Ecosystems monitoring powered by environmental genomics: A review of current strategies with an implementation roadmap

Molecular Ecology, Год журнала: 2020, Номер 30(13), С. 2937 - 2958

Опубликована: Май 16, 2020

Abstract A decade after environmental scientists integrated high‐throughput sequencing technologies in their toolbox, the genomics‐based monitoring of anthropogenic impacts on biodiversity and functioning ecosystems is yet to be implemented by regulatory frameworks. Despite broadly acknowledged potential genomics this end, technical limitations conceptual issues still stand way its broad application end‐users. In addition, multiplicity implementation strategies may contribute a perception that routine methodology premature or “in development”, hence restraining regulators from binding these tools into legal Here, we review recent implementations methods, applied biomonitoring ecosystems. By taking general overview, without narrowing our perspective particular habitats groups organisms, paper aims compare, discuss strengths four for monitoring: (a) Taxonomy‐based analyses focused identification known bioindicators described taxa; (b) De novo bioindicator analyses; (c) Structural community metrics including inferred ecological networks; (d) Functional (metagenomics metatranscriptomics). We emphasise utility three latter integrate meiofauna microorganisms are not traditionally utilised because difficult taxonomic identification. Finally, propose roadmap programmes leverage analytical advancements, while pointing out current future research needs.

Язык: Английский

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Machine learning applications in microbial ecology, human microbiome studies, and environmental monitoring

Computational and Structural Biotechnology Journal, Год журнала: 2021, Номер 19, С. 1092 - 1107

Опубликована: Янв. 1, 2021

Advances in nucleic acid sequencing technology have enabled expansion of our ability to profile microbial diversity. These large datasets taxonomic and functional diversity are key better understanding ecology. Machine learning has proven be a useful approach for analyzing community data making predictions about outcomes including human environmental health. applied profiles been used predict disease states health, quality presence contamination the environment, as trace evidence forensics. appeal powerful tool that can provide deep insights into communities identify patterns data. However, often machine models black boxes specific outcome, with little how arrived at predictions. Complex algorithms may value higher accuracy performance sacrifice interpretability. In order leverage more translational research related microbiome strengthen extract meaningful biological information, it is important interpretable. Here we review current trends applications ecology well some challenges opportunities broad application communities.

Язык: Английский

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Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods

The Science of The Total Environment, Год журнала: 2021, Номер 818, С. 151783 - 151783

Опубликована: Ноя. 19, 2021

Environmental DNA (eDNA) metabarcoding (parallel sequencing of DNA/RNA for identification whole communities within a targeted group) is revolutionizing the field aquatic biomonitoring. To date, most studies aiming to assess ecological status ecosystems have focused on water eDNA and macroinvertebrate bulk samples. However, has also been applied soft sediment samples, mainly assessing microbial or meiofaunal biota. Compared classical methodologies based manual sorting morphological benthic taxa, offers potentially important advantages environmental quality sediments. The methods protocols utilized can vary considerably among studies, standardization efforts are needed improve their robustness, comparability use regulatory frameworks. Here, we review available information with focus sampling, preservation, extraction steps. We discuss challenges specific analysis, including variety different sources states its persistence in sediment. This paper aims identify good-practice strategies facilitate method harmonization routine future monitoring.

Язык: Английский

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Machine learning in marine ecology: an overview of techniques and applications

ICES Journal of Marine Science, Год журнала: 2023, Номер 80(7), С. 1829 - 1853

Опубликована: Авг. 3, 2023

Abstract Machine learning covers a large set of algorithms that can be trained to identify patterns in data. Thanks the increase amount data and computing power available, it has become pervasive across scientific disciplines. We first highlight why machine is needed marine ecology. Then we provide quick primer on techniques vocabulary. built database ∼1000 publications implement such analyse ecology For various types (images, optical spectra, acoustics, omics, geolocations, biogeochemical profiles, satellite imagery), present historical perspective applications proved influential, serve as templates for new work, or represent diversity approaches. Then, illustrate how used better understand ecological systems, by combining sources Through this coverage literature, demonstrate an proportion studies use learning, pervasiveness images source, dominance classification-type problems, shift towards deep all types. This overview meant guide researchers who wish apply methods their datasets.

Язык: Английский

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TICI: a taxon-independent community index for eDNA-based ecological health assessment

PeerJ, Год журнала: 2024, Номер 12, С. e16963 - e16963

Опубликована: Фев. 26, 2024

Global biodiversity is declining at an ever-increasing rate. Yet effective policies to mitigate or reverse these declines require ecosystem condition data that are rarely available. Morphology-based bioassessment methods difficult scale, limited in scope, suffer prohibitive costs, skilled taxonomists, and can be applied inconsistently between practitioners. Environmental DNA (eDNA) metabarcoding offers a powerful, reproducible scalable solution survey across the tree-of-life with relatively low cost minimal expertise for sample collection. However, there remains need condense complex, multidimensional community information into simple, interpretable metrics of ecological health environmental management purposes. We developed riverine taxon-independent index (TICI) objectively assigns indicator values amplicon sequence variants (ASVs), significantly improves statistical power utility eDNA-based bioassessments. The TICI model training step uses Chessman iterative learning algorithm assign scores large number ASVs commonly encountered wide geographic range. New sites then evaluated by averaging value present site. trained on eDNA dataset from 53 well-studied monitoring Zealand, each sampled high level biological replication ( n = 16). Eight short-amplicon assays were used generate broad taxonomic range, including bacteria, microeukaryotes, fungi, plants, animals. Site-specific strongly correlated historical stream macroinvertebrate assessments (macroinvertebrate MCI; R 2 0.82), variation replicates was (CV 0.013). Taken together, this demonstrates potential analysis provide reliable, robust low-cost assessment accessible managers, decision makers, wider community.

Язык: Английский

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Environmental DNA for biomonitoring

Molecular Ecology, Год журнала: 2021, Номер 30(13), С. 2931 - 2936

Опубликована: Июнь 27, 2021

In 2012, Molecular Ecology published a special issue on environmental DNA, which provided an overview of the field eDNA research and presented selection papers studies (Taberlet et al., 2012). This also introduced concept Biomonitoring 2.0, advocating for use DNA-based identification taxa in biodiversity surveys ecosystem assessment (Baird & Hajibabaei, Since then, hundreds have been covering various aspects eDNA-based biomonitoring from single-species detection to community impact assessments. Numerous reviews summarized these both freshwater marine environments (Bohmann 2014; Thomsen Willerslev, 2015). The progress made during last ten years has spectacular 2018). Although basic concepts workflow DNA barcoding metabarcoding not changed, technological advances high-throughput sequencing greatly facilitated access data. It become possible monitor with unprecedented precision depth. Massive genomic datasets rapidly generated at relatively low cost. analysis using machine learning other taxonomy-free approaches opened wide doors new groups bioindicators infer ecological status (Cordier 2018, 2019; Pawlowski al. At same time, constant efforts fill gaps reference databases considerably increased effectiveness taxonomic data (Weigand 2019). Astonishingly, rapid technologies are rather timidly implemented routine (Hering 2018; Shackleton 2021). 2.0 is widely endorsed, its acceptance practice hampered reasons. There no consensus whether should only apply conventional (Renovate) or include (Rebuild) (Revolutionize) (see Figure 1). Moreover, three main steps roadmap developed equally. attention given development optimization generation analysis. standardization methods their translation into legislatory framework remain very early stage. One issues impeding application tools concerns lack congruence between results traditional molecular analyses (Aylagas 2020). expected that method "safe use" if it provides almost as one. However, obtaining such perfect often impossible because character different (e.g., abundance individuals vs reads). "ecology" can hardly be translated directly species ecology. numerous biological technical biases affect processing data, impacting interpretation. addresses some challenges by presenting latest discussing strengths limitations when applied biomonitoring. comprises 29 grouped four sections applications. accompanied opinion paper, clarifies terminology relation (Pawlowski first section series analytical (e.g. learning), types shotgun sequencing) status. followed dedicated fish eDNA, whose most advanced. third dealing methodological comparison methods. final presents few examples applications population genetics. genomics enables monitoring microbial meiofaunal communities were previously inaccessible our knowledge ecology limited therefore analytic necessary integrate them bioassessment. begins review implementation strategies diagnostics authors introduce broad categories strategies, including (1) known bioindicators, (2) discovery (3) structural metrics, (4) functional metrics. Each adapted particular type (metabarcoding, metagenomics, metatranscriptomics) rely computational order provide Among tools, seems promising way predict this issue, performance tested case benthic diatoms index used quality rivers streams (Apothéloz-Perret-Gentil study shows supervised performs better than assignment, but predictions similar those obtained assignment approach. efficiency strongly depends completeness database, highlighting need existing gaps, particularly bioindicator taxa. ability de novo prokaryotic multiple anthropogenic impacts estuarine coastal demonstrated Lanzén (2021). compare macrofauna-based indices discuss advantages they more sensitive abiotic pressures. Similar conclusions reached aquaculture (Frühe 2021) oil gas industry (Mauffrey Both demonstrate promote environments. two explore directions further ecogenomic diagnostics. Broman (2021) RNA (eRNA) analyse organic enrichment micro-eukaryotic communities. Compared majority studies, eRNA advantage overcome potential PCR amplification capture organismic response pressures targeting predominantly active cells. Ibrahim historical analyze eutrophication lake phytoplankton 20th century. demonstrates paleo-metabarcoding characterize past establish conditions future monitoring. second diversity. We focus among important perspective advanced (Pont database common regions close (Knebelsberger 2015), fish-specific markers well defined (M. Miya 2015; Valentini 2016; Zhang 2020) protocols sampling established (Masaki 2020; 2016). Currently, considerable directed solve challenging related quantitative inferring Two address proposing estimate Fukaya numerical hydrodynamic models simulate spatial temporal distribution aquatic By integrating measures concentration, estimates comparable echo sounder method. Yates improve correlation concentration allometric scaling coefficients. Such coefficients help adjust values production taking consideration density, biomass metabolic rates characteristic taxon. A understanding how shaped biotic factors, subject following papers. Littlefair seasonal variations thermal stratification influence lakes. show follows niche species, turn may certain seasons. amphibian lentic system was investigated experimentally Brys indicates high decay dispersal, reinforcing accuracy retrieving spatiotemporal occupancy patterns. survey populations section. McColl-Gausden showed generally electrofishing conducting streams, while Aglieri strong complementarity visual capture-based General requires benchmarking against morphotaxonomy-based approaches. commonly achieved samples parallel assessing fit approaches, considered ground truth. bulk morphology-based They present propose solutions outcomes processing. comparative Suter evaluate water zooplankton open ocean, currently monitored continuous plankton recorders. recover morphological analyses, however, selected marker. conclude promising, still refinement before routinely drawn sediment macrofauna salmon farms (He found coherence relative inferred observed much stronger meiofauna, usually included studies. Significant differences extracts adjacent (Antich concluded poor proxy communities, although do exclude taxon-specific could importance marker emphasized macrobenthos metabarcoding. markers, key insect orders (Ephemeroptera, Plecoptera Trichoptera) Ficetola complexity process advocate cover widest range Combining shown match macrobenthic morphotaxonomic (Meyer multimarker approach recommended macroinvertebrate preservative (Martins Despite presence heavily sclerotized exoskeleton act limiting factor reported Gleason accurately represents local stream community, being overwhelmed non-metazoan sequences. difference comparing inventories pond macroinvertebrates (Harper consider complementary suggest combined comprehensive invertebrate community. tool ecosystems highlighted van Loos Nijland affecting improvements overcoming future. five sites Brazilian Atlantic forest one site Cerrado grasslands allowed Lopes (2020) significantly improves methods, confirming frog undetected For years, invertebrate-derived (iDNA) leech blood-meal track mammalian (Schnell Here, Drinkwater assess diversity across gradient degradation Borneo. elusive mammals, iDNA complements camera trapping. optimizations aiming improving surveys. Guerrieri soil preservation richness composition. guidelines optimizing agreement objectives practical constraints project. On hand, Mächler analysis, investigating stringency filtering estimates. Hill numbers comparisons differ articles ground-breaking biodiversity. Martel clearly paired modelling uncover metapopulation dynamics drivers. information endangered distributed metapopulations quite difficult obtain via inventories. Shum Palumbi reanalyzed dataset concerning cobble within kelp ecosystems. focussed intraspecific level structure demographic trends. increases scope value opening towards metaphylogeography (Turon Finally, Sigsgaard successfully tracked insects cow dungs environments, efficient diversity, easy As collection highly diverse. Their ranges tracking surveying impact. Some bioindication systems, whereas others expand inconspicuous, overlooked All attest major done methodology every step contribute understand factors analyses. Yet, despite huge advantages, taken off. now time move transform truly science. crisis global changes call urgent modernization environment. here, top levels scientific excellence many areas. Certainly, there inherent specificity, reason technology less morpho-taxonomic actions ensure build confidence through intercalibration tests. view substantial illustrated content reasonable expect will long coming. Open Access Funding Universite Geneve. conflict interest regarding paper.

Язык: Английский

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Planning and licensing for marine aquaculture

Reviews in Aquaculture, Год журнала: 2023, Номер 15(4), С. 1374 - 1404

Опубликована: Янв. 11, 2023

Marine aquaculture has the potential to increase its contribution global food system and provide valuable ecosystem services, but appropriate planning, licensing regulation systems must be in place enable sustainable development. At present, approaches vary considerably throughout world, several national regional investigations have highlighted need for reforms if marine is fulfil potential. This article aims map evaluate challenges of planning growth aquaculture. Despite range species, production circumstances, this study found a number common themes literature; complicated fragmented licensing, property rights licence operate, competition space spatial emerging species diversifying (seaweed production, Integrated Multi-Trophic Aquaculture [IMTA], nutrient carbon offsetting with aquaculture, offshore co-location multiuse platforms), address knowledge gaps use decision-support tools. Planning can highly complicated, so UK used as case show more detailed examples that highlight uncertainty industry, regulators policymakers face across interacting jurisdictions. There are many complexities, shows countries undergone, or undergoing, similar challenges, suggesting lessons learned by sharing experiences, even different systems, rather than having insular focus.

Язык: Английский

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Monitoring the ecological status of rivers with diatom eDNA metabarcoding: A comparison of taxonomic markers and analytical approaches for the inference of a molecular diatom index

Molecular Ecology, Год журнала: 2020, Номер 30(13), С. 2959 - 2968

Опубликована: Сен. 26, 2020

Abstract Recently, several studies demonstrated the usefulness of diatom eDNA metabarcoding as an alternative to assess ecological quality rivers and streams. However, choice taxonomic marker well methodology for data analysis differ between these studies, hampering comparison their results effectiveness. The aim this study was compare two markers commonly used in three distinct analytical approaches infer a molecular index. We values classical morphological index benchmark comparison. amplified sequenced both fragment rbc L gene V4 region 18S rRNA 112 epilithic samples from Swiss French rivers. inferred using approaches: by computing it directly taxonomically assigned sequences, calibrating de novo ecovalues all metabarcodes, supervised machine learning algorithm train predictive models. In general, obtained “taxonomy‐free” approaches, encompassing assignment learning, were closer correlated than based on sequences. correlations higher case compared marker, highlighting importance reference database which is more complete marker. Our confirms effectiveness operational tool assessment shows that by‐passing assignments are particularly efficient when databases incomplete.

Язык: Английский

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Environmental DNA gives comparable results to morphology-based indices of macroinvertebrates in a large-scale ecological assessment

PLoS ONE, Год журнала: 2021, Номер 16(9), С. e0257510 - e0257510

Опубликована: Сен. 21, 2021

Anthropogenic activities are changing the state of ecosystems worldwide, affecting community composition and often resulting in loss biodiversity. Rivers among most impacted ecosystems. Recording their current with regular biomonitoring is important to assess future trajectory Traditional monitoring methods for ecological assessments costly time-intensive. Here, we compared macroinvertebrates based on environmental DNA (eDNA) sampling traditional kick-net biodiversity patterns at 92 river sites covering all major Swiss catchments. From data, a biotic index (IBCH) 145 indicator taxa had been established. The was matched by taxonomically annotated eDNA data using machine learning approach. Our comparison diversity only uses zero-radius Operational Taxonomic Units assigned taxa. Overall, found strong congruence between both assessment total (gamma diversity). However, when assessing site level (alpha diversity), were less consistent gave complementary composition. Specifically, retrieved significantly fewer per than Importantly, however, subsequent classification rivers detected indicators resulted similar scores that classified random forest majority predictions (72%) from same status categories as Thus, validly communities and, combined learning, provided reliable classifications rivers. while gives macroinvertebrate approach, subsequently calculated indices nevertheless directly comparable consistent.

Язык: Английский

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Comparing sediment DNA extraction methods for assessing organic enrichment associated with marine aquaculture

PeerJ, Год журнала: 2020, Номер 8, С. e10231 - e10231

Опубликована: Окт. 27, 2020

Marine sediments contain a high diversity of micro- and macro-organisms which are important in the functioning biogeochemical cycles. Traditionally, anthropogenic perturbation has been investigated by identifying macro-organism responses along gradients. Environmental DNA (eDNA) analyses have recently advocated as rapid cost-effective approach to measuring ecological impacts efforts underway incorporate eDNA tools into monitoring. Before these methods can replace or complement existing methods, robustness repeatability each analytical step be demonstrated. One area that requires further investigation is selection sediment extraction method. samples were obtained disturbance gradient adjacent Chinook ( Oncorhynchus tshawytscha ) salmon farm Otanerau Bay, New Zealand. was extracted using four kits (Qiagen DNeasy PowerSoil, Qiagen PowerSoil Pro, RNeasy Total RNA/DNA extraction/elution Favorgen FavorPrep Soil Isolation Midi Kit) three volumes (0.25, 2, 5 g). Prokaryotic eukaryotic communities amplified primers targeting 16S 18S ribosomal RNA genes, respectively, sequenced on an Illumina MiSeq. Diversity community composition estimates from kit, well their relative performance established metabarcoding biotic indices. Differences observed quality quantity amongst with two performing best. Significant differences both prokaryotes eukaryotes p < 0.001) richness among kits. A small proportion amplicon sequence variants (ASVs) shared (~3%) although ASVs accounted for majority reads (prokaryotes: 59.9%, eukaryotes: 67.2%). abundance taxonomic classes revealed kit. Multivariate analysis showed there significant interaction between “distance” “kit” explaining communities, distance being stronger determinant composition. Comparison against bacterial index suggested all similar patterns environmental gradient. Overall, we advocate use when characterizing prokaryotic marine sediments. We base this conclusion higher values achieved compared other kits/amounts study. The additional advantage Kits extractions performed extractor robot, offering standardization reproducibility results.

Язык: Английский

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