Using low volume eDNA methods to sample pelagic marine animal assemblages.

Environmental DNA (eDNA) is an increasingly useful method for detecting pelagic animals in the ocean but typically requires large water volumes to sample diverse assemblages. Ship-based pelagic sampling programs that could implement eDNA methods generally have restrictive water budgets. Studies that quantify how eDNA methods perform on low water volumes in the ocean are limited, especially in deep-sea habitats with low animal biomass and poorly described species assemblages. Using 12S rRNA and COI gene primers, we quantified assemblages comprised of micronekton, coastal forage fishes, and zooplankton from low volume eDNA seawater samples (n = 436, 380-1800 mL) collected at depths of 0-2200 m in the southern California Current. We compared diversity in eDNA samples to concurrently collected pelagic trawl samples (n = 27), detecting a higher diversity of vertebrate and invertebrate groups in the eDNA samples. Differences in assemblage composition could be explained by variability in size-selectivity among methods and DNA primer suitability across taxonomic groups. The number of reads and amplicon sequences variants (ASVs) did not vary substantially among shallow (<200 m) and deep samples (>600 m), but the proportion of invertebrate ASVs that could be assigned a species-level identification decreased with sampling depth. Using hierarchical clustering, we resolved horizontal and vertical variability in marine animal assemblages from samples characterized by a relatively low diversity of ecologically important species. Low volume eDNA samples will quantify greater taxonomic diversity as reference libraries, especially for deep-dwelling invertebrate species, continue to expand.

Taxonomic accuracy and complementarity between bulk and eDNA metabarcoding provides an alternative to morphology for biological assessment of freshwater macroinvertebrates.

Determining biological status of freshwater ecosystems is critical for ensuring ecosystem health and maintaining associated services to such ecosystems. Freshwater macroinvertebrates respond predictably to environmental disturbances and are widely used in biomonitoring programs. However, many freshwater species are difficult to capture and sort from debris or substrate and morphological identification is challenging, especially larval stages, damaged specimens, or hyperdiverse groups such as Diptera. The advent of high throughput sequencing technologies has enhanced DNA barcoding tools to automatise species identification for whole communities, as metabarcoding is increasingly used to monitor biodiversity. However, recent comparisons have revealed little congruence between morphological and molecular-based identifications. Using broad range universal primers for DNA barcode marker cox1, we compare community composition captured between morphological and molecular-based approaches from different sources - tissue-based (bulk benthic and bulk drift samples) and environmental DNA (eDNA, filtered water) metabarcoding - for samples collected along a gradient of anthropogenic disturbances. For comparability, metabarcoding taxonomic assignments were filtered by taxa included in the standardised national biological metric IBMWP. At the family level, bulk benthic metabarcoding showed the highest congruence with morphology, and the most abundant taxa were captured by all techniques. Richness captured by morphology and bulk benthic metabarcoding decreased along the gradient, whereas richness recorded by eDNA remained constant and increased downstream when sequencing bulk drift. Estimates of biological metrics were higher using molecular than morphological identification. At species level, diversity captured by bulk benthic samples were higher than the other techniques. Importantly, bulk benthic and eDNA metabarcoding captured different and complementary portions of the community - benthic versus water column, respectively - and their combined use is recommended. While bulk benthic metabarcoding can likely replace morphology using similar benthic biological indices, water eDNA will require new metrics because this technique sequences a different portion of the community.

Spatial distribution of benthic taxonomic and functional diversity in the Yellow River Basin: From ecological processes to associated determinant factors.

One of the fundamental objectives in ecology is to investigate the ecological processes and associated factors governing the abundance and spatial distribution patterns of biodiversity. However, the reaction of biological communities to environmental degradation remains relatively unknown, even for ecologically crucial communities like macroinvertebrates in aquatic ecosystems. Here, we sampled 117 locations to quantify relative contributions of geographical and environmental factors, including water quality, land use, climate, and hydrological factors, to determine the absolute and relative compositions of macroinvertebrate communities and their spatial distribution in the Yellow River Basin (YRB), the sixth-longest river system on Earth. We assessed relative roles of species sorting and dispersal in determining macroinvertebrate community structure along YRB. Our results demonstrated that alpha and beta diversity indices showed an increase from the up- to low-reaches of YRB. The middle and low-reaches exhibited elevated species diversity and both regions exhibited relatively stable community compositions. The biodiversity of macroinvertebrates was influenced by a combination of geographical factors and environmental variables, with environmental factors predominantly serving as the principal determinants. Results of multiple linear regression and variance decomposition showed that the effect of environmental factors was approximately three times greater than that of spatial factors. These findings provide support for the hypothesis that species sorting, driven by environmental gradients, plays a significant role in shaping the community structure of macroinvertebrates in running water ecosystems at the basin scales. Moreover, the factors contributing to substantial shifts in biodiversity across different segments of YRB indicate that distinct river sections have been influenced by varying stressors, with downstream areas being more susceptible to the impacts of water pollution and urbanization resulting from human activities.

A study of macroinvertebrate community structure and diversity in response to land use type in the Yiluo River Basin.

Land use types have a significant impact on river ecosystems. The Yiluo River is the largest tributary below Xiaolangdi Reservoir in the middle reaches of the Yellow River, and is one of the important water conservation areas in the Yellow River Basin. Studying the ecological status of the Yiluo River under varied land use types in this basin is crucial for both ecological protection and the high-quality development of the Yellow River Basin. This study investigated the impacts of land use types on the macroinvertebrate community and functional structure in the Yiluo River Basin and introduced the concept of the land use health index (LUI). During the survey period, a total of 11,894 macroinvertebrates were collected, and 143 species were identified, belonging to 4 phyla, 7 orders, 22 families, and 75 families. The results showed that LUI had the most significant impact on macroinvertebrate community structure, with substrate type, dry plant weight, total phosphorus, turbidity, and attached algae biomass also playing significant roles in affecting macroinvertebrate communities. The species richness, the Shannon-Wiener index, and the Margalef richness index exhibited a nonlinear positive correlation with LUI of the sampling site, increasing as LUI enhancing and eventually reaching a plateau. Functional richness showed a linear and positive correlation with LUI, increasing with its enhancement, while functional evenness and functional divergence exhibited a nonlinear correlation with LUI. Functional evenness initially increased and then decreased with the enhancement of LUI, while functional divergence decreased with LUI enhancement. This study can provide a scientific reference for river ecological management under various land use scenarios.The Yiluo River is the largest tributary below Xiaolangdi Reservoir in the middle reaches of the Yellow River, and is one of the important water conservation areas in the Yellow River Basin. Studying the ecological status of the Yiluo River under varied land use types in this basin is crucial for both ecological protection and the high-quality development of the Yellow River Basin. This study investigated the impacts of land use types on the macroinvertebrate community and functional structure in the Yiluo River Basin and introduced the concept of the land use health index (LUI). During the survey period, a total of 11,894 macroinvertebrates were collected, and 143 species were identified, belonging to 4 phyla, 7 orders, 22 families, and 75 families. The results showed that LUI had the most significant impact on macroinvertebrate community structure, with substrate type, dry plant weight, total phosphorus, turbidity, and attached algae biomass also playing significant roles in affecting macroinvertebrate communities. The species richness, the Shannon-Wiener index, and the Margalef richness index exhibited a nonlinear positive correlation with LUI of the sampling site, increasing as LUI enhancing and eventually reaching a plateau. Functional richness showed a linear and positive correlation with LUI, increasing with its enhancement, while functional evenness and functional divergence exhibited a nonlinear correlation with LUI. Functional evenness initially increased and then decreased with the enhancement of LUI, while functional divergence decreased with LUI enhancement. This study can provide a scientific reference for river ecological management under various land use scenarios.

Sediment DNA metabarcoding and morphology provide complementary insight into macrofauna and meiobenthos response to environmental gradients in an Arctic glacial fjord.

Arctic fjords ecosystems are highly dynamic, with organisms exposed to various natural stressors along with productivity clines driven by advection of water masses from shelves. The benthic response to these environmental clines has been extensively studied using traditional, morphology-based approaches mostly focusing on macroinvertebrates. In this study we analyse the effects of glacially mediated disturbance on the biodiversity of benthic macrofauna and meiobenthos (meiofauna and Foraminifera) in a Svalbard fjord by comparing morphology and eDNA metabarcoding. Three genetic markers targeting metazoans (COI), meiofauna (18S V1V2) and Foraminifera (18S 37f) were analyzed. Univariate measures of alpha diversity and multivariate compositional dissimilarities were calculated and tested for similarities in response to environmental gradients using correlation analysis. Our study showed different taxonomic composition of morphological and molecular datasets for both macrofauna and meiobenthos. Some taxonomic groups while abundant in metabarcoding data were almost absent in morphology-based inventory and vice versa. In general, species richness and diversity measures in macrofauna morphological data were higher than in metabarcoding, and similar for the meiofauna. Both methodological approaches showed different patterns of response to the glacially mediated disturbance for the macrofauna and the meiobenthos. Macrofauna showed an evident distinction in taxonomic composition and a dramatic cline in alpha diversity indices between the outer and inner parts of fjord, while the meiobenthos showed a gradual change and more subtle responses to environmental changes along the fjord axis. The two methods can be seen as complementing rather than replacing each other. Morphological approach provides more accurate inventory of larger size species and more reliable quantitative data, while metabarcoding allows identification of inconspicuous taxa that are overlooked in morphology-based studies. As different taxa may show different sensitivities to environmental changes, both methods shall be used to monitor marine biodiversity in Arctic ecosystems and its response to dramatically changing environmental conditions.

The southernmost Errina antarctica hydrocoral savannah in Patagonian waters.

Marine animal forest (MAF) are animal-dominated megabenthic communities that support high biodiversity levels and play key roles in ecosystem functioning. However, there is limited data available in Patagonian waters related to the presence of these vulnerable benthic communities. We report a monospecific MAF of Errina antartica in Angostura Tomms, which represents the southernmost known living MAF of this species. With coverages reaching up to 28.5% of the substrate from 1.23 m to, at least, 33 m depth is the shallowest stylasterid assemblage described worldwide to date. The size of the colonies ranged from 0.14 to 15.8 cm, with small colonies (< 10 cm) being the most abundant (99%). We hypothesize that this MAF might correspond to a recent colonization of a space, extending its distribution range towards shallower areas or it could be an assemblage formed at the limit of the species' distribution in which the environmental conditions are not optimal for the major development of the colonies. Additionally, results showed that habitats structured by three-dimensional sessile invertebrate such as E. antarctica showed higher values of species richness and alpha diversity than non-biogenic habitats. Analyses were based on 297 photos taken at 22 different sites in the western Strait of Magellan, along vertical transects from 5 to 25 m depth. Our study highlights the importance of the benthic communities existing in Patagonian waters, evidencing the need to act actively to ensure their maintenance.

Density data for Lake Erie benthic invertebrate assemblages from 1930 to 2019.

Benthic invertebrates are important trophic links in food webs and useful bioindicators of environmental conditions, but long-term benthic organism abundance data across broad geographic areas are rare and historic datasets are often not readily accessible. This dataset provides densities of benthic macroinvertebrates collected from 1930 to 2019 during surveys in Lake Erie, a Laurentian Great Lake. The surveys were funded by the governments of the United States and Canada to investigate the status and changes in the benthic community. From the total of 21 lake-wide and basin-wide benthic surveys conducted in Lake Erie from 1929 to 2019, we were able to acquire data for 17 surveys, including species-level data for 10 surveys and data by higher taxonomic groups for seven surveys. Our amassed Lake Erie dataset includes data from 11 surveys (including five with species-level data) conducted in the western basin in 1930-2019, seven surveys (six with species-level data) in the central basin, and eight surveys (seven with species-level data) in the eastern basin (1973-2019). This Lake Erie dataset represents the most extensive temporal dataset of benthic invertebrates available for any of the Laurentian Great Lakes. Benthic samples were collected using Ponar or Shipek bottom dredges and taxa densities were calculated as individuals per square meter using the area of the dredge. Density data are provided for taxa in the Annelida, Arthropoda, Mollusca, Cnidaria, Nemertea, and Platyhelminthes phyla. Current taxonomy was used for most groups but, in a few cases, older taxonomic names were used for consistency with historical data. Analysis of this dataset indicates that eutrophication, water quality improvement, and dreissenid introduction were the major drivers of changes in the benthic community in the western basin, while hypoxia was a major factor in the central basin, and dreissenid introduction was the most important driver in the eastern basin. Considering the rarity of high taxonomic resolution long-term benthic data for lake ecosystems, this dataset could be useful to explore broader aspects of ecological theory, including effects of eutrophication, hypoxia, invasive species, and other factors on community organization, phylogenetic and functional diversity, and spatial and temporal scales of variation in community structure. In addition, the dataset could be useful for studies on individual species, including abundance and distribution, species co-occurrence, and how the patterns of dominance and rarity change over space and time. Use of this dataset for academic or educational purposes is encouraged as long as this data paper is properly cited.

Development of Macroinvertebrate Multimetric Index for Assessment of Large Rivers in Thailand.

Human activities are a significant threat to the health of river ecosystems, especially in developing countries. In Thailand, benthic macroinvertebrates have been widely used for bioassessment for aquatic ecosystem evaluation. However, most of them focuses on streams, which may not be applicable to large rivers. This study aimed to fill this gap by developing a macroinvertebrate multimetric index for Thailand's large rivers. Sampling was conducted in 15 rivers, and 41 sites across Thailand. Physico-chemical parameters, habitat characteristics, and macroinvertebrates were analyzed. Macroinvertebrate data were analyzed and metrics calculated. The seven selected core metrics, including Plecoptera taxa, EPT taxa, insect individuals %, Crustaceans and Mollusca individuals %, collector-gatherers taxa, intolerant taxa in BMWPThai, and Hilsenhoff Biotic Index, showed a strong response to anthropogenic disturbance. The final Thailand Large River Multimetric Index (TLMI) classified river health from "Excellent" to "Very Poor" condition. The validation of TLMI confirmed its ability to distinguish river health conditions. Overall, the TLMI can used as an assessing and monitoring ecological health tool for Thailand's large rivers, that can be applied for river management and conservation.

Simple, Robust Invertebrate DNA Barcoding: Chelex-Based DNA Extraction and Optimized COI Amplification.

Chelex-based DNA extractions are well suited for student DNA barcoding research because they are simple, safe, and inexpensive and can be performed without specialized laboratory equipment, allowing them to be performed in classrooms or at home. Extracted DNA is stable in Chelex solution for at least a week at ambient temperature, allowing collection of DNA samples from remote students. These extractions provide quality DNA for many taxa and are optimal for barcoding invertebrates, especially in combination with novel cytochrome c oxidase I (COI) primer cocktails and PCR cycling conditions.

Evaluation of water ecological health of Yanhe River based on benthic fauna integrity index.

Yanhe River Basin is located in the hilly gully area of the Loess Plateau with serious soil erosion. Strong human activities in the middle and lower reaches lead to fragile ecological environment. Soil erosion status varies among different geomorphic units within the watershed (loess liang hilly and gully region, loess mao hilly and gully region, and broken platform region). In this study, we surveyed the benthic community from the Yanhe River Basin in April (spring) and October (autumn) of 2021. To evaluate the water ecological health status of the watershed and investigate the effects of different geomorphic units on the benthic integrity of the benthos, we constructed the benthic-index of biotical integrity (B-IBI) based on the biological data. We identified a total of 113 species of 73 genera in 4 phyla of benthic fauna, with aquatic insects as the dominant taxa in both seasons. Through screening 26 candidate indicators, we found that the spring B-IBI consisted of three indicators: relative abundance of individuals of dominant taxonomic units, family biotic index (FBI), and relative abundance of predator individuals, and that autumn B-IBI was composed of the number of taxonomic units of Ephemeroptera, FBI value, and the relative abundance of predator individuals. Results of the B-IBI evaluation showed that 83.3% of the sampling sites in the upper mainstem and tributaries were at a healthy condition, while only 28.6% sampling sites in the middle and lower mainstem and tributaries were at a healthy condition. In addition, the health status of the watershed was better in spring than in autumn. The Kruskal-Wallis nonparametric tests showed that benthic density, species number, and B-IBI percentile scores in the fragmented loess area were significantly higher in spring than in autumn, and significantly lower in autumn than in the loess liang hilly and gully region and loess mao hilly and gully region, being mainly caused by the increasing erosion due to the concentrated rainfall in wet season. Results of the redundancy analysis showed that key environmental factors affecting benthic community structure in spring were boulder substrate, chlorophyll-a, oxidation reduction potential, turbidity, conductivity, and dissolved oxygen, and were nitrate-nitrogen, oxidation reduction potential, and pH in autumn.

The recovery of European freshwater biodiversity has come to a halt.

Owing to a long history of anthropogenic pressures, freshwater ecosystems are among the most vulnerable to biodiversity loss1. Mitigation measures, including wastewater treatment and hydromorphological restoration, have aimed to improve environmental quality and foster the recovery of freshwater biodiversity2. Here, using 1,816 time series of freshwater invertebrate communities collected across 22 European countries between 1968 and 2020, we quantified temporal trends in taxonomic and functional diversity and their responses to environmental pressures and gradients. We observed overall increases in taxon richness (0.73% per year), functional richness (2.4% per year) and abundance (1.17% per year). However, these increases primarily occurred before the 2010s, and have since plateaued. Freshwater communities downstream of dams, urban areas and cropland were less likely to experience recovery. Communities at sites with faster rates of warming had fewer gains in taxon richness, functional richness and abundance. Although biodiversity gains in the 1990s and 2000s probably reflect the effectiveness of water-quality improvements and restoration projects, the decelerating trajectory in the 2010s suggests that the current measures offer diminishing returns. Given new and persistent pressures on freshwater ecosystems, including emerging pollutants, climate change and the spread of invasive species, we call for additional mitigation to revive the recovery of freshwater biodiversity.

How many metazoan species live in the world's largest mineral exploration region?

The global surge in demand for metals such as cobalt and nickel has created unprecedented interest in deep-sea habitats with mineral resources. The largest area of activity is a 6 million km2 region known as the Clarion-Clipperton Zone (CCZ) in the central and eastern Pacific, regulated by the International Seabed Authority (ISA). Baseline biodiversity knowledge of the region is crucial to effective management of environmental impact from potential deep-sea mining activities, but until recently this has been almost completely lacking. The rapid growth in taxonomic outputs and data availability for the region over the last decade has allowed us to conduct the first comprehensive synthesis of CCZ benthic metazoan biodiversity for all faunal size classes. Here we present the CCZ Checklist, a biodiversity inventory of benthic metazoa vital to future assessments of environmental impacts. An estimated 92% of species identified from the CCZ are new to science (436 named species from a total of 5,578 recorded). This is likely to be an overestimate owing to synonyms in the data but is supported by analysis of recent taxonomic studies suggesting that 88% of species sampled in the region are undescribed. Species richness estimators place total CCZ metazoan benthic diversity at 6,233 (+/-82 SE) species for Chao1, and 7,620 (+/-132 SE) species for Chao2, most likely representing lower bounds of diversity in the region. Although uncertainty in estimates is high, regional syntheses become increasingly possible as comparable datasets accumulate. These will be vital to understanding ecological processes and risks of biodiversity loss.

Continent-wide declines in shallow reef life over a decade of ocean warming.

Human society is dependent on nature1,2, but whether our ecological foundations are at risk remains unknown in the absence of systematic monitoring of species' populations3. Knowledge of species fluctuations is particularly inadequate in the marine realm4. Here we assess the population trends of 1,057 common shallow reef species from multiple phyla at 1,636 sites around Australia over the past decade. Most populations decreased over this period, including many tropical fishes, temperate invertebrates (particularly echinoderms) and southwestern Australian macroalgae, whereas coral populations remained relatively stable. Population declines typically followed heatwave years, when local water temperatures were more than 0.5 °C above temperatures in 2008. Following heatwaves5,6, species abundances generally tended to decline near warm range edges, and increase near cool range edges. More than 30% of shallow invertebrate species in cool latitudes exhibited high extinction risk, with rapidly declining populations trapped by deep ocean barriers, preventing poleward retreat as temperatures rise. Greater conservation effort is needed to safeguard temperate marine ecosystems, which are disproportionately threatened and include species with deep evolutionary roots. Fundamental among such efforts, and broader societal needs to efficiently adapt to interacting anthropogenic and natural pressures, is greatly expanded monitoring of species' population trends7,8.

AjTGFß alleviates V. splendidus-induced inflammation through SMADs pathway in Apostichopus japonicus.

The inhibition of inflammatory response is an essential process to control the development of inflammation and is an important step to protect the organism from excessive inflammatory damage. As a pleiotropic cytokine, transforming growth factor beta (TGF-ß) plays a regulatory role in inhibiting inflammation in vertebrates. To investigate the role of TGF-ß in the regulation of inflammation in invertebrates, we cloned and characterized the TGF-ß gene from Apostichopus japonicus via rapid amplification of cDNA ends, and the sample was designated as AjTGF-ß. For Vibrio splendidus-challenged sea cucumbers, the expression of AjTGF-ß mRNAs in coelomocytes decreased at 96 h (0.27-fold), which was contrary to the trend of inflammation. AjTGF-ß was expressed in all tissues with the highest expression in the body wall. When AjTGF-ß was knocked down by using small interfering RNA (siRNA-KD) to 0.45-fold, AjSMAD 2/3 and AjSMAD6 were downregulated to 0.32- and 0.05-fold compared with the control group, respectively. Furthermore, when the damaged sea cucumber was challenged by V. splendidus co-incubated with rAjTGF-ß, the damage area had no extensive inflammation, and damaged repair appeared at 72 h compared with the Vs + BSA group, in which the expression of AjSMAD 2/3 was upregulated by 1.35-fold. Under this condition, AjSMAD 2/3 silencing alleviated rAjTGF-ß-induced damage recovery. Moreover, rAjTGF-ß slightly induced the collagen I expression from 6.13 ng/mL to 7.84 ng/mL, and collagen III was upregulated from 6.23 ng/mL to 6.89 ng/mL compared with the Vs + BSA group. This finding indicates that AjTGF-ß negatively regulated the inflammatory progress and accelerated the repair of damage by AjSMADs to regulate the collagens expression.

Effect of environmental characteristics on the diversity of aquatic macroinvertebrates in Andean rivers regulated for hydroelectric generation / Efecto de características ambientales en la diversidad de macroinvertebrados acuáticos en ríos andinos regulados para generación hidroeléctrica

Introduction: The Andes are characterized by an abundance of water resources and flows are frequently regulated by reservoirs for the generation of energy. The effects of regulation on aquatic macroinvertebrate communities are not well known in Colombia. Objective: To test the hypothesis that regulated currents have less macroinvertebrate diversity. Methods: We collected water and organism samples before, and after, the regulation of the Tafetanes, Calderas and Arenosa rivers, in Antioquia, Colombia, during various hydrological cycles (rain, transition and drought) and climatic phenomena (ENSO/El Niño Phenomenon) between 2016 and 2018. Results: We collected 53 214 individuals, from 165 taxa, mostly from the orders Ephemeroptera, Plecoptera, Trichoptera and Diptera (90 % of captures). Changes in diversity responded to spatial differences rather than to physicochemical variables: diversity was higher in non-regulated sites, regardless of the hydrological period or associated ENSO. Most species were found in all sampling sites, but abundance was higher in the site with the best habitat conservation status. Conclusion: The results support the hypothesis that physical barriers have effects on macroinvertebrate diversity at the local scale, however, the condition of adjacent habitats also seems to play an important role in preserving richness and abundance. The conservation of forest adjacent to the riverbed could mitigate the impacts of regulation.

Introducción: Los Andes se caracterizan por tener gran abundancia de recursos hídricos y las corrientes son frecuentemente reguladas por embalses para la generación de energía. Los efectos de la regulación en las comunidades de macroinvertebrados acuáticos no se conocen bien en Colombia. Objetivo: Probar la hipótesis de que las corrientes reguladas presentan menor diversidad de macroinvertebrados. Métodos: Recolectamos muestras de agua y organismos, antes y después de la regulación de los ríos Tafetanes, Calderas y La Arenosa, en Antioquia, Colombia, durante varios ciclos hidrológicos (lluvia, transición y sequía) y fenómenos climáticos (ENSO/Fenómeno de El Niño) entre 2016 y 2018. Resultados: Recolectamos 53 214 individuos, de 165 táxones, en su mayoría de los órdenes Ephemeroptera, Plecoptera, Trichoptera y Diptera (90 % de las capturas). Los cambios en la diversidad respondieron a las diferencias espaciales más que a las variables fisicoquímicas: la diversidad fue mayor en sitios no regulados, independientemente del periodo hidrológico o del ENSO. La mayoría de las especies se encontraron en todos los sitios de muestreo, pero su abundancia fue mayor en el sitio de mejor estado de conservación del hábitat. Conclusiones: Los resultados apoyan la hipótesis de que las barreras físicas tienen efectos sobre la diversidad de macroinvertebrados a escala local, sin embargo, el estado de los hábitats adyacentes también parece jugar un papel importante en la preservación de la riqueza y abundancia. La conservación del bosque adyacente podría mitigar los impactos generados por la regulación.

Community structure of benthic macroinvertebrates in native and introduced mangroves of northern Beibu Gulf, China: Implication for restoring mangrove ecosystems.

Introduced mangroves are widely used to restore mangrove ecosystems in South China. Results of potential impacts on indicative benthic macroinvertebrates are divergent. We explored the community structure of benthic macroinvertebrates in the mangrove ecosystem of northern Beibu Gulf, China across four habitats: native Avicennia marina mangrove, introduced Laguncularia racemosa mangrove, native-introduced mixed mangrove, and unvegetated intertidal flat. Based on the Hill number, community structure was estimated from the dimensions of estimated species richness, diversity, evenness, and species composition similarity. Benthic macroinvertebrates in the unvegetated flat significantly differed from the other three assemblages in mangroves; introduced L. racemosa mangrove had relatively distinct benthic macroinvertebrate assemblage from the native A. marina and the mixed mangroves, with lower species richness and similarity but higher diversity and evenness. Considering the lack of unanimous conclusion of potential impact on benthic macroinvertebrates under complex species interactions, native mangroves should be of top priority in ecosystem restoration.

Sinking Down or Floating Up? Current State of Taxonomic Studies on Marine Invertebrates in Japan Inferred from the Number of New Species Published between the Years 2003 and 2020.

Taxonomic studies on marine invertebrates have been prominent in Japan since the 19th century. Globally, taxonomy was reported to have been in recession since the early 21st century, but it is not clear if it is still in hardship or is making a recovery in recent years in Japan. In order to comprehend the status quo of taxonomic studies on marine invertebrates in Japan, we compiled a list of marine invertebrate species newly described from the exclusive economic zone of this country during the period between 2003 and 2020 and investigated trends by making comparisons of higher taxa and academic journals in terms of the numbers of new species and taxonomic authors. We noticed that recruitment of new researchers into taxonomic studies is evident in some taxa. We also found that certain articles with descriptions of new species are now being published in journals aimed at general biology/zoology, not oriented principally to taxonomy. We consider from our analyses that taxonomic studies on marine invertebrates in Japan show signs of resurgence, but development of new taxonomists is awaited in certain taxa.

DNA metabarcoding reveals human impacts on macroinvertebrate communities in polluted headwater streams: Evidence from the Liao River in northeast China.

Headwater streams are a hotspot of freshwater biodiversity, carrying indispensable resource pools of aquatic species. However, up to now, there remain many challenges to accurately and efficiently characterize the responses of this vulnerable ecosystem to human-induced changes. Here, we collected macroinvertebrate data from 12 different headwater streams in the Liao River of northeast China by DNA metabarcoding approach, to reveal biodiversity changes and ecological thresholds affected by human beings. Our data showed that the community composition and structure of headwater streams had unique and significant differences under human impacts, and 5-day biological oxygen demand (BOD5) and ammonia nitrogen (NH3-N) were the key variables explaining the variation in community structure. Although α diversity had a unimodal relationship with nutrients and organic loads, ß diversity and its turnover component (species replacement) increased significantly. In addition, 22 and 33 indicative taxa were identified to have significant negative responses to BOD5 and NH3-N, respectively, and the change points derived from Threshold Indicator Taxa Analysis (TITAN) for the negative response of their frequency and abundance were BOD5 >3.42 mg/L and NH3-N >0.14 mg/L. Overall, this study reveals the biodiversity changes in headwater streams from the aspects of α and ß diversity, and also determines the thresholds of BOD5 and NH3-N pollutants for one reach at one date from 12 headwater streams, suggesting the potential of DNA metabarcoding approach for threshold analyses in headwater streams.

Viromes in marine ecosystems reveal remarkable invertebrate RNA virus diversity.

Little is known about ocean viromes and the ecological drivers of the evolution of aquatic RNA viruses. This study employed a meta-transcriptomic approach to characterize the viromes of 58 marine invertebrate species across three seas. This revealed the presence of 315 newly identified RNA viruses in nine viral families or orders (Durnavirales, Totiviridae, Bunyavirales, Hantaviridae, Picornavirales, Flaviviridae, Hepelivirales, Solemoviridae, and Tombusviridae), with most of them being sufficiently divergent to the already documented viruses. Notably, this study revealed three marine invertebrate hantaviruses that are rooted to vertebrate hantaviruses, further supporting that hantaviruses may have a marine origin. We have also found evidence for possible host sharing and switch events during virus evolution. Overall, we have revealed the hidden diversity of marine invertebrate RNA viruses.

CompoDynamics: a comprehensive database for characterizing sequence composition dynamics.

Sequence compositions of nucleic acids and proteins have significant impact on gene expression, RNA stability, translation efficiency, RNA/protein structure and molecular function, and are associated with genome evolution and adaptation across all kingdoms of life. Therefore, a devoted resource of sequence compositions and associated features is fundamentally crucial for a wide range of biological research. Here, we present CompoDynamics (https://ngdc.cncb.ac.cn/compodynamics/), a comprehensive database of sequence compositions of coding sequences (CDSs) and genomes for all kinds of species. Taking advantage of the exponential growth of RefSeq data, CompoDynamics presents a wealth of sequence compositions (nucleotide content, codon usage, amino acid usage) and derived features (coding potential, physicochemical property and phase separation) for 118 689 747 high-quality CDSs and 34 562 genomes across 24 995 species. Additionally, interactive analytical tools are provided to enable comparative analyses of sequence compositions and molecular features across different species and gene groups. Collectively, CompoDynamics bears the great potential to better understand the underlying roles of sequence composition dynamics across genes and genomes, providing a fundamental resource in support of a broad spectrum of biological studies.