PubMed · 14341813
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H A WEIJERS, J H VAN DE KAMER. 1965-08-07. [FERMENTATION DIARRHEA].. https://pubmed.ncbi.nlm.nih.gov/14341813/
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Investigation of carbohydrate metabolism in lactic acid bacteria is essential for the rational selection of strains for fermentation processes, particularly in emerging applications involving non-conventional substrates or building of synthetic microbial consortia. However, establishing robust genotype-phenotype relationships remains challenging, as gene presence alone often fails to explain observed metabolic traits without considering the genomic context and regulatory architecture. In the present study, we combined hybrid genome assembly (Illumina and Oxford Nanopore) with high-throughput phenotype profiling (Biolog GENIII and PM2A) to investigate carbohydrate utilization in five Lacticaseibacillus strains. Phenotypic assays revealed clear intra- and inter-specific variability in substrate utilization. We therefore investigated whether such differences could be attributed to the organization and regulatory context of carbohydrate-associated loci, rather than to gene presence alone. Functional annotation based on COG and CAZyme databases revealed candidate genomic regions potentially involved in carbohydrate metabolism. Comparative analysis between predicted and experimentally observed substrate usage highlighted specific loci associated with carbohydrate utilization profile. The trehalose (tre) operon was conserved across all strains, while at least two distinct cellobiose-associated loci were detected in each genome. Despite the presence of these loci, L. paracasei strains were unable to metabolize cellobiose, a phenotype likely linked to the presence of a downstream TetR-type transcriptional repressor within the cellobiose (cel) operon. Additionally, a genomic region uniquely found in L. rhamnosus strains was associated with gentiobiose utilization, consistent with phenotypic observations. Overall, these findings highlight the importance of integrating phenotypic validation with complete genome context to support the identification of candidate structural and regulatory determinants of carbohydrate utilization in lactic acid bacteria. KEY POINTS: • Phenotype microarrays reveal metabolic traits of interest in isolated strains. • Regulatory context is key to understanding carbohydrate metabolism differences. • Basis of subspecies-dependent cellobiose metabolism in L. paracasei is provided.
Here we report the draft genome sequence of Naganishia friedmannii (formerly Cryptococcus friedmannii) isolate, a Basidiomycota yeast commonly found in some of the most extreme environments of the Earth's cryosphere. We isolated N. friedmannii strain Llullensis from soils at 6000 m above sea level on Volcán Llullaillaco, Argentina. The genome was 22.2 Mb with 6251 identified protein coding genes. Proteins known to be associated with thermal, osmotic, and radiation stress were identified in the genome. Comparative analysis with seven other Naganishia genomes revealed unique features underlying its polyextremophilic lifestyle. Naganishia friedmannii showed an expansion of genes involved in breaking down plant-derived carbohydrates, supporting the hypothesis that it survives at high elevations by metabolizing wind-deposited organic matter. Surprisingly, many genes involved in cell-cycle checkpoints and DNA repair were missing, as in several other Naganishia species. This extensive loss may be adaptive in extreme environments prone to abiotic stress, where a high mutation rate could generate advantageous traits, and reduced cell-cycle control may allow for faster reproduction that would be advantageous for rapid growth during brief periods of soil wetting following rare snow events.
Previous studies have led to contrasting results about the role of overwintering leaves as storage sites, which is related to leaf longevity and life-form. The aim of this study was to evaluate the functional role of the leaves of four species of Mediterranean sub-shrubs, with different leaf phenology, as sources of nitrogen (N) and non-structural carbohydrates (NSC) for shoot growth. The seasonal dynamics of the concentrations and pools of N and NSC were assessed monthly in the leaves and woody organs of each species. Overwintering and spring leaves served as N and NSC sources for shoot growth in the evergreen species analyzed, providing up to 73 % and 324 % of the N demand for spring and autumn growth, respectively. Excess autumn N was stored in woody structures which contributed to the N and NSC requirements of spring growth. In the winter deciduous species, woody organs were the main N source for spring growth, while current photosynthesis from immature brachyblasts seemed to be the main carbon (C) source. Due to their short lifespan, overwintering and spring leaves did not show several translocation processes throughout their life time, their contribution to new growth being made during senescence. The successive exchange of leaf cohorts displayed by Mediterranean sub-shrubs might serve as a mechanism to recycle N and C between consecutive cohorts as plants perform the pheno-morphological changes needed to adapt their morphology to the seasonality of their environment.