Microbiome of Field Grown Hemp Reveals Potential Microbial Interactions With Root and Rhizosphere Soil

Abstract

Hemp (Cannabis sativa L.) is a crop bred and grown for the production of fiber, grain, and floral extracts that contribute to health and wellness. Hemp plants interact with a myriad of microbiota inhabiting the phyllosphere, endosphere, rhizoplane, and rhizosphere. These microbes offer many ecological services, particularly those of below ground biotopes which are involved in nutrient cycling, uptake, and alleviating biotic and abiotic stress. The microbiota communities of the hemp rhizosphere in the field are not well documented. To discover core microbiota associated with field grown hemp, we cultivated single C. sativa cultivar, “TJ’s CBD,” in six different fields in New York and sampled hemp roots and their rhizospheric soil. We used Illumina MiSeq amplicon sequencing targeting 16S ribosomal DNA of bacteria and ITS of fungi to study microbial community structure of hemp roots and rhizospheres. We found that Planctobacteria and Ascomycota dominated the taxonomic composition of hemp associated microbial community. We identified potential core microbiota in each community (bacteria: eight bacterial amplicon sequence variant – ASV, identified as Gimesia maris, Pirellula sp. Lacipirellula limnantheis, Gemmata sp. and unclassified Planctobacteria; fungi: three ASVs identified as Fusarium oxysporum, Gibellulopsis piscis, and Mortierella minutissima). We found 14 ASVs as hub taxa [eight bacterial ASVs (BASV) in the root, and four bacterial and two fungal ASVs in the rhizosphere soil], and 10 BASV connected the root and rhizosphere soil microbiota to form an extended microbial communication in hemp. The only hub taxa detected in both the root and rhizosphere soil microbiota was ASV37 (Caulifigura coniformis), a bacterial taxon. The core microbiota and Network hub taxa can be studied further for biocontrol activities and functional investigations in the formulation of hemp bioinoculants. This study documented the microbial diversity and community structure of hemp grown in six fields, which could contribute toward the development of bioinoculants for hemp that could be used in organic farming.

Mycorrhizal-based inoculants in the root microbiome enhanced phytocannabinoid production in medical Cannabis cultivars

“…Bacterial 16S rDNA and fungal ITS regions were ampli ed by PCR according to previously published methods [13,14]. The PCR reaction was performed in a 25 µL reaction volume according to our previous study [7,14]. We used negative PCR controls without DNA.…”

“…In the root, EEA cultivar had the most co-occurrences (456 nodes and 2023 edges), while THE cultivar had the most co-occurrences in the soil (959 nodes and 10,278 edges). We investigated at the interkingdom network in the root and rhizosphere soil for each cultivar, then analyzed the meta-co-occurrence network interconnecting root and rhizosphere soil microbiome to nd hub taxa as de ned by Ahmed et al ( 2021) [14]. This involved creating a module made up of a network of each hub taxon and its associated ASVs, with modular hub taxa being ASV-centered within a module.…”

“…and it is in the Ferticann inoculum composition. Streptomyces lincolnensi was identi ed as a root indicator species in our recent studies of eld-grown hemp microbiome (Ahmed et al, 2021). Streptomyces sp.…”

“…In addition to bene cial microbes, we also found F. concentricum, F. oxysporium and F. solani as core microbiome. Although Fusarium is known for its negative impacts on Cannabis plants [48], its presence as a core microbiome in bulk soil of eld-grown hemp [14] supports its widespread occurrence, as well as studying the interactions of host-dependent pathogens to better understand the soil health of Cannabis. It has been reported that Fusarium sp.…”

“…Lacipirellula limnantheis, and Gemmata sp.) and three fungal (Fusarium oxysporum, Gibellulopsis piscis, and Fusarium equiseti) core microbiome [14].…”