A sequential co-extraction method for DNA, RNA and protein recovery from soil for future system-based approaches

A co-extraction protocol that sequentially isolates core biopolymer fractions (DNA, RNA, protein) from edaphic microbial communities is presented. In order to confirm compatibility with downstream analyses, bacterial T-RFLP profiles were generated from the DNA- and RNA-derived fractions of an arid-based soil, with metaproteomics undertaken on the corresponding protein fraction.National Research Foundation Grant no. 81779 (South Africa).http://www.elsevier.com/ locate/jmicmethhb2016Genetic

Namib Desert edaphic bacterial, fungal and archaeal communities assemble through deterministic processes but are influenced by different abiotic parameters

The central Namib Desert is hyperarid, where limited plant growth ensures that biogeochemical processes are largely driven by microbial populations. Recent research has shown that niche partitioning is critically involved in the assembly of Namib Desert edaphic communities. However, these studies have mainly focussed on the Domain Bacteria. Using microbial community fingerprinting, we compared the assembly of the bacterial, fungal and archaeal populations of microbial communities across nine soil niches from four Namib Desert soil habitats (riverbed, dune, gravel plain and salt pan). Permutational multivariate analysis of variance indicated that the nine soil niches presented significantly different physicochemistries (R 2 = 0.8306, P ≤ 0.0001) and that bacterial, fungal and archaeal populations were soil niche specific (R 2 ≥ 0.64, P ≤ 0.001). However, the abiotic drivers of community structure were Domain-specific (P < 0.05), with P, clay and sand fraction, and NH4 influencing bacterial, fungal and archaeal communities, respectively. Soil physicochemistry and soil niche explained over 50% of the variation in community structure, and communities displayed strong non-random patterns of co-occurrence. Taken together, these results demonstrate that in central Namib Desert soil microbial communities, assembly is principally driven by deterministic processes.The South African National Research Foundation (Grant Number N00113-95565) and the University of Pretoria (UP).http://link.springer.com/journal/7922018-01-31hb2017Genetic

Financial leverage and stock returns: evidence from an emerging economy

The aim of this research was to examine the propositions of Campbell et al. and Mirza et al. on pricing of leverage in stock returns using a comprehensive set of firms listed on the Karachi Stock Exchange (KSE) over a period of 13 years. Our results suggest that while size, value and, more importantly, financial leverage are systematic in nature, market risk premium is not a relevant factor. The results confirm the notion of leverage premium and have important implications for financial managers, investment analysts and other market participants who use asset pricing frameworks for investment appraisals. These findings have global relevance, notably for other emerging and developing economies where default risk is of importance due to cyclical nature of cash flows and low recovery rates owing to weaknesses of legal structure

Microbial ecology of hot desert edaphic systems

A significant proportion of the Earth's surface is desert or in the process of desertification. The extreme environmental conditions that characterize these areas result in a surface that is essentially barren, with a limited range of higher plants and animals. Microbial communities are probably the dominant drivers of these systems, mediating key ecosystem processes. In this review, we examine the microbial communities of hot desert terrestrial biotopes (including soils, cryptic and refuge niches and plant-root-associated microbes) and the processes that govern their assembly. We also assess the possible effects of global climate change on hot desert microbial communities and the resulting feedback mechanisms. We conclude by discussing current gaps in our understanding of the microbiology of hot deserts and suggest fruitful avenues for future research.South African National Research Foundation, the University of Pretoria and the Genomics Research Institute.http://femsre.oxfordjournals.org2016-03-31hb201

Ecology and biogeochemistry of cyanobacteria in soils, permafrost, aquatic and cryptic polar habitats

Polar Regions (continental Antarctica and the Arctic) are characterized by a range of extreme environmental conditions, which impose severe pressures on biological life. Polar cold-active cyanobacteria are uniquely adapted to withstand the environmental conditions of the high latitudes. These adaptations include high ultra-violet radiation and desiccation tolerance, and mechanisms to protect cells from freeze–thaw damage. As the most widely distributed photoautotrophs in these regions, cyanobacteria are likely the dominant contributors of critically essential ecosystem services, particularly carbon and nitrogen turnover in terrestrial polar habitats. These habitats include soils, permafrost, cryptic niches (including biological soil crusts, hypoliths and endoliths), ice and snow, and a range of aquatic habitats. Here we review current literature on the ecology, and the functional role played by cyanobacteria in various Arctic and Antarctic environments. We focus on the ecological importance of cyanobacterial communities in Polar Regions and assess what is known regarding the toxins they produce. We also review the responses and adaptations of cyanobacteria to extreme environments.University of Pretoria Research Development Program (TPM),Genomics Research Institute,The National Research Foundation (NRF) of SouthAfrica’s National Antarctic Program (SANAP program) (TPM, AV, EG.MW VG, DAC) and Ministeriode Economıa y Competitividad (Spain) : Grantref CTM 2011-28736 (DV,AQ).http://link.springer.com/journal/105312016-03-10hb201

A functional approach to characterising the microbial communities underpinning low temperature anaerobic digestion

Low-temperature anaerobic digestion (LTAD) presents a sustainable, cost-efficient technology for the treatment of a vast array of wastewater streams. However, this microbially-mediated process requires further understanding and experimental characterisation if large-scale application of LTAD is to be realised. The objective of this thesis was to employ a functional-based approach to characterise the microbial communities underpinning low-temperature anaerobic digestion. Firstly, the key microbial functional groups present in end-point samples taken from three, laboratory-scale, expanded granular sludge bed (EGSB) bioreactors; R1 (37°C), R2 (15°C) and R3 (7°C) were characterised. Metaproteomics, in conjunction with 16S rRNA gene phylogenetic approaches (clone libraries, qPCR), was applied to record microbial community composition and metaproteomic profiles as a function of bioreactor operating temperature. Clone libraries indicated a predominance of the Chloroflexi (21%) and ¿-Proteobacteria (61%) bacterial groups in R1, with Firmicutes (24%) and Bacteroidetes (46%) prominent in both R2 and R3. The Methanosaeta genus was strongly represented in archaeal clone libraries (29% [R1], 76% [R2] and 91% [R3]). This was reflected in the metaproteomic results with 26 (65%) differentially expressed proteins assigned to this methanogenic group. Also evident from the metaproteomic data were proteins assigned to the bacterial phyla Proteobacteria, Firmicutes and Actinobacteria, while the archaeal orders Methanobacteriales, and Methanomicrobiales were also represented. Interestingly, the identification of a protein assigned to Methanosarcina sp. was not consistent with DNA-based community profiling data, where this methanogenic group was not detected, confirming the importance of employing a functional-based approach in this study. A pure culture proteomic (iTRAQ, 2-DGE) approach was then employed to uncover the sub-mesophilic functional characteristics of a Methanosarcina strain (optimum growth temperature, 37¿C), with proteins assigned to this group detected in previous LTAD bioreactor trials. New insights into the low-temperature adaptation capacity of this mesophilic methanogen, including differentially expressed proteins during low temperature growth, e.g. elongation factor protein expression during sub-mesophilic adaptation, with high levels of viable cells recorded through this \u27adaptation\u27 stage (84% [±9.65% SE; n = 10] of cells were viable after 17 days of growth at 15degrees C). Therefore, through this polyphasic approach, the psychrotolerant capacity of this organism was characterised. Finally, two EGSB bioreactors (R1 & R2) were operated, initially at 37°C with a subsequent temperature drop to 15°C, with biomass samples being taken throughout the trial. PCR-based (clone libraries, qPCR, DGGE [RNA- DNA- derived]) and PCR-independent (specific methanogenic activity [SMA] profiling, microautoradiography fluorescent in situ hybridisation [MAR-FISH], and metaproteomics) approaches were employed to investigate the microbial community structure and key functional groups throughout the trial, with particular emphasis on the methanogenic archaea. Once again Methanosaeata were prominenet in archaeal community and functional analysis with consistent proteomic profiles recorded between the two LTAD bioreator trials investigated in this study. For example, a bifunctional protein (Mcon_1383) with possible function in riboulose monophosphate (RuMP) pathway was significantly expressed in low temperature biomass for both studies. Overall, community profiling techniques (clone libraries, qPCR) linked with functional-based (RNA-based DGGE, metaproteomics) approaches employed in this research illustrated the importance and metabolic complexity of Methanosaeta in a well functioning LTAD system. Also, the incorporation of functional analysis was justified through the uncovering of discrete community information missed through traditional DNA-based community profiling methods e.g. Methanospirillum importance in low temperature biomass during LTAD trial confirmed through metaproteomic and RNA-based DGGE profiles

Exploring mixed microbial community functioning: recent advances in metaproteomics

System approaches to elucidate ecosystem functioning constitute an emerging area of research within microbial ecology. Such approaches aim at investigating all levels of biological information (DNA, RNA, proteins and metabolites) to capture the functional interactions occurring in a given ecosystem and track down characteristics that could not be accessed by the study of isolated components. In this context, the study of the proteins collectively expressed by all the microorganisms present within an ecosystem (metaproteomics) is not only crucial but can also provide insights into microbial functionality. Overall, the success of metaproteomics is closely linked to metagenomics, and with the exponential increase in the availability of metagenome sequences, this field of research is starting to experience generation of an overwhelming amount of data, which requires systematic analysis. Metaproteomics has been employed in very diverse environments, and this review discusses the recent advances achieved in the context of human biology, soil, marine and freshwater environments as well as natural and bioengineered systems