Metagenomic analysis provides insights into functional capacity in a hyperarid desert soil niche community

Autores
Vikram, Surendra; Guerrero, Leandro Demián; Makhalanyane, Thulani P.; Le, Phuong T.; Seely, Mary; Cowan, Don A.
Año de publicación
2016
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
In hyperarid ecosystems, macroscopic communities are often restricted to cryptic niches, 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 productivity, the functional guilds implicated in these processes remain unclear. Here, we describe the metagenomic sequencing, assembly and analysis of hypolithic microbial communities from the Namib Desert. Taxonomic analyses using Small Subunit phylogenetic markers showed that bacterial phylotypes (93%) dominated the communities, with relatively small proportions of archaea (0.43%) and fungi (5.6%). Refseq-viral database analysis 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. Hypolithons demonstrated an extensive genetic capacity for the degradation of phosphonates and mineralization of organic sulphur. Surprisingly, we were unable to show the presence of genes representative of complete nitrogen cycles. Taken together, our analyses suggest an extensive capacity for carbon, phosphate and sulphate cycling but only limited nitrogen biogeochemistry.
Fil: Vikram, Surendra. University of Pretoria; Sudáfrica
Fil: Guerrero, Leandro Demián. University of Pretoria; Sudáfrica. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina
Fil: Makhalanyane, Thulani P.. University of Pretoria; Sudáfrica
Fil: Le, Phuong T.. University of Pretoria; Sudáfrica
Fil: Seely, Mary. Gobabeb Research and Training Centr; Namibia
Fil: Cowan, Don A.. University of Pretoria; Sudáfrica
Materia
Environmental Microbiology
Metagenomics
Desert
Hypoliths
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/69929
Acceder
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network_name_str CONICET Digital (CONICET)
spelling Metagenomic analysis provides insights into functional capacity in a hyperarid desert soil niche communityVikram, SurendraGuerrero, Leandro DemiánMakhalanyane, Thulani P.Le, Phuong T.Seely, MaryCowan, Don A.Environmental MicrobiologyMetagenomicsDesertHypolithshttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1In hyperarid ecosystems, macroscopic communities are often restricted to cryptic niches, 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 productivity, the functional guilds implicated in these processes remain unclear. Here, we describe the metagenomic sequencing, assembly and analysis of hypolithic microbial communities from the Namib Desert. Taxonomic analyses using Small Subunit phylogenetic markers showed that bacterial phylotypes (93%) dominated the communities, with relatively small proportions of archaea (0.43%) and fungi (5.6%). Refseq-viral database analysis 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. Hypolithons demonstrated an extensive genetic capacity for the degradation of phosphonates and mineralization of organic sulphur. Surprisingly, we were unable to show the presence of genes representative of complete nitrogen cycles. Taken together, our analyses suggest an extensive capacity for carbon, phosphate and sulphate cycling but only limited nitrogen biogeochemistry.Fil: Vikram, Surendra. University of Pretoria; SudáfricaFil: Guerrero, Leandro Demián. University of Pretoria; Sudáfrica. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; ArgentinaFil: Makhalanyane, Thulani P.. University of Pretoria; SudáfricaFil: Le, Phuong T.. University of Pretoria; SudáfricaFil: Seely, Mary. Gobabeb Research and Training Centr; NamibiaFil: Cowan, Don A.. University of Pretoria; SudáfricaWiley Blackwell Publishing, Inc2016-06info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/69929Vikram, Surendra; Guerrero, Leandro Demián; Makhalanyane, Thulani P.; Le, Phuong T.; Seely, Mary; et al.; Metagenomic analysis provides insights into functional capacity in a hyperarid desert soil niche community; Wiley Blackwell Publishing, Inc; Environmental Microbiology; 18; 6; 6-2016; 1875-18881462-29121462-2920CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1111/1462-2920.13088info:eu-repo/semantics/altIdentifier/url/https://onlinelibrary.wiley.com/doi/abs/10.1111/1462-2920.13088info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:35:01Zoai:ri.conicet.gov.ar:11336/69929instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-29 10:35:01.543CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Metagenomic analysis provides insights into functional capacity in a hyperarid desert soil niche community
title Metagenomic analysis provides insights into functional capacity in a hyperarid desert soil niche community
spellingShingle Metagenomic analysis provides insights into functional capacity in a hyperarid desert soil niche community
Vikram, Surendra
Environmental Microbiology
Metagenomics
Desert
Hypoliths
title_short Metagenomic analysis provides insights into functional capacity in a hyperarid desert soil niche community
title_full Metagenomic analysis provides insights into functional capacity in a hyperarid desert soil niche community
title_fullStr Metagenomic analysis provides insights into functional capacity in a hyperarid desert soil niche community
title_full_unstemmed Metagenomic analysis provides insights into functional capacity in a hyperarid desert soil niche community
title_sort Metagenomic analysis provides insights into functional capacity in a hyperarid desert soil niche community
dc.creator.none.fl_str_mv Vikram, Surendra
Guerrero, Leandro Demián
Makhalanyane, Thulani P.
Le, Phuong T.
Seely, Mary
Cowan, Don A.
author Vikram, Surendra
author_facet Vikram, Surendra
Guerrero, Leandro Demián
Makhalanyane, Thulani P.
Le, Phuong T.
Seely, Mary
Cowan, Don A.
author_role author
author2 Guerrero, Leandro Demián
Makhalanyane, Thulani P.
Le, Phuong T.
Seely, Mary
Cowan, Don A.
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv Environmental Microbiology
Metagenomics
Desert
Hypoliths
topic Environmental Microbiology
Metagenomics
Desert
Hypoliths
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv In hyperarid ecosystems, macroscopic communities are often restricted to cryptic niches, 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 productivity, the functional guilds implicated in these processes remain unclear. Here, we describe the metagenomic sequencing, assembly and analysis of hypolithic microbial communities from the Namib Desert. Taxonomic analyses using Small Subunit phylogenetic markers showed that bacterial phylotypes (93%) dominated the communities, with relatively small proportions of archaea (0.43%) and fungi (5.6%). Refseq-viral database analysis 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. Hypolithons demonstrated an extensive genetic capacity for the degradation of phosphonates and mineralization of organic sulphur. Surprisingly, we were unable to show the presence of genes representative of complete nitrogen cycles. Taken together, our analyses suggest an extensive capacity for carbon, phosphate and sulphate cycling but only limited nitrogen biogeochemistry.
Fil: Vikram, Surendra. University of Pretoria; Sudáfrica
Fil: Guerrero, Leandro Demián. University of Pretoria; Sudáfrica. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina
Fil: Makhalanyane, Thulani P.. University of Pretoria; Sudáfrica
Fil: Le, Phuong T.. University of Pretoria; Sudáfrica
Fil: Seely, Mary. Gobabeb Research and Training Centr; Namibia
Fil: Cowan, Don A.. University of Pretoria; Sudáfrica
description In hyperarid ecosystems, macroscopic communities are often restricted to cryptic niches, 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 productivity, the functional guilds implicated in these processes remain unclear. Here, we describe the metagenomic sequencing, assembly and analysis of hypolithic microbial communities from the Namib Desert. Taxonomic analyses using Small Subunit phylogenetic markers showed that bacterial phylotypes (93%) dominated the communities, with relatively small proportions of archaea (0.43%) and fungi (5.6%). Refseq-viral database analysis 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. Hypolithons demonstrated an extensive genetic capacity for the degradation of phosphonates and mineralization of organic sulphur. Surprisingly, we were unable to show the presence of genes representative of complete nitrogen cycles. Taken together, our analyses suggest an extensive capacity for carbon, phosphate and sulphate cycling but only limited nitrogen biogeochemistry.
publishDate 2016
dc.date.none.fl_str_mv 2016-06
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/69929
Vikram, Surendra; Guerrero, Leandro Demián; Makhalanyane, Thulani P.; Le, Phuong T.; Seely, Mary; et al.; Metagenomic analysis provides insights into functional capacity in a hyperarid desert soil niche community; Wiley Blackwell Publishing, Inc; Environmental Microbiology; 18; 6; 6-2016; 1875-1888
1462-2912
1462-2920
CONICET Digital
CONICET
url http://hdl.handle.net/11336/69929
identifier_str_mv Vikram, Surendra; Guerrero, Leandro Demián; Makhalanyane, Thulani P.; Le, Phuong T.; Seely, Mary; et al.; Metagenomic analysis provides insights into functional capacity in a hyperarid desert soil niche community; Wiley Blackwell Publishing, Inc; Environmental Microbiology; 18; 6; 6-2016; 1875-1888
1462-2912
1462-2920
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1111/1462-2920.13088
info:eu-repo/semantics/altIdentifier/url/https://onlinelibrary.wiley.com/doi/abs/10.1111/1462-2920.13088
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Wiley Blackwell Publishing, Inc
publisher.none.fl_str_mv Wiley Blackwell Publishing, Inc
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
_version_ 1844614367549587456
score 13.070432

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