Environmental DNA Sequencing Research Articles

Robust Archaeal and Bacterial Communities Inhabit Shallow Subsurface Sediments of the Bonneville Salt Flats.

We report the first census of natural microbial communities of the Bonneville Salt Flats (BSF), a perennial salt pan at the Utah-Nevada border. Environmental DNA sequencing of archaeal and bacterial 16S rRNA genes was conducted on samples from multiple evaporite sediment layers collected from the upper 30 cm of the surface salt crust. Our results show that at the time of sampling (September 2016), BSF hosted a robust microbial community dominated by diverse halobacteria and Salinibacter species. Sequences identical to Geitlerinema sp. strain PCC 9228, an anoxygenic cyanobacterium that uses sulfide as the electron donor for photosynthesis, are also abundant in many samples. We identified taxonomic groups enriched in each layer of the salt crust sediment and revealed that the upper gypsum sediment layer found immediately under the uppermost surface halite contains a robust microbial community. In these sediments, we found an increased presence of Thermoplasmatales, Hadesarchaeota, Nanoarchaeaeota, Acetothermia, Desulfovermiculus, Halanaerobiales, Bacteroidetes, and Rhodovibrio This study provides insight into the diversity, spatial heterogeneity, and geologic context of a surprisingly complex microbial ecosystem within this macroscopically sterile landscape.IMPORTANCE Pleistocene Lake Bonneville, which covered a third of Utah, desiccated approximately 13,000 years ago, leaving behind the Bonneville Salt Flats (BSF) in the Utah West Desert. The potash salts that saturate BSF basin are extracted and sold as an additive for agricultural fertilizers. The salt crust is a well-known recreational and economic commodity, but the biological interactions with the salt crust have not been studied. This study is the first geospatial analysis of microbially diverse populations at this site using cultivation-independent environmental DNA sequencing methods. Identification of the microbes present within this unique, dynamic, and valued sedimentary evaporite environment is an important step toward understanding the potential consequences of perturbations to the microbial ecology on the surrounding landscape and ecosystem.

A method for the reintroduction of entire benthic invertebrate communities in formerly degraded streams

Reintroduction is a commonly used tool in wildlife conservation. Although freshwater ecosystems are among the most threatened worldwide, reintroductions of entire benthic invertebrate communities have never been reported before. Here, for the first time, we developed a comprehensive method for the reintroduction of entire communities in formerly degraded streams that describes the selection of donor and recipient streams, the transfer of specimens, mortality rates, and a monitoring scheme. The stream selection procedure of the new method is based on widely available environmental variables and richness metrics that are regularly monitored by water authorities to fulfill the requirements of water policy frameworks (e.g. EU WFD). The sampling and transfer of specimens is also based on common and simply applicable methods (i.e. kick sampling). For each recipient stream, three donor streams were selected with a complementary set of reference species missing at the recipient stream. The sampling at each donor stream was done six times a year to cover different seasons and life stages. We applied our method to one stream (10 km2) and one river (1608 km2) in central Germany. In total, we transferred 325,197 and 401,233 specimens from three different donor streams, including 45 (28,682 specimens) and 50 (47,716 specimens) missing reference taxa into each recipient stream and river, respectively. Average mortality rates varied between 0.97% for all specimens and 1.72% for reference specimens. We recommend a post-reintroduction monitoring that includes new methods, i.e. environmental DNA and high throughput sequencing. Our proposed reintroduction method is based on commonly used variables, metrics and sampling techniques. Accordingly, this method requires only minor modifications to become applicable in other countries. The simultaneous reintroduction of a large number of reference taxa will increase the likelihood to reestablish near-natural benthic invertebrate communities in formerly degraded streams. This may increase the public and political acceptance of costly river restoration projects that so far, do not often reach a good ecological status even after decades, due to a large-scale depletion of potential source populations. Our method will help in the reintroduction of reference species in restored streams where natural recolonization is not possible.

Checklist of the planktonic marine dinoflagellates of New Zealand

ABSTRACTPlanktonic dinoflagellate records for New Zealand are substantial due to intense monitoring programmes that have taken place on behalf of New Zealand’s biotoxin regulators and the shellfish industry since 1993. At that time a Karenia bloom caused human illnesses and shellfish harvesting ceased until monitoring was instigated. Phytoplankton records are based on morphological identification using light microscopy but are backed up by government funded research programmes which implement techniques such as electron microscopy, DNA sequencing, molecular detection assays and high throughput sequencing of environmental DNA. This checklist will support management of aquaculture industries, recreational shellfish harvests and environmental health initiatives. Some genera are considered benthic or epiphytic, but have lengthy planktonic life stages. Forty-five genera in the class Dinophyceae Fritsch are reported: Akashiwo, Alexandrium, Amphidinium, Amylax, Azadinium, Biecheleria, Bysmatrum, Cachonina, Cochlodinium (synonym: Margalefidinium), Coolia, Dicroerisma, Dinophysis, Diploneis, Diplopsalis, Fragilidium, Glenodinium, Gonyaulax, Gymnodinium, Gyrodinium, Heterocapsa, Karenia, Karlodinium, Lepidodinium, Lingulodinium, Margalefidinium, Ostreopsis, Oxyphysis, Pelagodinium, Pentapharsodinium, Phalacroma, Podolampas, Polarella, Polykrikos, Prorocentrum, Protodinium, Protoodinium, Protoperidinium, Pseliodinium, Scrippsiella, Takayama, Togula, Torodinium, Tripos, Vulcanodinium, Wolosynska. Other genera belonging to the Infraphylum Dinoflagellata also occur in New Zealand waters. They are not in the list but include Noctiluca, Pronoctiluca and Spatulodinium (Class: Noctilucophyceae) and Oxyrrhis (Class: Oxyrrhidophyceae).

Uncovering the dark matter of the metagenome one read at a time

Contemporary metagenomic annotation methods have proven insufficient in our attempts to better understand the complex environments around us. We call the yet to be annotated part of a metagenome it’s ‘dark matter’. The Gene Ontology (GO) is a hierarchical vocabulary used to describe gene product function and a large collection of curated genes with GO annotations already exists. DeepGO utilises deep learning to build models from these curated genes and gene products to predict GO categories for novel proteins. One of the major problems with metagenomic studies today is the process of assembling the environmental DNA sequences into their original genomes. This is difficult, with chimeric metagenomically assembled genomes being common. To avoid this and the computational and time expense, we have modified DeepGO to perform protein function prediction directly from sequence reads with limited protein coding sequence prediction. Three independent models were trained as the following; The first 50 amino acids of a protein were used for training, The last 50 amino acids were used for training, A phasing window of 50 amino acids was used to train across the entirety of a protein sequence. These models were chosen to learn from the different parts of a protein sequence we are likely to capture from only the short unassembled sequence reads. We compared the three models by producing a mock metagenomic community consisting of 6 model bacterial genomes. We evaluated the functions predicted from the unassembled sequence reads and the protein coding sequences predicted from the assembled metagenome.

SLIM: a flexible web application for the reproducible processing of environmental DNA metabarcoding data

BackgroundHigh-throughput amplicon sequencing of environmental DNA (eDNA metabarcoding) has become a routine tool for biodiversity survey and ecological studies. By including sample-specific tags in the primers prior PCR amplification, it is possible to multiplex hundreds of samples in a single sequencing run. The analysis of millions of sequences spread into hundreds to thousands of samples prompts for efficient, automated yet flexible analysis pipelines. Various algorithms and software have been developed to perform one or multiple processing steps, such as paired-end reads assembly, chimera filtering, Operational Taxonomic Unit (OTU) clustering and taxonomic assignment. Some of these software are now well established and widely used by scientists as part of their workflow. Wrappers that are capable to process metabarcoding data from raw sequencing data to annotated OTU-to-sample matrix were also developed to facilitate the analysis for non-specialist users. Yet, most of them require basic bioinformatic or command-line knowledge, which can limit the accessibility to such integrative toolkits. Furthermore, for flexibility reasons, these tools have adopted a step-by-step approach, which can prevent an easy automation of the workflow, and hence hamper the analysis reproducibility.ResultsWe introduce SLIM, an open-source web application that simplifies the creation and execution of metabarcoding data processing pipelines through an intuitive Graphic User Interface (GUI). The GUI interact with well-established software and their associated parameters, so that the processing steps are performed seamlessly from the raw sequencing data to an annotated OTU-to-sample matrix. Thanks to a module-centered organization, SLIM can be used for a wide range of metabarcoding cases, and can also be extended by developers for custom needs or for the integration of new software. The pipeline configuration (i.e. the modules chaining and all their parameters) is stored in a file that can be used for reproducing the same analysis.ConclusionThis web application has been designed to be user-friendly for non-specialists yet flexible with advanced settings and extensibility for advanced users and bioinformaticians. The source code along with full documentation is available on the GitHub repository (https://github.com/yoann-dufresne/SLIM) and a demonstration server is accessible through the application website (https://trtcrd.github.io/SLIM/).

Environmental DNA sequencing of archaeal and bacterial 16S rRNA genes from Bonneville Salt Flats Sediment Samples

Environmental DNA sequencing of archaeal and bacterial 16S rRNA genes from Bonneville Salt Flats Sediment Samples

Changes in Trophic Groups of Protists With Conversion of Rainforest Into Rubber and Oil Palm Plantations.

Protists, abundant but enigmatic single-celled eukaryotes, are important soil microbiota providing numerous ecosystem functions. We employed high-throughput sequencing of environmental DNA, targeting the V4 region of the 18S rRNA gene, to characterize changes in their abundance, species richness, and community structure with conversion of lowland rainforest into rubber agroforest (jungle rubber), and rubber and oil palm plantations; typical agricultural systems in Sumatra, Indonesia. We identified 5,204 operational taxonomic units (OTUs) at 97% identity threshold of protists from 32 sites. Protists species richness was similar in rainforest, jungle rubber and oil palm plantations but significantly lower in rubber plantations. After standardization, 4,219 OTUs were assigned to five trophic groups, and inspected for effects of land-use change, and potential biotic and abiotic driving factors. The most abundant trophic group was phagotrophs (52%), followed by animal parasites (29%), photoautotrophs (12%), plant parasites (1%), and symbionts (<1%). However, the relative abundance and OTU richness of phagotrophs and photoautotrophs increased significantly with increasing land-use intensity. This was similar, but less pronounced, for the relative abundance of symbionts. Animal and plant parasites decreased significantly in abundance and species richness with increasing land-use intensity. Community compositions and factors affecting the structure of individual trophic groups differed between land-use systems. Parasites were presumably mainly driven by the abundance and species richness of their hosts, while phagotrophs by changes in soil pH and increase in Gram-positive bacteria, and photoautotrophs by light availability. Overall, the results show that relative species richness, relative abundance, and community composition of individual trophic groups of protists in tropical lowland rainforest significantly differ from that in converted ecosystems. This is likely associated with changes in ecosystem functioning. The study provides novel insight into protist communities and their changes with land-use intensity in tropical lowland ecosystems. We show, that trophic groups of protists are powerful indicators reflecting changes in the functioning of ecosystems with conversion of rainforest into monoculture plantations.

Digging for DNA at depth: rapid universal metabarcoding surveys (RUMS) as a tool to detect coral reef biodiversity across a depth gradient.

BackgroundEffective biodiversity monitoring is fundamental in tracking changes in ecosystems as it relates to commercial, recreational, and conservation interests. Current approaches to survey coral reef ecosystems center on the use of indicator species and repeat surveying at specific sites. However, such approaches are often limited by the narrow snapshot of total marine biodiversity that they describe and are thus hindered in their ability to contribute to holistic ecosystem-based monitoring. In tandem, environmental DNA (eDNA) and next-generation sequencing metabarcoding methods provide a new opportunity to rapidly assess the presence of a broad spectrum of eukaryotic organisms within our oceans, ranging from microbes to macrofauna.MethodsWe here investigate the potential for rapid universal metabarcoding surveys (RUMS) of eDNA in sediment samples to provide snapshots of eukaryotic subtropical biodiversity along a depth gradient at two coral reefs in Okinawa, Japan based on 18S rRNA.ResultsUsing 18S rRNA metabarcoding, we found that there were significant separations in eukaryotic community assemblages (at the family level) detected in sediments when compared across different depths ranging from 10 to 40 m (p = 0.001). Significant depth zonation was observed across operational taxonomic units assigned to the class Demospongiae (sponges), the most diverse class (contributing 81% of species) within the phylum Porifera; the oldest metazoan phylum on the planet. However, zonation was not observed across the class Anthozoa (i.e., anemones, stony corals, soft corals, and octocorals), suggesting that the former may serve as a better source of indicator species based on sampling over fine spatial scales and using this universal assay. Furthermore, despite their abundance on the examined coral reefs, we did not detect any octocoral DNA, which may be due to low cellular shedding rates, assay sensitivities, or primer biases.DiscussionOverall, our pilot study demonstrates the importance of exploring depth effects in eDNA and suggest that RUMS may be applied to provide a baseline of information on eukaryotic marine taxa at coastal sites of economic and conservation importance.

Targeted Amplification and Sequencing of Ancient Environmental and Sedimentary DNA.

All organisms release their DNA into the environment through processes such as excretion and the senescence of tissues and limbs. This DNA, often referred to as environmental DNA (eDNA) or sedimentary ancient DNA (sedaDNA), can be recovered from both present-day and ancient soils, fecal samples, bodies of water and lake cores, and even air. While eDNA is a potentially useful record of past and present biodiversity, several challenges complicate data generation and interpretation of results. Most importantly, eDNA samples tend to be highly taxonomically mixed, and the target organism or group of organisms may be present at very low abundance within this mixture. To overcome this challenge, enrichment approaches are often used to target specific taxa of interest. Here, we describe a protocol to amplify metabarcodes or short, variable loci that identify lineages within broad taxonomic groups (e.g., plants, mammals), using the polymerase chain reaction (PCR) with established generic "barcode" primers. We also provide a catalog of animal and plant barcode primers that, because they target relatively short fragments of DNA, are potentially suitable for use with degraded DNA.

Analysis of the diversity of aerobic, thermophilic endospore-forming bacteria in two Algerian hot springs using cultural and non-cultural methods

Terrestrial hot environments are important resources for isolation of thermophilic microorganisms. Few studies have been made on microbial diversity of Algerian geothermal sites. This paper reports the diversity of thermophilic, aerobic endospore-forming bacteria from water and sediment samples taken from Hammam Ouled Ali and Hammam Debagh, two hot springs with a wide range of temperatures and a very rich mineral composition, located in the region of Guelma, north-east of Algeria using culture-dependent and culture-independent approaches Sequences of the V4 region of the 16S rRNA gene from environmental DNA extracted from sediment samples were analyzed and a set of isolates from water and sediment have been characterized by phenotypic and molecular methods. Phylogenetic surveys using environmental DNA sequences indicated that three families dominated the two hot springs: Planococcaceae, Bacillaceae, and Paenibacillaceae. Phenotypic characterization revealed the morphological, biochemical, and physiological properties of these microorganisms, all of which exhibited a range of common extracellular enzymatic activities. Amplified ribosomal DNA restriction analysis (ARDRA) was used to cluster isolates into different phylotypic groups and phylogenetic analysis of 16S rRNA gene sequences of selected isolates showed that all were closely related to four genera of thermophilic Bacilli: Bacillus, Anoxybacillus, Geobacillus, and Brevibacillus. Our results provide important insights into the microbial ecology of Guelma hot springs. They showed that the phylogenetic diversity of bacterial communities within the two studied hot springs was mostly aerobic, with the presence of taxonomic groups of great biotechnological interest. Bioprospection of thermozymes and other biomolecules within these communities will probably provide a data basis for their industrial exploitation.

Inventory of chytrid diversity in two temporary forest ponds using a multiphasic approach

ABSTRACTFood webs in temporary forest ponds are driven by decomposition of terrestrial inputs. Chytrid fungi are important components of the fungal community, degrading leaf litter in streams reliant on terrestrial inputs and in lake ecosystems where they may stabilize the food web. However, little is known about chytrid fungi in temporary forest ponds. We inventoried the chytrid diversity present in two temporary forest ponds via light microscopy of baited samples and ion semiconductor (Ion Torrent) sequencing of environmental DNA. We quantified trends of chytrid alpha and beta diversity as a function of spatial and temporal factors. A total of 59 chytrid taxa were detected throughout the study. Beta diversity exhibited variation across the sampled months for both the entire fungal community as well as for chytrids alone. Shifts in community composition were also apparent, although diversity metrics and composition patterns did not meet adjusted P values. The results of this study highlight the diversity of chytrid fungi in temporary forest ponds and the need for further studies on the spatial and temporal dynamics of chytrid species.

Toward an ecoregion scale evaluation of eDNA metabarcoding primers: A case study for the freshwater fish biodiversity of the Murray-Darling Basin (Australia).

High‐throughput sequencing of environmental DNA (i.e., eDNA metabarcoding) has become an increasingly popular method for monitoring aquatic biodiversity. At present, such analyses require target‐specific primers to amplify DNA barcodes from co‐occurring species, and this initial amplification can introduce biases. Understanding the performance of different primers is thus recommended prior to undertaking any metabarcoding initiative. While multiple software programs are available to evaluate metabarcoding primers, all programs have their own strengths and weaknesses. Therefore, a robust in silico workflow for the evaluation of metabarcoding primers will benefit from the use of multiple programs. Furthermore, geographic differences in species biodiversity are likely to influence the performance of metabarcoding primers and further complicate the evaluation process. Here, an in silico workflow is presented that can be used to evaluate the performance of metabarcoding primers on an ecoregion scale. This workflow was used to evaluate the performance of published and newly developed eDNA metabarcoding primers for the freshwater fish biodiversity of the Murray–Darling Basin (Australia). To validate the in silico workflow, a subset of the primers, including one newly designed primer pair, were used in metabarcoding analyses of an artificial DNA community and eDNA samples. The results show that the in silico workflow allows for a robust evaluation of metabarcoding primers and can reveal important trade‐offs that need to be considered when selecting the most suitable primer. Additionally, a new primer pair was described and validated that allows for more robust taxonomic assignments and is less influenced by primer biases compared to commonly used fish metabarcoding primers.

Diversity and Evolutionary History of the Symbiontida (Euglenozoa)

Several lineages of euglenozoans are enveloped with epibiotic bacteria and live in low oxygen and anoxic marine sediments, such as Bihospites bacati and Calkinsia aureus. A combination of shared ultrastructural traits and molecular phylogenetic inferences demonstrate that these lineages belong to a clade called the “Symbiontida”. Bihospites and Calkinsia possess all of the synapomorphies for the Euglenozoa plus several novel traits. Bihospites has a distinctive cell surface organization reminiscent of the pellicle strips in euglenids, a robust C-shaped feeding apparatus that encircles the nucleus, and a diverse community of epibiotic bacteria. Calkinsia has a novel “extrusomal pocket” and a thick (orange) extracellular matrix beneath a uniform layer of epibiotic bacteria. Despite the absence of molecular phylogenetic data, similar ultrastructural traits in Postgaardi mariagerensis and its epibiotic bacteria strongly suggest that this species is also a member of the Symbiontida. Molecular phylogenetic trees inferred from small subunit (SSU) ribosomal DNA sequences have shown that Bihospites and Calkinsia group strongly with a diverse set of environmental DNA sequences (eDNA) generated from low-oxygen marine samples collected at different depths from different locations around the world. These data demonstrate a diverse array of symbiontids that have yet to be characterized at the genomic, cellular, and behavior levels, which underscores how poorly we currently understand the biology and ecology of the group. Moreover, current data suggest that the communities of epibiotic bacteria associated with Bihospites, Calkinsia and Postgaardi co-evolved with their hosts and are metabolically integrated with modified mitochondria positioned immediately beneath the host’s plasma membrane. No symbiontid species has ever been cultivated, so improved knowledge about these eukaryotic organisms and their intimate relationships with bacteria in low oxygen environments will likely be achieved using culture-independent approaches, such as isolated-cell metagenomics.

The evolutionary signal in metagenome phyletic profiles predicts many gene functions

BackgroundThe function of many genes is still not known even in model organisms. An increasing availability of microbiome DNA sequencing data provides an opportunity to infer gene function in a systematic manner.ResultsWe evaluated if the evolutionary signal contained in metagenome phyletic profiles (MPP) is predictive of a broad array of gene functions. The MPPs are an encoding of environmental DNA sequencing data that consists of relative abundances of gene families across metagenomes. We find that such MPPs can accurately predict 826 Gene Ontology functional categories, while drawing on human gut microbiomes, ocean metagenomes, and DNA sequences from various other engineered and natural environments. Overall, in this task, the MPPs are highly accurate, and moreover they provide coverage for a set of Gene Ontology terms largely complementary to standard phylogenetic profiles, derived from fully sequenced genomes. We also find that metagenomes approximated from taxon relative abundance obtained via 16S rRNA gene sequencing may provide surprisingly useful predictive models. Crucially, the MPPs derived from different types of environments can infer distinct, non-overlapping sets of gene functions and therefore complement each other. Consistently, simulations on > 5000 metagenomes indicate that the amount of data is not in itself critical for maximizing predictive accuracy, while the diversity of sampled environments appears to be the critical factor for obtaining robust models.ConclusionsIn past work, metagenomics has provided invaluable insight into ecology of various habitats, into diversity of microbial life and also into human health and disease mechanisms. We propose that environmental DNA sequencing additionally constitutes a useful tool to predict biological roles of genes, yielding inferences out of reach for existing comparative genomics approaches.

BBI: an R package for the computation of Benthic Biotic Indices from composition data

The monitoring of impacts of anthropic activities in marine environments, such as aquaculture, oil-drilling platforms or deep-sea mining, relies on Benthic Biotic Indices (BBI). Several indices have been formalised to reduce the multivariate composition data into a single continuous value that is ascribed to a discrete ecological quality status. Such composition data is traditionally obtained from macrofaunal inventories, which is time-consuming and expertise-demanding. Important efforts are ongoing towards using High-Throughput Sequencing of environmental DNA (eDNA metabarcoding) to replace or complement morpho-taxonomic surveys for routine biomonitoring. The computation of BBI from such composition data is usually being undertaken by practitioners with excel spreadsheets or through custom script. Hence, the updating of reference morpho-taxonomic tables and cross studies comparison could be hampered. Here we introduce the R package BBI for the computation of BBI from composition data, either obtained from traditional morpho-taxonomic inventories or from metabarcoding data. Its aim is to provide an open-source, transparent and centralised method to compute BBI for routine biomonitoring.

Considerations and consequences of allowing DNA sequence data as types of fungal taxa

Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.

Assessment of Passive Traps Combined with High-Throughput Sequencing To Study Airborne Fungal Communities.

Techniques based on high-throughput sequencing (HTS) of environmental DNA have provided a new way of studying fungal diversity. However, these techniques suffer from a number of methodological biases which may appear at any of the steps involved in a metabarcoding study. Air is one of the most important environments where fungi can be found, because it is the primary medium of dispersal for many species. Looking ahead to future developments, it was decided to test 20 protocols, including different passive spore traps, spore recovery procedures, DNA extraction kits, and barcode loci. HTS was performed with the Illumina MiSeq platform targeting two subloci of the fungal internal transcribed spacer. Multivariate analysis and generalized linear models showed that the type of passive spore trap, the spore recovery procedure, and the barcode all impact the description of fungal communities in terms of richness and diversity when assessed by HTS metabarcoding. In contrast, DNA extraction kits did not significantly impact these results. Although passive traps may be used to describe airborne fungal communities, a study using specific real-time PCR and a mock community showed that these kinds of traps are affected by environmental conditions that may induce losses of biological material, impacting diversity and community composition results.IMPORTANCE The advent of high-throughput sequencing (HTS) methods, such as those offered by next-generation sequencing (NGS) techniques, has opened a new era in the study of fungal diversity in different environmental substrates. In this study, we show that an assessment of the diversity of airborne fungal communities can reliably be achieved by the use of simple and robust passive spore traps. However, a comparison of sample processing protocols showed that several methodological biases may impact the results of fungal diversity when assessed by metabarcoding. Our data suggest that identifying these biases is of paramount importance to enable a correct identification and relative quantification of community members.

GGBN Data Portal, GGBN Data Standard and GGBN Document Library

The GGBN Data Standard (https://terms.tdwg.org/wiki/GGBN_Data_Standard) provides a platform based on a documented agreement to promote the efficient sharing and usage of genomic sample material and associated specimen information in a consistent way. It builds upon existing standards commonly used within the community extending them with the capability to exchange data on tissue, environmental and DNA samples as well as sequences. The standard has been recently extended to support environmental DNA and High Throughput Sequencing (HTS) library samples. Both, eDNA and HTS library sample use cases have been published in the GGBN Sandbox (http://sandbox.ggbn.org) and will be presented here. The use case collection is documented in the GGBN wiki (http://wiki.ggbn.org/ggbn/Use_Case_Collection). In addition a general overview of the GGBN Data Portal (http://www.ggbn.org) will be given. Based on ABCD, DwC and the GGBN Data Standard the GGBN Data Portal is the gateway to standardized access of DNA, tissue and environmental samples and their associated specimens. The third core piece of GGBN is the GGBN Document Library (https://library.ggbn.org), today containing more than 300 documents about research, management and legal aspects of biodiversity biobanks. We will provide an overview of covered topics and gaps that the community can help to fill. Finally an outlook of goals and priority tasks for the next two years will be given.

Metagenomic sequencing of environmental DNA reveals marine faunal assemblages from the West Antarctic Peninsula

The West Antarctic Peninsula (WAP) is the fastest warming region in Antarctica where climate impact on the cold-adapted marine ecosystem is already visible. To monitor faunal changes in remote vast bodies of Antarctic waters, efficient and informative tools are essential. High-throughput sequencing of environmental DNA (eDNA) has emerged as one such tool for monitoring biodiversity and ecosystems, as it increases detection sensitivity of taxa, and sampling is often simpler and less costly than traditional collection methods. We collected water samples from four WAP shallow (≤300m) shelf regions, recovered the eDNA therein, and performed metagenomic shotgun sequencing and analyses to determine the effectiveness of this method to assess marine benthic faunal diversity; this includes the detection of deep-water predatory king crabs whose potential shoreward expansion to warming shelves has sparked much concern. Using a customized bioinformatics pipeline, we identified abundant signatures of common benthic invertebrate fauna, endemic notothenioid fishes, as well as lithodid king crabs. We also uncovered species richness and diversity comparable to biological inventories compiled by the use of traditional survey methods, supporting the efficacy of the eDNA shotgun sequencing approach. As the rate of eDNA degradation affects faunal detection sensitivity, we also quantified mitochondrial ND2 gene copies in eDNA derived from a WAP icefish and found ND2 copies persisted to at least 20days in the cold WAP water, much longer than values reported for temperate environments. We propose that eDNA metagenomic sequencing complements traditional sampling, and combining both will enable more inclusive biodiversity detection and faunal change monitoring in the vast Southern Ocean.

No single driver of biodiversity: divergent responses of multiple taxa across land use types

AbstractUnderstanding the responses of biodiversity to different land use regimes is critical for managing biodiversity in the face of future land use change. However, there is still significant uncertainty around how consistent the responses of different taxonomic groups to land use change are. Here, we use a combination of high‐throughput environmental DNA sequencing and traditional field‐based survey methods to examine how patterns of richness and community composition correlate among four domains/kingdoms (bacteria, fungi, plants, and metazoans) and the four most‐abundant animal taxonomic groups (arachnids, Collembola, insects, and nematodes) across five different land use types (natural forest, planted forest, unimproved grassland, improved grassland, and vineyards). Richness for each taxonomic group varied between land use types, yet different taxa showed inconsistent responses to land use, and their richness was rarely correlated. This contrasted with community composition of taxonomic groups, for which there was relatively good discrimination of land use types and there was strong correlation between group responses. We found little evidence for consistent drivers of taxonomic richness, yet identified several significant drivers of community composition that were shared across many groups. Drivers of composition were not the same as the drivers of diversity, suggesting diversity and composition are independently controlled. While land use intensification has been viewed as having generally negative effects on biodiversity, our results provide evidence that different taxa respond divergently across different land uses. Further, our study demonstrates the power of high‐throughput sequencing of environmental DNA as a tool for addressing broad ecological patterns relating to landscape biodiversity.