Unlocking the bacterial and fungal communities assemblages of sugarcane microbiome

Abstract

Plant microbiome and its manipulation herald a new era for plant biotechnology with the potential to benefit sustainable crop production. However, studies evaluating the diversity, structure and impact of the microbiota in economic important crops are still rare. Here we describe a comprehensive inventory of the structure and assemblage of the bacterial and fungal communities associated with sugarcane. Our analysis identified 23,811 bacterial OTUs and an unexpected 11,727 fungal OTUs inhabiting the endophytic and exophytic compartments of roots, shoots, and leaves. These communities originate primarily from native soil around plants and colonize plant organs in distinct patterns. The sample type is the primary driver of fungal community assemblage, and the organ compartment plays a major role in bacterial community assemblage. We identified core bacterial and fungal communities composed of less than 20% of the total microbial richness but accounting for over 90% of the total microbial relative abundance. The roots showed 89 core bacterial families, 19 of which accounted for 44% of the total relative abundance. Stalks are dominated by groups of yeasts that represent over 12% of total relative abundance. The core microbiome described here comprise groups whose biological role underlies important traits in plant growth and fermentative processes.

Figure 1. Main factors driving the microbiota composition of bacterial and fungal communities.

The principal coordinate analyses (PCoA) of pairwise Bray-Curtis distance matrixes of filtered OTU tables rarefied to 18,000 reads. PCoA analyses were performed independently in two groups of samples, “root, bulk soil and young shoot” (belowground) and “stalks and leaves” (aboveground) for the bacterial and fungi datasets. For each group, the same graph was differentially colored to emphasize the influence of compartment, sample type and stage of development in the community assemblage. Compartment is the major driving factor for bacterial community assemblage for all samples. Fungal community assemblage is primarily driven by the sample type and compartment in aboveground samples and by the stage of development in belowground samples.

Figure 2. Soil serves as the main reservoir for bacterial and fungal groups that colonize sugarcane plant organs.

(a) Number of shared OTUs among sample groups for bacteria (i) and fungi (ii). Samples were grouped according to their Bray-Curtis distance matrix similarity. Numbers in parenthesis indicate the total sum of OTUs in a given grouped sample. Numbers in overlapping regions indicate OTUs shared among grouped samples. (b) Taxon enrichment across sample types. Statistical significance was tested using Kruskal-Wallis, FDR-corrected P < 0.001 at the order level for bacterial (i) and fungal (ii) communities. Orders with an average relative abundance below 1% were grouped as “others”. Un.: Unkown; Exo.: Exo.; Endo.: Endo.

Figure 3. Heatmaps showing bacterial and fungal genera that significantly contribute to sample differentiation.

(a) A total of 49 bacterial genera were significantly responsible (P < 0.001) for the distinct enrichment and depletion patterns found at the order level (Fig. 2b(i)). Among them, 20 genera were assigned as unidentified (Un.). (b) In the fungal community, a set of 45 genera significantly contributed to the enrichment and depletion pattern (P < 0.001), 8 of which were assigned as unidentified (Un.). Heatmaps were colored on the basis of row z-scores calculated on relative abundance. Exo.: Exophytic; Endo.: Endophytic.

Figure 4. Relative abundance and richness of OTUs belonging to the core microbiome.

Blue and red bars indicate the total relative abundance of core and non-core OTUs, respectively. Core OTUs richness is expressed as a fraction (%) of total OTU counts. (a) Bacterial core community (b) Fungi core community. Although there is a huge OTU richness for each sample, only a small fraction of OTUs belongs to the core microbiome. Inversely, this small fraction comprises most of the total relative abundance. Exo.: Exophytic; Endo.: Endophytic.; Med.: Medium.

Figure 5. Sample types show a distinct pattern of core colonizers.

The heatmap shows a distribution pattern of core OTUs across sample types based on relative abundance (column z-score). Samples were hierarchically grouped (group-average linkage) based on the pairwise Bray-Curtis similarity of the core OTU table. OTUs were organized by family-level classification. (a) Bacterial core OTUs. Belowground samples have similar colonizer profiles. Aboveground samples from the same compartment have similar colonizer profiles independent of the plant organ. (b) Fungal core OTUs. Samples from the same plant organ have similar profiles. Bot.: Bottom; Med.: Medium; Up.: Upper; Exo.: Exophytic; Endo.: Endophytic.

Figure 6. Untapped diversity in fungal and bacterial communities.

Dots represent the relative abundance of core OTUs in a given sample type. Each assigned genus was searched in the literature for isolated members with growth-promoting traits (Supplementary Tables 5 and 6). The vast majority of core OTUs have no evidence of functional whole in association with plants. (a) Core bacterial OTUs. (b) Core fungal OTUs. Exo.: Exophytic; Endo.: Endophytic.