Bibliographic survey of microbial diversity from Chilean soils
Description
This dataset is a recopilation of research works published from 1975 to 2023 presenting original studies of soil microbial diversity in Chile. The considered microorganisms are bacteria, archaea, and fungi. The studies selected here focused on the diverse environmental biomes represented in Chile, from arid desert and salt flats in the North, to cultivated lands and forests in the medium South, and steppes and glaciers in the extreme South down to the Antarctic peninsula. The dataset includes different methodological approaches such as cultivation, sequencing, metabarcoding, metagenomics, as well as functional characterization of microbial communities. The main objectives of this work are (i) to describe quantitatively and qualitatively the existing research effort for microbial diversity understanding in Chilean soils (i.e., number of studies, type of methodological approaches, and origin of funding), (ii) to compare the extent of research in the different Chilean regions (including the Antarctic Peninsula) and along time since 1975, and (iii) to identify the main research scopes and current knowledge gaps in soil biodiversity in Chile and Antarctic Peninsula. The studies included in this dataset adressed different main concerns, as follows: potential biotechnological applications of soil microorganisms; impact of climate change on soil microorganisms; microbial diversity of extreme environments; identification of new species; effect of disturbances on soil microorganisms; insights in the functionnal capacities of microbial diversity; biogeographic distribution of soil microorganisms.
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Steps to reproduce
1. Literature search We created a dataset following the method described by Guerra et al. (2020) (https://www.nature.com/articles/s41467-020-17688-2) adapted to our topic of interest. Briefly, we collected published literature on studies of soil microbial biodiversity. For this literature search, we conducted independent searches in the Web of Knowledge (WOS), the SCOPUS and the PUBMED databases on June 23rd, 2023 within papers published between 1975 and 2023. For the first search, we used the keywords (soil OR sand) AND (Chile*) AND (*bacteria* OR fung* OR *archaea* OR vir* OR microbi* OR metagen* OR metatranscript* OR metataxon* OR genom*) using the ‘Topic’ search option, which includes title, abstract, author keywords, and Keywords Plus. 2. Rationale of data selection The initial search returned 1,429 publications, which were further manually selected based on the following inclusion criteria: (1) soil samples excluding biocrusts, marine and lacustrine sediments (the “sand*” keyword being not selective enough to exclude sediments); (2) in situ soil samples were not modified by researchers prior to analysis (e.g. excluding microcosm or mesocosm incubation); (3) soil samples were not collected after atypical events that may have caused a major change on natural microbial communities (e.g. following a wildfire); (4) study was conducted in the Chilean claimed territory (including Antarctic Peninsula) (the “Chile*” keyword being not selective enough to exclude studies outside Chile); (5) only original studies (i.e., reviews were excluded); (6) only studies with diversity data (i.e., studies with only microbial activity measurements were excluded).