Compartment Niche Shapes the Assembly and Network of Cannabis sativa-Associated Microbiome

Abstract

Interactions between plants and microbes may promote the growth of plants and regulate the production of secondary metabolites. Hemp (Cannabis sativa) is an annual herb and an important commercial crop. However, the assembly and network of hemp-associated microbiomes inhabiting in soil and plant compartments have not been comprehensively understood. This work investigated the assembly and network of bacterial and fungal communities living in soils (bulk and rhizosphere) and plant compartments (root, stem, leaf, and flower) of four hemp ecotypes cultivated in the same habitat. Microbiome assembly was predominantly shaped by compartment niche. Microbial alpha diversity was the highest in soil, continually decreased from root to flower. Core bacterial genera Pseudomonas, Bacillus, Rhizobium, Planococcus, and Sphingomonas were mostly enriched in aerial endosphere niches; Clitopilus, Plectosphaerella, and Mortierella were enriched in belowground endosphere. Microbial network complexity and connectivity decreased from root to flower. According to source tracking analysis, hemp microbiota primarily originated from soil and were subsequently filtered in different plant compartments. This work provides details on hemp-associated microbiome along the soil–plant continuum and a comprehensive understanding of the origin and transmission mode of endophytes in hemp.

Correlations Between the Metabolome and the Endophytic Fungal Metagenome Suggests Importance of Various Metabolite Classes in Community Assembly in Horseradish (Armoracia rusticana, Brassicaceae) Roots

“…At genus resolution, plant samples showed a high abundance of genera that have been already described as endophytes: Exophiala (Yu et al, 2021), Monosporascus (Guo and Zou, 2020), Paraphoma (Kang et al, 2021), Plectospherella (Feng et al, 2021;Wei et al, 2021), Podospora (Penner and Sapir, 2021). Some of these genera were even identified in Brassicaceae plant endospheres, including Exophiala (Maciá-Vicente et al, 2016), Plectosphaerella (Plaszkó et al, 2020;Ważny et al, 2021), Setophoma (Szűcs et al, 2018;Poveda et al, 2020), or as a common pathogen: Thanatephorus (teleomorph of Rhizoctonia) (Dean et al, 2012).…”

Compartment and Plant Identity Shape Tree Mycobiome in a Subtropical Forest

“…For example, microbial communities are essential to maintaining soil homeostasis and to improving host productivity via the production of secondary metabolites ( 4 , 5 ), the suppression of pathogens ( 6 , 7 ), and the promotion of plant growth ( 8 ). However, different compartments provide various ecological niches, which are inhabited by highly distinct microbial communities ( 9 ), though the microbial diversity, community compositions, and assemblies among different compartment niches are still less documented. In order to improve our ability to predict the responses of ecosystem functions ( 10 ), it is crucial to seek a better understanding of the relationships between plants and microbes.…”

“…For example, Fusarium , Ilyonectria , Cladosporium and Aspergillus were observed to have a distinctive abundance in the rhizosphere and phyllosphere of Vaccinium macrocarpon ( 25 ). Fungal Clitopilus and Mortierella were significantly enriched in the soil and root endosphere samples of the Cannabis sativa plant species compared with those of the aerial parts ( 9 ), and Phyllosticta vaccinii and P. elongata were frequently isolated from the developing ovaries of cranberry ( 26 ). All of these studies indicate that niche differentiation can result in compositional and structural variations in microbial communities across different plant-related compartments.…”

Colonization and Interaction of Bacteria Associated With Chinese Chives Affected by Ecological Compartments and Growth Conditions

“…Therefore, it is speculated that Chinese chives contain endophytic bacteria or associate with rhizospheric microorganisms that can inhibit pathogens. In the microbial analysis of various ecological compartments of other plants, it can be found that ecological compartments have effects on microbial composition and microbial community function (Wei et al, 2021 ). However, the current studies on plant ecological compartments are mostly between underground compartments (especially in the rhizosphere and root surface), and the composition differences of soil microorganisms, rhizosphere microorganisms, and root endosphere microorganisms and the screening mechanism of roots are studied (Reinhold Hurek et al, 2015 ).…”