Characterization and genomic analysis of two novel psychrotolerant Acidithiobacillus ferrooxidans strains from polar and subpolar environments

Extremophiles and Extremophilic Behaviour-New Insights and Perspectives

Extremophiles, throughout evolutionary time, have evolved a plethora of unique strategies to overcome hardships associated with the environments they are found in. Modifying their genome, showing a bias towards certain amino acids, redesigning their proteins, and enhancing their membranes and other organelles with specialised chemical compounds are only some of those strategies. Scientists can utilise such attributes of theirs for a plethora of biotechnological and astrobiological applications. Moreover, the rigorous study of such microorganisms regarding their evolution and ecological niche can offer deep insight into science's most paramount inquiries such as how life originated on Earth and whether we are alone in the universe. The intensification of studies involving extremophiles in the future can prove to be highly beneficial for humanity, even potentially ameliorating modern problems such as those related to climate change while also expanding our knowledge about the complex biochemical reactions that ultimately resulted in life as we know it today.

Exploration of the advantages of targeted isolation of deep-sea microorganisms and genetically engineered strains

Oil, mineral processing and environmental restoration can be dangerous processes. Attempts are often made to apply microorganisms to reduce the risks, but the adaptability of terrestrial organisms is often weak. Although genetically engineered strains can improve their environmental adaptability through targeted modification, there are problems such as metabolite accumulation, poor plasmid stability and potential pathogenicity. Screening of extremophiles from the natural environment has become an inevitable choice. The special environment in the deep sea (high pressure, low temperature, low nutrition, high salinity) is a natural place for extremophiles to grow and survive, thus screening of extremophiles from the deep sea is conducive to the green and sustainable development of industry. In this paper, the application status and problems of genetically engineered strains are reviewed based on the microorganisms needed for extreme industry. This paper focuses on the application status and advantages of deep-sea microorganisms. It is found that their advantages are strong adaptability, stable gene, friendly environment, simple and convenient technology (compared with genetic engineering), which has a broad industry processes application prospect. This review broadens the scope of microbial applications.

Leveraging protein language model embeddings and logistic regression for efficient and accurate in-silico acidophilic proteins classification

The increasing demand for eco-friendly technologies in biotechnology necessitates effective and sustainable catalysts. Acidophilic proteins, functioning optimally in highly acidic environments, hold immense promise for various applications, including food production, biofuels, and bioremediation. However, limited knowledge about these proteins hinders their exploration. This study addresses this gap by employing in silico methods utilizing computational tools and machine learning. We propose a novel approach to predict acidophilic proteins using protein language models (PLMs), accelerating discovery without extensive lab work. Our investigation highlights the potential of PLMs in understanding and harnessing acidophilic proteins for scientific and industrial advancements. We introduce the ACE model, which combines a simple Logistic Regression model with embeddings derived from protein sequences processed by the ProtT5 PLM. This model achieves high performance on an independent test set, with accuracy (0.91), F1-score (0.93), and Matthew's correlation coefficient (0.76). To our knowledge, this is the first application of pre-trained PLM embeddings for acidophilic protein classification. The ACE model serves as a powerful tool for exploring protein acidophilicity, paving the way for future advancements in protein design and engineering.

Assessment of microbial communities from cold mine environments and subsequent enrichment, isolation and characterization of putative antimony- or copper-metabolizing microorganisms

Mining activities, even in arctic regions, create waste materials releasing metals and metalloids, which have an impact on the microorganisms inhabiting their surroundings. Some species can persist in these areas through tolerance to meta(loid)s via, e.g., metabolic transformations. Due to the interaction between microorganisms and meta(loid)s, interest in the investigation of microbial communities and their possible applications (like bioremediation or biomining) has increased. The main goal of the present study was to identify, isolate, and characterize microorganisms, from subarctic mine sites, tolerant to the metalloid antimony (Sb) and the metal copper (Cu). During both summer and winter, samples were collected from Finnish mine sites (site A and B, tailings, and site C, a water-treatment peatland) and environmental parameters were assessed. Microorganisms tolerant to Sb and Cu were successfully enriched under low temperatures (4°C), creating conditions that promoted the growth of aerobic and fermenting metal(loid) tolerating or anaerobic metal(loid) respiring organism. Microbial communities from the environment and Sb/Cu-enriched microorganisms were studied via 16S rRNA amplicon sequencing. Site C had the highest number of taxa and for all sites, an expected loss of biodiversity occurred when enriching the samples, with genera like Prauserella, Pseudomonas or Clostridium increasing their relative abundances and others like Corynebacterium or Kocuria reducing in relative abundance. From enrichments, 65 putative Sb- and Cu-metabolizing microorganisms were isolated, showing growth at 0.1 mM to 10 mM concentrations and 0°C to 40°C temperatures. 16S rRNA gene sequencing of the isolates indicated that most of the putative anaerobically Sb-respiring tolerators were related to the genus Clostridium. This study represents the first isolation, to our knowledge, of putative Sb-metabolizing cold-tolerant microorganisms and contributes to the understanding of metal (loid)-tolerant microbial communities in Arctic mine sites.

Bacillus velezensis YXDHD1-7 Prevents Early Blight Disease by Promoting Growth and Enhancing Defense Enzyme Activities in Tomato Plants

Bacillus velezensis is well known as a plant growth-promoting rhizobacteria (PGPR) and biocontrol agent. Nevertheless, there are very few reports on the study of B. velezensis on tomato early blight, especially the biocontrol effects among different inoculation concentrations. In this study, an IAA-producing strain, Bacillus velezensis YXDHD1-7 was isolated from the tomato rhizosphere soil, which had the strongest inhibitory effect against Alternaria solani. Inoculation with bacterial suspensions of this strain promoted the growth of tomato seedlings effectively. Furthermore, inoculations at 106, 107, and 108 cfu/mL resulted in control efficacies of 100%, 83.15%, and 69.90%, respectively. Genome sequencing showed that it possesses 22 gene clusters associated with the synthesis of antimicrobial metabolites and genes that are involved in the production of IAA. Furthermore, it may be able to produce spermidine and volatile compounds that also enhance plant growth and defense responses. Our results suggest that strain YXDHD1-7 prevents early blight disease by promoting growth and enhancing the defense enzyme activities in tomato plants. This strain is a promising candidate for an excellent microbial inoculant that can be used to enhance tomato production.

Application of extremophile cell factories in industrial biotechnology

Due to the extreme living conditions, extremophiles have unique characteristics in morphology, structure, physiology, biochemistry, molecular evolution mechanism and so on. Extremophiles have superior growth and synthesis capabilities under harsh conditions compared to conventional microorganisms, allowing for unsterilized fermentation processes and thus better performance in low-cost production. In recent years, due to the development and optimization of molecular biology, synthetic biology and fermentation technology, the identification and screening technology of extremophiles has been greatly improved. In this review, we summarize techniques for the identification and screening of extremophiles and review their applications in industrial biotechnology in recent years. In addition, the facts and perspectives gathered in this review suggest that next-generation industrial biotechnology (NGIBs) based on engineered extremophiles holds the promise of simplifying biofuturing processes, establishing open, non-sterilized continuous fermentation production systems, and utilizing low-cost substrates to make NGIBs attractive and cost-effective bioprocessing technologies for sustainable manufacturing.

Interplay between desiccation and oxidative stress responses in iron-oxidizing acidophilic bacteria

Variations in water availability represent a foremost stress factor affecting the growth and survival of microorganisms. Acidophilic bioleaching bacteria are industrially applied for releasing metals from mineral sulphides, and they are considered extremely tolerant to oxidative conditions prevailing in acidic bioleaching environments. Such processes usually are performed in heaps and thus these microorganisms are also exposed to intermittent desiccations or high osmolarity periods that reduce the water availability. However, the tolerance to water stress and the molecular basis of adaptation to it are still largely unknown. The aim of this work was to determine the cellular response to desiccation stress and establish its relationship to oxidative stress response in the acidophilic iron-oxidizing bacteria Acidithiobacillus ferrooxidans ATCC 23270 and Leptospirillum ferriphilum DSM 14647. Results showed that the exposure of cell cultures to desiccation (0-120 min) led to a significant reduction in cell growth, and to an increase in content in reactive oxygen species in both bacteria. However, Leptospirillum ferriphilum turned out to be more tolerant than Acidithiobacillus ferrooxidans. In addition, the pre-treatment of the cell cultures with compatible solutes (trehalose and ectoine), and antioxidants (glutathione and cobalamin) restored all stress parameters to levels exhibited by the control cultures. To evaluate the role of the osmotic and redox homeostasis mechanisms in coping with desiccation stress, the relative expression of a set of selected genes was approached by RT-qPCR experiments in cells exposed to desiccation for 30 min. Results showed a generalized upregulation of genes that code for mechanosensitive channels, and enzymes related to the biosynthesis of compatible solutes and oxidative stress response in both bacteria. These data suggest that acidophiles show variable tolerance to desiccation and allow to establish that water stress can trigger oxidative stress, and thus anti-oxidative protection capability can be a relevant mechanism when cells are challenged by desiccation or other anhydrobiosis states.

Eurypsychrophilic acidophiles: From (meta)genomes to low-temperature biotechnologies

Low temperature and acidic environments encompass natural milieus such as acid rock drainage in Antarctica and anthropogenic sites including drained sulfidic sediments in Scandinavia. The microorganisms inhabiting these environments include polyextremophiles that are both extreme acidophiles (defined as having an optimum growth pH < 3), and eurypsychrophiles that grow at low temperatures down to approximately 4°C but have an optimum temperature for growth above 15°C. Eurypsychrophilic acidophiles have important roles in natural biogeochemical cycling on earth and potentially on other planetary bodies and moons along with biotechnological applications in, for instance, low-temperature metal dissolution from metal sulfides. Five low-temperature acidophiles are characterized, namely, Acidithiobacillus ferriphilus, Acidithiobacillus ferrivorans, Acidithiobacillus ferrooxidans, “Ferrovum myxofaciens,” and Alicyclobacillus disulfidooxidans, and their characteristics are reviewed. Our understanding of characterized and environmental eurypsychrophilic acidophiles has been accelerated by the application of “omics” techniques that have aided in revealing adaptations to low pH and temperature that can be synergistic, while other adaptations are potentially antagonistic. The lack of known acidophiles that exclusively grow below 15°C may be due to the antagonistic nature of adaptations in this polyextremophile. In conclusion, this review summarizes the knowledge of eurypsychrophilic acidophiles and places the information in evolutionary, environmental, biotechnological, and exobiology perspectives.