Counting with DNA in metabarcoding studies: How should we convert sequence reads to dietary data?

Molecular Ecology, Journal Year: 2018, Volume and Issue: 28(2), P. 391 - 406

Published: June 2, 2018

Abstract Advances in DNA sequencing technology have revolutionized the field of molecular analysis trophic interactions, and it is now possible to recover counts food sequences from a wide range dietary samples. But what do these mean? To obtain an accurate estimate consumer's diet should we work strictly with data sets summarizing frequency occurrence different taxa, or use relative number sequences? Both approaches are applied semi‐quantitative summaries, but often promoted as more conservative reliable option due taxa‐specific biases recovery sequences. We explore representative metabarcoding point out that summaries based on overestimate importance consumed small quantities (potentially including low‐level contaminants) sensitive count threshold used define occurrence. Our simulations indicate using read abundance ( RRA ) information provides view population‐level even moderate incorporated; however, impacting common taxa. when mean taxa samples small. The ideas presented here highlight need consider all sources bias justify methods interpret studies. encourage researchers continue addressing methodological challenges acknowledge unanswered questions help spur future investigations this rapidly developing area research.

Language: Английский

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Feeding habits and multifunctional classification of soil‐associated consumers from protists to vertebrates

Biological reviews/Biological reviews of the Cambridge Philosophical Society, Journal Year: 2022, Volume and Issue: 97(3), P. 1057 - 1117

Published: Jan. 20, 2022

Soil organisms drive major ecosystem functions by mineralising carbon and releasing nutrients during decomposition processes, which supports plant growth, aboveground biodiversity and, ultimately, human nutrition. ecologists often operate with functional groups to infer the effects of individual taxa on services. Simultaneous assessment roles multiple is possible using food-web reconstructions, but our knowledge feeding habits many insufficient based limited evidence. Over last two decades, molecular, biochemical isotopic tools have improved understanding various soil organisms, yet this still be synthesised into a common framework. Here, we provide comprehensive review consumers in soil, including protists, micro-, meso- macrofauna (invertebrates), soil-associated vertebrates. We integrated existing group classifications findings gained novel methods compiled an overarching classification across focusing key universal traits such as food resource preferences, body masses, microhabitat specialisation, protection hunting mechanisms. Our summary highlights strands evidence that commonly used ecology models are types resources. In cases, omnivory observed down species level taxonomic resolution, challenging realism traditional distinct resource-based energy channels. Novel methods, stable isotope, fatty acid DNA gut content analyses, revealed previously hidden facets trophic relationships consumers, assimilation, multichannel levels, niche differentiation importance alternative food/prey, well transfers compartments. Wider adoption development open interoperable platforms assemble morphological, ecological data will enable refinement expansion multifunctional soil. The serve reference for working changes biodiversity-ecosystem functioning relationships, making research more accessible reproducible.

Language: Английский

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A Paradigm Shift in the Trophic Importance of Jellyfish?

Trends in Ecology & Evolution, Journal Year: 2018, Volume and Issue: 33(11), P. 874 - 884

Published: Sept. 20, 2018

Language: Английский

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Feeding studies take guts – critical review and recommendations of methods for stomach contents analysis in fish

Journal of Fish Biology, Journal Year: 2019, Volume and Issue: 95(6), P. 1364 - 1373

Published: Oct. 7, 2019

Abstract Studies on the feeding ecology of fish are essential for exploring and contrasting trophic interactions population community dynamics within among aquatic ecosystems. In this respect, many different methods have been adopted analysis stomach contents. No consensus has, however, reached a standardised methodology despite that several decades there has an ongoing debate about which methodical approaches should be preferred. Here, we critically review scrutinise methods, addressing their strengths weaknesses emphasising inherent problems possible pitfalls in use. Although our critical assessment reveals no completely ideal approach exists, appropriate reliable procedures can through careful considerations implementation. particular, advocate objectives require choice method therefore closely linked to research questions addressed. For standardisation recommend combination relative‐fullness presence–absence as optimal commonly applied studies relative dietary composition terms prey diversity abundance. Additionally, gravimetric related quantification food consumption rates numerical selection studies. DNA‐based provides new promising complementary visual examination contents, although some technical challenges still exist. The suggested facilitates comparisons across species, ecosystems time will enhance applicability benefits research.

Language: Английский

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Causes and consequences of ontogenetic dietary shifts: a global synthesis using fish models

Biological reviews/Biological reviews of the Cambridge Philosophical Society, Journal Year: 2018, Volume and Issue: 94(2), P. 539 - 554

Published: Sept. 24, 2018

ABSTRACT Ontogenetic dietary shifts (ODSs), the changes in diet utilisation occurring over life span of an individual consumer, are widespread animal kingdom. Understanding ODSs provides fundamental insights into biological and ecological processes that function at individual, population community levels, is critical for development testing hypotheses around key concepts trophic theory on model organisms. Here, we synthesise historic contemporary research fishes, identify where further required. Numerous biotic abiotic factors can directly or indirectly influence ODSs, but most influential these may vary spatially, temporally interspecifically. Within constraints imposed by prey availability, identified competition predation risk as major drivers fishes. These do not affect ontogeny have indirect effect trajectories through ontogenetic habitat use concomitant availability. The synthesis compelling evidence profound consequences fish by, example, enhancing growth lifetime reproductive output reducing mortality. also food‐web dynamics facilitate coexistence sympatric species resource partitioning, currently lack a holistic understanding population, ecosystem functioning. Studies attempting to address knowledge gaps largely focused theoretical approaches, empirical under natural conditions, including phylogenetic evolutionary considerations, required test concepts. Research focusing inter‐individual variation has been limited, with complex relationships between behaviour environmental heterogeneity representing particularly promising area future research.

Language: Английский

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Connected macroalgal‐sediment systems: blue carbon and food webs in the deep coastal ocean

Ecological Monographs, Journal Year: 2019, Volume and Issue: 89(3)

Published: May 23, 2019

Abstract Macroalgae drive the largest CO 2 flux fixed globally by marine macrophytes. Most of resulting biomass is exported through coastal ocean as detritus and yet almost no field measurements have verified its potential net sequestration in sediments. This gap limits scope for inclusion macroalgae within blue carbon schemes that support globally, understanding role their plays distal food webs. Here, we pursued three lines evidence (eDNA sequencing, Bayesian Stable Isotope Mixing Modeling, benthic‐pelagic process measurements) to generate needed, novel data addressing this gap. To end, a 13‐month study was undertaken at deep sedimentary site English Channel, surrounding shoreline Plymouth, UK. The eDNA sequencing indicated from most shores occurs deep, sediments, with supply reflecting seasonal ecology individual species. stable isotope mixing modeling [C N] highlighted vital supporting benthic web (22–36% diets), especially when other resources are seasonally low. magnitude uptake sediments varies seasonally, an average organic macroalgal 8.75 g C·m −2 ·yr −1 . particulate 58.74 , two rates corresponding 4–5% 26–37% those associated mangroves, salt marshes, seagrass beds, systems more readily identified habitats. These provide important first estimates help contextualize importance macroalgal‐sedimentary connectivity webs, measured fluxes constrain global can policy development. At time climate change mitigation foreground environmental development, embracing full regulation via necessity.

Language: Английский

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Methylmercury exposure in wildlife: A review of the ecological and physiological processes affecting contaminant concentrations and their interpretation

The Science of The Total Environment, Journal Year: 2019, Volume and Issue: 711, P. 135117 - 135117

Published: Nov. 21, 2019

Language: Английский

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Studying animal niches using bulk stable isotope ratios: an updated synthesis

Oecologia, Journal Year: 2020, Volume and Issue: 193(1), P. 27 - 51

Published: May 1, 2020

Language: Английский

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Advancing the integration of multi‐marker metabarcoding data in dietary analysis of trophic generalists

Molecular Ecology Resources, Journal Year: 2019, Volume and Issue: 19(6), P. 1420 - 1432

Published: July 23, 2019

Abstract The application of DNA metabarcoding to dietary analysis trophic generalists requires using multiple markers in order overcome problems primer specificity and bias. However, limited attention has been given the integration information from markers, particularly when they partly overlap taxa amplified, vary taxonomic resolution biases. Here, we test use a mix universal specific provide criteria integrate multi‐marker data python script implement such produce single list ingested per sample. We then compare results based on morphological methods, proposed combination markers. study was 115 faeces small passerine, Black Wheatears ( Oenanthe leucura ). Morphological detected far fewer plant (12) than either 18S marker (57) or trn L (124). This may reflect detection secondary ingestion by molecular methods. identification also (23) (91) arthropod IN16STK (244) ZBJ (231), though each method missed underestimated some prey items. Integration provided more detailed any estimated higher frequencies occurrence all taxa. Overall, our show value integrating multiple, taxonomically overlapping an example set.

Language: Английский

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How much is enough? Effects of technical and biological replication on metabarcoding dietary analysis

Molecular Ecology, Journal Year: 2018, Volume and Issue: 28(2), P. 165 - 175

Published: June 25, 2018

DNA metabarcoding is increasingly used in dietary studies to estimate diversity, composition and frequency of occurrence prey items. However, few have assessed how technical biological replication affect the accuracy diet estimates. This study addresses these issues using European free-tailed bat Tadarida teniotis, involving high-throughput sequencing a small fragment COI gene 15 separate faecal pellets 15-pellet pool per each 20 bats. We investigated descriptors were affected by variability among (a) individuals, (b) individual (c) PCRs pellet. In addition, we impact (d) analysing vs. pellet pools. found that diversity estimates increased steadily with number analysed individual, seven required detect ~80% species. Most variation was associated differences bats, followed The bat, highest error rates recorded for consumed infrequently many individuals. Pools provided poor occurrence, which comparable single consistently missed less common Overall, our results stress maximizing critical emphasize several samples rather than pooled produce more accurate results.

Language: Английский

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