Advances in HTS-Based Identification of Species and Ecological Interactions

A special issue of Diversity (ISSN 1424-2818). This special issue belongs to the section "Biodiversity Conservation".

Deadline for manuscript submissions: closed (16 December 2021) | Viewed by 7521

Special Issue Editors


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Guest Editor
ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.za della Scienza 2, 20126-I Milano, Italy
Interests: integrative taxonomy; DNA barcoding; DNA metabarcoding; metazoans; diet analysis; food authenticity; high-throughput sequencing; ecosystem services
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Guest Editor
Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
Interests: pollination ecology; community ecology; plant-pollinator network; rare species; biogeography; species interactions; threatened pollinators

Special Issue Information

Dear Colleagues,

In the last decade, high-throughput sequencing (HTS) techniques have been largely proposed or directly applied to investigate biodiversity and ecosystem functioning, ranging from the assessment of communities inhabiting various environments (e.g., soil and water) to studies dealing with ecological interactions (e.g., pollination, prey–predator, host–parasite, and various commensalism and competition cases). In all these studies, HTS increased the resolution of the investigation, in order to describe changes of biodiversity over time and space, with studies spanning from ancient biological residues (e.g., lake sediments) up to the impacts of climate change, of human activities and of pollution of the current times.

More recently, HTS technologies related to DNA-based identifications, has devoted great attention to bioinformatic tools aimed at assigning the sequencing products to taxonomic units. At the same time, additional renewal of the field has been provided by the exploitation of fast-evolving automatic tools and statistical approaches, e.g., based on machine learning systems.

This Special Issue is focused on new approaches and advances in species and interaction identification based on HTS techniques. Special attention will be paid to studies addressing the new frontiers of HTS application in the context of biodiversity, biomonitoring, and ecosystem functioning, or that elucidate novel and robust analytical and bioinformatics pipelines. We particularly encourage studies with practical and applied scopes, and that integrate various scientific disciplines.

We cordially invite researchers working actively in these fields to submit their original research manuscripts to this Special Issue.

Dr. Andrea Galimberti
Dr. Paolo Biella
Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Diversity is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Biomonitoring
  • Ecosystem services
  • Diet analysis
  • High-throughput sequencing advances
  • Species assignment pipelines
  • DNA metabarcoding
  • Species interaction networks
  • eDNA
  • Human impacts on biodiversity

Published Papers (2 papers)

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Research

20 pages, 852 KiB  
Article
Harnessing the Power of Metabarcoding in the Ecological Interpretation of Plant-Pollinator DNA Data: Strategies and Consequences of Filtering Approaches
by Nicola Tommasi, Andrea Ferrari, Massimo Labra, Andrea Galimberti and Paolo Biella
Diversity 2021, 13(9), 437; https://doi.org/10.3390/d13090437 - 10 Sep 2021
Cited by 12 | Viewed by 3703
Abstract
Although DNA metabarcoding of pollen mixtures has been increasingly used in the field of pollination biology, methodological and interpretation issues arise due to its high sensitivity. Filtering or maintaining false positives, contaminants, and rare taxa or molecular features could lead to different ecological [...] Read more.
Although DNA metabarcoding of pollen mixtures has been increasingly used in the field of pollination biology, methodological and interpretation issues arise due to its high sensitivity. Filtering or maintaining false positives, contaminants, and rare taxa or molecular features could lead to different ecological results. Here, we reviewed how this choice has been addressed in 43 studies featuring pollen DNA metabarcoding, which highlighted a very high heterogeneity of filtering methods. We assessed how these strategies shaped pollen assemblage composition, species richness, and interaction networks. To do so, we compared four processing methods: unfiltering, filtering with a proportional 1% of sample reads, a fixed threshold of 100 reads, and the ROC approach (Receiver Operator Characteristic). The results indicated that filtering impacted species composition and reduced species richness, with ROC emerging as a conservative approach. Moreover, in contrast to unfiltered networks, filtering decreased network Connectance and Entropy, and it increased Modularity and Connectivity, indicating that using cut-off thresholds better describes interactions. Overall, unfiltering might compromise reliable ecological interpretations, unless a study targets rare species. We discuss the suitability of each filtering type, plead for justifying filtering strategies on biological or methodological bases and for developing shared approaches to make future studies more comparable. Full article
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14 pages, 1660 KiB  
Article
Unravelling the Symbiotic Microalgal Diversity in Buellia zoharyi (Lichenized Ascomycota) from the Iberian Peninsula and Balearic Islands Using DNA Metabarcoding
by Patricia Moya, Salvador Chiva, Arantzazu Molins, Isaac Garrido-Benavent and Eva Barreno
Diversity 2021, 13(6), 220; https://doi.org/10.3390/d13060220 - 21 May 2021
Cited by 10 | Viewed by 2987
Abstract
Buellia zoharyi is a crustose placodioid lichen, usually occurring on biocrusts of semiarid ecosystems in circum-Mediterranean/Macaronesian areas. In previous work, we found that this lichenized fungus was flexible in its phycobiont choice in the Canary Islands. Here we test whether geography and habitat [...] Read more.
Buellia zoharyi is a crustose placodioid lichen, usually occurring on biocrusts of semiarid ecosystems in circum-Mediterranean/Macaronesian areas. In previous work, we found that this lichenized fungus was flexible in its phycobiont choice in the Canary Islands. Here we test whether geography and habitat influence phycobiont diversity in populations of this lichen from the Iberian Peninsula and Balearic Islands using Sanger and high throughput sequencing (HTS). Additionally, three thallus section categories (central, middle and periphery) were analyzed to explore diversity of microalgal communities in each part. We found that B. zoharyi populations hosted at least three different Trebouxia spp., and this lichen can associate with distinct phycobiont strains in different habitats and geographic regions. This study also revealed that the Trebouxia composition of this lichen showed significant differences when comparing the Iberian Peninsula with the Balearics thalli. No support for differences in microalgal communities was found among thallus sections; however, several thalli showed different predominant Trebouxia spp. at each section. This result corroborate that thallus parts selected for DNA extraction in metabarcoding analyses are key to not bias the total phycobiont diversity detected. This study highlights that inclusion of HTS analysis is crucial to understand lichen symbiotic microalgal diversity. Full article
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