Physiological and multi-omic insights into the adaptation mechanisms of Planococcus halotolerans SCU63T to high-salinity and low-temperature co-stress.
The strain Planococcus halotolerans SCU63T can survive under extreme conditions of 15% NaCl and 0 °C and provides a promising microbial resource for the remediation of saline soils in winter and high-salt as well as low-temperature industrial wastewater.
Abstract
High-salinity and low-temperature co-stress often impairs microbial function and disrupts their ecological balance, and thus understanding the adaptive mechanisms of psychrotolerant and halotolerant microorganisms is essential for their application in environmental remediation. The strain Planococcus halotolerans SCU63T can survive under extreme conditions of 15% NaCl and 0 °C. Physiological analyses revealed that, under co-stress, cells developed a thicker capsule, accumulated more intracellular sodium (increased from 2.25 to 3.41 g/kg), and exhibited significantly elevated membrane permeability. Genome annotation identified numerous co-stress-responsive genes, including but not limited to cspA, desA, betA/B, opuA/D, proX, nhaC, mnhA-G, trkA, and trkH. Transcriptomic data further demonstrated that these genes regulate ABC transporters, branched-chain amino acid and osmoprotectant metabolism, membrane transport, and cellular homeostasis. Metabolomic profiling confirmed that, under co‑stress, the strain not only accumulated proline derivatives and upregulated glycosylated products and certain alkaloids, but also underwent significant changes in molecules associated with membrane lipid remodeling and fatty acid derivatives. Collectively, these findings advance our understanding of microbial tolerance to concurrent stressors and provide a promising microbial resource for the remediation of saline soils in winter and high-salt as well as low-temperature industrial wastewater.
Under severe stress, GO and KEGG enrichment consistently revealed the reinforcement of central carbon and energy metabolism, peroxisome-associated fatty acid turnover, oxidoreductase/redox activities, and translation and nucleotide metabolic pathways.
Dingkang Wang, Li Wang, Yue Xiao et al.· Journal of Proteome Research· 0 citations
A primary factor preventing the spread of the invasive plant Praxelis clematidea to higher latitudes and altitudes is the low-temperature stress induced by global climate change. The present study investigated the impact of low-temperature stress on the rhizosphere soil micro-ecosystem of P. clematidea, with the aim of examining its adaptive micro-ecological mechanisms via a comprehensive multi-omics approach. The rhizosphere soils of plants were compared under low-temperature (LT, 5 °C) or normal-temperature (HT, 25 °C) treatments. Using soil physicochemical analysis, enzyme activity assay, metagenomics, and non-targeted metabolomics, we observed that LT stress did not significantly alter microbial alpha diversity but strongly shifted the community structure. This change enriched cold-tolerant bacterial taxa, including Nocardiopsis, Sphingobium and Azoarcus. The LT stress was associated with altered carbon and nitrogen cycling, as indicated by increased soil urease activity but decreased alkaline phosphatase and catalase activities. The nitrate-N and ammonium-N levels increased, but total nitrogen, total organic carbon, and organic matter were reduced. Additionally, metagenomic study revealed overexpression of major microbial carbon metabolism genes (e.g., TCA cycle and glycolysis) and downregulation of nitrogen assimilation genes (e.g., glnA and NasA). Furthermore, metabolomics indicated a rise in carbohydrates and vitamins, along with a notable accumulation of stress-resistant secondary metabolites such as phenolic acids, flavonoids, and terpenes in the rhizosphere soils under LT stress. Correlation analysis indicated strong positive associations between the enriched cold-tolerant genera and these stress-resistant metabolites (e.g., costunolide and choline sulfate). Functional enrichment analysis suggested a metabolic reprogramming signature coupled with low-temperature treatment. Finally, this integrated multi-omics study reveals that P. clematidea is associated with an altered rhizosphere microbiome, differential functional gene abundance, and reorganized metabolic networks under low-temperature conditions. These findings offer a vital micro-ecological elucidation for P. clematidea effective colonization and propagation in novel, colder habitats.
Xiaowen Liu, Wen-Zhi Cheng, Chunhong Li et al.· Frontiers in Microbiology· 0 citations
The proteomic basis of thermal adaptation in P. plecoglossicida is revealed and molecular targets for engineering thermotolerant strains to optimize industrial 2-KGA fermentation are provided.
Daming Wang, Yu-Ming Jing, Qing-hong Wang et al.· 3 Biotech· 0 citations
ABSTRACT Deep-sea extreme environments harbor microorganisms with unique adaptive mechanisms. Fungi play significant ecological roles in these ecosystems, yet the regulatory pathways governing their adaptation to extreme conditions remain poorly understood. Here, we investigated the hadal-derived fungus Aspergillus sydowii DM1 as a model strain. Using CRISPR–Cas9 technology, we constructed a sho1 gene knockout mutant to examine its phenotypic and molecular responses to osmotic stress, oxidative stress, and high hydrostatic pressure (HHP). Our results showed that Sho1 contributed to cell wall integrity, was associated with changes in secondary metabolite profiles, and modulated the high-osmolarity glycerol (HOG) responses. Under osmotic stress, deletion of sho1 enhanced colony growth and conidiation under moderate-to-high salinity, and was accompanied by altered asexual developmental progression and HOG-associated gene expression. Under oxidative stress, loss of Sho1 led to increased reactive oxygen species (ROS) accumulation, and reduced spore viability. Under HHP, deletion of sho1 impaired early pressure-responsive signaling, increased ROS accumulation, and reduced spore germination during recovery. Comparative analysis of A. sydowii strains from different ecological niches further suggested that the deep-sea strain may possess a more coordinated pressure-response pattern associated with the Sho1–Hog1 pathway. Together, these findings indicate that Sho1 functions as an important upstream coordinator linking environmental sensing with osmotic adaptation, oxidative homeostasis, developmental regulation, and pressure-associated recovery in a hadal filamentous fungus, offering new insights into fungal signal transduction and adaptive evolution in extreme environments. IMPORTANCE Deep-sea fungi live under extreme conditions, yet the signaling mechanisms that help them survive remain poorly understood. Using a hadal isolate of Aspergillus sydowii, we show that the membrane sensor Sho1 contributes to fungal responses to osmotic stress, oxidative stress, and high hydrostatic pressure. Loss of sho1 altered growth, development, redox balance, and recovery after pressure exposure, indicating that this upstream signaling component coordinates multiple adaptive traits in a deep-sea fungus. These findings extend current knowledge of fungal stress signaling beyond model organisms and suggest that conserved signaling modules can be repurposed for life in the deep ocean. This study provides a useful genetic framework for understanding how fungi adapt to extreme marine environments. Deep-sea fungi live under extreme conditions, yet the signaling mechanisms that help them survive remain poorly understood. Using a hadal isolate of Aspergillus sydowii, we show that the membrane sensor Sho1 contributes to fungal responses to osmotic stress, oxidative stress, and high hydrostatic pressure. Loss of sho1 altered growth, development, redox balance, and recovery after pressure exposure, indicating that this upstream signaling component coordinates multiple adaptive traits in a deep-sea fungus. These findings extend current knowledge of fungal stress signaling beyond model organisms and suggest that conserved signaling modules can be repurposed for life in the deep ocean. This study provides a useful genetic framework for understanding how fungi adapt to extreme marine environments.
Hongfu Lai, Guangzhao Hu, Yukun Cui et al.· Applied and Environmental Mi...· 0 citations
ABSTRACT Human ureaplasmas are minimal-genome bacteria and pathobionts of the urogenital tract. They must adapt to fluctuating pH conditions despite the absence of canonical transcriptional regulatory systems. However, the mechanisms underlying these responses remain unclear. This study aimed to construct a system-level model of pH adaptation in this minimal pathogen. We used an integrated multi-omics platform combining proteomics, metabolomics, and RNA modification profiling to construct a system-level model of pH adaptation. The results revealed a bifurcated strategy governed by the differential activation of preexisting, co-regulated functional modules. Under neutral pH conditions (pH 7), Ureaplasma parvum activated energy metabolism and upregulated ATP synthesis while forming a stress-counteracting proteostasis pathway. This may suggest a biological energy state under high stress conditions. Conversely, under acidic stress (pH 5), it activated biosynthesis/translation, showing significant upregulation of ribosomal proteins and accumulation of translation precursors and the polyamine spermidine. This may represent a state of expanded translational capacity. This adaptive switch is accompanied by dynamic reorganization of the epitranscriptome, highlighting the importance of post-transcriptional regulation. This study suggests mechanisms by which minimal organisms achieve adaptive plasticity through sophisticated post-transcriptional and metabolic control, providing a new framework for understanding Ureaplasma physiology and the biology of genome-reduced organisms. IMPORTANCE Minimal bacteria challenge canonical views of cellular regulation. In organisms with radically reduced genomes and sparse transcription factors, how adaptive plasticity is achieved remains a core question. Our study proposes a model in which a simple physicochemical cue—extracellular pH—selects among prewired cellular programs, while post-transcriptional and epitranscriptomic layers fine-tune execution. The findings of this study suggest a multi-omics scheme for how organisms adapt to environmental changes and ensure survival without inducing new circuits or complex transcriptional regulation. Conceptually, it proposes regulation via RNA modifications in processes, such as metabolism, proteostasis, and translation. This framework may be generalizable to other genome-reduced microorganisms. Beyond microbiology, it provides design principles for synthetic biology and offers a mechanistic interpretation of phenotypic tolerance to stress factors. It may encourage the use of pH-linked epitranscriptome signals as measurable indicators of cellular state. Minimal bacteria challenge canonical views of cellular regulation. In organisms with radically reduced genomes and sparse transcription factors, how adaptive plasticity is achieved remains a core question. Our study proposes a model in which a simple physicochemical cue—extracellular pH—selects among prewired cellular programs, while post-transcriptional and epitranscriptomic layers fine-tune execution. The findings of this study suggest a multi-omics scheme for how organisms adapt to environmental changes and ensure survival without inducing new circuits or complex transcriptional regulation. Conceptually, it proposes regulation via RNA modifications in processes, such as metabolism, proteostasis, and translation. This framework may be generalizable to other genome-reduced microorganisms. Beyond microbiology, it provides design principles for synthetic biology and offers a mechanistic interpretation of phenotypic tolerance to stress factors. It may encourage the use of pH-linked epitranscriptome signals as measurable indicators of cellular state.
H. Hase, Y. Nakura, Yuki Shimada et al.· Microbiology spectrum· 0 citations
Owing to natural or anthropogenic factors, dissolved oxygen (DO) levels in aquatic environments frequently experience drastic fluctuations. Because fish are directly exposed to aquatic environments, DO fluctuations can disrupt physiological homeostasis, thereby inhibiting growth, reducing disease resistance, and potentially leading to mortality. To alleviate economic losses caused by hypoxia in Larimichthys crocea farming, we bred a novel strain with enhanced hypoxia tolerance. To elucidate the mechanisms underlying this enhanced tolerance, we conducted physiological, transcriptomic, and metabolomic analyses of both the hypoxia-tolerant (T) and control (N) groups under hypoxic stress to identify differentially expressed genes and metabolites. GO and KEGG enrichment analyses revealed that the T group adopted a more effective strategy when confronted with low oxygen levels, primarily by promoting glycolysis and the TCA cycle and enhancing the biosynthesis of carbohydrates, amino acids, terpenoids, and N-glycans. By contrast, the N group exhibited a relatively weaker glycolytic flux under hypoxic stress, with significant suppression of the tricarboxylic acid cycle and biosynthesis of energy-related substances and a greater reliance on oxygen-dependent lipid metabolism pathways. Overall, multi-omics analysis revealed hypoxia-induced alterations in metabolites and genes, providing crucial insights into the hypoxia tolerance mechanism of the L. crocea and offering evidence supporting the improved hypoxia tolerance of the selected population.
Yibo Zhang, Jie Ding, Xuelei Wang et al.· Marine Pollution Bulletin· 0 citations