Diversity and flexibility of algal symbiont community in globally distributed larger benthic foraminifera of the genus Amphistegina

Abstract Background Understanding the specificity and flexibility of the algal symbiosis-host association is fundamental for predicting how species occupy a diverse range of habitats. Here we assessed the algal symbiosis diversity of three species of larger benthic foraminifera from the genus Amphistegina and investigated the role of habitat and species identity in shaping the associated algal community. Results We used next-generation sequencing to identify the associated algal community, and DNA barcoding to identify the diatom endosymbionts associated with species of A. lobifera, A. lessonii, and A. radiata, collected from shallow habitats (< 15 m) in 16 sites, ranging from the Mediterranean Sea to French Polynesia. Next-generation sequencing results showed the consistent presence of Ochrophyta as the main algal phylum associated with all species and sites analysed. A significant proportion of phylotypes were classified as Chlorophyta and Myzozoa. We uncovered unprecedented diversity of algal phylotypes found in low abundance, especially of the class Bacillariophyta (i.e., diatoms). We found a significant influence of sites rather than host identity in shaping algal communities in all species. DNA barcoding revealed the consistent presence of phylotypes classified within the order Fragilariales as the diatoms associated with A. lobifera and A. lessonii, while A. radiata specimens host predominately diatoms of the order Triceratiales. Conclusions We show that local habitat is the main factor influencing the overall composition of the algal symbiont community. However, host identity and the phylogenetic relationship among hosts is relevant in shaping the specific endosymbiont diatom community, suggesting that the relationship between diatom endosymbiont and hosts plays a crucial role in the evolutionary history of the genus Amphistegina. The capacity of Amphistegina species to associate with a diverse array of diatoms, and possibly other algal groups, likely underpins the ecological success of these crucial calcifying organisms across their extensive geographic range.

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Temporal Detection Limits of Remnant Larval Bloodmeals in Nymphal Ixodes scapularis (Say, Ixodida: Ixodidae) Using Two Next-Generation Sequencing DNA Barcoding Assays

Journal of Medical Entomology ◽

10.1093/jme/tjaa192 ◽

2020 ◽

Author(s):

Genevieve A M Lumsden ◽

Evgeny V Zakharov ◽

Sarah Dolynskyj ◽

J Scott Weese ◽

L Robbin Lindsay ◽

...

Keyword(s):

Next Generation Sequencing ◽

Dna Barcoding ◽

Ixodes Scapularis ◽

Life Stage ◽

Next Generation ◽

Host Detection ◽

Host Identification ◽

Species Specific ◽

Generation Sequencing ◽

Assay Detection

Abstract Using next-generation sequencing DNA barcoding, we aimed to determine: 1) if the larval bloodmeal can be detected in Ixodes scapularis nymphs and 2) the post-moult temporal window for detection of the larval bloodmeal. Subsets of 30 nymphs fed on a domestic rabbit (Oryctolagus cuniculus Linnaeus, Lagomorphia: Leporidae) as larvae were reared and frozen at 11 time points post-moult, up to 150 d. Vertebrate DNA was amplified using novel universal (UP) and species-specific primers (SSP) and sequenced for comparison against cytochrome c oxidase subunit I barcodes to infer host identification. Detectable bloodmeals decreased as time since moult increased for both assays. For the SSP assay, detection of bloodmeals decreased from 96.7% (n = 29/30) in day 0 nymphs to 3.3% (n = 1/30) and 6.7% (n = 2/30) at 4- and 5-mo post-moult, respectively. A shorter temporal detection period was achieved with the UP assay, declining from 16.7% (n = 5/30) in day 0 nymphs to 0/30 in 3-d-old nymphs. Bloodmeal detection was nonexistent for the remaining cohorts, with the exception of 1/30 nymphs at 2-mo post-moult. Host detection was significantly more likely using the SSP assay compared to the UP assay in the first three time cohorts (day 0: χ 2 = 39.1, P < 0.005; day 2: χ 2 = 19.2, P < 0.005; day 3: χ 2 = 23.3, P < 0.005). Regardless of the primer set used, the next-generation sequencing DNA barcoding assay was able to detect host DNA from a larval bloodmeal in the nymphal life stage; however, a short window with a high proportion of detection post-moult was achieved.

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Assessing wild bee diversity using next generation sequencing

10.35662/unine-thesis-2792 ◽

2019 ◽

Author(s):

◽

Morgan Gueuning

Keyword(s):

Next Generation Sequencing ◽

Dna Barcoding ◽

Species Delimitation ◽

Morphological Identification ◽

Next Generation ◽

Wild Bees ◽

Wild Bee ◽

Monitoring Programs ◽

The Cost ◽

Generation Sequencing

Wild bees are essential pollinators and therefore play a key role in both natural and agricultural ecosystems. However, bees have often been neglected in conservation studies and policies worldwide, which is surprising given their ecological importance. As a result, little is known on the conservation status of the vast majority of wild bee species in Europe, and even less worldwide. Limited surveys suggest important declines in the abundance and diversity of most wild bee communities worldwide. It is therefore urgent to implement targeted measures for the conservation of these keystone species. Once implemented, the effectiveness of these measures must be evaluated using adequate monitoring programs. To date, wild bee surveys are entirely based on morphological identification, which is both labor intensive and time consuming. Consequently, an affordable, high-throughput identification method is needed to reduce costs and improve bee monitoring. The objective of this thesis was to evaluate novel genetic techniques based on Next Generation Sequencing (NGS) methods for facilitating surveys of wild bees. NGS tools were mainly investigated for bridging two important impediments to wild bee conservation efforts, i.e., the cost of biodiversity assessment schemes and taxonomic incompleteness. With the development of NGS techniques, DNA barcoding has gained enormous momentum, enabling cost-effective, fast and accurate identifications. Before these methods can be routinely used in monitoring programs, there are however still important knowledge gaps to fill. These gaps mainly concern the detection of rare species and the acquisition of accurate quantitative data on species abundance; more generally the cost and labour effectiveness of these methods need to be evaluated. To provide a comprehensive presentation of the advantages and weaknesses of different NGS-based identification methods, we assessed three of the most promising ones, namely metabarcoding, mitogenomics and NGS barcoding. Using a regular monitoring data, we found that NGS barcoding performed best for both species’ presence/absence and abundance data, producing only few false positives and no false negatives. The other methods investigated were less reliable in term of species detection and inference of abundance data, and partly led to erroneous ecological conclusions. In terms of workload and cost, we showed that NGS techniques were more expensive than morphological identification with our dataset, although these techniques would become slightly more economical in large-scale monitoring programs. A second aim of this thesis was to provide an easy and robust genomic solution to alleviate taxonomical incompleteness, one of the major impediments to the effective conservation of many insect taxa. For conservation purposes, having stable and well-delimited species hypotheses is essential. Currently, most species are delimitated based on morphology and/or DNA barcoding. These methods are however associated with important limitations, and it is widely accepted that species delimitation should rely on multi-locus genomic markers. To overcome these limitations, ultraconserved elements (UCEs) were tested as a fast and robust approach using different species-complexes harbouring cryptic diversity, mitochondrial introgression, or mitochondrial paraphyly. Phylogenetic analyses of UCEs were highly conclusive and yielded meaningful species delimitation hypotheses in all cases. These results provide strong evidence for the potential of UCEs as a fast method for delimiting species even in cases of recently diverged lineages. Advantages and limitations of UCEs for shallow phylogenetic studies are further discussed.

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What Else Is in Salviae officinalis folium? Comprehensive Species Identification of Plant Raw Material by DNA Metabarcoding

Planta Medica ◽

10.1055/s-0043-121470 ◽

2017 ◽

Vol 84 (06/07) ◽

pp. 428-433 ◽

Cited By ~ 1

Author(s):

Corinna Schmiderer ◽

Brigitte Lukas ◽

Joana Ruzicka ◽

Johannes Novak

Keyword(s):

Next Generation Sequencing ◽

Dna Barcoding ◽

Species Identification ◽

Internal Transcribed Spacer ◽

Raw Material ◽

Next Generation ◽

Additional Species ◽

Internal Transcribed Spacer 2 ◽

Dna Metabarcoding ◽

Generation Sequencing

AbstractQuality control of drugs consists of identifying the raw material to avoid unwanted admixtures or exchange of material as well as looking for abiotic and biotic contaminations. So far, identity and microbial contamination are analyzed by separate processes and separate methods. Species identification by their DNA (“DNA barcoding”) has the potential to supplement existing methods of identification. The introduction of next-generation sequencing methods offers completely new approaches like the identification of whole communities in one analysis, termed “DNA metabarcoding”. Here we present a next-generation sequencing assessment to identify plants and fungi of two commercial sage samples (Salvia officinalis) using the standard DNA barcoding region “internal transcribed spacer” consisting of internal transcribed spacer 1 and internal transcribed spacer 2, respectively. The main species in both samples was identified as S. officinalis. The spectrum of accompanying plant and fungal species, however, was completely different between the samples. Additionally, the composition between internal transcribed spacer 1 and internal transcribed spacer 2 within the samples was different and demonstrated the influence of primer selection and therefore the need for harmonization. This next-generation sequencing approach does not result in quantitative species composition but gives deeper insight into the composition of additional species. Therefore, it would allow for a better knowledge-based risk assessment than any other method available. However, the method is only economically feasible in routine analysis if a high sample throughput can be guaranteed.

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