BSR LAB and the brewing environment
Niche adaptation and horizontal gene transfer
Distinction between differently adapted LAB isolates lies not only with the analysis of the LAB core genomes, but also in the investigation of chromosomal sequences that appear to have originated in another species and mobile genetic elements (MGEs) such as plasmids (Broadbent et al., 2012). The latter two genetic features are frequently acquired through horizontal gene transfer (HGT) between isolates of the same or different species. By comparing recently divergent as well as ecologically distinct genomes, it is revealed that HGT is important for the transfer of sequences or clusters of sequences, and drives the existence of diversification (Heuer and Smalla, 2007; Wiedenbeck and Cohan 2011). In fact, HGT events are promoted by environmental stress, resulting in faster adaptation or ‘short-term' evolution in challenging environments (Dziewit and Bartosik, 2014).
For LAB, HGT events mediated by plasmids are important to a variety of industries (de Angelis and Gobetti, 2011; Cai et al., 2009). In the brewing industry, conventional genetic markers of beer spoilage such as the exopolysaccharide gene gtf, and the hop tolerance genes hitA, horA, and horC are all plasmid-encoded and exhibit a very high degree of sequence identity in many different species (Suzuki, 2011; Walling et al., 2005). The existence of these markers suggests not only the occurrence and support of HGT in and by the brewery, but also the importance of investigating other plasmid-harboured genes that demarcate BSR from non-BSR LAB.
Given that the ecological diversity among LAB appears to be driven in general by genome reduction mechanisms, the acquisition of niche-specific genes through the transfer of plasmids is an important area of investigation (Schroeter and Klaenham- mer, 2009). Indeed, recent omics-based studies support the notion that plasmids are important for conferring beer spoilage ability. New genomic data for several L. brevis isolates has revealed that an increased number of plasmids may correlate with the ability of isolates to withstand increasingly harsh and specific environments. For example, L. brevis KB290 originally isolated from a traditional Japanese fermented vegetable and also able to grow in simulated gastric and intestinal juices, has nine plasmids ranging in size from 5.8 to 42 kb (Fukao et al., 2013). Similarly, the rapid beer-spoiling isolate L. brevis BSO 464 has eight plasmids ranging from 2.3 to 85 kb (Bergsveinson et al., 2015a). These two isolates are incapable of growth in the other isolate's niche-environment ( J. Bergsveinson, unpublished), indicating that each possesses specific genes that do not confer immediate cross-resistance to another stressful environment; as such, these isolates have niche-specific tolerance genes. In contrast, the type strain L. brevis ATCC 367T only harbours two plasmids (13 and 35 Kb) (Makarova et al., 2006) and is unable to spoil beer and cannot grow in gastric juices ( J. Bergsveinson, unpublished; Fukao et al., 2013). This further suggests that increased plasmidcoding capacity likely supports the ability of L. brevis strains to infiltrate diverse environments. This idea is supported by a recent study showing that the sequential loss of plasmids from L. brevis BSO 464 results in loss of its original beer spoilage phenotype, indicating that beer spoilage is mediated by specific plasmid-encoded functions (Bergsveinson et al., 2015a). Similarly, transcriptomic analysis performed on BSR LAB L. brevis BSO 464 (Lb464) (Bergsveinson et al., 2016b) and P. claussenii ATCC BAA-344T (Pc344) (Pittet et al. 2013) reveals that several significant plasmid-based transcripts were active across their respective eight plasmids when in the beer environment, notably on the plasmids that already harbour hop tolerance genes (horC for Lb464 and horA for Pc344) (Bergsveinson et al., 2015a, 2016b; Pittet et al., 2010, 2013). Collectively, these results strongly suggest that specific plasmids encode previously undescribed beer spoilage-related functions and that detailed investigation of plasmid genes in relation to growth in niche environments, beer, brewery, or otherwise, will prove useful.