The microbiome of cereal plants: The current state of knowledge and the potential for future applications

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TL;DR

This review synthesizes 302 microbiome studies (2013–2021) on the four major cereal crops—wheat, maize, rice, and barley—finding that belowground compartments and bacterial communities dominate the research landscape, while fungi, archaea, and aboveground tissues remain understudied. Key commonalities across cereals include shared prevalent bacterial phyla (Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, Acidobacteria, Chloroflexi) and the frequent identification of beneficial genera such as Pseudomonas and Bacillus with plant growth-promoting and biocontrol potential. The authors highlight the potential of harnessing cereal microbiomes to reduce agrochemical use and improve stress tolerance, but call for more holistic, functional, and multi-kingdom approaches to translate knowledge into agricultural applications.

Full summary

4,504 CHARS

**Background:** The plant microbiome holds promise for improving agricultural sustainability, analogous to the Green Revolution. Cereals—wheat, maize, rice, and barley—account for >50% of global daily caloric intake and are cultivated on ~622 million ha. Harnessing their microbiomes could enhance yield, stress tolerance, and reduce reliance on agrochemicals. This review summarizes the current knowledge base from high-throughput sequencing studies of cereal microbiomes.

**Methods:** An extensive literature search was conducted in PubMed and Google Scholar from 02 February 2021 to 13 July 2021. Keywords for each crop (e.g., 'wheat', 'Triticum', 'maize', 'Zea', 'rice', 'Oryza', 'barley', 'Hordeum', 'cereals') were combined with 'microbiome' or 'microbiota'. Additional articles were identified via cited references. Studies not based on high-throughput sequencing and reviews were excluded. A total of 302 articles published between 2013 and 2021 were selected. A table (Supplementary Table 1) was compiled cataloguing microorganisms, plant compartments, and general topics. Percentages were calculated by dividing the number of entries for a topic by the total number of entries (not total publications), as many studies covered multiple topics. A meta-analysis of alpha diversity (Chao1 index or ASV richness) was performed on data extracted from 160 manuscripts.

**Key Results:** The distribution of studies roughly matched cultivation area: wheat (32.4% of entries), maize (31.8%), rice (28.6%), and barley (7.2%). Across all crops, belowground compartments dominated: soil (23.7–26.9%), rhizosphere (31.4–43.8%), and roots (18.1–24.1%). Aboveground compartments were addressed in 11.3–22.4% of studies, with seeds specifically in 6.5–16.2%. Bacteria were the focus in 64.9–74.1% of studies, fungi in 18.7–30.1%, and archaea in 0–8.1%. Prevalent bacterial phyla across all four cereals included Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, Acidobacteria, and Chloroflexi. Common beneficial genera included Pantoea, Pseudomonas, Rhizobium, Sphingomonas, and Stenotrophomonas. The most commonly addressed research topic was comparative assessments (31.0–40.0% of entries per crop), followed by agronomic management (10.0–15.2%) and fertilizers (4.9–16.8%). Fertilizer studies were most prominent in maize (16.8%). Soil contamination studies were most common in rice (9.1%). Abiotic stress was a minor focus (average 4.1%). The meta-analysis found no significant difference in microbial diversity between the four plant types in any compartment, though soil compartments had substantially higher diversity than endosphere samples. Fungal communities were dominated by Ascomycota and Basidiomycota. Archaea were most studied in rice paddies due to methanogens (Euryarchaeota, Crenarchaeota), while Nitrososphaerota dominated in wheat. Key specific findings included: (1) plant developmental stage had a stronger impact on bacterial than fungal communities in wheat; (2) benzoxazinoids in maize influenced herbivore defence across generations via microbiome changes; (3) the seed-endophytic bacterium Sphingomonas melonis conferred resistance against Burkholderia plantarii in rice by producing anthranilic acid; (4) barley plants grown in field soil showed higher resistance to Blumeria graminis than those in potting soil, attributed to higher microbial diversity.

**Clinical Implications:** This is not a clinical study. The review has agricultural and public health implications: cereal crops provide staple food for over half the world's population, and pre-harvest losses due to biotic/abiotic factors can reach 35%, with another 20% lost during storage. Harnessing the microbiome could reduce pesticide use by half (aligned with the EU Farm to Fork Strategy), reduce overfertilization, and improve crop resilience. Identified biocontrol strains include Pseudomonas piscium and Pantoea agglomerans against Fusarium head blight in wheat, Sphingomonas melonis for rice seedling blight, and Enterobacter cloacae for maize stalk and ear rot. Nitrogen-use efficiency improvements linked to the NRT1.1B transporter in indica rice varieties offer a pathway to reduce fertilizer inputs. The review emphasizes that most research is descriptive (amplicon-based) and calls for functional studies combining metagenomics/metatranscriptomics with cultivation-based approaches, as well as greater attention to understudied kingdoms (archaea, protists, viruses) and aboveground compartments.