dc.contributor.author |
Vikram, Surendra
|
|
dc.contributor.author |
Guerrero, Leandro D.
|
|
dc.contributor.author |
Makhalanyane, Thulani Peter
|
|
dc.contributor.author |
Le, Phuong T.
|
|
dc.contributor.author |
Seely, Mary
|
|
dc.contributor.author |
Cowan, Don A.
|
|
dc.date.accessioned |
2016-08-01T08:25:47Z |
|
dc.date.issued |
2016-06 |
|
dc.description.abstract |
Environmental stressors such as low water activity and temperature extremes impose severe
limitations on the productivity of soils in hyperarid deserts. In such ecosystems, macroscopic
communities are often restricted to cryptic niche habitats, such as hypoliths (microbial
communities found beneath translucent rocks), which are widely distributed in hyperarid
desert environments. While hypolithic communities are considered to play a major role in the
productivity of hyperarid habitats, the functional guilds implicated in these processes remain
unclear. Here, we describe the Illumina-based metagenomic sequencing (± 30 Gb), assembly
and analysis of hypolithic microbial communities from the south-west African Namib Desert.
Taxonomic analyses using Small Subunit (SSU) phylogenetic markers showed that bacterial
phylotypes (93%) dominated the communities, with relatively small proportions of archaea
(0.43%) and fungi (5.6%). BlastX analysis against the refseq-viral database showed the
presence of double stranded DNA viruses (7.8% contigs), dominated by Caudovirales
(59.2%). Analysis of functional genes and metabolic pathways revealed that cyanobacteria
were primarily responsible for photosynthesis with the presence of multiple copies of genes
for both photosystems I and II, with a smaller but significant fraction of proteobacterial
anoxic photosystem II genes. Hypolithic community members demonstrated an extensive
genetic capacity for the degradation of phosphonates and mineralization of organic sulfur.
Our data suggest that Proteobacterial guilds may be more significant in desert niches than
previously recognized, as they showed widespread genetic capacity for mediating key stages
in all biogeochemical cycles. Surprisingly, we were unable to show the presence of genes
representative of complete nitrogen cycles. The diversity of nif genes was low, and the
metagenome showed no evidence of other key N-cycling genes. Taken together, our analyses
suggest an extensive capacity for carbon, phosphate and sulphate cycling but only limited
nitrogen biogeochemistry. |
en_ZA |
dc.description.department |
Genetics |
en_ZA |
dc.description.embargo |
2017-07-01 |
|
dc.description.librarian |
hb2016 |
en_ZA |
dc.description.sponsorship |
The authors (SV, LDG, TPM, PTL, DAC) gratefully acknowledge
funding support from the National Research Foundation
and the University of Pretoria Genomics Research Institute
(TPM, DAC) and computational support from the Centre for
High Performance Computing, Cape Town, South Africa and
bioinformatics at University of Pretoria, Pretoria, South Africa. |
en_ZA |
dc.description.uri |
http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1462-2920 |
en_ZA |
dc.identifier.citation |
Vikram, S, Guerrero, LD, Makhalanyane, TP, Le, PT, Seely, M & Cowan, DA 2016, 'Metagenomic analysis provides insights into functional capacity in a hyperarid desert soil niche community', Environmental Microbiology, vol. 18, no. 6, pp. 1875-1888. |
en_ZA |
dc.identifier.issn |
1462-2912 (print) |
|
dc.identifier.issn |
1462-2920 (online) |
|
dc.identifier.other |
10.1111/1462-2920.13088 |
|
dc.identifier.uri |
http://hdl.handle.net/2263/56154 |
|
dc.language.iso |
en |
en_ZA |
dc.publisher |
Wiley |
en_ZA |
dc.rights |
© 2015 Society for Applied Microbiology and John Wiley & Sons Ltd. This is the pre-peer reviewed version of the following article : Metagenomic analysis provides insights into functional capacity in a hyperarid desert soil niche community, Environmental Microbiology, vol. 18, no. 6, pp. 1875-1888, 2016. doi : 10.1111/1462-2920.13088. The definite version is available at : http://onlinelibrary.wiley.comjournal/10.1111/(ISSN)1462-2920. |
en_ZA |
dc.subject |
Metagenomic analysis |
en_ZA |
dc.subject |
Functional capacity |
en_ZA |
dc.subject |
Hyperarid desert soil |
en_ZA |
dc.title |
Metagenomic analysis provides insights into functional capacity in a hyperarid desert soil niche community |
en_ZA |
dc.type |
Postprint Article |
en_ZA |