CMEG Research Projects

 

 

Molecular Ecology of cold (Antarctic) desert soils

In a major collaboration with Professors Ian Hogg and Craig Cary (University of Waikato, NZ), Dr Mark Stevens (Adelaide University, AU) and Professor Steve Pointing (Auckland University of Technology, NZ), CMEG researchers are investigating the structure and function of microbial communities in the cold desert soils of the McMurdo Dry Valleys of Antarctica.

 

The mineral soils of the Antarctic Dry Valleys are one of the most extreme environments on Earth. The extreme conditions to which soil microorganisms are exposed include very low temperatures (-50oC), low water availability, oligotrophy, high salinity and periodic high radiation levels. In response to these extremes, microbial communities are restricted to ‘refuge’ habitats (such as hypoliths and cryptoendoliths; microbial communities which exist either under translucent rocks, or inside the rock structure), where some protection against the the environmental extremes exist.

 

Cryptoendolithic cyanobacteria in a sandstone rock

 

 

Using metagenomics to understand microbial function and adaptation

CMEG researchers use a range of modern molecular and Next Generation DNA sequencing methods, including population phylogenetics and comparative metagenomics, to investigate the diversity of bacteria, fungi, archaea and viruses in soil samples, and to study the metabolic capacity and stress-response adaptations in individual microbial genomes.  This program is supported by the National Research Foundation, Antarctica NZ and the New Zealand Antarctic Research Institute, who provide the logistics for annual field expeditions.

We are using comparative metagenomics, involving the comparisons of multiple entire metagenomes in order to understand the variation in functional traits across different habitats and microenvironments. We have also been successful in reconstructing complete bacterial genomes from metagenomics sequence data, allowing us to probe the physiological capacity and adaptive strategies of microorganisms which have never been cultured.

 

Schematic reconstruction of key genes and pathways in a novel Bacteroidetes genome, reconstructed from a soil metagenome
 
 

Metagenomics of sub-Antarctic peat bogs

 

Peat bog ecosystems store approximately one third of the total global soil carbon pool. The role of these ecosystems in carbon sequestration is attributed to factors such as low rates of organic matter decomposition, low temperatures, low pH, anoxia and chemically complex substrates. However, these long-existing ecosystems are extremely sensitive to climate change. For example, it is expected that an increase in temperature will promote in situ peat bog microbial activity, resulting in a substantially increased potential for greenhouse-gas emissions (i.e., CO2, CH4 and N2O).

In collaboration with Prof Gabriela Mataloni (Universidad Nacional de San Martín, Argentina) and combining metagenomic and metatranscriptomic studies on Argentinian peat bogs, we aim to gain information on the microbial communities that thrive in these ecosystems. We are particularly interested in the genomic potential for soil organic carbon transformation and in the identification of the active microorganisms that drive these processes: methanogens and methanotrophs, for example. This information, when combined with experimental tests using microcosms, will allow us to better understand the role of microbes in the soil carbon cycle and to make predictions on future CH4 and CO2 emissions from peat bog soils.

     
 Peat bog sampling near Ushuaia, with Gabriela

 

Molecular ecology of hot (Namibian) desert soils

In collaboration with many international and local researchers including Prof. Marla Tuffin (IMBM, UWC), Prof David Hopkins (Heriot-Watt U., UK), Prof Ian Hogg (Waikato University, New Zealand), Prof Steve Pointing (AUT, New Zealand), Prof. Christoph Syldakt (KIT, Germany), Dr Asun de los Rios (CNR, Spain), Dr Weidong Kong (IPTCAS, China), Prof. Ed Rybicki (MCB, UCT), Dr Frank Eckardt (Geology, UCT) and Drs Gillian Maggs-Kölling and Mary Seely of the Gobabeb Research and Training Centre, Namibia, we are undertaking a large scale holistic research program on the microbial ecology of the Namib Desert. The Namib is one of the oldest deserts in the world and one of the most interesting. For example, the differences in water relations across the east (rainfall zone) to west (fog zone) desert-scape have major impacts on primary productivity, plant diversity and, as we have discovered, microbial community structures.

 

Shifting dunes of the Namib Sand Sea (Namib Desert)

 

The CMEG Namib Desert research project has many elements: the role of water availability in dictating community structure and function; the impact of seasonal lignocellulosic carbon productivity on soil microbial populations; the diversity and role of soil cyanobacteria, the structure and function of hypolithic communities; water-capture species as drivers for microbial community development; and the role of bacteriophage and viruses in the trophic structure of desert soil communities.

Several projects focus on particularly charismatic elements of the Namib Desert region: the unusual desert ‘fairy circles’, the enigmatic desert plant Welwitschia mirabilis, and the hypolithic microbial communities living underneath quartz pebbles in the desert pavement.

 

Researchers during a sampling trip in 2012 (Gobabeb, Namib Desert)

 

 

Unraveling the mysteries of ‘Fairy Circles’

In the Namib Desert, an enigmatic and natural phenomenon which has been studied for more than 30 years and has still not revealed its secrets: The Fairy Circles (FCs). These features are circular barren patches of soils surrounded by a grass matrix and have been detected in the dunes and gravel plains of the Namib Desert and recently in the Australian outback. Since first reported, a remarkable number of alternate hypotheses have been advanced to explain their origin, development and maintenance (such as UFOs, underground dragons, abiotic gas seepages, micro-faunal activities and/or vegetative self-organization). 

 

Enigmatic fairy circles of the Namib Desert

 

At CMEG, we work on the original hypothesis that FCs are related to microbial phytopathogenic activities: that it, that pathogenic microorganisms infect the grasses, causing death shortly after germination. Our hypothesis is consistent with the lifestyle of Fairy Circles, in that they appear to be ‘born’, to ‘grow’, and to eventually ‘die’. To test our hypothesis, we are using a combination of modern ‘omics’ technologies (metabarcoding, metaproteomics, metaviromics, and shotgun metagenome sequencing).

In collaboration with a team from the Auckland University of Technology (NZ) we also have initiated a drone survey to evaluate the distribution of Fairy Circles in the two dominant Namib Desert habitat types: the gravel deserts and the dunes. Our first results are promising as we have detected FC-specific microbial phylotypes in both the Namib Desert dune and gravel plain FCs, some of which being affiliated to known phytopathogenic taxa. 

 

 

Estimating microbial population dynamics in desert niche communities

 

In a long-term experiment initiated in 2015, we established a series of artificial hypolith arrays in different parts of the Namib Desert. Local quartz rocks and pre-cut marble blocks were cleaned, sterilized and laid out on the desert pavement surface.  Each year (for up to 9 years), we will sample the underlying soil of a set of the artificial hypoliths, and use molecular phylogenetics and metagenome sequencing to monitor two important parameters (about which we currently know almost nothing): the rate of development of hypolithic communities, and the evolutionary path of the community.

 

An artificial Namib Desert hypolith array

 

Desert Soil Metaviromics

Eukaryotic and bacterial viruses (bacteriophage) are key elements of all ecosystems, but little studied in terrestrial habitats. We have initiated a metaviromic survey of our hot (Namib) and cold (Antarctic Dry Valley) desert study sites in order to understand the diversity of bacteriophage in these biotopes, as a prelude for understanding the role of phage in microbial community structure and function.


We are using modern Next Generate Sequencing methods to analyse the diversity of double-stranded DNA bacteriophage. We have demonstrated that both hot and cold desert soils are dominated by common soil phage taxa (members of the Caudovirales), but that megaviruses (Mimiviridae) are common in both soil types. Our current research is focused on understanding the role that desert soil bacteriophage play in microbial community dynamics, on using both culture-dependent and culture-independent approaches to identify and characterize virus-host networks, infection modes and virus-host interactions and on the isolation of terrestrial cyanophage, about which very little is known.

 

Electron micrographs of viruses isolated from the Namib Desert

 

Microinvertebrates in Desert Soils

A modern method for characterizing the genetic diversity and relative species abundance of microinvertebrates is DNA barcoding, using the CO1 (cytochrome oxidase 1) phylogenetic marker sequence technique.  With Professor Ian Hogg from Waikato University, NZ, we have used this method to determine the genetic diversity of springtails across Namib Desert transects, and to explore the environmental parameters that have an effect on shaping springtail diversity and distribution.  The few previous studies conducted on the genetic diversity of southern African springtails have suggested that genetic diversity is very low: only two species have previously been identified in the Namib region. Our studies have already shown that the genetic diversity is high, with as many as 12 different species identified across the 200km coast-to-mountain transect, with some showing very localized distribution. These unexpected and intriguing results pave the way for a much wider analysis of microinvertebrate phylogeography, and a deeper understanding of the possible impacts of major climatic and environmental changes on desert soil organisms. 

 

CMEG student hunting for springtails

 

Namib Desert Field Expeditions


Our research in the Namib Desert is strongly driven by an annual week-long field expedition where a team of national and international researchers, typically from 20 to 30 staff and students, undertake a range of sampling programs, establish short- and long-term field experiments, and deploy microsensor arrays or download micro-environmental data from existing sensor arrays. These field expeditions provide a basis for developing long-term collaborations with national and international researchers, provide valuable field training for researchers from CMEG, the Gobabeb Research and Training Centre and from our partner laboratories, and have an important team building element.  Since initiating our Namib Desert research program, we have developed an increasingly sophisticated understanding of the composition and function of microbial communities in this desert ecosystem, and published over 20 research papers in high quality international journals.

 

Our Namib Desert studies have important implications for future desert ecology and conservation. With increasing impacts from climate change, it is vital to understand the biological complexity of dry-land ecosystems so that the impacts can be both predicted and monitored.

The 2016 CMEG team and international collaborators at the Gobabeb Research and Training Centre

 

Marine microbial ecology of the Southern Ocean

Microbial communities form the basis of marine food webs and mediating important marine biogeochemical processes. The Southern Ocean is a crucial ecosystem and has been shown to connect the world’s oceans. There is considerable evidence showing that this ecosystem harbors a high diversity of macrofauna, but even higher levels of microbial diversity.

We will use the existing SA Agulhas southern ocean monitoring-and-sampling lines to profile microbial communities (bacteria, archaea, fungi and Protista) at three depths (i.e. surface, middle, deep), during both summer and winter seasons, over a three-year period.

The project involves an analysis of microbial community structure and gene content (metagenomics), functional analysis (metaproteomics), and the profiling the secondary metabolites and bioactive compounds (metabolomics). These data will allow us to profile microbial responses to changing environmental conditions at a variety of levels, and should lead to a better understand the relationships between microbial diversity and functional processes in cold oceanic habitats.

 

The SA Agulhas 

 

The African Soil Microbiology Project

In a new research initiative funded by USAID and with collaborating partners from many sub-Saharan African countries, we are planning to undertake a wide-ranging survey of soil microbial community composition across parts of sub-Saharan Africa.  

There is an increasing awareness of the vital role that soil microorganisms play in the ‘agricultural health’ of soils.  Here, in collaboration with colleagues from South Africa, Namibia, Botswana, Zimbabwe, Mozambique, Zambia, Kenya, Ethiopia, Benin and Côte d’Ivoire, we have initiated a baseline study of soil microbial community structure, using modern molecular phylogenetic bar-coding methods. We will correlate the microbial community fingerprinting data with macro- and micro-environmental parameters. This survey paves the way for more localized and focused investigations of the critical roles of other variables (climate, water relations, vegetation cover, land use, and agricultural practice).  In its first phase of the research, we aim to analyze 1000 soil samples from across sub-Saharan Africa.

The AfSM project was formally initiated in July 2016, with a meeting of consortium members at the University of Pretoria. We aim to complete the soil sampling by mid-2016. Researchers from each of the partner laboratories will participate in the phylogenetic analyses and data interpretation. 

 

The AfSM team in the CMEG laboratory at the University of Pretoria, 2016

 

 

Phylogeography and Functional Ecology of South African dry-land Microbial Communities

 

Arid or dry environments represent a third of all the terrestrial biomes as well as ~20% and ~80% of the Earth’s and South Africa's land surface, respectively. Predictive models show that, through intensive land usage and Global Climate Change, dry-land areas will increase in scale; a process termed desertification.

To date, the soil microbiomes of South African arid lands have never been comprehensively studied. However, such studies are important since, in environments where the macro-fauna and -flora are sparsely distributed, microbial communities constitute the main ‘ecosystem engineers’. 

In a new project funded by the NRF Foundational Biodiversity program, a multidisciplinary team of national international researchers led by CMEG and in collaboration with SANParks will implement a phylogenetic survey of the desert soil microbiota in multiple natural soil types located in different aridity zones across South Africa.  This study will also probe the functional capacities and process rates of soil microbial communities under different Global Change-related climate scenarios. An increasing volume of literature supports the view that microbial processes should be taken into account in order to improve the modelling of Global Climate Change processes.

CMEG researcher collecting soil samples in Limpopo

 

 

AADMEN (the African-Arabian Desert Microbial Ecology Network) and the microbiology of Tunisian deserts

In a collaborative network jointly led with Professor Ameur Cherif (University of Manouba, Tunisia) and Professor Daniele Daffonchio (King Abdullah University of Science and Technology, Saudi Arabia), CMEG researchers are expanding their studies of the microbial ecology of hot desert soils into north Africa and the Arabian Peninsula. Recent field expeditions to both Tunisia and Saudi Arabia have generated soil samples and phylogenetic data sets which can be used as comparisons with dry-land soil data sets obtained from other regions (the Namib, the Karoo and the Kalahari), and in the future will enable us to undertake a continent-wide phylogeographic assessment of soil microbiology. The collaborative network (AADMEN) involves researchers from many other countries, all of whom have interests in the microbiology of desert and desert soils.

 

The eastern margins of the Sahara Desert

 

 

The impact of global climate change on microbial biodiversity and functionality in arid ecosystems

 

Soils store a third of total terrestrial carbon (C). Soil organic carbon (SOC) is the core of ecosystems functioning and therefore essential for soil fertility and health, which in turn sustain agriculture. Global change has led to alterations in temperatures and decreased more variable rainfall regimes. These factors have led to an increased proportion of areas, which are now under threat due to desertification (the transition of lands towards greater aridity).

This study aims to undertake a survey of microbial communities (comprising bacteria, archaea, fungi, and protista) along a 1500km aridity gradient. Soils will be collected from multiple locations from the arid Nama Karoo  to the Grassland biomes of Kwazulu-Natal. We will also measure soil carbon levels along this transect, and correlate these data with microbial diversity and measurements of functional (enzymatic assay) activity. The aim is to determine the contribution of microbial guilds to important soil-related processes.

 

Microbial ecology of South African crop plant rhizospheres

Rhizosphere microbial communities influence the fitness of plants, either negatively, by acting as pathogens, or positively, by increasing the stress tolerance of the plant, assisting with the uptake of phosphorus and nitrogen, producing phytohormones, preventing colonization or reducing the infection of plant tissues by pathogens.

Previous work from our laboratory and elsewhere suggests that soil properties are the dominant factors structuring rhizosphere microbial communities. However, other factors such as plant species identity or microbe-microbe interactions can influence these communities and the way the function.

Using crop plants such as sorghum and maize, together with modern molecular technologies (e.g., metagenomics, metaproteomics), ecological theories (e.g., food web theory, niche theory), and recent computational and statistical advances (e.g., structural equation modeling, co-occurrence networks), we aim to link microbial community composition and dynamics with ecological functions. More specifically, our objective is to identify the core species of the “root microbiome” that associated with a particular plant and are critical to its health and performance. Ultimately, such knowledge can be used to manipulate these microbial communities to enhance the health and productivity of agricultural crops.

 

 

In planta stress adaption by genetic engineering

A serious consequence of global climate change is the increased desertification of those regions which are already impacted by water deficit. Equatorial areas of the African continent are most likely affected with increased negative impacts on agriculture. There is therefore an urgent need to identify innovative approaches for enhancing cropping ranges, particularly into regions which are drought-prone or impacted by soil salinity. One such approach is the development of new crop cultivars which have enhanced drought and salt resistance, through the identification and in planta expression of novel stress-response elements. Functional metagenomics library screening is one approach that has already become an established method for the identification of novel genes and gene products.

In 2011, members of our research group collected soil samples in an Antarctic expedition and prepared a large fosmid metagenome library. In a close collaboration between microbiologists and bioinformaticians from different countries and continents (Africa, Europe and India) and by applying modern wet-lab and bioinformatics tools, screening of the Antarctic soil metagenomic library under stress conditions identified a novel bacterial gene product (the WHy protein), homologous to a known anti-stress protein domain. Intensive studies in our laboratories have shown that this novel bacterial protein elicits significant protection against cold and drought stress in recombinant model organisms like E. coli and Arabidopsis plants.

Based on these findings we are now addressing the question of whether this novel bacterial protein can be functionally expressed in crop plants such as soybean, maize and sorghum, and whether its functional properties can expand the growth range and performance of these important economic species. 
 

 

A drought stress experiment with Arabidopsis. Left: Wild-type, with no drought stress; Centre: Recombinant plant expressing the Why gene, after drought stress; Right: wild-type, after drought stress.

 

 

Bacterial canker of stone fruit trees

Bacterial canker of stone fruit trees has been known to occur in South Africa since the 1980s. Since then there has been limited research conducted on this disease.  In recent years, however, there have been increased reports of tree death in the Western Cape.   Affected trees were of different cultivars and ages, and there was a random distribution of dead/dying trees within the orchards.  It was suggested that a combination of abiotic and biotic factors played a role in causing these deaths. Nematodes were considered to be the primary suspect but typical bacterial canker symptoms were also observed.  Studies are now underway to determine whether abiotic (drought) and biotic (ring nematodes) play a role in bacterial canker outbreaks.

Surveys were undertaken in commercial stone fruit orchards in South Africa and bacteria were isolated from typical bacterial canker symptoms. Pseudomonas syringae pv. syringae was identified and proven to be the causative agent of the disease.   As this pathogen has a wide host range, infecting both herbaceous and woody hosts, the genomes of strains were sequenced in an attempt to understand the mechanisms this pathogen uses to adapted and infect these two very different host types.

 

Pantoea ananatis genomics

Pantoea ananatis is a ubiquitous bacterium. It occupies diverse and unusual ecological niches where it functions as a successful saprophyte. It is also capable of causing bacteremia in humans. When it is associated with plants it can occur as an epiphyte, endophyte or even as a pathogen, where it infects a broad range of plant species. Despite its widespread occurrence, little is known about how it causes disease symptoms in its host plants. Teresa Coutinho and her team are using genomic approaches to identify a number of pathogenicity factors in P. ananatis, including motility, quorum sensing and small RNAs.

 
The conserved and variable genes in the different flagellin glycosylation island (FGI) types of P. ananatis chosen for genetic screening.

 

 

African Ancient DNA Research

CMEG researchers Riaan Rifkin and Jean-Baptiste Ramond are recovering ancient DNA from local archaeological sites which span the past 100,000 years. Their goal is to reconstruct the African disease baseline before our ancestors left Africa some 65,000 years ago. They have obtained soil and bone samples from caves, and extracted and sequenced the ancient (a)DNA. They will now reassemble the fragmented snippets of aDNA into sequences typical of pathogens (e.g. viruses and bacteria).


But why investigate ancient diseases, and how can novel data about prehistoric pathogens benefit us? It is widely thought that modern human diseases arose during the Neolithic age some 12,000 years ago, but we believe that the original state of human disease susceptibility is preserved in our African archaeological heritage. Diseases can severely impact humans; up to 60% of modern hunter-gatherers succumb to disease before reaching 15 years of age. So, even in our modern day and age, we are not immune against pathogens. Epidemics like Zika virus and Avian Influenza still plaque modern society. Information about ancient pathogens can provide many benefits to modern society: it can be used to anchor pathogen mutation rates and reconstruct evolutionary processes, and even help to develop new vaccines. Ancient disease data can also facilitate the discovery of pathogens that might pose significant future disease threats to humanity.

 

 

Understanding the effect of lifestyle, diet and geography on the human gut microbiome

Microbial communities and their genes (the “human microbiome”) are recognized to significantly affect health. However, crucial aspects on the structure, function and diversity of healthy human microbiota remain poorly understood, especially in understudied populations such as in South Africa. This study aims to reduce this knowledge deficit regarding the state of the gut microbiota of South African populations through application of “omic-based’ methods. Specifically, the study aims to apply metagenomics, metaproteomics and metabolomics to assess the effect of lifestyle, diet and geographic location on the human gut microbiome. Through application of metagenomics, we will obtain direct knowledge of microbial composition and genetic capacity of microbes within the gut. The analysis of the metaproteomics and metabolomics will allow us to understand the relationship between microbial composition and function. This project will provide the first, extensive dataset on the gut microbiomes of South African communities.

 

The Microbiomics of Human Disease


Our lack of understanding of the etiology and the role of different physiological systems in complex disorders such as Alzheimer’s disease (AD) has left us with a growing incidence of these disorders globally. Alzheimer’s disease is a devastating condition that results in the inexorable loss of intellectual and social capabilities. While various mechanisms have been proposed to explain AD, none has been causally linked to the disease, and the condition remains untreated with no prospect of curative therapy in the near future.

Our group investigates the role of microorganisms in health and disease. We are exploring the nature of the blood microbiome and how this differs in people with diseases such as AD. Our work also investigates the close relationship of the immune system with the “human microbiome” to gain new insights into the role of the aging immune system in complex disorders. We aim to identify the mechanisms that may underlie the disease onset and progression of AD. The research methodology that we are currently developing and optimizing in our facility will provide the basis to elucidate the role of microorganisms, particularly those in the blood, in other human diseases

 

Geobacillus Genomics

The genus Geobacillus contains a large and diverse group of obligately thermophilic and catabolically and ubiquitous species. Geobacillus species have long been of biotechnological interest as sources of thermostable enzymes, and more recently have been utilized in other industrial processes such as biofuel production and bioremediation. Using phylogenomic strategies, we recently proposed a revision of the genus Geobacillus, with the description of a new genus, Parageobacillus, consisting of four type strains and one genomo-species. With this new phylogenomic framework, genomes of more Geobacillus and Parageobacillus species are currently being sequenced and assembled by our group.

In the second phase of the work, we will apply genomic and comparative genomic strategies to elucidate the evolutionary histories and genome dynamics of the ‘geobacilli’. Information gained from the genomic studies will be utilized to catalogue important metabolic pathways that can be exploited for the identification of novel bioactive molecules. To gain further insights into the molecular determinants of specific functions, various multi-omic and mutagenesis approaches will be used. Ultimately, we will be able to use synthetic biology methods to engineer specific ‘geobacilli’ for enhanced production of biocatalysts and other bioactive molecules.

 

Published by Alacia Armstrong

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