Nature Ecology & Evolution, Год журнала: 2020, Номер 4(5), С. 712 - 724
Опубликована: Янв. 13, 2020
Язык: Английский
Communications Biology, Год журнала: 2021, Номер 4(1)
Опубликована: Фев. 22, 2021
Abstract Environmental DNA (eDNA) metabarcoding is a sensitive and widely used approach for species detection biodiversity assessment. The most common eDNA collection method in aquatic systems actively filtering water through membrane, which time consuming requires specialized equipment. Ecological studies investigating abundance or distribution often require more samples than can be practically collected with current filtration methods. Here we demonstrate how passively both tropical temperate marine by directly submerging filter membranes (positively charged nylon non-charged cellulose ester) the column. Using universal fish assay, show that passive detect as effectively active methods also provide similar estimates of total biodiversity. Furthermore, enables greater levels biological sampling, increases range ecological questions address.
Язык: Английский
Процитировано
110
Metabarcoding and Metagenomics, Год журнала: 2022, Номер 6
Опубликована: Июль 22, 2022
The worldwide rapid declines in insect and plant abundance diversity that have occurred the past decades gained public attention demand for political actions to counteract these are growing. Rapid large-scale biomonitoring can aid observing changes provide information decisions land management species protection. Malaise traps long been used sampling when insects captured traps, they carry traces of plants visited on body surface or as digested food material gut contents. Metabarcoding offers a promising method identifying traces, providing insight into with which directly interacting at given time. To test efficacy DNA metabarcoding sample types, 79 samples from 21 sites across Germany were analysed ITS2 barcode. This study, our knowledge, is first examination trap samples. Here, we report feasibility sequencing analysis resulting taxa, usage cultivated by near nature conservancy areas detection rare neophyte species. Due frequency contamination false positive reads, isolation PCR negative controls should be every reaction. has advantages efficiency resolution over microscopic identification pollen only possible other could broad utility future studies plant-insect interactions.
Язык: Английский
Процитировано
109
Methods in Ecology and Evolution, Год журнала: 2021, Номер 13(3), С. 694 - 710
Опубликована: Дек. 4, 2021
Abstract Metabarcoding provides a powerful tool for investigating biodiversity and trophic interactions, but the high sensitivity of this methodology makes it vulnerable to errors, resulting in artefacts final data. studies thus often utilise minimum sequence copy thresholds (MSCTs) remove that remain datasets; however, there is no consensus on best practice use MSCTs. To mitigate erroneous reporting results inconsistencies, study discusses guidance best‐practice filtering metabarcoding data ascertainment conservative accurate Several most commonly used MSCTs were applied example datasets Eurasian otter Lutra lutra cereal crop spider (Araneae: Linyphiidae Lycosidae) diets. Changes both method threshold value considerably affected resultant Of tested, was concluded optimal examples given combined sample‐based with removal maximum taxon contamination, providing stringent while retaining target Choice differed between due variation artefact abundance sequencing depth, should employ controls (mock communities, negative DNA unused MID tag combinations) select values appropriate each individual study.
Язык: Английский
Процитировано
106
Science, Год журнала: 2019, Номер 364(6436), С. 173 - 177
Опубликована: Март 8, 2019
Populations of the world's largest carnivores are declining and now occupy mere fractions their historical ranges. Theory predicts that when apex predators disappear, large herbivores become less fearful, new habitats, modify those habitats by eating food plants. Yet experimental support for this prediction has been difficult to obtain in large-mammal systems. After extirpation leopards African wild dogs from Mozambique's Gorongosa National Park, forest-dwelling antelopes [bushbuck (Tragelaphus sylvaticus)] expanded into treeless floodplains, where they consumed novel diets suppressed a common plant [waterwort (Bergia mossambicensis)]. By experimentally simulating predation risk, we demonstrate behavior was reversible. Thus, whereas anthropogenic predator extinction disrupted trophic cascade enabling rapid differentiation prey behavior, carnivore restoration may just as rapidly reestablish cascade.
Язык: Английский
Процитировано
141
Nature, Год журнала: 2019, Номер 570(7759), С. 58 - 64
Опубликована: Июнь 5, 2019
Язык: Английский
Процитировано
141
Ecological Entomology, Год журнала: 2019, Номер 45(3), С. 373 - 385
Опубликована: Дек. 30, 2019
1. DNA metabarcoding is a cost‐effective species identification approach with great potential to assist entomological ecologists. This review presents practical guide help ecologists design their own studies and ensure that sound ecological conclusions can be obtained. 2. The considers approaches field sampling, laboratory work, bioinformatic analyses, the aim of providing background knowledge needed make decisions at each step workflow. 3. Although most conventional sampling methods adapted metabarcoding, this highlights techniques will suitable preservation during storage. also calls for greater understanding occurrence, transportation, deposition environmental when applying different ecosystems. 4. Accurate detection needs consider biases introduced extraction PCR amplification, cross‐contamination resulting from inappropriate amplicon library preparation, downstream analyses. Quantifying abundance in its infancy, yet recent demonstrate promise estimating relative sequencing reads. 5. Given bioinformatics one biggest hurdles researchers new several useful graphical user interface programs are recommended sequence data processing, application emerging technologies discussed.
Язык: Английский
Процитировано
141
Environmental DNA, Год журнала: 2020, Номер 2(4), С. 493 - 504
Опубликована: Фев. 20, 2020
Abstract Fish biodiversity can be measured by capturing and then sequencing free DNA present in water. Such environmental (eDNA) methods offer an effective, noninvasive tool for species diversity measurement, although standardized protocols are not yet developed. We investigate how metrics of fish revealed through eDNA analysis water influenced sampling volume. Water samples were collected from the intertidal reef Browse Island, a tropical, remote island Timor Sea. Aliquots single 20,700‐ml sample multiple 2,000‐ml filtered various volumes (25–2,000 ml) across two membrane sizes (0.20 0.45 µm). A metabarcoding assay was used to characterize within aliquots. All samples, except one, yielded sequences. Two hundred nine operational taxonomic units (cf. species) representing 48 families identified complete collection contained all comparable 200 detected using conventional surveys at this location. Notable additions cryptic nocturnal species. Nevertheless, large differences composition (<60% overlap) between aliquots identical demonstrate that seawater is patchy estimates strongly volume filtered. suggest studies maximize as much logistically possible if aim detect greatest number taxa accumulation curves provided indication adequacy.
Язык: Английский
Процитировано
132
Environmental DNA, Год журнала: 2020, Номер 2(4), С. 391 - 406
Опубликована: Авг. 17, 2020
Abstract Fine‐scale estimation of trophic interactions is an important subject in the field ecology. Diet analysis based on fecal DNA metabarcoding has been accepted as a noninvasive, accurate, and time‐ cost‐effective tool to determine animal diets. Here, we summarize trends studies well methodological characteristics using 155 original papers published from 2009 March 2020. We calculated frequencies methods conditions used each experimental procedure bioinformatics approach. Mammals were major target taxa for metabarcoding. A few or dominated procedure: sampling, extraction, PCR, sequencing, bioinformatics, which might be specialized degraded DNA. However, disadvantages common noted some studies, further optimizations are required obtain more accurate dietary data with high taxonomic resolution quantitative performance. This review will help metabarcode users, especially new scientists who considering their understand process also hope this facilitate technical improvements method.
Язык: Английский
Процитировано
128
Molecular Ecology Resources, Год журнала: 2019, Номер 19(6), С. 1420 - 1432
Опубликована: Июль 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.
Язык: Английский
Процитировано
107
Ecology and Evolution, Год журнала: 2018, Номер 9(1), С. 631 - 639
Опубликована: Дек. 21, 2018
Abstract Diets play a key role in understanding trophic interactions. Knowing the actual structure of food webs contributes greatly to our biodiversity and ecosystem functioning. The research prey preferences different predators requires knowledge not only consumed, but also what is available. In this study, we applied DNA metabarcoding analyze diet 4 bird species (willow tits Poecile montanus , Siberian cinctus great Parus major blue Cyanistes caeruleus ) by using feces nestlings. availability their assumed (Lepidoptera) was determined from larvae (frass) collected main foraging habitat, birch ( Betula spp.) canopy. We identified 53 nestling feces, which 11 (21%) were detected frass samples (eight lepidopterans). Approximately 80% represented lepidopterans, line with earlier studies on parids' diet. A subsequent laboratory experiment showed threshold for fecal sample size barcoding success, suggesting that smallest do contain enough larval be high‐throughput sequencing. To summarize, apply first time combined approach identify available (through frass) consumed (via feces), expanding scope precision future dietary insectivorous birds.
Язык: Английский
Процитировано
102