Linking soil microbial community structure to potential carbon mineralization: A continental scale assessment of reduced tillage

Potential carbon mineralization (Cmin) is a commonly used indicator of soil health, with greater Cmin values interpreted as healthier soil. While Cmin values are typically greater in agricultural soils managed with minimal physical disturbance, the mechanisms driving the increases remain poorly understood. This study assessed bacterial and archaeal community structure and potential microbial drivers of Cmin in soils maintained under various degrees of physical disturbance. Potential carbon mineralization, 16S rRNA sequences, and soil characterization data were collected as part of the North American Project to Evaluate Soil Health Measurements (NAPESHM). Results showed that type of cropping system, intensity of physical disturbance, and soil pH influenced microbial sensitivity to physical disturbance. Furthermore, 28% of amplicon sequence variants (ASVs), which were important in modeling Cmin, were enriched under soils managed with minimal physical disturbance. Sequences identified as enriched under minimal disturbance and important for modeling Cmin, were linked to organisms which could produce extracellular polymeric substances and contained metabolic strategies suited for tolerating environmental stressors. Understanding how physical disturbance shapes microbial communities across climates and inherent soil properties and drives changes in Cmin provides the context necessary to evaluate management impacts on standardized measures of soil microbial activity

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Conifers: Species Diversity and Improvement Status in Kenya

A wide range of exotic conifer species have been successfully introduced in Kenya since 1910 for the purpose of supplying wood, mainly for timber, pulp, and plywood industries. Among the conifers introduced, Cupressus lusitanica and Pinus patula have adapted well to local growing conditions and are now the key species widely planted in commercial plantations. The other conifer species are planted at secondary level or as ornamentals. In order to increase productivity, the key conifer species have been subjected to genetic improvement through selection, breeding, and hybridization. Results of tree improvement work on C. lusitanica and P. patula showed growth and productivity increase from 20 to 25 m3/ha/yr. for C. lusitanica and from 25 to 30 m3/ha/yr. for P. patula. Scaling up conifer plantations using the tree improvement technologies drawn for the two species is one of the strategies for closing the annual wood supply–demand deficit which is currently estimated at 10.3 million m3. It is also one of the strategies for achieving 10% tree cover which is currently at 7.2%. The strategy encompasses the application of principles of tree breeding, improved germplasm, silviculture, pests and disease control. This presentation is a review of the status of conifer species since their introduction in Kenya

Data from: Evidence of high genetic diversity and significant population structuring in Vachellia tortilis (Forsk.) Galasso & Bonfi population in Kenya

Context: Vachellia tortilis is an important dryland tree species valued for fuelwood and fodder production, however, no strategy has been put in place for sustainable management of the species genetic resources. Furthermore, there is inadequate information on the species population genetics to facilitate development of such strategies. Aim: We evaluated the amount and structure of neutral genetic diversity of V. tortilis population in Kenya and provided recommendations necessary for improvement and conservation of the species genetic resources. We hypothesised that the current genetic diversity of V. tortilis is high because of it is demographic history and that no population structuring was expected to occur due to the presumed long distance and effective gene flow within the species. Methods: Leaf tissues were collected from fifteen putative natural populations of V. tortilis covering the whole distribution range in Kenya. DNA was isolated from the leaf tissues and analysed using microsatellite markers. In total, 450 trees were genotyped using 10 polymorphic nuclear microsatellite loci, and genetic diversity and population structure parameters determined Results: We found high levels of genetic diversity within the populations with a mean gene diversity at 0.85. However, significant population differentiation was evident (FST = 0.026, P = 0.007; RST = 0.032, P = 0.004) despite large number of migrants per generation (Nm = 5.3). Population structure detected suggests presence of two clusters, although, some populations showed mixed ancestry. The groups reflect the influence of geographic patterns and historical population gene flow. Conclusion: There exist high genetic diversity in V. tortilis in Kenya with significant population structuring into two clusters. We recommend consideration of the two distinct groups in the development of the species improvement, breeding and conservation programmes. Such programmes should ensure maintenance of the majority of the extant genetic diversity

Development and characterization of microsatellite markers for Osyris lanceolata Hochst. & Steud., an endangered African sandalwood tree species

Osyris lanceolataHochst. & Steud. isa multipurpose tree species widely spread in many of the sub-Saharan countries ranging from Algeria to Ethiopia all the way to South Africa. In Kenya, the species is endemic to the Arid and Semi-Arid Lands (ASALs). It is highly valued for its essential oils used in the cosmetic and pharmaceutical industries. Despite its endangered status and economic importance, little is known about its genetic diversity status and only few conservation strategies exist for the species.Overexploitation of the species hasresulted in the decline of its population and reduced availability of its products. The mode of harvesting of sandalwood is destructive and unsustainable. This is because the whole tree is usually uprooted to get the heartwood from the stem, stump and roots. The exploitation of African sandalwood could soon drive the species to extinction unless proper control measures are put in place through regulation of its trade and development of conservation strategies. Despite its endangered status and economic importance, no genetic study has been carried out on the species to provide information vital for conservation strategies. This paper reports the development and characterization of a set of 12 polymorphic and five (5) monomorphic microsatellite markers isolated and characterized of O. lanceolata

Synchrony in Leafing, Flowering, and Fruiting Phenology of Senegalia senegal within Lake Baringo Woodland, Kenya: Implication for Conservation and Tree Improvement

Leafing, flowering, and fruiting patterns of Senegalia senegal were studied over a period of 24 months from January 2014 to December 2015. The phenological events of the species are bimodal and follow the rainfall patterns. The leafing phase starts during the onset of rains and lasts for 18 weeks. New leaves continued to appear on the new shoots while old leaves persisted to the leaf fall period. Flowering event takes 12 weeks and is concentrated in the months of high relative humidity (April and October) with one-month peak flowering period. Fruiting phase starts at the peak of the rainy seasons (May and November) and peaks in June and December. This phase lasted for 14 weeks. The fruits mature towards the end of the rainy season (January/February and July/August). The fruits open for dispersal mainly in February/March and September during the peak dry season. High synchrony index (SI) was found in leafing (SI: 0.87), flowering (SI: 0.75), and fruiting (SI: 0.85) events among the populations. Temperature, precipitation, and soil moisture content were significantly correlated with the phenological events. Significant variations in floral morphology and fruits traits were also evident. Seed collections should be undertaken in the months of January/February and July/August

Genetic Diversity and Population Structure of Acacia senegal (L) Willd. in Kenya

The level of genetic diversity and population structure of Acacia senegal variety kerensis in Kenya was examined using seven polymorphic nuclear microsatellite loci and two chloroplast microsatellite loci. In both chloroplast and nuclear datasets, high levels of genetic diversity were found within all populations and genetic differentiation among populations was low, indicating extensive gene flow. Analysis of population structure provided support for the presence of two groups of populations, although all individuals had mixed ancestry. Groups reflected the influence of geography on gene flow, with one representing Rift Valley populations whilst the other represented populations from Eastern Kenya. The similarities between estimates derived from nuclear and chloroplast data suggest highly effective gene dispersal by both pollen and seed in this species, although population structure appears to have been influenced by distributional changes in the past. The few contrasts between the spatial patterns for nuclear and chloroplast data provided additional support for the idea that, having fragmented in the past, groups are now thoroughly mixed as a result of extensive gene flow. For the purposes of conservation and in situ management of genetic resources, sampling could target a few, large populations ideally distributed among the spatial groups identified. This should ensure the majority of extant variation is preserved, and facilitate the investigation of variation in important phenotypic traits and development of breeding populations

Per capita FSW in the towns mapped in Western and Rift Valley provinces, Kenya.

<p>Per capita FSW in the towns mapped in Western and Rift Valley provinces, Kenya.</p

Estimated number of active FSW spots and population sizes in the towns mapped in Western and Rift Valley provinces, Kenya.

a<p>Based on point estimate for FSW population.</p