Profiling eukaryotic and bacterial communities of high- and low-productivity blueberry farm and forest soils

Highbush blueberry (Vaccinium corymbosum) is native to North America, commercially cultivated, and grows in acidic soils with high organic content. We attempted to characterize the core microbiome of two different highbush blueberry farm soils compared to forest soils. Stable isotope probing (SIP) was employed on two low-productivity, two high-productivity blueberry farm, and two nearby forest soils using 13C-15N-Bioexpress (amino acids mixture) to detect the differences between the resident and amino acid-active soil microbial communities. The SIP experiments were coupled with bacterial and eukaryotic near full-length ribosomal profiling using Oxford Nanopore MinION sequencing technology. Bacterial rRNA operons were screened against the EzBioCloud database to characterize the resident and active rhizosphere bacterial communities, while eukaryotic rRNA operon sequences were screened against the UNITE/all eukaryotes database. Over 13,000 distinct taxonomic units were detected including a number of very abundant ones and thousands of rare members of the bacterial and eukaryotic communities inhabiting these soil systems. The results demonstrated that multiple Bacillus species were abundant in the amino acid-active communities of low-productivity soils, while high-productivity soils were dominated by amino acid-active Paraburkholderia species. Profiling the eukaryotic members of these communities indicated that mycorrhizal fungi belonging to the Glomeromycota phylum were abundant in high-productivity soils, while low-productivity soils were enriched with fungi-like organisms of the phyla Rozellomycota and Oomycota (found in the amino acid-active community fraction only). Secondly, we tried to understand whether there was hidden diversity within a subset of the most abundant fungal and bacterial taxonomic units detected in this study. High-quality and unambiguous ribosomal RNA operons of several abundant fungal and bacteria were reconstructed from the best BLAST hits by generating long-read consensus sequences (LRC). The phylogenetic analysis of the fungal LRCs was performed based on the 18S and 28S rRNA genes, while bacterial LRCs were compared based on the 16S rRNA gene. The data demonstrate that most taxonomic assignments by BLAST were accurate, but new bacterial species and/or strains were shown to potentially exist in these soil systems. Novel clades of fungi (Glomeraceae- and Rozellomycota-related) were detected as well. In conclusion, SIP and MinION sequencing elucidated the resident and active microbial communities, as well as demonstrated the differences between high- and low-productivity farm soils. In the future, this approach can be applied using other heavy isotope-containing substrates for SIP to better characterize the active members of these communities that may be crucial in shaping blueberry plant health and productivity. In addition, this approach coupled with sequencing whole genomes should provide more useful information about the individual phylogenies of the detected organisms as well as their metabolic and functional capabilities that are responsible for unique plant-microbe interactions.M.S.Includes bibliographical reference