Assessment of benthic invertebrate diversity and river ecological status along an urbanized gradient using environmental DNA metabarcoding and a traditional survey method

Comparison of Environmental DNA Metabarcoding and a Traditional Survey Method for Assessing Fish Diversity and Distribution Along Salinity Gradient in an Urban Brackish Reservoir, China

With the decrease in fish diversity, the monitoring of fish has become a current research hotspot. Here, the fish diversity and spatial distribution along a salinity gradient (0.28‱-3.32‱) in Xinglinwan Reservoir, China, were investigated using eDNA and the TSM. With the combination of both methods, 12 species from 6 orders, 9 families, and 11 genera were observed. The invasive species Oreochromis niloticus had the highest relative abundance, accounting for 56.91% in the TSM and 89.80% in eDNA, respectively. eDNA detected 83.33% of the species detected using the TSM, and an additional six species (50.0% of the total species) were detected via only eDNA. Moreover, eDNA supplemented the unavailable abundance data from the TSM. The TSM revealed that the diversity and relative abundance of fish inhabiting seawater and brackish water increased with an increase in salinity, but this was not found using eDNA. Thus, our study highlights that Xinglinwan Reservoir has a low species richness and is suffering from the great harm of ecological invasion. Our findings also show that eDNA could be reliable for providing a comprehensive picture of fish, but discriminating the spatial heterogeneity of fish communities is a challenge for its widespread adoption in lentic brackish systems.

Similarities and differences in bacterial communities between the Pearl River (Guangzhou section) and its estuary

BACKGROUND

The Pearl River and its estuary are highly exposed to anthropogenic disturbance. Because bacterial communities play an indispensable role in aquatic ecosystems, there has been an increased research focus on the statuses of these communities under human-induced perturbations.

METHODS AND RESULTS

This study investigated the composition, diversity, and structure of bacterial communities across 29 sites from the Guangzhou section of the Pearl River (GZ) to the Pearl River Estuary (PRE) using 16S rRNA gene amplicons. The results revealed similar dominant phyla of bacteria in both GZ and PRE, as well as significant differences in bacterial community composition and diversity between the two sections. Proteobacteria and Cyanobacteria were identified as the primary drivers of compositional differences between GZ and PRE. The Cyanobacteria Dolichospermum_NIES41 and Cuspidothrix issatschenkoi were only present in GZ, whereas the marine Gram-negative bacteria of Porticoccus litoralis and Thalassolituus oleivorans were unique to PRE.

CONCLUSIONS

Bacterial community composition and diversity exhibit both similarities and differences between GZ and PRE; Proteobacteria and Cyanobacteria are key factors underlying these variations. Bacterial communities in both GZ and PRE are strongly influenced by human activities, and salinity is an important factor in controlling their differences. This study provides a comprehensive analysis of the bacterial communities in GZ and PRE, establishing a foundation for better management of aquatic ecosystems impacted by anthropogenic activities.

From land to sea: Environmental DNA is correlated with long-term water quality indicators in an urbanized estuary

Estuaries provide critical ecosystem services, and yet are increasingly under threat from urbanization. Non-invasive approaches to monitor biodiversity resident to or migrating through estuaries is critical to evaluate the holistic health of these ecosystems, often based entirely on water quality. In this study we compared tree of life metabarcoding (ToL-metabarcoding) biodiversity detections with measurements of physico-chemical variables (chlorophyll a, turbidity, total nitrogen, total phosphorous, dissolved oxygen) at eight sites of varying degrees of water quality in the Gold Coast Broadwater Estuary (Queensland, Australia). These sites were ranked according to an adapted Water Quality Index (WQI) score. Here, we detected 787 unique taxa, adding 137 new biodiversity records to the region, mostly micro-organisms such as bacteria, ciliates, diatoms, dinoflagellates, and cryptomonads. Sites with the lowest WQI were characterised by higher turbidity, lower dissolved oxygen, as well as higher total nitrogen and phosphorous, which correlated with an increased diversity of bacteria, ciliates, and green algae. Similarly, the composition of taxa was significantly different between sites with variable WQI values for most taxa but was less apparent for larger vertebrate groups. These findings suggest that rapid ToL-metabarcoding biodiversity detections, particularly for lower order taxonomic groups, can serve as valuable indicators of flora and fauna across the tree of life associated with dynamically shifting estuarine health along urbanized coastlines.

Assessing benthic macroinvertebrate communities' spatial heterogeneity in Mediterranean transitional waters through eDNA metabarcoding

Transitional waters are important habitats both for biodiversity and ecological functions, providing valuable natural resources and relevant ecosystem services. However, they are highly susceptible to climate changes and anthropogenic pressures responsible for biodiversity losses and require specific biomonitoring programs. Benthic macroinvertebrates are suitable as ecological indicators of transitional waters, being affected by biological, chemical, and physical conditions of the ecosystems about their life cycles and space-use behaviour. The advent of high-throughput sequencing technologies has allowed biodiversity investigations, at the molecular level, in multiple ecosystems and for different ecological guilds. Benthic macroinvertebrate communities' composition has been investigated, at the molecular level, mainly through DNA extracted from sediments in marine and riverine ecosystems. In this work, benthic macroinvertebrate communities are explored through eDNA metabarcoding from water samples in a Mediterranean transitional water ecosystem. This research highlighted the validity of eDNA metabarcoding as an efficient tool for the assessment of benthic macroinvertebrate community structure in transitional waters, unveiling the spatial heterogeneity of benthic macroinvertebrate communities correlated to the measured environmental gradients. The results suggest that peculiar features of transitional water ecosystems, such as shallow waters and limited currents, facilitate the assessment of benthic macroinvertebrate communities through environmental DNA analysis from surface water samples, opening for more rapid and accurate monitoring programs for these valuable ecosystems.

From DNA to diagnostics: A case study using macroinvertebrate metabarcoding to assess the effectiveness of restoration measures in a Dutch stream

Stream ecosystems are under pressure due to multiple stressors. Restoration measures can halt further degradation and improve their ecological status. However, assessment of the effectiveness of the implemented measures is often insufficient because of logistic and financial constraints. DNA-metabarcoding has been proposed to scale up sample processing, although its application as a diagnostic tool has received less attention. The aim of our study was to evaluate if DNA-metabarcoding of stream macroinvertebrates can be used to compute a stressor-specific index to assess the effectiveness of a stream restoration project. For this purpose, we sampled the upstream, restored, and downstream section of a recently restored lowland stream in the Netherlands. At each site, we applied three different methods of macroinvertebrate identification: morphological identification of bulk samples (morphology), DNA-metabarcoding of the same bulk samples (DNA) and metabarcoding of eDNA extracted from the water (eDNA). First, we compared the community composition identified by each method. The communities identified by morphology and DNA were highly similar, whereas the communities generated by the eDNA differed. Second, we analysed whether the identification methods could be used to assess the effectiveness of the restoration project, focussing on a stressor-specific index for flow as the restoration measures aimed at improving flow conditions. Both the morphology and bulk DNA samples indicated improved flow conditions in the restored section of the stream (i.e., less stress from the reduction or absence of flow than in the unrestored sections). Contrary, the eDNA-water samples did not differentiate the amount of stress throughout the catchment, although applying recent developments in eDNA sampling could lead to more robust results. In conclusion, this study forms proof of concept that DNA from bulk samples can be utilized to assess the effectiveness of restoration measures, showing the added value of this approach for water managers.

Ditch control and land reclamation promote vegetation recovery in Loess Plateau

This study aimed to assess the impact of land consolidation projects and climate change on changes in vegetation in the Loess Plateau during 2012-2021. The study also explored the impacts of human activities and climate change on the ecological quality of the Loess Plateau during this period. The spatial and temporal normalized difference combined meteorological monitoring data, project data, and normalized difference vegetation index (NDVI) data that was used to create the vegetation index dataset spanning from 2012-2021. The study discussed and assessed the effectiveness of the project, revealing the following results: 1) A significant increase was observed in the vegetation index of the Loess Plateau region from 2012 to 2021, with an upward trend of 0.0024 per year (P < 0.05). 2) Contributions to changes in vegetation attributed to climatic factors and the anthropogenic factors of the ditch construction project were 82.74 and 17.62%, respectively, with climatic factors dominating and the degree of response of the ditch construction project increasing annually. 3) In the Loess Plateau, climatic variables dominated changes in vegetation. However, land consolidation projects in vegetation factors played a key role in changes in vegetation, and the degree of influence was gradually increasing.

Assessing the Impact of Anthropic Pressures on Aquatic Macroinvertebrates: A Functional Trait Approach in the Irtysh River Watershed

Little is known about how changes in the biodiversity and functional traits of macroinvertebrates in rivers respond to the responses of anthropic pressures and their driving factors. Macroinvertebrates were sampled at 17 sites in the Irtysh River Basin and classified macroinvertebrates into 10 traits and 38 categories between May and August 2022. Then, we performed R-mode linked to Q-mode (RLQ) analysis and calculated functional richness, evenness, divergence, and Rao's quadratic entropy (RaoQ) for each site and community-weighted means for each trait category. Our results indicated that there were pronounced alterations in species variability in the urban region. Functional divergence indicated fierce competition among species and considerable niche overlap in the urban region. Functional evenness indicated that species abundance distribution and interspecific functional distance were not uniform in the urban region. Functional richness indicated that the urban region was the strongest region in terms of niche occupation, resource utilization, and buffering capacity for environmental fluctuations. Rao's quadratic entropy showed that the trait difference of macroinvertebrates was the largest in all regions, which was caused by the gradient environmental difference. Research has revealed that urbanization significantly influences the evolutionary trajectory of macroinvertebrate fauna, culminating in an upsurge in pollution-tolerant species and a convergence of functional traits. We recommend strengthening the control of urban and industrial pollution and wise planning and management of land and water resources to mitigate the impact of anthropogenic destruction on habitat fragmentation in the Irtysh River Basin.

It Is Not Only Data-Freshwater Invertebrates Misused in Biological Monitoring

The article presents and discusses the issues of the use of free-living invertebrates to assess the ecological status of freshwater environments with different methods of biological monitoring. Invertebrates are excluded from ethical consideration in the procedures of environmental protection, which results in the killing of many more individuals during sampling than necessary. Biomonitoring is used as a routine method for environmental protection that results in the cruel death of even millions of aquatic animals annually. In many cases, the mortality of animals used in such types of activities has been shown as excessive, e.g., because the vast majority die due to unnecessary subsampling procedures. Improperly planned and conducted procedures which result in excessive mortality have or may have a negative impact on the environment and biodiversity. Their existence as sensitive beings is reduced to an information function; they become only data useful for biomonitoring purposes. The main problem when trying to determine the mortality of invertebrates due to biomonitoring activities and its impact on natural populations seems to be the lack of access to raw data presenting how many animals were killed during sampling.

Assessing arthropod diversity metrics derived from stream environmental DNA: spatiotemporal variation and paired comparisons with manual sampling

Background

Benthic invertebrate (BI) surveys have been widely used to characterize freshwater environmental quality but can be challenging to implement at desired spatial scales and frequency. Environmental DNA (eDNA) allows an alternative BI survey approach, one that can potentially be implemented more rapidly and cheaply than traditional methods.

Methods

We evaluated eDNA analogs of BI metrics in the Potomac River watershed of the eastern United States. We first compared arthropod diversity detected with primers targeting mitochondrial 16S (mt16S) and cytochrome c oxidase 1 (cox1 or COI) loci to that detected by manual surveys conducted in parallel. We then evaluated spatial and temporal variation in arthropod diversity metrics with repeated sampling in three focal parks. We also investigated technical factors such as filter type used to capture eDNA and PCR inhibition treatment.

Results

Our results indicate that genus-level assessment of eDNA compositions is achievable at both loci with modest technical noise, although database gaps remain substantial at mt16S for regional taxa. While the specific taxa identified by eDNA did not strongly overlap with paired manual surveys, some metrics derived from eDNA compositions were rank-correlated with previously derived biological indices of environmental quality. Repeated sampling revealed statistical differences between high- and low-quality sites based on taxonomic diversity, functional diversity, and tolerance scores weighted by taxon proportions in transformed counts. We conclude that eDNA compositions are efficient and informative of stream condition. Further development and validation of scoring schemes analogous to commonly used biological indices should allow increased application of the approach to management needs.