Microbial ecology of hot and cold desert edaphic communities

Philosophiae Doctor - PhDThis thesis presents significant advances into the microbial ecology of hypolithic communities in two hyperarid deserts. Deserts account for one fifth of the Earths total surface area. These zones differ substantially in terms of climate, geomorphology, hydrology and vegetation. Desert biomes are, however, generally depauperate with particularly with respect to macroorganisms. Hypoliths, photosynthetic microbial assemblages associated with quartz rocks, are widely distributed in hot and cold desert environs where they may represent a large fraction of the standing biomass and mediate key ecosystem processes, including nutrient cycling. However, important questions regarding their (i) development (ii) community structure and assembly patterns and (iii) functional structure remain unaddressed. Here, molecular tools (T-RFLP, clone libraries and pyrosequencing) and multivariate data analyses were used to address these questions. This study presents evidence of species recruitment in the development of hypolithic communities in the Namib Desert. Hypolithic bacterial communities were compared at a fine scale (10 m radius). Multivariate analysis of T-RFLP-derived data showed that hypolithic and open soil communities were structurally distinct. Applying the ecological concept of ‘indicator species’, 6 and 9 indicator lineages were identified for hypoliths and soil, respectively. Hypolithic communities were dominated by cyanobacteria affiliated to Pleurocapsales, whereas actinobacteria were prevalent in the open soil. These results are consistent with the concept of species sorting and suggest that the underside of the quartz rocks provide conditions suitable for the development of discrete and demonstrably different microbial assemblages.However, strong evidence for neutral assembly processes was found, as almost 90% of the taxa present in the hypoliths were also detected in the open soil. All together, these results suggest that hypolithons do not develop independently from microbial communities found in the surrounding soil, but selectively recruit from local populations.The bacterial community structure and assembly patterns in hypolithons from Miers Valley (Antarctica) were investigated. Previous studies in this valley have identified three morphologically distinct hypolithic community types: cyanobacteria dominated(Type I), fungus dominated (Type II) and moss dominated (Type III). The bacterial composition of surface soils and hypolithic communities were shown to be clearly and robustly distinct, using T-RFLP analysis. Moreover, the bacterial assemblages were similar in Type II and Type III hypolithons and clearly distinct from those foundin Type I. Using16S ribosomal RNA gene (rRNA) 454 pyrosequencing,Proteobacteria were shown to be the most important bacterial component of all three types of hypolithic communities. As expected, Cyanobacteria dominated Type I hypolithons, whereas Actinobacteria dominated Types II and III hypolithons. Using a probabilistic dissimilarity metric and random sampling, deterministic processes were demonstrated to be relatively more important in shaping the structure of the bacterial community found in Type II and Type III hypolithons. Taken together, these results suggest that hypolithic development favors a sequential pathway with Type II hypolithons serving as an intermediate development state between Type I and Type In a more in depth analysis of the diversity patterns of key nutrient cycling genes in Antarctic Miers Valley edaphic communities, genes coding for carbon fixation (greenand red-like cbbL), nitrogen fixation (nifH), nitrification (amoA) and denitrification(nirK and nirS), were targeted. Multivariate analysis (PERMANOVA) showed that hypolithic and open soil communities were functionally distinct. Type I hypoliths were functionally more diverse than soils, suggesting higher potential for enzymatic activities. Taxonomic structure (derived from 16S rRNA data) showed congruence with functional traits (genes involved in C and N cycling). Redundancy analysis suggested that chemical variables (S, F, and NO3) were important structuring forces in the different communities. Taken together, the results suggest that stochastic processes such as dispersion cannot override the influence of environmental factors on functional diversity patterns

The diversity of key anabolic genes in antarctic hypolithons

>Magister Scientiae - MScAntarctica is known for its pristine environments. A variety of unsuitable environmental conditions were once thought to render the continent unsuitable for sustaining life. However, metagenomic data have revealed a wealth of species diversity in a range of biotopes.Hypolithons, photosynthetic communities which live under translucent rocks in climatically extreme environments, are an important input source for both carbon (C) and nitrogen (N) in this hyperarid desert environment. Microbial contribution to biogeochemical cycling resulting in fixation of both C and N remains poorly understood. Moreover, there is a reported close interplay between both cycles, with nitrogen being reported to be a limiting factor in carbon assimilation.In this study the diversity of C and N fixing organisms was investigated by using the cbbL and nifH genes as phylogenetic and functional markers. High Molecular weight metagenomic DNA and RNA was extracted from hypolithons. PCR amplification was carried out using cbbL (800 bp for red-like, 1,100 bp for green-like) and nifH (360 bp) gene specific primers.Resultant PCR products were used to construct libraries which were screened for correct sized inserts. Restriction Fragment Length Polymorphism (RFLP) was used to de-replicate clones prior to sequencing. Phylogenetic positions from both clone libraries were established by aligning nucleotide sequences and constructing similarity trees using NJ clustering methods.BLASTn results indicated the presence of previously uncultured organisms which contain cbbL and nifH genes. BLASTn results were characterized by low percentages of maximum identity (typically <95%), a potential indicator of novel taxa. Sequences from respective libraries clustered with cyanobacteria such as Nostoc, Scytonema, and Tolypothrix and α-, β-, and γ-Proteobacteria such as Azotobacter, Agrobacterium and Mesorhizobium. Generally sequence results indicate a largely homogenous, being dominated by specific taxa. Each group may contain potential keystone species, essential for both biogeochemical cycling in oligotrophic environment

Energy from thin air

Advanced genomic-analysis techniques now suggest that microbial communities in cold, nutrient-poor Antarctic soils can acquire their energy from the oxidation of trace gases, rather than by photosynthesis.http://www.nature.com/nature2018-06-06hj2018Genetic

Comparative metagenomic analysis reveals mechanisms for stress response in hypoliths from extreme hyperarid deserts

Understanding microbial adaptation to environmental stressors is crucial for interpreting broader ecological patterns. In the most extreme hot and cold deserts, cryptic niche communities are thought to play key roles in ecosystem processes and represent excellent model systems for investigating microbial responses to environmental stressors. However, relatively little is known about the genetic diversity underlying such functional processes in climatically extreme desert systems. This study presents the first comparative metagenome analysis of cyanobacteria-dominated hypolithic communities in hot (Namib Desert, Namibia) and cold (Miers Valley, Antarctica) hyperarid deserts. The most abundant phyla in both hypolith metagenomes were Actinobacteria, Proteobacteria, Cyanobacteria and Bacteroidetes with Cyanobacteria dominating in Antarctic hypoliths. However, no significant differences between the twometagenomeswere identified. The Antarctic hypolithicmetagenome displayed a high number of sequences assigned to sigma factors, replication,recombination andrepair, translation, ribosomal structure,andbiogenesis. In contrast, theNamibDesert metagenome showed a high abundance of sequences assigned to carbohydrate transport and metabolism. Metagenome data analysis also revealed significantdivergence inthe geneticdeterminantsof aminoacidandnucleotidemetabolismbetween these two metagenomes and those of soil from other polar deserts, hot deserts, and non-desert soils. Our results suggest extensive niche differentiation in hypolithic microbial communities from these two extreme environments and a high genetic capacity for survival under environmental extremes.Fil: Le, Phuong Thi. University of Pretoria; Sudáfrica. Vlaams Instituut voor Biotechnologie; Bélgica. University of Ghent; BélgicaFil: Makhalanyane, Thulani P.. University of Pretoria; SudáfricaFil: Guerrero, Leandro Demián. University of Pretoria; Sudáfrica. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; ArgentinaFil: Vikram, Surendra. University of Pretoria; SudáfricaFil: Van De Peer, Yves. University of Pretoria; Sudáfrica. Vlaams Instituut voor Biotechnologie; Bélgica. University of Ghent; BélgicaFil: Cowan, Don A.. University of Pretoria; Sudáfric

Contrasting assembly processes in a bacterial metacommunity along a desiccation gradient

Understanding the relative influence of deterministic and stochastic processes in driving community assembly is a major goal in microbial ecology. Here, we have investigated the influence of these processes on bacterial community assembly in the lateral sediments of a salt pan along a desiccation gradient over a three-year period. We show that the role of deterministic processes increases in communities distant from the waterline (shaped by drought), probably as a result of the interplay between abiotic and biotic factors. By contrast, the influence of stochastic processes on bacterial community assembly was higher in the sediments closest to the waterline ,more likely due to lower levels of abiotic stress.Our results demonstrate that both deterministic and stochastic processes influence bacterial community assembly in salt pan sediments, and that their relative influence varies along a desiccation gradient.National Research Foundation (South Africa)http://www.frontiersin.org/Microbiologytm201

A reservoir of 'historical' antibiotic resistance genes in remote pristine Antarctic soils

Background: Soil bacteria naturally produce antibiotics as a competitive mechanism, with a concomitant evolution, and exchange by horizontal gene transfer, of a range of antibiotic resistance mechanisms. Surveys of bacterial resistance elements in edaphic systems have originated primarily from human-impacted environments, with relatively little information from remote and pristine environments, where the resistome may comprise the ancestral gene diversity. Methods: We used shotgun metagenomics to assess antibiotic resistance gene (ARG) distribution in 17 pristine and remote Antarctic surface soils within the undisturbed Mackay Glacier region. We also interrogated the phylogenetic placement of ARGs compared to environmental ARG sequences and tested for the presence of horizontal gene transfer elements flanking ARGs. Results: In total, 177 naturally occurring ARGs were identified, most of which encoded single or multi-drug efflux pumps. Resistance mechanisms for the inactivation of aminoglycosides, chloramphenicol and beta-lactam antibiotics were also common. Gram-negative bacteria harboured most ARGs (71%), with fewer genes from Gram-positive Actinobacteria and Bacilli (Firmicutes) (9%), reflecting the taxonomic composition of the soils. Strikingly, the abundance of ARGs per sample had a strong, negative correlation with species richness (r=-0.49, P < 0.05). This result, coupled with a lack of mobile genetic elements flanking ARGs, suggests that these genes are ancient acquisitions of horizontal transfer events. Conclusions: ARGs in these remote and uncontaminated soils most likely represent functional efficient historical genes that have since been vertically inherited over generations. The historical ARGs in these pristine environments carry a strong phylogenetic signal and form a monophyletic group relative to ARGs from other similar environments

Contrasting assembly processes in a bacterial metacommunity along a desiccation gradient

Understanding the relative influence of deterministic and stochastic processes in driving community assembly is a major goal in microbial ecology. Here, we have investigated the influence of these processes on bacterial community assembly in the lateral sediments of a salt pan along a desiccation gradient over a three-year period. We show that the role of deterministic processes increases in communities distant from the waterline (shaped by drought), probably as a result of the interplay between abiotic and biotic factors. By contrast, the influence of stochastic processes on bacterial community assembly was higher in the sediments closest to the waterline ,more likely due to lower levels of abiotic stress.Our results demonstrate that both deterministic and stochastic processes influence bacterial community assembly in salt pan sediments, and that their relative influence varies along a desiccation gradient.National Research Foundation (South Africa)http://www.frontiersin.org/Microbiologytm201

Cyanobacteria drive community composition and functionality in rock-soil interface communities

Most ecological research on hypoliths, significant primary producers in hyperarid deserts, has focused on the diversity of individual groups of microbes (i.e. bacteria). However, microbial communities are inherently complex, and the interactions between cyanobacteria, heterotrophic bacteria, protista and metazoa, are likely to be very important for ecosystem functioning. Cyanobacterial and heterotrophic bacterial communities were analysed by pyrosequencing, while metazoan and protistan communities were assessed by T-RFLP analysis. Microbial functionality was estimated using carbon substrate utilization. Cyanobacterial community composition was significant in shaping community structure and function in hypoliths. Ecological network analysis showed that most significant co-occurrences were positive, representing potential synergistic interactions. There were several highly interconnected associations (modules) and specific cyanobacteria were important in driving the modular structure of hypolithic networks. Together, our results suggest that hypolithic cyanobacteria have strong effects on higher trophic levels and ecosystem functioning.National Research Foundation (South Africa) and the University of Pretoria.http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1755-09982016-02-28hb201

Microbial diversity and functional capacity in polar soils

Global change is disproportionately affecting cold environments (polar and high elevation regions), with potentially negative impacts on microbial diversity and functional processes. In most cold environments the combination of low temperatures, and physical stressors, such as katabatic wind episodes and limited water availability result in biotic systems, which are in trophic terms very simple and primarily driven by microbial communities. Metagenomic approaches have provided key insights on microbial communities in these systems and how they may adapt to stressors and contribute towards mediating crucial biogeochemical cycles. Here we review, the current knowledge regarding edaphic-based microbial diversity and functional processes in Antarctica, and the Artic. Such insights are crucial and help to establish a baseline for understanding the impact of climate change on Polar Regions.South African National Research Foundation. South African National Antarctic Program. Foundational Biodiversity Program.University of Pretoria for funding through the Research Development Program (TPM) and the Genomics Research Institute.http://www.journals.elsevier.com/current-opinion-in-biotechnology2017-04-30hb2016Genetic

Cyanobacteria drive community composition and functionality in rock-soil interface communities

Most ecological research on hypoliths, significant primary producers in hyperarid deserts, has focused on the diversity of individual groups of microbes (i.e. bacteria). However, microbial communities are inherently complex, and the interactions between cyanobacteria, heterotrophic bacteria, protista and metazoa, are likely to be very important for ecosystem functioning. Cyanobacterial and heterotrophic bacterial communities were analysed by pyrosequencing, while metazoan and protistan communities were assessed by T-RFLP analysis. Microbial functionality was estimated using carbon substrate utilization. Cyanobacterial community composition was significant in shaping community structure and function in hypoliths. Ecological network analysis showed that most significant co-occurrences were positive, representing potential synergistic interactions. There were several highly interconnected associations (modules) and specific cyanobacteria were important in driving the modular structure of hypolithic networks. Together, our results suggest that hypolithic cyanobacteria have strong effects on higher trophic levels and ecosystem functioning.National Research Foundation (South Africa) and the University of Pretoria.http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1755-09982016-02-28hb201