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.

Bacterial diversity in the haloalkaline Lake Elmenteita, Kenya.

Lake Elmenteita is one of the alkaline saline lakes within the Kenyan Rift valley. The lake is situated on the floor of the Kenyan Rift Valley at 1,776 m above sea level and has no direct outlet. The microbial diversity of the lake was investigated using a culture-independent approach. Five different sampling points were selected randomly within the lake. Wet sediments and water samples were collected from each sampling point. In addition, dry mud cake was collected from three points where the lake had dried. DNA was extracted from the samples and the 16S rRNA genes amplified using universal primers for Bacteria. Thirteen clone libraries were constructed using the PCR amplified 16S rRNA genes. A total of 1,663 clones were picked. Representative clones were selected using ARDRA technique for sequencing. 655 partial and non-chimeric clone sequences indicated the presence of 37 orders in the Domain Bacteria. Cyanobacteria were the most abundant clones in terms of numbers whereas members of the phylum Firmicutes group were the second in terms of numbers but the most diverse in terms of genera represented. All clones affiliated to the class Betaproteobacteria originated from DNA obtained from the water samples. Analysis using BLAST showed that 93.1% of the sequenced clones had similarity values below 98% to both cultured and as yet uncultured bacteria, resulting in 596 phylotypes. Therefore, it can be concluded that Lake Elmenteita harbours phylogenetically diverse groups of bacteria involved in complex metabolic interactions within the Lake's ecosystem.

Attraction response of adult Rhipicephalus appendiculatus and Rhipicephalus pulchellus (Acari: Ixodidae) ticks to extracts from Calpurnia aurea (Fabaceae).

Experiments were carried out to investigate the response of two tick species Rhipicephalus pulchellus Gerstaker, 1873 and Rhipicephalus appendiculatus Neumann, 1901 to three different extracts (acetone, aqueous and oil) of the dried leaves of Calpurnia aurea (Aiton) Benth in both an inverted glass tube and a dual choice T-olfactometer. The oil extract at 50 and 100mg/ml attracted 46.7% and 65.9% of R. appendiculatus, respectively, in the inverted glass tube assay, which was comparable to 47.8% of the attraction-aggregation-attachment pheromone (AAAP) used as positive control. At a dose of 100mg/ml the oil extract attracted 52.4% of R. pulchellus in the T-olfactometer bioassay. The relative attraction of both tick species to plant extract was also tested in semi-field plot experiments using a trap baited with different concentrations of emulsifiable extract of C. aurea. A dose of 100mg/ml attracted 52.2% of R. pulchellus and 44.4% of R. appendiculatus from a distance of 1m while 14.4% of R. pulchellus and 12.2% of R. appendiculatus were attracted from 5m distance at the same dose. Addition of CO(2) to the plant extract-baited-trap at the dose of 100mg/ml increased the range of attraction of adult R. pulchellus (44.4% from 5m distance) and up to 33.3% of adult R. appendiculatus tick from a distance of 4m. The results of this study suggest that extracts from C. aurea can potentially be used as baits in a trap for the control of ticks in the field.

Isolation and characterisation of bacteria from the haloalkaline Lake Elmenteita, Kenya.

Culture-independent studies show that soda lake environments harbour diverse groups of bacteria and archaea. In this study different enrichment and isolation media were used in an attempt to isolate novel groups of bacteria from Lake Elmenteita. Different media were prepared using filter-sterilised water from the lake. The isolates recovered were purified on tryptic soy agar supplemented with 1% sodium carbonate and 4% sodium chloride. Phylogenetic analysis of 181 partial 16S rRNA gene sequences with excellent quality showed that the majority of the isolates were affiliated to the class Gammaproteobacteria and to the genus Bacillus. Isolates from the genus Halomonas and Bacillus constituted 37 and 31% of the total sequenced isolates, respectively. Other groups recovered were related to Marinospirillum, Idiomarina, Vibrio, Enterococcus, Alkalimonas, Alkalibacterium, Amphibacillus, Marinilactibacillus and the actinobacteria Nocardiopsis and Streptomyces. Fifty-one different genera were represented with 31 and 15 cultures scoring with their nearest neighbour similarities below 98 and 97%, respectively. Some novel taxa were identified which had not been isolated previously from the soda environment. The results show that the use of different media with varying compositions can help retrieve novel bacterial diversity from the soda lake environment.

Molecular typing and antibiotic susceptibility patterns of enteropathogenic and shigatoxin producing Escherichia coli isolated from food handlers in three areas of Kenya.

OBJECTIVES: To determine the aetiology, epidemiology and sanitary factors of carriage of enteropathogenic Escherichia coli (EPEC) and Shiga-toxin producing E. coli (STEC) in food-handlers working in tourist hotels in three popular tourist destinations in Kenya. DESIGN: Cross sectional laboratory based study. SETTING: Three tourist destinations of Nairobi, Malindi and Diani in Kenya. SUBJECTS: Food handlers who were working in hotels frequented by tourists in the three study sites. RESULTS: Overall, during the period of April 2003 to May 2004, a total of 1399 food handlers stool samples were collected and analysed. EPEC expressing the eaeA gene and STEC expressing the stx2 gene were detected in 11/1399 (0.8%) and 2/1399 (0.1%) of the study subjects respectively. The mean age of the subjects from whom EPEC and STEC were isolated was similar (32.6 years) to those from whom no EPEC and STEC were isolated (32.5 years). Prior use of antibiotics, water source and toilet types were not significantly associated with the isolation of EPEC and STEC (p>0.05). There were 11 resistance patterns with six isolates (6/13, 46.2%) showing multidrug resistance. High prevalence of resistance was observed to co-trimoxazole (55.6%), chloramphenicol (33.3%), ampicillin (22.2%) and tetracycline (22.2%). High concentrations of antibiotics were required to achieve MIC90 for tetracycline, (>64 mg ml(-1)) and ampicillin (>256 mg ml(-1)). Cluster analysis of the Pulse Field Gel Electrophoresis profiles revealed that the EPEC and STEC isolates belonged to two main genotypes with 11 distinct DNA fragment profiles. CONCLUSION: This is the first report in Africa on the isolation of STEC from food handlers working in tourist hotels. These food handlers who carry the STEC and EPEC could potentially infect tourists and other people through food or water contamination in the hotel settings and thus our findings are of great public health importance.