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Shedding light on the composition of extreme microbial dark matter: alternative approaches for culturing extremophiles

More than 20,000 species of prokaryotes (less than 1% of the estimated number of Earth’s microbial species) have been described thus far. However, the vast majority of microbes that inhabit extreme environments remain uncultured and this group is termed “microbial dark matter.” Little is known regar...

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Autores principales: Schultz, Júnia, Modolon, Flúvio, Peixoto, Raquel Silva, Rosado, Alexandre Soares
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10272570/
https://www.ncbi.nlm.nih.gov/pubmed/37333658
http://dx.doi.org/10.3389/fmicb.2023.1167718
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author Schultz, Júnia
Modolon, Flúvio
Peixoto, Raquel Silva
Rosado, Alexandre Soares
author_facet Schultz, Júnia
Modolon, Flúvio
Peixoto, Raquel Silva
Rosado, Alexandre Soares
author_sort Schultz, Júnia
collection PubMed
description More than 20,000 species of prokaryotes (less than 1% of the estimated number of Earth’s microbial species) have been described thus far. However, the vast majority of microbes that inhabit extreme environments remain uncultured and this group is termed “microbial dark matter.” Little is known regarding the ecological functions and biotechnological potential of these underexplored extremophiles, thus representing a vast untapped and uncharacterized biological resource. Advances in microbial cultivation approaches are key for a detailed and comprehensive characterization of the roles of these microbes in shaping the environment and, ultimately, for their biotechnological exploitation, such as for extremophile-derived bioproducts (extremozymes, secondary metabolites, CRISPR Cas systems, and pigments, among others), astrobiology, and space exploration. Additional efforts to enhance culturable diversity are required due to the challenges imposed by extreme culturing and plating conditions. In this review, we summarize methods and technologies used to recover the microbial diversity of extreme environments, while discussing the advantages and disadvantages associated with each of these approaches. Additionally, this review describes alternative culturing strategies to retrieve novel taxa with their unknown genes, metabolisms, and ecological roles, with the ultimate goal of increasing the yields of more efficient bio-based products. This review thus summarizes the strategies used to unveil the hidden diversity of the microbiome of extreme environments and discusses the directions for future studies of microbial dark matter and its potential applications in biotechnology and astrobiology.
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spelling pubmed-102725702023-06-17 Shedding light on the composition of extreme microbial dark matter: alternative approaches for culturing extremophiles Schultz, Júnia Modolon, Flúvio Peixoto, Raquel Silva Rosado, Alexandre Soares Front Microbiol Microbiology More than 20,000 species of prokaryotes (less than 1% of the estimated number of Earth’s microbial species) have been described thus far. However, the vast majority of microbes that inhabit extreme environments remain uncultured and this group is termed “microbial dark matter.” Little is known regarding the ecological functions and biotechnological potential of these underexplored extremophiles, thus representing a vast untapped and uncharacterized biological resource. Advances in microbial cultivation approaches are key for a detailed and comprehensive characterization of the roles of these microbes in shaping the environment and, ultimately, for their biotechnological exploitation, such as for extremophile-derived bioproducts (extremozymes, secondary metabolites, CRISPR Cas systems, and pigments, among others), astrobiology, and space exploration. Additional efforts to enhance culturable diversity are required due to the challenges imposed by extreme culturing and plating conditions. In this review, we summarize methods and technologies used to recover the microbial diversity of extreme environments, while discussing the advantages and disadvantages associated with each of these approaches. Additionally, this review describes alternative culturing strategies to retrieve novel taxa with their unknown genes, metabolisms, and ecological roles, with the ultimate goal of increasing the yields of more efficient bio-based products. This review thus summarizes the strategies used to unveil the hidden diversity of the microbiome of extreme environments and discusses the directions for future studies of microbial dark matter and its potential applications in biotechnology and astrobiology. Frontiers Media S.A. 2023-06-02 /pmc/articles/PMC10272570/ /pubmed/37333658 http://dx.doi.org/10.3389/fmicb.2023.1167718 Text en Copyright © 2023 Schultz, Modolon, Peixoto and Rosado. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Schultz, Júnia
Modolon, Flúvio
Peixoto, Raquel Silva
Rosado, Alexandre Soares
Shedding light on the composition of extreme microbial dark matter: alternative approaches for culturing extremophiles
title Shedding light on the composition of extreme microbial dark matter: alternative approaches for culturing extremophiles
title_full Shedding light on the composition of extreme microbial dark matter: alternative approaches for culturing extremophiles
title_fullStr Shedding light on the composition of extreme microbial dark matter: alternative approaches for culturing extremophiles
title_full_unstemmed Shedding light on the composition of extreme microbial dark matter: alternative approaches for culturing extremophiles
title_short Shedding light on the composition of extreme microbial dark matter: alternative approaches for culturing extremophiles
title_sort shedding light on the composition of extreme microbial dark matter: alternative approaches for culturing extremophiles
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10272570/
https://www.ncbi.nlm.nih.gov/pubmed/37333658
http://dx.doi.org/10.3389/fmicb.2023.1167718
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