The Himalayan Onion (Allium wallichii Kunth) Harbors Unique Spatially Organized Bacterial Communities.

Plant-associated microorganisms are known to contribute with various beneficial functions to the health and productivity of their hosts, yet the microbiome of most plants remains unexplored. This especially applies to wild relatives of cultivated plants, which might harbor beneficial microorganisms that were lost during intensive breeding. We studied bacterial communities of the Himalayan onion (Allium wallichii Kunth), a wild relative of onion native to mountains in East Asia. The bacterial community structure was assessed in different plant microhabitats (rhizosphere, endosphere, anthosphere) by sequencing of 16S rRNA gene fragment amplicons. Targeted bioinformatic analyses were implemented in order to identify unique features in each habitat and to map the overall community in the first representative of the Amaryllidaceae plant family. The highest bacterial diversity was found for bulk soil (Shannon index, H' 9.3) at the high-altitude sampling location. It was followed by the plant rhizosphere (H' 8.9) while communities colonizing flowers (H' 6.1) and the endosphere (H' 6.5 and 5.6) where less diverse. Interestingly, we observed a non-significant rhizosphere effect. Another specificity of the microbiome was its high evenness in taxonomic distribution, which was so far not observed in plant microbiomes. Pseudomonas was identified among additional 10 bacterial genera as a plant-specific signature. The first insights into the microbiome of a plant in the widespread Allium genus will facilitate upcoming comparisons with its domesticated relatives while additionally providing a detailed microbiome mapping of the plant's microhabitats to facilitate bioresource mining.

The tea leaf microbiome shows specific responses to chemical pesticides and biocontrol applications.

The plant microbiome is known to be influenced by certain biotic as well as abiotic factors. Nevertheless, the drivers for specific changes in microbial community composition and structure are largely unknown. In the present study, the effects of chemical and biological treatments for plant protection on the indigenous microbiome of Camellia sinensis (L.) Kuntze were contrasted. Assessment of bacteria-specific ribosomal RNA gene fragment amplicons from a representative set of samples showed an increased microbial diversity in treated plants when compared to untreated samples. Moreover, distinct microbial fingerprints were found for plants subjected to a conventional pesticide treatment with lime sulfur as well as for plants that were biologically treated with a Piriformospora indica spore solution. The bacterial community of pesticide-treated plants was augmented by 11 taxa assigned to Proteobacteria and Actinobacteria. In contrast, plants from biological control treatments were augmented by 10 taxa representing a more diversified community enrichment and included members of Actionobacteria, Proteobacteria, Bacteroidetes, Planctomycetes, and Verrucomicrobia. Complementary, molecular quantification of fungi in the samples showed a significantly lower number of internal transcribed spacer copies in plants subjected to biological control treatments, indicating the highest efficiency against fungal pathogens. The overall results show that leaves that are used for tea production show distinct microbiome shifts that are elicited by common pest and pathogen management practices. These shifts in the microbial population indicate non-target effects of the applied treatments.

Deciphering functional diversification within the lichen microbiota by meta-omics.

BACKGROUND: Recent evidence of specific bacterial communities extended the traditional concept of fungal-algal lichen symbioses by a further organismal kingdom. Although functional roles were already assigned to dominant members of the highly diversified microbiota, a substantial fraction of the ubiquitous colonizers remained unexplored. We employed a multi-omics approach to further characterize functional guilds in an unconventional model system. RESULTS: The general community structure of the lichen-associated microbiota was shown to be highly similar irrespective of the employed omics approach. Five highly abundant bacterial orders-Sphingomonadales, Rhodospirillales, Myxococcales, Chthoniobacterales, and Sphingobacteriales-harbor functions that are of substantial importance for the holobiome. Identified functions range from the provision of vitamins and cofactors to the degradation of phenolic compounds like phenylpropanoid, xylenols, and cresols. CONCLUSIONS: Functions that facilitate the persistence of Lobaria pulmonaria under unfavorable conditions were present in previously overlooked fractions of the microbiota. So far, unrecognized groups like Chthoniobacterales (Verrucomicrobia) emerged as functional protectors in the lichen microbiome. By combining multi-omics and imaging techniques, we highlight previously overlooked participants in the complex microenvironment of the lichens.