Mechanism of TonB-dependent transport system in Halomonas alkalicola CICC 11012s in response to alkaline stress

Identifying the Alkaline Tolerance-Related Genes Through Transcriptome Analysis of Halomonas alkalicola CICC 11012 s

Halomonas alkalicola CICC 11012 s is the strongest alkaliphile in the genus Halomonas. So far, studies have focused on the genome level and functional validation of a single gene, providing an overview and partial analysis of the adaptive mechanisms. As such, the comprehensive adaptations of alkaliphiles to extremely alkaline stress remain largely unclear. Therefore, in this study, the transcriptome profiling of H. alkalicola under neutral and alkaline conditions was compared to explore its global adaptation mechanisms towards pH homeostasis. In addition, the different up-regulated genes of this strain grown at pH 11.0 were compared with those grown at pH 7.0. The results revealed that the up-regulated genes were mainly distributed in six categories, including glycosyl transferase, fimbrial assembly protein, TonB-dependent transport system, C4-dicarboxylate TRAP transport system, transposase, and toxin-antitoxin system. This result indicated that H. alkalicola developed various adaptive strategies to survive under extremely alkaline pressure, from modifying their cell wall structure to enhancing their membrane transport activities and intracellular metabolism homeostasis. Furthermore, the function of the gene cluster tonB-exbB-exbB2-exbD under extreme alkaline stress was verified by the CRISPR-Cas9 gene-editing system, indicating that the TonB-dependent transport system significantly affected the growth of the strain under extreme alkaline stresses.

Transcriptomics with metabolomics reveals the mechanism of alkaline tolerance in Halomonas alkalicola CICC 11012s

The potential of alkaline-tolerant bacteria as cell factories for the production of functional molecules and bulk chemicals has been increasingly recognized owing to in-depth studies of their metabolic pathways and products combined with their tolerance to alkaline environments. To further explore the cell factory potential of alkaline-tolerant bacteria, it is necessary to systematically analyze and explore the genes and metabolites related to alkaline tolerance. Halomonas alkalicola CICC 11012s is currently the strongest alkaliphile of the genus Halomonas, which can grow at pH 12.5. This study aimed to elucidate the molecular mechanisms underlying the response of H. alkalicola CICC 11012s to alkaline stress, using transcriptomic and metabolomic analyses. The expression of 259 genes and 401 metabolites was significantly altered. Important metabolic pathways included nucleotide, amino acid, and carbohydrate metabolism, as well as membrane transport. Furthermore, an integrative pathway analysis revealed that two pathways, glycine, serine, and threonine metabolism and biotin metabolism, were significantly enriched under high-alkaline conditions (pH 11.0). These findings highlight that deletion of the gene cluster tonB-exbB-exbB2-exbD significantly affects the synthesis of L-aspartate, leading to a decrease in the alkaline tolerance of H. alkalicola.

Analysis of the Alkaline Resistance Mechanism of Halomonas alkalicola CICC 11012 s by Proteomics and Metabolomics

In recent years, as excellent industrial microorganisms, Halomonas has become a potential chassis cell of the next generation of industrial biotechnology because of its advantages of low complexity, antipollution ability, and rapid fermentation. Therefore, there is an urgent need to study the genome information, synthetic biology, multiomics, and other technologies of Halomonas, and it is also highly important to study its tolerance to extreme environments. Halomonas alkalicola CICC 11012 s is the most alkaliphilic bacterium in the genus Halomonas and is an excellent alkali-resistant bacterium that was independently isolated in our laboratory; this bacterium plays a certain role in industrial pollution control and the application of synthetic biology chassis cells. The H. alkalicola mutant was designed and constructed via CRISPR technology in the early stage of this experiment, which verified that the tonb gene plays an important role in the alkali resistance mechanism of this strain. Therefore, the molecular mechanism of the response of H. alkalicola CICC 11012 s to alkaline stress was explored through combined proteomic and metabolomic analysis. The experimental results revealed that the wild-type and mutant strains evolved multilevel adaptive strategies to regulate pH homeostasis in response to alkaline stress, including increasing their membrane transport activities and synthesizing carbohydrates and amino acids. In summary, the experimental results provide a deep understanding of the alkaline response mechanism of alkalophilic bacteria, thereby further promoting their application in different environments.

New insights into the typical nitrogen-containing heterocyclic compound-quinoline degradation and detoxification by microbial consortium: Integrated pathways, meta-transcriptomic analysis and toxicological evaluation

As the primary source of COD in industrial wastewater, quinoline has aroused increasing attention because of its potential teratogenic, carcinogenic, and mutagenic effects in the environment. The activated sludge isolate quinoline-degrading microbial consortium (QDMC) efficiently metabolizes quinoline. However, the molecular underpinnings of the degradation mechanism of quinoline by QDMC have not been elucidated. High-throughput sequencing revealed that the dominant genera included Diaphorobacter, Bacteroidia, Moheibacter and Comamonas. Furthermore, a positive strong correlation was observed between the key bacterial communities (Diaphorobact and Bacteroidia) and quinoline degradation. According to metatranscriptomics, genes associated with quorum sensing, ABC transporters, component systems, carbohydrate, aromatic compound degradation, energy metabolism and amino metabolism showed high expression, thus improving adaptability of microbial community to quinoline stress. In addition, the mechanism of QDMC in adapting and resisting to extreme environmental conditions in line with the corresponding internal functional properties and promoting biogegradation efficiency was illustrated. Based on the identified products, QDMC effectively mineralized quinoline into low-toxicity metabolites through three major metabolic pathways, including hydroxyquinoline, 1,2,3,4-H-quinoline, 5,6,7,8-tetrahydroquinoline and 1-oxoquinoline pathways. Finally, toxicological, genotoxicity and phytotoxicity studies supported the detoxification of quinoline by the QDMC. This study provided a promising approach for the stable, environmental-friendly and efficient bioremediation applications for quinoline-containing wastewater.

Halo-alkaliphilic microbes as an effective tool for heavy metal pollution abatement and resource recovery: challenges and future prospects

The current study presents an overview of heavy metals bioremediation from halo-alkaline conditions by using extremophilic microorganisms. Heavy metal remediation from the extreme environment with high pH and elevated salt concentration is a challenge as mesophilic microorganisms are unable to thrive under these polyextremophilic conditions. Thus, for effective bioremediation of extreme systems, specialized microbes (extremophiles) are projected as potential bioremediating agents, that not only thrive under such extreme conditions but are also capable of remediating heavy metals from these environments. The physiological versatility of extremophiles especially halophiles and alkaliphiles and their enzymes (extremozymes) could conveniently be harnessed to remediate and detoxify heavy metals from the high alkaline saline environment. Bibliometric analysis has shown that research in this direction has found pace in recent years and thus this review is a timely attempt to highlight the importance of halo-alkaliphiles for effective contaminant removal in extreme conditions. Also, this review systematically presents insights on adaptive measures utilized by extremophiles to cope with harsh environments and outlines the role of extremophilic microbes in industrial wastewater treatment and recovery of metals from waste with relevant examples. Further, the major challenges and way forward for the effective applicability of halo-alkaliphilic microbes in heavy metals bioremediation from extremophilic conditions are also highlighted.

Cadmium sulfide nanoparticle biomineralization and biofilm formation mediate cadmium resistance of the deep-sea bacterium Pseudoalteromonas sp. MT33b

Cadmium (Cd) is a common toxic heavy metal in the environment, and bacteria have evolved different strategies to deal with Cd toxicity. Here, a bacterium designated Pseudoalteromonas sp. MT33b possessing strong Cd resistance was isolated from the Mariana Trench sediments. Supplement of cysteine significantly increased bacterial Cd resistance and removal rate. Biofilm formation was demonstrated to play a positive role toward bacterial Cd resistance. Transcriptome analysis showed the supplement of cysteine effectively prevented Cd²⁺ from entering bacterial cells, promoted saccharide metabolism and thereby facilitating energy production, which consists well with bacterial growth trend analysed under the same conditions. Notably, the expressions of many biofilm formation related genes including flagellar assembly, signal transduction, bacterial secretion and TonB-dependent transfer system were significantly upregulated when facing Cd stress, indicating their important roles in determining bacterial biofilm formation and enhancing Cd resistance. Overall, this study indicates the formation of insoluble CdS precipitates and massive biofilm is the major strategy adopted by Pseudoalteromonas sp. MT33b to eliminate Cd stress. Our results provide a good model to investigate how heavy metals impact biofilm formation in the deep-sea ecosystems, which may facilitate a deeper understanding of microbial environmental adaptability and better utilization of these microbes for bioremediation purposes in the future.