About this Research Topic
Extreme habitats exist across the globe and span over three quarters of our planet. They can be widely different from a physical-chemical perspective as they include diverse types of extreme, such as temperature, pH, salinity, radiation, pressure, low water activity, low nutrient availability, etc. Organisms capable of adjusting, surviving, or thriving in those habitats, which are so hostile that they were previously thought to be adverse or lethal for life, are called “extremophiles”.
All three Domains of Life are represented in each type of extreme environment. However, the vast majority of them are prokaryotes, which is not surprising considering their remarkable adaptation capabilities and overwhelming abundance. The discovery, study and classification of novel microbial extremophiles is of enormous interest, given their potential biotechnological applications and the ever-increasing expectation to find life on other planets, where conditions might be similar to those of the extreme environments on Earth. In this sense, next generation sequencing and bioinformatics can enhance our knowledge concerning these microorganisms.
Next generation sequencing platforms have been evolving for the last decade. Recent development such as currently short read Ilumina platforms and new emerging long read technologies hold promise for dense, accurate and inexpensive sequence information retrieval. In parallel, the development of new computing tools now provides the necessary means to deal with such a huge amount of data.
Extreme environments possess a larger than expected microbial diversity, considering the harshness of the conditions that they need to cope with. Many efforts have been made to characterize and describe prokaryotic dwellers and their metabolic functions within these habitats using culture-dependent approaches. Nevertheless, it is estimated that around 80 % of microbial genera remain uncultured, meaning that most of the diversity and functions of extremophiles remain undiscovered. Fortunately, high-performance sequencing and computation-based analysis now allow the recovery of metagenome-assembled genomes (MAGs) and single-cell genomes, in addition to complete (or high-quality draft) genomes of cultured microorganisms. These approaches allow us to finally characterize and describe the extremophilic microbial dark matter and their ecological role in the environments they inhabit.
The use genomic data of both cultured and uncultured extremophiles is also valuable to infer phylogenetic relationships and to establish a robust and accurate classification system. Most of the existing taxa of extremophiles were proposed based on classical but increasingly old-fashioned 16S rRNA gene sequence and DNA-DNA hybridization approaches. These have been overtaken by genome relatedness indexes and phylogenomic studies. Therefore, assessment of current taxonomy of extremophile-containing groups using genomic information seems necessary. The ever-increasing access to public genomic databases and the ever-decreasing cost of next generation sequencing technologies makes this a particularly timely Research Topic and grants us an exceptional opportunity to address this issue.
The present Research Topic on “Extremophiles: microbial genomics and taxogenomics” aims to assemble contributions from scientists working with genomic sequencing data on the fields of comparative genomics, metagenomics, biodiversity and taxonomy of extremophiles. Here, we would like to encourage authors to contribute research articles that are interdisciplinary, including original research, methods, reviews and mini-reviews, as well as opinion articles. Broadly, we would like contributions covering the following areas of research:
- Genome sequencing and comparative analysis of cultured extremophiles
- Use of genomic information to isolate highly-abundant, fastidious microorganisms
- Characterization and description of uncultured extremophiles inferred from genomic and environmental data
- Environmental role and metabolic functions of extremophiles
- Adaptation to extreme conditions
- Phylogeny, taxonomy and biodiversity of extremophiles
Please note that Frontiers in Microbiology does not consider submissions limited to standard genome report submissions or descriptive studies such as observational “omics” data alone lacking a hypothesis or application.
All three Domains of Life are represented in each type of extreme environment. However, the vast majority of them are prokaryotes, which is not surprising considering their remarkable adaptation capabilities and overwhelming abundance. The discovery, study and classification of novel microbial extremophiles is of enormous interest, given their potential biotechnological applications and the ever-increasing expectation to find life on other planets, where conditions might be similar to those of the extreme environments on Earth. In this sense, next generation sequencing and bioinformatics can enhance our knowledge concerning these microorganisms.
Next generation sequencing platforms have been evolving for the last decade. Recent development such as currently short read Ilumina platforms and new emerging long read technologies hold promise for dense, accurate and inexpensive sequence information retrieval. In parallel, the development of new computing tools now provides the necessary means to deal with such a huge amount of data.
Extreme environments possess a larger than expected microbial diversity, considering the harshness of the conditions that they need to cope with. Many efforts have been made to characterize and describe prokaryotic dwellers and their metabolic functions within these habitats using culture-dependent approaches. Nevertheless, it is estimated that around 80 % of microbial genera remain uncultured, meaning that most of the diversity and functions of extremophiles remain undiscovered. Fortunately, high-performance sequencing and computation-based analysis now allow the recovery of metagenome-assembled genomes (MAGs) and single-cell genomes, in addition to complete (or high-quality draft) genomes of cultured microorganisms. These approaches allow us to finally characterize and describe the extremophilic microbial dark matter and their ecological role in the environments they inhabit.
The use genomic data of both cultured and uncultured extremophiles is also valuable to infer phylogenetic relationships and to establish a robust and accurate classification system. Most of the existing taxa of extremophiles were proposed based on classical but increasingly old-fashioned 16S rRNA gene sequence and DNA-DNA hybridization approaches. These have been overtaken by genome relatedness indexes and phylogenomic studies. Therefore, assessment of current taxonomy of extremophile-containing groups using genomic information seems necessary. The ever-increasing access to public genomic databases and the ever-decreasing cost of next generation sequencing technologies makes this a particularly timely Research Topic and grants us an exceptional opportunity to address this issue.
The present Research Topic on “Extremophiles: microbial genomics and taxogenomics” aims to assemble contributions from scientists working with genomic sequencing data on the fields of comparative genomics, metagenomics, biodiversity and taxonomy of extremophiles. Here, we would like to encourage authors to contribute research articles that are interdisciplinary, including original research, methods, reviews and mini-reviews, as well as opinion articles. Broadly, we would like contributions covering the following areas of research:
- Genome sequencing and comparative analysis of cultured extremophiles
- Use of genomic information to isolate highly-abundant, fastidious microorganisms
- Characterization and description of uncultured extremophiles inferred from genomic and environmental data
- Environmental role and metabolic functions of extremophiles
- Adaptation to extreme conditions
- Phylogeny, taxonomy and biodiversity of extremophiles
Please note that Frontiers in Microbiology does not consider submissions limited to standard genome report submissions or descriptive studies such as observational “omics” data alone lacking a hypothesis or application.
Keywords: Extreme environments, microbial diversity, comparative genomics, phylogenomics, taxonomy
Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.
