Life in acid: pH homeostasis in acidophiles

Mechanism of nitrogen conversion and microbial communities controlling the acidification and storage of pig farm fecal water

The effect of acidifiers on nitrogen transformation during manure wastewater storage remains unclear. In this study, we investigate the effects of two types of acidifiers on nitrogen transformation, bacterial structure, and functional genes during manure wastewater storage. The results indicate that the internal reactions in manure wastewater storage could be divided into three stages, i.e., nitrification (first 35 days), denitrification (mainly from days 36-84), and the final stage during which the internal environment of the manure wastewater stabilized. The addition of acidifiers effectively reduced nitrogen loss, with the total nitrogen content increasing from 12.8 to 25.83 %, and ammonia emissions decreasing from 31.67 to 43.81 %. The optimal nitrogen retention effect was observed for sulfuric acid. Furthermore, acidifiers primarily inhibited microbial activity and the abundance of functional genes, without altering the dominant bacterial community structure or nitrogen transformation pathways. These results provide a foundation for the use of acidifiers to reduce nitrogen loss during manure wastewater storage.

Exploring the ecological niche of comammox Nitrospira by in-situ enrichment within mainstream nitrification systems

Complete-ammonia-oxidization bacteria (Comammox Nitrospira) hold promising potential for reducing carbon footprint in mainstream wastewater treatment. However, the inadequate understanding of comammox Nitrospira within wastewater systems has greatly hindered the utilization of these novel microbial resources. This study explored the ecological niche of comammox Nitrospira within mainstream nitrification systems by enriching them under varied operational conditions. The joint analysis of multiple linear regression and random forest model have identified in-situ ammonium concentration and pH as the two most important parameters influencing the growth of comammox Nitrospira, followed by nitrogen loading rate, nitrogen source type, and dissolved oxygen (DO). Meanwhile, the ecological niche preference of comammox Nitrospira was revealed. The optimal ranges of in-situ ammonium concentration and pH for comammox Nitrospira was found below 0.5 mg NH4+-N/L and 6.5-7.5, respectively, indicating that low free ammonia conditions favor their growth. Furthermore, comammox Nitrospira exhibited a competitive advantage over Nitrosomonas under weakly acidic pH (6.0-6.5), and adapted to DO fluctuations by interspecies shifts, whereas Nitrosomonas preferred relatively high DO (1.5-2 mg O2/L). Comparative genomics further confirmed the above niche differentiation of two groups from reconstructed comammox Nitrospira and Nitrosomonas genomes. Overall, these findings provide guidance for the application of comammox process in wastewater treatment, thereby supporting the transition of mainstream nitrification process toward a more sustainable and energy-efficient pathway.

Mineral-Based Advanced Oxidation Processes for Enhancing the Removal of Antibiotic Resistance Genes from Domestic Wastewater

Wastewater treatment plants (WWTPs) release antibiotic-resistant bacteria (ARB) and antibiotic-resistant genes (ARGs) into the environment. Advanced oxidation processes (AOPs) can remove ARB and ARGs, but they often require impractically high chemical or energy use. Here, we explore a low-energy AOP that uses Fe-bearing clay mineral (NAu-1) either combined with H2O2 (H2O2/NAu-1) or as prereduced structural Fe (rNAu-1) to degrade selected ARGs (i.e., tetM, tetQ, and bla OXA-10), int1 (a mobile genetic element), and the 16S rRNA gene in postsecondary WWTP effluents. Addition of H2O2/NAu-1 significantly increased tetM and int1 removals relative to UV irradiation and H2O2/UV (p ≤ 0.02). Removals increased with greater H2O2 doses and contact times, reaching maximum values of 1.2 and 2.3 log units at H2O2 doses of 0.26 and 10 mM and contact times of 4 and 8 h, respectively. Bacterial regrowth after 24 h of contact was probably due to H2O2 depletion. However, the addition of rNAu-1 achieved the highest removals, up to 2.9 log units after 0.5 h, and suppressed bacterial regrowth over 24 h. Similar removals were observed with rNAu-1 under oxic and anoxic conditions. Results show that mineral-based AOPs offer the potential for elevated ARG removal and lower chemical and energy demands in tertiary wastewater treatment.

Vanadium Stress-Driven Microbial Acclimation Enhances Biological Denitrification in Recycling of Vanadium-Containing Industrial Wastewater

Recirculation in vanadium mining enhances resource efficiency but risks ammonia nitrogen (NH3-N) accumulation, severely compromising leaching yields. To address this bottleneck, we developed a bioaugmentation strategy using Pseudomonas sp. S.P-1 acclimated to vanadium stress. Under optimized conditions (sodium citrate as a carbon source, C/N = 5, 5% inoculum, and pH = 8), the strain achieved exceptional NH3-N (2000 mg·L-1) removal (>99.25% within 16 days; residual NH4+ < 15 mg·L-1), 12.7% higher than the original bacteria. Mechanistic studies revealed that vanadium exposure triggered dual adaptive responses: enhanced biosorption via the stimulated synthesis of extracellular polymeric substances (EPS) enriched with negatively charged functional groups (C=O, -COOH-, and C-N), improving NH4+ adsorption capacity, and metabolic activation via an elevated transmembrane electrochemical potential and an accelerated substrate uptake due to cell membrane permeability, while up-regulation of ammonia monooxygenase (AMO) activity (123.11%) facilitated efficient NH4+→NH2OH conversions. Crucially, this bio-process enabled simultaneous NH3-N degradation (89.2% efficiency) and vanadium recovery, demonstrating its dual role in pollution control and critical metal recycling. By integrating microbial resilience with circular economy principles, our strategy offers a scalable prototype for sustainable vanadium extraction, aligning with low-carbon metallurgy demands in clean energy transitions. This study investigated the ability of vanadium stress to enhance microbial ammonia nitrogen metabolism, and by acclimatizing S.P-1 to vanadium-containing solutions, we aimed to address the dual problems of NH3-N accumulation and vanadium toxicity in wastewater recirculation.

Unravelling the key factors for the dominance of Leuconostoc starters during kimchi fermentation

Recent studies aim to prevent kimchi spoilage and enhance the sensory and nutritional qualities using lactic acid bacteria, particularly Leuconostoc species, as kimchi starters. However, the factors enabling the successful adaptation and predominance of Leuconostoc species remain unclear. This study investigates the factors that contribute to the successful adaptation of Leuconostoc starter strains WiKim32, WiKim33, WiKim0121 and CBA3628 during kimchi fermentation using a comprehensive multi-omics approach. Our findings reveal that ATP-dependent molecular chaperones, which respond to cold and acidic kimchi environments, play crucial roles in successfully adapting Leuconostoc starter strains. Moreover, genes involved in carbohydrate metabolic pathways enhance ATP production, thereby supporting chaperone activity and bacterial growth. This study highlights the practical use of Leuconostoc starter strains WiKim32, WiKim33 and WiKim0121 and identifies essential factors for their successful adaptation and predominance during kimchi fermentation.

Identification of microorganisms at different times in a bioleaching process for the recovery of gold and silver from minerals in oxide form

In this study, gold and silver were recovered through a bioleaching process conducted at room temperature over 11 days. Native bacteria and varying ratios of mineral pulp to culture medium (20/80, 37.5/62.5, and 50/50 %) from a mining operation in Zacatecas, Mexico, were evaluated. The mineral was crushed to a particle size of 0.125 inches or smaller, containing gold and silver concentrations of 0.609 g/ton and 138.89 g/ton, respectively. Four native microorganisms were identified using molecular biology techniques and a 16S rRNA gene fragment: Acidovorax citrulli, Brevundimonas albigilva, Sphingomonas korenensis, and Methylobacterium organophilum. The bioleaching system achieved metal extractions of 84.12 % and 63.93 % for gold and silver, respectively. Different microorganisms were identified at various processing times: Sphingomonas korenensis (days 1, 2, 5, 8, and 11), Methylobacterium organophilum (days 1 and 2), Paenibacillus dongdonensis (days 1 and 2), Brevundimonas albigilva (day 5), Ureibacillus manganicus (day 5), Peribacillus simplex (day 8), Niallia circulans (day 8), Massilia atriviolacea (day 11), and Bacillus licheniformis (day 11). The dominant bacterium throughout the process was Sphingomonas korenensis, which appeared at all stages of the experiment.

Where the microbes aren't

Although a large fraction of Earth's volume and most places beyond the planet lack life because physical and chemical conditions are too extreme, intriguing scientific questions are raised in many environments within or at the edges of life's niche space in which active life is absent. This review explores the environments in which active microorganisms do not occur. Within the known niche space for life, uninhabited, but habitable physical spaces potentially offer opportunities for hypothesis testing, such as using them as negative control environments to investigate the influence of life on planetary processes. At the physico-chemical limits of life, questions such as whether spaces devoid of actively metabolizing or reproducing life constitute uninhabitable space or space containing vacant niches that could be occupied with appropriate adaptation are raised. We do not know the extent to which evolution has allowed life to occupy all niche space within its biochemical potential. The case of habitable extraterrestrial environments and the scientific and ethical questions that they raise is discussed.

Extremophilic Microorganisms as a Source of Emerging Enzymes for the Food Industry: A Review

Modern-day consumers are interested in highly nutritious and safe foods with corresponding organoleptic qualities. Such foods are increasingly subjected to various processing techniques which include the use of enzymes. These enzymes like amylases, lipases, proteases, xylanases, laccases, pullulanase, chitinases, pectinases, esterases, isomerases, and dehydrogenases could be derived from extremophilic organisms such as thermophiles, psychrophiles, acidophiles, alkaliphiles, and halophiles. As these organisms can grow under severe environmental conditions, they can produce functional enzymes (extremozymes) used in producing safe foods (such as gluten-free, lactose-free, lower acrylamide, or lower trans-fat products). The extremozymes also enhance nutrient bioavailability and bioaccessibility (e.g., predigested nourishments like baby formulae), and improve nourishment functionalities such as surface, sensory, and bioactive properties. Therefore, exploring alternative sources of enzymes for better compatibility and long-term adaptability in the processing stages is a promising approach for obtaining novel food products. This review will establish novel discovery methods of extremozymes from psychrophiles, thermophiles, acidophiles, alkaliphiles, and halophiles, the enzymes' types, mechanisms of action, and their food applications. It will also contribute to their commercial relevance and the furtherance of their discovery.

Outstanding enrichment of ladderane lipids in anammox bacteria: Overlooked effect of pH

Ladderane lipids synthesised by anammox bacteria hold significant potential for applications in jet fuel, drug delivery, and optoelectronics. Despite the widespread use of anammox bacteria in nitrogen removal from wastewater, the optimal conditions for maximising ladderane production remain unclear, limiting their broader application. To address this, we operated a fed-batch bioreactor with anammox bacteria, gradually adjusting the pH from 6.5 to 7.5 while regularly sampling for microbial community composition (Illumina sequencing), proteins, and ladderane lipids (UHPLC-HRMS). Our findings reveal that ladderane production positively correlates with rising pH increasing nearly fivefold as pH rose from 6.5 to 7.5, with a notable shift towards lipids containing two ladderane alkyl chains at higher pH. However, the conditions at an alkaline pH range also induced mild stress in anammox bacteria, as evidenced by our proteomic and microbial community data. Therefore, we propose maintaining a pH above 7.5 to enrich ladderane-rich anammox biomass but emphasise the need for gradual adaptation. This approach could optimise anammox installations for producing high-value ladderane lipids from wastewater.

Accurately predicting optimal conditions for microorganism proteins through geometric graph learning and language model

Proteins derived from microorganisms that survive in the harshest environments on Earth have stable activity under extreme conditions, providing rich resources for industrial applications and enzyme engineering. Due to the time-consuming nature of experimental determinations, it is imperative to develop computational models for fast and accurate prediction of protein optimal conditions. Previous studies were limited by the scarcity of data and the neglect of protein structures. To solve these problems, we constructed an up-to-date dataset with 175,905 non-redundant proteins and proposed a new model GeoPoc based on geometric graph learning for the protein optimal temperature, pH, and salt concentration prediction. GeoPoc leverages protein structures and sequence embeddings extracted from pre-trained language model, and further employs a geometric graph transformer network to capture the sequence and spatial information. We first focused on in-house validation for optimal temperature prediction for robustness assessment, and achieved a PCC of 0.78. The algorithm is further confirmed in an independent test set, where GeoPoc surpasses the state-of-the-art method by 2.3% in AUC. Additionally, GeoPoc was extended to pH and salt concentration prediction, and obtained AUC scores of 0.78 and 0.77, respectively. Through further interpretable analysis, GeoPoc elucidates the critical physicochemical properties that contribute to enhancing protein thermostability.

Dual-biased metal oxide electrolyte-gated thin-film transistors for enhanced protonation in complex biofluids

pH sensing technology is pivotal for monitoring aquatic ecosystems and diagnosing human health conditions. Indium-gallium-zinc oxide electrolyte-gated thin-film transistors (IGZO EGTFTs) are highly regarded as ion-sensing devices due to the pH-dependent surface chemistry of their sensing membranes. However, applying EGTFT-based pH sensors in complex biofluids containing diverse charged species poses challenges due to ion interference and inherently low sensitivity constrained by the Nernst limit. Here, we propose a dual-biased (DB) EGTFT pH sensing platform, acquiring back-gate-assisted sensitivity enhancement and recyclable redox-coupled protonation at the semiconductor-biofluid interface. A solution-processed amorphous IGZO film, used as the proton-sensitive membrane, ensures scalable uniformity across a 6-inch wafer. These devices demonstrate exceptional pH resistivity over several hours when submerged in solutions with pH levels of 4 and 8. In-depth electrochemical investigations reveal that back-gate bias significantly enhances sensitivity beyond the Nernst limit, reaching 85 mV/pH. This improvement is due to additional charge accumulation in the channel, which expands the sensing window. As a proof of concept, we observe consistent variations in threshold voltage during repeated pH cycles, not only in standard solutions but also in physiological electrolytes such as phosphate-buffered saline (PBS) and artificial urine, confirming the potential for reliable operation in complex biological environments.

Antimicrobial Activity of Glycyrrhizinic Acid Is pH-Dependent

In recent years, antimicrobial hydrogels have attracted much attention in biomedical applications due to their biocompatibility and high water content. Glycyrrhizin (GA) is an antimicrobial that can form pH-dependent hydrogels due to the three carboxyl groups of GA that differ in pKa value. The influence of GA protonation on the antimicrobial activity, however, has never been studied before. Therefore, we investigated the effect of the pH on the antimicrobial activity of GA against Pseudomonas aeruginosa, Staphylococcus aureus, MRSA, Staphylococcus epidermidis, Acinetobacter baumannii, Klebsiella pneumoniae, Klebsiella aerogenes, and two strains of Escherichia coli. In general, the antimicrobial activity of GA increases as a function of decreasing pH (and thus increasing protonation of GA). More specifically, fully protonated GA hydrogels (pH = 3) are required for growth inhibition and killing of E. coli UTI89 and Klebsiella in the suspension above the hydrogel, while the staphylococci strains and A. baumannii are already inhibited by fully deprotonated GA (pH = 6.8). P. aeruginosa and E. coli DH5α showed moderate susceptibility, as they are completely inhibited by a hydrogel at pH 3.8, containing partly protonated GA, but not by fully deprotonated GA (pH = 6.8). The antimicrobial activity of the hydrogel cannot solely be attributed to the resulting pH decrease of the suspension, as the presence of GA significantly increases the activity. Instead, this increased activity is due to the release of GA from the hydrogel into the suspension, where it directly interacts with the bacteria. Moreover, we provide evidence indicating that the pH dependency of the antimicrobial activity is due to differences in GA protonation state by treating the pathogens with GA solutions differing in their GA protonation distribution. Finally, we show by LC-MS that there is no chemical or enzymatic breakdown of GA. Overall, our results demonstrate that the pH influences not only the physical but also the antimicrobial properties of the GA hydrogels.

Multi-stress adaptive lifestyle of acidophiles enhances their robustness for biotechnological and environmental applications

Acidophiles are a group of organisms typically found in highly acidic environments such as acid mine drainage. These organisms have several physiological features that enable them to thrive in highly acidic environments (pH ≤3). Considering that both acid mine drainage and solfatara fields exhibit extreme and dynamic ecological conditions for acidophiles, it is crucial to gain deeper insights into the adaptive mechanisms employed by these unique organisms. The existing literature reveals a notable gap in understanding the multi-stress conditions confronting acidophiles and their corresponding coping mechanisms. Therefore, the current review aims to illuminate the intricacies of the metabolic lifestyles of acidophiles within these demanding habitats, exploring how their energy demands contribute to habitat acidification. In addition, the unique adaptive mechanisms employed by acidophiles were emphasized, especially the pivotal role of monolayer membrane-spanning lipids, and how these organisms effectively respond to a myriad of stresses. Beyond mere survival, understanding the adaptive mechanisms of these unique organisms could further enhance their use in some biotechnological and environmental applications. Lastly, this review explores the strategies used to engineer these organisms to promote their use in industrial applications.

The mechanism of survival and degradation of phenol by Acinetobacter pittii in an extremely acidic environment

The treatment efficiency of acidic phenol-containing wastewater is hindered by the absence of efficient acid-resistant phenol-degrading bacteria, and the acid-resistant mechanism of such bacteria remains poorly studied. In this study, the acid-resistant strain Hly3 was used as a research model to investigate its ability to degrade phenol and its underlying mechanism of acid resistance. Strain Hly3 exhibited robust acid resistance, capable of surviving in extremely acidic environments (pH 3) and degrading 1700 mg L-1 phenol in 72 h. Through the physiological response analysis of strain Hly3 to pH, the results indicated: firstly, the strain could reduce the relative permeability of the cell membrane and increase EPS secretion to prevent H+ from entering the cell (shielding effect); secondly, the strain could accumulate more buffering substances to neutralize the intracellular H+ (neutralization effect); thirdly, the strain could expel H+ from the cell by enhancing H+-ATPase activity (pumping effect); finally, the strain produced more active scavengers to reduce the toxicity of acid stress on cells (antioxidant effect). Subsequently, combining liquid chromatography-mass spectrometry (LC-MS) technology with exogenous addition experiments, it was verified that the acid resistance mechanism of microorganisms is achieved through the activation of acid-resistant response systems by glutamine, thereby enhancing functions such as shielding, neutralization, efflux, and antioxidation. This study elucidated the acid resistance mechanism of Acinetobacter pittii, providing a theoretical basis and guidance for the treatment of acidic phenol-containing wastewater.

Bacterial extracellular biopolymers: Eco-diversification, biosynthesis, technological development and commercial applications

Synthetic polymers have been widely thriving as mega industries at a commercial scale in various commercial sectors over the last few decades. The extensive use of synthetic polymers has caused several negative repercussions on the health of humans and the environment. Recently, biopolymers have gained more attention among scientists of different disciplines by their potential therapeutic and commercial applications. Biopolymers are chain-like repeating units of molecules isolated from green sources. They are self-degradable, biocompatible, and non-toxic in nature. Recently, eco-friendly biopolymers such as extracellular polymeric substances (EPSs) have received much attention for their wide applications in the fields of emulsification, flocculation, preservatives, wastewater treatment, nanomaterial functionalization, drug delivery, cosmetics, glycomics, medicinal chemistry, and purification technology. The dynamicity of applications has raised the industrial and consumer demands to cater to the needs of mankind. This review deals with current insights and highlights on database surveys, potential sources, classification, extremophilic EPSs, bioprospecting, patents, microenvironment stability, biosynthesis, and genetic advances for production of high valued ecofriendly polymers. The importance of high valued EPSs in commercial and industrial applications in the global market economy is also summarized. This review concludes with future perspectives and commercial applications for the well-being of humanity.

Methylene Blue: An FDA-Approved NIR-II Fluorogenic Probe with Extremely Low pH Responsibility for Hyperchlorhydria Imaging

Methylene blue (MB) is an FDA (Food and Drug Administration)-approved contrast agent with donor-acceptor (D-A) structure integrated with carbonyl-containing nitrogen-heterocycles. MB can be converted into MBH (protonated MB) by protonation, which not only induces the fluorescence emission red-shifted from the first near-infrared window (NIR-I, 650-950 nm) to the second near-infrared window (NIR-II, 1000-1700 nm) but also achieves ACQ-to-AIE conversion. MB has been successfully demonstrated in hyperacidemia imaging with an extremely low pH value (<1).

Impact of nutrient excess on physiology and metabolism of Sulfolobus acidocaldarius

Overflow metabolism is a well-known phenomenon that describes the seemingly wasteful and incomplete substrate oxidation by aerobic cells, such as yeasts, bacteria, and mammalian cells, even when conditions allow for total combustion via respiration. This cellular response, triggered by an excess of C-source, has not yet been investigated in archaea. In this study, we conducted chemostat cultivations to compare the metabolic and physiological states of the thermoacidophilic archaeon Sulfolobus acidocaldarius under three conditions, each with gradually increasing nutrient stress. Our results show that S. acidocaldarius has different capacities for the uptake of the two C-sources, monosodium glutamate and glucose. A saturated tricarboxylic acid cycle at elevated nutrient concentrations affects the cell's ability to deplete its intermediates. This includes deploying additional cataplerotic pathways and the secretion of amino acids, notably valine, glycine, and alanine, while glucose is increasingly metabolized via glycogenesis. We did not observe the secretion of common fermentation products, like organic acids. Transcriptomic analysis indicated an upregulation of genes involved in fatty acid metabolism, suggesting the intracellular conservation of energy. Adapting respiratory enzymes under nutrient stress indicated high metabolic flexibility and robust regulatory mechanisms in this archaeon. This study enhances our fundamental understanding of the metabolism of S. acidocaldarius.

Acidophilic sulphate-reducing bacteria: Diversity, ecophysiology, and applications

Acidophilic sulphate-reducing bacteria (aSRB) are widespread anaerobic microorganisms that perform dissimilatory sulphate reduction and have key adaptations to tolerate acidic environments (pH <5.0), such as proton impermeability and Donnan potential. This diverse prokaryotic group is of interest from physiological, ecological, and applicational viewpoints. In this review, we summarize the interactions between aSRB and other microbial guilds, such as syntrophy, and their roles in the biogeochemical cycling of sulphur, iron, carbon, and other elements. We discuss the biotechnological applications of aSRB in treating acid mine drainage (AMD, pH <3), focusing on their ability to produce biogenic sulphide and precipitate metals, particularly in the context of utilizing microbial consortia instead of pure isolates. Metal sulphide nanoparticles recovered after AMD treatment have multiple potential technological uses, including in electronics and biomedicine, contributing to a cost-effective circular economy. The products of aSRB metabolisms, such as biominerals and isotopes, could also serve as biosignatures to understand ancient and extant microbial life in the universe. Overall, aSRB are active components of the sulphur and carbon cycles under acidic conditions, with potential natural and technological implications for the world around us.

Utilization of formic acid by extremely thermoacidophilic archaea species

The exploration of novel hosts with the ability to assimilate formic acid, a C1 substrate that can be produced from renewable electrons and CO2, is of great relevance for developing novel and sustainable biomanufacturing platforms. Formatotrophs can use formic acid or formate as a carbon and/or reducing power source. Formatotrophy has typically been studied in neutrophilic microorganisms because formic acid toxicity increases in acidic environments below the pKa of 3.75 (25°C). Because of this toxicity challenge, utilization of formic acid as either a carbon or energy source has been largely unexplored in thermoacidophiles, species that possess the ability to produce a variety of metabolites and enzymes of high biotechnological relevance. Here we investigate the capacity of several thermoacidophilic archaea species from the Sulfolobales order to tolerate and metabolize formic acid. Metallosphaera prunae, Sulfolobus metallicus and Sulfolobus acidocaldarium were found to metabolize and grow with 1-2 mM of formic acid in batch cultivations. Formic acid was co-utilized by this species alongside physiological electron donors, including ferrous iron. To enhance formic acid utilization while maintaining aqueous concentrations below the toxicity threshold, we developed a bioreactor culturing method based on a sequential formic acid feeding strategy. By dosing small amounts of formic acid sequentially and feeding H2 as co-substrate, M. prunae could utilize a total of 16.3 mM of formic acid and grow to higher cell densities than when H2 was supplied as a sole electron donor. These results demonstrate the viability of culturing thermoacidophilic species with formic acid as an auxiliary substrate in bioreactors to obtain higher cell densities than those yielded by conventional autotrophic conditions. Our work underscores the significance of formic acid metabolism in extreme habitats and holds promise for biotechnological applications in the realm of sustainable energy production and environmental remediation.

Rubisco kinetic adaptations to extreme environments

Photosynthetic and chemosynthetic extremophiles have evolved adaptations to thrive in challenging environments by finely adjusting their metabolic pathways through evolutionary processes. A prime adaptation target to allow autotrophy in extreme conditions is the enzyme Rubisco, which plays a central role in the conversion of inorganic to organic carbon. Here, we present an extensive compilation of Rubisco kinetic traits from a wide range of species of bacteria, archaea, algae, and plants, sorted by phylogenetic group, Rubisco type, and extremophile type. Our results show that Rubisco kinetics for the few extremophile organisms reported up to date are placed at the margins of the enzyme's natural variability. Form ID Rubisco from thermoacidophile rhodophytes and form IB Rubisco from halophile terrestrial plants exhibit higher specificity and affinity for CO2 than their non-extremophilic counterparts, as well as higher carboxylation efficiency, whereas form ID Rubisco from psychrophile organisms possess lower affinity for O2. Additionally, form IB Rubisco from thermophile cyanobacteria shows enhanced CO2 specificity when compared to form IB non-extremophilic cyanobacteria. Overall, these findings highlight the unique characteristics of extremophile Rubisco enzymes and provide useful clues to guide next explorations aimed at finding more efficient Rubiscos.

Lessons from Extremophiles: Functional Adaptations and Genomic Innovations across the Eukaryotic Tree of Life

From hydrothermal vents, to glaciers, to deserts, research in extreme environments has reshaped our understanding of how and where life can persist. Contained within the genomes of extremophilic organisms are the blueprints for a toolkit to tackle the multitude of challenges of survival in inhospitable environments. As new sequencing technologies have rapidly developed, so too has our understanding of the molecular and genomic mechanisms that have facilitated the success of extremophiles. Although eukaryotic extremophiles remain relatively understudied compared to bacteria and archaea, an increasing number of studies have begun to leverage 'omics tools to shed light on eukaryotic life in harsh conditions. In this perspective paper, we highlight a diverse breadth of research on extremophilic lineages across the eukaryotic tree of life, from microbes to macrobes, that are collectively reshaping our understanding of molecular innovations at life's extremes. These studies are not only advancing our understanding of evolution and biological processes but are also offering a valuable roadmap on how emerging technologies can be applied to identify cellular mechanisms of adaptation to cope with life in stressful conditions, including high and low temperatures, limited water availability, and heavy metal habitats. We shed light on patterns of molecular and organismal adaptation across the eukaryotic tree of life and discuss a few promising research directions, including investigations into the role of horizontal gene transfer in eukaryotic extremophiles and the importance of increasing phylogenetic diversity of model systems.

Eco-evolutionary strategies for relieving carbon limitation under salt stress differ across microbial clades

With the continuous expansion of saline soils under climate change, understanding the eco-evolutionary tradeoff between the microbial mitigation of carbon limitation and the maintenance of functional traits in saline soils represents a significant knowledge gap in predicting future soil health and ecological function. Through shotgun metagenomic sequencing of coastal soils along a salinity gradient, we show contrasting eco-evolutionary directions of soil bacteria and archaea that manifest in changes to genome size and the functional potential of the soil microbiome. In salt environments with high carbon requirements, bacteria exhibit reduced genome sizes associated with a depletion of metabolic genes, while archaea display larger genomes and enrichment of salt-resistance, metabolic, and carbon-acquisition genes. This suggests that bacteria conserve energy through genome streamlining when facing salt stress, while archaea invest in carbon-acquisition pathways to broaden their resource usage. These findings suggest divergent directions in eco-evolutionary adaptations to soil saline stress amongst microbial clades and serve as a foundation for understanding the response of soil microbiomes to escalating climate change.

Metagenomic analysis of a thermophilic bacterial consortium and its use in the bioremediation of a petroleum-contaminated soil

Biodegradation is difficult at high temperatures due to the limited capacity of microorganisms to survive and function outside their optimum temperature range. Here, a thermophilic petroleum-degrading consortium was enriched from compost at a temperature of 55 °C. 16S rDNA and metagenomic techniques were used to analyze the composition of the consortium and the mechanisms of degradation. The consortium degraded 17000 mg total petroleum hydrocarbons (TPHs) L-1 with a degradation efficiency of 81.5% in 14 days. The consortium utilized a range of substrates such as n-hexadecane, n-docosane, naphthalene and pyrene and grew well over a wide range of pH (4-10) and salinity (0-90 g L-1). The hydrocarbon-degrading extremophilic consortium contained, inter alia, (relative abundance >1%) Caldibacillus, Geobacillus, Mycolicibacterium, Bacillus, Chelatococcus, and Aeribacillus spp. Metagenomic analysis was conducted to discover the degradation and environmental tolerance functional genes of the consortium. Two alkane hydroxylase genes, alkB and ladA, were found. A microcosm study shows that the consortium promoted the bioremediation of soil TPHs. The results indicate that the consortium may be a good candidate for the high-temperature bioremediation of petroleum-contaminated soils.

Lowering pH optimum of activity of SshEstI, a slightly alkaliphilic archaeal esterase of the hormone-sensitive lipase family

SshEstI, a carboxylesterase from the thermoacidophilic archaeon Saccharolobus shibatae, is a member of the hormone-sensitive lipase family that displays slightly alkaliphilic activity with an optimum activity at pH 8.0. In this study, three distinct strategies were explored to confer acidophilic properties to SshEstI. The first strategy involved engineering the oxyanion hole by replacing Gly81 with serine or aspartic acid. The G81S mutant showed optimum activity at pH 7.0, whereas the aspartic acid mutant (G81D) rendered the enzyme slightly acidophilic with optimum activity observed at pH 6.0; however, kcat and kcat/Km values were reduced by these substitutions. The second strategy involved examining the effects of surfactant additives on the pH-activity profiles of SshEstI. The results showed that cetyltrimethylammonium bromide (CTAB) enhanced wild-type enzyme (WT) activity at acidic pH values. In the presence of 0.1 mM CTAB, G81S and G81D were acidophilic enzymes with optimum activity at pH 6.0 and 4.0, respectively, although their enzyme activities were low. The third strategy involved engineering the active site to resemble that of kumamolisin-As (kuma-As), an acidophilic peptidase of the sedolisin family. The catalytic triad of kuma-As was exchanged into SshEstI using site-directed mutagenesis. X-ray crystallographic analysis of the mutants (H274D and H274E) revealed that the potential hydrogen donor-acceptor distances around the active site of WT were fully maintained in these mutants. However, these mutants were inactive at pH 4-8.

Hell's Gate Globin-I from Methylacidiphilum infernorum Displays a Unique Temperature-Independent pH Sensing Mechanism Utililized a Lipid-Induced Conformational Change

Hell's Gate globin-I (HGb-I) is a thermally stable globin from the aerobic methanotroph Methylacidiphilium infernorum. Here we report that HGb-I interacts with lipids stoichiometrically to induce structural changes in the heme pocket, changing the heme iron distal ligation coordination from hexacoordinate to pentacoordinate. Such changes in heme geometry have only been previously reported for cytochrome c and cytoglobin, linked to apoptosis regulation and enhanced lipid peroxidation activity, respectively. However, unlike cytoglobin and cytochrome c, the heme iron of HGb-I is altered by lipids in ferrous as well as ferric oxidation states. The apparent affinity for lipids in this thermally stable globin is highly pH-dependent but essentially temperature-independent within the range of 20-60 °C. We propose a mechanism to explain these observations, in which lipid binding and stability of the distal endogenous ligand are juxtaposed as a function of temperature. Additionally, we propose that these coupled equilibria may constitute a mechanism through which this acidophilic thermophile senses the pH of its environment.

Iron bioleaching and polymers accumulation by an extreme acidophilic bacterium

In many European regions, both local metallic and non-metallic raw materials are poorly exploited due to their low quality and the lack of technologies to increase their economic value. In this context, the development of low cost and eco-friendly approaches, such as bioleaching of metal impurities, is crucial. The acidophilic strain Acidiphilium sp. SJH reduces Fe(III) to Fe(II) by coupling the oxidation of an organic substrate to the reduction of Fe(III) and can therefore be applied in the bioleaching of iron impurities from non-metallic raw materials. In this work, the physiology of Acidiphilium sp. SJH and the reduction of iron impurities from quartz sand and its derivatives have been studied during growth on media supplemented with various carbon sources and under different oxygenation conditions, highlighting that cell physiology and iron reduction are tightly coupled. Although the organism is known to be aerobic, maximum bioleaching performance was obtained by cultures cultivated until the exponential phase of growth under oxygen limitation. Among carbon sources, glucose has been shown to support faster biomass growth, while galactose allowed highest bioleaching. Moreover, Acidiphilium sp. SJH cells can synthesise and accumulate Poly-β-hydroxybutyrate (PHB) during the process, a polymer with relevant application in biotechnology. In summary, this work gives an insight into the physiology of Acidiphilium sp. SJH, able to use different carbon sources and to synthesise a technologically relevant polymer (PHB), while removing metals from sand without the need to introduce modifications in the process set up.

Acidophilic heterotrophs: basic aspects and technological applications

Acidophiles comprise a group of microorganisms adapted to live in acidic environments. Despite acidophiles are usually associated with an autotrophic metabolism, more than 80 microorganisms capable of utilizing organic matter have been isolated from natural and man-made environments. The ability to reduce soluble and insoluble iron compounds has been described for many of these species and may be harnessed to develop new or improved mining processes when oxidative bioleaching is ineffective. Similarly, as these microorganisms grow in highly acidic media and the chances of contamination are reduced by the low pH, they may be employed to implement robust fermentation processes. By conducting an extensive literature review, this work presents an updated view of basic aspects and technological applications in biomining, bioremediation, fermentation processes aimed at biopolymers production, microbial electrochemical systems, and the potential use of extremozymes.

Sustained bacterial N2O reduction at acidic pH

Nitrous oxide (N2O) is a climate-active gas with emissions predicted to increase due to agricultural intensification. Microbial reduction of N2O to dinitrogen (N2) is the major consumption process but microbial N2O reduction under acidic conditions is considered negligible, albeit strongly acidic soils harbor nosZ genes encoding N2O reductase. Here, we study a co-culture derived from acidic tropical forest soil that reduces N2O at pH 4.5. The co-culture exhibits bimodal growth with a Serratia sp. fermenting pyruvate followed by hydrogenotrophic N2O reduction by a Desulfosporosinus sp. Integrated omics and physiological characterization revealed interspecies nutritional interactions, with the pyruvate fermenting Serratia sp. supplying amino acids as essential growth factors to the N2O-reducing Desulfosporosinus sp. Thus, we demonstrate growth-linked N2O reduction between pH 4.5 and 6, highlighting microbial N2O reduction potential in acidic soils.

Microbial assisted multifaceted amelioration processes of heavy-metal remediation: a clean perspective toward sustainable and greener future

Rapidly increasing heavy metal waste has adversely affected the environment and the Earth's health. The lack of appropriate remediation technologies has worsened the issue globally, especially in developing countries. Heavy-metals contaminants have severely impacted the environment and led to devastating conditions owing to their abundance and reactivity. As they are nondegradable, the potential risk increases even at a low concentration. However, heavy-metal remediation has increased with the up-gradation of technologies and integration of new approaches. Also, of all the treatment methodologies, microbial-assisted multifaceted approach for ameliorating heavy metals is a promising strategy for propagating the idea of a green and sustainable environment with minimal waste aggregation. Microbial remediation combined with different biotechniques could aid in unraveling new methods for eradicating heavy metals. Thus, the present review focuses on various microbial remediation approaches and their affecting factors, enabling recapitulation of the interplay between heavy-metals ions and microorganisms. Additionally, heavy-metals remediation mechanisms adapted by microorganisms, the role of genetically modified (GM) microorganisms, life cycle assessment (LCA), techno-economic assessment (TEA) limitations, and prospects of microbial-assisted amelioration of heavy-metals have been elaborated in the current review with focus toward "sustainable and greener future."

Dynamics and thermal stability of the bypass polymerase, DinB homolog (Dbh)

The DinB homolog polymerase (Dbh) is a member of the Y-family of translesion DNA polymerases that can synthesize using a damaged DNA template. Since Dbh comes from the thermophilic archaeon Sulfolobus acidocaldarius, it is capable of functioning over a wide range of temperatures. Existing X-ray structures were determined at temperatures where the protein is least active. Here we use NMR and circular dichroism to understand how the structure and dynamics of Dbh are affected by temperature (2°C-65°C) and metal ion binding in solution. We measured hydrogen exchange protection factors, temperature coefficients, and chemical shift perturbations with and without magnesium and manganese. We report on regions of the protein that become more dynamic as the temperature is increased toward the functional temperature. Hydrogen exchange protection factors and temperature coefficients reveal that both the thumb and finger domains are very dynamic relative to the palm and little-finger (LF) domains. These trends remain true at high temperature with dynamics increasing as temperatures increase from 35°C to 50°C. Notably, NMR spectra show that the Dbh tertiary structure cold denatures beginning at 25°C and increases in denaturation as the temperature is lowered to 5°C with little change observed by CD. Above 35°C, chemical shift perturbation analysis in the presence and absence of magnesium and manganese reveals three ion binding sites, without DNA bound. In contrast, these bound metals are not apparent in any Dbh crystal structures of the protein without DNA. Two ion binding sites are confirmed to be near the active site, as reported in other Y-family polymerases, and we report a novel ion binding site in the LF domain. Thus, the solution-state structure of the Dbh polymerase is distinct from that of the solid-state structures and shows an unusually high cold denaturation temperature.

Trace gas oxidation sustains energy needs of a thermophilic archaeon at suboptimal temperatures

Diverse aerobic bacteria use atmospheric hydrogen (H2) and carbon monoxide (CO) as energy sources to support growth and survival. Such trace gas oxidation is recognised as a globally significant process that serves as the main sink in the biogeochemical H2 cycle and sustains microbial biodiversity in oligotrophic ecosystems. However, it is unclear whether archaea can also use atmospheric H2. Here we show that a thermoacidophilic archaeon, Acidianus brierleyi (Thermoproteota), constitutively consumes H2 and CO to sub-atmospheric levels. Oxidation occurs across a wide range of temperatures (10 to 70 °C) and enhances ATP production during starvation-induced persistence under temperate conditions. The genome of A. brierleyi encodes a canonical CO dehydrogenase and four distinct [NiFe]-hydrogenases, which are differentially produced in response to electron donor and acceptor availability. Another archaeon, Metallosphaera sedula, can also oxidize atmospheric H2. Our results suggest that trace gas oxidation is a common trait of Sulfolobales archaea and may play a role in their survival and niche expansion, including during dispersal through temperate environments.

Acidithiobacillia class members originating at sites within the Pacific Ring of Fire and other tectonically active locations and description of the novel genus 'Igneacidithiobacillus'

Recent studies have expanded the genomic contours of the Acidithiobacillia, highlighting important lacunae in our comprehension of the phylogenetic space occupied by certain lineages of the class. One such lineage is 'Igneacidithiobacillus', a novel genus-level taxon, represented by 'Igneacidithiobacillus copahuensis' VAN18-1T as its type species, along with two other uncultivated metagenome-assembled genomes (MAGs) originating from geothermally active sites across the Pacific Ring of Fire. In this study, we investigate the genetic and genomic diversity, and the distribution patterns of several uncharacterized Acidithiobacillia class strains and sequence clones, which are ascribed to the same 16S rRNA gene sequence clade. By digging deeper into this data and contributing to novel MAGs emerging from environmental studies in tectonically active locations, the description of this novel genus has been consolidated. Using state-of-the-art genomic taxonomy methods, we added to already recognized taxa, an additional four novel Candidate (Ca.) species, including 'Ca. Igneacidithiobacillus chanchocoensis' (mCHCt20-1TS), 'Igneacidithiobacillus siniensis' (S30A2T), 'Ca. Igneacidithiobacillus taupoensis' (TVZ-G3 TS), and 'Ca. Igneacidithiobacillus waiarikiensis' (TVZ-G4 TS). Analysis of published data on the isolation, enrichment, cultivation, and preliminary microbiological characterization of several of these unassigned or misassigned strains, along with the type species of the genus, plus the recoverable environmental data from metagenomic studies, allowed us to identify habitat preferences of these taxa. Commonalities and lineage-specific adaptations of the seven species of the genus were derived from pangenome analysis and comparative genomic metabolic reconstruction. The findings emerging from this study lay the groundwork for further research on the ecology, evolution, and biotechnological potential of the novel genus 'Igneacidithiobacillus'.

Chapter 6: The Breadth and Limits of Life on Earth

Scientific ideas about the potential existence of life elsewhere in the universe are predominantly informed by knowledge about life on Earth. Over the past ∼4 billion years, life on Earth has evolved into millions of unique species. Life now inhabits nearly every environmental niche on Earth that has been explored. Despite the wide variety of species and diverse biochemistry of modern life, many features, such as energy production mechanisms and nutrient requirements, are conserved across the Tree of Life. Such conserved features help define the operational parameters required by life and therefore help direct the exploration and evaluation of habitability in extraterrestrial environments. As new diversity in the Tree of Life continues to expand, so do the known limits of life on Earth and the range of environments considered habitable elsewhere. The metabolic processes used by organisms living on the edge of habitability provide insights into the types of environments that would be most suitable to hosting extraterrestrial life, crucial for planning and developing future astrobiology missions. This chapter will introduce readers to the breadth and limits of life on Earth and show how the study of life at the extremes can inform the broader field of astrobiology.

Impact of temperature on the virulence of Streptococcus agalactiae in Indonesian aquaculture: A better vaccine design is required

Due to their poikilothermic nature, fish are very sensitive to changes in temperature. Due to climate change, the average global temperature has increased by 1.5°C in the last century, which may have caused an increase in farmed fish mortality recently. Predictions using the model estimate that a 1°C increase in temperature could cause 3%-4% and 4%-6% mortality due to infectious diseases in organisms living in warm and temperate waters, respectively. There is a need to determine whether there is a relationship between increasing environmental temperature and disease virulence. This review examines the influence and impact of increasing temperatures due to climate change on the physiology and pathogenicity of Streptococcus agalactiae, which causes streptococcosis in tilapia and causes significant economic losses. Changes in the pathogenicity of S. agalactiae, especially its virulence properties due to increasing temperature, require changes in the composition design of the fish vaccine formula to provide better protection through the production of protective antibodies.

Acidithiobacillus species drive the formation of ferric-silica cemented microstructure: Insights into early hardpan development for mine site rehabilitation

Hardpan-based profiles naturally formed under semi-arid climatic conditions have substantial potential in rehabilitating sulfidic tailings, resulting from their aggregation microstructure regulated by Fe-Si cements. Nevertheless, eco-engineered approaches for accelerating the formation of complex cementation structure remain unclear. The present study aims to investigate the microbial functions of extremophiles on mineral dissolution, oxidation, and aggregation (cementation) through a microcosm experiment containing pyrites and polysilicates, of which are dominant components in typical sulfidic tailings. Microspectroscopic analysis revealed that pyrite was rapidly dissolved and massive microbial corrosion pits were displayed on pyrite surfaces. Synchrotron-based X-ray absorption spectroscopy demonstrated that approximately 30 % pyrites were oxidized to jarosite-like (ca. 14 %) and ferrihydrite-like minerals (ca. 16 %) in talc group, leading to the formation of secondary Fe precipitates. The Si ions co-dissolved from polysilicates may be embedded into secondary Fe precipitates, while these clustered Fe-Si precipitates displayed distinct morphology (e.g., "circular" shaped in the talc group, "fine-grained" shaped in the chlorite group, and "donut" shaped in the muscovite group). Moreover, the precipitates could join together and act as cementing agents aggregating mineral particles together, forming macroaggregates in talc and chlorite groups. The present findings revealed critical microbial functions on accelerating mineral dissolution, oxidation, and aggregation of pyrite and various silicates, which provided the eco-engineered feasibility of hardpan-based technology for mine site rehabilitation.

Microbes of biotechnological importance in acidic saline lakes in the Yilgarn Craton, Western Australia

Acidic salt lakes are environments that harbor an array of biologically challenging conditions. Through 16S rRNA, 18S rRNA, and ITS amplicon sequencing of eight such lakes across the Yilgarn Craton of Western Australia, we aim to understand the microbial ecology of these lakes with a focus on iron- and sulfur-oxidizing and reducing microorganisms that have theoretical application in biomining industries. In spite of the biological challenges to life in these lakes, the microbial communities were highly diverse. Redundancy analysis of soil samples revealed sulfur, ammonium, organic carbon, and potassium were significant diversities of the microbial community composition. The most abundant microbes with a hypothetical application in biomining include the genus 9 M32 of the Acidithiobacillus family, Alicyclobacillus and Acidiphilium, all of which are possible iron- and/or sulfur-oxidizing bacteria. It is evident through this study that these lakes harbor multiple organisms with potential in biomining industries that should be exploited and studied further.

Electrochemical and structural characterization of recombinant respiratory proteins of the acidophilic iron oxidizer Ferrovum sp. PN-J47-F6 suggests adaptations to the acidic pH at protein level

The tendency of the periplasmic redox proteins in acidophiles to have more positive redox potentials (Em) than their homologous counterparts in neutrophiles suggests an adaptation to acidic pH at protein level, since thermodynamics of electron transfer processes are also affected by acidic pH. Since this conclusion is mainly based on the electrochemical characterization of redox proteins from extreme acidophiles of the genus Acidithiobacillus, we aimed to characterize three recombinant redox proteins of the more moderate acidophile Ferrovum sp. PN-J47-F6. We applied protein film voltammetry and linear sweep voltammetry coupled to UV/Vis spectroscopy to characterize the redox behavior of HiPIP-41, CytC-18, and CytC-78, respectively. The Em-values of HiPIP-41 (571 ± 16 mV), CytC-18 (276 ± 8 mV, 416 ± 2 mV), and CytC-78 (308 ± 7 mV, 399 ± 7 mV) were indeed more positive than those of homologous redox proteins in neutrophiles. Moreover, our findings suggest that the adaptation of redox proteins with respect to their Em occurs more gradually in response to the pH, since there are also differences between moderate and more extreme acidophiles. In order to address structure function correlations in these redox proteins with respect to structural features affecting the Em, we conducted a comparative structural analysis of the Ferrovum-derived redox proteins and homologs of Acidithiobacillus spp. and neutrophilic proteobacteria. Hydrophobic contacts in the redox cofactor binding pockets resulting in a low solvent accessibility appear to be the major factor contributing to the more positive Em-values in acidophile-derived redox proteins. While additional cysteines in HiPIPs of acidophiles might increase the effective shielding of the [4Fe-4S]-cofactor, the tight shielding of the heme centers in acidophile-derived cytochromes is achieved by a drastic increase in hydrophobic contacts (A.f. Cyc41), and by a larger fraction of aromatic residues in the binding pockets (CytC-18, CytC-78).

Acetic acid stress response of the acidophilic sulfate reducer Acididesulfobacillus acetoxydans

Acid mine drainage (AMD) waters are a severe environmental threat, due to their high metal content and low pH (pH <3). Current technologies treating AMD utilize neutrophilic sulfate-reducing microorganisms (SRMs), but acidophilic SRM could offer advantages. As AMDs are low in organics these processes require electron donor addition, which is often incompletely oxidized into organic acids (e.g., acetic acid). At low pH, acetic acid is undissociated and toxic to microorganisms. We investigated the stress response of the acetotrophic Acididesulfobacillus acetoxydans to acetic acid. A. acetoxydans was cultivated in bioreactors at pH 5.0 (optimum). For stress experiments, triplicate reactors were spiked until 7.5 mM of acetic acid and compared with (non-spiked) triplicate reactors for physiological, transcriptomic, and membrane lipid changes. After acetic acid spiking, the optical density initially dropped, followed by an adaptation phase during which growth resumed at a lower growth rate. Transcriptome analysis revealed a downregulation of genes involved in glutamate and aspartate synthesis following spiking. Membrane lipid analysis revealed a decrease in iso and anteiso fatty acid relative abundance; and an increase of acetyl-CoA as a fatty acid precursor. These adaptations allow A. acetoxydans to detoxify acetic acid, creating milder conditions for other microorganisms in AMD environments.

Microbial diversity and community structure dynamics in acid mine drainage: Acidic fire with dissolved heavy metals

Acid mine drainage (AMD) is one of the leading causes of environmental pollution and is linked to public health and ecological consequences. Microbes-mineral interaction generates AMD, but microorganisms can also remedy AMD pollution. Exploring the microbial response to AMD effluents may reveal survival strategies in extreme ecosystems. Three distinct sites across a mine (inside the mine, the entrance of the mine, and outside) were selected to study their heavy metal concentrations due to significant variations in pH and physicochemical characteristics, and high-throughput sequencing was carried out to investigate the microbial diversity. The metal and ion concentrations followed the order SO42-, Fe, Cu, Zn, Mg, Pb, Co, Cr, and Ni from highest to lowest, respectively. Maximum sequences were allocated to Proteobacteria and Firmicutes. Among archaea, the abundance of Thaumarchaeota and Euryarchaeota was higher outside of mine. Most of the genera (23.12 %) were unclassified and unknown. The average OTUs (operational taxonomic units) were significantly higher outside the mine; however, diversity indices were not significantly different across the mine sites. Hierarchical clustering of selective genera and nMDS ordination of OTUs displayed greater segregation resolution inside and outside of mine, whereas the entrance samples clustered with greater similarity. Heterogeneous selection might be the main driver of community composition outside the mine, whereas stochastic processes became prominent inside the mine. However, the ANOSIM test shows a relatively even distribution of community composition within and between the groups. Microbial phyla showed both positive and negative correlations with physicochemical factors. A greater number of biomarkers were reported outside of the mine. Predictive functional investigation revealed the existence of putative degradative, metabolic, and biosynthetic pathways. This study presents a rare dataset in our understanding of microbial diversity and distribution as shaped by the ecological gradient and potential novelty in phylogenetic/taxonomic diversity in AMD, with potential biotechnological applications.

A transcriptomic atlas of acute stress response to low pH in multiple Issatchenkia orientalis strains

IMPORTANCE

Issatchenkia orientalis is a promising industrial chassis to produce biofuels and bioproducts due to its high tolerance to multiple environmental stresses such as low pH, heat, and other chemicals otherwise toxic for the most widely used microbes. Yet, little is known about specific mechanisms of such tolerance in this organism, hindering our ability to engineer this species to produce valuable biochemicals. Here, we report a comprehensive study of the mechanisms of acidic tolerance in this species via transcriptome profiling across variable pH for 12 different strains with different phenotypes. We found multiple regulatory mechanisms involved in tolerance to low pH in different strains of I. orientalis, marking potential targets for future gene editing and perturbation experiments.

Temperature, pH, and oxygen availability contributed to the functional differentiation of ancient Nitrososphaeria

Ammonia-oxidizing Nitrososphaeria are among the most abundant archaea on Earth and have profound impacts on the biogeochemical cycles of carbon and nitrogen. In contrast to these well-studied ammonia-oxidizing archaea (AOA), deep-branching non-AOA within this class remain poorly characterized because of a low number of genome representatives. Here, we reconstructed 128 Nitrososphaeria metagenome-assembled genomes from acid mine drainage and hot spring sediment metagenomes. Comparative genomics revealed that extant non-AOA are functionally diverse, with capacity for carbon fixation, carbon monoxide oxidation, methanogenesis, and respiratory pathways including oxygen, nitrate, sulfur, or sulfate, as potential terminal electron acceptors. Despite their diverse anaerobic pathways, evolutionary history inference suggested that the common ancestor of Nitrososphaeria was likely an aerobic thermophile. We further surmise that the functional differentiation of Nitrososphaeria was primarily shaped by oxygen, pH, and temperature, with the acquisition of pathways for carbon, nitrogen, and sulfur metabolism. Our study provides a more holistic and less biased understanding of the diversity, ecology, and deep evolution of the globally abundant Nitrososphaeria.

Comparative analysis of reconstructed ancestral proteins with their extant counterparts suggests primitive life had an alkaline habitat

To understand the origin and early evolution of life it is crucial to establish characteristics of the primordial environment that facilitated the emergence and evolution of life. One important environmental factor is the pH of the primordial environment. Here, we assessed the pH-dependent thermal stabilities of previously reconstructed ancestral nucleoside diphosphate kinases and ribosomal protein uS8s. The selected proteins were likely to be present in ancient organisms such as the last common ancestor of bacteria and that of archaea. We also assessed the thermal stability of homologous proteins from extant acidophilic, neutralophilic, and alkaliphilic microorganisms as a function of pH. Our results indicate that the reconstructed ancestral proteins are more akin to those of extant alkaliphilic bacteria, which display greater stability under alkaline conditions. These findings suggest that the common ancestors of bacterial and archaeal species thrived in an alkaline environment. Moreover, we demonstrate the reconstruction method employed in this study is a valuable technique for generating alkali-tolerant proteins that can be used in a variety of biotechnological and environmental applications.

Growth of soil ammonia-oxidizing archaea on air-exposed solid surface

Soil microorganisms often thrive as microcolonies or biofilms within pores of soil aggregates exposed to the soil atmosphere. However, previous studies on the physiology of soil ammonia-oxidizing microorganisms (AOMs), which play a critical role in the nitrogen cycle, were primarily conducted using freely suspended AOM cells (planktonic cells) in liquid media. In this study, we examined the growth of two representative soil ammonia-oxidizing archaea (AOA), Nitrososphaera viennensis EN76 and "Nitrosotenuis chungbukensis" MY2, and a soil ammonia-oxidizing bacterium, Nitrosomonas europaea ATCC 19718 on polycarbonate membrane filters floated on liquid media to observe their adaptation to air-exposed solid surfaces. Interestingly, ammonia oxidation activities of N. viennensis EN76 and "N. chungbukensis" MY2 were significantly repressed on floating filters compared to the freely suspended cells in liquid media. Conversely, the ammonia oxidation activity of N. europaea ATCC 19718 was comparable on floating filters and liquid media. N. viennensis EN76 and N. europaea ATCC 19718 developed microcolonies on floating filters. Transcriptome analysis of N. viennensis EN76 floating filter-grown cells revealed upregulation of unique sets of genes for cell wall and extracellular polymeric substance biosynthesis, ammonia oxidation (including ammonia monooxygenase subunit C (amoC3) and multicopper oxidases), and defense against H2O2-induced oxidative stress. These genes may play a pivotal role in adapting AOA to air-exposed solid surfaces. Furthermore, the floating filter technique resulted in the enrichment of distinct soil AOA communities dominated by the "Ca. Nitrosocosmicus" clade. Overall, this study sheds light on distinct adaptive mechanisms governing AOA growth on air-exposed solid surfaces.

Strategies of chemolithoautotrophs adapting to high temperature and extremely acidic conditions in a shallow hydrothermal ecosystem

BACKGROUND

Active hydrothermal vents create extreme conditions characterized by high temperatures, low pH levels, and elevated concentrations of heavy metals and other trace elements. These conditions support unique ecosystems where chemolithoautotrophs serve as primary producers. The steep temperature and pH gradients from the vent mouth to its periphery provide a wide range of microhabitats for these specialized microorganisms. However, their metabolic functions, adaptations in response to these gradients, and coping mechanisms under extreme conditions remain areas of limited knowledge. In this study, we conducted temperature gradient incubations of hydrothermal fluids from moderate (pH = 5.6) and extremely (pH = 2.2) acidic vents. Combining the DNA-stable isotope probing technique and subsequent metagenomics, we identified active chemolithoautotrophs under different temperature and pH conditions and analyzed their specific metabolic mechanisms.

RESULTS

We found that the carbon fixation activities of Nautiliales in vent fluids were significantly increased from 45 to 65 °C under moderately acidic condition, while their heat tolerance was reduced under extremely acidic conditions. In contrast, Campylobacterales actively fixed carbon under both moderately and extremely acidic conditions under 30 - 45 °C. Compared to Campylobacterales, Nautiliales were found to lack the Sox sulfur oxidation system and instead use NAD(H)-linked glutamate dehydrogenase to boost the reverse tricarboxylic acid (rTCA) cycle. Additionally, they exhibit a high genetic potential for high activity of cytochrome bd ubiquinol oxidase in oxygen respiration and hydrogen oxidation at high temperatures. In terms of high-temperature adaption, the rgy gene plays a critical role in Nautiliales by maintaining DNA stability at high temperature. Genes encoding proteins involved in proton export, including the membrane arm subunits of proton-pumping NADH: ubiquinone oxidoreductase, K+ accumulation, selective transport of charged molecules, permease regulation, and formation of the permeability barrier of bacterial outer membranes, play essential roles in enabling Campylobacterales to adapt to extremely acidic conditions.

CONCLUSIONS

Our study provides in-depth insights into how high temperature and low pH impact the metabolic processes of energy and main elements in chemolithoautotrophs living in hydrothermal ecosystems, as well as the mechanisms they use to adapt to the extreme hydrothermal conditions. Video Abstract.

Metagenomic Thermometer

Various microorganisms exist in environments, and each of them has its optimal growth temperature (OGT). The relationship between genomic information and OGT of each species has long been studied, and one such study revealed that OGT of prokaryotes can be accurately predicted based on the fraction of seven amino acids (IVYWREL) among all encoded amino-acid sequences in its genome. Extending this discovery, we developed a 'Metagenomic Thermometer' as a means of predicting environmental temperature based on metagenomic sequences. Temperature prediction of diverse environments using publicly available metagenomic data revealed that the Metagenomic Thermometer can predict environmental temperatures with small temperature changes and little influx of microorganisms from other environments. The accuracy of the Metagenomic Thermometer was also confirmed by a demonstration experiment using an artificial hot water canal. The Metagenomic Thermometer was also applied to human gut metagenomic samples, yielding a reasonably accurate value for human body temperature. The result further suggests that deep body temperature determines the dominant lineage of the gut community. Metagenomic Thermometer provides a new insight into temperature-driven community assembly based on amino-acid composition rather than microbial taxa.

Microbial communities from weathered outcrops of a sulfide-rich ultramafic intrusion, and implications for mine waste management

The Duluth Complex (DC) contains sulfide-rich magmatic intrusions that represent one of the largest known economic deposits of copper, nickel, and platinum group elements. Previous work showed that microbial communities associated with experimentally-weathered DC waste rock and tailings were dominated by uncultivated taxa and organisms not typically associated with mine waste. However, those experiments were designed for kinetic testing and do not necessarily represent the conditions expected for long-term environmental weathering. We used 16S rRNA gene methods to characterize the microbial communities present on the surfaces of naturally-weathered and historically disturbed outcrops of DC material. Rock surfaces were dominated by diverse uncultured Ktedonobacteria, Acetobacteria, and Actinobacteria, with abundant algae and other phototrophs. These communities were distinct from microbial assemblages from experimentally-weathered DC rocks, suggesting different energy and nutrient resources in environmental samples. Sulfide mineral incubations performed with and without algae showed that photosynthetic microorganisms could have an inhibitory effect on autotrophic populations, resulting in slightly lower sulfate release and differences in dominant microorganisms. The microbial assemblages from these weathered outcrops show how communities develop during weathering of sulfide-rich DC rocks and represent baseline data that could evaluate the effectiveness of future reclamation of waste produced by large-scale mining operations.

Genomics of soil depth niche partitioning in the Thaumarchaeota family Gagatemarchaeaceae

Knowledge of deeply-rooted non-ammonia oxidising Thaumarchaeota lineages from terrestrial environments is scarce, despite their abundance in acidic soils. Here, 15 new deeply-rooted thaumarchaeotal genomes were assembled from acidic topsoils (0-15 cm) and subsoils (30-60 cm), corresponding to two genera of terrestrially prevalent Gagatemarchaeaceae (previously known as thaumarchaeotal Group I.1c) and to a novel genus of heterotrophic terrestrial Thaumarchaeota. Unlike previous predictions, metabolic annotations suggest Gagatemarchaeaceae perform aerobic respiration and use various organic carbon sources. Evolutionary divergence between topsoil and subsoil lineages happened early in Gagatemarchaeaceae history, with significant metabolic and genomic trait differences. Reconstruction of the evolutionary mechanisms showed that the genome expansion in topsoil Gagatemarchaeaceae resulted from extensive early lateral gene acquisition, followed by progressive gene duplication throughout evolutionary history. Ancestral trait reconstruction using the expanded genomic diversity also did not support the previous hypothesis of a thermophilic last common ancestor of the ammonia-oxidising archaea. Ultimately, this study provides a good model for studying mechanisms driving niche partitioning between spatially related ecosystems.

Dechlorination of wastewater from shell-based glucosamine processing by mangrove wetland-derived fungi

Wastewater from processing crustacean shell features ultrahigh chloride content. Bioremediation of the wastewater is challenging due to the high chloride ion content, making it inhospitable for most microorganisms to survive and growth. In this study, mangrove wetland-derived fungi were first tested for their salt tolerance, and the highly tolerant isolates were cultured in shrimp processing wastewater and the chloride concentration was monitored. Notably, the filamentous fungal species Aspergillus piperis could remove over 70% of the chloride in the wastewater within 3 days, with the fastest biomass increase (2.01 times heavier) and chloride removal occurring between day one and two. The chloride ions were sequestered into the fungal cells. The genome of this fungal species contained Cl- conversion enzymes, which may have contributed to the ion removal. The fungal strain was found to be of low virulence in larval models and could serve as a starting point for further considerations in bioremediation of shell processing wastewater, promoting the development of green technology in the shell processing industry.

Extremophiles: the species that evolve and survive under hostile conditions

Extremophiles possess unique cellular and molecular mechanisms to assist, tolerate, and sustain their lives in extreme habitats. These habitats are dominated by one or more extreme physical or chemical parameters that shape existing microbial communities and their cellular and genomic features. The diversity of extremophiles reflects a long list of adaptations over millions of years. Growing research on extremophiles has considerably uncovered and increased our understanding of life and its limits on our planet. Many extremophiles have been greatly explored for their application in various industrial processes. In this review, we focused on the characteristics that microorganisms have acquired to optimally thrive in extreme environments. We have discussed cellular and molecular mechanisms involved in stability at respective extreme conditions like thermophiles, psychrophiles, acidophiles, barophiles, etc., which highlight evolutionary aspects and the significance of extremophiles for the benefit of mankind.

One-step synthesis of a pH switched pyrene-based fluorescent probe for ratiometric detection of HS- in real water samples

Only a few probes are suited for highly acidic environments and sensitive to pH values below 4. Thus, finding a solution for detecting strong acidic (pH value below 2) conditions is still challenging. Herein, we constructed and created a pH-switched fluorescent probe based on pyrene and a heteroatom containing pyridine unit. When exposed to acidic environments (pH 2.0), the probe's fluorescence redshifted with distinct colour and fluorescence changes owing to protonation on the nitrogen atom containing pyridine moiety, which could be deprotonated by HS- selectively compared to other competing analytes. Pyr can detect HS- with a rapid response within 5 s and showed very good quantum yield under acidic environments. The sensing mechanism was confirmed by Density Functional Theory (DFT) studies using the B3LYP and 6-31G+ (d) basis sets. Furthermore, the probe was utilized to monitor HS- in actual water samples and identify H2S gas by a simple paper strip test.