A Review and Perspective of eDNA Application to Eutrophication and HAB Control in Freshwater and Marine Ecosystems

Soil eDNA biomonitoring reveals changes in multitrophic biodiversity and ecological health of agroecosystems

Soil health is integral to sustainable agroecosystem management. Current monitoring and assessment practices primarily focus on soil physicochemical properties, yet the perspective of multitrophic biodiversity remains underexplored. Here we used environmental DNA (eDNA) technology to monitor multitrophic biodiversity in four typical agroecosystems, and analyzed the species composition and diversity changes in fungi, bacteria and metazoan, and combined with the traditional physicochemical variables to establish a soil health assessment framework centered on biodiversity data. First, eDNA technology detected rich multitrophic biodiversity in four agroecosystems, including 100 phyla, 273 classes, 611 orders, 1026 families, 1668 genera and 1146 species with annotated classification, and the relative sequence abundance of dominant taxa fluctuates tens of times across agroecosystems. Second, significant differences in soil physicochemical variables such as organic matter (OM), total nitrogen (TN) and available phosphorus (AP) were observed among different agroecosystems, nutrients were higher in cropland and rice paddies, while heavy metals were higher in fish ponds and lotus ponds. Third, biodiversity metrics, including α and β diversity, also showed significant changes across agroecosystems, the soil biota was generally more sensitive to nutrients (e.g., OM, TN or AP), while the fungal communities were mainly affected by heavy metals in October (e.g., Cu and Cr). Finally, we screened 48 sensitive organismal indicators and found significant positive consistency between the developed eDNA indices and the traditional soil quality index (SQI, reaching up to R2 = 0.58). In general, this study demonstrated the potential of eDNA technology in soil health assessment and underscored the importance of a multitrophic perspective for efficient monitoring and managing agroecosystems.

Environmental DNA for the surveillance of biosecurity threats in Mediterranean lagoons

Invasive species that outcompete endemic ones and toxic harmful algae that cause algal blooms threaten marine resources like fisheries, aquaculture, and even tourism. Environmental DNA (eDNA) metabarcoding can help as a method for early alert. In this study, we have analyzed communities inhabiting six lagoons within the Gulf of Lion (northwest Mediterranean Sea) with spatial protection as RAMSAR and Natura 2000 sites. Employing the COI gene as the only metabarcode, we found 15 genera that have caused recognized algal bloom outbreaks in the studied lagoons since 2000. In addition, seven alien invasive species that can pose risks to the rich marine resources of the zone and lagoons were also found. The results found from eDNA are consistent with events of toxic algae blooms before and after the sampling moment and with reported occurrences of the invasive species in nearby Mediterranean areas. Multivariate multiple analysis showed the importance of anthropic pressure in the abundance of these nuisance species. Mitigation actions and routine eDNA metabarcoding in zones of special interest like these fragile French Mediterranean lagoons are recommended for early alert of nuisance species in order to plan timely management actions.

Ultrasonic-assisted extraction of total flavonoids from Zanthoxylum bungeanum residue and their allelopathic mechanism on Microcystis aeruginosa

Water eutrophication has emerged as a pressing concern for massive algal blooms, and these harmful blooms can potentially generate harmful toxins, which can detrimentally impact the aquatic environment and human health. Consequently, it is imperative to identify a safe and efficient approach to combat algal blooms to safeguard the ecological safety of water. This study aimed to investigate the procedure for extracting total flavonoids from Z. bungeanum residue and assess its antioxidant properties. The most favorable parameters for extracting total flavonoids from Z. bungeanum residue were a liquid-solid ratio (LSR) of 20 mL/g, a solvent concentration of 60%, an extraction period of 55 min, and an ultrasonic temperature of 80 °C. Meanwhile, the photosynthetic inhibitory mechanism of Z. bungeanum residue extracts against M. aeruginosa was assessed with a particular focus on the concentration-dependent toxicity effect. Z. bungeanum residue extracts damaged the oxygen-evolving complex structure, influenced energy capture and distribution, and inhibited the electron transport of PSII in M. aeruginosa. Furthermore, the enhanced capacity for ROS detoxification enables treated cells to sustain their photosynthetic activity. The findings of this study hold considerable relevance for the ecological management community and offer potential avenues for the practical utilization of resources in controlling algal blooms.

Water and sediment chemistry drivers of chlorophyll-a dynamics within a Ramsar declared floodplain pan wetland system

Floodplain pans are hydrologically dynamic in nature and characterised by variables such as chlorophyll-a (chl-a), water, and sediment chemistry over their hydroperiods. The present study investigated the spatio-temporal variations in water and sediment physico-chemical, and chlorophyll-a concentration characteristics of six floodplain pans found in the Ramsar declared Makuleke wetlands, Kruger National Park, South Africa. The water and sediment physico-chemical variable values were generally elevated during the high-water period, whereas chlorophyll-a concentrations varied across pans and hydroperiod. Benthic chl-a concentration significantly varied across pans with concentrations ranging from 161 to 1036.2 mg m2. The two-way ANOVA showed significant differences in benthic chl-a concentration among hydroperiods, and no significant differences were observed in pelagic chl-a across pans and hydroperiods. Generally, pelagic and benthic chl-a concentration increased as water and sediment chemistry variables increased. Furthermore, three sediment variables, i.e. pH, calcium, and magnesium, and water conductivity were found to be significant in structuring benthic chlorophyll-a dynamics in pans. However, none of the sediment and water variables had a significant effect on pelagic chl-a. Hydroperiod had a significant effect on influencing chl-a concentration, with high and low water level periods being characterised by low and high chl-a concentration, respectively. The n-MDS results showed strong overlaps in chl-a biomass among the Makuleke floodplain pans across hydroperiods. The increasing chl-a concentration in these floodplain pans due to potential bioturbation effects as a result of large mammals could potentially lead to eutrophication, which in turn could affect the system's primary productivity and aquatic biota. Therefore, it is important to establish a continuous monitoring programme on these pans to inform sound management decisions.

Heterogeneous bacterial communities affected by phytoplankton community turnover and microcystins in plateau lakes of Southwestern China

Both phytoplankton and bacteria are fundamental organisms with key ecological functions in lake ecosystems. However, the mechanistic interactions through which phytoplankton community change and bacterial communities interact remain poorly understood. Here, the responses of bacterial communities to the community structure, resource-use efficiency (RUE), and community turnover of phytoplankton and microcystins (MCs) were investigated in Lake Dianchi, Lake Xingyun, and Lake Erhai of Southwestern China across two seasons (May and October 2020). Among phytoplankton, Cyanobacteria was the dominant species in all three lakes and attained greater dominance in October than in May due to variation in the RUE of nitrogen and phosphorus and environmental changes. The production of MCs, including MC_LR, MC_RR and MC_YR, was the result of the massive Cyanobacteria. Decreases in diversity and increases in heterogeneity were observed in the bacterial community structure. Nutrient levels, environmental factors and MCs (especially MC_YR) jointly affected the bacterial community in lakes, namely its diversity and community assembly. The cascading effects in lakes mediated by environmental conditions, phytoplankton community composition, RUE, community turnover, and MCs on bacterial communities were revealed in this study. These findings underscore the importance of relating phytoplankton community change and MCs to the bacterial community, which is fundamental for better understanding the lake ecosystem functioning and potential risks of MCs.

Insights in Pharmaceutical Pollution: The Prospective Role of eDNA Metabarcoding

Environmental pollution is a growing threat to natural ecosystems and one of the world's most pressing concerns. The increasing worldwide use of pharmaceuticals has elevated their status as significant emerging contaminants. Pharmaceuticals enter aquatic environments through multiple pathways related to anthropogenic activity. Their high consumption, insufficient waste treatment, and the incapacity of organisms to completely metabolize them contribute to their accumulation in aquatic environments, posing a threat to all life forms. Various analytical methods have been used to quantify pharmaceuticals. Biotechnology advancements based on next-generation sequencing (NGS) techniques, like eDNA metabarcoding, have enabled the development of new methods for assessing and monitoring the ecotoxicological effects of pharmaceuticals. eDNA metabarcoding is a valuable biomonitoring tool for pharmaceutical pollution because it (a) provides an efficient method to assess and predict pollution status, (b) identifies pollution sources, (c) tracks changes in pharmaceutical pollution levels over time, (d) assesses the ecological impact of pharmaceutical pollution, (e) helps prioritize cleanup and mitigation efforts, and (f) offers insights into the diversity and composition of microbial and other bioindicator communities. This review highlights the issue of aquatic pharmaceutical pollution while emphasizing the importance of using modern NGS-based biomonitoring actions to assess its environmental effects more consistently and effectively.

Evaluation of sediment dredging in remediating toxic metal contamination - a systematic review

Toxic metal pollution is a leading environmental concern for aquatic systems globally, and remedial dredging has been widely employed to mitigate its harmful impacts. In terms of the short-term impacts of remedial dredging, mixed results are reported in several studies. Despite its immediate negative impacts including saturation of water with toxic metals, increased turbidity, and sediment resuspension, positive impacts can be recorded over a stabilization period of 6-24 months after dredging. Nevertheless, the sustainability of these recorded positive effects cannot be ascertained as some studies have reported long-term regression in remediated sites' conditions. Evaluation of success determinants, site-measure compatibility, and determination of supplementary measures are keys to achieving and sustaining the projected benefits of remedial dredging and justifying its overall cost. This multicomponent study reviewed published literatures that documented the outcomes of short- and long-term dredging projects in toxic metal-polluted systems globally with a broad goal of examining how sediment removal impacts toxic metal dynamics in the aquatic system and understanding why the sustenance of positive impacts is controversial. In the meantime, this study also explored the preventative and remedial management strategies for attaining and sustaining positive dredging outcomes. The purpose of this study is to provide key recommendations for decision-making and policy development in aquatic toxic metal remediation.

The increasing role of structural proteomics in cyanobacteria

Cyanobacteria, also known as blue–green algae, are ubiquitous organisms on the planet. They contain tremendous protein machineries that are of interest to the biotechnology industry and beyond. Recently, the number of annotated cyanobacterial genomes has expanded, enabling structural studies on known gene-coded proteins to accelerate. This review focuses on the advances in mass spectrometry (MS) that have enabled structural proteomics studies to be performed on the proteins and protein complexes within cyanobacteria. The review also showcases examples whereby MS has revealed critical mechanistic information behind how these remarkable machines within cyanobacteria function.

Does filter pore size introduce bias in DNA sequence-based plankton community studies?

The cell size of microbial eukaryotic plankton normally ranges from 0.2 to 200 μm. During the past decade, high-throughput sequencing of DNA has been revolutionizing their study on an unprecedented scale. Nonetheless, it is currently unclear whether we can accurately, effectively, and quantitatively depict the microbial eukaryotic plankton community using size-fractionated filtration combined with environmental DNA (eDNA) molecular methods. Here we assessed the microbial eukaryotic plankton communities with two filtering strategies from two subtropical reservoirs, that is one-step filtration (0.2–200 μm) and size-fractionated filtration (0.2–3 and 3–200 μm). The difference of 18S rRNA gene copy abundance between the two filtering treatments was less than 50% of the 0.2–200 μm microbial eukaryotic community for 95% of the total samples. Although the microbial eukaryotic plankton communities within the 0.2–200 μm and the 0.2–3 and 3–200 μm size fractions had approximately identical 18S rRNA gene copies, there were significant differences in their community composition. Furthermore, our results demonstrate that the systemic bias introduced by size-fractionation filtration has more influence on unique OTUs than shared OTUs, and the significant differences in abundance between the two eukaryotic plankton communities largely occurred in low-abundance OTUs in specific seasons. This work provides new insights into the use of size-fractionation in molecular studies of microbial eukaryotes populating the plankton.

Can biogenic n-heptadecane be utilized to represent algae cell density dynamics in water environment? Evidences from field investigation and laboratory validation

The monitoring and prediction of algae cell density are the fundamental supports for eutrophication management. As the molecular marker of algae, n-heptadecane has been successfully utilized to reflect algae biomass in sedimentary studies. However, whether biogenic n-heptadecane (bio C17) can be utilized to represent algae cell density dynamics in water environment still remains an issue. Current study aims to provide novel evidences from both field investigation and laboratory validation for it. Firstly, we found a strinkingly positive correlation between algae cell density dynamics and bio C17 variations (p = 4.34 × 10-10) via meta-analysis using field dataset in Lake Chaohu. Then, we selected Microcystis aeruginosa, Chlorella vulgaris and Melosira sp. as model species of cyanobacteria, green algae and diatom, respectively, for laboratory validation. Our results illustrated that n-heptadecane was synchronized with the growth for cyanobacteria and green algae but not for diatom. The association between bio C17 and algae cell density was species-dependent, and the relationship between bio C17 and cell density was linear within 107 cells∙mL-1. Therefore, we established and optimized a generalized additive model to fit observed algae cell density in Lake Chaohu. In the optimal model, bio C17, Pielou evenness index J and Shannon-Wiener index H' were included, totally explaining 66% of the variance of algae cell density. Model comparisons revealed that considering algae community could indeed improve the interpretation of algae cell density in natural environment. In conclusion, our study provided novel evidences that bio C17 can be utilized to represent the cell density dynamics of cyanobacteria and green algae in the environment.

Eco-bioengineering tools in ecohydrological assessment of eutrophic water bodies

Eutrophication of water bodies and deterioration of water quality are emerging environmental crises. The root causes and consequences of eutrophication are multidirectional. Thus, they provide a huge scope of risk-analysis and risk-assessment in the domain of remediation studies. However, recent restoration studies reveal a global trend of utilizing traditional restoration methods combined with advanced pioneer innovative techniques developed in the field of science and technology. This review introduces a novel approach to consider ecohydrological assessment of eutrophication by classical biomanipulation practices emphasising on their evolution into innovative 'eco-bioengineering' methods. The main objective of this study is to critically analyse and recognize the research gaps in classical biomanipulation and appreciate the reproducibility and efficacy of eco-bioengineering methods at micro- and macrolevel aquatic ecosystems. Comprehensive literature review was conducted on offline and online platforms. Our survey revealed (a) continuation of a historical trend in classical biomanipulation practices (61.64%) and (b) an ascending drift in eco-bioengineering research (38.36%) in the last decade (2010-2021). At a global scale, recent biomanipulation research has a skewed distribution in Europe (41.10%), East Asia (32.88%), North America (10.96%), South Africa (4.11%), South America (2.74%), Middle East (1.37%), Oceania (1.37%), and non-specific regions (5.48%). Finally, this review analysis revealed the comprehensiveness of eco-bioengineering methods and their strong ecological resilience to recurrence of eutrophication and fluctuating environmental flows in the future. Therefore, our review reinforces the supremacy of eco-bioengineering methods as cost-effective green technologies providing sustainable solutions to restore the eutrophic waters at a global scale.

eDNA revealed in situ microbial community changes in response to Trapa japonica in Lake Qionghai and Lake Erhai, southwestern China

Trapa japonica was observed to have inhibiting effects and could be used as a potential environment-friendly control strategy for cyanobacterial blooms in freshwater. However, the changes and effecting mechanisms in eukaryotic and prokaryotic communities by T. japonica are not yet clear. In this study, the effects of T. japonica on microbial communities were assessed in Lake Qionghai and Lake Erhai by 18S rRNA and 16S rRNA amplicon sequencing, respectively. The results showed that T. japonica can improve biodiversity and change the microbial community structures to varying degrees in both lakes. The alpha diversity indexes of microbial communities (e.g., Shannon, Sobs, Ace and Chao 1) were higher in the water inhabited by T. japonica (TJ group) than the water uninhabited by T. japonica (control) (P < 0.05). The PCoA results suggested that the microbial community compositions differed between the two groups (PERMANOVA P = 0.001). In Lake Qionghai, the relative abundances of dominant taxa and nutrients level showed little differences between the two groups. These may result from the homogenous water condition in Lake Qionghai. While the genera Cyanobium_PCC-6307, the majority of Cyanobacteria, decreased significantly in TJ group than control according to 16S rRNA gene sequencing. In Lake Erhai, environmental variables were distinctly affected by T. japonica, which was found to drive Cryptophyceae to become the main taxa through taxonomic analysis of 18S rRNA. Based on 16S rRNA gene sequencing, T. japonica reduced the relative abundance of Cyanobacteria, such as Planktothrix_NIVA-CYA_15 and Cyanobium_PCC-6307, by enriching cyanobactericidal bacteria and growth-inhibiting bacteria (e.g., Limnohabitans and Flavobacterium) and changing environmental parameters. Our results revealed that T. japonica acts in shaping microbial communities in lakes on the community level, shedding new lights on eutrophication mitigation, one of the most serious global ecological problems we are facing.

Comparative growth characteristics and interspecific competitive interaction of two cyanobacteria, Phormidium autumnale and Nostoc sp.

This study examined the growth characteristics and competitive interaction of two cyanobacteria, Phormidium autumnale GJ_2B_I1 and Nostoc sp. DS_2B_I1, which were newly isolated from a southeast river (Nakdong) during the cyanobacterial harmful algal bloom (CyanoHAB) season in Korea. As major environmental parameters, water temperature (25 and 30 °C) and alkalinity (19-78 mg CaCO₃ L^-1 ) and nitrate concentration (1.5-3.5 mg NO₃ -N L^-1 ) were selected based on the water environmental monitoring data during the CyanoHAB season. Unlike P. autumnale, Nostoc sp. has a relatively high growth rate under both monoculture and co-culture and prefers the maximum environmental conditions (30 °C and 78 mg CaCO₃ L^-1 ; pH 9) during the CyanoHAB season. In addition, the growth of P. autumnale is relatively unaffected by alkalinity. Nitrogen (N) stress also has a limiting effect in the interspecific interactions of both cyanobacterial strains. All other cases except for Nostoc sp. in a co-culture showed a considerable increase in growth rate with increasing N content (1.5-3.5 mg NO₃ -N L^-1 ), showing 20-64% under the minimum field conditions (25 °C and 19 mg CaCO₃ L^-1 ; pH 7) and 18-140% under the maximum field conditions. The results show that the growth of P. autumnale can be stimulated by enhanced N stress. On the other hand, Nostoc sp. is less affected by N stress compared with P. autumnale. Therefore, it has excellent potential to be a major group of CyanoHABs because of their relatively high growth rate, particularly in the range of N tested.

Genetic detection of freshwater harmful algal blooms: A review focused on the use of environmental DNA (eDNA) in Microcystis aeruginosa and Prymnesium parvum

Recurrence and severity of harmful algal blooms (HABs) are increasing due to a number of factors, including human practices and climate change. Sensitive and robust methods that allow for early and expedited HAB detection across large landscape scales are needed. Among the suite of HAB detection tools available, a powerful option exists in genetics-based approaches utilizing environmental sampling, also termed environmental DNA (eDNA). Here we provide a detailed methodological review of three HAB eDNA approaches (quantitative PCR, high throughput sequencing, and isothermal amplification). We then summarize and synthesize recently published eDNA applications covering a variety of HAB surveillance and research objectives, all with a specific emphasis in the detection of two widely problematic freshwater species, Microcystis aeruginosa and Prymnesium parvum. In our summary and conclusion we build on this literature by discussing ways in which eDNA methods could be advanced to improve HAB detection. We also discuss ways in which eDNA data could be used to potentially provide novel insight into the ecology, mitigation, and prediction of HABs.

Experimental Study of the Adsorption of Nitrogen and Phosphorus by Natural Clay Minerals

Nitrogen and phosphorus are commonly recognized as causing eutrophication in aquatic systems, and their transport in subsurface environments has also aroused great public attention. This research presented four natural clay minerals (NCMs) evaluated for their effectiveness of NH4+ and PO43- adsorption from wastewater. All the NCMs were fully characterized by X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), BET analysis, and adsorption kinetics and isotherms to better understand the adsorption mechanism-property relationship. The results show that the adsorption efficiency of the four NCMs for phosphate was better than that for ammonia nitrogen. The removal rate of phosphate was higher than 65%, generally in the range of 80%-90%, while the removal rate of ammonia nitrogen was less than 50%. The adsorption kinetic behavior followed the pseudo-second-order kinetic model. The ammonia nitrogen adsorption isotherm was in good agreement with the Freundlich isotherm equilibrium model, and the phosphate adsorption isotherm matched the Langmuir model. Among all the NCMs studied, bentonite (7.13 mg/g) and kaolinite (5.37 mg/g) showed higher adsorption capacities for ammonia nitrogen, while zeolite (0.21 mg/g) and attapulgite (0.17 mg/g) showed higher adsorption capacities for phosphate. This study provides crucial baseline knowledge for the adsorption of nitrogen and phosphate by different kinds of NCMs.

Retrieval and Evaluation of Chlorophyll-a Concentration in Reservoirs with Main Water Supply Function in Beijing, China, Based on Landsat Satellite Images

Remote sensing retrieval is an important technology for studying water eutrophication. In this study, Guanting Reservoir with the main water supply function of Beijing was selected as the research object. Based on the measured data in 2016, 2017, and 2019, and Landsat-8 remote sensing images, the concentration and distribution of chlorophyll-a in the Guanting Reservoir were inversed. We analyzed the changes in chlorophyll-a concentration of the reservoir in Beijing and the reasons and effects. Although the concentration of chlorophyll-a in the Guanting Reservoir decreased gradually, it may still increase. The amount and stability of water storage, chlorophyll-a concentration of the supply water, and nitrogen and phosphorus concentration change are important factors affecting the chlorophyll-a concentration of the reservoir. We also found a strong correlation between the pixel values of adjacent reservoirs in the same image, so the chlorophyll-a estimation model can be applied to each other.

A sustainable approach by using microalgae to minimize the eutrophication process of Mar Menor lagoon

The present study evaluates the removal capacity of microalgae photobioreactors of environmental pollutants present in wastewater from the dry riverbed El Albujón, as a way to minimize the eutrophication process of the Mar Menor. Particularly, the capacity of four autochthonous microalgae consortia collected from different locations of the salty lagoon to remove emerging contaminants (simazine, atrazine, terbuthylazine, adenosine and ibuprofen), nitrates, and phosphates, was evaluated. Among the four microalgae consortia, consortium 1 was the best in terms of biomass productivity (0.11 g L^-1 d^-1) and specific growth rate (0.14 d^-1), providing 100% removal of emerging contaminants (simazine, atrazine, terbuthylazine, adenosine and ibuprofen), and a maximal reduction and consumption of macronutrients, especially nitrates and phosphates, reaching levels below 28 mg L^-1, that is, a decrease of 89.90 and 99.70% of nitrates and phosphates, respectively. Therefore, this consortium (Monoraphidium sp., Desmodesmus subspicatus, Nannochloris sp.) could be selected as a green filter for successful large-scale applications. This study is the first one that combines the successful removal of herbicides, ibuprofen and adenosine as emerging contaminants, and nitrate removal.

Environmental DNA and RNA as Records of Human Exposome, Including Biotic/Abiotic Exposures and Its Implications in the Assessment of the Role of Environment in Chronic Diseases

Most of environment-related diseases often result from multiple exposures of abiotic and/or biotic stressors across various life stages. The application of environmental DNA/RNA (eDNA/eRNA) to advance ecological understanding has been very successfully used. However, the eminent extension of eDNA/eRNA-based approaches to estimate human exposure to biotic and/or abiotic environmental stressors to understand the environmental causes of chronic diseases has yet to start. Here, we introduce the potential of eDNA/eRNA for bio-monitoring of human exposome and health effects in the real environmental or occupational settings. This review is the first of its kind to discuss how eDNA/eRNA-based approaches can be applied for assessing the human exposome. eDNA-based exposome assessment is expected to rely on our ability to capture the genome- and epigenome-wide signatures left behind by individuals in the indoor and outdoor physical spaces through shedding, excreting, etc. Records of eDNA/eRNA exposome may reflect the early appearance, persistence, and presence of biotic and/or abiotic-exposure-mediated modifications in these nucleic acid molecules. Functional genome- and epigenome-wide mapping of eDNA offer great promise to help elucidate the human exposome. Assessment of longitudinal exposure to physical, biological, and chemical agents present in the environment through eDNA/eRNA may enable the building of an integrative causal dynamic stochastic model to estimate environmental causes of human health deficits. This model is expected to incorporate key biological pathways and gene networks linking individuals, their geographic locations, and random multi-hits of environmental factors. Development and validation of monitoring of eDNA/eRNA exposome should seriously be considered to introduce into safety and risk assessment and as surrogates of chronic exposure to environmental stressors. Here we highlight that eDNA/eRNA reflecting longitudinal exposure of both biotic and abiotic environmental stressors may serve as records of human exposome and discuss its application as molecular tools for understanding the toxicogenomics basis of environment-related health deficits.