The dynamics of indigenous epiphytic bacterial and fungal communities of barley grains through the commercial malting process in Western Canada

Abstract

Microbial activity is present at every step of the malting process. It is, therefore, critical to manage the grain-associated microbial communities for the production of high-quality malts. This study characterized barley and malt epiphytic microbiota by metabarcoding the internal transcribed spacer (ITS) 2 region and the 16S rRNA gene V1-V4 metabarcodes, respectively. We elucidated the changes in the diversity and the compositional and functional changes of the grain-associated microbiota and inferred the impact of such changes on malting efficiency and premature yeast flocculation (PYF) of the commercial malt end product. Through the malting process, the fungal diversity decreased while bacterial community diversity increased. Lactic acid bacteria (LAB) and some mycotoxin-producing fungi (e.g. Fusarium spp.) were found to be significantly enriched in malts. Most potential fungal pathogens, however, did not change in abundance through the malting process. Fungi (e.g. Aureobasidium, Candida) and bacteria (e.g. LAB, Arthrobacter, Brachybacterium) with the potential to generate organic acids or exhibit high hydrolytic enzymatic activity for degrading the endosperm cell walls and storage proteins were detected in greater abundance in kilned malt, suggesting their contribution to malting efficiency. Bacterial and fungal operational taxonomic units (OTUs) associated with PYF-positive malt were mainly identified as Aureobasidium, Candida, and Leuconostoc, while Pleosporaceae, Steptococcus, and Leucobacter were associated with PYF-negative malt. The ecological networks of the field and steeped barley samples were found to be larger and denser, while that of the malt microbiome was smaller and less connected. A decrease in the proportion of negative interactions through the malting process suggested that malting destabilized the microbial networks. In summary, this study profiled the microbiota of commercial malting barley and malt samples in western Canada; the findings expanded our knowledge in the microbiology of malting while providing potential insights regarding the management of microbial-associated problems, such as PYF, in commercial malting.

Keywords: Barley grain; Commercial malting; Microbiome; Mycotoxin-producing fungi; Premature yeast flocculation (PYF).

Graphical abstract

Fig. 1

Diversity of the fungal and bacterial communities associated with the field barley grains, steeped barley grains, and kilned malts at the OTU level. Alpha-diversity indices of (A & C) fungi and (B & D) bacteria at the three malting stages (with malt samples separated depending on the kilning batch). Beta-diversity analysis using non-metric multidimensional scaling (NMDS) ordination plots based on the Bray-Curtis distances of the (E) fungi and (F) bacteria communities, calculated for hellinger transformed OTU abundance matrices. Significant differences in relative abundance between barley and malt are denoted by: ***p ≤ 0.001; ** 0.001 < p ≤ 0.01; * 0.01 < p ≤ 0.05.

Fig. 2

Changes in the abundance of (A) fungal genera, (B) fungal genera containing mycotoxin-producing species groups, (C) bacterial phyla, and (D) bacterial genera, through the malting process. (E) The phylogenetic tree of the 38 Fusarium ITS OTUs recovered through the malting process.

Fig. 3

(A) Enrichment of lactic acid bacteria through the malting process. (B) Fungal and bacterial OTUs associated with PYF-positive (PYF+ve) and PYF-negative (PYF-ve) samples. The PYF value in Fig. 3B was scaled to zero mean and unit variance.

Fig. 4

A heatmap showing the metabolic pathways that were potentially enriched or depleted through the malting process.

Fig. 5

Co-occurrence networks of fungal and bacterial OTUs in (A) field barley grains, (B) steeped barley grains, and (C) kilned malts. Fungal and bacterial OTU nodes are shown in blue and pink, respectively. Correlations are depicted by the green (positive correlations) or purple (negative correlations) linkages. Nodes are proportionally sized depending on their degree. Top figures display the whole ecological network, while bottom figures show the associations between fermentation bacteria and potential plant pathogens. Barley and steeped barley networks are larger, more connected, and have a higher proportion of negative interactions than those of kilned malts. The malt community has a higher proportion of bacteria with fermentation capacities that are positively correlated. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)