Identification of genomic groups in the genus Stenotrophomonas using gyrB RFLP analysis

Stenotrophomonas maltophilia isolates have been recovered from various clinical samples, including the respiratory tract of cystic fibrosis (CF) patients, but this organism is also widespread in nature. Previously it has been shown that there is a considerable genomic diversity within S. maltophilia . The aims of our study were to determine the taxonomic resolution of restriction fragment length polymorphism (RFLP) analysis of the polymerase chain reaction-amplified gyrB gene for the genus Stenotrophomonas . Subsequently, we wanted to use this technique to screen a set of S. maltophilia isolates (with emphasis on a specific subset, isolates recovered from CF patients), to assess the genomic diversity within this group. In this study we investigated 191 Stenotrophomonas sp. isolates (including 40 isolates recovered from CF patients) by means of gyrB RFLP. The taxonomic resolution of gyrB RFLP, and hence its potential as an identification tool, was confirmed by comparison with results from published and novel DNA–DNA hybridisation experiments. Our data also indicate that the majority of CF isolates grouped in two clusters. This may indicate that isolates from specific genomic groups have an increased potential for colonisation of the respiratory tract of CF patients.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/72378/1/S0928-8244_03_00307-9.pd

Suitability of root, tuber, and banana crops in Central Africa can be favoured under future climates

Context Climate change is projected to negatively impact food systems in Sub-Saharan Africa. The magnitude of these impacts is expected to be amplified by the extensive reliance on rainfed agriculture and the prevalence of subsistence farming. In the Great Lakes Region of Central Africa, smallholder farming households are largely dependent on root, tuber and banana crops. However, the potential impacts of various climate change scenarios on these crops are not well reported. Yet, data-rich insights about the future impacts of climate change on these crops and the adaptive capacity of food systems in the Great Lakes Region is critical to inform research and development investments towards regional climate change adaptation. Objectives We aimed to gain insights of potential impacts of climate change on root, tuber, and banana crops in the Great Lakes Region, specifically investigating changes to localised crop suitability, planting dates, and identifying potential ‘climate-proof’ variety types of each crop for specific geographies. Methods We developed a modified version of the EcoCrop model to analyse the suitability of future climates for four key root, tuber, and banana crops (banana, cassava, potato, and sweetpotato) and a suite of varieties for each (typical, heat-tolerant, drought-tolerant, and early maturing). The model considers only the direct impacts of climate change on crop suitability. It does not consider how climate change impacts crop suitability by affecting the occurrence of extreme weather events or indirect effects on incidence and severity of pest and disease outbreaks. Results and conclusions Our results demonstrate that climate change will be somewhat favourable to root, tuber, and banana-based systems, with only widespread negative impacts seen for potato. These changes should be qualified by the observation that in most cases the environmental suitability for banana, cassava, and sweetpotato will remain constant or improve if farmers shift planting schedules. Location- and crop-dependent shifts to different variety types were found to be effective in improving suitability under future climates. Significance Data driven insights generated from this work can be used as a first step in developing spatially explicit recommendations for both farmers and decision-makers on how to adapt to climate change and plan investment in the research needed to adapt root, tuber, and banana-based livelihoods and systems to those long-term changes

Genomics of an endemic cystic fibrosis Burkholderia multivorans strain reveals low within-patient evolution but high between-patient diversity

In many countries, Burkholderia multivorans is the most prevalent species within the Burkholderia cepacia complex (Bcc) found infecting the lungs of patients with cystic fibrosis (CF). Its positive identification is of immediate concern to the health of the patient as it is notoriously hard to eradicate using antibiotics and can cause necrosis of the lung tissues (cepacia syndrome). Infection control measures reduced the prevalence of B. cenocepacia in CF wards, but patients continue to acquire infections by B. multivorans from environmental sources. In most reported cases, the infecting strains are unique except in rare cases in which cross-infection is observed between patients. We report here an endemic strain of B. multivorans with sequence type ST-742 that has been infecting multiple patients, without evidence for cross-infection. We investigated the epidemiology and genomics of this ST-742 strain and show that it is microdiverse, as isolates between-patients exhibit numerous genomic differences, at scales that have not been observed previously when looking at evolutionary trajectories within-patients. Additionally, we found that the specific genomic background of a given strain may dictate the strategy of adaptation within the CF lung. Burkholderia multivorans is a member of the Burkholderia cepacia complex (Bcc), notorious for its pathogenicity in persons with cystic fibrosis. Epidemiological surveillance suggests that patients predominantly acquire B. multivorans from environmental sources, with rare cases of patient-to-patient transmission. Here we report on the genomic analysis of thirteen isolates from an endemic B. multivorans strain infecting four cystic fibrosis patients treated in different pediatric cystic fibrosis centers in Belgium, with no evidence of cross-infection. All isolates share an identical sequence type (ST-742) but whole genome analysis shows that they exhibit peculiar patterns of genomic diversity between patients. By combining short and long reads sequencing technologies, we highlight key differences in terms of small nucleotide polymorphisms indicative of low rates of adaptive evolution within patient, and well-defined, hundred Kbps-long segments of high enrichment in mutations between patients. In addition, we observed large structural genomic variations amongst the isolates which revealed different plasmid contents, active roles for transposase IS3 and IS5 in the deactivation of genes, and mobile prophage elements. Our study shows limited within-patient B. multivorans evolution and high between-patient strain diversity, indicating that an environmental microdiverse reservoir must be present for this endemic strain, in which active diversification is taking place. Furthermore, our analysis also reveals a set of 30 parallel adaptations across multiple patients, indicating that the specific genomic background of a given strain may dictate the route of adaptation within the cystic fibrosis lung

Quantifying rice yield gaps and their causes in Eastern and Southern Africa

The demand for rice in Eastern and Southern Africa is rapidly increasing because of changes in consumer preferences and urbanization. However, local rice production lags behind consumption, mainly due to low yield levels. In order to set priorities for research and development aimed at improving rice productivity, there is a need to characterize the rice production environments, to quantify rice yield gaps —i.e. the difference between average on-farm yield and the best farmers’ yield— and to identify causes of yield gaps. Such information will help identifying and targeting technologies to alleviate the main constraints, and consequently to reduce existing yield gaps. Yield gap surveys were conducted on 357 rice farms at eight sites (19-50 farmers per site) across five rice-producing countries in Eastern and Southern Africa —i.e. Ethiopia, Madagascar, Rwanda, Tanzania and Uganda— for one or two years (2012-13) to collect both quantitative and qualitative data at field and farm level. Average farm yields measured at the eight sites ranged from 1.8 to 4.3 t ha–1 and the average yield gap ranged from 0.8 to 3.4 t ha–1. Across rice growing environments, major causes for yield variability were straw management, weeding frequency, growth duration of the variety, weed cover, fertilizer (mineral and organic) application frequency, levelling and iron toxicity. Land levelling increased the yield by 0.74 t ha–1, bird control increased the yield by 1.44 t ha–1, and sub-optimal management of weeds reduced the yield by 3.6 to 4.4 t ha–1. There is great potential to reduce the current rice yield gap in ESA, by focusing on improvements of those crop management practices that address the main site-specific causes for suboptimal yields

Status quo of chemical weed control in rice in sub-Saharan Africa

If future rice production is to contribute to food security for the increasing population of sub-Saharan Africa (SSA), effective strategies are needed to control weeds, the crop’s fiercest competitors for resources. To gain better insights into farmers’ access to, and use of, herbicides as part of weed control strategies, surveys were conducted in key rice production locations across SSA. Farm surveys were held among 1965 farmers across 20 countries to collect data on rice yields, farmer’s weed management practices, herbicide use, frequencies of interventions and information sources regarding herbicides. Markets were surveyed across 17 countries to collect data on herbicide availability, brand names and local prices (converted to US$ha−1). Herbicides are used by 34$17 ha−1). They are also the most popular herbicides among farmers. For advice on herbicide application methods, farmers primarily rely on their peers, and only a few receive advice from extension services (<23%) or inform themselves by reading the product label (<16%). Herbicide application timings are therefore often (38%) sub-optimal. Herbicide technologies can contribute to reduced production losses in rice in SSA. However, through negative effects on crop, environment and human health, incorrect herbicide use may unintentionally counteract efforts to increase food security. Moving away from this status quo will require strict implementation and monitoring of national pesticide regulations and investment in research and development to innovate and diversify the currently followed weed management strategies, agricultural service provision and communications with farmers

Nutrient-dense orange-fleshed sweetpotato: advances in drought-tolerance breeding and understanding of management practices for sustainable next-generation cropping systems in sub-Saharan Africa

Almost half of children <5 years old living in sub-Saharan Africa (SSA) suffer from vitamin A deficiency and 60% suffer from iron deficiency. Thus, there has been a strong commitment to breeding for, promoting awareness of, and delivering adapted pro-vitamin A rich orange-fleshed sweetpotato (OFSP) in SSA during the past two decades and for enhanced iron content since 2014. This review article focuses on major breeding efforts in SSA to enhance the drought tolerance of OFSP and reviews integrated crop management practices for improved and sustained sweetpotato production in SSA farming systems. Under climate change, the frequency and severity of droughts is expected to increase. Technical issues are presented in the context of addressing challenges along the entire value chain to ensure adoption. First, the use of an accelerated breeding scheme reduced the breeding cycle from 8–10 to 4–5 years. Since 2010, 19 drought-tolerant OFSP cultivars have been released in Mozambique, 7 in Malawi, and 2 in South Africa. Moreover, research in four breeding populations using the heterosis exploiting breeding scheme (HEBS) demonstrated that within one breeding cycle of 5 years, clones with significantly higher root yield, abiotic tolerance, host plant resistance to pests and diseases, and early maturity can be produced. In the future, HEBS will be combined with greater use of modern genomic tools, new phenotyping tools, and CRISPR/Cas9-mediated gene editing. Second, beyond genetic enhancements, evidence is presented that using improved crop management systems, existing sweetpotato yields can be increased 2–4 times. Current knowledge is reviewed concerning sweetpotato's role in diverse farming systems, but integrated crop management is clearly under researched. Third, the outlook for drought tolerance breeding indicates that two distinct classes of nutrient-rich cultivars are emerging: (1) Early maturing cultivars (<4 month growing period) that escape drought but also serve humid environments with small landholding size per capita; and (2) Medium maturing (4–6 month growing period) cultivars that avoid drought, are drought tolerant and exhibit continuous root formation. Increasing commercialization of the crop and climate change will drive demand, and the willingness of farmers to invest in improved sweetpotato crop management

Growth in Stewart's medium is a simple, rapid and inexpensive screening tool for the identification of Burkholderia cepacia complex

AbstractNinety-one percent of Burkholderia cepacia complex reference strains (66 out of 72) displayed a yellow slope–green butt colour reaction after growth in Stewart's medium indicating the oxidation of glucose and the absence of an arginine dihydrolase system. This same colour reaction was observed for Burkholderia gladioli and several Ralstonia species, but not for Pseudomonas aeruginosa, Stenotrophomonas, Achromobacter, Pandoraea and several other Gram-negative non-fermenting bacilli. We therefore consider growth in Stewart's medium a useful, simple, rapid and inexpensive screening test to reduce the number of false positive isolates from B. cepacia complex selective media