Characterisation of the arsenic resistance genes in Bacillus sp. UWC isolated from maturing fly ash acid mine drainage neutralised solids

An arsenic resistant Bacillus sp. UWC was isolated from fly ash acid mine drainage (FA-AMD) neutralised solids. A genomic library was prepared and screened in an arsenic sensitive mutant Escherichia coli strain for the presence of arsenic resistance (ars) genes. Sequence analysis of a clone conferring resistance to both sodium arsenite and sodium arsenate revealed homologues to the arsR (regulatory repressor), arsB (membrane located arsenite pump), arsC (arsenate reductase), arsD (second regulatory repressor and a metallochaperone) and arsA (ATPase) genes from known arsenic resistance operons. The Bacillus sp. UWC arsRBCDA genes were shown to be arranged in an unusual manner with the arsDA genes immediately downstream of arsC

Micro-eukaryotic diversity in hypolithons from Miers Valley, Antarctica

The discovery of extensive and complex hypolithic communities in both cold and hot deserts has raised many questions regarding their ecology, biodiversity and relevance in terms of regional productivity. However, most hypolithic research has focused on the bacterial elements of the community. This study represents the first investigation of micro-eukaryotic communities in all three hypolith types. Here we show that Antarctic hypoliths support extensive populations of novel uncharacterized bryophyta, fungi and protists and suggest that well known producer-decomposer-predator interactions may create the necessary conditions for hypolithic productivity in Antarctic deserts

Extremophiles in biofuel synthesis

The current global energy situation has demonstrated an urgent need for the development of alternative fuel sourcesto the continually diminishing fossil fuel reserves. Much research to address this issue focuses on the developmentof financially viable technologies for the production of biofuels. The current market for biofuels, defined as fuelproducts obtained from organic substrates, is dominated by bioethanol, biodiesel, biobutanol and biogas, relying onthe use of substrates such as sugars, starch and oil crops, agricultural and animal wastes, and lignocellulosic biomass.This conversion from biomass to biofuel through microbial catalysis has gained much momentum as biotechnologyhas evolved to its current status. Extremophiles are a robust group of organisms producing stable enzymes, which areoften capable of tolerating changes in environmental conditions such as pH and temperature. The potentialapplication of such organisms and their enzymes in biotechnology is enormous, and a particular application is inbiofuel production. In this review an overview of the different biofuels is given, covering those already producedcommercially as well as those under development. The past and present trends in biofuel production are discussed,and future prospects for the industry are highlighted. The focus is on the current and future application ofextremophilic organisms and enzymes in technologies to develop and improve the biotechnological production ofbiofuels

Biodiversity: so much more than legs and leaves

Microorganisms inhabit virtually every possible niche on Earth, including those at the outer envelope of survival. However, the focus of most conservation authorities and ecologists is the ‘legs and leaves’ side of biology – the ‘macrobiology’ that can be seen with the naked eye. There is little apparent concern for the preservation of microbial diversity, or of unique microbial habitats. Here we show examples of the astounding microbial diversity supported by South Africa’s ecosystems and argue that because microbes constitute the vast majority of our planet’s species they should be considered seriously in the future protection of our genetic resources.Web of Scienc

High-level diversity of tailed phages, eukaryote-associated viruses, and virophage-like elements in the metaviromes of Antarctic soils

The metaviromes of two distinct Antarctic hyperarid desert soil communities have been characterized. Hypolithic communities, cyanobacterium-dominated assemblages situated on the ventral surfaces of quartz pebbles embedded in the desert pavement, showed higher virus diversity than surface soils, which correlated with previous bacterial community studies. Prokaryotic viruses (i.e., phages) represented the largest viral component (particularly Mycobacterium phages) in both habitats, with an identical hierarchical sequence abundance of families of tailed phages (Siphoviridae>Myoviridae>Podoviridae). No archaeal viruses were found. Unexpectedly, cyanophages were poorly represented in both metaviromes and were phylogenetically distant from currently characterized cyanophages. Putative phage genomes were assembled and showed a high level of unaffiliated genes, mostly from hypolithic viruses. Moreover, unusual gene arrangements in which eukaryotic and prokaryotic virus-derived genes were found within identical genome segments were observed. Phycodnaviridae and Mimiviridae viruses were the second-mostabundant taxa and more numerous within open soil. Novel virophage-like sequences (within the Sputnik clade) were identified. These findings highlight high-level virus diversity and novel species discovery potential within Antarctic hyperarid soils and may serve as a starting point for future studies targeting specific viral groups.IS

A novel bacterial Water Hypersensitivity-like protein shows in vivo protection against cold and freeze damage

Metagenomic library screening, by functional or sequence analysis, has become an established method for the identification of novel genes and gene products, including genetic elements implicated in microbial stress response and adaptation. We have identified, using a sequence based approach, a fosmid clone from an Antarctic desert soil metagenome library containing a novel gene which codes for a protein homologous to a Water Hypersensitive domain (WHy). The WHy domain is typically found as a component of specific LEA (Late Embryogenesis Abundant) proteins, particularly the LEA-14 (LEA-8) variants, which occur widely in plants, nematodes, bacteria and archaea and which are typically induced by exposure to stress conditions. The novel Why-like protein, (165 amino acid, 18.6 kDa) exhibits a largely invariant NPN motif at the N-terminus and has high sequence identity to genes identified in Pseudomonas genomes. Expression of this protein in E. coli significantly protected the recombinant host against cold and freeze stress.South African National Antarctic Program of the National Research Foundation.http://femsle.oxfordjournals.org2016-08-31hb201

Normalization of environmental metagenomic DNA enhances the discovery of under-represented microbial community members

Normalization is a procedure classically employed to detect rare sequences in cellular expression profiles (i.e. cDNA libraries). Here, we present a normalization protocol involving the direct treatment of extracted environmental metagenomic DNA with S1 nuclease; referred to as Normalization of metagenomic DNA: NmDNA. We demonstrate that NmDNA, prior to post hoc PCR based experiments (16S rRNA gene T-RFLP fingerprinting and clone library), increased the diversity of sequences retrieved from environmental microbial communities by detection of rarer sequences. This approach could be used to enhance the resolution of detection of ecologically relevant rare members in environmental microbial assemblages.National Research Foundation (NRF) of South Africa (BlueSkies program 81693).http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1472-765X2016-04-30hb201

Draft genome sequence of the Antarctic polyextremophile Nesterenkonia sp. strain AN1

Nesterenkonia sp. strain AN1 was isolated from Antarctic soil and is a polyextremophile, being tolerant of low temperatures, high salt concentrations, and high alkalinity. Here we report the draft genome sequence of this strain.This project was partially supported by the National Research Foundation– South African National Antarctic Research Programme (NRFSANAP) (award 80256) and the Genomics Research Institute (GRI), University of Pretoria.http://genomea.asm.org/am201

Evidence of variability in the structure and recruitment of rhizospheric and endophytic bacterial communities associated with arable sweet sorghum (Sorghum bicolor (L) Moench)

Sorghum is the second most cultivated crop in Africa and is a staple food source of many African communities. Exploiting the associated plant growth promoting bacteria (PGPB) has potential as an agricultural biotechnology strategy to enhance sorghum growth, yield and nutritional properties. Here we use Terminal-Restriction Fragment Length Polymorphism (TRFLP) and Denaturing Gradient Gel Electrophoresis (DGGE) to evaluate the factors that potentially shape rhizospheric and endophytic bacterial communities associated with sorghum farmed in South Africa. Microbial diversity was typically higher in the rhizosphere and rhizoplane compared to the endophytic zones (root, shoot and stem). Geographical location was one of the main drivers in describing microbial community assemblages found in rhizospheric and endophytic sorghum-linked niches. NO3-N, total nitrogen and pH were clearly identified as the main abiotic factors shaping sorghum-associated soil communities. Our results also suggest that specific bacterial taxa with potential N-fixing capacities (Acetobacter sp., Azospirillum sp., Pantoea sp., Bacillus sp. and cyanobacteria) are consistently detected in sorghum-created rhizospheric and endophytic environments, irrespective of environmental factor effects.The South African National Research Foundation (NRF)http://link.springer.com/journal/11104hb2016Genetic

Engineering pyruvate decarboxylase-mediated ethanol production in the thermophilic host Geobacillus thermoglucosidasius

This study reports the expression, purification and kinetic characterization of a PDC from Gluconobacter oxydans. Kinetic analyses showed the enzyme to have high affinity for pyruvate (120μM at pH 5), high catalytic efficiency (4.75 x 105 M-1s-1 at pH 5), a pHopt of approximately 4.5 and an in vitro temperature optimum at approximately 55°C (the highest yet reported for a bacterial PDC). Due to good in vitro thermostablity (approximately 40% enzyme activity retained after 30 minutes at 65°C) this PDC was considered to be a suitable candidate for heterologous expression in the thermophile Geobacillus thermoglucosidasius. Initial studies using a variety of methods failed to detect activity at any growth temperature. However, the application of codon harmonization (i.e., mimicry of the heterogeneous host’s transcription and translational rhythm) yielded a protein that was fully functional in the thermophilic strain at 45°C (as determined by enzyme activity, Western blot, mRNA detection and ethanol productivity). Here we describe the successful expression of PDC in a true thermophile. Yields as high as 0.35 g/g ±0.04 ethanol per gram of glucose consumed were detected, highly competitive to those reported in ethanologenic thermophilic mutants. Although activities could not be detected at temperatures approaching the growth optimum for the strain, this study highlights that the possibility that previously unsuccessful expression of pdcs in Geobacillus spp. may be the result of ineffective transcription / translation coupling.National Research Foundation South Africahttp://link.springer.com/journal/253hb201