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

Xiaoyulong Chen, Lisa Krug, Maofa Yang, Gabriele Berg, Tomislav Cernava*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish
Pages (from-to)909–918
Number of pages10
JournalMicrobial Ecology
Issue number4
Publication statusPublished - Nov 2021


  • Bacterial communities
  • Endophytic bacteria
  • Phyllosphere
  • Plant microbiome
  • Rhizosphere

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Soil Science
  • Ecology


Dive into the research topics of 'The Himalayan Onion (Allium wallichii Kunth) Harbors Unique Spatially Organized Bacterial Communities'. Together they form a unique fingerprint.

Cite this