Biogeographical survey of soil microbiomes across sub-Saharan Africa: structure, drivers, and predicted climate-driven changes.

BACKGROUND: Top-soil microbiomes make a vital contribution to the Earth's ecology and harbor an extraordinarily high biodiversity. They are also key players in many ecosystem services, particularly in arid regions of the globe such as the African continent. While several recent studies have documented patterns in global soil microbial ecology, these are largely biased towards widely studied regions and rely on models to interpolate the microbial diversity of other regions where there is low data coverage. This is the case for sub-Saharan Africa, where the number of regional microbial studies is very low in comparison to other continents. RESULTS: The aim of this study was to conduct an extensive biogeographical survey of sub-Saharan Africa's top-soil microbiomes, with a specific focus on investigating the environmental drivers of microbial ecology across the region. In this study, we sampled 810 sample sites across 9 sub-Saharan African countries and used taxonomic barcoding to profile the microbial ecology of these regions. Our results showed that the sub-Saharan nations included in the study harbor qualitatively distinguishable soil microbiomes. In addition, using soil chemistry and climatic data extracted from the same sites, we demonstrated that the top-soil microbiome is shaped by a broad range of environmental factors, most notably pH, precipitation, and temperature. Through the use of structural equation modeling, we also developed a model to predict how soil microbial biodiversity in sub-Saharan Africa might be affected by future climate change scenarios. This model predicted that the soil microbial biodiversity of countries such as Kenya will be negatively affected by increased temperatures and decreased precipitation, while the fungal biodiversity of Benin will benefit from the increase in annual precipitation. CONCLUSION: This study represents the most extensive biogeographical survey of sub-Saharan top-soil microbiomes to date. Importantly, this study has allowed us to identify countries in sub-Saharan Africa that might be particularly vulnerable to losses in soil microbial ecology and productivity due to climate change. Considering the reliance of many economies in the region on rain-fed agriculture, this study provides crucial information to support conservation efforts in the countries that will be most heavily impacted by climate change. Video Abstract.

Microbiomics of Namib Desert habitats.

The Namib Desert is one of the world's only truly coastal desert ecosystem. Until the end of the 1st decade of the twenty-first century, very little was known of the microbiology of this southwestern African desert, with the few reported studies being based solely on culture-dependent approaches. However, from 2010, an intense research program was undertaken by researchers from the University of the Western Cape Institute for Microbial Biotechnology and Metagenomics, and subsequently the University of Pretoria Centre for Microbial Ecology and Genomics, and their collaborators, led to a more detailed understanding of the ecology of the indigenous microbial communities in many Namib Desert biotopes. Namib Desert soils and the associated specialized niche communities are inhabited by a wide array of prokaryotic, lower eukaryotic and virus/phage taxa. These communities are highly heterogeneous on both small and large spatial scales, with community composition impacted by a range of macro- and micro-environmental factors, from water regime to soil particle size. Community functionality is also surprisingly non-homogeneous, with some taxa retaining functionality even under hyper-arid soil conditions, and with subtle changes in gene expression and phylotype abundances even on diel timescales. Despite the growing understanding of the structure and function of Namib Desert microbiomes, there remain enormous gaps in our knowledge. We have yet to quantify many of the processes in these soil communities, from regional nutrient cycling to community growth rates. Despite the progress that has been made, we still have little knowledge of either the role of phages in microbial community dynamics or inter-species interactions. Furthermore, the intense research efforts of the past decade have highlighted the immense scope for future microbiological research in this dynamic, enigmatic and charismatic region of Africa.

Isotopic evidence for the provenance and turnover of organic carbon by soil microorganisms in the Antarctic dry valleys.

The extremely cold and arid Antarctic dry valleys are one of the most environmentally harsh terrestrial ecosystems supporting organisms in which the biogeochemical transformations of carbon are exclusively driven by microorganisms. The natural abundance of (13)C and (15)N in source organic materials and soils have been examined to obtain evidence for the provenance of the soil organic matter and the C loss as CO(2) during extended incubation (approximately 1200 days at 10 degrees C under moist conditions) has been used to determine the potential decay of soil organic C. The organic matter in soils remote from sources of liquid water or where lacustrine productivity was low had isotope signatures characteristic of endolithic (lichen) sources, whereas at more sheltered and productive sites, the organic matter in the soils that was a mixture mainly lacustrine detritus and moss-derived organic matter. Soil organic C declined by up to 42% during extended incubation under laboratory conditions (equivalent to 50-73 years in the field on a thermal time basis), indicating relatively fast turnover, consistent with previous studies indicating mean residence times for soil organic C in dry valley soils in the range 52-123 years and also with recent inputs of relatively labile source materials.

Controls on the distribution of productivity and organic resources in Antarctic Dry Valley soils.

The Antarctic Dry Valleys are regarded as one of the harshest terrestrial habitats on Earth because of the extremely cold and dry conditions. Despite the extreme environment and scarcity of conspicuous primary producers, the soils contain organic carbon and heterotrophic micro-organisms and invertebrates. Potential sources of organic compounds to sustain soil organisms include in situ primary production by micro-organisms and mosses, spatial subsidies from lacustrine and marine-derived detritus, and temporal subsidies ('legacies') from ancient lake deposits. The contributions from these sources at different sites are likely to be influenced by local environmental conditions, especially soil moisture content, position in the landscape in relation to lake level oscillations and legacies from previous geomorphic processes. Here we review the abiotic factors that influence biological activity in Dry Valley soils and present a conceptual model that summarizes mechanisms leading to organic resources therein.

The relationship between microbial carbon and the resource quality of soil carbon.

The biological health of soil is an important aspect of soil quality because of the many critical functions performed by organisms in soil. Various indicators of soil quality have been proposed, but measurements of microbial biomass are most commonly used. During decomposition of plant residues in soil the relative intensities of the O-alkyl-C signal decreases and the alkyl-C signal increases in nuclear magnetic resonance (NMR) spectra. This leads to the suggestion that the alkyl-C to O-alkyl-C ratio of a soil may indicate the degree of decomposition. Consequently, the overall resource quality of soil C as a substrate for heterotrophic microorganisms may be inversely related to the alkyl-C to O-alkyl-C ratio. Our hypothesis is that a relationship exists between the size of the soil microbial community (microbial biomass) and the quality of soil carbon as a resource for microorganisms. New data have been combined with previously published data to show that there was a significant, negative correlation between the biomass C to total C (Cmic, to Corg) ratio and the alkyl-C to O-alkyl-C ratio (p < 0.01), which supports our hypothesis.

Application of 13C NMR to investigate the transformations and biodegradation of organic materials by wood- and soil-feeding termites, and a coprophagous litter-dwelling dipteran larva.

Solid-state 13C nuclear magnetic resonance spectroscopy has been used to characterize the C in samples of the food (wood), gut contents and faeces from the wood-feeding termite, Microcerotermes parvus; soil in the guts and mound material from the soil-feeding termite, Thoracotermes macrothorax; and the food and faeces from the litter-feeding, coprophagous larvae of the dipteran fly, Bibio marci. Spectra from the wood-feeding termite indicated preferential loss of polysaccharide and accumulation of lignin with some modification to the O-aromatic-C and methoxyl-C (O-methyl-C) components during passage through the gut. Spectra for the soil-feeding termite indicated little change in the distribution of 13C between resonances following passage through the gut, except for some evidence of preferential polysaccharide loss. Interpretation of the spectra from these organisms was restricted by the relatively low C content of the soils and mound material, and by the large contribution to the NMR spectra from the gut tissue rather than the gut contents. Spectra for the litter-feeding dipteran larvae indicated preferential feeding on the polysaccharide-rich component of the litter and then overall loss of polysaccharide-C and accumulation of both aromatic-C and methoxyl-C in the gut. These changes were greater for the second passage than for the first passage through the gut, suggesting that principally mechanical and physical changes occurred initially and that chemical digestion was prevalent during the second passage.

Acceleration of dark reversion of phytochrome in vitro by calcium and magnesium.

Rates of dark reversion of the far red-absorbing form of phytochrome, Pfr, to the red-absorbing form, Pr, have been determined in the presence of several salts. Low concentrations of calcium chloride and magnesium chloride (up to 3 mm) accelerated the rate of dark reversion at all stages of purification of phytochrome from etiolated rye (Secale cereale L. cv. Balbo) seedlings. The complex kinetics of the dark reversion could be resolved into two first-order components. The effect of the added divalent cations was on the relative proportion of the fast and slow reacting components, rather than on the rate constants of the two populations. It was possible to reverse the effects of the cations by adding the chelating agents ethylene-bis-(oxyethylene-nitrilo) tetraacetic acid or ethylenediaminetetraacetate. The effect of the divalent cations is not a nonspecific ionic strength effect. The relative proportion of the two populations was also affected by the degree of purity of the phytochrome samples.

Immunochemical and spectroscopic evidence for protein conformational changes in phytochrome transformations.

Phytochrome was examined by immunochemical and spectroscopic techniques to detect differences between the protein moieties of red- and far red-absorbing phytochrome (P(r) and P(fr)). No differences in the reaction of P(r) and P(fr) with phytochrome antibody were discernible on Ouchterlony double diffusion plates. However, the microcomplement fixation assay showed a greater degree of antibody reaction with P(fr) than with P(r), indicating some difference in the surface characteristics of the two forms. Circular dichroism spectroscopy between 300 and 200 nanometers revealed differences between P(r) and P(fr) which may reflect differences in the protein conformation. The circular dichroism spectrum of P(r) showed a negative band at 285 nanometers which was not present in the spectrum of P(fr), and the large negative circular dichroism band at 222 nanometers with P(fr), associated with the alpha-helical content, was shifted 2 nanometers to shorter wave length with P(r) although there was no change of magnitude of this band. The absorbancy of P(r) and P(fr) is very nearly the same in the 280 nanometer spectral region, but sensitive difference spectra between P(r) and P(fr) did reveal spectra which were similar to solvent perturbation spectra obtained by others with different proteins. In total, the experiments indicate that there are conformational differences between the protein moieties of P(r) and P(fr) but that these differences are rather slight from a standpoint of gross structure.