Metabarcoding data reveal vertical multitaxa variation in topsoil communities during the colonization of deglaciated forelands

Abstract

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Towards exhaustive community ecology via DNA metabarcoding

“…In order to overcome the limitations of strategies 3.1 and 3.2, it is possible to analyse the same DNA using both specific primers targeting taxa with particular ecological role (e.g., taxa with taxonomic diversity or with a major functional role), and universal primers. For instance, for the analysis of soil biodiversity it is possible to complement primers amplifying insects, springtails, earthworms and fungi, with a primer that amplifies all the eukaryotes and can give an idea of the diversity of groups not amplified with the previous ones (e.g., microeukaryotes, nematodes, rotifers) (Bloor et al, 2021; Calderón‐Sanou et al, 2022; Guerrieri et al, 2022). This approach has the advantage of providing a reasonable representation of biodiversity, with good information on selected key taxa and few completely missing, and might thus allow exploring complex relationships between multiple taxonomic groups (Bloor et al, 2021; Calderón‐Sanou et al, 2022).…”

“…The complete list of studies is provided in Table S1. [Colour figure can be viewed at wileyonlinelibrary.com] N target taxa vs. journal impact factor an idea of the diversity of groups not amplified with the previous ones (e.g., microeukaryotes, nematodes, rotifers) (Bloor et al, 2021;Calderón-Sanou et al, 2022;Guerrieri et al, 2022). This approach has the advantage of providing a reasonable representation of biodiversity, with good information on selected key taxa and few completely missing, and might thus allow exploring complex relationships between multiple taxonomic groups (Bloor et al, 2021;Calderón-Sanou et al, 2022).…”

“…In principle, we can amplify the DNA extracted from one single environmental or bulk sample using multiple primers, and then combine the results to attempt an overall reconstruction of biodiversity (Jurburg et al, 2021). For example, we might study the majority of soil biodiversity by analysing markers specific for bacteria, fungi, earthworms, insects and springtails, while a large portion of freshwater diversity can be assessed by combining primers that amplify bacteria, protists, insects, fishes and amphibians (Bloor et al, 2021; Guerrieri et al, 2022; Li et al, 2023).…”

Insights into Ecological & Evolutionary Processes via community metabarcoding

“…Guerrieri et al. (2022) use multi‐locus metabarcoding to explore the development of successional communities in recently deglaciated soils, focusing on six groups (Eukaryota, Bacteria, Mycota, Collembola, Insecta and Oligochaeta) and asking how soil communities change through time following deglaciation, and how this change differs between different soil layers. They were able to show increasing diversity within, but also increasing biotic homogenization between, soil layers, with increasing time since deglaciation.…”

Editorial 2024

“…Collectively the articles in this Special Issue 'underline the huge impact of the anthropogenic environment in microbial evolution, including the emergence and spread of pathogens as well as the benefits provided by domesticated or mutualistic fungi and bacteria'(Giraud et al, 2023).Finally, our third Special Issue, Insights into Ecological & Evolutionary Processes via Community Metabarcoding includes 'papers that highlight the power of high-throughput sequencing (HTS) data to address classic questions in ecology and evolution, particularly focused on metabarcoding (amplicon) datasets in conjunction with complementary -omics data types and/or models/theory to infer overall ecosystem processes'(Gillespie et al, 2023). The impressive collection of 44 manuscripts covers a wide range of topics: community assembly processes(Andujar et al, 2022;Arjona et al, 2022;Emerson et al, 2022;Govender et al, 2022;Guerrieri et al, 2022;Ip, Chang, Oh, et al, 2022;Kiemel et al, 2022;Li et al, 2022;Macheriotou et al, 2023;Menéndez-Serra et al, 2023;Nappi et al, 2022;Noguerales et al, 2023;Overcast et al, 2023;Pino et al, 2023;Van der Loos et al, 2022;Wang et al, 2022), interaction networks(Ando et al, 2022;Bell et al, 2022;Dürrbaum et al, 2022;Encinas-Viso et al, 2022;Ficetola & Taberlet, 2023;Graham et al, 2022;Ip, Chang, Tun, et al, 2022;Lowe et al, 2022;Lu et al, 2022;Lue et al, 2022;Pitteloud et al, 2022;Srivathsan et al, 2022;Tommasi et al, 2022), cross-scale interactions and microbiomes(Brinker et al, 2022;Câmara dos Reis et al, 2022...…”