A root nodule microbiome sequencing data set from red alder (Alnus rubra Bong.)

Area of Science:

• Plant-microbe interactions
• Microbial ecology
• Symbiotic nitrogen fixation

Background:

• Alnus root nodules frequently host multiple Frankia strains, but their relative contributions remain unquantified.
• The diversity and functional roles of other microbes within these nodules are not well understood.

Purpose of the Study:

• To quantitatively assess the diversity and abundance of Frankia strains within Alnus rubra root nodules.
• To characterize the broader bacterial microbiota in Alnus rubra root nodules and identify potentially beneficial microbes.
• To investigate the spatial distribution of bacterial strains within root nodule structures.

Main Methods:

• Utilized Illumina short-read sequencing for high-resolution analysis of Alnus rubra root nodule microbiota.
• Employed k-mer based read classification with KrakenUniq and Bracken for accurate taxonomic assignment and abundance estimation.
• Performed single-end 76 bp sequencing to a median depth of 96 million reads per sample.

Main Results:

• Quantified the presence of multiple Cluster 1A Frankia strains and, in some cases, Cluster 4 strains within single Alnus rubra nodules.
• Discovered a diverse bacterial community, including genera with known plant growth-promoting species.
• Observed evidence suggesting partitioning of certain bacterial strains between older and younger root nodule lobes.

Conclusions:

• This study provides the first high-resolution, quantitative assessment of microbial communities in Alnus root nodules using next-generation sequencing.
• The findings highlight the complex microbial ecology within Alnus nodules, including multiple Frankia symbionts and beneficial bacteria.
• Further research into these interactions could optimize nitrogen fixation and plant growth in Alnus species.