Exploring the Microbiota of East African Indigenous Leafy Greens for Plant Growth, Health, and Resilience

Abstract

Indigenous leafy green vegetable crops provide a promising nutritious alternative for East African agriculture under a changing climate; they are better able to cope with biotic and abiotic stresses than cosmopolitan vegetable crops. To verify our hypothesis that the associated microbiome is involved, we studied archaeal and bacterial communities of four locally popular leafy green crops in Uganda (Bidens pilosa, Solanum scabrum, Abelmoschus esculentus, and Gynandropsis gynandra) and of four plant microhabitats (phyllosphere, root endosphere, rhizosphere, and soil) by complementary analyses of amplicon and isolate libraries. All plants shared an unusually large core microbiome, comprising 18 procaryotic families but primarily consisting of Bacillus, Sphingobium, Comamonadaceae, Pseudomonas, and one archaeon from the soil crenarchaeotic group. Microbiome composition did not differ significantly for plant species but differed for microhabitats. The diversity was, in general, higher for bacteria (27,697 ASVs/H = 6.91) than for archaea (2,995 ASVs/H = 4.91); both groups form a robust network of copiotrophic bacteria and oligotrophic archaea. Screening of selected isolates for stress and plant health protecting traits showed that strains of Bacillus and Sphingomonas spp. div. constituted a substantial portion (15-31%) of the prokaryotic plant-associated communities. Across plant species, microbiota were characterized by a high proportion of potential copiotrophic and plant-beneficial species, which was not specific by plant species. The use of identified plant-beneficial isolates could provide the basis for the development of consortia of isolates for both abiotic and biotic stress protection to improve plant and ecosystem health, ensuring food security in East Africa.

Insights into the microbiome assembly during different growth stages and storage of strawberry plants

“…Sphingomonas and Pseudomonas were previously found to be abundant in apple flower [75] and fruit [76] microbiomes. Moreover, phyllosphere-adapted bacterial genera like Methylobacterium and Sphingomonas [2,77] are known to commonly compose the core of phyllosphere microbiomes where they can have implications for plant growth promotion and pathogen suppression [11,[78][79][80], and even for strawberry flavor [12]. Sphingomonas was previously shown to have a high niche versatility in the phyllosphere; it was detected in the core microbiomes of tomato trichomes as well as apple fruits [76,81].…”

The indoor environment - a potential source for intact human-associated anaerobes

“…It is made The copyright holder for this preprint this version posted December 2, 2020. ; https://doi.org/10.1101/2020.12.02.406132 doi: bioRxiv preprint from direct seeding during vaginal birth. It is yet unknown whether methanogens such as Methanobrevibacter* are acquired perinatally and escape detection early in life or if they colonise the GIT via another source such as the BE or dietary products like yoghurt, organic milk and vegetables (Brusa et al, 1998;Taffner, Bergna, et al, 2020;Taffner, Laggner, et al, 2020;van de Pol et al, 2017). The latter scenario is plausible as methanogens coevolved with animals (Borrel et al, 2017;Youngblut et al, 2020) and thus, show strong adaption to the human GIT.…”

“…This introduces a new potential transmission pathway, which is especially interesting with respect to infants, as it presents another way in which they can acquire microbes aside from direct seeding during vaginal birth. It is still not know whether methanogens such as Methanobrevibacter * are acquired perinatal and escape detection early in life or colonise the GIT via another source, such as the BE or dietary products like yoghurt, organic milk and vegetables [96–99]. The latter scenario is plausible, as methanogens co-evolved with animals [56, 100] and, thus, have adapted to the human GIT.…”

A review on the potential of underutilized Blackjack (Biden Pilosa) naturally occurring in sub-Saharan Africa

“…[ 37 ] India 2001 Experiment B. Pilosa can exert inhibitory effect and hence control the development of weeds The use of B. Pilosa to control other weeds Tembo et al. [ 38 ] Tanzania and Malawi 2018 Experiment Safety of botanical pesticides such as bioactive from B. Pilosa The use of bioactive from B. Pilosa as botanical pesticides Taffner and Coallegues [ 39 ] Uganda, East Africa 2020 Complementary scrutinises amplicon and isolate libraries An unusually large core microbiome shared by plants, including procaryotic families such as comamonadaceae, bacillus, sphingobium, pseudomonas, and one archaeon from the soil crenarchaeotic group. Microbiome composition did not differ significantly for plant species but differed for microhabitats.…”

“…Blackjack plants can flourish soils with light, moderate and heavy rains and flourish in loose soil containing high organic matter. In addition, blackjack can tolerate saline soil as it can survive in the soil with pH ranging from 4 to 9 [ 39 ]. Generally, blackjack plants grow in rich soil in the wild, planting fields, and home gardens.…”