Nutrient availability shapes the microbial community structure in sugarcane bagasse compost-derived consortia

Abstract

Microbial communities (MCs) create complex metabolic networks in natural habitats and respond to environmental changes by shifts in the community structure. Although members of MCs are often not amenable for cultivation in pure culture, it is possible to obtain a greater diversity of species in the laboratory setting when microorganisms are grown as mixed cultures. In order to mimic the environmental conditions, an appropriate growth medium must be applied. Here, we examined the hypothesis that a greater diversity of microorganisms can be sustained under nutrient-limited conditions. Using a 16 S rRNA amplicon metagenomic approach, we explored the structure of a compost-derived MC. During a five-week time course the MC grown in minimal medium with sugarcane bagasse (SCB) as a sole carbon source showed greater diversity and enrichment in lignocellulose-degrading microorganisms. In contrast, a MC grown in nutrient rich medium with addition of SCB had a lower microbial diversity and limited number of lignocellulolytic species. Our approach provides evidence that factors such as nutrient availability has a significant selective pressure on the biodiversity of microorganisms in MCs. Consequently, nutrient-limited medium may displace bacterial generalist species, leading to an enriched source for mining novel enzymes for biotechnology applications.

Figure 1

Number of colony forming units (CFUs) of compost-derived consortia grown in (a) minimal medium and (b) PCS. Supernatant from liquid cultures after incubation for one and two weeks was collected and spread as serial dilutions on solid agar plates supplemented with carboxymethyl cellulose (CMC). Subsequently, colonies were removed and plates were stained with Congo red. The proportion of isolates producing clearance zones − indicative to cellulolytic activity − is presented in the figure.

Figure 2

Relative abundance of bacterial (a) phyla and (b) classes for phylotypes identified in compost-derived consortia grown on minimal medium and PCS using 16 S rRNA sequencing. Number next to the medium abbreviation represents week when sample was collected. y-axis = relative abundance [%].

Figure 3. Diversity analysis of compost-derived consortia.

(a) Venn diagram presenting number of unique and shared OTUs for MM- and PCS-grown compost derived consortia. (b) Rarefaction curves showing the calculated rarefaction using phylogenetic diversity (PD) versus the number of reads sequenced per sample. Other diversity indices, such as chao1 and observed_species, were also tested showing similar results. (c) Box-whisker plot of the calculated Shannon’s diversity index. The results were grouped by the medium used for growth. The asterisk (*) denotes a significant difference (p ≤ 0.05, Student’s t-test) between MM- and PCS-grown cultures diversity indexes. (d) PCoA of weighted UniFrac distances. Consortia obtained from the same growth medium clustered together, as presented in the figure.