Amplicon sequencing dataset (454 pyrosequencing) of Bacteria (16S ssu rRNA gene, v3 region) in hy... more Amplicon sequencing dataset (454 pyrosequencing) of Bacteria (16S ssu rRNA gene, v3 region) in hypolithic and soil environments of Miers Valley, Antarctica
Actinobacteria are ubiquitous in soil, freshwater and marine ecosystems. Although various studies... more Actinobacteria are ubiquitous in soil, freshwater and marine ecosystems. Although various studies have focused on the microbial ecology of this phylum, data is scant on the ecology of actinobacteria endemic to hot springs. Here, we have investigated the molecular diversity of eubacteria, with specific focus on the actinobacteria in hot springs in Zambia, China, New Zealand and Kenya. Temperature and pH values at sampling sites ranged between 44.5-86.5oC and 5-10, respectively. Non-metric multidimensional scaling analysis of 16S rRNA gene T-RFLP patterns showed that samples could be separated by geographical location. Multivariate analysis showed that actinobacterial community composition was best predicted by changes in pH and temperature, whereas temperature alone was the most important variable explaining differences in bacterial community structure. Using 16S rRNA gene libraries, 28 major actinobacterial OTUs were found. Both molecular techniques indicated that many of the actino...
The rise in antibiotic-resistant bacteria has spurred efforts to identify novel compounds with an... more The rise in antibiotic-resistant bacteria has spurred efforts to identify novel compounds with antimicrobial activity. This brief report describes the genome sequence of threeBacillusspecies isolates from South African marine sponges, which produce compounds with antimicrobial activity. A search for secondary metabolite clusters revealed several secondary metabolite pathways in these genomes, which may hold promise as novel antibiotics.
Viral communities of two different salt pans located in the Namib Desert, Hosabes and Eisfeld, we... more Viral communities of two different salt pans located in the Namib Desert, Hosabes and Eisfeld, were investigated using a combination of multiple displacement amplification of metaviromic DNA and deep sequencing, and provided comprehensive sequence data on both ssDNA and dsDNA viral community structures. Read and contig annotations through online pipelines showed that the salt pans harbored largely unknown viral communities. Through network analysis, we were able to assign a large portion of the unknown reads to a diverse group of ssDNA viruses. Contigs belonging to the subfamily Gokushovirinae were common in both environmental datasets. Analysis of haloarchaeal virus contigs revealed the presence of three contigs distantly related with His1, indicating a possible new lineage of salterproviruses in the Hosabes playa. Based on viral richness and read mapping analyses, the salt pan metaviromes were novel and most closely related to each other while showing a low degree of overlap with ...
Applied microbiology and biotechnology, Jan 4, 2015
Geobacillus thermoglucosidasius is a promising platform organism for the production of biofuels a... more Geobacillus thermoglucosidasius is a promising platform organism for the production of biofuels and other metabolites of interest. G. thermoglucosidasius fermentations could be subject to bacteriophage-related failure and financial loss. We develop two strains resistant to a recently described G. thermoglucosidasius-infecting phage GVE3. The phage-encoded immunity gene, imm, was overexpressed in the host leading to phage resistance. A phage-resistant mutant was isolated following expression of a putative anti-repressor-like protein and phage challenge. A point mutation was identified in the polysaccharide pyruvyl transferase, csaB. A double crossover knockout mutation of csaB confirmed its role in the phage resistance phenotype. These resistance mechanisms appear to prevent phage DNA injection and/or lysogenic conversion rather than just reducing efficiency of plating, as no phage DNA could be detected in resistant bacteria challenged with GVE3 and no plaques observed even at high p...
Hypolithic microbial communities are specialized desert communities inhabiting the underside of t... more Hypolithic microbial communities are specialized desert communities inhabiting the underside of translucent rocks. Here, we present the first study of the viral fraction of these communities isolated from the hyperarid Namib Desert. The taxonomic composition of the hypolithic viral communities was investigated and a functional assessment of the sequences determined. Phylotypic analysis showed that bacteriophages belonging to the order Caudovirales, in particular the family Siphoviridae, were most prevalent. Functional analysis and comparison with other metaviromes revealed a relatively high frequency of cell wall-degrading enzymes, ribonucleotide reductases (RNRs) and phage-associated genes. Phylogenetic analyses of terL and phoH marker genes indicated that many of the sequences were novel and distinct from known isolates, and the class distribution of the RNRs suggests that this is a novel environment. The composition of the viral hypolith fraction containing many Bacillus-infectin...
Biofuels currently feature heavily on scientific, social, and political agenda, and particular fo... more Biofuels currently feature heavily on scientific, social, and political agenda, and particular focus is reserved for liquid fuels that may act as a substitute or blending agent for petroleum. Many pertinent questions arise when a thorough analysis of the feasibility of liquid alcohol ...
The Dry Valleys Desert of Eastern Antarctica is an ice-free region of 4800 km2, which accounts fo... more The Dry Valleys Desert of Eastern Antarctica is an ice-free region of 4800 km2, which accounts for less than 2% of the total Antarctic landmass. Previously, it was thought that the prevailing environmental conditions of these hyper-arid cold deserts, such as strong katabatic winds, low temperatures, and low humidity, would severely limit the ability of microorganisms to survive in this habitat, and the Dry Valleys could only support low microbial populations [Wynn-Williams, 1990]. However, recent culture-independent ...
A transposon, TnAtcArs, that carries a set of arsenic-resistance genes was isolated from a strain... more A transposon, TnAtcArs, that carries a set of arsenic-resistance genes was isolated from a strain of the moderately thermophilic, sulfur-oxidizing, biomining bacteriumAcidithiobacillus caldus. This strain originated from a commercial plant used for the bio-oxidation of gold-bearing arsenopyrite concentrates. Continuous selection for arsenic resistance over many years had made the bacterium resistant to high concentrations of arsenic. Sequence analysis indicated that TnAtcArsis 12 444 bp in length and has 40 bp terminal inverted repeat sequences and divergently transcribed resolvase and transposase genes that are related to the Tn21-transposon subfamily. A series of genes consisting ofarsR, two tandem copies ofarsAandarsD, two ORFs (7 and 8) andarsBis situated between the resolvase and transposase genes. Although some commercial strains ofAt. calduscontained thearsDAduplication, when transformed intoEscherichia coli, thearsDAduplication was unstable and was frequently lost during cul...
Amplicon sequencing dataset (454 pyrosequencing) of Bacteria (16S ssu rRNA gene, v3 region) in hy... more Amplicon sequencing dataset (454 pyrosequencing) of Bacteria (16S ssu rRNA gene, v3 region) in hypolithic and soil environments of Miers Valley, Antarctica
Actinobacteria are ubiquitous in soil, freshwater and marine ecosystems. Although various studies... more Actinobacteria are ubiquitous in soil, freshwater and marine ecosystems. Although various studies have focused on the microbial ecology of this phylum, data is scant on the ecology of actinobacteria endemic to hot springs. Here, we have investigated the molecular diversity of eubacteria, with specific focus on the actinobacteria in hot springs in Zambia, China, New Zealand and Kenya. Temperature and pH values at sampling sites ranged between 44.5-86.5oC and 5-10, respectively. Non-metric multidimensional scaling analysis of 16S rRNA gene T-RFLP patterns showed that samples could be separated by geographical location. Multivariate analysis showed that actinobacterial community composition was best predicted by changes in pH and temperature, whereas temperature alone was the most important variable explaining differences in bacterial community structure. Using 16S rRNA gene libraries, 28 major actinobacterial OTUs were found. Both molecular techniques indicated that many of the actino...
The rise in antibiotic-resistant bacteria has spurred efforts to identify novel compounds with an... more The rise in antibiotic-resistant bacteria has spurred efforts to identify novel compounds with antimicrobial activity. This brief report describes the genome sequence of threeBacillusspecies isolates from South African marine sponges, which produce compounds with antimicrobial activity. A search for secondary metabolite clusters revealed several secondary metabolite pathways in these genomes, which may hold promise as novel antibiotics.
Viral communities of two different salt pans located in the Namib Desert, Hosabes and Eisfeld, we... more Viral communities of two different salt pans located in the Namib Desert, Hosabes and Eisfeld, were investigated using a combination of multiple displacement amplification of metaviromic DNA and deep sequencing, and provided comprehensive sequence data on both ssDNA and dsDNA viral community structures. Read and contig annotations through online pipelines showed that the salt pans harbored largely unknown viral communities. Through network analysis, we were able to assign a large portion of the unknown reads to a diverse group of ssDNA viruses. Contigs belonging to the subfamily Gokushovirinae were common in both environmental datasets. Analysis of haloarchaeal virus contigs revealed the presence of three contigs distantly related with His1, indicating a possible new lineage of salterproviruses in the Hosabes playa. Based on viral richness and read mapping analyses, the salt pan metaviromes were novel and most closely related to each other while showing a low degree of overlap with ...
Applied microbiology and biotechnology, Jan 4, 2015
Geobacillus thermoglucosidasius is a promising platform organism for the production of biofuels a... more Geobacillus thermoglucosidasius is a promising platform organism for the production of biofuels and other metabolites of interest. G. thermoglucosidasius fermentations could be subject to bacteriophage-related failure and financial loss. We develop two strains resistant to a recently described G. thermoglucosidasius-infecting phage GVE3. The phage-encoded immunity gene, imm, was overexpressed in the host leading to phage resistance. A phage-resistant mutant was isolated following expression of a putative anti-repressor-like protein and phage challenge. A point mutation was identified in the polysaccharide pyruvyl transferase, csaB. A double crossover knockout mutation of csaB confirmed its role in the phage resistance phenotype. These resistance mechanisms appear to prevent phage DNA injection and/or lysogenic conversion rather than just reducing efficiency of plating, as no phage DNA could be detected in resistant bacteria challenged with GVE3 and no plaques observed even at high p...
Hypolithic microbial communities are specialized desert communities inhabiting the underside of t... more Hypolithic microbial communities are specialized desert communities inhabiting the underside of translucent rocks. Here, we present the first study of the viral fraction of these communities isolated from the hyperarid Namib Desert. The taxonomic composition of the hypolithic viral communities was investigated and a functional assessment of the sequences determined. Phylotypic analysis showed that bacteriophages belonging to the order Caudovirales, in particular the family Siphoviridae, were most prevalent. Functional analysis and comparison with other metaviromes revealed a relatively high frequency of cell wall-degrading enzymes, ribonucleotide reductases (RNRs) and phage-associated genes. Phylogenetic analyses of terL and phoH marker genes indicated that many of the sequences were novel and distinct from known isolates, and the class distribution of the RNRs suggests that this is a novel environment. The composition of the viral hypolith fraction containing many Bacillus-infectin...
Biofuels currently feature heavily on scientific, social, and political agenda, and particular fo... more Biofuels currently feature heavily on scientific, social, and political agenda, and particular focus is reserved for liquid fuels that may act as a substitute or blending agent for petroleum. Many pertinent questions arise when a thorough analysis of the feasibility of liquid alcohol ...
The Dry Valleys Desert of Eastern Antarctica is an ice-free region of 4800 km2, which accounts fo... more The Dry Valleys Desert of Eastern Antarctica is an ice-free region of 4800 km2, which accounts for less than 2% of the total Antarctic landmass. Previously, it was thought that the prevailing environmental conditions of these hyper-arid cold deserts, such as strong katabatic winds, low temperatures, and low humidity, would severely limit the ability of microorganisms to survive in this habitat, and the Dry Valleys could only support low microbial populations [Wynn-Williams, 1990]. However, recent culture-independent ...
A transposon, TnAtcArs, that carries a set of arsenic-resistance genes was isolated from a strain... more A transposon, TnAtcArs, that carries a set of arsenic-resistance genes was isolated from a strain of the moderately thermophilic, sulfur-oxidizing, biomining bacteriumAcidithiobacillus caldus. This strain originated from a commercial plant used for the bio-oxidation of gold-bearing arsenopyrite concentrates. Continuous selection for arsenic resistance over many years had made the bacterium resistant to high concentrations of arsenic. Sequence analysis indicated that TnAtcArsis 12 444 bp in length and has 40 bp terminal inverted repeat sequences and divergently transcribed resolvase and transposase genes that are related to the Tn21-transposon subfamily. A series of genes consisting ofarsR, two tandem copies ofarsAandarsD, two ORFs (7 and 8) andarsBis situated between the resolvase and transposase genes. Although some commercial strains ofAt. calduscontained thearsDAduplication, when transformed intoEscherichia coli, thearsDAduplication was unstable and was frequently lost during cul...
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