Special Issue "Genetics and Genomics of Acidophiles"

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Microbial Genetics and Genomics".

Deadline for manuscript submissions: 31 August 2019.

Special Issue Editors

Guest Editor
Prof. Eric Boyd

Montana State University
Website | E-Mail
Interests: Hyperthermophiles; acidophiles; extremophiles; elemental sulfur reduction; hydrogen metabolism; origin of life; metalloenzyme evolution; geobiology
Guest Editor
Dr. Dan Colman

Montana State University
E-Mail
Interests: Archaea; thermophiles; acidophiles; ecological distributions; community assembly; subsurface environments; thermal springs; evolutionary ecology; geobiological interactions
Guest Editor
Dr. Maximiliano Amenabar

Montana State University
E-Mail
Interests: Extremophiles; thermophiles; acidophiles; sulfur metabolism; iron metabolism; bioenergetics; physiology; subsurface biosphere

Special Issue Information

Dear Colleagues,

Acidic environments and the organisms that they host are of significant interest to disciplines ranging from microbiology, biotechnology, Earth sciences, to astrobiology, and have been subject to extensive research to understand the processes that contribute to their formation and the adaptations that allow for their habitation. Acidophiles, organisms that grow optimally at acidic pH, are distributed across all three domains of life and exhibit substantial physiological diversity. Acidophiles grow in environments with pH as low as 0 and at temperatures as high as ~90 oC. As such, they display a wide diversity of metabolic lifestyles and physiological adaptations. Further, the metabolic activities of lithotrophic acidophiles are important in the formation of acidic environments where they influence metal cycling and metal availability. The insights gained from the study of acidophiles have provided new insights into the physiological limits of life and have uncovered unique adaptations that allow life to thrive under pH extremes.  

The low taxonomic diversity of communities in acidic habitats has allowed for the development and application of cutting edge technologies in environmental microbiology such as metagenomics, metatranscriptomics, and proteomics. Moreover, the low diversity of acidophilic communities has allowed for testing of macrobiological theories on microbial ecosystems, including the concept of island biogeography. These advances have led to numerous new insights into the physiological diversity of acidophiles and the ecological drivers of their diversification. However, numerous key questions regarding acidophiles remain unanswered including: When did acidophiles and their habitats evolve? What role has horizontal gene transfer had in promoting acidophily? What regulatory systems underpin the ability of acidophiles to survive and persist in acidic environments? How do acidophile protein systems facilitate microbe-mineral interactions and influence biogeochemical cycles? What is the relationship between acidophilic adaptation and aerobic metabolism? What is the most acidic habitat tolerated by an anaerobe? How have viruses evolved alongside their acidophilic hosts?

This Special Issue is focused on the genetics and genomics of acidophiles and their viruses and seeks studies that focus on comparative genomics, genetic systems, the genetic/genomic mechanisms of acidophilic adaptations and/or microbe-mineral interactions, genomic evolution, and genetic exchange, among other interrelated topics. Submissions of original research studies and reviews related to the above, or related, topics and questions regarding acidophiles are invited to be featured as part of this Special Issue in Genes.

Prof. Eric Boyd
Dr. Dan Colman
Dr. Maximiliano Amenabar
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

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. Genes 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 1800 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

  • Acidophiles
  • Archaea
  • Bacteria
  • Eukaryotes
  • viruses
  • geochemical cycles
  • metals
  • ore leaching
  • aerobes

Published Papers (1 paper)

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Research

Open AccessArticle
Diversity of “Ca. Micrarchaeota” in Two Distinct Types of Acidic Environments and Their Associations with Thermoplasmatales
Received: 16 April 2019 / Revised: 30 May 2019 / Accepted: 11 June 2019 / Published: 15 June 2019
PDF Full-text (2821 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Candidatus Micrarchaeota” are widely distributed in acidic environments; however, their cultivability and our understanding of their interactions with potential hosts are very limited. Their habitats were so far attributed with acidic sites, soils, peats, freshwater systems, and hypersaline mats. Using cultivation and [...] Read more.
Candidatus Micrarchaeota” are widely distributed in acidic environments; however, their cultivability and our understanding of their interactions with potential hosts are very limited. Their habitats were so far attributed with acidic sites, soils, peats, freshwater systems, and hypersaline mats. Using cultivation and culture-independent approaches (16S rRNA gene clonal libraries, high-throughput amplicon sequencing of V3-V4 region of 16S rRNA genes), we surveyed the occurrence of these archaea in geothermal areas on Kamchatka Peninsula and Kunashir Island and assessed their taxonomic diversity in relation with another type of low-pH environment, acid mine drainage stream (Wales, UK). We detected “Ca. Micrarchaeota” in thermophilic heterotrophic enrichment cultures of Kunashir and Kamchatka that appeared as two different phylotypes, namely “Ca. Mancarchaeum acidiphilum”-, and ARMAN-2-related, alongside their potential hosts, Cuniculiplasma spp. and other Thermoplasmatales archaea without defined taxonomic position. These clusters of “Ca. Micrarchaeota” together with three other groups were also present in mesophilic acid mine drainage community. Present work expands our knowledge on the diversity of “Ca. Micrarchaeota” in thermophilic and mesophilic acidic environments, suggests cultivability patterns of acidophilic archaea and establishes potential links between low-abundance species of thermophilic “Ca. Micrarchaeota” and certain Thermoplasmatales, such as Cuniculiplasma spp. in situ. Full article
(This article belongs to the Special Issue Genetics and Genomics of Acidophiles)
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