Many microorganisms are refractory to laboratory cultivation. One possible explanation, known as the great plate count anomaly, is metabolic dependencies among community members. However, systematic studies of these interactions in communities like soil are missing, hindering advances in understanding these ecologically important ecosystems. Here, we address this issue by systematically analysing 6,931 bacterial isolates of 27 soil microbial communities. We find that the growth of up to 50% of all community members depended essentially on supplementation with amino acids, vitamins, or nucleotides. In 73% of cases, supplementation with multiple amino acids was necessary. Genomic analysis of 62 strains revealed that accumulation of insertion sequences and specific gene loss was associated with the observed auxotrophies. Finally, genome-scale metabolic models, computational analyses, and cocultivation experiments demonstrated that other co-occurring genotypes complemented the metabolic needs of auxotrophs, thus facilitating their growth. Our results demonstrate that soil bacteria exist within integrated metabolic networks, which hampers their cultivation.
Ghada Yousif, Francisco Zorrilla, Swagatika Dash et al.· bioRxiv· 9 citations· ⚡1
Yeasts are key microbial members of several ecosystems. Yet, the impact of widespread chemical pollutants on yeasts is only sparsely studied. Here we report the effect of >1000 chemical pollutants on fourteen diverse yeast species spanning the Saccharomycotina subphylum. Starmerella bombicola, a symbiont of various bee species, was the most sensitive and inhibited by several fungicides as well as by non-fungicides. To identify the molecular basis of this ultra-sensitivity, we selected resistant lineages against nine chemicals using adaptive laboratory evolution. Whole-genome-sequencing uncovered convergent evolution on YBP1, a key regulator of oxidative stress. Proteomic analysis confirmed the protective role of oxidative stress response pathways, including proteins encoded by horizontally transferred bacterial genes. We find that the evolved S. bombicola stably colonized the bee gut and ameliorated the negative effect of paclobutrazol, a plant hormone regulator, on gut microbes, sucrose responsiveness, and learning. Our findings demonstrate how laboratory evolution can be used to mitigate the negative impact of chemical pollutants on pollinators.
Simone Mozzachiodi, Flavia Di Cesare, S. Kamrad et al.· bioRxiv· 0 citations
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