during the wet season, while yellow-banded millipedes were the most important dry season prey in one community and hunting billbugs the most important in the other. Despite limited spatiotemporal sampling effort, our results indicated that cane toad was consuming arthropod taxa considered pests in the urban ecosystem. Further studies are needed to investigate the potential effects of human activities and environmental variability on the cane toad diet and to determine whether cane toads act as a biological control for pest populations. [ABSTRACT FROM AUTHOR]

Simple Summary: eDNA metabarcoding is a relatively novel method for studying the diet of wild animals. This study compares eDNA metabarcoding with microscopy, in order to determine the diet of four species of waterfowl. In total, 56 plants were identified at the species level. The study concluded that the combination of morphological analysis and DNA metabarcoding can yield adequate information to address pertinent ecological inquiries. Understanding diets and structural food webs are keys to the apprehension of ecological communities, upon which conservation and management biology are based. The understanding of grazing and habitat choice for waterfowl is one of the most important topics for avian ecologists today and can, to some degree, be answered by dietary analysis. Droppings collected from four waterfowl, the Eurasian wigeon (Anas penelope), Greylag goose (Anser anser), pink-footed goose (Anser brachyrhynchus) and Barnacle goose (Branta leucopsis) in Vejlerne (Denmark), were analysed microscopically and through eDNA metabarcoding with the use of next generation sequencing (NGS) to accumulate knowledge about the diet of these waterfowl. In total, 120 dropping samples were microscopically analysed, of which the eDNA metabarcoding analysis was done on 79 samples. The prey items were identified according to the taxonomic level of species, and a qualitative method, frequency of occurrence (FO) and FO calculated as a percentage, was used in order to compare the results from the two methods. As neither of the methods was able to encompass all species discovered when combining the two methods, it was concluded in this study that the two methods can support each other in a dietary analysis of waterfowl, but not replace one another. [ABSTRACT FROM AUTHOR]

Streamflow-duration assessment methods (SDAMs) are rapid, indicator-based tools for classifying streamflow duration (e.g., intermittent vs perennial flow) at the reach scale. Indicators are easily assessed stream properties used as surrogates of flow duration, which is too resource intensive to measure directly for many reaches. Invertebrates are commonly used as SDAM indicators because many are not highly mobile, and different species have life stages that require flow for different durations and times of the year. The objectives of this study were to 1) identify invertebrate taxa that can be used as SDAM indicators to distinguish between stream reaches having intermittent and perennial flow, 2) to compare indicator strength across different taxonomic and numeric resolutions, and 3) to assess the relative importance of season and habitat type on the ability of invertebrates to predict streamflow-duration class. We used 2 methods, random forest models and indicator species analysis, to analyze aquatic and terrestrial invertebrate data (presence/absence, density, and biomass) at the family and genus levels from 370 samples collected from both erosional and depositional habitats during both wet and dry seasons. In total, 36 intermittent and 53 perennial reaches were sampled along 31 forested headwater streams in 4 level II ecoregions across the United States. Random forest models for family- and genus-level datasets had stream classification accuracy ranging from 88.9 to 93.2%, with slightly higher accuracy for density than for presence/absence and biomass datasets. Season (wet/dry) tended to be a stronger predictor of streamflow-duration class than habitat (erosional/depositional). Many taxa at the family (58.8%) and genus level (61.6%) were collected from both intermittent and perennial reaches, and most taxa that were exclusive to 1 streamflow-duration class were rarely collected. However, 23 family-level or higher taxa (20 aquatic and 3 terrestrial) and 44 aquatic genera were identified as potential indicators of streamflow-duration class for forested headwater streams. The utility of the potential indicators varied across level II ecoregions in part because of representation of intermittent and perennial reaches in the dataset but also because of variable ecological responses to drying among species. Aquatic invertebrates have been an important field indicator of perennial reaches in existing SDAMs, but our findings highlight how including aquatic and terrestrial invertebrates as indicators of intermittent reaches can further maximize the data collected for streamflow-duration classifications. [ABSTRACT FROM AUTHOR]

The delivery of consistent and accurate fine‐resolution data on biodiversity using metabarcoding promises to improve environmental assessment and research. Whilst this approach is a substantial improvement upon traditional techniques, critics note that metabarcoding data are suitable for establishing taxon occurrence, but not abundance. We propose a novel hierarchical approach to recovering abundance information from metabarcoding, and demonstrate this technique using benthic macroinvertebrates. To sample a range of abundance structures without introducing additional changes in composition, we combined seasonal surveys with fish‐exclusion experiments at Catamaran Brook in northern New Brunswick, Canada. Five monthly surveys collected 31 benthic samples for DNA metabarcoding divided between caged and control treatments. A further six samples per survey were processed using traditional morphological identification for comparison. By estimating the probability of detecting a single individual, multispecies abundance models infer changes in abundance based on changes in detection frequency. Using replicate detections of 184 genera (and 318 species) from metabarcoding samples, our analysis identified changes in abundance arising from both seasonal dynamics and the exclusion of fish predators. Counts obtained from morphological samples were highly variable, a feature that limited the opportunity for more robust comparison, and emphasizing the difficulty standard methods also face to detect changes in abundance. Our approach is the first to demonstrate how quantitative estimates of abundance can be made using metabarcoding, both among species within sites as well as within species among sites. Many samples are required to capture true abundance patterns, particularly in streams where counts are highly variable, but few studies can afford to process entire samples. Our approach allows study of responses across whole communities, and at fine taxonomic resolution. We discuss how ecological studies can use additional sampling to capture changes in abundance at fine resolution, and how this can complement broad‐scale biomonitoring using DNA metabarcoding. [ABSTRACT FROM AUTHOR]

Bipartite network analysis is a powerful tool to study the processes structuring interactions in ecological communities. In applying the method, it is assumed that the sampled interactions provide an accurate representation of the actual community. However, acquiring a representative sample may be difficult as not all species are equally abundant or easily identifiable. Two potential sampling issues can compromise the conclusions of bipartite network analyses: failure to capture the full range of interactions (sampling completeness) and use of a taxonomic level higher than species to evaluate the network (taxonomic resolution). We asked how commonly used descriptors of bipartite antagonistic communities (modularity, nestedness, connectance, and specialization [H2′]) are affected by reduced host sampling completeness, parasite taxonomic resolution, and their crossed effect, as they are likely to co‐occur. We used a quantitative niche model to generate weighted bipartite networks that resembled natural host–parasite communities. The descriptors were more sensitive to uncertainty in parasite taxonomic resolution than to host sampling completeness. When only 10% of parasite taxonomic resolution was retained, modularity and specialization decreased by ~76% and ~12%, respectively, and nestedness and connectance increased by ~114% and ~345% respectively. The loss of taxonomic resolution led to a wide range of possible communities, which made it difficult to predict its effects on a given network. With regards to host sampling completeness, standardized nestedness, connectance, and specialization were robust, whereas modularity was sensitive (~30% decrease). The combination of both sampling issues had an additive effect on modularity. In communities with low effort for both sampling issues (50%–10% of sampling completeness and taxonomic resolution), estimators of modularity, and nestedness could not be distinguished from those of random assemblages. Thus, the categorical description of communities with low sampling effort (e.g., if a community is modular or not) should be done with caution. We recommend evaluating both sampling completeness and taxonomic certainty when conducting bipartite network analyses. Care should also be exercised when using nonrobust descriptors (the four descriptors for parasite taxonomic resolution; modularity for host sampling completeness) when sampling issues are likely to affect a dataset. [ABSTRACT FROM AUTHOR]

The use of macroinvertebrates as indicators of water quality is an effective and low-cost tool, which is widely implemented in biomonitoring programmes. Certain taxa are characteristic of impaired watercourses (e.g. Oligochaeta, Chironomidae and Amphipoda), while others are characteristic of good-quality watercourses (e.g. Ephemeroptera, Plecoptera and Trichoptera; EPT). In this work, we evaluated the response of the macroinvertebrate assemblages to different land uses. For this purpose, artificial substrate colonization experiments were conducted in streams including urban (U, n = 3), intensive agriculture and dairy production (AD, n = 4) and extensive cattle ranching (CR, n = 4) land uses. Because in Uruguay pristine ecosystems are practically non-existent and streams of low order streams associated with extensive cattle production represent the lowest deterioration water quality condition, CR sites were used as control reference streams. Physicochemical water parameters were measured. For macroinvertebrate sampling, 10 artificial substrates were installed in each stream. A total of 110 artificial substrates were analysed. Each sample/site consisted of a plastic mesh bag of 1.2 cm opening, which were filled with 160 cm3 (including 73.3 ± 5.8 cm3 interstitial water) of stones sieved between 1.3 and 1.5 cm. During the summer of 2018 (February), devices were left in streams for 15 days for communities to colonize them. U and AD land use represented the stressors with the highest impact on the attributes and composition of the macroinvertebrate communities. Abundance of EPT was higher in CR, meanwhile Caenogastropoda dominated in AD, and Amphipoda in U sites. Macroinvertebrate groups to order level classification were able to effectively discriminate between different land uses. The use of artificial substrate also demonstrated to be efficient method for monitoring macroinvertebrate community. We did not find a correlation between the physicochemical water parameters and the macroinvertebrate community. In this context, we propose a rapid and cost-effective biomonitoring approach, capable of estimating the degree of impact of different land uses. [ABSTRACT FROM AUTHOR]

Artificial substrates are ideal for the settlement of biofouling communities. Oyster cages used in mariculture are known to provide substrate for a diversity of epibiotic organisms to settle and grow. While oyster farmers regularly clean their cages of these epibionts, diverse biofouling communities can still develop and contribute to the composition of the overall ecosystem surrounding mariculture farms. Colonization by biofouling organisms, including algae and animals, can be sudden and have rapid development. Biofouling on cages can have deleterious impacts on the farmed oysters, ultimately increasing operational expenses and decreasing farmer profits. Identifying seasonal and spatial patterns in biofouling community composition and their relationship to environmental conditions is essential for effectively addressing the impact these organisms pose. Here, we examined changes in taxonomic composition of biofouling communities over time at multiple oyster mariculture farms in the Gulf of Alaska with the intent of answering our overarching research question: Does composition of biofouling communities vary seasonally and spatially? To address this question, we took bi-monthly photographs of oyster cages from March to September of 2023 at three farms in Kachemak Bay and one sampling was done in September 2023 in Prince William Sound to assess seasonal and spatial differences in biofouling community composition. A subset of photographs taken at all sites in September were paired with scrape collections for biomass to compare surveying methods. Though there were notable differences in taxonomic resolution between the two sampling methods, both resulted in similar diversity measurements and spatial patterns of composition. Diatom mats and red filamentous algae were predominant contributors to biofouling. Additionally, the spatial differences in community variability and composition were stronger than seasonal differences, and salinity was found to best correlate with patterns in biofouling communities. Altogether, these findings have practical implications for monitoring impacts of biofouling on mariculture, as the methodological approach can be catered to specific research goals or resource constraints. • Investigation of biofouling communities on oyster farms in Alaska. • Spatial differences in community variability and composition were stronger than seasonal differences. • Methodological approach can be catered to specific research goals or resource constraints. [ABSTRACT FROM AUTHOR]

We investigated the diet of cane toads (Rhinella marina) inhabiting urbanized areas in southwest Florida to provide high taxonomic resolution of prey items, contrast toad diets between sampling seasons and sexes, and assess this invasive species’ ecological role in the urban landscape. A pest control agency collected cane toads from two golf course communities in Naples, Florida, USA during November–December 2018 (early dry season) and June–July 2019 (early wet season), and faunal stomach contents were quantified from a random subsample of 240 adult toads (30 males and 30 females from each community and season). Yellow-banded millipedes (Anadenobolus monilicornis), big-headed ants (Pheidole spp.), and hunting billbugs (Sphenophorus venatus vestitus) were the most frequently consumed prey items and had the highest total numbers and/or volume with corresponding highest indices of relative importance. There was considerable overlap in the seasonal prey importance values for each golf course community and little if any difference in the importance values between toad sexes in each community. Nonetheless, big-headed ants were the most important prey in both communities during the wet season, while yellow-banded millipedes were the most important dry season prey in one community and hunting billbugs the most important in the other. Despite limited spatiotemporal sampling effort, our results indicated that cane toad was consuming arthropod taxa considered pests in the urban ecosystem. Further studies are needed to investigate the potential effects of human activities and environmental variability on the cane toad diet and to determine whether cane toads act as a biological control for pest populations.

Aim: This study aimed at investigating the taxonomic resolutions (TRs) of benthic macroinvertebrates for freshwater assessments in the scope of the functional trait approach (FTA). Location: Macroinvertebrate samples were collected in 22 locations within the Paute River Basin (PRB), Ecuador, over three years (2010, 2011 and 2012). Methods: Biological traits were allocated as scores to the macroinvertebrate data (at genus level) through fuzzy coding, using published data. The scores of each genus were used to derive scores for the corresponding family. These two sets of scores were standardized and compared, they were similar in 82% of the cases. Functional diversity (FD) was described by the rRao index, which showed no significant differences between coarse (family level) and fine (genus level) TRs. Cluster analyses using the K‐means algorithm were performed to determine similarities between both rRao data sets. The WQ cluster number (K) was varied between 2 and 5 to determine a threshold K value (Kth), after which a WQ assessment differed as a function of the TR being used. Results: Kth was 3. Family‐level identification in the framework of the FTA in the PRB was suitable in detecting changes of macroinvertebrate assemblages (until Kth = 3). Main conclusions: The proposed methodology could be implemented in other basins where decision‐makers could decide whether the level of functional trait data similarity is sufficient for WQ management purposes and whether the defined Kth is acceptable. The reliability of the key methodological steps was assessed using performance statistics that have rarely been applied to ecological studies. Despite related research performed in other regions, the present study is the first South American attempt to investigate the effects of TR of benthic macroinvertebrates on freshwater bioassessments using functional traits. [ABSTRACT FROM AUTHOR]

Recent advances in molecular ecology have dramatically improved our knowledge of soil microbial diversity and offers new indicators of soil quality. The usefulness of diversity indices has never been greater as the astronomical amounts of data generated in the literature needs to be synthesized. Despite technical guidelines have been proposed to characterize soil microbiomes using high throughput sequencing, the effect of taxonomic resolution on diversity indices is still largely unknown. Here, we explored how downscaling to higher taxonomic resolution levels may affect α- and β-diversity indices of bacterial communities exposed to different soil organic matter management. To this aim, we collected soil samples in a long-term experimental site (Ultuna, Sweden) where different mineral and organic fertilizers have been applied for since 1956. We used both massive amplicon sequencing from phylum to species (OTU) and molecular fingerprints (PLFA, DGGE and T-RFLP). Our results showed that the discrimination potential increased at finer taxonomic resolution for β-diversity but not for α-diversity indices such as richness and evenness. Also, the relative importance of hierarchical drivers of soil microbial communities such as C, N and pH varied depending on the taxonomic resolution. This study also demonstrated that indicators generated by molecular fingerprints such as PLFA, DGGE and T-RFLP are still consistent to monitor the effect of agricultural management on β-diversity but not on α-diversity, which is useful information as it allows for a better use of results in past literature. We encourage performing such comparative studies on wider surveys, including different contexts and other indicators, in order to increase the efficiency and the robustness of the use of sequencing data in soil biodiversity monitoring.

Environmental management is one of the most important activities in ecological conservation at present. Faced with various socioeconomic impacts (e.g., urbanization, agriculture, and logging), practical and effective ways to analyze and determine how biodiversity is affected by these anthropogenic activities are essential. Utilizing niche theory helps to understand how similar groups of organisms respond to environmental changes based on the assumption that organisms with some niche overlap (i.e., similar resources) will respond similarly to these changes. Members of the order Odonata are frequently used as biological indicators due to their low survey costs, relatively easy taxonomic identification, and sensibility to environmental changes. In this study, using the PROTEST method, we analyze the cross-taxon congruence between Odonata and two aquatic organisms in Brazilian savanna streams: Gerromorpha and fishes. Although congruence was found between aquatic insects (~ 45%), this result changed when we only considered the species’ genera: no congruence for the aquatic insects was found, but instead we found a congruence between Odonata and fishes (~ 44%). Since Odonata showed congruence with the other groups in different taxonomical resolutions and it is a relatively easy and cheap group to collect and identify, we suggest that Odonata could be used as an indicator of disturbance for this set of organisms and hence serve as an alternative method to traditional environmental management techniques. [ABSTRACT FROM AUTHOR]

Background: Pollinators are important ecological elements due to their role in the maintenance of ecosystem health, wild plant reproduction, crop production and food security. The pollinator-plant interaction supports the preservation of plant and animal populations and it also improves the yield in pollination dependent crops. Having knowledge about the plant-pollinator interaction is necessary for development of pesticide risk assessment of pollinators and conservation of endangering species. Results: Traditional methods to discover the relatedness of insects and plants are based on tracing the visiting pollinators by field observations as well as palynology. These methods are time-consuming and needs expert taxonomists to identify different groups of pollinators such as insects or identify flowering plants through palynology. With pace of technology, using molecular methods become popular in identification and classification of organisms. DNA metabarcoding, which is the combination of DNA barcoding and high throughput sequencing, can be applied as an alternative method in identification of mixed origin environmental samples such as pollen loads attached to the body of insects and has been used in DNA-based discovery of plant-pollinator relationship. Conclusions: DNA metabarcoding is practical for plant-pollinator studies, however, lack of reference sequence in online databases, taxonomic resolution, universality of primers are the most crucial limitations. Using multiple molecular markers is preferable due to the limitations of developed universal primers, which improves taxa richness and taxonomic resolution of the studied community. [ABSTRACT FROM AUTHOR]

The Arabian Gulf is a natural laboratory to examine how subtropical coral reef ecosystems might change in responding to recurring heating events because of uniquely high water temperature and relatively low fish diversity. Several statistical methods were applied to long-term (30 yrs) monitoring data in the western Arabian Gulf to extract clean signals of the fish abundances, to reveal common trends in the multivariate time series, and to test for nonlinear and lagged effects of coral coverage and sea surface temperature as predictors. Data were analyzed at three taxonomic resolutions: species (29 species out of a total of 148 species, contributing to 69% of total observations), genus (24 genera, 81%), and family (19 families, 96%), to test the taxonomic sufficiency hypothesis, which asserts that there is no significant loss of information at higher taxonomic levels for detecting changes in the fish assemblages. Multivariate abundance time series can be summarized by dynamic factor models of four common trends, which were supported by time series clustering and good model fitting performances. The taxonomic sufficiency hypothesis is supported for the first two common trends, which showed similarity among the three taxonomic resolutions. The effects of changes in coral coverage on the fish community are nonlinear and significantly lagged with lags mostly of 8 yrs, while the effects of mean sea surface temperature were significant but inconclusive. The fish communities in the coral reefs of the western Arabian Gulf are degrading in general with decreasing abundance at the three taxonomic resolutions. Analyzing data at coarser taxonomic resolutions can be informative in revealing the general trends of the abundance of coral reef fish communities, at the cost of ignoring variations at finer resolutions. This study further highlights the importance of long-term and continuous monitoring of the coral reef ecosystem at the finest possible taxonomic level to fully reveal slow but crucial changes in fish communities, as well as to detect signs of communities' degradation to take timely restoration actions. [ABSTRACT FROM AUTHOR]

It is essential to explore and define the level of taxonomic identification and quantification approaches for diversity and biomonitoring studies, given their potential influence on assessing and interpreting ecological outcomes. This study assessed the response of benthic macroinvertebrate communities to restore and construct gravel bars in a dam-impacted river, with non-dam influenced tributaries serving as reference sites. Additionally, we evaluated the performance of different taxonomic and numerical (i.e., abundance vs. presence/absence data) resolutions of DNA metabarcoding with consequent comparison to morphology-based identification and how it affects assessment outcomes. DNA metabarcoding detected 93% of the morphologically identified individuals and provided finer taxonomic resolution. We also detected significant correlations between morphological sample abundance, biomass, and DNA metabarcoding-read abundance. Furthermore, we observed a relatively high and significant congruence in macroinvertebrate community structure and composition between different taxonomic and numerical resolutions of both methods. This indicates a satisfactory surrogacy between the two approaches and their varying identification levels and data transformation. Additionally, community–environmental associations were significant for all datasets but showed significant varying associations with physicochemical parameters. Our observations imply that coarser taxonomic resolution could be highly advantageous for DNA metabarcoding-based applications in situations where the lack of taxonomic information, e.g., poor reference database, might severely affect biological assessment quality.

Metabarcoding of bulk or environmental DNA has great potential for biomonitoring of freshwater environments. However, successful application of metabarcoding to biodiversity monitoring requires universal primers with high taxonomic coverage that amplify highly variable, short metabarcodes with high taxonomic resolution. Moreover, reliable and extensive reference databases are essential to match the outcome of metabarcoding analyses with available taxonomy and biomonitoring indices. Benthic invertebrates, particularly insects, are key taxa for freshwater bioassessment. Nevertheless, few studies have so far assessed markers for metabarcoding of freshwater macrobenthos. Here we combined in silico and laboratory analyses to test the performance of different markers amplifying regions in the 18S rDNA (Euka02), 16S rDNA (Inse01) and COI (BF1_BR2‐COI) genes, and developed an extensive database of benthic macroinvertebrates of France and Europe, with a particular focus on key insect orders (Ephemeroptera, Plecoptera and Trichoptera). Analyses on 1,514 individuals representing different taxa of benthic macroinvertebrates showed very different amplification success across primer combinations. The Euka02 marker showed the highest universality, while the Inse01 marker showed excellent performance for the amplification of insects. BF1_BR2‐COI showed the highest resolution, while the resolution of Euka02 was often limited. By combining our data with GenBank information, we developed a curated database including sequences representing 822 genera. The heterogeneous performance of the different primers highlights the complexity in identifying the best markers, and advocates for the integration of multiple metabarcodes for a more comprehensive and accurate understanding of ecological impacts on freshwater biodiversity. [ABSTRACT FROM AUTHOR]

The polychaete Capitella capitata is historically one of the most commonly used indicators of organic enrichment in marine benthic environments. However, this taxon has been used to refer to several cryptic species with distinct environmental tolerances, which may compromise ecological assessment and monitoring programs. In this study, we aimed to (1) assess the overlap and patterns of dominance in the spatial and temporal distribution and response to environmental variability of different species of the C. capitata complex in an urbanized coastal area and (2) investigate how the taxonomic resolution (species vs genera) could affect the observed patterns (i.e., whether the acknowledgement of cryptic species may affect the outcome of ecological assessments). Eight sampling campaigns were carried out from September 2011 to September 2013 in a heavily anthropized tidal flat in Southeastern Brazil. Four species of the complex were identified. Capitella nonatoi was the most abundant (~80% of the total abundance). Overall, the four species of Capitella showed high overlap in spatial distribution, especially between the most abundant ones. At community level, taxonomic resolution did not influence the perceived relationships with environmental and spatial variables, a result likely driven by the dominance of C. nonatoi and relatively high spatial overlap among species. The assemblage was influenced mainly by chlorophyll a and hydrocarbons, corroborating the indicator status of the taxa. At species level, however, individual response to environmental variability differed, suggesting that species may have distinct requirements. Thus, the use of a particular taxonomic resolution in ecological studies depends on the questions to be addressed. The recognition of cryptic diversity may be important for biodiversity assessments and studies at the population level (i.e., dynamics, behavior). Although further studies are needed to corroborate the observed patterns of dominance at larger scales, for community-level assessments, our results suggest that identifying Capitella to species level may not be needed for local ecological monitoring. [ABSTRACT FROM AUTHOR]

Environmental surveillance is a critical tool for combatting public health threats represented by the global COVID-19 pandemic and the continuous increase of antibiotic resistance in pathogens. With its power to detect entire microbial communities, metagenomics-based methods stand out in addressing the need. However, several hurdles remain to be overcome in order to generate actionable interpretations from metagenomic sequencing data for infection prevention. Conceptually and technically, we focus on viability assessment, taxonomic resolution, and quantitative metagenomics, and discuss their current advancements, necessary precautions and directions to further development. We highlight the importance of building solid conceptual frameworks and identifying rational limits to facilitate the application of techniques. We also propose the usage of internal standards as a promising approach to overcome analytical bottlenecks introduced by low biomass samples and the inherent lack of quantitation in metagenomics. Taken together, we hope this perspective will contribute to bringing accurate and consistent metagenomics-based environmental surveillance to the ground.

Environmental surveillance is a critical tool for combatting public health threats represented by the global COVID-19 pandemic and the continuous increase of antibiotic resistance in pathogens. With its power to detect entire microbial communities, metagenomics-based methods stand out in addressing the need. However, several hurdles remain to be overcome in order to generate actionable interpretations from metagenomic sequencing data for infection prevention. Conceptually and technically, we focus on viability assessment, taxonomic resolution, and quantitative metagenomics, and discuss their current advancements, necessary precautions and directions to further development. We highlight the importance of building solid conceptual frameworks and identifying rational limits to facilitate the application of techniques. We also propose the usage of internal standards as a promising approach to overcome analytical bottlenecks introduced by low biomass samples and the inherent lack of quantitation in metagenomics. Taken together, we hope this perspective will contribute to bringing accurate and consistent metagenomics-based environmental surveillance to the ground. [ABSTRACT FROM AUTHOR]

A wide knowledge base regarding the ecological preferences of benthic macroinvertebrates is synthesized in public databases. This knowledge can assist in disentangling the influence of multiple environmental factors on the probability of occurrence of macroinvertebrates and in identifying anthropogenic impacts on the macroinvertebrate assemblage. We aimed to examine and extend current knowledge on ecological preferences by confronting it with independent biomonitoring datasets and to assess how the taxonomic resolution of datasets and the prevalence of taxa affects our ability to do so. We used a habitat suitability-based multi-species distribution model (HS-MSDM) and applied Bayesian inference to confront current knowledge (formalized as prior probability distributions) against independent biomonitoring data across rivers in Switzerland. Shifts in the resulting posterior probability distributions relative to the priors indicate a disagreement with the current knowledge of ecological preferences. Ecological preferences for temperature and organic matter had the highest influence on the predicted occurrence of macroinvertebrates in the model, followed by flow velocity, insecticide pollution, and substratum. Three-fold cross-validation tests demonstrated that the HS-MSDM predicted the distribution of taxa with a relative frequency of occurrence between 0.2 and 0.8 considerably better than a model without consideration of environmental factors. However, it was less able to predict the distribution of taxa with a frequency of occurrence <0.1 or >0.9. Nine taxa with a frequency of occurrence between 0.4 and 0.8 were identified as potentially useful bioindicators, given their strong association with the environmental factors in the model. We also identified 29 taxa for which part of the ecological preference data, particularly temperature and flow-velocity preferences, should be re-examined. For river morphology, 18 sensitive and 10 insensitive taxa were identified, although direct and uniquely linked prior knowledge regarding morphology was lacking for all taxa. Phylogenetically derived information on ecological preferences could be integrated and updated to fill gaps in ecological preference databases. However, the taxonomic resolution of the biomonitoring and ecological preference data plays an important role, as we show by identifying families comprising species that respond differently to environmental factors. These results demonstrate the value of conducting biomonitoring at the most detailed taxonomic level possible. [ABSTRACT FROM AUTHOR]

The Eurasian otter (Lutra lutra) is a semi-aquatic predator that lives in a wide range of aquatic habitats. Knowledge of the diet of predators is essential for the management and conservation of the species and their habitats. We assessed the diet of otters in fifty-three faecal samples (spraints) by morphological analysis of undigested prey remains and by DNA metabarcoding approaches with two different blocking primers. The blocking primers were shown to be similarly effective in repressing host DNA, improving amplification of non-host taxa. The analyses were conducted to compare the accuracy of the two methods. The prey items were categorized to the highest possible taxonomic resolution, and relative frequency of occurrence was applied in order to compare the morphological and DNA results. The bulk score for difference prey items in the spraints was based on volume estimates in macroscopic observations. The two methods had an overlap of identified prey species ranging from 69.9 to 72.9% (depending on the kind of primers) meaning that a large portion of prey items found by one method was replaced by other prey items in the other method and that most prey items found through DNA-metabarcoding are considered new when compared with the morphological analysis. Therefore, applying both morphological and DNA analysis is crucial in order to determine the diet of otters and, possibly, other predatory species. [ABSTRACT FROM AUTHOR]

Abstract Background Chironomids, or non-biting midges, often dominate stream invertebrate communities in terms of biomass, abundance, and species richness and play an important role in riverine food webs. Despite these clear facts, the insect family Chironomidae is often treated as a single family in ecological studies or bioassessments given the difficulty to determine specimens further. We investigated stressor responses of single chironomid operational taxonomic units (OTUs) to three globally important stressors (increased salinity, fine sediment and reduced water flow velocity) in a highly replicated mesocosm experiment using a full-factorial design (eight treatment combinations with eight replicates each). Results In total, 183 chironomid OTUs (97% similarity) were obtained by applying a quantitative DNA metabarcoding approach. Whereas on the typically applied family level, chironomids responded positively to added fine sediment and reduced water velocity in the streambed and negatively to reduced velocity in the leaf litter, an OTU-level analysis revealed a total of 15 different response patterns among the 35 most common OTUs only. The response patterns ranged from (a) insensitivity to any experimental manipulation over (b) highly specific sensitivities to only one stressor to (c) additive multiple-stressor effects and even (d) complex interactions. Conclusion Even though most OTUs (> 85%) could not be assigned to a formally described species due to a lack of accurate reference data bases at present, the results indicate increased explanatory power with higher taxonomic resolution. Thus, our results highlight the potential of DNA-based approaches when studying environmental impacts, especially for this ecologically important taxon and in the context of multiple stressors.

ABSTRACT The present study evaluated the potential for the reduction of sampling effort in studies of ephemeropteran nymphs in Brazilian Amazon streams, Pará State, Brazil, without the loss of ecological information (species composition, abundance, and richness), and the congruence of different levels of taxonomic resolution (morphospecies, genus, family and functional group). Test groups of 15, 10 and five subsamples were selected from the 20 subsamples collected per stream (40 streams sampled), and were compared in terms of their species richness and abundance (ANOVA), and composition (Procrustes). Taxonomic resolution was also analyzed in Procrustes. Species abundance (F(3, 156) = 25.426; p < 0.001) and richness (F(3, 156) = 13.866, p < 0.001) varied significantly among sample groups, while the results of the 15-S group were statistically similar, in both cases, to those of the 20-S group. A similar pattern was found for species composition. The genus-level taxonomic resolution produced results 99% similar to those found for the species-level data. The results indicate that the reduction in sampling effort from 20 to 15 subsamples per site and a genus-level taxonomic resolution would not affect the reliability of analyses significantly. A reduction of five samples per site would result in a decrease of effort in the field and the amount of material to be processed, reducing laboratory time. In addition to a reduction in the time and resources needed to identify specimens, the adoption of a genus-level taxonomic resolution could help minimize errors of under- or over-estimation in the processing of the results.

The complexity and natural variability of ecosystems present a challenge for reliable detection of change due to anthropogenic influences. This issue is exacerbated by necessary trade-offs that reduce the quality and resolution of survey data for assessments at large scales. The Peace-Athabasca Delta (PAD) is a large inland wetland complex in northern Alberta, Canada. Despite its geographic isolation, the PAD is threatened by encroachment of oil sands mining in the Athabasca watershed and hydroelectric dams in the Peace watershed. Methods capable of reliably detecting changes in ecosystem health are needed to evaluate and manage risks. Between 2011 and 2016, aquatic macroinvertebrates were sampled across a gradient of wetland flood frequency, applying both microscope-based morphological identification and DNA metabarcoding. By using multispecies occupancy models, we demonstrate that DNA metabarcoding detected a much broader range of taxa and more taxa per sample compared to traditional morphological identification and was essential to identifying significant responses to flood and thermal regimes. We show that family-level occupancy masks high variation among genera and quantify the bias of barcoding primers on the probability of detection in a natural community. Interestingly, patterns of community assembly were nearly random, suggesting a strong role of stochasticity in the dynamics of the metacommunity. This variability seriously compromises effective monitoring at local scales but also reflects resilience to hydrological and thermal variability. Nevertheless, simulations showed the greater efficiency of metabarcoding, particularly at a finer taxonomic resolution, provided the statistical power needed to detect change at the landscape scale. [ABSTRACT FROM AUTHOR]

Ecologists are increasingly interested in plant–pollinator networks that synthesize in a single object the species and the interactions linking them within their ecological context. Numerous indices have been developed to describe the structural properties and resilience of these networks, but currently, these indices are calculated for a network resolved to the species level, thus preventing the full exploitation of numerous datasets with a lower taxonomic resolution. Here, we used datasets from the literature to study whether taxonomic resolution has an impact on the properties of plant–pollinator networks.For a set of 41 plant–pollinator networks from the literature, we calculated nine network index values at three different taxonomic resolutions: species, genus, and family. We used nine common indices assessing the structural properties or resilience of networks: nestedness (estimated using the nestedness index based on overlap and decreasing fill [NODF], weighted NODF, discrepancy [BR], and spectral radius [SR]), connectance, modularity, robustness to species loss, motifs frequencies, and normalized degree.We observed that modifying the taxonomic resolution of these networks significantly changes the absolute values of the indices that describe their properties, except for the spectral radius and robustness. After the standardization of indices measuring nestedness with the Z‐score, three indices—NODF, BR, and SR for binary matrices—are not significantly different at different taxonomic resolutions. Finally, the relative values of all indices are strongly conserved at different taxonomic resolutions.We conclude that it is possible to meaningfully estimate the properties of plant–pollinator interaction networks with a taxonomic resolution lower than the species level. We would advise using either the SR or robustness on untransformed data, or the NODF, discrepancy, or SR (for weighted networks only) on Z‐scores. Additionally, connectance and modularity can be compared between low taxonomic resolution networks using the rank instead of the absolute values. [ABSTRACT FROM AUTHOR]

Underwater imagery is increasingly used as an effective and repeatable method to monitor benthic ecosystems. Nevertheless, extracting ecologically relevant information from a large amount of raw images remains a time-consuming and somewhat laborious challenge. Thus, underwater imagery processing needs to strike a compromise between time-efficient image annotation and accuracy in quantifying benthic community composition. Designing and implementing robust image sampling and image annotation protocols are therefore critical to rationally address these trade-offs between ecological accuracy and processing time. The aim of this study was to develop and to optimize a reliable image scoring strategy based on the point count method using imagery data acquired on tide-swept macroepibenthic communities. Using a stepwise approach, we define an underwater imagery processing protocol that is effective in terms of (i) time allocated to overall image, (ii) reaching a satisfactory accuracy to estimate the occurrence of dominant benthic taxa, and (iii) adopting a sufficient taxonomic resolution to describe changes in community composition. We believe that our method is well adapted to investigate the composition of epibenthic communities on artificial reefs and can be useful in surveying colonization of other human structures (wind turbine foundations, pipelines, etc.) in coastal areas. Our strategy meets the increasing demand for inexpensive and time-effective tools for monitoring changes in benthic communities in a context of increasing coastal artificialization pressures. [ABSTRACT FROM AUTHOR]

An ongoing challenge for ecological studies has been the collection of data with high precision and accuracy at a suitable scale to detect and manage critical global change processes. A major hurdle has been the time-consuming and challenging process of sorting and identification of organisms, but the rapid development of DNA metabarcoding as a biodiversity observation tool provides a potential solution. As high-throughput sequencing becomes more rapid and cost-effective, a “big data” revolution is anticipated, based on higher and more accurate taxonomic resolution, more efficient detection, and greater sample processing capacity. These advances have the potential to amplify the power of ecological studies to detect change and diagnose its cause, through a methodology termed “Biomonitoring 2.0.” Despite its promise, the unfamiliar terminology and pace of development in high-throughput sequencing technologies has contributed to a growing concern that an unproven technology is supplanting tried and tested approaches, lowering trust among potential users, and reducing uptake by ecologists and environmental management practitioners. While it is reasonable to exercise caution, we argue that any criticism of new methods must also acknowledge the shortcomings and lower capacity of current observation methods. Broader understanding of the statistical properties of metabarcoding data will help ecologists to design, test and review evidence for new hypotheses. We highlight the uncertainties and challenges underlying DNA metabarcoding and traditional methods for compositional analysis, specifically comparing the interpretation of otherwise identical bulk-community samples of freshwater benthic invertebrates. We explore how taxonomic resolution, sample similarity, taxon misidentification, and taxon abundance affect the statistical properties of these samples, but recognize these issues are relevant to applications across all ecosystem types. In conclusion, metabarcoding has the capacity to improve the quality and utility of ecological data, and consequently the quality of new research and efficacy of management responses.

Microeukaryotic plankton communities are keystone components for keeping aquatic primary productivity. Currently, variations in microeukaryotic plankton diversity have often been explained by local ecological factors but not by evolutionary constraints. We used amplicon sequencing of 100 water samples across five years to investigate the ecological preferences of the microeukaryotic plankton community in a subtropical riverine ecosystem. We found that microeukaryotic plankton diversity was less associated with bacterial abundance (16S rRNA gene copy number) than bacterial diversity. Further, environmental effects exhibited a larger influence on microeukaryotic plankton community composition than bacterial community composition, especially at fine taxonomic levels. The evolutionary constraints of microeukaryotic plankton community increased with decreasing taxonomic resolution (from 97% to 91% similarity levels), but not significant change from 85% to 70% similarity levels. However, compared with the bacterial community, the evolutionary constraints were shown to be more affected by environmental variables. This study illustrated possible controlling environmental and bacterial drivers of microeukaryotic diversity and community assembly in a subtropical river, thereby indirectly reflecting on the quality status of the water environment by providing new clues on the microeukaryotic community assembly., Competing Interests: The authors declare no competing interests., (© The Author(s) 2024. Published by Oxford University Press on behalf of the International Society for Microbial Ecology.)

Carbon (δ13C) and nitrogen (δ15N) stable isotope ratios of zooplankton are potentially good indicators of energy and nutrient fluxes, and trophic interactions in lake food‐webs, yet, are poorly understood.Based on a synoptic survey of 233 boreal lakes, we evaluated the relationships of water chemistry, hydromorphological, and land cover variables (lake/catchment‐specific factors), and the spatial position of lakes in the landscape (representing potential regional factors) with the δ13C and δ15N of nine meso‐zooplankton taxa.The δ13C variation of most taxa was negatively related to water chemistry variables associated with allochthonous inputs (colour/dissolved organic carbon), and positively correlated with nutrient concentrations (together explaining 12–69% of variation). Most of the δ13C variation explained by significant hydromorphological and land cover variables (% peat area, drainage basin area:lake area, shoreline development index, and lake area, explaining 26–47% of variation) was shared by significant water chemistry variables. Together, this suggests that δ13C variation of zooplankton reflects different environmental influences on δ13C of lake primary producers.The δ15N variation of most taxa was significantly related to pH, total phosphorous concentration (water chemistry variables, explaining 8–64% of variation), and water retention time (hydromorphological variable, explaining 13–87% of variation). These relationships are probably reflective of the association of zooplankton δ15N with terrestrial organic matter flux, environmentally‐induced biogeochemical nitrogen transformations and phytoplankton 15N fractionation.Specific water chemistry, hydromorphological, and land cover predictors of δ13C and δ15N and the direction of their effects (i.e. positive or negative) were largely similar among taxa. However, their degree of importance varied among taxa particularly for δ13C, probably due to contrasting feeding selectivity and resulting differences in allochthony. This suggests that δ13C of different taxa may respond differently to changes in limnological gradients due to environmental perturbations affecting boreal regions.The lake/catchment‐specific factors were more important than regional factors (lithology, soil properties and atmospheric nitrogen deposition; which are represented by the spatial position of lakes) in explaining δ13C and δ15N variation of zooplankton. Hence, before inferring regional effects in stable isotope studies, the influence of lake/catchment‐specific factors needs to be explicitly quantified. [ABSTRACT FROM AUTHOR]

Summary: The phylogenetic depth at which arbuscular mycorrhizal (AM) fungi harbor a coherent ecological niche is unknown, which has consequences for operational taxonomic unit (OTU) delineation from sequence data and the study of their biogeography.We tested how changes in AM fungi community composition across habitats (beta diversity) vary with OTU phylogenetic resolution. We inferred exact sequence variants (ESVs) to resolve phylotypes at resolutions finer than provided by traditional sequence clustering and analyzed beta diversity profiles up to order‐level sequence clusters.At the ESV level, we detected the environmental predictors revealed with traditional OTUs or at higher genetic distances. However, the correlation between environmental predictors and community turnover steeply increased at a genetic distance of c. 0.03 substitutions per site. Furthermore, we observed a turnover of either closely or distantly related taxa (respectively at or above 0.03 substitutions per site) along different environmental gradients.This study suggests that different axes of AM fungal ecological niche are conserved at different phylogenetic depths. Delineating AM fungal phylotypes using DNA sequences should screen different phylogenetic resolutions to better elucidate the factors that shape communities and predict the fate of AM symbioses in a changing environment. [ABSTRACT FROM AUTHOR]

Phytoplankton are aquatic, microscopically small primary producers, accounting for almost half of the worldwide carbon fixation. As early indicators of environmental change, they play a crucial role in water quality management. Human activities like climate change, eutrophication, or international shipping traffic strongly impact diversity of these organisms. Phytoplankton monitoring is a crucial step in the recognition of changes in community composition. The common standard for monitoring programs is manual microscopic counting, which strongly limits sample number and sampling frequency. In contrast, high‐throughput technologies like standard flow cytometry (FCM) are restricted to a low taxonomic resolution, which makes them unsuitable for the identification of indicator species. Imaging flow cytometers (IFC) could overcome these limitations as they combine microscopy and high‐throughput analysis. In comparison to single fluorescence values, image information not only allows for a wide variety of possibilities to characterize different species as well as immediate and fast measurements but also provides an archivable data output. Taxonomic resolution of IFC (ImageStream X Mk II) was proven comparable to standard FCM (FACSAria II) by the help of numerical evaluations. This is demonstrated on different levels of taxonomic differentiation of laboratory grown cultures in this study. Phytoplankton species discrimination by an imaging flow cytometer could be useful as supportive tool to make machine‐learning classifications more robust, reliable, and flexible. Furthermore, this study provides examples, demonstrating the possibility of discrimination between species with similar fluorescence properties, strains, and even subpopulations. In contrast to standard FCM, each cell is not only represented as a dot in a cytogram but is also linked to microscopic brightfield and the author presents a new way to visualize this as image‐based cytograms. The source code is supplied and could be useful for all kind of IFC data in general. © 2019 The Authors. Cytometry Part A published by Wiley Periodicals, Inc. on behalf of International Society for Advancement of Cytometry. [ABSTRACT FROM AUTHOR]

Animals that have similar morphological traits are expected to share similar ecological niches. This statement applies to individual animals within a species and thus species often serve as the functional units in ecological studies. Species are further grouped into higher‐ranked taxonomic units based on their morphological similarity and thus are also expected to be ecologically similar. On the other hand, theory predicts that strong competition between closely related species may result in differentiation of ecological niches. Due to high diversity and limited taxonomic expertise, soil food webs are often resolved using supraspecific taxa such as families, orders or even classes as functional units.Here, we tested the trophic differentiation and consistency of supraspecific taxa across major lineages of temperate forest soil invertebrates: Annelida, Chelicerata, Myriapoda, Crustacea and Hexapoda. Published data on stable isotope compositions of carbon and nitrogen were used to infer basal resources and trophic level, and explore the relationship between taxonomic and trophic dissimilarity of local populations.Genera and families had normal and unimodal distributions of isotopic niches, suggesting that supraspecific taxa are trophically consistent. The isotopic niche of local populations varied considerably resulting in large overlap of niches among species. Within the same genus, the effect of species identity on stable isotope composition of populations was not significant in 92% of cases. More than 50% of the variability in Δ15N values (trophic level) across lineages was explained by classes and orders, while the variability in Δ13C values (basal resources) was explained mostly by families and genera. The variability in stable isotope composition in Chelicerata and Hexapoda was explained by lower taxonomic ranks than in Myriapoda.We compiled a comprehensive list of mean Δ13C and Δ15N values of invertebrate taxa from temperate forest soils allowing to refine soil food web models when measurements of trophic niches of local populations are not feasible. Supraspecific taxa are meaningful as trophic nodes in food web studies, but the consistency varies among taxa and the choice of taxonomic resolution depends on the research question; generally, identification of taxa should be more detailed in more diverse taxonomic groups. A plain language summary is available for this article. [ABSTRACT FROM AUTHOR]