The diversity of key anabolic genes in antarctic hypolithons
>Magister Scientiae - MSc Antarctica is known for its pristine environments. A variety of unsuitable environmental conditions were once thought to render the continent unsuitable for sustaining life. However, metagenomic data have revealed a wealth of species diversity in a range of biotopes.Hypo...
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ftunivwesterncap:oai:etd.uwc.ac.za:11394/3337 2023-05-15T14:02:11+02:00 The diversity of key anabolic genes in antarctic hypolithons Makhalanyane, Thulani Peter Cowan, D.A. Tuffin, Marla 2009 http://hdl.handle.net/11394/3337 en eng http://hdl.handle.net/11394/3337 Antarctica Metagenomic data Diversity Biotopes Hypolithons Photosynthetic communities Translucent rocks Climatically extreme environments Carbon (C) Nitrogen (N) Hyperarid desert environment Thesis 2009 ftunivwesterncap 2021-06-17T16:09:28Z >Magister Scientiae - MSc Antarctica is known for its pristine environments. A variety of unsuitable environmental conditions were once thought to render the continent unsuitable for sustaining life. However, metagenomic data have revealed a wealth of species diversity in a range of biotopes.Hypolithons, photosynthetic communities which live under translucent rocks in climatically extreme environments, are an important input source for both carbon (C) and nitrogen (N) in this hyperarid desert environment. Microbial contribution to biogeochemical cycling resulting in fixation of both C and N remains poorly understood. Moreover, there is a reported close interplay between both cycles, with nitrogen being reported to be a limiting factor in carbon assimilation.In this study the diversity of C and N fixing organisms was investigated by using the cbbL and nifH genes as phylogenetic and functional markers. High Molecular weight metagenomic DNA and RNA was extracted from hypolithons. PCR amplification was carried out using cbbL (800 bp for red-like, 1,100 bp for green-like) and nifH (360 bp) gene specific primers.Resultant PCR products were used to construct libraries which were screened for correct sized inserts. Restriction Fragment Length Polymorphism (RFLP) was used to de-replicate clones prior to sequencing. Phylogenetic positions from both clone libraries were established by aligning nucleotide sequences and constructing similarity trees using NJ clustering methods.BLASTn results indicated the presence of previously uncultured organisms which contain cbbL and nifH genes. BLASTn results were characterized by low percentages of maximum identity (typically <95%), a potential indicator of novel taxa. Sequences from respective libraries clustered with cyanobacteria such as Nostoc, Scytonema, and Tolypothrix and α-, β-, and γ-Proteobacteria such as Azotobacter, Agrobacterium and Mesorhizobium. Generally sequence results indicate a largely homogenous, being dominated by specific taxa. Each group may contain potential keystone species, essential for both biogeochemical cycling in oligotrophic environment. Thesis Antarc* Antarctic Antarctica University of the Western Cape: Electronic Thesis and Dissertation Library Antarctic |
institution |
Open Polar |
collection |
University of the Western Cape: Electronic Thesis and Dissertation Library |
op_collection_id |
ftunivwesterncap |
language |
English |
topic |
Antarctica Metagenomic data Diversity Biotopes Hypolithons Photosynthetic communities Translucent rocks Climatically extreme environments Carbon (C) Nitrogen (N) Hyperarid desert environment |
spellingShingle |
Antarctica Metagenomic data Diversity Biotopes Hypolithons Photosynthetic communities Translucent rocks Climatically extreme environments Carbon (C) Nitrogen (N) Hyperarid desert environment Makhalanyane, Thulani Peter The diversity of key anabolic genes in antarctic hypolithons |
topic_facet |
Antarctica Metagenomic data Diversity Biotopes Hypolithons Photosynthetic communities Translucent rocks Climatically extreme environments Carbon (C) Nitrogen (N) Hyperarid desert environment |
description |
>Magister Scientiae - MSc Antarctica is known for its pristine environments. A variety of unsuitable environmental conditions were once thought to render the continent unsuitable for sustaining life. However, metagenomic data have revealed a wealth of species diversity in a range of biotopes.Hypolithons, photosynthetic communities which live under translucent rocks in climatically extreme environments, are an important input source for both carbon (C) and nitrogen (N) in this hyperarid desert environment. Microbial contribution to biogeochemical cycling resulting in fixation of both C and N remains poorly understood. Moreover, there is a reported close interplay between both cycles, with nitrogen being reported to be a limiting factor in carbon assimilation.In this study the diversity of C and N fixing organisms was investigated by using the cbbL and nifH genes as phylogenetic and functional markers. High Molecular weight metagenomic DNA and RNA was extracted from hypolithons. PCR amplification was carried out using cbbL (800 bp for red-like, 1,100 bp for green-like) and nifH (360 bp) gene specific primers.Resultant PCR products were used to construct libraries which were screened for correct sized inserts. Restriction Fragment Length Polymorphism (RFLP) was used to de-replicate clones prior to sequencing. Phylogenetic positions from both clone libraries were established by aligning nucleotide sequences and constructing similarity trees using NJ clustering methods.BLASTn results indicated the presence of previously uncultured organisms which contain cbbL and nifH genes. BLASTn results were characterized by low percentages of maximum identity (typically <95%), a potential indicator of novel taxa. Sequences from respective libraries clustered with cyanobacteria such as Nostoc, Scytonema, and Tolypothrix and α-, β-, and γ-Proteobacteria such as Azotobacter, Agrobacterium and Mesorhizobium. Generally sequence results indicate a largely homogenous, being dominated by specific taxa. Each group may contain potential keystone species, essential for both biogeochemical cycling in oligotrophic environment. |
author2 |
Cowan, D.A. Tuffin, Marla |
format |
Thesis |
author |
Makhalanyane, Thulani Peter |
author_facet |
Makhalanyane, Thulani Peter |
author_sort |
Makhalanyane, Thulani Peter |
title |
The diversity of key anabolic genes in antarctic hypolithons |
title_short |
The diversity of key anabolic genes in antarctic hypolithons |
title_full |
The diversity of key anabolic genes in antarctic hypolithons |
title_fullStr |
The diversity of key anabolic genes in antarctic hypolithons |
title_full_unstemmed |
The diversity of key anabolic genes in antarctic hypolithons |
title_sort |
diversity of key anabolic genes in antarctic hypolithons |
publishDate |
2009 |
url |
http://hdl.handle.net/11394/3337 |
geographic |
Antarctic |
geographic_facet |
Antarctic |
genre |
Antarc* Antarctic Antarctica |
genre_facet |
Antarc* Antarctic Antarctica |
op_relation |
http://hdl.handle.net/11394/3337 |
_version_ |
1766272299408818176 |