Agulhas Current properties shape microbial community diversity and potential functionality

Understanding the impact of oceanographic features on marine microbial ecosystems remains a major ecological endeavour. Here we assess microbial diversity, community structure and functional capacity along the Agulhas Current system and the Subtropical Front in the South Indian Ocean (SIO). Samples collected from the epipelagic, oxygen minimum and bathypelagic zones were analysed by 16S rRNA gene amplicon and metagenomic sequencing. In contrast to previous studies, we found high taxonomic richness in surface and deep water samples, but generally low richness for OMZ communities. Beta-diversity analysis revealed significant dissimilarity between the three water depths. Most microbial communities were dominated by marine Gammaproteobacteria, with strikingly low levels of picocyanobacteria. Community composition was strongly influenced by specific environmental factors including depth, salinity, and the availability of both oxygen and light. Carbon, nitrogen and sulfur cycling capacity in the SIO was linked to several autotrophic and copiotrophic Alphaproteobacteria and Gammaproteobacteria. Taken together, our data suggest that the environmental conditions in the Agulhas Current system, particularly depth-related parameters, substantially influence microbial community structure. In addition, the capacity for biogeochemical cycling of nitrogen and sulfur is linked primarily to the dominant Gammaproteobacteria taxa, whereas ecologically rare taxa drive carbon cycling

Towards developing a new host-vector system for high-level protein expression

Filamentous fungi are critical for the production of many commercial enzymes and organic compounds. Due to their decomposer lifestyle, they have a natural potential for large scale production of proteins, many of these extracellular. The concept of this project was to exploit the protein synthesis and secretory capability of a large number of indigenous fungi as the basis to generate a new fungal expression platform. Filamentous fungi were obtained from the culture collection (CMW) of the Forestry and Agricultural Biotechnology Institute (FABI) University of Pretoria, South Africa. Screening of the isolates for extracellular protein expression in malt extract liquid medium shake flasks, led to the identification of a Clonostachys rosea 17970 isolate after internal transcribed spacer (ITS) sequencing and morphological studies. A ~35 kDa protein secreted at high levels was identified through LC-MS/MS as a cuticle-degrading serine protease (Cdsp). The optimum pH and temperature for protein production were found to be 9.0 and 32°C respectively, after 96 h of incubation on malt extract liquid media. Designed primers were used for the PCR amplification of an internal fragment of the cdsp gene from chromosomal DNA. Sequence data was used for further PCR-amplification of the up and downstream regions through chromosome walking using Inverse and SiteFinding PCR technology. Analysis of the assembled cdsp gene fragment (2,923 bp) revealed that the gene harbours a 5 upstream region (1,141 bp), coding region (1,300 bp) and 3 downstream region (509 bp). The coding region contains three introns. Reverse transcriptase-PCR of the coding region revealed a 1,140 bp open reading frame that encodes Cdsp. The putative cdsp signal peptide, promoter and terminator regions were identified in silico and are predicted to be important elements for the construction of an expression vector. Overall, these results demonstrate that C. rosea 17970 could be a good source for extracellular protein production and is a potential candidate for development as a new host-vector system based on its secretory capability and identified regulatory regions via in silico analysis.Dissertation (MSc)--University of Pretoria, 2015.Microbiology and Plant PathologyMScUnrestricte

Depth-dependent variables shape community structure and functionality in the Prince Edward Islands

Physicochemical variables limit and control the distribution of microbial communities in all environments. In the oceans, this may significantly influence functional processes such the consumption of dissolved organic material and nutrient sequestration. Yet, the relative contributions of physical factors, such as water mass variability and depth, on functional processes are underexplored. We assessed microbial community structure and functionality in the Prince Edward Islands (PEIs) using 16S rRNA gene amplicon analysis and extracellular enzymatic activity assays, respectively. We found that depth and nutrients substantially drive the structural patterns of bacteria and archaea in this region. Shifts from epipelagic to bathypelagic zones were linked to decreases in the activities of several extracellular enzymes. These extracellular enzymatic activities were positively correlated with several phyla including several Alphaproteobacteria (including members of the SAR 11 clade and order Rhodospirillales) and Cyanobacteria. We show that depth-dependent variables may be essential drivers of community structure and functionality in the PEIs.The South African National Antarctic Programme (SANAP 110717) of the National Research Foundation (NRF) and the University of Pretoria.http://link.springer.com/journal/248hj2022BiochemistryGeneticsMicrobiology and Plant Patholog