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Comparative metagenomic analysis reveals mechanisms for stress response in hypoliths from extreme hyperarid deserts

Phuong LE, Thulani P Makhalanyane, Leandro D Guerrero, Surendra Vikram, Yves Van de Peer UGent and Don A Cowan (2016) GENOME BIOLOGY AND EVOLUTION. 8(9). p.2737-2747
abstract
Understanding microbial adaptation to environmental stressors is crucial for interpreting broader ecological patterns. In the most extreme hot and cold deserts, cryptic niche communities are thought to play key roles in ecosystem processes and represent excellent model systems for investigating microbial responses to environmental stressors. However, relatively little is known about the genetic diversity underlying such functional processes in climatically extreme desert systems. This study presents the first comparative metagenome analysis of cyanobacteria-dominated hypolithic communities in hot (Namib Desert, Namibia) and cold (Miers Valley, Antarctica) hyperarid deserts. The most abundant phyla in both hypolith metagenomes were Actinobacteria, Proteobacteria, Cyanobacteria and Bacteroidetes with Cyanobacteria dominating in Antarctic hypoliths. However, no significant differences between the two metagenomes were identified. The Antarctic hypolithic metagenome displayed a high number of sequences assigned to sigma factors, replication, recombination and repair, translation, ribosomal structure, and biogenesis. In contrast, the Namib Desert metagenome showed a high abundance of sequences assigned to carbohydrate transport and metabolism. Metagenome data analysis also revealed significant divergence in the genetic determinants of amino acid and nucleotide metabolism between these two metagenomes and those of soil from other polar deserts, hot deserts, and non-desert soils. Our results suggest extensive niche differentiation in hypolithic microbial communities from these two extreme environments and a high genetic capacity for survival under environmental extremes.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
CLIMATE-CHANGE, BACTERIAL COMMUNITIES, NAMIB DESERT, ENVIRONMENTAL GRADIENTS, ROSS SEA REGION, ANTARCTIC DRY VALLEY, SOIL MICROBIAL COMMUNITIES, biomes, soils, hypoliths, Namib Desert, Antarctica, comparative metagenomics, deserts, stress response, ECOSYSTEM FUNCTION, BACILLUS-SUBTILIS, ORTHOLOG GROUPS
journal title
GENOME BIOLOGY AND EVOLUTION
Genome Biol. Evol.
volume
8
issue
9
pages
2737 - 2747
Web of Science type
Article
Web of Science id
000384307900008
JCR category
GENETICS & HEREDITY
JCR impact factor
3.979 (2016)
JCR rank
42/166 (2016)
JCR quartile
2 (2016)
ISSN
1759-6653
DOI
10.1093/gbe/evw189
project
Bioinformatics: from nucleotids to networks (N2N)
language
English
UGent publication?
yes
classification
A1
copyright statement
I have retained and own the full copyright for this publication
id
8174114
handle
http://hdl.handle.net/1854/LU-8174114
date created
2016-11-28 10:49:34
date last changed
2016-12-19 15:48:17
@article{8174114,
  abstract     = {Understanding microbial adaptation to environmental stressors is crucial for interpreting broader ecological patterns. In the most extreme hot and cold deserts, cryptic niche communities are thought to play key roles in ecosystem processes and represent excellent model systems for investigating microbial responses to environmental stressors. However, relatively little is known about the genetic diversity underlying such functional processes in climatically extreme desert systems. This study presents the first comparative metagenome analysis of cyanobacteria-dominated hypolithic communities in hot (Namib Desert, Namibia) and cold (Miers Valley, Antarctica) hyperarid deserts. The most abundant phyla in both hypolith metagenomes were Actinobacteria, Proteobacteria, Cyanobacteria and Bacteroidetes with Cyanobacteria dominating in Antarctic hypoliths. However, no significant differences between the two metagenomes were identified. The Antarctic hypolithic metagenome displayed a high number of sequences assigned to sigma factors, replication, recombination and repair, translation, ribosomal structure, and biogenesis. In contrast, the Namib Desert metagenome showed a high abundance of sequences assigned to carbohydrate transport and metabolism. Metagenome data analysis also revealed significant divergence in the genetic determinants of amino acid and nucleotide metabolism between these two metagenomes and those of soil from other polar deserts, hot deserts, and non-desert soils. Our results suggest extensive niche differentiation in hypolithic microbial communities from these two extreme environments and a high genetic capacity for survival under environmental extremes.},
  author       = {LE, Phuong and Makhalanyane, Thulani P and Guerrero, Leandro D and Vikram, Surendra and Van de Peer, Yves and Cowan, Don A},
  issn         = {1759-6653},
  journal      = {GENOME BIOLOGY AND EVOLUTION},
  keyword      = {CLIMATE-CHANGE,BACTERIAL COMMUNITIES,NAMIB DESERT,ENVIRONMENTAL GRADIENTS,ROSS SEA REGION,ANTARCTIC DRY VALLEY,SOIL MICROBIAL COMMUNITIES,biomes,soils,hypoliths,Namib Desert,Antarctica,comparative metagenomics,deserts,stress response,ECOSYSTEM FUNCTION,BACILLUS-SUBTILIS,ORTHOLOG GROUPS},
  language     = {eng},
  number       = {9},
  pages        = {2737--2747},
  title        = {Comparative metagenomic analysis reveals mechanisms for stress response in hypoliths from extreme hyperarid deserts},
  url          = {http://dx.doi.org/10.1093/gbe/evw189},
  volume       = {8},
  year         = {2016},
}

Chicago
LE, Phuong, Thulani P Makhalanyane, Leandro D Guerrero, Surendra Vikram, Yves Van de Peer, and Don A Cowan. 2016. “Comparative Metagenomic Analysis Reveals Mechanisms for Stress Response in Hypoliths from Extreme Hyperarid Deserts.” Genome Biology and Evolution 8 (9): 2737–2747.
APA
LE, P., Makhalanyane, T. P., Guerrero, L. D., Vikram, S., Van de Peer, Y., & Cowan, D. A. (2016). Comparative metagenomic analysis reveals mechanisms for stress response in hypoliths from extreme hyperarid deserts. GENOME BIOLOGY AND EVOLUTION, 8(9), 2737–2747.
Vancouver
1.
LE P, Makhalanyane TP, Guerrero LD, Vikram S, Van de Peer Y, Cowan DA. Comparative metagenomic analysis reveals mechanisms for stress response in hypoliths from extreme hyperarid deserts. GENOME BIOLOGY AND EVOLUTION. 2016;8(9):2737–47.
MLA
LE, Phuong, Thulani P Makhalanyane, Leandro D Guerrero, et al. “Comparative Metagenomic Analysis Reveals Mechanisms for Stress Response in Hypoliths from Extreme Hyperarid Deserts.” GENOME BIOLOGY AND EVOLUTION 8.9 (2016): 2737–2747. Print.