Recent progress in the application of omics technologies in the study of bio-mining microorganisms from extreme environments

Re-vitalizing wastewater: Nutrient recovery and carbon capture through microbe-algae synergy using omics-biology

Increasing amounts of wastewater is the most pervasive and challenging environmental problem globally. Conventional treatment methods are costly and entail huge energy, carbon consumption and greenhouse gas emissions. Owing to their unique ability of carbon capturing and resource recovery, microalgae-microbiome based treatment is a potential approach and is widely used for carbon-neutral wastewater treatment. Microalgae-bacteria synergy (i.e., the functionally beneficial microbial synthetic communities) performs better and enhances carbon-sequestration and nutrient recovery from wastewater treatment plants. This review presents a comprehensive information regarding the potential of microalgae-microbiome as a sustainable agent for wastewater and discusses synergistic approaches for effective nutrient removal. Moreover, this review discusses, the role of omics-biology and Insilco approaches in unravelling and understanding the algae-microbe synergism and their response toward wastewater treatment. Finally, it discusses various microbiome engineering approaches for developing the effective microalgae-bacteria partners for carbon sequestration and nutrient recovery from wastewater, and summarizes future research perspectives on microalgae-microbiome based bioremediation.

Harnessing the potential of the microbial sulfur cycle for environmental biotechnology

The sulfur cycle is a complex biogeochemical cycle characterized by the high variability in the oxidation states of sulfur. While sulfur is essential for life processes, certain sulfur compounds, such as hydrogen sulfide, are toxic to all life forms. Micro-organisms facilitate the sulfur cycle, playing a prominent role even in extreme environments, such as soda lakes, acid mine drainage sites, hot springs, and other harsh habitats. The activity of these micro-organisms presents unique opportunities for mitigating sulfur-based pollution and enhancing the recovery of sulfur and metals. This review highlights the application of sulfur-oxidizing and -reducing micro-organisms in environmental biotechnology through three illustrative examples. Additionally, it discusses the challenges, recent trends, and prospects associated with these applications.

Integrated Proteomics and Metabolomics Reveal Altered Metabolic Regulation of Xanthobacter autotrophicus under Electrochemical Water-Splitting Conditions

Biological-inorganic hybrid systems are a growing class of technologies that combine microorganisms with materials for a variety of purposes, including chemical synthesis, environmental remediation, and energy generation. These systems typically consider microorganisms as simple catalysts for the reaction of interest; however, other metabolic activity is likely to have a large influence on the system performance. The investigation of biological responses to the hybrid environment is thus critical to the future development and optimization. The present study investigates this phenomenon in a recently reported hybrid system that uses electrochemical water splitting to provide reducing equivalents to the nitrogen-fixing bacteria Xanthobacter autotrophicus for efficient reduction of N2 to biomass that may be used as fertilizer. Using integrated proteomic and metabolomic methods, we find a pattern of differentiated metabolic regulation under electrochemical water-splitting (hybrid) conditions with an increase in carbon fixation products glycerate-3-phosphate and acetyl-CoA that suggests a high energy availability. We further report an increased expression of proteins of interest, namely, those responsible for nitrogen fixation and assimilation, which indicate increased rates of nitrogen fixation and support previous observations of faster biomass accumulation in the hybrid system compared to typical planktonic growth conditions. This work complicates the inert catalyst view of biological-inorganic hybrids while demonstrating the power of multiomics analysis as a tool for deeper understanding of those systems.

Omics technology draws a comprehensive heavy metal resistance strategy in bacteria

The rapid industrial revolution significantly increased heavy metal pollution, becoming a major global environmental concern. This pollution is considered as one of the most harmful and toxic threats to all environmental components (air, soil, water, animals, and plants until reaching to human). Therefore, scientists try to find a promising and eco-friendly technique to solve this problem i.e., bacterial bioremediation. Various heavy metal resistance mechanisms were reported. Omics technologies can significantly improve our understanding of heavy metal resistant bacteria and their communities. They are a potent tool for investigating the adaptation processes of microbes in severe conditions. These omics methods provide unique benefits for investigating metabolic alterations, microbial diversity, and mechanisms of resistance of individual strains or communities to harsh conditions. Starting with genome sequencing which provides us with complete and comprehensive insight into the resistance mechanism of heavy metal resistant bacteria. Moreover, genome sequencing facilitates the opportunities to identify specific metal resistance genes, operons, and regulatory elements in the genomes of individual bacteria, understand the genetic mechanisms and variations responsible for heavy metal resistance within and between bacterial species in addition to the transcriptome, proteome that obtain the real expressed genes. Moreover, at the community level, metagenome, meta transcriptome and meta proteome participate in understanding the microbial interactive network potentially novel metabolic pathways, enzymes and gene species can all be found using these methods. This review presents the state of the art and anticipated developments in the use of omics technologies in the investigation of microbes used for heavy metal bioremediation.

Genome-wide transcriptional response to silver stress in extremely halophilic archaeon Haloferax alexandrinus DSM 27206 T

BACKGROUND

The extremely halophilic archaeon Haloferax (Hfx.) alexandrinus DSM 27206 T was previously documented for the ability to biosynthesize silver nanoparticles while mechanisms underlying its silver tolerance were overlooked. In the current study, we aimed to assess the transcriptional response of this haloarchaeon to varying concentrations of silver, seeking a comprehensive understanding of the molecular determinants underpinning its heavy metal tolerance.

RESULTS

The growth curves confirmed the capacity of Hfx. alexandrinus to surmount silver stress, while the SEM-EDS analysis illustrated the presence of silver nanoparticles in cultures exposed to 0.5 mM silver nitrate. The RNA-Seq based transcriptomic analysis of Hfx. alexandrinus cells exposed to 0.1, 0.25, and 0.5 mM silver nitrate revealed the differential expression of multiple sets of genes potentially employed in heavy-metal stress response, genes mostly related to metal transporters, basic metabolism, oxidative stress response and cellular motility. The RT-qPCR analysis of selected transcripts was conducted to verify and validate the generated RNA-Seq data.

CONCLUSIONS

Our results indicated that copA, encoding the copper ATPase, is essential for the survival of Hfx. alexandrinus cells in silver-containing saline media. The silver-exposed cultures underwent several metabolic adjustments that enabled the activation of enzymes involved in the oxidative stress response and impairment of the cellular movement capacity. To our knowledge, this study represents the first comprehensive analysis of gene expression in halophillic archaea facing increased levels of heavy metals.

The mechanism of polysaccharide synthesis of Sanghuangporus sanghuang based on multi-omic analyses and feedback inhibition

S. sanghuang polysaccharide has various biological roles in promoting human health, however, the underlying mechanism of polysaccharide synthesis in S. sanghuang remain elusive. In the present study, the molecular structure of novel polysaccharide in the mutant S. sanghuang strain A130 with high yield of polysaccharide was characterized. The critical genes/proteins and pathways involved in polysaccharide synthesis were investigated via comparative transcriptomic, proteomic, and integrative analysis between wildtype strain SH-1 and A130. An integrated analysis of transcriptomic and proteomic results was also performed to locate potential regulators in the production of polysaccharides. The genes of cellobiohydrolase1 (CBH1) and MutS Homolog 6 (MSH6) related to glycolysis/gluconeogenesis were differentially expressed between A130 and SH-1, suggesting the potential involvement of these genes in regulating the production of polysaccharide. Proteomic analysis revealed that the abundance of Tyrosinase (TYR) and Trehalase (TREH) were substantially different between A130 and SH-1. The potential involvement of TYR in polysaccharide production was confirmed by transcriptomic-proteomic integrated analysis. The biological role of TYR and TREH in polysaccharide production was further verified by feedback inhibition of kojic acid and validamycin A, respectively. Overall, our study provides critical insights for the polysaccharide synthesis and high yield of polysaccharide through genes/pathways regulating in S. sanghuang.

The Rising Role of Omics and Meta-Omics in Table Olive Research

Table olives are often the result of fermentation, a process where microorganisms transform raw materials into the final product. The microbial community can significantly impact the organoleptic characteristics and safety of table olives, and it is influenced by various factors, including the processing methods. Traditional culture-dependent techniques capture only a fraction of table olives' intricate microbiota, prompting a shift toward culture-independent methods to address this knowledge gap. This review explores recent advances in table olive research through omics and meta-omics approaches. Genomic analysis of microorganisms isolated from table olives has revealed multiple genes linked to technological and probiotic attributes. An increasing number of studies concern metagenomics and metabolomics analyses of table olives. The former offers comprehensive insights into microbial diversity and function, while the latter identifies aroma and flavor determinants. Although proteomics and transcriptomics studies remain limited in the field, they have the potential to reveal deeper layers of table olives' microbiome composition and functionality. Despite the challenges associated with implementing multi-omics approaches, such as the reliance on advanced bioinformatics tools and computational resources, they hold the promise of groundbreaking advances in table olive processing technology.

From Genes to Bioleaching: Unraveling Sulfur Metabolism in Acidithiobacillus Genus

Sulfur oxidation stands as a pivotal process within the Earth's sulfur cycle, in which Acidithiobacillus species emerge as skillful sulfur-oxidizing bacteria. They are able to efficiently oxidize several reduced inorganic sulfur compounds (RISCs) under extreme conditions for their autotrophic growth. This unique characteristic has made these bacteria a useful tool in bioleaching and biological desulfurization applications. Extensive research has unraveled diverse sulfur metabolism pathways and their corresponding regulatory systems. The metabolic arsenal of the Acidithiobacillus genus includes oxidative enzymes such as: (i) elemental sulfur oxidation enzymes, like sulfur dioxygenase (SDO), sulfur oxygenase reductase (SOR), and heterodisulfide reductase (HDR-like system); (ii) enzymes involved in thiosulfate oxidation pathways, including the sulfur oxidation (Sox) system, tetrathionate hydrolase (TetH), and thiosulfate quinone oxidoreductase (TQO); (iii) sulfide oxidation enzymes, like sulfide:quinone oxidoreductase (SQR); and (iv) sulfite oxidation pathways, such as sulfite oxidase (SOX). This review summarizes the current state of the art of sulfur metabolic processes in Acidithiobacillus species, which are key players of industrial biomining processes. Furthermore, this manuscript highlights the existing challenges and barriers to further exploring the sulfur metabolism of this peculiar extremophilic genus.

Molecular Identification and Acid Stress Response of an Acidithiobacillus thiooxidans Strain Isolated from Rio Tinto (Spain)

Acidithiobacillus thiooxidans is of paramount importance in the development of biomining technologies. Being widely recognized as an extreme acidophile, extensive research has been dedicated to understanding its significant role in the extraction of several ores in recent years. However, there still exist significant molecular uncertainties surrounding this species. This study focuses on developing a taxonomic assignment method based on the sequencing of the 16S-5S rRNA cluster, along with a qPCR-based technology enabling precise growth determination. Additionally, an approach to understanding its response to acid stress is explored through RT-PCR and MALDI-TOF analysis. Our findings indicate that when subjected to pH levels below 1, the cell inhibits central (carbon fixation and metabolism) and energy (sulfur metabolism) metabolism, as well as chaperone synthesis, suggesting a potential cellular collapse. Nevertheless, the secretion of ammonia is enhanced to raise the environmental pH, while fatty acid synthesis is upregulated to reinforce the cell membrane.

Genome-resolved metagenomics inferred novel insights into the microbial community, metabolic pathways, and biomining potential of Malanjkhand acidic copper mine tailings

Mine tailing sites provide profound opportunities to elucidate the microbial mechanisms involved in ecosystem functioning. In the present study, metagenomic analysis of dumping soil and adjacent pond around India's largest copper mine at Malanjkhand has been done. Taxonomic analysis deciphered the abundance of phyla Proteobacteria, Bacteroidetes, Acidobacteria, and Chloroflexi. Genomic signatures of viruses were predicted in the soil metagenome, whereas Archaea and Eukaryotes were noticed in water samples. Mesophilic chemolithotrophs, such as Acidobacteria bacterium, Chloroflexi bacterium, and Verrucomicrobia bacterium, were predominant in soil, whereas, in the water sample, the abundance of Methylobacterium mesophilicum, Pedobacter sp., and Thaumarchaeota archaeon was determined. The functional potential analysis highlighted the abundance of genes related to sulfur, nitrogen, methane, ferrous oxidation, carbon fixation, and carbohydrate metabolisms. The genes for copper, iron, arsenic, mercury, chromium, tellurium, hydrogen peroxide, and selenium resistance were found to be predominant in the metagenomes. Metagenome-assembled genomes (MAGs) were constructed from the sequencing data, indicating novel microbial species genetically related to the phylum predicted through whole genome metagenomics. Phylogenetic analysis, genome annotations, functional potential, and resistome analysis showed the resemblance of assembled novel MAGs with traditional organisms used in bioremediation and biomining applications. Microorganisms harboring adaptive mechanisms, such as detoxification, hydroxyl radical scavenging, and heavy metal resistance, could be the potent benefactions for their utility as bioleaching agents. The genetic information produced in the present investigation provides a foundation for pursuing and understanding the molecular aspects of bioleaching and bioremediation applications.

Exploring Oxidoreductases from Extremophiles for Biosynthesis in a Non-Aqueous System

Organic solvent tolerant oxidoreductases are significant for both scientific research and biomanufacturing. However, it is really challenging to obtain oxidoreductases due to the shortages of natural resources and the difficulty to obtained it via protein modification. This review summarizes the recent advances in gene mining and structure-functional study of oxidoreductases from extremophiles for non-aqueous reaction systems. First, new strategies combining genome mining with bioinformatics provide new insights to the discovery and identification of novel extreme oxidoreductases. Second, analysis from the perspectives of amino acid interaction networks explain the organic solvent tolerant mechanism, which regulate the discrete structure-functional properties of extreme oxidoreductases. Third, further study by conservation and co-evolution analysis of extreme oxidoreductases provides new perspectives and strategies for designing robust enzymes for an organic media reaction system. Furthermore, the challenges and opportunities in designing biocatalysis non-aqueous systems are highlighted.

Multi-scale analysis of nickel ion tolerance mechanism for thermophilic Sulfobacillus thermosulfidooxidans in bioleaching

Bioleaching is intensively investigated for recovering valuable metals such as Li, Co, Ni and Cu. Nickel ion stress threatens the health of microorganisms when Ni²⁺ starts to accumulate in the leachate during the bioleaching of materials that are rich in Ni, such as spent lithium-ion batteries. The possible mechanisms underlying the response of S. thermosulfidooxidans to nickel ion stress were analyzed using a multi-scale approach. Under the condition of nickel ion stress, high concentrations of nickel ions were immobilized by extracellular polymeric substances, while concentrations of nickel ions inside the cells remained low. The intracellular adenosine triphosphate (ATP) concentration and H⁺-ATPase activity increased to maintain normal cell growth and metabolic activities. Scavenging abilities of S. thermosulfidooxidans for hydrogen peroxide and superoxide anion were enhanced to reduce oxidative damage induced by nickel ion stress. There were 734 differentially expressed genes identified by RNA-seq under nickel ion stress. Most of them were involved in oxidative phosphorylation, glutathione metabolism and genetic information processing, responsible for intracellular energy utilization, intracellular antioxidant capacity and DNA damage repair, respectively. The results of this study are of major significance for in-depth understanding of the mechanisms of acidophilic microorganisms' resistance to metal ions.

Advances in experimental and computational methodologies for the study of microbial-surface interactions at different omics levels

The study of the biological response of microbial cells interacting with natural and synthetic interfaces has acquired a new dimension with the development and constant progress of advanced omics technologies. New methods allow the isolation and analysis of nucleic acids, proteins and metabolites from complex samples, of interest in diverse research areas, such as materials sciences, biomedical sciences, forensic sciences, biotechnology and archeology, among others. The study of the bacterial recognition and response to surface contact or the diagnosis and evolution of ancient pathogens contained in archeological tissues require, in many cases, the availability of specialized methods and tools. The current review describes advances in in vitro and in silico approaches to tackle existing challenges (e.g., low-quality sample, low amount, presence of inhibitors, chelators, etc.) in the isolation of high-quality samples and in the analysis of microbial cells at genomic, transcriptomic, proteomic and metabolomic levels, when present in complex interfaces. From the experimental point of view, tailored manual and automatized methodologies, commercial and in-house developed protocols, are described. The computational level focuses on the discussion of novel tools and approaches designed to solve associated issues, such as sample contamination, low quality reads, low coverage, etc. Finally, approaches to obtain a systems level understanding of these complex interactions by integrating multi omics datasets are presented.

Development of a Prediction Method of Cell Density in Autotrophic/Heterotrophic Microorganism Mixtures by Machine Learning Using Absorbance Spectrum Data

Microflora is actively used to produce value-added materials in industry, and each cell density should be controlled for stable microflora use. In this study, a simple system evaluating the cell density was constructed with artificial intelligence (AI) using the absorbance spectra data of microflora. To set up the system, the prediction system for cell density based on machine learning was constructed using the spectra data as the feature from the mixture of Saccharomyces cerevisiae and Chlamydomonas reinhardtii. As the results of predicting cell density by extremely randomized trees, when the cell densities of S. cerevisiae and C. reinhardtii were shifted and fixed, the coefficient of determination (R²) was 0.8495; on the other hand, when the cell densities of S. cerevisiae and C. reinhardtii were fixed and shifted, the R² was 0.9232. To explain the prediction system, the randomized trees regressor of the decision tree-based ensemble learning method as the machine learning algorithm and Shapley additive explanations (SHAPs) as the explainable AI (XAI) to interpret the features contributing to the prediction results were used. As a result of the SHAP analyses, not only the optical density, but also the absorbance of the Soret and Q bands derived from the chloroplasts of C. reinhardtii could contribute to the prediction as the features. The simple cell density evaluating system could have an industrial impact.

Harnessing synthetic biology for sustainable biomining with Fe/S-oxidizing microbes

Biomining is a biotechnological approach where microorganisms are used to recover metals from ores and waste materials. While biomining applications are motivated by critical issues related to the climate crisis (e.g., habitat destruction due to mine effluent pollution, metal supply chains, increasing demands for cleantech-critical metals), its drawbacks hinder its widespread commercial applications: lengthy processing times, low recovery, and metal selectivity. Advances in synthetic biology provide an opportunity to engineer iron/sulfur-oxidizing microbes to address these limitations. In this forum, we review recent progress in synthetic biology-enhanced biomining with iron/sulfur-oxidizing microbes and delineate future research avenues.

Perspectives on the microorganism of extreme environments and their applications

Extremophiles are organisms that can survive and thrive in conditions termed as "extreme" by human beings. Conventional methods cannot be applied under extreme conditions like temperature and pH fluctuations, high salinity, etc. for a variety of reasons. Extremophiles can function and are adapted to thrive in these environments and are sustainable, cheaper, and efficient, therefore, they serve as better alternatives to the traditional methods. They adapt to these environments with biochemical and physiological changes and produce products like extremolytes, extremozymes, biosurfactants, etc., which are found to be useful in a wide range of industries like sustainable agriculture, food, cosmetics, and pharmaceuticals. These products also play a crucial role in bioremediation, production of biofuels, biorefinery, and astrobiology. This review paper comprehensively lists out the current applications of extremophiles and their products in various industries and explores the prospects of the same. They help us understand the underlying basis of biological mechanisms exploring the boundaries of life and thus help us understand the origin and evolution of life on Earth. This helps us in the research for extra-terrestrial life and space exploration. The structure and biochemical properties of extremophiles along with any possible long-term effects of their applications need to be investigated further.

The Interaction among Microbiota, Epigenetic Regulation, and Air Pollutants in Disease Prevention

Environmental pollutants can influence microbiota variety, with important implications for the general wellbeing of organisms. In subjects at high-risk of cancer, gut, and lung microbiota are distinct from those of low-risk subjects, and disease progression is associated with microbiota alterations. As with many inflammatory diseases, it is the combination of specific host and environmental factors in certain individuals that provokes disease outcomes. The microbiota metabolites influence activity of epigenetic enzymes. The knowledge of the mechanisms of action of environmental pollution now includes not only the alteration of the gut microbiota but also the interaction between different human microbiota niches such as the lung–gut axis. The epigenetic regulations can reprogram differentiated cells in response to environmental changes. The microbiota can play a major role in the progression and suppression of several epigenetic diseases. Accordingly, the maintenance of a balanced microbiota by monitoring the environmental stimuli provides a novel preventive approach for disease prevention. Metagenomics technologies can be utilized to establish new mitigation approaches for diseases induced by polluted environments. The purpose of this review is to examine the effects of particulate matter exposure on the progression of disease outcomes as related to the alterations of gut and lung microbial communities and consequent epigenetic modifications.