Charles Staver

Banana-Associated Microbial Communities in Uganda Are Highly Diverse but Dominated by Enterobacteriaceae

ABSTRACT Bananas are among the most widely consumed foods in the world. In Uganda, the country with the second largest banana production in the world, bananas are the most important staple food. The objective of this study was to analyze banana-associated microorganisms and to select efficient antagonists against fungal pathogens which are responsible for substantial yield losses. We studied the structure and function of microbial communities (endosphere, rhizosphere, and soil) obtained from three different traditional farms in Uganda by cultivation-independent (PCR-SSCP fingerprints of 16S rRNA/ITS genes, pyrosequencing of enterobacterial 16S rRNA gene fragments, quantitative PCR, fluorescence in situ hybridization coupled with confocal laser scanning microscopy, and PCR-based detection of broad-host-range plasmids and sulfonamide resistance genes) and cultivation-dependent methods. The results showed microhabitat-specific microbial communities that were significant across sites and treatments. Furthermore, all microhabitats contained a high number and broad spectrum of indigenous antagonists toward identified fungal pathogens. While bacterial antagonists were found to be enriched in banana plants, fungal antagonists were less abundant and mainly found in soil. The banana stem endosphere was the habitat with the highest bacterial counts (up to 109 gene copy numbers g−1). Here, enterics were found to be enhanced in abundance and diversity; they provided one-third of the bacteria and were identified by pyrosequencing with 14 genera, including not only potential human (Escherichia, Klebsiella, Salmonella, and Yersinia spp.) and plant (Pectobacterium spp.) pathogens but also disease-suppressive bacteria (Serratia spp.). The dominant role of enterics can be explained by the permanent nature and vegetative propagation of banana and the amendments of human, as well as animal, manure in these traditional cultivations.

TRANSFORMING IMPACT ASSESSMENT: BEGINNING THE QUIET REVOLUTION OF INSTITUTIONAL LEARNING AND CHANGE

SUMMARY Scores of assessments of the impacts of agricultural research have been carried out over the years. However, few appear to have been used to improve decision making and the effectiveness of research programmes. The Institutional Learning and Change (ILAC) Initiative emerged within the Consultative Group on International Agricultural Research (CGIAR), with the goal of strengthening learning from experience and using lessons to improve pro-poor innovation. It is testing approaches for expanding the contributions of impact assessment and evaluation to learning, decision making and improvement.

Agroforestry leads to shifts within the gammaproteobacterial microbiome of banana plants cultivated in Central America

Bananas (Musa spp.) belong to the most important global food commodities, and their cultivation represents the worlds largest monoculture. Although the plant-associated microbiome has substantial influence on plant growth and health, there is a lack of knowledge of the banana microbiome and its influencing factors. We studied the impact of (i) biogeography, and (ii) agroforestry on the banana-associated gammaproteobacterial microbiome analyzing plants grown in smallholder farms in Nicaragua and Costa Rica. Profiles of 16S rRNA genes revealed high abundances of Pseudomonadales, Enterobacteriales, Xanthomonadales, and Legionellales. An extraordinary high diversity of the gammaproteobacterial microbiota was observed within the endophytic microenvironments (endorhiza and pseudostem), which was similar in both countries. Enterobacteria were identified as dominant group of above-ground plant parts (pseudostem and leaves). Neither biogeography nor agroforestry showed a statistically significant impact on the gammaproteobacterial banana microbiome in general. However, indicator species for each microenvironment and country, as well as for plants grown in Coffea intercropping systems with and without agri-silvicultural production of different Fabaceae trees (Inga spp. in Nicaragua and Erythrina poeppigiana in Costa Rica) could be identified. For example, banana plants grown in agroforestry systems were characterized by an increase of potential plant-beneficial bacteria, like Pseudomonas and Stenotrophomonas, and on the other side by a decrease of Erwinia. Hence, this study could show that as a result of legume-based agroforestry the indigenous banana-associated gammaproteobacterial community noticeably shifted.

Members of Gammaproteobacteria as indicator species of healthy banana plants on Fusarium wilt-infested fields in Central America

Culminating in the 1950’s, bananas, the world’s most extensive perennial monoculture, suffered one of the most devastating disease epidemics in history. In Latin America and the Caribbean, Fusarium wilt (FW) caused by the soil-borne fungus Fusarium oxysporum f. sp. cubense (FOC), forced the abandonment of the Gros Michel-based export banana industry. Comparative microbiome analyses performed between healthy and diseased Gros Michel plants on FW-infested farms in Nicaragua and Costa Rica revealed significant shifts in the gammaproteobacterial microbiome. Although we found substantial differences in the banana microbiome between both countries and a higher impact of FOC on farms in Costa Rica than in Nicaragua, the composition especially in the endophytic microhabitats was similar and the general microbiome response to FW followed similar rules. Gammaproteobacterial diversity and community members were identified as potential health indicators. Healthy plants revealed an increase in potentially plant-beneficial Pseudomonas and Stenotrophomonas, while diseased plants showed a preferential occurrence of Enterobacteriaceae known for their plant-degrading capacity. Significantly higher microbial rhizosphere diversity found in healthy plants could be indicative of pathogen suppression events preventing or minimizing disease expression. This first study examining banana microbiome shifts caused by FW under natural field conditions opens new perspectives for its biological control.

Using Ecological Knowledge and Molecular Tools to Develop Effective and Safe Biocontrol Strategies

Today’s farming systems undermine the well-being of communities in many ways: farming has destroyed huge regions of natural habitats, which also implies a loss of species and their ecosystem services (Sachs et al., 2010). Plant protection measures also causes problems for human health (Horrigan et al., 2002), and agriculture is responsible for about 30% of greenhouse-gas-emission (IPCC, 2007). Furthermore, emerging, re-emerging and endemic plant pathogens continue to challenge our ability to safeguard plant growth and health worldwide (Miller et al., 2009). Therefore, one of the major challenges for the 21st century will be an environmentally sound and sustainable crop production. Microbial inoculants containing microorganisms with beneficial plant-microbe interactions have a great potential to contribute to this objective (Berg, 2009; Bhattacharjee et al., 2008). Over the past 150 years, research has demonstrated repeatedly that bacteria and fungi have an intimate interaction with their host plants and are able to promote plant growth as well as to suppress plant pathogens (Compant et al., 2005; Lugtenberg & Kamilova, 2009; Weller et al., 2002; Weller, 2007; Whipps, 2001). All plant-associated microenvironments, especially the rhizosphere, are colonized in high abundances by antagonistic microbes (Berg et al., 2005a). Between 1 and 35% of the microbial inhabitants showed antagonistic capacity to inhibit the growth of pathogens in vitro (Berg et al., 2002, 2006). The proportion of isolates, which express plant growth promoting traits is much higher in general, and was found up to 2/3 of the cultivable population (Cattelan et al., 1999; Furnkranz et al., 2009; Lottmann et al., 1999). Diverse microbial inoculants, which were selected from this promising indigenous potential, are already on the market. In recent years, the popularity of microbial inoculants has increased substantially, as extensive and systematic research has enhanced their effectiveness and consistency (Berg, 2009). New molecular and microscopic techniques are one reason for progress in biocontrol research. These techniques have enhanced our understanding about the plant and especially

Transgenic banana plants expressing Xanthomonas wilt resistance genes revealed a stable non-target bacterial colonization structure

Africa is among the continents where the battle over genetically modified crops is currently being played out. The impact of GM in Africa could potentially be very positive. In Uganda, researchers have developed transgenic banana lines resistant to banana Xanthomonas wilt. The transgenic lines expressing hrap and pflp can provide a timely solution to the pandemic. However, the impact of the transgenes expression on non-target microorganisms has not yet been investigated. To study this effect, transgenic and control lines were grown under field conditions and their associated microbiome was investigated by 16S rRNA gene profiling combining amplicon sequencing and molecular fingerprinting. Three years after sucker planting, no statistically significant differences between transgenic lines and their non-modified predecessors were detected for their associated bacterial communities. The overall gammaproteobacterial rhizosphere microbiome was highly dominated by Xanthomonadales, while Pseudomonadales and Enterobacteriales were accumulated in the pseudostem. Shannon indices revealed much higher diversity in the rhizosphere than in the pseudostem endosphere. However, the expression of the transgenes did not result in changes in the diversity of Gammaproteobacteria, the closest relatives of the target pathogen. In this field experiment, the expression of the resistance genes appears to have no consequences for non-target rhizobacteria and endophytes.

Fusarium Wilt of Banana: Current Knowledge on Epidemiology and Research Needs Toward Sustainable Disease Management

Banana production is seriously threatened by Fusarium wilt (FW), a disease caused by the soil-borne fungus Fusarium oxysporum f. sp. cubense (Foc). In the mid-twentieth century FW, also known as “Panama disease”, wiped out the Gros Michel banana industry in Central America. The devastation caused by Foc race 1 was mitigated by a shift to resistant Cavendish cultivars, which are currently the source of 99% of banana exports. However, a new strain of Foc, the tropical race 4 (TR4), attacks Cavendish clones and a diverse range of other banana varieties. Foc TR4 has been restricted to East and parts of Southeast Asia for more than 20 years, but since 2010 the disease has spread westward into five additional countries in Southeast and South Asia (Vietnam, Laos, Myanmar, India, and Pakistan) and at the transcontinental level into the Middle East (Oman, Jordan, Lebanon, and Israel) and Africa (Mozambique). The spread of Foc TR4 is of great concern due to the limited knowledge about key aspects of disease epidemiology and the lack of effective management models, including resistant varieties and soil management approaches. In this review we summarize the current knowledge on the epidemiology of FW of banana, highlighting knowledge gaps in pathogen survival and dispersal, factors driving disease intensity, soil and plant microbiome and the dynamics of the disease. Comparisons with FW in other crops were also made to indicate possible differences and commonalities. Our current understanding of the role of main biotic and abiotic factors on disease intensity is reviewed, highlighting research needs and futures directions. Finally, a set of practices and their impact on disease intensity are discussed and proposed as an integrative management approach that could eventually be used by a range of users, including plant protection organizations, researchers, extension workers and growers.

The effect of Banana Xanthomonas Wilt on beer-banana value chains in central Uganda

Purpose - – Beer-bananas in Central Uganda are important for smallholder farmers’ livelihoods, especially for those that process the banana into beer and spirits. The purpose of this paper is to understand how actors in the beer-banana value chain are affected and how they are managing disease has become an important issue since the outbreak of the bacterial banana disease Xanthomonas Wilt. Design/methodology/approach - – The authors conducted an exploratory study focusing on producers of beer-bananas; brewers and non-brewers, and on retailers in Central Uganda and in Kampala. The authors conducted surveys with these value chain actors and we used baseline data, collected through a household survey in the project sites. Findings - – Results showed that Banana Xanthomonas Wilt (BXW) has drastically reduced productivity of beer-banana systems, resulting in reduced sales volumes of beer-bananas and processed products and consequently reduced incomes. Application of disease control measures was generally higher among those farmers that brew. Research limitations/implications - – This being an exploratory study, the samples for the different value chain actors were rather small. Future research should address: product quality and opportunities for differentiation; effects of beer-banana processing on rural communities; adoption of BXW control measures. Originality/value - – Beer-bananas are often neglected in research; this paper shows that is unfounded since beer-banana production and processing are important for many people’s livelihood. More insight into what motivates farmers to control the disease is essential to protect these people’s livelihoods.