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Comparative Genomics Unravels the Functional Roles of Co-occurring Acidophilic Bacteria in Bioleaching Heaps

The spatial-temporal distribution of populations in various econiches is thought to be potentially related to individual differences in the utilization of nutrients or other resources, but their functional roles in the microbial communities remain elusive. We compared differentiation in gene reperto...

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Autores principales: Zhang, Xian, Liu, Xueduan, Liang, Yili, Xiao, Yunhua, Ma, Liyuan, Guo, Xue, Miao, Bo, Liu, Hongwei, Peng, Deliang, Huang, Wenkun, Yin, Huaqun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5418355/
https://www.ncbi.nlm.nih.gov/pubmed/28529505
http://dx.doi.org/10.3389/fmicb.2017.00790
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author Zhang, Xian
Liu, Xueduan
Liang, Yili
Xiao, Yunhua
Ma, Liyuan
Guo, Xue
Miao, Bo
Liu, Hongwei
Peng, Deliang
Huang, Wenkun
Yin, Huaqun
author_facet Zhang, Xian
Liu, Xueduan
Liang, Yili
Xiao, Yunhua
Ma, Liyuan
Guo, Xue
Miao, Bo
Liu, Hongwei
Peng, Deliang
Huang, Wenkun
Yin, Huaqun
author_sort Zhang, Xian
collection PubMed
description The spatial-temporal distribution of populations in various econiches is thought to be potentially related to individual differences in the utilization of nutrients or other resources, but their functional roles in the microbial communities remain elusive. We compared differentiation in gene repertoire and metabolic profiles, with a focus on the potential functional traits of three commonly recognized members (Acidithiobacillus caldus, Leptospirillum ferriphilum, and Sulfobacillus thermosulfidooxidans) in bioleaching heaps. Comparative genomics revealed that intra-species divergence might be driven by horizontal gene transfer. These co-occurring bacteria shared a few homologous genes, which significantly suggested the genomic differences between these organisms. Notably, relatively more genes assigned to the Clusters of Orthologous Groups category [G] (carbohydrate transport and metabolism) were identified in Sulfobacillus thermosulfidooxidans compared to the two other species, which probably indicated their mixotrophic capabilities that assimilate both organic and inorganic forms of carbon. Further inspection revealed distinctive metabolic capabilities involving carbon assimilation, nitrogen uptake, and iron-sulfur cycling, providing robust evidence for functional differences with respect to nutrient utilization. Therefore, we proposed that the mutual compensation of functionalities among these co-occurring organisms might provide a selective advantage for efficiently utilizing the limited resources in their habitats. Furthermore, it might be favorable to chemoautotrophs' lifestyles to form mutualistic interactions with these heterotrophic and/or mixotrophic acidophiles, whereby the latter could degrade organic compounds to effectively detoxify the environments. Collectively, the findings shed light on the genetic traits and potential metabolic activities of these organisms, and enable us to make some inferences about genomic and functional differences that might allow them to co-exist.
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spelling pubmed-54183552017-05-19 Comparative Genomics Unravels the Functional Roles of Co-occurring Acidophilic Bacteria in Bioleaching Heaps Zhang, Xian Liu, Xueduan Liang, Yili Xiao, Yunhua Ma, Liyuan Guo, Xue Miao, Bo Liu, Hongwei Peng, Deliang Huang, Wenkun Yin, Huaqun Front Microbiol Microbiology The spatial-temporal distribution of populations in various econiches is thought to be potentially related to individual differences in the utilization of nutrients or other resources, but their functional roles in the microbial communities remain elusive. We compared differentiation in gene repertoire and metabolic profiles, with a focus on the potential functional traits of three commonly recognized members (Acidithiobacillus caldus, Leptospirillum ferriphilum, and Sulfobacillus thermosulfidooxidans) in bioleaching heaps. Comparative genomics revealed that intra-species divergence might be driven by horizontal gene transfer. These co-occurring bacteria shared a few homologous genes, which significantly suggested the genomic differences between these organisms. Notably, relatively more genes assigned to the Clusters of Orthologous Groups category [G] (carbohydrate transport and metabolism) were identified in Sulfobacillus thermosulfidooxidans compared to the two other species, which probably indicated their mixotrophic capabilities that assimilate both organic and inorganic forms of carbon. Further inspection revealed distinctive metabolic capabilities involving carbon assimilation, nitrogen uptake, and iron-sulfur cycling, providing robust evidence for functional differences with respect to nutrient utilization. Therefore, we proposed that the mutual compensation of functionalities among these co-occurring organisms might provide a selective advantage for efficiently utilizing the limited resources in their habitats. Furthermore, it might be favorable to chemoautotrophs' lifestyles to form mutualistic interactions with these heterotrophic and/or mixotrophic acidophiles, whereby the latter could degrade organic compounds to effectively detoxify the environments. Collectively, the findings shed light on the genetic traits and potential metabolic activities of these organisms, and enable us to make some inferences about genomic and functional differences that might allow them to co-exist. Frontiers Media S.A. 2017-05-05 /pmc/articles/PMC5418355/ /pubmed/28529505 http://dx.doi.org/10.3389/fmicb.2017.00790 Text en Copyright © 2017 Zhang, Liu, Liang, Xiao, Ma, Guo, Miao, Liu, Peng, Huang and Yin. http://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) or licensor 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
Zhang, Xian
Liu, Xueduan
Liang, Yili
Xiao, Yunhua
Ma, Liyuan
Guo, Xue
Miao, Bo
Liu, Hongwei
Peng, Deliang
Huang, Wenkun
Yin, Huaqun
Comparative Genomics Unravels the Functional Roles of Co-occurring Acidophilic Bacteria in Bioleaching Heaps
title Comparative Genomics Unravels the Functional Roles of Co-occurring Acidophilic Bacteria in Bioleaching Heaps
title_full Comparative Genomics Unravels the Functional Roles of Co-occurring Acidophilic Bacteria in Bioleaching Heaps
title_fullStr Comparative Genomics Unravels the Functional Roles of Co-occurring Acidophilic Bacteria in Bioleaching Heaps
title_full_unstemmed Comparative Genomics Unravels the Functional Roles of Co-occurring Acidophilic Bacteria in Bioleaching Heaps
title_short Comparative Genomics Unravels the Functional Roles of Co-occurring Acidophilic Bacteria in Bioleaching Heaps
title_sort comparative genomics unravels the functional roles of co-occurring acidophilic bacteria in bioleaching heaps
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5418355/
https://www.ncbi.nlm.nih.gov/pubmed/28529505
http://dx.doi.org/10.3389/fmicb.2017.00790
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