Metabarcoding for Biodiversity Estimation

Elsevier eBooks, Journal Year: 2023, Volume and Issue: unknown, P. 388 - 407

Published: Oct. 18, 2023

Language: Английский

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Insights into Ecological & Evolutionary Processes via community metabarcoding

Molecular Ecology, Journal Year: 2023, Volume and Issue: 32(23), P. 6083 - 6092

Published: Nov. 24, 2023

This Special Issue brings together papers that highlight the power of high-throughput sequencing (HTS) data to address classic questions in ecology and evolution, particularly focused on metabarcoding (amplicon) datasets conjunction with complementary -omics types and/or models/theory infer overall ecosystem processes. We key show new technology related to: (i) dynamics community assembly how these may change across environmental conditions, successional processes extended evolutionary time; (ii) interaction networks, can predictable patterns over spatial temporal gradients, providing insights into biotic resilience. Studies also examined (iii) cross-scale interactions host-microbiome associations, critical developments demonstrating ease comparison integration scales organismic complexity allow at one scale inform other. These approaches are amenable (iv) studies invasive species homogenization, shifts alpha- beta-diversity a wide range scales. Biodiversity—the multiplicity life, from microbes macro-organisms genes ecosystems—is crisis, yet we have little understanding factors sustain biodiversity enhance its resilience perturbations (IPBES, 2019; Oliver et al., 2015). Key remain include interplay between niche neutral shaping communities (Mittelbach & McGill, 2019) associated role stochastic deterministic governing (Menéndez-Serra 2023); complexity-stability paradox (Domínguez-García 2019); metacommunity connection local regional diversity (Thompson 2020); extent which given exist equilibrium or steady state (Qian Akçay, 2020) concepts alternative stable states (Van Nes 2016), among others. been focus much theoretical development past, but ability generate needed validate theories has limited by difficulty sampling biological scale. However, without answers fundamental questions, left major gaps our resilience, sustainability strategies for restoration, all so effective conservation management ecosystems. The advance molecular profiling methods (e.g. metabarcoding-marker gene amplicon-based metagenomics, metatranscriptomics) recently provided remarkably toolkit measuring presents opportunity answer outstanding mentioned above. Moreover, because harness common tools both macro- micro-organisms, macroecological composition work Brown 2020). technological initiated dramatic shift measure ecological metrics within entire micro-organismal communities, they space time. In this Issue, as outline below, authors use high throughput technologies evolution make predictions. Describing structure their responses stressors primary objective research since inception. still struggle understand predict mechanisms accommodate collapse face (Urban 2016). Community methods, abundance taxa sites different age, nutrient availability forth, unprecedented assembly. New modelling (Overcast 2019, 2021) now being applied provide components govern process, hence might dictate issue, Overcast al. (2023) describe an eco-evolutionary simulation model uses community-scale genetic study there detectable signatures non-neutral simulated profiles. Applying soil microarthropod Cyprus, widespread low-elevation structured processes, while isolated high-elevation habitats shaped category included terrestrial marine systems, micro-organism assembly, comparisons complexity. For several respective roles filtering, conservatism/lability isolation animal site. Noguerales whole organism bulk DNA (Creedy 2022) operational taxonomic unit (OTU) level amplicon sequence variant (ASV) tease apart filtering microarthropods. showed OTU (species) richness follows altitudinal gradient, presumably niche-based processes; ASV contrasting pattern decline anthropogenic disturbance. paper Andujar (2022) mesofauna Canary Islands importance conservatism driver insular showing evidence lability, strong geographic structure. Likewise, Arjona focuses arthropod depths, highlighting (many records), results supporting hypothesis deeper beetle more dispersal compared those closer surface. Focusing loss Gaoligongshan National Park southwestern China, Li barcoding compare scenarios climate-change-induced loss, simulating extinction clustered season, elevation latitude. expectation was close relatives (as inferred phylogenetic affinities) would be buffered against history; is, if went extinct, clade represented other members. find not adequately shared history remaining after extinction. promise is presented Emerson who potential complement such barcode deep learning image recognition workflows way whole. Considering Macheriotou phylogenetics approach assess nematode ocean depth gradient. They increases up bathyal zone (200–4000 m), then decreases; moreover, clustering ASVs suggests assembled through filtering. Kiemel again (cytochrome oxidase, COI, 18S ribosomal RNA) ask zooplankton spatially temporally connected, what influencing underlying system. There no difference ephemeral permanent kettle holes (ponds formed retreating glaciers) suggest mainly based pH, water temperature, hole size hydroperiod. Species sorting dominant studied metacommunity. Likewise Govender point that, sheltered bights around South Africa lower pelagic due structural homogeneity, actually represent important fish spawning grounds (with ramifications fisheries higher-level consumers). case, measures could thus used proxy importance. Finally, Ip, Chang, Oh, combine standardised using Autonomous Reef Monitoring Structures (ARMS) test whether coral cover shapes organisms inhabiting hidden spaces reef matrix (the “cryptobiome”). fungi, bacteria, phytoplankton planktonic were impacted primarily abiotic (depth, particles column distance mainland), larger-sized metazoans cover. A number explicitly microbial communities. example, Pino 16S rRNA ITS microbiomes (bacteria fungi) large edaphic climatic gradients Australia science macroecology: Are broad classifications sufficient capture function, large-scale determine turnover composition? classes predictive bacterial fungal regardless proximity, natural cultivated soils reliably distinct microbiomes, drivers microbiome differences pH temperature cycles. Van der Loos explore environment host genotype stability variability composition. Using seaweed-associated along salinity able identify small group core possibly involved adaptation host. experimental Nappi tested effects two strains succession green macroalga Ulva australis. Both exert priority effect, strain (D2) causing initially temporary changes profile community, second (D323) weaker consistent predominantly facilitatory benefit algal Priority do appear simple replacement functionally equivalent taxa, result functional community. Besides implications ecology, provides probiotics human health agriculture). examine (macro- micro-organisms). Wang microorganisms (bacteria, mostly influenced larger (nematodes) deterministic; independent habitat (including topographic variables) plant attributes significantly decreased increasing body size; leaf phosphorus directly distribution soil-available phosphorus, indicates indirect impact Data multitrophic explained some above-ground attributes. Guerrieri multi-locus deglaciated soils, focusing six groups (Eukaryota, Bacteria, Mycota, Collembola, Insecta Oligochaeta) asking time following deglaciation, differs layers. within, homogenization between, layers, deglaciation. likely during succession. Another area properties networks reflect functioning macro-organismal (Banerjee (Peixoto Metabarcoding ideal relating quantitative assessment perturbation. Highlighting holistic interacting assemblages trophic groups, Ficetola Taberlet review reveal response global change. information only occurrences, interactions, traits, information, machine algorithms multitaxa interactions. means detecting Yin cryptic Sow 2019). novel long-read approaches, Lu focussed comparing mycobiomes marine, gut samples; found highest diversity, unknown species, followed sediments. Recent revealed entirely plant-pollinator Bell opportunities modification land-use. consider particular, time, including impacts climate stressors. Similar shown (eDNA) flowers pollinating bumblebees complex (Harper 2023). Lowe empirical example pollen honey samples honeybee (Apis mellifera) seasonal diet specialisation according resource availability. Because degree linked network highlighted vulnerability. Along similar lines, Encinas-Viso drive beta alpine By analysing insect loads generated diverse less specialised observational data. supported leads fine-scale Tommasi fragmentation networks. metabarcoding, analysed pollinator richness, pollination efficiency landscapes levels Maldives Islands. Contrary expectations, moderate increase pollinators, intermediate disturbance hypothesis. Despite harbouring fragmented resulted detrimental service. concerning finding preference native pollinators additionally speeding spread. look dietary partitioning. Ando hundreds faecal seven ducks partitioning opportunistic foraging when invertebrates available food source. Several gradients. Srivathsan tests fly-vertebrate any specialisation. sampled dung carrion fly gradient swamp forest remnant Singapore. While vertebrate effect roads presence endangered rainforest eDNA monitoring tool. Pitteloud faeces specific hypotheses regarding plant–orthoptera bipartite governed position where herbivores feed plants identity abundance, proportion species. aspects shape particular nitrogen content warmer environments, phenolics terpenoids colder environments. Dürrbaum urbanisation levels. herbivorous bees prey wasp nests, predator–prey levels, negative stronger predators than herbivores, increased requirement larger, unfragmented habitat. control reviewed Lue it identification hyperparasitism multiparasitism, disrupt introduced agents. High-throughput set Tun, multilocus reefs parallel corals coral-associated inversion pyramid events numbers (secondary tertiary consumers) predation eggs planktivorous fish. Over Graham Hawaiian Island geological become progressively 5 million year period. arthropod-plant average per (linkage density), ratio (vulnerability), uniformity energy flow (interaction evenness) suggesting progression towards adoption avenues scales, animals sharing same analytical profiling. When samples, suite sequencing-based methodologies enables characterisation organismal ranging macro−/micro-organismal function down traits individual taxa. Thus, conduct analyses micro-scale parallels, Câmara dos Reis relative ecologically bloom-forming Through combination (field sampling) (microcosm) bloom succession, phytoplanktonic whereas prevalent outside blooms. microbiome, looking niche. Michel investigate geographically genetically differentiated populations critically Grauer's gorilla. marked (though populations, social, ecological, factors. Manthey holometabolous microbiota rapidly remoulds metamorphosis, allowing exploration niches ontogenesis. ontogeny, higher insects hemimetabolous insects. shedding ontogenesis open explain success considered affect biogeochemical cycling web dynamics. viral infection dynamics, Merges activity bacteria bacteriophages co-declines elevational transcriptome transect Swiss Alps metabolic declined elevation, did not, gap relationships contributions carbon, cycling. Pereira tunicate remineralisation. pellet processing tunicates webs nitrogen, sulphur carbon Hu examines protistan separated deep-sea hydrothermal vent Their suggested archaea, turn chemistry environment. highlights influence selective pressures eukaryotic vents. fine adaptation. To relationships, Molina climate, site, variables structuring sapwood-inhabiting climatic, site North Patagonian Nothofagus forests. Remarkable tight relationship hosts microbiome. Rolshausen measured predictability multi taxon holobiont genome analysis fungal, lichen holobionts chemically morphologically indistinguishable, exhibit pronounced compositional elevation. happens concerted fashion three components, coadaptation diversification. Kivistik combined (salinity antibiotics) gastrointestinal aquatic gastropods. transition led viability, generalists gut. Brinker population structure, conditions endosymbiont simultaneously investigated parasitic similarity Wolbachia infected (asexually reproducing) uninfected (sexually hosts. High imparting disease Navine resistance avian malaria birds Hawaii, native, introduced. Neither alpha nor covaried infection, 149 positive associations survivors, possible candidates facilitate immunity birds. component observed patterns, something difficult. Perez-Lamarque Morlon evaluated widely inferring cophylogenetic aim differentiate vertical transmission host-switching. simulations type-I error rate trade-offs computational statistical performance methods. conclude current method optimal recommendations under most appropriate. Homogenization seascapes arrival non-native subsequent erosion services (Díaz 2018) buffering tipping points regime (Nyström teasing them out natives difficult task, especially phyla (Essl 2018). Perhaps difficulty, argued must incorporated decisions (Sax 2022), though scientific rationale establish substantial literature indicating co-evolved nature (Pauchard First, detectability, systems (Valentin addition, intriguing tool signature derived separate, bioinformatically, (Andersen employed special issue (Graham 2022; Kennedy 2022). developed context equally invasions humans assemblages. demonstrate disturbed paves applying biodiversity, modification. Hampel undersea “built habitats” (shipwrecks) causes surrounding sediments (extending 300 m wrecks). Specific archaeal enrichment shipwrecks, chemolithoautotrophy proximate Similarly, Andrés homogenising shipping, route-based models ship-borne dissimilarity, reduce dissimilarity commercial port habitats. As previous sections, invasion and, phenomenon resistance, reduction maintained resident (Levine 2004). Notably, age comparable MY timeframe. Results lowest (on youngest island), infiltration highest. survey community-wide incursion non-natives archipelagos Pacific. island each differ respect area, habitat, defined predictions surveys. older correspondingly invasion, lead degraded forests archipelagos. made theme areas above, recurring themes emerged multiple studies: Museums play approaches. many gained sequences alone, reference collection (i.e. barcodes identified specimens) adds dimensionality allows us morphological every sample, status introduced, relationships. specimen thoroughly confirmed, misidentification flawed interpretations. rather diminishing museums vast increasingly (Valdivia-Carrillo 2021). vetted curated library studies. emphasise limitations inference database, introduce operon database (FRODO) 1116 taxonomically museum specimens historic past bee decadal plants, (Bell Gous shows (Heindler parasite–host (Greiman Early generally grouped Operational Taxonomic Units (OTUs), assumed correspond purpose step remove known noise data, grouping denoising gaining population-level (Noguerales aspect tremendously informative Large tremendous amount potentially about structures, well like remotely sensed bioclimatic variables. Moving beyond descriptive statistics correlations massive will require adopting powerful manuscripts exemplified. visual effectively (2022). supervised sediment sample proximity shipwrecks frequency (Hampel Machine paired interact demonstrated (2023). relation precipitation, nutrients, anthropogenically modifications. specimens, ancient sediments, sub-fossils diet, host-associations, parasitism, changed; chronosequences periods. includes mixture studies, approximately half macro-organisms, microorganisms. here real microorganisms, learned robust, easier realise intractable science. All worked develop served editors manuscripts. HMB wrote first draft manuscript, RGG, contributing final version. largely conceived working sEcoEvo -Biodiversity Dynamics: Nexus Between Space Time, sDiv, Synthesis Centre German Integrative Biodiversity Research (iDiv), additional workshop Science Foundation DEB 2135502: Insights Macro-Ecology Macro-Evolution Assessment (PI RGG) 1927510 Rules Of Life (RoLE) Model Uncover Fundamental Processes Governing AJR). declare conflict interest. applicable article created analyzed study.

Language: Английский

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Metagenomic ecosystem monitoring of soft scale insects and mealybug communities

OENO One, Journal Year: 2023, Volume and Issue: 57(4)

Published: Nov. 17, 2023

Soft scale insects and mealybugs are phloem-feeding Hemipterans that considered major pests in agriculture horticulture throughout the world. However, correct taxonomic identification field can be difficult, making it hard for growers to implement control strategies. In viticulture, soft a issue due their ability secrete honeydew, which facilitates development of sooty mould, propensity being transmission vectors several viral diseases grapevine. To facilitate rapid quantification vineyard-associated metagenomic-based bioinformatic pipeline (MitoMonitor) was developed generalised ecosystem monitoring, automated assembly classification insect mitochondrial genomes from shotgun sequencing data using Barcode Life Database API. The proof-of-concept application MitoMonitor on metagenomic obtained eight samples South Australian vineyards led Parthenolecanium corni (European fruit scale)—which thought absent vineyards—as dominant coccoid species across samples, with less frequent, also lower abundance Pseudococcus viburni (obscure mealybug) Pseudo. longispinus (long-tailed mealybug). addition, parisitoidism by Coccophagus scutellaris (Aphelinidae) wasps detected. discovery Parth. as member communities these has significant implications effective strategies this important group affected areas.

Language: Английский

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Prospects of pollinator community surveillance using terrestrial environmental DNA metagenetics

Environmental DNA, Journal Year: 2023, Volume and Issue: 6(1)

Published: Dec. 21, 2023

Abstract Current pollinator survey methods exhibit bias, require highly‐trained practitioners, and are difficult to scale large sample sizes. High‐throughput sequencing of terrestrial eDNA could provide a complementary tool for studying communities, but have not been extensively evaluated. We conducted metagenetic analysis whole arthropod community from 20 flower seven honey bee‐collected pollen samples compared eDNA‐derived data with traditional netting‐based surveys the communities present during sampling. focused our on Anthophila (bees) detected eight bee genera belonging four families across COI, 16S, 28S markers. Results varied considerably by marker substrate. Detected were plausible study system about 43 percent total both net‐based surveys, though netting resulted in more detections wider diversity genera. Data sequenced controls suggest that identifications unlikely cross‐contamination. Our results demonstrate can be documented techniques choice substrate substantially influences detection. Future improvements required, appear well‐suited characterize diverse novel sampling perspectives within plant‐pollinator networks. efforts should focus improving selection markers available metagenetics, addressing taxonomic gaps reference sequence databases optimizing isolation protocols. anticipate such highly feasible will useful those who pollinators interactions.

Language: Английский

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Design and partial validation of novel eDNA qPCR assays for three common North American tick (Arachnida: Ixodida) species

Environmental DNA, Journal Year: 2024, Volume and Issue: 6(2)

Published: March 1, 2024

Abstract The range expansion of ticks to higher latitudes poses a severe threat human health exposing populations who had no prior contact with several harmful tick‐borne diseases. Early detection in new areas is critical help inform the public and medical professionals dangers associated tick encounters. Environmental DNA represents novel survey method that could provide reliable records occurrences timely warnings their expansions. In this study, we designed eDNA qPCR assays for three common North American species ( Dermacentor variabilis , Amblyomma americanum Ixodes scapularis ) tested them on 51 samples grasses leaf litter collected from 12 grassland forest sites central southern Illinois. We silico vitro validation all assays; however, were unable generate any positive detections field samples. Our lack likely stems low deposition rates coupled rapid degradation grasslands forests, problem exacerbated by terrestrial sampling methods limited volume substrate. recommendations improving sample collection increase probability future efforts. Continued research should focus viability detect small invertebrates, like ticks, it potential as early warning indicator spread vector‐borne

Language: Английский

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Spatio-temporal variation in arthropod-plant interactions: A direct comparison of eDNA metabarcoding of tree crop flowers and digital video recordings

Ecological Indicators, Journal Year: 2024, Volume and Issue: 169, P. 112827 - 112827

Published: Nov. 12, 2024

Language: Английский

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Metagenomic ecosystem monitoring of soft scale and mealybug infestations in Australian vineyards

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: July 30, 2023

Abstract Soft scale insects and mealybugs are phloem feeding Hemipterans that considered majors pests in agricultural horticultural settings throughout the world. Viticulturally, a major issue due to their ability secrete honeydew, which facilitates development of sooty mould for propensity as transmission vectors several viral diseases grapevine. To facilitate rapid identification quantification vineyard-associated metagenomic-based bioinformatic pipeline was developed generalised ecosystem monitoring automated assembly classification insect mitochondrial genomes from shotgun sequencing data using Barcode Life Database API. Parthenolecanium corni (European fruit scale), thought be absent Australian grapevines, identified dominant coccid species infesting all vines sampled, along with secondary infestation by Pseudococcus viburni (obscure mealybug) Pseudo. longispinus (long-tailed mealybug). In addition, parisitoidism Coccophagus scutellaris (Aphelinidae) wasps also detected. The discovery Parth. significant member infestations Australia has implications effective control strategies this important group pests.

Language: Английский

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