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

Abstract

<jats:title>ABSTRACT</jats:title><jats:p>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<jats:italic>in situ</jats:italic>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 10<jats:sup>9</jats:sup>gene copy numbers g<jats:sup>−1</jats:sup>). 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 (<jats:named-content content-type="genus-species">Escherichia</jats:named-content>,<jats:named-content content-type="genus-species">Klebsiella</jats:named-content>,<jats:named-content content-type="genus-species">Salmonella</jats:named-content>, and<jats:named-content content-type="genus-species">Yersinia</jats:named-content>spp.) and plant (<jats:named-content content-type="genus-species">Pectobacterium</jats:named-content>spp.) pathogens but also disease-suppressive bacteria (<jats:named-content content-type="genus-species">Serratia</jats:named-content>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.</jats:p>

A New Approach to Analyzing Endophytic Actinobacterial Population in the Roots of Banana Plants (Musa sp., AAA)

“…The actinobacterial taxa were not consistent with previous results. Streptomyces was the most frequently isolated genus from surface-sterilized banana roots [7] , nevertheless, it can not be isolated or detected in previous studies [1,6,22] . In the study, total 11 reads belonged to Streptomyces or Streptomycetaceae were detected by Illumina-based analysis.…”

“…Bananas and plantains grown in the tropic and subtropic regions are among the important crops worldwide [1] . Nevertheless, fusarium wilt of banana (Panama disease) is one of the most devastating diseases of banana.…”

“…It is a major problem throughout most of the banana production regions of the world. Since the Fusarium clamydospores persist in the soil for decades, no cultural or agronomic practices that are useful for the growth susceptible cultivars on infested soils have been identified [1] . No effective chemical method exists to control fusarium wilt of banana; however, biological control using endophytes provides promising perspective for sustainable control of fusarium wilt [2] .…”

Culture-Independent Molecular Tools for Soil and Rhizosphere Microbiology

“…Typical problems with this technique are the occurrence of three bands due to several conformations of one product. Recently, this technique has been used for the rapid profiling of soil microbial communities [84,85] and phylogenetic studies [86]. An interesting study on diversity and distribution of polyhydroxyalkanoate-producing bacteria has used SSCP as a culture-independent approach.…”

“…In this study, Trichoderma-specific communities which play a major role in soil health exhibited low diversity [88]. An improved variation of this technique, namely the Capillary Electrophoresis-Single Strand Conformation Polymorphism (CE-SSCP) fingerprinting has been developed and used to profile communities with low complexity [85], but its application for highly diverse environments is still under evaluation. An alternative of this variation is polymerase chain reaction-free; however it has also been tested only in low diversity samples [89].…”