Rare Biosphere Reveals a Decoupling Between Microbial Abundance and Intrinsic Physiological Potential in Shanxi Aged Vinegar Fermentation

Abstract

The discrepancy between in situ microbial abundance and actual metabolic performance represents a critical challenge for interpreting microbial function from meta-omic data. Here, we integrated metagenomic and metatranscriptomic sequencing to investigate this decoupling between microbial abundance and cultivation-based physiological potential in Shanxi aged vinegar (SAV) solid-state fermentation. Lactobacillus acetotolerans dominated the community at both the genomic (40.89%) and transcriptomic (55.36%) levels, whereas Pediococcus acidilactici accounted for only 0.11%—a canonical rare-biosphere member. Source tracking via Sankey analysis showed that genes involved in acetate production were primarily attributed to Acetobacter pasteurianus, whereas genes involved in lactate production were predominantly associated with Lactobacillus spp. However, L. acetotolerans exhibited limited acid tolerance and lactic acid production, whereas the low-abundance P. acidilactici AAF1-5 displayed robust stress tolerance and superior lactic acid production under fermentation-relevant conditions—a striking contrast between microbial abundance and physiological performance. Metabolic interaction network analysis predicted that P. acidilactici may be co-inhibited by L. acetotolerans (Ixy = −2.737, resource competition) and A. pasteurianus (Ixy = −1.887, acid stress). To test whether ecological constraints, rather than intrinsic metabolic capacity, underlie this low abundance, we heterologously expressed the heat shock co-chaperone gene grpE from A. pasteurianus in P. acidilactici AAF1-5 as an experimental tool. The recombinant strain P. acidilactici-grpE exhibited significantly enhanced viability under acetic acid stress and, in simulated SAV fermentation, lactic acid content increased by 23.63% compared with the wild-type control. These results demonstrate that meta-omic abundance does not necessarily predict physiological performance and that low abundance may reflect ecological constraints rather than intrinsic functional deficiency. Our study provides an ecological framework for linking microbial abundance with physiological function beyond sequence-based abundance inference in complex fermentation microbiomes.