Towards exhaustive community ecology via DNA metabarcoding

Development of universal PCR primers for the environmental DNA metabarcoding of cephalopod (Mollusca) diversity

Cephalopods play crucial roles in marine ecosystems, acting as both predators and prey for apex predators, thereby contributing to the distribution of energy and nutrients across the food web. Traditional net capture methods are often ineffective for studying cephalopods owing to their wide distribution in marine environments, necessitating the development of simple and efficient surveying techniques to assess cephalopod diversity. Therefore, in this study, we aimed to establish universal polymerase chain reaction primers specifically targeting mitochondrial 16S rRNA genes for environmental DNA metabarcoding in cephalopods. Two primer sets, Cep16S_D and Cep16S_O, were designed for squids and octopuses, respectively. Taxonomic specificity, resolution, and coverage of these primers were evaluated via in silico and in vitro analyses. Additionally, efficiency of these primer sets was assessed using tissue samples and mock communities. Finally, their applicability and performance were tested at various depths. The developed primers exhibited a relatively large amplification size with mixed bases that enhanced their amplification efficiency and sensitivity for cephalopod detection. We successfully identified cephalopod species with different body sizes, from small species, such as Heteroteuthis dagamensis, to large species, such as Architeuthis dux, at varying water depths. Overall, the primer sets established in this study serve as powerful tools to study cephalopod diversity and exhibit great potential for barcoding and genetic diversity investigations.

Environmental effects monitoring of offshore oil and gas activities on the Norwegian continental shelf: A review

This review examines the evolution and findings of Norway's offshore environmental monitoring (OEM) program over the past five decades. The program targets soft sediments, water column organisms, and deep-water epifauna across the Norwegian Continental Shelf (NCS) to assess the impacts of offshore oil and gas activities. The program is required by Norwegian authorities and financed by oil and gas companies operating on the NCS. Initially prompted by widespread effects from oil-contaminated drill cuttings (OBM-DC) discharges, the first sediment quality monitoring came in 1973, and grew into a regional sediment quality monitoring program in 1995. A ban on discharge of OBM cuttings on the NCS was implemented in 1993, and the following years saw a clear reduction in areas with impacted sediments. Currently, significant contamination and macrofauna disturbances are typically confined within 250-500 m of DC discharge points. In the 1990s, concerns over increasing produced water (PW) discharges led to development of effect monitoring in the water column, with focus on fish and mussels as bioindicators. These in situ effect surveys have shown localized impacts near PW outlets. Other fish surveys have revealed elevated DNA adduct levels in demersal fish (haddock) in several areas on the NCS, but the causality of this phenomenon remains unclear. Deep-water petroleum exploration has necessitated visual surveys to map protected benthic epifauna communities, such as corals and sponges, though the methodology's suitability for assessing biological impact is uncertain. Future recommendations include redesigning sediment surveys to address combined stressors from the petroleum industry, fisheries, and climate change, adopting recent methodological and statistical advancements, and improving integration across program elements. This review describes how the offshore monitoring on the NCS has evolved in response to changing environmental concerns, regulations and industrial practices, providing insights for enhancing ecological protection in offshore petroleum activities.

Advancing molecular macrobenthos biodiversity monitoring: a comparison between Oxford Nanopore and Illumina based metabarcoding and metagenomics

DNA-based methods and developments of sequencing technologies are integral to macrobenthos biodiversity studies, and their implementation as standardized monitoring methods is approaching. Evaluating the efficacy and reliability of these technological developments is crucial for macrobenthos biodiversity assessments. In this study, we compared three DNA-based techniques for assessing the diversity of bulk macrobenthos samples from the Belgian North Sea. Specifically, we compared amplicon sequencing using Illumina MiSeq and portable real-time sequencing of Oxford Nanopore versus shotgun sequencing using Illumina NovaSeq sequencing. The 313 bp mitochondrial cytochrome c oxidase subunit I (COI) metabarcoding fragment served as the target region for the metabarcoding analysis. Our results indicate that Oxford Nanopore and MiSeq metabarcoding had similar performances in terms of alpha and beta diversity, revealing highly similar location-specific community compositions. The NovaSeq metagenomics method also resulted in similar alpha diversity, but slightly different community compositions compared to the metabarcoding approach. Despite these differences, location-specific community compositions were maintained across all platforms. Notably, read counts from the NovaSeq metagenomic analysis showed the weakest correlation to size corrected morphological abundance and there were mismatches between morphological identification and all DNA based findings which are likely caused by a combination of factors such as primer efficiency and an incomplete reference database. Our findings underscore the critical importance of database completeness prior to implementing DNA-based techniques as standardized monitoring method, especially for metagenomics. Nevertheless, our findings emphasize that Oxford Nanopore metabarcoding proves to be a viable alternative to the conventional Illumina MiSeq metabarcoding platform for macrobenthos biodiversity monitoring.

Protein Coding Low-Copy rpb2 and ef1-α Regions Are Viable Fungal Metabarcoding DNA Markers Which Can Supplement ITS for Better Accuracy

The nuclear ribosomal DNA Internal Transcribed Spacer (ITS) region is used as a universal fungal barcode marker, but often lacks a significant DNA barcoding gap between sister taxa. Here we tested the reliability of protein coding low-copy genes as alternative barcode markers. Mock communities of three unrelated agaric genera (Dermoloma, Hodophilus, and Russula) representing lineages of closely related species were sequenced by the Illumina platform targeting the ITS1, ITS2, the second largest subunit of RNA polymerase II gene (rpb2) and the transcription elongation factor 1-alpha gene (ef1-α) regions. Species representation and their relative abundances were similar across all tested barcode regions, despite a lower copy number in protein coding markers. ITS1 and ITS2 required more sophisticated sequence filtering because they produced a high number of chimeric sequences requiring reference-based chimera removal and had a higher number of sequence variants per species. Although clustering of filtered ITS sequences resulted in an average higher number of correctly clustered units at optimal similarity thresholds, these thresholds varied substantially among genera. Best-fitted thresholds of low-copy markers were more consistent across genera but frequently lacked species resolution due to low intraspecific variability. At some thresholds, we observed multiple species lumped together, and at the same time, species split into multiple partial clusters, which should be taken into consideration when assessing the best clustering thresholds and taxonomic identity of clusters. To achieve the best taxonomic resolution and improve species detection, we recommend combining different markers and applying additional reference-based sorting of clusters. The current availability of rpb2 and ef1-α reference sequences in public databases is far from being complete for all fungal groups, but a combined marker approach can be used for group-specific studies that can build reference data for their own purposes.

The chemical ecology and physiological functions of type I polyketide natural products: the emerging picture

Covering: up to 2024.For many years, the value of complex polyketides lay in their medical properties, including their antibiotic and antifungal activities, with little consideration paid to their native functions. However, more recent evidence gathered from the study of inter-organismal interactions has revealed the influence of these metabolites upon the ecological adaptation and distribution of their hosts, as well as their modes of communication. The increasing number of sequenced genomes and associated transcriptomes has also unveiled the widespread occurrence of the underlying biosynthetic enzymes across all kingdoms of life, and the important contributions they make to physiological events specific to each organism. This review depicts the diversity of roles fulfilled by type I polyketides, particularly in light of studies carried out during the last decade, providing an initial overall picture of their diverse functions.

Describing functional diversity of communities from environmental DNA

Comprehensive assessments of functional diversity are needed to understand ecosystem alterations under global changes. The 'Fun-eDNA' approach characterises functional diversity by assigning traits to taxonomic units obtained through environmental DNA (eDNA) sampling. By simultaneously analysing an unprecedented number of taxa over broad spatial scales, the approach provides a whole-ecosystem perspective of functional diversity. Fun-eDNA is increasingly used to tackle multiple questions, but aligning eDNA with traits poses several conceptual and technical challenges. Enhancing trait databases, improving the annotation of eDNA-based taxonomic inventories, interdisciplinary collaboration, and conceptual harmonisation of traits are key steps to achieve a comprehensive assessment of diverse taxa. Overcoming these challenges can unlock the full potential of eDNA in leveraging measures of ecosystem functions from multi-taxa assessments.

Cross-taxa assessment of species diversity and phylogenetic structure of benthic communities in a dam-impacted river undergoing habitat restoration

Exploring diversity and community composition patterns across evolutionary and functionally diverse organisms is critical for understanding the general processes that shape biodiversity in response to environmental changes. Knowledge of multi-trophic relationships offers valuable insights to support the effective assessment and management of freshwater ecosystems. In this study, we conducted a cross-taxa assessment of benthic macroinvertebrates and microorganisms using metabarcoding-based surveys to evaluate habitat restoration in a dam-impacted river. We found no correlation between the α-diversity of the benthic macroinvertebrate and microbial communities. This suggests that factors influencing the α-diversity of different trophic groups might operate independently or through different mechanisms, even within the same habitat. In contrast, we observed positively correlated β-diversity patterns between the two benthic communities influenced by dam fragmentation and gravel bar restoration. This suggests that environmental heterogeneity between sites may have a common influence on the patterns of pairwise dissimilarities in the benthic communities, even though they have significant differences in key traits, e.g., species composition, functional roles, or trophic level. Additionally, phylogenetic structure analysis revealed a greater dam impact on benthic macroinvertebrates than microbial communities. Benthic microorganisms consistently formed phylogenetically clustered communities regardless of dam impact, while the macroinvertebrates shifted from competitive exclusion to environmental filtering in response to dam fragmentation. Our cross-taxa assessment further explained the relationships among benthic communities and their associations with environmental factors in a river ecosystem undergoing habitat restoration. Our study highlights the significant implications of evaluating different biological communities across trophic levels for river restoration strategies and ecosystem assessment.

Functional changes of protist communities in soil after glacier retreat

Soil hosts key components of terrestrial biodiversity providing essential services to the below- and above-ground ecosystems. The worldwide retreat of glaciers is exposing new deglaciated terrains, offering a unique opportunity to understand the development of soil ecosystems under a changing climate. Many studies have investigated how biotic communities change after deglaciation, but protists have often been overlooked despite their key role in multiple ecosystem functions. Here, we aim to understand how protist communities develop along glacier forelands, describing their successional trajectories. Protist communities were characterized in 1251 soil samples from 46 glacier forelands across four continents. We used environmental DNA metabarcoding to identify the Molecular Operational Taxonomic Units (MOTUs) of protists based on a universal eukaryotic marker. The detected MOTUs were combined with information on multiple traits to assess how the functional diversity and composition of protist communities vary through time. Immediately after glacier retreat, protist communities are like those of polar and high-altitude habitats, with consumers being the dominant trophic group, followed by a relevant presence of phototrophs, while parasites were underrepresented. Over the succession, we detected an increase in taxonomic and functional diversity, but some highly specialized groups (e.g. phototrophic algae) declined. The use of a trait-based approach allowed us to identify distinct successional patterns depending on functional groups. Through the functional characterization of a crucial but understudied component of soil biotic communities, our study added one of the final pieces needed to predict how soil ecosystems will develop in the rapidly changing environment of glacier forelands.

Rapid expansion and ecosystem health risk of invasive biopollutants dispersed by maritime traffic in French Polynesia

The introduction of biopollutant species challenge ecosystem health and economy in remote islands. Here we checked the advance of invasive fouling species in five French Polynesian islands. Expansion of invasive species (Acantophora spicifera, Bugula neritina, Chthamalus proteus, Dendostrea frons) was detected using individual barcoding (COI for animals, RBLC for algae), and metabarcoding on biofouling (COI and 18S sequences). They were especially abundant in Port Phaeton (Tahiti), Bora Bora and Rangiroa atoll. Chthamalus proteus is a vector of bacterial diseases and may harm native French Polynesian mollusks. Dendostrea frons is a vector of Perkinsus, a parasite to which black pearl oysters, the mainstay of the Polynesian economy, are susceptible. High ecological and epidemiological risks were estimated for C. proteus and D. frons, and ecological risks also for A. spicifera and especially for B. neritina. Strengthening marine biosecurity measures is highly recommended to conserve these unique ecosystems and their associated services.

The One Health approach in urban ecosystem rehabilitation: An evidence-based framework for designing sustainable cities

Rapid urbanization has led to negative, and sometimes unintended, consequences on biodiversity and human health. While cities offer numerous advantages in meeting the basic needs of a growing population, they also pose less apparent and longer-term health costs. To address the multifaceted impacts of urbanization, an evidence-based design framework for establishing mitigation and regeneration actions is essential. Via a "One Health" approach, this perspective provides recommendations and strategies for the urban ecosystem rehabilitation of future cities, placing biodiversity and ecosystem services at the core of designing healthy and sustainable urban spaces. The framework we propose is based on a Hub and Spoke model to integrate diverse perspectives from public and private sectors and declined in a six-building-blocks structure. This will ensure that efforts are sustainable, health-centered, socially inclusive, and grounded in high-quality data, reinforcing the essential connection between healthy environments and thriving communities.

Enhancing metabarcoding efficiency and ecological insights through integrated taxonomy and DNA reference barcoding: A case study on beach meiofauna

Molecular techniques like metabarcoding, while promising for exploring diversity of communities, are often impeded by the lack of reference DNA sequences available for taxonomic annotation. Our study explores the benefits of combining targeted DNA barcoding and morphological taxonomy to improve metabarcoding efficiency, using beach meiofauna as a case study. Beaches are globally important ecosystems and are inhabited by meiofauna, microscopic animals living in the interstitial space between the sand grains, which play a key role in coastal biodiversity and ecosystem dynamics. However, research on meiofauna faces challenges due to limited taxonomic expertise and sparse sampling. We generated 775 new cytochrome c oxidase I DNA barcodes from meiofauna specimens collected along the Netherlands' west coast and combined them with the NCBI GenBank database. We analysed alpha and beta diversity in 561 metabarcoding samples from 24 North Sea beaches, a region extensively studied for meiofauna, using both the enriched reference database and the NCBI database without the additional reference barcodes. Our results show a 2.5-fold increase in sequence annotation and a doubling of species-level Operational Taxonomic Units (OTUs) identification when annotating the metabarcoding data with the enhanced database. Additionally, our analyses revealed a bell-shaped curve of OTU richness across the intertidal zone, aligning more closely with morphological analysis patterns, and more defined community dissimilarity patterns between supralittoral and intertidal sites. Our research highlights the importance of expanding molecular reference databases and combining morphological taxonomy with molecular techniques for biodiversity assessments, ultimately improving our understanding of coastal ecosystems.

The development of terrestrial ecosystems emerging after glacier retreat

The global retreat of glaciers is dramatically altering mountain and high-latitude landscapes, with new ecosystems developing from apparently barren substrates1-4. The study of these emerging ecosystems is critical to understanding how climate change interacts with microhabitat and biotic communities and determines the future of ice-free terrains1,5. Here, using a comprehensive characterization of ecosystems (soil properties, microclimate, productivity and biodiversity by environmental DNA metabarcoding6) across 46 proglacial landscapes worldwide, we found that all the environmental properties change with time since glaciers retreated, and that temperature modulates the accumulation of soil nutrients. The richness of bacteria, fungi, plants and animals increases with time since deglaciation, but their temporal patterns differ. Microorganisms colonized most rapidly in the first decades after glacier retreat, whereas most macroorganisms took longer. Increased habitat suitability, growing complexity of biotic interactions and temporal colonization all contribute to the increase in biodiversity over time. These processes also modify community composition for all the groups of organisms. Plant communities show positive links with all other biodiversity components and have a key role in ecosystem development. These unifying patterns provide new insights into the early dynamics of deglaciated terrains and highlight the need for integrated surveillance of their multiple environmental properties5.

Marine eDNA sampling from submerged surfaces with paint rollers

Environmental DNA (eDNA) analyses of species present in marine environments is the most effective biological diversity measurement tool currently available. eDNA sampling methods are an intrinsically important part of the eDNA biodiversity analysis process. Identification and development of eDNA sampling methods that are as rapid, affordable, versatile and practical as possible will improve rates of detection of marine species. Optimal outcomes of eDNA biodiversity surveys come from studies employing high levels of sampling replication, so any methods that make sampling faster and cheaper will improve scientific outcomes. eDNA sampling methods that can be applied more widely will also enable sampling from a greater range of marine surface micro-habitats, resulting in detection of a wider range of organisms. In this study, we compared diversity detection by several methods for sampling eDNA from submerged marine surfaces: polyurethane foam, nylon swabs, microfibre paint rollers, and sediment scoops. All of the methods produced a diverse range of species identifications, with >250 multicellular species represented by eDNA at the study site. We found that widely-available small paint rollers were an effective, readily available and affordable method for sampling eDNA from underwater marine surfaces. This approach enables the sampling of marine eDNA using extended poles, or potentially by remotely operated vehicles, where surface sampling by hand is impractical.

Unlocking rivers' hidden diversity and ecological status using DNA metabarcoding in Northwest Spain

Rivers are crucial ecosystems supporting biodiversity and human well-being, yet they face increasing degradation globally. Traditional river biomonitoring methods based on morphological identification of macroinvertebrates present challenges in terms of taxonomic resolution and scalability. This study explores the application of DNA metabarcoding analysis in both bulk and environmental DNA (eDNA) samples for comprehensive assessment of macrozoobenthic biodiversity, detection of invasive and endangered species, and evaluation of river ecological status in northwestern Spain. DNA metabarcoding of homogenized bulk samples and water eDNA revealed a mean of 100 and 87 macrozoobenthos species per sample respectively. However, the specific composition was significantly different with only 27.3% of the total species being shared. It was not possible to identify all the OTUs to species level; only 17.43% and 49.4% of the OTUs generated could be identified to species level in the bulk and eDNA samples, respectively. Additionally, a total of 11 exotic species (two first records for the Iberian Peninsula and another three first records for Asturias region) and one endangered species were detected by molecular tools. Molecular methods showed significant correlations with morphological identification for EQR values (Ecological Quality Ratio) of IBMWP index, yet differences in inferred river ecological status were noted, with bulk samples tending to indicate higher status. Overall, DNA metabarcoding offers a promising approach for river biomonitoring, providing insights into biodiversity, invasive species, and ecological status within a single analysis. Further optimization and intercalibration are required for its implementation in routine biomonitoring programmes, but its scalability and multi-tasking capabilities position it as a valuable tool for integrated monitoring of river ecosystems.

Decoding Seafood: Multi-Marker Metabarcoding for Authenticating Processed Seafood

Given the recognized nutritional value of fish and shifting consumer lifestyles, processed seafood has become increasingly prevalent, comprising a significant portion of global food production. Although current European Union labeling regulations do not require species declaration for these products, food business operators often voluntarily provide this information on ingredient lists. Next Generation Sequencing (NGS) approaches are currently the most effective methods for verifying the accuracy of species declarations on processed seafood labels. This study examined the species composition of 20 processed seafood products, each labeled as containing a single species, using two DNA metabarcoding markers targeting the mitochondrial cytochrome c oxidase I (COI) and 16S rRNA genes. The combined use of these markers revealed that the majority of the products contained multiple species. Furthermore, two products were found to be mislabeled, as the declared species were not detected. These findings underscore that NGS is a robust technique that could be adopted to support routine food industry activities and official control programs, thereby enhancing the 'From Boat to Plate' strategy and combating fraudulent practices in the complex fisheries supply chain.

Distinct multitrophic biodiversity composition and community organization in a freshwater lake and a hypersaline lake on the Tibetan Plateau

Alpine lakes play pivotal roles in plateau hydrological processes but are highly sensitive to climate change, yet we lack comprehensive knowledge of their multitrophic biodiversity patterns. Here, we compared the biodiversity characteristics of diverse taxonomic groups across water depths and in surface sediments from a freshwater lake and a hypersaline lake on the northwestern Tibetan Plateau. Using multi-marker environmental DNA metabarcoding, we detected 134 cyanobacteria, 443 diatom, 1,519 invertebrate, and 28 vertebrate taxa. Each group had a substantially different community composition in the two lakes, and differences were also found between water and sediments within each lake. Cooccurrence network analysis revealed higher network complexity, lower modularity, and fewer negative cohesions in the hypersaline lake, suggesting that high salinity may destabilize ecological networks. Our results provide the first holistic view of Tibetan lake biodiversity under contrasting salinity levels and reveal structural differences in the ecological networks that may impact ecosystem resilience.

Genomics for monitoring and understanding species responses to global climate change

All life forms across the globe are experiencing drastic changes in environmental conditions as a result of global climate change. These environmental changes are happening rapidly, incur substantial socioeconomic costs, pose threats to biodiversity and diminish a species' potential to adapt to future environments. Understanding and monitoring how organisms respond to human-driven climate change is therefore a major priority for the conservation of biodiversity in a rapidly changing environment. Recent developments in genomic, transcriptomic and epigenomic technologies are enabling unprecedented insights into the evolutionary processes and molecular bases of adaptation. This Review summarizes methods that apply and integrate omics tools to experimentally investigate, monitor and predict how species and communities in the wild cope with global climate change, which is by genetically adapting to new environmental conditions, through range shifts or through phenotypic plasticity. We identify advantages and limitations of each method and discuss future research avenues that would improve our understanding of species' evolutionary responses to global climate change, highlighting the need for holistic, multi-omics approaches to ecosystem monitoring during global climate change.

Novel community data in ecology-properties and prospects

New technologies for monitoring biodiversity such as environmental (e)DNA, passive acoustic monitoring, and optical sensors promise to generate automated spatiotemporal community observations at unprecedented scales and resolutions. Here, we introduce 'novel community data' as an umbrella term for these data. We review the emerging field around novel community data, focusing on new ecological questions that could be addressed; the analytical tools available or needed to make best use of these data; and the potential implications of these developments for policy and conservation. We conclude that novel community data offer many opportunities to advance our understanding of fundamental ecological processes, including community assembly, biotic interactions, micro- and macroevolution, and overall ecosystem functioning.

Mock community experiments can inform on the reliability of eDNA metabarcoding data: a case study on marine phytoplankton

Environmental DNA metabarcoding is increasingly implemented in biodiversity monitoring, including phytoplankton studies. Using 21 mock communities composed of seven unicellular diatom and dinoflagellate algae, assembled with different composition and abundance by controlling the number of cells, we tested the accuracy of an eDNA metabarcoding protocol in reconstructing patterns of alpha and beta diversity. This approach allowed us to directly evaluate both qualitative and quantitative metabarcoding estimates. Our results showed non-negligible rates (17-25%) of false negatives (i.e., failure to detect a taxon in a community where it was included), for three taxa. This led to a statistically significant underestimation of metabarcoding-derived alpha diversity (Wilcoxon p = 0.02), with the detected species richness being lower than expected (based on cell numbers) in 8/21 mock communities. Considering beta diversity, the correlation between metabarcoding-derived and expected community dissimilarities was significant but not strong (R2 = 0.41), indicating suboptimal accuracy of metabarcoding results. Average biovolume and rDNA gene copy number were estimated for the seven taxa, highlighting a potential, though not exhaustive, role of the latter in explaining the recorded biases. Our findings highlight the importance of mock communities for assessing the reliability of phytoplankton eDNA metabarcoding studies and identifying their limitations.