Establishing arthropod community composition using metabarcoding: Surprising inconsistencies between soil samples and preservative ethanol and homogenate from Malaise trap catches

Marquina, Daniel; Esparza‐Salas, Rodrigo; Roslin, Tomas; Ronquist, Fredrik

doi:10.1111/1755-0998.13071

Cited by 73 publications

(137 citation statements)

References 73 publications

(169 reference statements)

Supporting

Mentioning

122

Contrasting

Order By: Relevance

“…However, these methods are still in development. Recent results show surprising inconsistencies in metabarcoding results for Malaise trap samples depending on whether the preservative ethanol or tissue homogenate is used [57]. Specifically, it appears that small and weakly sclerotized insects, which are detected in preservative ethanol, are easily missed in tissue homogenate because the signal is swamped by the DNA from larger insects.…”

Section: Discussionmentioning

confidence: 99%

Completing Linnaeus’s inventory of the Swedish insect fauna: Only 5,000 species left?

et al. 2020

Self Cite

View full text Add to dashboard Cite

Despite more than 250 years of taxonomic research, we still have only a vague idea about the true size and composition of the faunas and floras of the planet. Many biodiversity inventories provide limited insight because they focus on a small taxonomic subsample or a tiny geographic area. Here, we report on the size and composition of the Swedish insect fauna, thought to represent roughly half of the diversity of multicellular life in one of the largest European countries. Our results are based on more than a decade of data from the Swedish Taxonomy Initiative and its massive inventory of the country's insect fauna, the Swedish Malaise Trap Project The fauna is considered one of the best known in the world, but the initiative has nevertheless revealed a surprising amount of hidden diversity: more than 3,000 new species (301 new to science) have been documented so far. Here, we use three independent methods to analyze the true size and composition of the fauna at the family or subfamily level: (1) assessments by experts who have been working on the most poorly known groups in the fauna; (2) estimates based on the proportion of new species discovered in the Malaise trap inventory; and (3) extrapolations based on species abundance and incidence data from the inventory. For the last method, we develop a new estimator, the combined non-parametric estimator, which we show is less sensitive to poor coverage of the species pool than other popular estimators. The three methods converge on similar estimates of the size and composition of the fauna, suggesting that it comprises around 33,000 species. Of

show abstract

Section: Discussionmentioning

confidence: 99%

Completing Linnaeus’s inventory of the Swedish insect fauna: Only 5,000 species left?

et al. 2020

Self Cite

View full text Add to dashboard Cite

show abstract

“…Additionally, since only gentle shaking is used with wet sieving, specimens are less damaged and might be used for morphological identification if non destructive metabarcoding is applied (using ethanol (Hajibabaei et al, 2012) or lysis buffer protocols (Nielsen et al, 2019)). However, non destructive methods can introduce additional biases to the metabarcoding process, in some cases detecting substantially less taxa than with morphology or homogenizing bulk samples (Erdozain et al, 2019;Marquina et al, 2019). To generate multiple size fractions, several sieves can be placed over each other.…”

Section: Discussionmentioning

confidence: 99%

Pooling size sorted malaise trap fractions to maximise taxon recovery with metabarcoding

Elbrecht

Bourlat

Hörren³

et al. 2020

Preprint

View full text Add to dashboard Cite

1) Small and rare specimens can remain undetected when metabarcoding bulk samples with a high size heterogeneity of specimens. This is especially critical for malaise trap samples, where most of the biodiversity is often contributed by small specimens. How to size sort and in which proportions to pool these samples has not been widely explored. We set out to find a size sorting strategy that maximizes taxonomic recovery but remains highly scalable and time efficient. 2) Three 3 malaise trap samples where size sorted into 4 size classes using dry sieving.Each fraction was homogenized and lysed. The corresponding lysates were pooled to simulate samples never sorted, pooled in equal proportions and in 4 different proportions favoring the small size fractions. DNA from the pooled fractions as well as the individual size classes were extracted and metabarcoded using the FwhF2 and Fol-degen-rev primer set. Additionally wet sieving strategies were explored. 3) The small size fractions harbored the highest diversity, and were best represented when pooling in favor of small specimens. Not size sorting a sample leads to a 45-77% decrease in taxon recovery compared to size sorted samples. A size separation into only 2 fractions (below 4 mm and above) can already double taxon recovery compared to not sorting. However, increasing the sequencing depth 3-4 fold can also increase taxon recovery to comparable levels, but remains biased toward biomass rich taxa in the sample. 4) We demonstrate that size fractionizing bulk malaise samples can increase taxon recovery. The most practical approach is wet sieving into two size fractions, and proportional pooling of the lysates in favor of the small size fraction (80-90% volume).However, in large projects with time constraints, increasing sequencing depth can also be an alternative solution.

show abstract

“…DNA may even be extracted directly from the collection medium (e.g., ethanol), because specimens leave trace amounts of DNA in the medium (Hajibabaei et al 2012;Martins et al 2019). However, the DNA recovered from nondestructive extraction of community samples may be biased toward those taxonomic groups that release DNA more readily than others, e.g., soft-bodied animals (Carew et al 2018;Marquina et al 2019).…”

Section: Community Metabarcodingmentioning

confidence: 99%

High-throughput sequencing for community analysis: the promise of DNA barcoding to uncover diversity, relatedness, abundances and interactions in spider communities

et al. 2020

View full text Add to dashboard Cite

Large-scale studies on community ecology are highly desirable but often difficult to accomplish due to the considerable investment of time, labor and, money required to characterize richness, abundance, relatedness, and interactions. Nonetheless, such large-scale perspectives are necessary for understanding the composition, dynamics, and resilience of biological communities. Small invertebrates play a central role in ecosystems, occupying critical positions in the food web and performing a broad variety of ecological functions. However, it has been particularly difficult to adequately characterize communities of these animals because of their exceptionally high diversity and abundance. Spiders in particular fulfill key roles as both predator and prey in terrestrial food webs and are hence an important focus of ecological studies. In recent years, large-scale community analyses have benefitted tremendously from advances in DNA barcoding technology. High-throughput sequencing (HTS), particularly DNA metabarcoding, enables community-wide analyses of diversity and interactions at unprecedented scales and at a fraction of the cost that was previously possible. Here, we review the current state of the application of these technologies to the analysis of spider communities. We discuss amplicon-based DNA barcoding and metabarcoding for the analysis of community diversity and molecular gut content analysis for assessing predator-prey relationships. We also highlight applications of the third generation sequencing technology for long read and portable DNA barcoding. We then address the development of theoretical frameworks for community-level studies, and finally highlight critical gaps and future directions for DNA analysis of spider communities.

show abstract

Establishing arthropod community composition using metabarcoding: Surprising inconsistencies between soil samples and preservative ethanol and homogenate from Malaise trap catches

Cited by 73 publications

References 73 publications

Completing Linnaeus’s inventory of the Swedish insect fauna: Only 5,000 species left?

Completing Linnaeus’s inventory of the Swedish insect fauna: Only 5,000 species left?

Pooling size sorted malaise trap fractions to maximise taxon recovery with metabarcoding

High-throughput sequencing for community analysis: the promise of DNA barcoding to uncover diversity, relatedness, abundances and interactions in spider communities

Contact Info

Product

Resources

About