(Acido)bacterial diversity in space and time

Recent technological achievements enabled microbiologists to fully grasp the vast diversity of microbial life that is resident in soils, highly complex matrices of alternating micro-habitats on very small scales. Since then, microbial community composition has been catalogued for many different terrestrial habitats. This triggered the investigation and definition of processes which shape these communities. In most cases, the environment determines community composition, and similar habitats may feature similar microbial communities despite being far apart. However, some habitats have been described as subjected to pronounced neutral processes, which are dispersal, ecological drift or speciation. The balance between these process types is now the subject of many studies looking at microbial communities. It is also clear that these processes need to be monitored on both temporal and spatial scales, as the two dimensions are inseparably interlinked. However, most microbial studies deal with only one aspect, but do not control for the other. In this work, the outcome of a highly sophisticated plot scale experiment is presented encompassing 358 sampling locations distributed between six intra-annual sampling points on a 10 m x 10 m unfertilized grassland site in the Swabian Alb. RNA was extracted from the A-horizon of each soil and the hypervariable region 3 of the ribosomal small subunit was amplified and sequenced with barcoded Illumina sequencing. Roughly 400 million eubacterial reads were obtained. The dataset was used to assess the population dynamics of Acidobacteria, as well as the spatio-temporal co-occurenze of functionally depending microorganism. Additionally, preliminary results motivated the assessment of common methods for the examination of rhizospheric communities. In combination, the diversity of bacterial communities in space and time was tested from different angles, reflecting different research question, and they all revealed a far more complex reality than previously thought

Molecular characterization of unique hepatitis c viral genotypes in South Africa

Hepatitis C is a notifiable disease in South Africa (SA), but there is a lack of surveillance and reporting systems. The availability of routine, reliable and validated methods of hepatitis C virus (HCV) detection and genotyping, together with better surveillance strategies is vital to ensure optimal patient diagnosis, treatment and disease management. This is the first extensive molecular study on the HCV in this country to identify circulating genotypes, host immuno-genetics and patients responses to combination therapy. HCV genotypes in the patient and blood donor groups were determined by sequencing of the 5’untranslated (5’UTR) and non-structural -5B (NS5B) regions. Three molecularbased tests, line probe assay (LiPA), real-time and palindromic nucleotide substitutions (PNS), were compared to the sequencing method. Molecular sequence analyses of the core, envelope 1(E1), NS4B and NS5B were determined. The inferred amino acid data was used to determine epitope variation across immunodominant regions. Viral load monitoring was performed on patients receiving combination treatment. A positive HCV polymerase chain reaction (PCR) result is necessary to confirm active infection. A National HCV surveillance database was established to collate patient demographics with results from public health laboratories. Genotype 5a predominates in patients with liver disease. Changing frequencies and introductions of other subtypes were determined. The LiPA (5’UTR) was found to surpass the other genotyping tests, as it was quick and easy. Geographical clustering within the genotype 5a clade was evident in the E1 and NS4B regions. The branching order of genotype 5a suggests that genotype 5a is older than genotype 3, inferring that patients with genotype 5a may respond better to therapy than those infected with genotype 3. The divergence estimate of genotype 5a was found to be between 100-156 years. Despite the homogeneity of genotypes 1 and 5 epitope sequences, well-published epitopes were predicted to bind sub-optimally to the common human leukocyte antigen (HLA) alleles, making a vaccine less effective in SA. The treatment response for genotype 5a was higher in this study compared to previous global studies. This new molecular knowledge on HCV genotypes circulating in SA will allow informed decisions when planning preventative and treatment strategies relevant to local viral and host genetics

Evolutionary History Of Subterranean Termites In The Geographic And Ecological Context Of The Appalachian Mountains In The United States

Termites in the genus Reticulitermes (Blattodea: Rhinotermitidae) are distributed across the eastern United States, including the southern Appalachian Mountains, a region incredibly rich in biodiversity. The eastern subterranean termite, Reticulitermes flavipes, has been uninentionally introduced to South America and Europe, and is predicted to further expand its geographic range. My goal was to determine how eco-evolutionary processes, operating at both long and short timescales, may have contributed to R. flavipes becoming an invasive species. I examined geographic and environmental influences at historical and contemporary timescales. To do this, I first determined the extent of niche divergence among three geographically overlapping Reticulitermes species, R. flavipes, R. malletei, and R. virginicus, and also identified the geographic areas and environmental conditions in which R. flavipes occurs to the exclusion of the other two species. Then, I assessed evidence for the influence of glacial-interglacial cycles on changes in the geographic distribution of R. flavipes, as well as potential genetic divergence within the species resulting from these past distributional shifts. In addition to historical eco-evolutionary processes, at the contemporary timescale I investigated how epigenetic mechanisms–specifically, DNA methylation–facilitate rapid responses to human-mediated disturbance of forest ecosystems. Finally, I developed a new landscape connectivity metric, MSconn, to help understand the effect spatial heterogeneity of environments plays on biological diversity at multiple levels of organization, from alleles to communities. In principle, MSconn can be integrated into an eco-evolutionary framework, making it possible to quantify the effect of biotic and abiotic environments on gene flow between populations, and vice versa, the effect of gene flow on species interactions within and between communities

Nitrogen fixing potential in extreme environments

Biological nitrogen fixation is a key process in providing accessible nitrogen to Earth s biosphere. This process has been studied in various habitats yet extreme environments still remain relatively unexplored. The nifH gene codes for the Fe protein component in the nitrogenase, which facilitates the nitrogen fixation. Our aims in this study were to assess diazotrophic diversity, richness and community structure in three unique environments and analyse potential adaptations in the Fe protein composition and structure. Our methods included a terminal-restriction fragment length polymorphism (T-RFLP) analysis on 16S rDNA, PCR amplification of the nifH gene, statistical t-test analysis of amino acid compositions, a novel evolutionary analysis and 3D modelling with the I-TASSER web server. Boulder Clay and Amorphous Glacier are two ice-free areas in Terra Nova Bay, Antarctica, which differ in their geological origins and physio-chemical properties. DNA yields from ice-core samples ranged from 0.29 ng L-1 in Amorphous Glacier to 88 ng L-1 in Boulder Clay. Bray-Curtis cluster analysis suggested Boulder Clay bacterial profiles were similar to each other, but cluster separately from Amorphous Glacier. The hypersaline (>70 ppt) bays of Shark Bay, Western Australia, are home to the stromatolites microbial mats. The microbial diversity of diazotrophs from two different years, 1996 and 2004, was investigated. Our analysis indicated columnar stromatolites included a common persisting cyanobacterial diazotroph, a Cyanothece or Xenoccocous. Both samples contained novel nifH gene sequences of low similarity to uncultured nifH clones from saline to hypersaline environments, and their inferred NifH amino acid sequences were highly similar to unicellular, non-heterocystous Cyanobacteria and γ,-Proteobacteria sequences. Paralana s hot radon springs (PHS, 57 C°) are situated in South Australia. Phylogenetic analysis indicated a rich and diverse group of amino acid NifH sequences from α-, γ-, and δ-Proteobacteria, Chloroflexi and Cyanobacteria phyla. These results suggested aerobic and anaerobic bacteria with conventional Mo nitrogenase might be involved in nitrogen fixation. Our bioinformatic analysis suggested that halophilic adaptations, with an increase in salt bridges, acidic residues and a decrease in bulkier hydrophobic amino acids, did occur in stromatolite diazotrophs and that partial thermophilic adaptations, mainly an increase in salt bridges, Pro and charged residues, did occur in the PHS diazotrophs. These studies provide new insight on the ongoing evolution of nitrogen fixation in extreme environments