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.

Functional expression of the catalytic domains of two cysteine proteinases from Trypanosoma congolense

The catalytic domains of two closely related cysteine proteinases (CP1 and CP2) from Trypanosoma congolense, referred to as C1 and C2, were expressed as proforms in Escherichia coli (C1) and in the baculovirus system (C1 and C2). While the bacterial expression system did not allow recovery of active C1, the baculovirus system led to secretion of inactive zymogens which could be processed at acidic pH into mature enzymes. Active C1 and C2 were purified from serum-free culture supernatants by anion-exchange chromatography and characterised. Their kinetic parameters and pH activity profiles confirmed the relatedness between C2 and native CP2 (congopain). These properties also underline major functional differences between C1 and C2, that appear to relate to discrete but essential sequence differences. It is likely that these two enzymes perform distinct roles in vivo, in the parasite and/or in the host-parasite relationships.

Immunisation of cattle with cysteine proteinases of Trypanosoma congolense: targetting the disease rather than the parasite

In order to test the hypothesis that trypanosome cysteine proteinases (CPs) contribute to pathology of trypanosomosis, cattle were immunised with CP1 and/or CP2, the major CPs of Trypanosoma congolense, and subsequently challenged with T. congolense. Immunisation had no effect on the establishment of infection and the development of acute anaemia. However, immunised cattle, unlike control cattle, maintained or gained weight during infection. Their haematocrit and leukocyte counts showed a tendency to recovery after 2-3 months of infection. Cattle immunised with CP2 mounted early and prominent IgG responses to CPs and to the variable surface glycoprotein following challenge. Thus trypanosome CPs may play a role in anaemia and immunosuppression; conversely, anti-CP antibody may modulate the trypanosome-induced pathology.

Trypanosoma congolense: a comparison of T-cell-mediated responses in lymph nodes of trypanotolerant and trypanosusceptible cattle during primary infection

A comparison of T-cell-mediated immune responses in trypanotolerant N'Dama and susceptible Boran cattle during primary infection with tsetse-transmitted Trypanosoma congolense was conducted to assess whether different patterns of T-cell activation occurred during trypanosome infection. Proliferation and IFN-gamma synthesis in response to trypanosome antigens and to the mitogen Con A were measured in LNC before infection and 10 and 35 days postinfection. Phenotypic analysis of LNC was also carried out. No significant differences in the in vitro proliferation of LNC to VSG, to hsp70/BiP, or to Con A were detected between the breeds. In contrast, IFN-gamma production in response to Con A was higher in Boran cattle at 35 days p.i. A reduction in the number of CD2+ and CD4+ T-cells and an increase in the percentage of B-cells, CD8+ T-cells, and gamma delta T-cells during infection in both N'Dama and Boran was revealed by cytofluorimetric analysis of lymph node cells.

Trypanosoma congolense: B-lymphocyte responses differ between trypanotolerant and trypanosusceptible cattle

Trypanosomiasis is a serious constraint to livestock production in sub-Saharan Africa. Some breeds of cattle are genetically more resistant to the pathogenic effects of trypanosome infection. We measured B-cell activation and the quantity and isotype of antibody produced at the cellular level in six trypanotolerant N'Dama and five trypanosusceptible Boran cattle. The frequencies of spleen cells secreting total and parasite-specific IgM and IgG were measured prior to and 16, 28, and 35 days after a primary challenge with Trypanosoma congolense. Boran cattle had higher frequencies of splenic cells secreting IgM specific for trypanosome-derived variable surface glycoprotein (VSG), cysteine protease (congopain, CP), and heat shock protein (hsp 70/BiP) and the nonparasite antigen, ovalbumin, than did N'Dama cattle. In contrast, the number of VSG-specific IgG-secreting cells was significantly greater in N'Dama than in Boran cattle. During infection, low titers of anti-VSG IgM were detected transiently in the serum of all animals. However, N'Dama had significantly more VSG-specific IgG in blood than Boran during infection. The peripheral blood mononuclear cell population of N'Dama cattle contained a higher percentage of surface IgM-positive B-cells prior to and throughout infection than were found in the blood of Boran. In addition, during infection N'Dama cattle had more circulating lymphocytes that could be activated in vitro to undergo differentiation into IgM- and IgG-secreting cells. These findings demonstrate differences in the frequency of trypanosome-specific antibody-secreting cells in the spleen and in the activation state of B-cells in the blood between N'Dama and Boran cattle during a primary infection with T. congolense.

Trypanosoma congolense: tissue distribution of long-term T- and B-cell responses in cattle

Memory T- and B-cell responses to trypanosome antigens were measured in peripheral blood mononuclear cells, spleen and lymph node cells obtained from four trypanotolerant N'Dama cattle which had been exposed to six experimental infections with Trypanosoma congolense. These cattle were treated with trypanocidal drugs following each infection and had remained aparasitemic for 3 years prior to this study. The antigens used were whole trypanosome lysate, variable surface glycoprotein, a 33-kDa cysteine protease (congopain) and a 70-kDa heat-shock protein. As parameters of T-cell-mediated immunity, we measured T-cell proliferation and IFN-gamma production. Lymph node cells, spleen cells and peripheral blood mononuclear cells all proliferated to a mitogenic stimulus (concanavalin A) but only lymph node cells responded to trypanosome antigens. Similarly, IFN-gamma was produced by both lymph node and spleen cells stimulated with concanavalin A but only by lymph node cells stimulated with variable surface glycoprotein and whole trypanosome lysate. T. congolense-specific antibodies were detected in sera and in supernatants of cultured lymph node and spleen cells after in vitro stimulation with lipopolysaccharide and recombinant bovine interleukin-2. In conclusion, we have demonstrated that memory T- and B-cell responses are detectable in various lymphoid organs in cattle 3 years following infection and treatment with T. congolense.

Trypanosoma congolense: proliferative responses and interleukin production in lymph node cells of infected cattle

T-cell-mediated immune responses to defined antigens of Trypanosoma congolense were measured in cattle undergoing primary infection. The antigens used were the variable surface glycoprotein and two invariant antigens, a 33-kDa cysteine protease (congopain) and a recombinant form of a 69-kDa heat-shock protein. Proliferative responses were highest during the second week postinfection and were detected in cells obtained from the lymph node draining the site of infection but not in peripheral blood mononuclear cells. Production of IL-2 and IFN-gamma was measured in supernatants from antigen-stimulated lymph node cell cultures. Expression of IL-2, IL-4, and IFN-gamma mRNA was detected in antigen-stimulated lymph node cells by reverse transcription-polymerase chain amplification.

A 69 kDa immunodominant antigen of Trypanosoma (Nannomonas) congolense is homologous to immunoglobulin heavy chain binding protein (BiP)

An immunodominant antigen in Trypanosoma congolense-infected cattle is a 69 kDa protein which is conserved among species and developmental stages of African trypanosomes. Immunoscreening of a cDNA expression library identified a 2.35 kbp clone which contains a complete open reading frame encoding a protein of 653 amino acids with a predicted molecular mass of 71 kDa. Protein sequence analyses revealed 45-65% identity with hsp70s from a broad range of organisms, the highest homology being with the mammalian BiP (immunoglobulin heavy chain binding protein). The 69 kDa trypanosome protein shares with other BiP-related molecules two characteristics that are associated with their localization in the endoplasmic reticulum and their function as chaperonins, i.e., a hydrophobic N-terminal signal sequence and a conserved C-terminal tetrapeptide (X)DEL. Divergence between the 69 kDa antigen and other BiP-homologues occurs in the C-terminal region. This may be responsible for the high immunogenicity of the trypanosome protein. The gene for the 69 kDa antigen appears to be present as a cluster of several copies which are not organized in tandem repeats. It is expressed in all developmental stages of T. congolense, but the specific mRNA levels are higher in metacyclics than in other stages.

Onset and development of hypertriglyceridemia in the Zucker rat (fa/fa)

Triglyceridemia was studied in genetically obese Zucker rats (fa/fa) and their lean littermates aged 1-8 wk. Hypertriglyceridemia was manifest in the obese from 2 wk onwards. Hepatic triacylglycerol secretion rate (TGSR) measured after administration of Triton WR-1339, was similar in obese and lean pups aged 2 wk. At 4 wk TGSR was twice as high in the obese as in the lean. Lipoprotein lipase (LPL) activity was abnormal in the tissues of obese animals, being either increased in white adipose tissue from 1 wk onwards or decreased in brown adipose tissue and cardiac and skeletal muscle from 2 wk onwards. The simultaneous appearance in the 2-wk-old obese of a decrease in LPL activity of the latter tissues, and hypertriglyceridemia strongly suggests a cause-effect relationship particularly since TGRS is normal. After weaning, LPL capacity of white adipose tissue in the obese, although considerably increased, was apparently not high enough to compensate for both an increased TGSR and a decreased LPL activity in other tissues.

Phenotypic variability in unweaned 3-week-old Zucker rats

At 3 weeks of age, Zucker rats could not be classified as normal or obese according to body or liver weight. On the other hand, determination of subcutaneous adipose tissue weight per 100 grams of body weight permitted both phenotypes to be distinguished, provided that the growth variations particular to each litter were taken into account. Rats whose future obesity is predictable using this method, have significantly elevated serum levels of triacylglycerols, total cholesterol and phospholipids. However, further analysis of these values indicated that in fact there were two subgroups of both obese and non-obese rats, i.e., those which had elevated serum lipid levels and those which did not.

Onset of genetic obesity in the absence of hyperphagia during the first week of life in the Zucker rat (fa/fa)

The aim of this study was to discover which of three major abnormalities of the genetically obese Zucker rat (fa/fa), namely hyperphagia, excess adiposity, and hyperlipidemia, is the first to appear prior to manifest obesity, i.e., before weaning. Suckling fa/fa rats, bred from heterozygous parents, were detected by sizing fat cells obtained from an inguinal fat pad biopsy. Cell hypertrophy was observed in fa/fa rats, compared to Fa/-littermates of the same sex, as soon as 5-7 days after birth. Prediction of fa/fa genotype at this age by this method was assessed using a series of 80 pups and proved to be totally successful. The identity of the "predicted" obese pups was confirmed morphologically at 6 weeks of age. Food (milk) intake was estimated from water turnover rates determined on 86 pups aged 2-8 days using tritiated water. The results show that 7-day-old fa/fa rats had heavier inguinal fat pads with larger adipocytes and higher lipoprotein lipase activity than their lean controls. There was no genotype effect on water intake adjusted to body weight during the first week of life. Moreover weight of stomach contents and triglyceridemia were similar in all animals at 7 days. These results show that excess adiposity develops in the fa/fa rat during the first week of life, before hypertriglyceridemia and hyperphagia, and raises the question of whether this adiposity results from a defect in energy expenditure or an abnormality of fat cell storage capacity, or both.

Lipoprotein lipase activity at onset of development of white adipose tissue in newborn rats

The low triacylglycerol concentration in inguinal tissue of newborn rats did not change during the first 6h after birth, despite the relatively high lipoprotein lipase activity in the tissue. Subsequently triacylglycerol concentration and enzyme activity rose in parallel. The results show that lipoprotein lipase activity was present in the tissue before fat accumulation.