Taxonomic Patterns Research Articles

Shallow shotgun sequencing of the microbiome recapitulates 16S amplicon results and provides functional insights.

Prevailing 16S rRNA gene-amplicon methods for characterizing the bacterial microbiome of wildlife are economical, but result in coarse taxonomic classifications, are subject to primer and 16S copy number biases, and do not allow for direct estimation of microbiome functional potential. While deep shotgun metagenomic sequencing can overcome many of these limitations, it is prohibitively expensive for large sample sets. Here we evaluated the ability of shallow shotgun metagenomic sequencing to characterize taxonomic and functional patterns in the faecal microbiome of a model population of feral horses (Sable Island, Canada). Since 2007, this unmanaged population has been the subject of an individual-based, long-term ecological study. Using deep shotgun metagenomic sequencing, we determined the sequencing depth required to accurately characterize the horse microbiome. In comparing conventional vs. high-throughput shotgun metagenomic library preparation techniques, we validate the use of more cost-effective laboratory methods. Finally, we characterize similarities between 16S amplicon and shallow shotgun characterization of the microbiome, and demonstrate that the latter recapitulates biological patterns first described in a published amplicon data set. Unlike for amplicon data, we further demonstrate how shallow shotgun metagenomic data provide useful insights regarding microbiome functional potential which support previously hypothesized diet effects in this study system.

Molecular genetic studies of microbiocenosis and microstructure of jejunum wall in young rams grown on biofortified feed additives

The research featured the effect of a diet fortified with essential microelements on the ruminal microbiota of young rams. Ruminal microbiota is largely responsible for feed digestibility and body functioning of cattle. The study involved the contents of the rumens and jejuna of seven-month-old rams of the Edilbaev breed, which were subjected to a biofortified diet. The diet included the Russian feed additives Yoddar-Zn and DAFS-25 represent a protein-carbohydrate complex with plant silicon. The microflora of the digestive tract was tested using the molecular genetic method of terminal restriction fragment length polymorphism (T-RFLP) sequestration. The microstructural studies of the jejunum samples exploited light microscopy. The feed additives increased the population of cellulolytic and lactate-fermenting bacteria, as well as the Prevotella sp. microbiome and bifidobacteria in the rumen samples. The data obtained revealed the effect of essential microelements on the taxonomic pattern of microorganisms and the microflora profile. The research revealed the ratio of normal, opportunistic, pathogenic, nonculturable, and transit microflora. The jejunum wall samples obtained from the experimental group that fed on Yoddar-Zn and DAFS-25 had a more distinct micropicture of mucous membrane. Their rumen microflora balance had fewer pathogenic and opportunistic microorganisms, which was also confirmed by the jejunum morphology. The feed additives DAFS-25 and Yoddar-Zn proved beneficial for ram diet and inhibited the negative effect of pathogenic treponemas on the rumen. The additives improved digestion, absorption, and assimilation of food nutrients, as well as increased the livestock yield.

Massive annotation of bacterial l-asparaginases reveals their puzzling distribution and frequent gene transfer events

l-Asparaginases, which convert l-asparagine to l-aspartate and ammonia, come in five types, AI-AV. Some bacterial type AII enzymes are a key element in the treatment of acute lymphoblastic leukemia in children, but new l-asparaginases with better therapeutic properties are urgently needed. Here, we search publicly available bacterial genomes to annotate l-asparaginase proteins belonging to the five known types. We characterize taxonomic, phylogenetic, and genomic patterns of l-asparaginase occurrences pointing to frequent horizontal gene transfer (HGT) events, also occurring multiple times in the same recipient species. We show that the reference AV gene, encoding a protein originally found and structurally studied in Rhizobium etli, was acquired via HGT from Burkholderia. We also describe the sequence variability of the five l-asparaginase types and map the conservation levels on the experimental or predicted structures of the reference enzymes, finding the most conserved residues in the protein core near the active site, and the most variable ones on the protein surface. Additionally, we highlight the most common sequence features of bacterial AII proteins that may aid in selecting therapeutic l-asparaginases. Finally, we point to taxonomic units of bacteria that do not contain recognizable sequences of any of the known l-asparaginase types, implying that those microorganisms most likely contain new, as yet unknown types of l-asparaginases. Such novel enzymes, when properly identified and characterized, could hold promise as antileukemic drugs.

Pathways of introduction of alien species in Norway: Analyses of an exhaustive dataset to prioritise management efforts

Abstract Alien species constitute one of the major threats to global biodiversity. Stopping alien species at an early stage, preferably before establishment, is crucial for the effectiveness of management actions. To enable early detection and prevent future introductions, knowledge of pathways of introduction and their absolute and relative importance is crucial. Based on an exhaustive impact assessment of alien species in Norway (all multicellular neobiota), the relations of taxonomy, lifestyle and ecological impact of alien species to their pathways of introduction are investigated. This taxonomically and ecologically unbiased dataset contains 2267 unique pathways of 1180 alien species. Ecological and taxonomic patterns indicate that terrestrial organisms were predominantly introduced by means of escape (mainly perennial plants escaped from gardens), parasites as contaminants (mainly fungi and insects parasitising plants), freshwater organisms by release (mainly vertebrates) and marine organisms as stowaways (mainly invertebrates and algae). Unaided introductions were most common among insects and marine organisms. Alien species with high ecological impact were mainly introduced along the same pathways as other alien species. In relative terms, high‐impact species were overrepresented among released species, even though this pathway was subordinate in absolute terms. The number of pathways and the overall introduction pressure were important predictors of ecological impact, especially of the species' invasion potential, and area of occupancy. Introduction rates of novel alien species have seen recent increases in all taxa and along almost all pathways. This acceleration was especially pronounced for insects and fungi introduced as contaminants and for marine organisms introduced as stowaways. In absolute terms, introduction rates were highest for plant escapes, reaching more than five novel species per year. Synthesis and applications. Introductions of new alien species cannot be prevented by closing one or two introduction pathways, since none can be singled out as the main pathway of high‐impact alien species. Yet each pathways closed makes a difference, as this reduces the overall introduction pressure. The highest priorities for management are the pathways that are easiest to address, such as release, and those with the highest volumes, such as plant trade.

Taxonomic, functional, and phylogenetic diversity patterns reveal different processes shaping river fish assemblages in the Eastern Huai River Basin, China

Understanding contributions of different environmental drivers to the structure and function of river biota is critical for biodiversity and environmental conservation. Yet, there is no consensus on which drivers have the greatest impact on fish diversity, especially in watersheds disturbed by multiple human activities. Fish taxonomic, phylogenetic, and functional diversity at both alpha and beta dimensions and their environmental drivers were studied in a total of 84 river sites from three watersheds, Huai River watershed (HRW), Sui River watershed (SRW), and Yishusi River watershed (YRW) in the Eastern Huai River Basin of China. Results showed that rivers in the three watersheds had no significant difference in both taxonomic and functional alpha diversity. Rivers in the HRW had significantly higher phylogenetic alpha diversity. For taxonomic and phylogenetic beta diversity, the overall beta diversity and turnover component were significant higher in the HRW. For functional beta diversity, the overall beta diversity was significantly lower in the HRW. Multiple linear regression (MLR) and redundancy analysis (RDA) showed that local (e.g., nutrients, dissolved oxygen, river width, transparency), regional (e.g., wetland), climate (e.g., temperature), and spatial variables structured alpha and beta fish diversity. Variation partitioning analysis indicated that the pure contributions of local and spatial variables were more important than that of climate and regional variables, which suggested that spatial effects and local environmental filtering were the main factors driving the beta diversity of fish assemblages in these rivers. The current study highlights the importance of considering multidimensional diversity and multiple environmental factors for conserving river fishes.

Succession of protistan functional traits is influenced by bloom timing

Surface ocean eukaryotic phytoplankton biogeography can be determined as chlorophyll-a using remote sensing techniques yet evaluating its community composition remains limited. Given our ability to track site-specific chlorophyll-a concentration, we tested which factors influenced protistan functional trait distribution, and whether the distributions can be inferred from bloom succession. Here we surveyed the Labrador Sea during spring over three consecutive years, sequenced 18S data over 15 stations and collected satellite-derived chlorophyll-a concentration from March to July for each year. We evaluated changes in distribution of taxonomic composition as well as the functional traits of protistan size, trophic strategy (defined as phototrophy, phagotrophy, and mixotrophy as capable of both), motility and dimethylsulfoxide or dimethylsulfoniopropionate production by building a functional trait database after an extensive literature review. More variability in the biogeography of protistan functional traits was explained across water masses, and among years than taxonomic composition and patterns in trait variability were more apparent when site-specific timing of peak chlorophyll-a was considered. We found that reconstructing bloom phenology using days before peak (DBP) chlorophyll explained a significant amount of variability in functional trait community structure that was previously attributed to water masses or years, suggesting that spatial and interannual variations can be explained by the sampling moment during succession. Approximately 30 days prior to peak, mixotrophy as a trophic strategy was replaced by phototrophic protists of typically larger size classes. Our work suggests DBP influences protistan community trait succession that could inform biogeochemical models, and likely acts a proxy for the onset of stratification.

Taxonomic and functional diversity patterns of stream fish assemblages from Brazilian Atlantic Rain Forest

Disentangling the hierarchical structure of river systems and multi-scale environmental effects is essential for understanding freshwater fish community structure and function. We sampled 70 stream stretches to investigate how the taxonomic and functional composition and diversity of fish assemblages responded to the environment considering a hierarchical organisation of streams in three Brazilian watersheds (Upper Sorocaba, Upper Paranapanema and Upper Ribeira de Iguape). Functional diversity indicated that stream fish community function was independent of the watershed. The most critical environmental variable was substrate gradient. In streams with a consolidated substrate, equitability and functional dispersion were low due to invertivores occurring in this type of substrate. Our results highlight the importance of local environmental filters for shaping streams fish assemblages across different basins. This shaping was more evident when functional descriptors of assemblages were analysed, thereby reinforcing the importance of an approach based on traits as a tool to elucidate local community assembly processes at broader spatial scales.

Lizards (Reptilia: Squamata) from the Caatinga, northeastern Brazil: Detailed and updated overview

AbstractThe Caatinga is the largest seasonal dry tropical forest in South America and it has been historically neglected in terms of its biodiversity. Regarding lizards, different studies led to the current knowledge of diversity and endemism in Caatinga, but detailed syntheses are scarce in the literature. We present the most detailed and up-to-date synthesis of knowledge about Caatinga lizards by providing a detailed (i) list of species; (ii) taxonomic richness patterns; (iii) knowledge gaps and spatial biases; and (iv) detailed distribution maps of all species that contain at least one occurrence record within Caatinga limits. We created a distribution database using occurrences of lizards in Caatinga based on scientific collections, field collection, and literature. We produce up-to-date distribution maps, calculate the Extent of Occurrence and provide the environmental and bioclimatic profile for each species recorded. We draw taxonomic richness and sampling gap maps. Our database has 20,538 records of occurrence of lizards of the Caatinga. We recorded 93 lizard species (13 families), 52.7% of which are endemic. Forthy-four percent of the species present restricted distributions. We identified that 53% of the Caatinga area (or 70% of the municipalities) has no record of occurrence of lizards. The data presented are an important step towards synthesizing in detail the accumulated knowledge about Caatinga lizards and is crucial for accurate strategies for the conservation planning. It directs actions to advance our knowledge on Caatinga lizards: to concentrate inventories in sample void areas; continuous update of the species occurrence database, advance in the generation of autoecology data for species.

Phylogeographic and phenotypic divergence between two subspecies of Testudo graeca (T. g. buxtoni and T. g. zarudnyi) across their contact zone in Iran

Contact zones are considered as windows into the evolutionary process, allowing identification of factors influencing the evolutionary forces. Here, we combined phylogenetic and morphometric analyses to explore the evolutionary process affecting the taxonomic pattern of two subspecies of Testudo graeca (T. g. buxtoni and T. g. zarudnyi) across their contact zone in Central Iran. Our results showed high levels of phylogeographic and phenotypic variation in the contact zone. Two monophyletic clades including, clade 1 (T. g. zarudnyi) and clade 2 (T. g. buxtoni) were identified. Furthermore, four distinct subclades were found in T. g. buxtoni, across a wide geographic range. Divergence time analysis suggests that the two subspecies diverged from one another after the uplifting of the Zagros Mountains during the early Pliocene. Using neutrality tests and mismatch distribution analysis, we found no evidence of recent population expansion. Morphological associations among geographical populations in the contact zone found more distinctions, with some significant adaptive and non-adaptive morphological variations in these populations. These distinctive morphological populations can be considered as management units (MUs) to conserve the evolutionary potential of this species. Finer scale evolutionary studies are required to address the southern part of the Zagros mountain range, where the overlapping of mitochondrial clades and subclades has occurred. Such information is essential for effective conservation of T. graeca populations, preventing translocation or mixing of individuals without comprehensive genetic and morphological assessment.

Spatiotemporal Distribution Patterns of Climbers along an Abiotic Gradient in Jhelum District, Punjab, Pakistan

Climber–abiotic parameter interactions can have important ramifications for ecosystem’s functions and community dynamics, but the extent to which these abiotic factors influence the spatial distributions of climber communities in the western Himalayas is unknown. The purpose of this study was to examine the taxonomic diversity, richness, and distribution patterns of climbers in relation to abiotic variables in the Jhelum District. The data were collected from 120 random transects between 2019 and 2021, from 360 sites within triplet quadrats (1080 quadrats), and classification and ordination analyses were used to categorize the sample transects. A total of 38 climber species belonging to 25 genera and 11 families were recorded from the study area. The Convolvulaceae were the dominant family (26.32%), followed by the Apocynaceae (21.05%), and Leguminosae (15.79%). The majority of the climbers were herbaceous in nature (71.05%), followed by woody (23.68%). Based on the relative density, the most dominant species was Vicia sativa (12.74). The majority of the species flowered during the months of March–April (28.04%), followed by August–September (26.31%). Abiotic factors have a significant influence on the distribution pattern and structure of climbers in the study area. The results show that the climbers react to the biotic environment in different ways. The findings will serve as the foundation for future botanical inventories and will be crucial for understanding the biological, ecological, and economic value of climbers in forest ecosystems. This will help forest management, conservation, and ecological restoration in the Himalayas.

Fish-parasite interaction networks reveal latitudinal and taxonomic trends in the structure of host-parasite associations.

In recent years, treating host–parasite associations as bipartite interaction networks has proven a powerful tool to identify structural patterns and their likely causes in communities of fish and their parasites. Network analysis allows for both community-level properties to be computed and investigated, and species-level roles to be determined. Here, using data from 31 host–parasite interaction networks from local fish communities around the world, we test for latitudinal trends at whole-network level, and taxonomic patterns at individual parasite species level. We found that while controlling for network size (number of species per network), network modularity, or the tendency for the network to be subdivided into groups of species that interact mostly with each other, decreased with increasing latitude. This suggests that tropical fish–parasite networks may be more stable than those from temperate regions in the event of community perturbations, such as species extinction. At the species level, after accounting for the effect of host specificity, we observed no difference in the centrality of parasite species within networks between parasites with different transmission modes. However, species in some taxa, namely branchiurans, acanthocephalans and larval trematodes, generally had higher centrality values than other parasite taxa. Because species with a central position often serve as module connectors, these 3 taxa may play a key role in whole-network cohesion. Our results highlight the usefulness of network analysis to reveal the aspects of fish–parasite community interactions that would otherwise remain hidden and advance our understanding of their evolution.

Microbiome differences between wild and aquarium whitespotted eagle rays (Aetobatus narinari)

BackgroundAnimal-associated microbiomes can be influenced by both host and environmental factors. Comparing wild animals to those in zoos or aquariums can help disentangle the effects of host versus environmental factors, while also testing whether managed conditions foster a ‘natural’ host microbiome. Focusing on an endangered elasmobranch species—the whitespotted eagle ray Aetobatus narinari—we compared the skin, gill, and cloaca microbiomes of wild individuals to those at Georgia Aquarium. Whitespotted eagle ray microbiomes from Georgia Aquarium were also compared to those of cownose rays (Rhinoptera bonasus) in the same exhibit, allowing us to explore the effect of host identity on the ray microbiome.ResultsLong-term veterinary monitoring indicated that the rays in managed care did not have a history of disease and maintained health parameters consistent with those of wild individuals, with one exception. Aquarium whitespotted eagle rays were regularly treated to control parasite loads, but the effects on animal health were subclinical. Microbiome α- and β-diversity differed between wild versus aquarium whitespotted eagle rays at all body sites, with α-diversity significantly higher in wild individuals. β-diversity differences in wild versus aquarium whitespotted eagle rays were greater for skin and gill microbiomes compared to those of the cloaca. At each body site, we also detected microbial taxa shared between wild and aquarium eagle rays. Additionally, the cloaca, skin, and gill microbiomes of aquarium eagle rays differed from those of cownose rays in the same exhibit. Potentially pathogenic bacteria were at low abundance in all wild and aquarium rays.ConclusionFor whitespotted eagle rays, managed care was associated with a microbiome differing significantly from that of wild individuals. These differences were not absolute, as the microbiome of aquarium rays shared members with that of wild counterparts and was distinct from that of a cohabitating ray species. Eagle rays under managed care appear healthy, suggesting that their microbiomes are not associated with compromised host health. However, the ray microbiome is dynamic, differing with both environmental factors and host identity. Monitoring of aquarium ray microbiomes over time may identify taxonomic patterns that co-vary with host health.

Effects of Terrestrial Inputs on Mesozooplankton Community Structure in Bohai Bay, China

Zooplankton play a pivotal role in connecting primary producers and high trophic levels, and changes in their temporal and spatial distribution may affect the entire marine ecosystem. The spatial and seasonal taxonomic composition patterns of mesozooplankton in Bohai Bay were investigated in relation to a number of water parameters. Bohai Bay is a eutrophic semi-enclosed bay with dynamic physico-chemical conditions influenced by terrestrial inputs and seawater intrusion. The results showed that under the condition of terrigenous input, the diversity of mesozooplankton species near the eutrophic Haihe River Estuary and Jiyun River Estuary was lower than that in the central Bohai Bay, with gelatinous Oikopleura dioica as the dominant species. The mesozooplankton diversity was highest in the bay mouth affected by seawater intrusion, and the dominant oceanic species, mainly copepods Corycaeus affinis, Calanus sinicus, and Oithona similis, entered the inner bay from the bay mouth. Meanwhile, the abundance of mesozooplankton in summer was significantly higher than that in autumn. Compared with historical data, the dominant species in Bohai Bay has evolved from arrow worm Sagitta crassa to copepod Paracalanus parvus, probably due to global warming, indicating the effects of human activities on the succession of mesozooplankton community.

The Miseno Lake (Central-Western Mediterranean Sea): An Overlooked Reservoir of Non-Indigenous and Cryptogenic Ascidians in a Marine Reserve

Ascidians are the largest and most diverse class of the subphylum Tunicata, and are important components of marine benthic communities. They are also renowned worldwide invaders, of growing concern due to ease of spread and impacts on native biota. We hereby combined bathymetric and habitat mapping, extensive transect and photo-quadrat sampling, and a morphological and molecular study on selected specimens to evaluate taxonomic composition, cover, and distribution pattern of ascidians in a marine reserve of the central-western Mediterranean Sea, the Miseno Lake (Bacoli, Naples, Italy). Twenty-four taxa were found, of which 9 were non-indigenous species (NIS), 5 cryptogenic, and 10 native, delineating the Miseno Lake as a major hotspot of NIS and cryptogenic ascidians. DNA barcoding yielded 114 sequences, confirming identification for 22 taxa but also revealing single to few mismatches per species. Taxonomic insights were offered in the text and the Supplementary Material for several taxa, including the understudied Ascidia colleta and Ascidia malaca. The presence of a new clade was discovered in the Distaplia bermudensis species complex. Didemnum pseudovexillum and Polyclinum constellatum were respectively first recorded in Italy and western Mediterranean, and the same holds true for other taxa whose accurate identification was only possible through molecular evidence. The analysis of photographic archives allowed backdating and georeferencing to the Miseno Lake of the first records of Aplidium accarense and Botrylloides niger in Italy and of P. constellatum in the Mediterranean. Generalized Additive Models revealed that the abundance of NIS increased with availability of hard substrates (rocks or litter), decreased with depth, and was the highest in the channels connecting to other water bodies, followed by the peripheral areas of the lake. No certain evidence of competitive restriction of native ascidians was found. Finally, introduction pathways, potential impacts, and additional insights were discussed for NIS. The present study provides a baseline to evaluate shifts in the ascidian communities in the future, suggests that constant monitoring programs constitute crucial steps to achieve solid NIS management, and confirms marine reserves as widely vulnerable to biological invasions, especially when they coincide with potential hotspots of arrival or spreading such as semi-enclosed basins.

Ecological and genomic responses of soil microbiomes to high-severity wildfire: linking community assembly to functional potential

Increasing wildfire severity, which is common throughout the western United States, can have deleterious effects on plant regeneration and large impacts on carbon (C) and nitrogen (N) cycling rates. Soil microbes are pivotal in facilitating these elemental cycles, so understanding the impact of increasing fire severity on soil microbial communities is critical. Here, we assess the long-term impact of high-severity fires on the soil microbiome. We find that high-severity wildfires result in a multi-decadal (>25 y) recovery of the soil microbiome mediated by concomitant differences in aboveground vegetation, soil chemistry, and microbial assembly processes. Our results depict a distinct taxonomic and functional successional pattern of increasing selection in post-fire soil microbial communities. Changes in microbiome composition corresponded with changes in microbial functional potential, specifically altered C metabolism and enhanced N cycling potential, which related to rates of potential decomposition and inorganic N availability, respectively. Based on metagenome-assembled genomes, we show that bacterial genomes enriched in our earliest site (4 y since fire) harbor distinct traits such as a robust stress response and a high potential to degrade pyrogenic, polyaromatic C that allow them to thrive in post-fire environments. Taken together, these results provide a biological basis for previously reported process rate measurements and explain the temporal dynamics of post-fire biogeochemistry, which ultimately constrains ecosystem recovery.

Metagenomic survey of the microbiome of ancient Siberian permafrost and modern Kamchatkan cryosols.

In the context of global warming, the melting of Arctic permafrost raises the threat of a reemergence of microorganisms some of which were shown to remain viable in ancient frozen soils for up to half a million years. In order to evaluate this risk, it is of interest to acquire a better knowledge of the composition of the microbial communities found in this understudied environment. Here, we present a metagenomic analysis of 12 soil samples from Russian Arctic and subarctic pristine areas: Chukotka, Yakutia and Kamchatka, including nine permafrost samples collected at various depths. These large datasets (9.2 × 1011 total bp) were assembled (525 313 contigs >5 kb), theirencoded protein contents predicted, and then used to perform taxonomical assignments of bacterial, archaeal and eukaryotic organisms, as well as DNA viruses. The various samples exhibited variable DNA contents and highly diverse taxonomic profiles showing no obvious relationship with their locations, depths or deposit ages. Bacteria represented the largely dominant DNA fraction (95%) in all samples, followed by archaea (3.2%), surprisingly little eukaryotes (0.5%), and viruses (0.4%). Although no common taxonomic pattern was identified, the samples shared unexpected high frequencies of β-lactamase genes, almost 0.9 copy/bacterial genome. In addition to known environmental threats, the particularly intense warming of the Arctic might thus enhance the spread of bacterial antibiotic resistances, today's major challenge in public health. β-Lactamases were also observed at high frequency in other types of soils, suggesting their general role in the regulation of bacterial populations.

A Detailed Ecological Exploration of the Distribution Patterns of Wild Poaceae from the Jhelum District (Punjab), Pakistan

The purpose of this study was to investigate the taxonomic diversity, richness, and distribution patterns of Poaceae in relation to abiotic factors in the Jhelum district of the Pakistan Himalayas. We used a random sampling technique from 80 grids within 240 sites with a rich diversity of wild grasses and 720 quadrates in triplets from each site across the Jhelum district between 2019 and 2021 to collect data on grass species and the associated environmental factors and conditions. After evaluating the important value index for each plant taxa and for the environmental data, we analyzed the data using ordination and cluster analysis techniques. Fifty-two Poaceae taxa from twenty-nine genera were recorded within the study area. From a total of 52 recorded Poaceae species, 45 were native and 7 were invasive species. The life form (biological) showed the dominancy of 27 therophyte species, followed by 24 hemicryptophyte species, and 1 geophyte species. Microphyll had the leading leaf size spectra (27 species), followed by nanophyll (12 species), macrophyll (10 species), and leptophyll (3 species). The trend of the life cycle was the maximum (27 spp.) during the monsoon season, followed by spring (11 spp.), winter (8 spp.), and summer (6 spp.). The leading genera were Setaria with 9.61% of the species, followed by Panicum, Cenchrus, and Brachiaria with 7.69% of the species. Aristida and Echinochloa made up 5.76% of the species while Chrysopogon, Digitaria, Eragrostis, Pennisetum, and Poa made up 3.84% of the species. Other genera recorded single species. The leaf size spectra of grasses were dominated by microphylls (50%) followed by nanophylls (23.07%), macrophylls (19.23%), and leptophylls (7.69%). On the basis of the importance value index, the most dominant species was Cynodon dactylon (68), followed by Dichanthium annulatum (58), Brachiaria ramose (38), Dactyloctenium aegyptium (37), Eleusine indica (35), Saccharum bengalense (33), and Cenchrus biflorus (28). Two-way cluster analyses classified the grasses into three plant community associations based on the indicator plant species. Soil parameters as subsamples were tested for moisture, pH, EC, OM, macronutrients (CaCO3, N, P, and K), and saturation while the ordination analysis revealed that they had a significant (p ≤ 0.002) effect on vegetation associations. Overall, this study contributes to a better understanding of the influence of environmental factors on the composition and associations of grass species and the development of scientifically informed management solutions for the ecological restoration of degraded habitats in this Himalayan region.

Economic costs of invasive bivalves in freshwater ecosystems

AbstractAimTo assess spatio‐temporal and taxonomic patterns of available information on the costs of invasive freshwater bivalves, as well as to identify knowledge gaps.LocationGlobal.Time period1980–2020.Taxon studiedBivalvia.MethodsWe synthesize published global economic costs of impacts from freshwater bivalves using the InvaCost database and associated R package, explicitly considering the reliability of estimation methodologies, cost types, economic sectors and impacted regions.ResultsCumulative total global costs of invasive macrofouling bivalves were $ 63.7 billion (2017 US$) across all regions and socio‐economic sectors between 1980 and 2020. Costs were heavily biased taxonomically and spatially, dominated by two families, Dreissenidae and Cyrenidae (Corbiculidae), and largely reported in North America. The greatest share of reported costs ($ 31.5 billion) did not make the distinction between damage and management. However, of those that did, damages and resource losses were one order of magnitude higher ($ 30.5 billion) than control or preventative measures ($ 1.7 billion). Moreover, although many impacted socio‐economic sectors lacked specification, the largest shares of costs were incurred by authorities and stakeholders ($ 27.7 billion, e.g., public and private sector interventions) and through impacts on public and social welfare ($ 10.1 billion, e.g., via power/drinking water plant and irrigation system damage) in North America. Average cost estimates over the entire period amounted to approximately $ 1.6 billion per year, most of which was incurred in North America.Main conclusionsOur results highlight the burgeoning economic threat caused by invasive freshwater bivalves, offering a strong economic incentive to invest in preventative management such as biosecurity and rapid response eradications. Even if the damages and resource losses are severely understated because economic impacts are lacking for most invaded countries and invasive bivalve species, these impacts are substantial and likely growing.

Incongruent latitudinal patterns of taxonomic, phylogenetic and functional diversity reveal different drivers of caddisfly community assembly across spatial scales

AbstractAimCommunity assembly processes are difficult to observe in nature but can be inferred from species diversity patterns. However, taxonomic patterns may be consistent with multiple explanations, such as habitat filtering or biogeographical processes, which can also act differently across spatial scales. Here, we assessed multiple facets of diversity to determine the relative contributions of local versus regional processes and historical versus contemporary factors in establishing macroecological patterns.LocationFrom the Mediterranean peninsulas to northern Scandinavia.Time periodSpecies occurrence data gathered since c. 1980.Major organism group studiedTrichoptera (Insecta).MethodsBased on an extensive functional space and a phylogenetic tree including 197 and 509 species, respectively, and the composition of 180 communities, we assessed the distribution of taxonomic, functional and phylogenetic diversity within 18 ecoregions (local α‐ and β‐diversity) and among those ecoregions (regional γ‐ and β‐diversity).ResultsLocal estimates of taxonomic, functional and phylogenetic α‐ and β‐diversity were similar across Europe, which reveals that all streams have similar carrying capacity even though the local abiotic factors involved are likely different among ecoregions. In contrast, regional taxonomic and phylogenetic diversities decreased as latitude increased, whereas functional richness and functional dispersion displayed unimodal relationships. The position of species on the functional space was not conserved, while northern species pools were found to be phylogenetically clustered and southern ones overdispersed. The nestedness component mainly contributed to the taxonomic and phylogenetic β‐diversity among northern communities, whereas in southern latitudes the turnover was dominant.Main conclusionsDecoupled latitudinal patterns of taxonomic, phylogenetic and functional diversity reveal the importance of regional environmental filtering over local factors in limiting species range and shaping the regional species pool. The biogeographical signature is still present; the northern recolonizations following the Pleistocene glaciations originated exclusively from central regions, instead of Mediterranean refugia, as was previously accepted.

Data and Diversity in the Development of Acute Water Quality Criteria in the United States.

The US Environmental Protection Agency (USEPA) is responsible for the development of water quality criteria, regulatory standards that protect aquatic organisms from harmful chemical exposure. Although these criteria are intended to be broadly protective of aquatic life, the data used to derive criteria do not necessarily reflect the actual diversity of natural communities nor are they available for most chemicals. In addition, although the USEPA's current procedures emphasize using toxicity data with a certain minimum amount of biological diversity, the quantitative impact of such diversity on criteria is unclear. In the present study we assessed the changes to acute toxicity data over time, determined the prevalence of significant taxonomic differences in sensitivity, and investigated the effect of biological diversity on criteria. We found major gaps in existing toxicity data that we hypothesize have contributed to the absence of acute criteria for the majority of chemical pollutants. Taxonomic patterns of sensitivity in these data are abundant, although the resolution of the patterns is relatively poor. In addition, we found that the amount of biological diversity in a toxicity data set and the data set's taxonomic composition does not quantitatively affect criteria in most cases. Because the USEPA has published acute criteria for fewer than 20% of priority pollutants and the persistence of major gaps in toxicity data over the last 37 years, we recommend that the USEPA consider revisions to their water quality criteria guidelines that will expedite the criteria development process and advance the responsible management of pollutants in the aquatic environment. Environ Toxicol Chem 2022;41:1333-1343. © 2022 SETAC.