Environmental DNA Metabarcoding Research Articles

The Tree of Life eDNA metabarcoding reveals a similar taxonomic richness but dissimilar evolutionary lineages between seaports and marine reserves.

Coastal areas host a major part of marine biodiversity but are seriously threatened by ever-increasing human pressures. Transforming natural coastlines into urban seascapes through habitat artificialization may result in loss of biodiversity and key ecosystem functions. Yet, the extent to which seaports differ from nearby natural habitats and marine reserves across the whole Tree of Life is still unknown. This study aimed to assess the level of α and β-diversity between seaports and reserves, and whether these biodiversity patterns are conserved across taxa and evolutionary lineages. For that, we used environmental DNA (eDNA) metabarcoding to survey six seaports on the French Mediterranean coast and four strictly no-take marine reserves nearby. By targeting four different groups-prokaryotes, eukaryotes, metazoans and fish-with appropriate markers, we provide a holistic view of biodiversity on contrasted habitats. In the absence of comprehensive reference databases, we used bioinformatic pipelines to gather similar sequences into molecular operational taxonomic units (MOTUs). In contrast to our expectations, we obtained no difference in MOTU richness (α-diversity) between habitats except for prokaryotes and threatened fishes with higher diversity in reserves than in seaports. However, we observed a marked dissimilarity (β-diversity) between seaports and reserves for all taxa. Surprisingly, this biodiversity signature of seaports was preserved across the Tree of Life, up to the order. This result reveals that seaports and nearby marine reserves share few taxa and evolutionary lineages along urbanized coasts and suggests major differences in terms of ecosystem functioning between both habitats.

Cost-effort analysis of Baited Remote Underwater Video (BRUV) and environmental DNA (eDNA) in monitoring marine ecological communities.

Monitoring the diversity and distribution of species in an ecosystem is essential to assess the success of restoration strategies. Implementing biomonitoring methods, which provide a comprehensive assessment of species diversity and mitigate biases in data collection, holds significant importance in biodiversity research. Additionally, ensuring that these methods are cost-efficient and require minimal effort is crucial for effective environmental monitoring. In this study we compare the efficiency of species detection, the cost and the effort of two non-destructive sampling techniques: Baited Remote Underwater Video (BRUV) and environmental DNA (eDNA) metabarcoding to survey marine vertebrate species. Comparisons were conducted along the Sussex coast upon the introduction of the Nearshore Trawling Byelaw. This Byelaw aims to boost the recovery of the dense kelp beds and the associated biodiversity that existed in the 1980s. We show that overall BRUV surveys are more affordable than eDNA, however, eDNA detects almost three times as many species as BRUV. eDNA and BRUV surveys are comparable in terms of effort required for each method, unless eDNA analysis is carried out externally, in which case eDNA requires less effort for the lead researchers. Furthermore, we show that increased eDNA replication yields more informative results on community structure. We found that using both methods in conjunction provides a more complete view of biodiversity, with BRUV data supplementing eDNA monitoring by recording species missed by eDNA and by providing additional environmental and life history metrics. The results from this study will serve as a baseline of the marine vertebrate community in Sussex Bay allowing future biodiversity monitoring research projects to understand community structure as the ecosystem recovers following the removal of trawling fishing pressure. Although this study was regional, the findings presented herein have relevance to marine biodiversity and conservation monitoring programs around the globe.

An eDNA metabarcoding of brittle stars: Examples from the Seto Inland Sea, a semi-closed marine area

Marine ecosystem are facing a crisis due to climate change and anthropogenic activities, and many marine organisms are threatened by declining biodiversity. Regular and extensive surveys of these organisms are necessary to conserve the biodiversity. Conventional methods, however, rely on direct observation and collection of specimens by experts with identification and sampling skills. Using environmental DNA (eDNA) metabarcoding methods, we detected a total of 15 brittle star species at two sites in the Seto Inland Sea, a semi-enclosed marine area in Japan. This study showed that brittle stars are useful environmental indicator organisms, and that the eDNA metabarcoding method specific to brittle star is expected to be a useful tool for a wide-ranging and simple investigation method for marine ecosystems. Further investigations will need to verify whether species detected by metabarcoding without being confirmed by direct observations are due to false positives and whether this is due to the semi-enclosed character of the area.

Environmental DNA-based biodiversity profiling along the Houdong River in north-eastern Taiwan.

This paper describes two datasets: species occurrences, which were determined by environmental DNA (eDNA) metabarcoding and their associated DNA sequences, originating from a research project which was carried out along the Houdong River (), Jiaoxi Township, Yilan, Taiwan. The Houdong River begins at an elevation of 860 m and flows for approximately 9 km before it empties into the Pacific Ocean. Meandering through mountains, hills, plains and alluvial valleys, this short river system is representative of the fluvial systems in Taiwan. The primary objective of this study was to determine eukaryotic species occurrences in the riverine ecosystem through the use of the eDNA analysis. The second goal was, based on the current dataset, to establish a metabarcoding eDNA data template that will be useful and replicable for all users, particularly the Taiwan community. The species occurrence data are accessible at the Global Biodiversity Information Facility (GBIF) portal and its associated DNA sequences have been deposited in the European Nucleotide Archive (ENA) at EMBL-EBI, respectively. A total of 12 water samples from the study yielded an average of 1.5 million reads. The subsequent species identification from the collected samples resulted in the classification of 432 Operational Taxonomic Units (OTUs) out of a total of 2,734. Furthermore, a total of 1,356 occurrences with taxon matches in GBIF were documented (excluding 4,941 incertae sedis, accessed 05-12-2023). These data will be of substantial importance for future species and habitat monitoring within the short river, such as assessment of biodiversity patterns across different elevations, zonations and time periods and its correlation to water quality, land uses and anthropogenic activities. Further, these datasets will be of importance for regional ecological studies, in particular the freshwater ecosystem and its status in the current global change scenarios. The datasets are the first species diversity description of the Houdong River system using either eDNA or traditional monitoring processes.

Phytophthora Communities Associated with Agathis australis (kauri) in Te Wao Nui o Tiriwa/Waitākere Ranges, New Zealand

Studies of Phytophthora impact in forests generally focus on individual species without recognition that Phytophthora occur in multispecies communities. This study investigated community structure of Phytophthora species in the rhizosphere of Agathis australis (kauri) in Te Wao Nui o Tiriwa/Waitākere Ranges, New Zealand, in the context of kauri dieback disease expression. Soil sampling and tree monitoring were conducted on 767 randomly selected mature kauri trees. Phytophthora species were detected using both soil baiting and DNA metabarcoding of environmental DNA (eDNA). Four species were detected with soil baiting (P. agathidicida, P. cinnamomi, P. multivora, and P. pseudocryptogea/P. cryptogea) and an additional three species with metabarcoding (P. kernoviae, P. cactorum/P. aleatoria and an unknown clade 7 species). Phytophthora cinnamomi was the most abundant species and was distributed throughout the forest. Both P. multivora and P. agathidicida were limited to forest edges, suggesting more recent introductions. P. agathidicida presence was strongly correlated with declining canopy health, confirming its role as the main driver of kauri dieback. The limited distribution of P. agathidicida and infrequent detections (11.0% samples) suggests that that this species is spreading as an introduced invasive pathogen and provide hope that with strategic management (including track upgrades and closures, restricting access to uninfected areas, and continual monitoring) uninfected areas of the forest can be protected. The frequent detections of P. cinnamomi and P. multivora from symptomatic trees in the absence of P. agathidicida suggest more research is needed to understand their roles in kauri forest health.

The Soil Microbiomes of American Ginseng (Panax quinquefolius) Cultivated in North America Differ by Location But Not Always by Disease Status

One of the greatest challenges faced by ginseng producers is control of fungal pathogens which adversely affects harvest yields and is a contributing factor to replant failure syndrome. The goal of this project was to survey the soil microbiome of healthy versus diseased American Ginseng grown in North America. Soil associated with healthy and diseased plants were collected from commercial farms in Garett County, Maryland and Marathon County, Wisconsin. Environmental DNA metabarcoding was used to compare the bacterial and fungal microbiomes of healthy versus diseased plants from both locations. The most common bacteria occurred within the phylum Proteobacteria, Firmicutes, and Bacteroidota and the most common fungi occurred within Ascomycota, Basidiomytoca, Mortierellomycota and Glomeromycota. Overall Alpha- and Beta- diversities were statistically significant between the two locations. Community analyses (beta-diversity) of the Maryland site revealed a significant difference in the bacterial composition of soils associated with healthy versus diseased plants but not fungi. Conversely, there was a significantly different assemblage of fungi in healthy versus diseased associated soils from the Wisconsin site, but not for bacteria. Our results when compared to previous metabarcoding studies suggest there is little congruence between the soil microbiomes associated with cultivated ginseng and that we are still in the early stages of ginseng soil rhizosphere exploration.

Combining environmental DNA and visual surveys can inform conservation planning for coral reefs

Environmental DNA (eDNA) metabarcoding has the potential to revolutionize conservation planning by providing spatially and taxonomically comprehensive data on biodiversity and ecosystem conditions, but its utility to inform the design of protected areas remains untested. Here, we quantify whether and how identifying conservation priority areas within coral reef ecosystems differs when biodiversity information is collected via eDNA analyses or traditional visual census records. We focus on 147 coral reefs in Indonesia's hyper-diverse Wallacea region and show large discrepancies in the allocation and spatial design of conservation priority areas when coral reef species were surveyed with underwater visual techniques (fishes, corals, and algae) or eDNA metabarcoding (eukaryotes and metazoans). Specifically, incidental protection occurred for 55% of eDNA species when targets were set for species detected by visual surveys and 71% vice versa. This finding is supported by generally low overlap in detection between visual census and eDNA methods at species level, with more overlap at higher taxonomic ranks. Incomplete taxonomic reference databases for the highly diverse Wallacea reefs, and the complementary detection of species by the two methods, underscore the current need to combine different biodiversity data sources to maximize species representation in conservation planning.

Diet breadth of a critically endangered owl presents challenges for invasive rodent management: a conservation conundrum

ABSTRACT Trophic interactions between threatened species complicate management. Similarly, interactions between threatened species and pest species present management challenges, given that pest control can lead to non-target impacts (e.g. trophic cascades or secondary poisoning). There are records of the critically endangered Norfolk Island Morepork Ninox novaeseelandiae undulata consuming both threatened songbirds and invasive rodents that are subject to management interventions. Nevertheless, the diet of the morepork remains largely unknown. We visually screened regurgitated pellets using a microscope, alongside environmental DNA (eDNA) screening of pellets and scats, to investigate the diet of the Norfolk Island Morepork. A total of 113 pellets and 19 scats were collected between October 2020 and June 2021. All moreporks screened with eDNA metabarcoding had consumed invasive rodents and at least one-third of samples contained rodents. The owls were also found to have consumed four of five endemic songbirds and possibly an endemic parrot, most of which are threatened. Environmental DNA metabarcoding detected more taxa overall, but visual screening identified a greater richness of Orthoptera and Coleoptera in the diet. The frequency with which the Norfolk Island Morepork consumed rodents presents a conundrum for conservation managers. Control of invasive rodents is considered essential to support threatened songbirds, yet this same action places the species at risk of secondary poisoning. Urgent investigations are needed to identify effective control methods for invasive rodents that are safe for non-target species.

Dynamics and drivers of mycorrhizal fungi after glacier retreat.

The development of terrestrial ecosystems depends greatly on plant mutualists such as mycorrhizal fungi. The global retreat of glaciers exposes nutrient-poor substrates in extreme environments and provides a unique opportunity to study early successions of mycorrhizal fungi by assessing their dynamics and drivers. We combined environmental DNA metabarcoding and measurements of local conditions to assess the succession of mycorrhizal communities during soil development in 46 glacier forelands around the globe, testing whether dynamics and drivers differ between mycorrhizal types. Mycorrhizal fungi colonized deglaciated areas very quickly (< 10 yr), with arbuscular mycorrhizal fungi tending to become more diverse through time compared to ectomycorrhizal fungi. Both alpha- and beta-diversity of arbuscular mycorrhizal fungi were significantly related to time since glacier retreat and plant communities, while microclimate and primary productivity were more important for ectomycorrhizal fungi. The richness and composition of mycorrhizal communities were also significantly explained by soil chemistry, highlighting the importance of microhabitat for community dynamics. The acceleration of ice melt and the modifications of microclimate forecasted by climate change scenarios are expected to impact the diversity of mycorrhizal partners. These changes could alter the interactions underlying biotic colonization and belowground-aboveground linkages, with multifaceted impacts on soil development and associated ecological processes.

Exploring fish communities in the mud volcano polluted river using environmental DNA metabarcoding

In ecosystems subjected to environmental disturbances such as mud volcanoes, understanding the dynamics of fish communities is essential for ecological assessment and conservation. This study employs environmental DNA (eDNA) metabarcoding for the first time to explore fish communities within a challenging and unique environment—a mud volcano-polluted river. High-throughput sequencing was utilized to assess alpha and beta diversity, revealing distinct patterns in fish community composition in response to mud discharge activity. The results indicate that affected sites exhibit remarkably different communities during active and inactive mud discharge, with the impact extending downstream to the river mouth. Notably, the application of eDNA metabarcoding identified a vulnerable species, Rasbora lateristriata, emphasizing its utility in detecting high-risk species. Despite challenges in species identification and reference databases, the use of longer 16S rRNA fragments offered enhanced taxonomic resolution and interspecific sequence variation. This approach showcases the potential of eDNA metabarcoding in assessing fish diversity and community dynamics in polluted aquatic ecosystems, emphasizing its significance in biodiversity surveys and ecological monitoring. The study underscores the value of eDNA metabarcoding as an efficient and comprehensive tool for studying freshwater ecosystems and highlights the need for expanding reference databases to address genetic coverage gaps, particularly in less-studied environments.

Comparative assessment of eDNA metabarcoding and longline deployments for elasmobranch surveying across a large tropical marine park network

Abstract Medium‐ to large‐scale marine protected areas (MPAs) are playing an increasingly important role in global marine biodiversity conservation. A key question is “how do we collect relevant data on biodiversity and population trends to inform their design and measure success?” This question is particularly relevant for marine taxa that are difficult to survey, such as sharks and rays, and where populations may occur over vast areas. Environmental DNA (eDNA) metabarcoding has proven to be an effective sampling method and may provide a solution to these challenges; however, it remains unclear how its sampling effectiveness compares with traditionally used methods for elasmobranch surveying. Here, we directly compared the efficacy of eDNA metabarcoding and demersal longline deployments to survey elasmobranchs across 31 sites over a 55,000 km2 area of the Kimberley and Roebuck Australian Marine Parks in Australia's North‐west Marine Parks Network. In total, we documented 49 unique elasmobranch taxa, 36 of which were detected by eDNA and 32 (from a total of 815 captured sharks) by longline. A combined approach yielded over 34% more elasmobranch taxa than either method alone. Site community compositions varied between the two survey methods; notably eDNA was able to detect species from outside of the immediate sampling area, although this was still consistent with a detection radius of a few kilometres, highlighting a particular use in rugose reef habitats where it is difficult to deploy longlines. In investigating the quantitative use of eDNA data, we report that eDNA metabarcoding read abundance (count) data was poorly correlated with longline aggregate catch (count and biomass) data across raw, relative and rank abundance measures. However, we found that in multivariate analyses, both binary (presence–absence) and abundance (after square‐root transformation) datasets produced highly similar ordination patterns, largely segregating method (eDNA vs. longline), followed by latitude and depth. Lastly, we identified required levels of eDNA replication and longline deployments to maximize captured elasmobranch diversity. This study sets an integrated, georeferenced baseline and long‐term monitoring approach for the management and conservation of elasmobranch diversity within this unique marine park network.

Environmental DNA highlights the influence of salinity and agricultural run-off on coastal fish assemblages in the Great Barrier Reef region

Agricultural run-off in Australia’s Mackay-Whitsunday region is a major source of nutrient and pesticide pollution to coastal and inshore ecosystems of the Great Barrier Reef. While the effects of run-off are well documented for the region’s coral and seagrass habitats, the ecological impacts on estuaries, the direct recipients of run-off, are less known. This is particularly true for fish communities, which are shaped by the physico-chemical properties of coastal waterways that vary greatly in tropical regions. To address this knowledge gap, we used environmental DNA (eDNA) metabarcoding to examine fish assemblages at four locations (three estuaries and a harbour) subjected to varying levels of agricultural run-off during a wet and dry season. Pesticide and nutrient concentrations were markedly elevated during the sampled wet season with the influx of freshwater and agricultural run-off. Fish taxa richness significantly decreased in all three estuaries (F = 164.73, P = <0.001), along with pronounced changes in community composition (F = 46.68, P = 0.001) associated with environmental variables (largely salinity: 27.48% contribution to total variance). In contrast, the nearby Mackay Harbour exhibited a far more stable community structure, with no marked changes in fish assemblages observed between the sampled seasons. Among the four sampled locations, variation in fish community composition was more pronounced within the wet season (F = 2.5, P = 0.001). Notably, variation in the wet season was significantly correlated with agricultural contaminants (phosphorus: 6.25%, pesticides: 5.22%) alongside environmental variables (salinity: 5.61%, DOC: 5.57%). Historically contaminated and relatively unimpacted estuaries each demonstrated distinct fish communities, reflecting their associated catchment use. Our findings emphasise that while seasonal effects play a key role in shaping the community structure of fish in this region, agricultural contaminants are also important contributors in estuarine systems.

Environmental heterogeneity caused by large-scale cultivation of Pyropia haitanensis shapes multi-group biodiversity distribution in coastal areas

The response of marine biodiversity to mariculture has long been a research focus in marine ecology. However, the effects of seaweed cultivation on biological community assembly are poorly understood, especially in diverse communities with distinct ecological characteristics. In this study, we used environmental DNA metabarcoding to investigate the spatial distribution patterns of bacterial, protistan, and metazoan diversity, aiming to reveal the mechanisms of community assembly in the Pyropia haitanensis cultivation zone along the Fujian coast, China. We found that, compared with the biological communities in control zones, those in P. haitanensis cultivation zones exhibited stronger geographic distance-decay patterns and displayed more complex and stable network structures. Deterministic processes (environmental selection) played a more important role in the assembly of bacterial, protistan, and metazoan communities in P. haitanensis cultivation zones, especially metazoan communities. Variance partitioning analysis showed that environmental variables made greater contributions to the diversity of the three types of communities within the P. haitanensis cultivation zones than in the control zones. Partial least squares path modeling analysis identified nitrate‑nitrogen (NO3-N), pH, particulate organic carbon (POC), and dissolved organic carbon (DOC) as the key environmental variables affecting biodiversity. Overall, the environmental heterogeneity caused by the large-scale cultivation of P. haitanensis could be the crucial factor influencing the composition and structure of various biological communities. Our results highlight the importance of the responses of multi-group organisms to the cultivation of seaweed, and provide insights into the coexistence patterns of biodiversity at the spatial scale.

Examination of the Utility of Environmental DNA Metabarcoding for Monitoring Fish Species in Han Rivr, Korea

Han River in Korea is a crucial water resource and fish habitat. Nonetheless, its biodiversity is declining because of anthropogenic activities, particularly pollution. Fish species sensitive to environmental changes are monitored to conserve biodiversity and pollution monitoring. Fish species can be monitored based on environmental DNA (eDNA) which is released by organisms into the environment eDNA metabarcoding can compensate for the difficulties of collection-based fish monitoring and can be used for efficient monitoring. This study aimed to examine the utility of eDNA metabarcoding for monitoring fish species by performing eDNA metabarcoding of fish 12S rRNA from water samples collected from three locations in the Han River. The results were compared with collection-based survey data from the Water Environment Information System (Ministry of Environment of Korea) from the last three years. The results revealed 32 species that were identified in three locations through eDNA metabarcoding analysis. At all locations, eDNA metabarcoding detected 74.4% of the 43 fish species compared with the collection-based survey data, confirming as a valuable tool for monitoring fish species in Han River. Additionally, eDNA metabarcoding can be used as a tool to compensate for the limitations of collection-based surveys by detecting species with hiding characteristics and nocturnal species that are difficult to detect in collection-based surveys. The results of this study can be used as primary data to contribute to the conservation of fish biodiversity in Han River in the future.

Environmental DNA metabarcoding for the detection of the silverlip pearl oyster (Pinctada maxima) offshore of Eighty Mile Beach in northwest Australia

Effective fishery management relies on accurate knowledge of the spatial distribution of stocks of target species to efficiently focus fishing efforts. However, the distribution and abundance of species such as the silverlip pearl oyster (Pinctada maxima) can be difficult to determine with traditional survey methods since populations are patchy, often occur in low densities, and individuals can be quite cryptic, living partially buried in sediment. Environmental DNA is increasingly used to survey marine species and has proven to be particularly useful in detecting rare or elusive organisms. Here, we compared the presence of silverlip pearl oysters detected via eDNA metabarcoding to traditional towed video surveys offshore of Eighty Mile Beach, northwest Australia. Seawater samples were collected at the end of towed video transects and sites were categorised into shallow (<40 m depth) or deep (40 m +) groups. We applied an oyster-specific 16S metabarcoding assay as well as a universal 18S assay to identify potential indicator taxa associated with the presence of pearl oysters. Using the 16S assay, we detected silverlip pearl oysters at three of the 12 sites sampled, and found that eDNA records generally matched towed video transect data, with both survey methods detecting the target species predominantly in inshore waters at depths <40 m. Our results indicate that metabarcoding of seawater eDNA can be applied to detect cryptic species of commercial importance but highlight limitations around detecting organisms at very low abundances.

Evaluation of the Effects of Environmental Factors on Seasonal Variations in Fish Diversity on a Coastal Island in Western Japan

Coastal habitats are crucial for supporting ecological processes and serve as vital ecosystems for diverse fish species, providing essential functions such as feeding, nursery provision, and reproductive habitats. Fish communities are ecologically important components of coastal ecosystems and are affected by multiple environmental factors. Despite their importance, determining the effects of environmental factors on seasonal variations in fish species diversity and community dynamics remains a challenge. The advent of environmental DNA (eDNA) technology, an environmentally conscious approach, has resulted in considerable advancements in recent years and has been progressively adopted for marine fish population monitoring. Here, we used environmental DNA metabarcoding to study seasonal variations in fish community structure on a coastal island, and we assessed the effects of environmental factors in structuring these communities. Our findings revealed a rich diversity of 72 fish species across 40 families and 23 orders in the seawater surrounding an island of the Seto Inland Sea (SIS), Western Japan. Notably, the composition of fish communities varied significantly between seasons, with seawater temperature, salinity, and dissolved inorganic phosphorus (DIP) concentration identified as important factors correlated with fish communities’ structures. In conclusion, our study provides useful information of fish diversity, and we suggest that eDNA is a valuable technique for monitoring fish diversity in coastal areas. These findings are crucial for ecological studies and the environmental monitoring of oceanic coastal environments.

Microeukaryotic plankton community dynamics under ecological water replenishment: Insights from eDNA metabarcoding

Ecological water replenishment (EWR) is an important strategy for river restoration globally, but timely evaluation of its ecological effects at a large spatiotemporal scale to further adjust the EWR schemes is of great challenge. Here, we examine the impact of EWR on microeukaryotic plankton communities in three distinct river ecosystems through environmental DNA (eDNA) metabarcoding. The three ecosystems include a long-term cut-off river, a short-term connected river after EWR, and long-term connected rivers. We analyzed community stability by investigating species composition, stochastic and deterministic dynamics interplay, and ecological network robustness. We found that EWR markedly reduced the diversity and complexity of microeukaryotic plankton, altered their community dynamics, and lessened the variation within the community. Moreover, EWR disrupted the deterministic patterns of community organization, favoring dispersal constraints, and aligning with trends observed in naturally connected rivers. The shift from an isolated to a temporarily connected river appeared to transition community structuring mechanisms from deterministic to stochastic dominance, whereas, in permanently connected rivers, both forces concurrently influenced community assembly. The ecological network in temporarily connected rivers post-EWR demonstrated significantly greater stability and intricacy compared to other river systems. This shift markedly bolstered the resilience of the ecological network. The eDNA metabarcoding insights offer a novel understanding of ecosystem resilience under EWR interventions, which could be critical in assessing the effects of river restoration projects throughout their life cycle.

Employing a triple metabarcoding approach to differentiate active, dormant and dead microeukaryotes in sediments.

Microbial communities are commonly characterised through the metabarcoding of environmental DNA. This DNA originates from both viable (including dormant and active) and dead organisms, leading to recent efforts to distinguish between these states. In this study, we further these approaches by distinguishing not only between viable and dead cells but also between dormant and actively growing cells. This is achieved by sequencing both rRNA and rDNA, in conjunction with propidium monoazide cross-linked rDNA, to partition the active, dormant and relic fractions in environmental samples. We apply this method to characterise the diversity and assemblage structure of these fractions of microeukaryotes in intertidal sediments during a wet-dry-rewet incubation cycle. Our findings indicate that a significant proportion of microeukaryotic phylotypes detected in the total rDNA pools originate from dormant and relic microeukaryotes in the sediments, both in terms of richness (dormant, 13 ± 2%; relic, 47 ± 5%) and read abundance (dormant, 20 ± 7%; relic, 14 ± 5%). The richness and sequence proportion of dormant microeukaryotes notably increase during the transition from wet to dry conditions. Statistical analyses suggest that the dynamics of diversity and assemblage structure across different activity fractions are influenced by various environmental drivers. Our strategy offers a versatile approach that can be adapted to characterise other microbes in a wide range of environments.

Environmental DNA metabarcoding of pan trap water to monitor arthropod‐plant interactions

AbstractGlobally, the diversity of arthropods and the plants upon which they rely are under increasing pressure due to a combination of biotic and abiotic anthropogenic stressors. Unfortunately, conventional survey methods used to monitor ecosystems are often challenging to conduct on large scales. Pan traps are a commonly used pollinator survey method and environmental DNA (eDNA) metabarcoding of pan trap water may offer a high‐throughput alternative to aid in the detection of both arthropods and the plant resources they rely on. Here, we examined if eDNA metabarcoding can be used to identify arthropods and plant species from pan trap water, and investigated the effect of different DNA extraction methods. We then compared plant species identified by metabarcoding with observation‐based floral surveys and also assessed the contribution of airborne plant DNA (plant DNA not carried by arthropods) using marble traps to reduce putative false positives in the pan trap dataset. Arthropod eDNA was only detected in 17% of pan trap samples and there was minimal overlap between the eDNA results and morphological identifications. In contrast, for plants, we detected 64 taxa, of which 53 were unique to the eDNA dataset, and no differences were identified between the two extraction kits. We were able to significantly reduce the contribution of airborne plant DNA to the final dataset using marble traps. This study demonstrates that eDNA metabarcoding of pan trap water can detect plant resources used by arthropods and highlights the potential for eDNA metabarcoding to be applied to investigations of arthropod‐plant interactions.

Soil Fertilization with Palm Oil Mill Effluent Has a Short-Term Effect on the Bacterial Diversity of an Amazonian Agricultural Land Area.

Palm oil derived from the fruits of Elaeis guineensis Jacq. has global economic importance and is largely produced in tropical regions. The palm oil production process leads to a highly polluting waste called palm oil mill effluent (POME). A strategy commonly used by producers to overcome environmental issues and to improve soil fertility is the reuse of POME as a fertilizer due to the chemical and biological characteristics of the effluent. In this research, three groups were analyzed: soil without POME application (control group) and soil samples after 4 and 9 days of POME application. An environmental DNA metabarcoding approach was used. eDNA was extracted, and the V4 region of the 16S rRNA gene was amplified and sequenced in the Illumina MiSeq platform. The abundance of Proteobacteria (48.1%) and Firmicutes (9.0%) was higher in fertilized soil, while Bacteroidetes (20.3%) and Verrucomicrobia (7.8%) were more abundant in control soil. Additionally, the effluent seemed to modify soil characteristics favoring taxa responsible for the mineralization of organic compounds and nitrogen fixation such as species of Gammaproteobacteria class. Our study highlights the influence of POME on soil biological components and contributes to the sustainable production of palm oil in the Amazon.