Advances and prospects of environmental DNA in neotropical rainforests. Tropical Ecosystems in the 21st Century. Elsevier; 2020. pp. 331-73. [DOI: 10.1016/bs.aecr.2020.01.001]

Species abundance, urn models, and neutrality

The neutral theory of biodiversity and biogeography has stimulated much research in community ecology. Here, exact results are used to apply neutral model predictions to large regional samples. Three complementary neutral models are presented: the Ewens canonical neutral model, a model of subdivided ecological communities, and a “diversity begets diversity” neutral model. For all three models, an exact sampling formula is provided, and a new R package neutr, is presented. This package is used to fit species abundances from regional inventories of tropical forest trees in the Amazon, tropical Africa and Southeast Asia. It is shown that the neutral models fit well empirical data for all but the few most abundant species (from 6 to 40 depending on the continent). When the parameter θ is taken as an index or regional diversity, the Amazonia and Southeast Asia emerge with similar regional diversities (θ = 654 for Amazonia, versus θ = 726 for Southeast Asia), with a less diverse tropical African tree flora (θ = 219). The model infers 10,141 tree species with at least 50 individuals in Amazonia, 3477 in tropical Africa and 9915 in Southeast Asia. The spatially subdivided neutral model provides clear evidence for a spatial substructure in all three regional floras. These results show how neutral models are useful to explore regional patterns of species abundance and to provide insights about regional species pools.

Widespread occurrence of fecal indicator bacteria in oligotrophic tropical streams. Are common culture-based coliform tests appropriate?

Monitoring of stream water quality is a key element of water resource management worldwide, but methods that are commonly used in temperate habitats may not be appropriate in humid tropical systems. We assessed the influence of four land uses on microbial water quality in 21 streams in the Panama Canal Watershed over a one-year period, using a common culture-based fecal indicator test and 16S rDNA metabarcoding. Each stream was located within one of four land uses: mature forest, secondary forest, silvopasture, and traditional cattle pasture. Culturing detected total coliforms and Escherichia coli across all sites but found no significant differences in concentrations between land uses. However, 16S rDNA metabarcoding revealed variability in the abundance of coliforms across land uses and several genera that can cause false positives in culture-based tests. Our results indicate that culture-based fecal indicator bacteria tests targeting coliforms may be poor indicators of fecal contamination in Neotropical oligotrophic streams and suggest that tests targeting members of the Bacteroidales would provide a more reliable indication of fecal contamination.

Merging two eDNA metabarcoding approaches and citizen-science-based sampling to facilitate fish community monitoring along vast Sub-Saharan coastlines

The coastline of Sub-Saharan Africa hosts highly diverse fish communities of great conservation value, which are also key resources for local livelihoods. However, many costal ecosystems are threatened by overexploitation and their conservation state is frequently unknown due to their vast spatial extent and limited monitoring budgets. Here, we evaluated the potential of citizen science-based eDNA surveys to alleviate such chronic data deficiencies and assessed fish communities in Mozambique using two 12S metabarcoding primer sets. Samples were either collected by scientific personnel or trained community members and results from the two metabarcoding primers were combined using a new data merging approach. Irrespective of the background of sampling personnel, a high average fish species richness was recorded (38 ± 20 OTUs per sample). Individual sections of the coastline largely differed in the occurrence of threatened and commercially important species, highlighting the need for regionally differentiated management strategies. A detailed comparison of the two applied primer sets revealed an important trade-off in primer choice with MiFish primers amplifying a higher number of species but Riaz primers performing better in the detection of threatened fish species. This trade-off could be partly resolved by applying our new data-merging approach, which was especially designed to increase the robustness of multiprimer assessments in regions with poor reference libraries. Overall, our study provides encouraging results but also highlights that eDNA-based monitoring will require further improvements of, for example, reference databases and local analytical infrastructure to facilitate routine applications in Sub-Saharan Africa.

Deforestation strengthens environmental filtering and competitive exclusion in Neotropical streams and rivers

Understanding how anthropization impacts the assembly of species onto communities is pivotal to go beyond the observation of biodiversity changes and reveal how disturbances affect the environmental and biotic processes shaping biodiversity. Here, we propose a simple framework to measure the assembly processes underpinning functional convergence/divergence patterns. We applied this framework to northern Amazonian fish communities inventoried using environmental DNA in 35 stream sites and 64 river sites. We found that the harsh and unstable environmental conditions characterizing streams conveyed communities towards functional convergence, by filtering traits related to food acquisition and, to a lower extent, dispersal. Such environmental filtering also strengthened competition by excluding species having less competitive food acquisition traits. Instead, random species assembly was more marked in river communities, which may be explained by the downstream position of rivers facilitating the dispersion of species. Although fish assembly rules differed between streams and river fish communities, anthropogenic disturbances reduced functional divergence in both ecosystems, with a reinforcement of both environmental filtering and weaker competitor exclusion. This may explain the substantial biodiversity alterations observed under slight deforestation levels in Neotropical freshwater ecosystems and underlines their vulnerability to anthropic disturbances that not only affect species persistence but also modify community assembly rules.

Arbuscular mycorrhizal fungi associated with the rhizosphere of an endemic terrestrial bromeliad and a grass in the Brazilian neotropical dry forest

Arbuscular mycorrhizal fungi form symbiotic associations with 80-90% of all known plants, allowing the fungi to acquire plant-synthesized carbon, and confer an increased capacity for nutrient uptake by plants, improving tolerance to abiotic and biotic stresses. We aimed at characterizing the mycorrhizal community in the rhizosphere of Neoglaziovia variegata (so-called `caroa`) and Tripogonella spicata (so-called resurrection plant), using high-throughput sequencing of the partial 18S rRNA gene. Both plants are currently undergoing a bioprospecting program to find microbes with the potential of helping plants tolerate water stress. Sampling was carried out in the Caatinga biome, a neotropical dry forest, located in northeastern Brazil. Illumina MiSeq sequencing of 37 rhizosphere samples (19 for N. variegata and 18 for T. spicata) revealed a distinct mycorrhizal community between the studied plants. According to alpha diversity analyses, T. spicata showed the highest richness and diversity based on the Observed ASVs and the Shannon index, respectively. On the other hand, N. variegata showed higher modularity of the mycorrhizal network compared to T. spicata. The four most abundant genera found (higher than 10%) were Glomus, Gigaspora, Acaulospora, and Scutellospora, with Glomus being the most abundant in both plants. Nonetheless, Gigaspora, Diversispora, and Ambispora were found only in the rhizosphere of N. variegata, whilst Scutellospora, Paraglomus, and Archaeospora were exclusive to the rhizosphere of T. spicata. Therefore, the community of arbuscular mycorrhizal fungi of the rhizosphere of each plant encompasses a unique composition, structure and modularity, which can differentially assist them in the hostile environment.

A spatial fingerprint of land-water linkage of biodiversity uncovered by remote sensing and environmental DNA

Aquatic and terrestrial ecosystems are tightly connected via spatial flows of organisms and resources. Such land-water linkages integrate biodiversity across ecosystems and suggest a spatial association of aquatic and terrestrial biodiversity. However, knowledge about the extent of this spatial association is limited. By combining satellite remote sensing (RS) and environmental DNA (eDNA) extraction from river water across a 740-km² mountainous catchment, we identify a characteristic spatial land-water fingerprint. Specifically, we find a spatial association of riverine eDNA diversity with RS spectral diversity of terrestrial ecosystems upstream, peaking at a 400 m distance yet still detectable up to a 2.0 km radius. Our findings show that biodiversity patterns in rivers can be linked to the functional diversity of surrounding terrestrial ecosystems and provide a dominant scale at which these linkages are strongest. Such spatially explicit information is necessary for a functional understanding of land-water linkages.

Conceptualizing the 3D niche and vertical space use

Spatial partitioning in ecological communities has predominantly been described in two dimensions, yet habitat is complex and 3D. Complex space use mediates community structure and interaction strength by expanding spatial, temporal, and dietary dimensions. Vertical stratification of resources provides opportunities for novel specializations, creating a 3D niche. Competition and predation are mediated by 3D space use, as individuals use the vertical axis to access prey, flee predators, or avoid competitors. The 3D niche is important for long-term conservation strategies as species must navigate tradeoffs in habitat use between strata-specific threats and suboptimal habitat patches. Ultimately, elucidating the 3D niche has implications for protected area management and corridor design that directly influence species persistence and ecosystem function in a rapidly changing world.

Monitoring fish communities through environmental DNA metabarcoding in the fish pass system of the second largest hydropower plant in the world

The Itaipu Hydroelectric Power Plant is the second largest in the world in power generation. The artificial barrier created by its dam imposes an obstacle for fish migration. Thus, in 2002, a fish pass system, named Piracema Channel, was built to allow fish to access areas upstream of the reservoir. We tested the potential of environmental DNA metabarcoding to monitor the impact of both the dam and associated fish pass system in the Paraná River fish communities and to compare it with traditional monitoring methods. Using a fragment of the 12S gene, we characterized richness and community composition based on amplicon sequence variants, operational taxonomic units, and zero-radius OTUs. We combined GenBank and in-house data for taxonomic assignment. We found that different bioinformatics approaches showed similar results. Also, we found a decrease in fish diversity from 2019 to 2020 probably due to the recent extreme drought experienced in southeastern Brazil. The highest alpha diversity was recorded in the mouth of the fish pass system, located in a protected valley with the highest environmental heterogeneity. Despite the clear indication that the reference databases need to be continuously improved, our results demonstrate the analytical efficiency of the metabarcoding to monitor fish species.

Taxonomic, phylogenetic and functional diversity of root-associated fungi in bromeliads: effects of host identity, life forms and nutritional modes

Bromeliads represent a major component of neotropical forests and encompass a considerable diversity of life forms and nutritional modes. Bromeliads explore highly stressful habitats and root-associated fungi may play a crucial role in this, but the driving factors and variations in root-associated fungi remain largely unknown. We explored root-associated fungal communities in 17 bromeliad species and their variations linked to host identity, life forms and nutritional modes by using ITS1 gene-based high-throughput sequencing and by characterizing fungal functional guilds. We found a dual association of mycorrhizal and nonmycorrhizal fungi. The different species, life forms and nutritional modes among bromeliad hosts had fungal communities that differ in their taxonomic and functional composition. Specifically, roots of epiphytic bromeliads had more endophytic fungi and dark septate endophytes and fewer mycorrhizal fungi than terrestrial bromeliads and lithophytes. Our results contribute to a fundamental knowledge base on different fungal groups in previously undescribed Bromeliaceae. The diverse root-associated fungal communities in bromeliads may enhance plant fitness in both stressful and nutrient-poor environments and may give more flexibility to the plants to adapt to changing environmental conditions.

eDNA sampled from stream networks correlates with camera trap detection rates of terrestrial mammals

Biodiversity monitoring delivers vital information to those making conservation decisions. Comprehensively measuring terrestrial biodiversity usually requires costly methods that can rarely be deployed at large spatial scales over multiple time periods, limiting conservation efficiency. Here we investigated the capacity of environmental DNA (eDNA) from stream water samples to survey terrestrial mammal diversity at multiple spatial scales within a large catchment. We compared biodiversity information recovered using an eDNA metabarcoding approach with data from a dense camera trap survey, as well as the sampling costs of both methods. Via the sampling of large volumes of water from the two largest streams that drained the study area, eDNA metabarcoding provided information on the presence and detection probabilities of 35 mammal taxa, 25% more than camera traps and for half the cost. While eDNA metabarcoding had limited capacity to detect felid species and provide individual-level demographic information, it is a cost-efficient method for large-scale monitoring of terrestrial mammals that can offer sufficient information to solve many conservation problems.

Amazonian mammal monitoring using aquatic environmental DNA

Environmental DNA (eDNA) metabarcoding has emerged as one of the most efficient methods to assess aquatic species presence. While the method can in theory be used to investigate nonaquatic fauna, its development for inventorying semi-aquatic and terrestrial fauna is still at an early stage. Here we investigated the potential of aquatic eDNA metabarcoding for inventorying mammals in Neotropical environments, be they aquatic, semi-aquatic or terrestrial. We collected aquatic eDNA in 96 sites distributed along three Guianese watersheds and compared our inventories to expected species distributions and field observations derived from line transects located throughout French Guiana. Species occurrences and emblematic mammalian fauna richness patterns were consistent with the expected distribution of fauna and our results revealed that aquatic eDNA metabarcoding brings additional data to line transect samples for diurnal nonaquatic (terrestrial and arboreal) species. Aquatic eDNA also provided data on species not detectable in line transect surveys such as semi-aquatic, aquatic and nocturnal terrestrial and arboreal species. Although the application of eDNA to inventory mammals still needs some developments to optimize sampling efficiency, it can now be used as a complement to traditional surveys.

Connecting high-throughput biodiversity inventories: Opportunities for a site-based genomic framework for global integration and synthesis

High-throughput sequencing (HTS) is increasingly being used for the characterization and monitoring of biodiversity. If applied in a structured way, across broad geographical scales, it offers the potential for a much deeper understanding of global biodiversity through the integration of massive quantities of molecular inventory data generated independently at local, regional and global scales. The universality, reliability and efficiency of HTS data can potentially facilitate the seamless linking of data among species assemblages from different sites, at different hierarchical levels of diversity, for any taxonomic group and regardless of prior taxonomic knowledge. However, collective international efforts are required to optimally exploit the potential of site-based HTS data for global integration and synthesis, efforts that at present are limited to the microbial domain. To contribute to the development of an analogous strategy for the nonmicrobial terrestrial domain, an international symposium entitled "Next Generation Biodiversity Monitoring" was held in November 2019 in Nicosia (Cyprus). The symposium brought together evolutionary geneticists, ecologists and biodiversity scientists involved in diverse regional and global initiatives using HTS as a core tool for biodiversity assessment. In this review, we summarize the consensus that emerged from the 3-day symposium. We converged on the opinion that an effective terrestrial Genomic Observatories network for global biodiversity integration and synthesis should be spatially led and strategically united under the umbrella of the metabarcoding approach. Subsequently, we outline an HTS-based strategy to collectively build an integrative framework for site-based biodiversity data generation.

DNA barcoding of phytopathogens for disease diagnostics and bio-surveillance

DNA barcoding has proven to be a versatile tool for plant disease diagnostics in the genomics era. As the mass parallel and next generation sequencing techniques gained importance, the role of specific barcodes came under immense scrutiny. Identification and accurate classification of phytopathogens need a universal approach which has been the main application area of the concept of barcode. The present review entails a detailed description of the present status of barcode application in plant disease diagnostics. A case study on the application of Internal Transcribed Spacer (ITS) as barcode for Aspergillus and Fusarium spp. sheds light on the requirement of other potential candidates as barcodes for accurate identification. The challenges faced while barcoding novel pathogens have also been discussed with a comprehensive outline of integrating more recent technologies like meta-barcoding and genome skimming for detecting plant pathogens.

Assessing the efficacy of eDNA metabarcoding for measuring microbial biodiversity within forest ecosystems

We investigated the nascent application and efficacy of sampling and sequencing environmental DNA (eDNA) in terrestrial environments using rainwater that filters through the forest canopy and understory vegetation (i.e., throughfall). We demonstrate the utility and potential of this method for measuring microbial communities and forest biodiversity. We collected pure rainwater (open sky) and throughfall, successfully extracted DNA, and generated over 5000 unique amplicon sequence variants. We found that several taxa including Mycoplasma sp., Spirosoma sp., Roseomonas sp., and Lactococcus sp. were present only in throughfall samples. Spiroplasma sp., Methylobacterium sp., Massilia sp., Pantoea sp., and Sphingomonas sp. were found in both types of samples, but more abundantly in throughfall than in rainwater. Throughfall samples contained Gammaproteobacteria that have been previously found to be plant-associated, and may contribute to important functional roles. We illustrate how this novel method can be used for measuring microbial biodiversity in forest ecosystems, foreshadowing the utility for quantifying both prokaryotic and eukaryotic lifeforms. Leveraging these methods will enhance our ability to detect extant species, describe new species, and improve our overall understanding of ecological community dynamics in forest ecosystems.

Lost and found: Frogs in a biodiversity hotspot rediscovered with environmental DNA

Declines and extinctions are increasing globally and challenge conservationists to keep pace with biodiversity monitoring. Organisms leave DNA traces in the environment, e.g., in soil, water, and air. These DNA traces are referred to as environmental DNA (eDNA). The analysis of eDNA is a highly sensitive method with the potential to rapidly assess local diversity and the status of threatened species. We searched for DNA traces of 30 target amphibian species of conservation concern, at different levels of threat, using an environmental DNA metabarcoding approach, together with an extensive sequence reference database to analyse water samples from six montane sites in the Atlantic Coastal Forest and adjacent Cerrado grasslands of Brazil. We successfully detected DNA traces of four declined species (Hylodes ornatus, Hylodes regius, Crossodactylus timbuhy, and Vitreorana eurygnatha); two locally disappeared (Phasmahyla exilis and Phasmahyla guttata); and one species that has not been seen since 1968 (putatively assigned to Megaelosia bocainensis). We confirm the presence of species undetected by traditional methods, underscoring the efficacy of eDNA metabarcoding for biodiversity monitoring at low population densities, especially in megadiverse tropical sites. Our results support the potential application of eDNA in conservation biology, to evaluate persistence and distribution of threatened species in surveyed habitats or sites, and improve accuracy of red lists, especially for species undetected over long periods.

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.