Functional redundancy of ubiquitin-like sulfur-carrier proteins facilitates flexible, efficient sulfur utilization in the primordial archaeon Thermococcus kodakarensis.

Ubiquitin-like proteins (Ubls) in eukaryotes and bacteria mediate sulfur transfer for the biosynthesis of sulfur-containing biomolecules and form conjugates with specific protein targets to regulate their functions. Here, we investigated the functions and physiological importance of Ubls in a hyperthermophilic archaeon by constructing a series of deletion mutants. We found that the Ubls (TK1065, TK1093, and TK2118) in Thermococcus kodakarensis are conjugated to their specific target proteins, and all three are involved in varying degrees in the biosynthesis of sulfur-containing biomolecules such as tungsten cofactor (Wco) and tRNA thiouridines. TK2118 (named UblB) is involved in the biosynthesis of Wco in a glyceraldehyde 3-phosphate:ferredoxin oxidoreductase, which is required for glycolytic growth, whereas TK1093 (named UblA) plays a key role in the efficient thiolation of tRNAs, which contributes to cellular thermotolerance. Intriguingly, in the presence of elemental sulfur (S0) in the culture medium, defective synthesis of these sulfur-containing molecules in Ubl mutants was restored, indicating that T. kodakarensis can use S0 as an alternative sulfur source without Ubls. Our analysis indicates that the Ubl-mediated sulfur-transfer system in T. kodakarensis is important for efficient sulfur assimilation, especially under low S0 conditions, which may allow this organism to survive in a low sulfur environment.IMPORTANCESulfur is a crucial element in living organisms, occurring in various sulfur-containing biomolecules including iron-sulfur clusters, vitamins, and RNA thionucleosides, as well as the amino acids cysteine and methionine. In archaea, the biosynthesis routes and sulfur donors of sulfur-containing biomolecules are largely unknown. Here, we explored the functions of Ubls in the deep-blanched hyperthermophilic archaeon, Thermococcus kodakarensis. We demonstrated functional redundancy of these proteins in the biosynthesis of tungsten cofactor and tRNA thiouridines and the significance of these sulfur-carrier functions, especially in low sulfur environments. We propose that acquisition of a Ubl sulfur-transfer system, in addition to an ancient inorganic sulfur assimilation pathway, enabled the primordial archaeon to advance into lower-sulfur environments and expand their habitable zone.

Effects of thermophilic and acidophilic microbial consortia on maize wet-milling steeping.

To understand the ecology of species and promote biotechnology through beneficial strain selection for improving starch yield in maize wet-milling steeping, bacterial diversity and community structure during the counter-current steeping process in a commercial steeping system were characterized and investigated. The microbial diversity in the steeping liquor, which consisted of 16 phyla, 131 families, and 290 genera, was more abundant compared to those present on the surface of unsteeped maize. As the counter-current steeping progressed, exposing newer maize to the older steepwater, Lactobacillus dominated, replacing Rahnella, Pseudomonas, Pantoea, and Serratia. The thermophilic and acidophilic microbial consortia were enriched through adaptive evolution engineering and employed to improve starch yield. Several steeping strategies were evaluated, including water alone, SO2 alone, mono-culture of B. coagulans, microbial consortia, and a combination of consortium and SO2. Combining the microbial consortium with SO2 significantly increased the starch yield to, about 66.4 ± 0.5%, a 22% and 46% increase over SO2 alone and the consortium alone, respectively. Scanning electron microscope (SEM) of steeped maize structure indicated that the combination of consortium and SO2 disrupted the protein matrix and widened gaps between starch granules in maize endosperm. This released proteins into the steepwater and left starch granules in the aleurone layer. The steeping strategy of using thermophilic and acidophilic microbial consortium as additives shows potential application as an environmentally friendly alternative to conventional maize steeping procedures.

Innovative hyper-thermophilic aerobic submerged membrane distillation bioreactor for wastewater reclamation.

For the first time, a hyper-thermophilic aerobic (>60 °C) bioreactor has been integrated with direct submerged membrane distillation (MD), highlighting its potential as an advanced wastewater treatment solution. The hyper-thermophilic aerobic bioreactor, operating up to 65 °C, is tailored for high organic removal, while MD efficiently produces clean water. Throughout the study, high removal rates of 99.5% for organic matter, 96.4% for ammonia, and 100% for phosphorus underscored the impressive adaptability of microorganisms to challenging hyper-thermophilic conditions and a successful combination with the MD process. Despite the extreme temperatures and substantial salinity accumulation reaching up to 12,532 µS/cm, the biomass of microorganisms increased by 1.6 times over a 92-day period, representing their remarkable resilience. The distillation flux ranged from 6.15 LMH to 8.25 LMH, benefiting from the temperature gradient in the hyper-thermophilic setting and the design of the tubular submerged MD membrane module. The system also excels in pH control, utilizing fewer alkali and nutritional resources than conventional systems. Meiothermus, Firmicutes, and Bacteroidetes, the three dominant species, played a crucial role, showcasing their significance in adapting to high salinity and decomposing organic matter.

A novel univariate interpolation and bivariate regression hybrid method application to biodegradation of bisphenol A diglycidyl ether using laccases from Geobacillus stearothermophilus and Geobacillus thermoparafinivorans strains.

Bisphenol A diglycidyl ether (BADGE), a derivative of the well-known endocrine disruptor Bisphenol A (BPA), is a potential threat to long-term environmental health due to its prevalence as a micropollutant. This study addresses the previously unexplored area of BADGE toxicity and removal. We investigated, for the first time, the biodegradation potential of laccase isolated from Geobacillus thermophilic bacteria against BADGE. The laccase-mediated degradation process was optimized using a combination of response surface methodology (RSM) and machine learning models. Degradation of BADGE was analyzed by various techniques, including UV-Vis spectrophotometry, high-performance liquid chromatography (HPLC), Fourier transform infrared (FTIR) spectroscopy, and gas chromatography-mass spectrometry (GC-MS). Laccase from Geobacillus stearothermophilus strain MB600 achieved a degradation rate of 93.28% within 30 min, while laccase from Geobacillus thermoparafinivorans strain MB606 reached 94% degradation within 90 min. RSM analysis predicted the optimal degradation conditions to be 60 min reaction time, 80°C temperature, and pH 4.5. Furthermore, CB-Dock simulations revealed good binding interactions between laccase enzymes and BADGE, with an initial binding mode selected for a cavity size of 263 and a Vina score of -5.5, which confirmed the observed biodegradation potential of laccase. These findings highlight the biocatalytic potential of laccases derived from thermophilic Geobacillus strains, notably MB600, for enzymatic decontamination of BADGE-contaminated environments.

Optimization of lactic acid production from apple and tomato pomaces by thermotolerant bacteria.

The production of lactic acid (LA) through biomass fermentation represents a promising alternative to the chemical synthesis. The use of agri-food by-products as fermentable carbohydrate sources can improve process sustainability by reducing waste and valorizing residual biomass. This study assessed the use of apple and tomato pomaces for producing LA through fermentation using thermotolerant bacteria under aerobic and non-sterile conditions. Three bacteria were evaluated and Heyndrickxia coagulans DSM 2314 was selected for its ability to produce LA from hydrolyzates of apple pomace (APH) and tomato pomace (TPH). The fermentation conditions were optimized to maximize LA production from APH, TPH and a mixture of both hydrolyzates. Therefore, LA productions ranged from 36.98 ± 0.41 to 40.72 ± 0.43 g/L, with yields from 0.86 ± 0.02 to 1.01 ± 0.01 g/g. Yeast extract was necessary as a nitrogen source for fermenting APH, while TPH and the mixture of both hydrolyzates did not require any supplementation. Other nitrogen sources, such as wine lees, urea and NH3Cl, were tested for fermenting APH. However, mixing this hydrolyzate with TPH proved to be the most viable alternative. This study demonstrates the potential for valorizing apple and tomato pomaces into LA under feasible fermentation conditions.

Rational design approach to improve the solubility of the ß-sandwich domain 1 of a thermophilic protein.

The ß-sandwich domain 1 (SD1) of islandisin is a stable thermophilic protein with surface loops that can be redesigned for specific target binding, architecturally comparable to the variable domain of immunoglobulin (IgG). SD1's propensity to aggregate due to incorrect folding and subsequent accumulation in Escherichia coli inclusion bodies limits its use in biotechnological applications. We rationally designed SD1 for improved variants that were expressed in soluble forms in E. coli while maintaining the intrinsic thermal stability of the protein (melting temperature (Tm) = 73). We used FoldX's ΔΔG predictions to find beneficial mutations and aggregation-prone regions (APRs) using Tango. The S26K substitution within protein core residues did not affect protein stability. Among the soluble mutants studied, the S26K/Q91P combination significantly improved the expression and solubility of SD1. We also examined the effects of the surface residue, pH, and concentration on the solubility of SD1. We showed that the surface polarity of proteins had little or no effect on solubility, whereas surface charges played a substantial role. The storage stability of several SD1 variants was impaired at pH values near their isoelectric point, and pH levels resulting in highly charged groups. We observed that mutations that create an uneven distribution of charged groups on the SD1 surface could enhance protein solubility by eliminating favorable protein-protein surface charge interactions. Our findings suggest that SD1 is mutationally tolerant to new functionalities, thus providing a novel perspective for the application of rational design to improve the solubility of targeted proteins.

2-Site versus 3-site models of ATP hydrolysis by F1-ATPase: definitive mathematical proof using combinatorics and conservation equations.

The F1-ATPase enzyme is the smallest-known molecular motor that rotates in 120° steps, driven by the hydrolysis of ATP. It is a multi-subunit enzyme that contains three catalytic sites. A central question is how the elementary chemical reactions that occur in the three sites are coupled to mechanical rotation. Various models and coupling schemes have been formulated in an attempt to answer this question. They can be classified as 2-site (bi-site) models, exemplified by Boyer's binding change mechanism first proposed 50 years ago, and 3-site (tri-site) models such as Nath's torsional mechanism, first postulated 25 years ago and embellished 1 year back. Experimental data collated using diverse approaches have conclusively shown that steady-state ATP hydrolysis by F1-ATPase occurs in tri-site mode. Hence older models have been continually modified to make them conform to the new facts. Here, we have developed a pure mathematical approach based on combinatorics and conservation laws to test if proposed models are 2-site or 3-site. Based on this novel combinatorial approach, we have proved that older and modified models are effectively bi‒site models in that catalysis and rotation in F1-ATPase occurs in these models with only two catalytic sites occupied by bound nucleotide. Hence these models contradict consensus experimental data. The recent 2023 model of ATP hydrolysis by F1-ATPase has been proved to be a true tri-site model based on our novel mathematical approach. Such pure mathematical proofs constitute an important step forward for ATP mechanism. However, in what must be considered an aspect with great scientific potential, the power of such mathematical proofs has not been fully exploited to solve molecular biological problems, in our opinion. We believe that the creative application of pure mathematical proofs (for another example see Nath in Theory Biosci 141:249-260, 2022) can help resolve with finality various longstanding molecular-level issues that arise as a matter of course in the analysis of fundamental biological problems. Such issues have proved extraordinarily difficult to resolve by standard experimental, theoretical, or computational approaches.

Thermophilic and mesophilic digestion of high-solid oily food waste: How to ensure long-term and stable continuous operation?

Commonly high lipid in food waste confronts anaerobic digestion with improved energy production and also inhibition risk from the intermediate long chain fatty acids (LCFAs). Combined with operation challenges from anaerobic digestion of food waste itself, coping strategies are necessitated to ensure stable operation for oily food waste (OFW). A parallel thermophilic (TD) and mesophilic digestion (MD) of high-solid OFW was conducted and operated continuously for a long term. It was clarified that challenges were mainly from acidification, trace metal deficiency and LCFA inhibition. Acidification resulted in an abrupt pH decline to even below 6.00, and over 75% drop of biogas production rate. In addition to the requirements of saturated strong alkali to maintain an appropriate range, supplementation of trace metals were proven effective in counteracting the sharp decrease of biogas production rate. The TD was observed more competent in coping with the acidification than the MD, while the TD needed more supplementation of trace metals at approximately 0.10 mg Fe/g chemical oxygen demand (COD)added, 0.01 mg Co/g CODadded and 0.01 mg Ni/g CODadded. The TD was more adaptable in LCFA conversion due to the stronger ability of overcoming the palmitic acid (C16:0) accumulation. The MD experienced a prolonged recovery period owing to LCFA inhibition shortly after acidification. Similar operation performance was ultimately achieved for the TD and MD by the counteractions, with a methane yield and volatile solids (VS) removal efficiency at about 0.60 L/g VSadded and 75.0%, respectively. In summary, combined pH control and trace metal supplementation, and prevention and recovery of LCFA inhibition were necessary for the stability insurance of a long-term continuous digestion of oily food waste.

Industrial biotechnology goes thermophilic: Thermoanaerobes as promising hosts in the circular carbon economy.

Transitioning away from fossil feedstocks is imperative to mitigate climate change, and necessitates the utilization of renewable, alternative carbon and energy sources to foster a circular carbon economy. In this context, lignocellulosic biomass and one-carbon compounds emerge as promising feedstocks that could be renewably upgraded by thermophilic anaerobes (thermoanaerobes) via gas fermentation or consolidated bioprocessing to value-added products. In this review, the potential of thermoanaerobes for cost-efficient, effective and sustainable bioproduction is discussed. Metabolic and bioprocess engineering approaches are reviewed to draw a comprehensive picture of current developments and future perspectives for the conversion of renewable feedstocks to chemicals and fuels of interest. Selected bioprocessing scenarios are outlined, offering practical insights into the applicability of thermoanaerobes at a large scale. Collectively, the potential advantages of thermoanaerobes regarding process economics could facilitate an easier transition towards sustainable bioprocesses with renewable feedstocks.

Acidothermus cellulolyticus E1 endoglucanase expressed in planta undergoes extensive hydroxyproline-O-glycosylation and exhibits enhanced impact on biomass digestibility.

KEY MESSAGE: E1 holoenzyme was extensively Hyp-O-glycosylated at the proline rich linker region in plants, which substantially increased the molecular size and improved the enzymatic digestibility of the biomass of transgenic plants. Thermophilic E1 endo-1,4-ß-glucanase derived from Acidothermus cellulolyticus has been frequently expressed in planta to reconstruct the plant cell wall to overcome biomass recalcitrance. However, the expressed holoenzyme exhibited a larger molecular size (~ 100 kDa) than the theoretical one (57 kDa), possibly due to posttranslational modifications in the recombinant enzyme within plant cells. This study investigates the glycosylation of the E1 holoenzyme expressed in tobacco plants and determines its impact on enzyme activity and biomass digestibility. The E1 holoenzyme, E1 catalytic domain (E1cd) and E1 linker (E1Lk) were each expressed in tobacco plants and suspension cells. The accumulation of holoenzyme was 2.0- to 2.3- times higher than that of E1cd. The proline-rich E1Lk region was extensively hydroxyproline-O-glycosylated with arabinogalactan polysaccharides. Compared with E1cd, the holoenzyme displayed a broader optimal temperature range (70 to 85 ºC). When grown in greenhouse, the expression of E1 holoenzyme induced notable phenotypic changes in plants, including delayed flowering and leaf variegation post-flowering. However, the final yield of plant biomass was not significantly affected. Finally, plant biomass engineering with E1 holoenzyme showed 1.7- to 1.8-fold higher saccharification efficiency than the E1cd lines and 2.4- to 2.7-fold higher than the wild-type lines, which was ascribed to the synergetic action of the E1Lk and cellulose binding module in reducing cell wall recalcitrance.

Production and characterization of rhamnolipid biosurfactant from thermophilic Geobacillus stearothermophilus bacterium isolated from Uhud mountain.

Introduction: Biosurfactants have been given considerable attention as they are potential candidates for several biotechnological applications. Materials and methods: In this study, a promising thermophilic biosurfactant-producing HA-2 was isolated from the volcanic and arid region of Uhud mountain, Madinah, Saudi Arabia. It was identified using 16S rRNA gene sequence analysis. The biosurfactant production ability was screened using different methods such as the drop collapse test, oil spreading test, hemolytic activity test, CTAB test, and emulsification index. The ability of rhamnolipid production by the tested strain was confirmed by the polymerase chain reaction (PCR) of rhlAB. The affinity of thermophilic HA-2 to hydrophobic substrates was also investigated. Optimization of biosurfactant production was conducted. The biological activities of produced surfactant were investigated. Results and discussion: The isolated HA-1 was identified as Geobacillus stearothermophilus strain OR911984. It could utilize waste sunflower frying oil (WSFF) oil as a low-cost carbon source. It showed high emulsification activity (52 ± 0.0%) and positive results toward other biosurfactant screening tests. The strain showed high cell adhesion to hexane with 41.2% cell surface hydrophobicity. Fourier-transform infrared (FTIR) spectra indicated the presence of hydrophobic chains that comprise lipids, sugars, and hydrophilic glycolipid components. The optimization results showed the optimal factors included potato peel as a carbon source with 68.8% emulsification activity, yeast extract as a nitrogen source with 60% emulsification activity, a pH of 9 (56.6%), and a temperature of 50° (72%). The kinetics showed that optimum biosurfactant production (572.4 mg/L) was recorded at 5 days of incubation. The produced rhamnolipid biosurfactant showed high antimicrobial activity against some human and plant pathogenic bacterial and fungal isolates and high antioxidant activity (90.4%). In addition, it enhanced wheat (Triticum aestivum) growth, with the greatest enhancement obtained with the 5% concentration. Therefore, thermophilic G. stearothermophilus is a promising rhamnolipid biosurfactant producer that utilizes many organic wastes. The produced biosurfactant could be applied as a promising emulsifier, antimicrobial, antioxidant, and plant growth promoter.

Genome-centric metagenomics and methanogenic pathway analysis for acclimated anaerobic digestion of chicken manure with high ammonia stressed under thermophilic condition.

Thermophilic anaerobic digestion (AD) of animal manure offers various environmental benefits but the process requires a microbial community acclimatized to high ammonia. In current study, a lab-scale continuous stirred tank reactor (CSTR) fed with chicken manure was operated under thermophilic condition for 450 days in total. Results showed that the volumetric methane production decreased from 445 to 328 and sharply declined to 153 mL L-1·d-1 with feeding total solid (TS) step increased from 5% to 7.5% and 10%, respectively. While, after a long-term stop feeding for 80 days, highly disturbed reactor was able to recover methane generation to 739 mL L-1·d-1 at feeding TS of 10%. Isotope analysis indicted acetate converted to methane through the syntrophic acetate oxidation and hydrogenotrophic methanogenesis (SAO-HM) pathway increased from 33% to 63% as the concentration of ammonium increased from 2493 to 6258 mg L-1. Significant different in the genome expression of the SAO bacterial from 0.09% to 1.23%, combining with main hydrogenotrophic partners (Methanoculleus spp. and Methanothermobacter spp.) contented of 2.1% and 99.9% during inhibitory and recovery stages, respectively. The highly expressed KEGG pathway in level 3 (enzyme genes) for the Recovery sludge combining with the extraordinary high abundance of genera Halocella sp. suggested that Halocella sp. might be a highly efficient hydrolytic and acidogenic microorganism and enhance the process of SAO during carbon metabolic flow to methane. This report will be a basis for further study of AD studies on high nitrogen content of poultry manure.

[High-temperature adaptation mechanisms and biotechnological potentials of thermophilic cyanobacteria].

Thermophilic cyanobacteria are prokaryotic organisms that possess exceptional heat-resistant characteristics. This group serves as an excellent model for investigating the heat tolerance of higher photosynthetic organisms, including higher plants, some protists (such as algae and euglena), and bacteria. Analyzing the mechanisms of high-temperature adaptation in thermophilic cyanobacteria can enhance our understanding of how photosynthetic organisms and microorganisms tolerate high temperatures at the molecular level. Additionally, these thermotolerant cyanobacteria have the potential to contribute to breeding heat-tolerant plants and developing microbial cell factories. This review summarizes current research on thermophilic cyanobacteria, focusing on their ecology, morphology, omics studies, and mechanisms of high-temperature tolerance. It offers insight into the potential biotechnological applications of thermophilic cyanobacteria and highlights future research opportunities. Specifically, attention is given to the photosynthetic physiology and metabolism of cyanobacteria, and the molecular basis of heat-tolerance mechanisms in thermophilic cyanobacteria is explored.

How Do Thermophiles Organize Their Genomes?

All cells must maintain the structural and functional integrity of the genome under a wide range of environments. High temperatures pose a formidable challenge to cells by denaturing the DNA double helix, causing chemical damage to DNA, and increasing the random thermal motion of chromosomes. Thermophiles, predominantly classified as bacteria or archaea, exhibit an exceptional capacity to mitigate these detrimental effects and prosper under extreme thermal conditions, with some species tolerating temperatures higher than 100°C. Their genomes are mainly characterized by the presence of reverse gyrase, a unique topoisomerase that introduces positive supercoils into DNA. This enzyme has been suggested to maintain the genome integrity of thermophiles by limiting DNA melting and mediating DNA repair. Previous studies provided significant insights into the mechanisms by which NAPs, histones, SMC superfamily proteins, and polyamines affect the 3D genomes of thermophiles across different scales. Here, I discuss current knowledge of the genome organization in thermophiles and pertinent research questions for future investigations.

Induction of Apoptosis with Silver Nanoparticles Obtained Using Thermophilic Bacteria.

Yeasts resistant to antifungals have become an increasing risk to human health. One of the best antimicrobial properties is reported to be present in silver nanoparticles (AgNPs); however, little is known about the antimicrobial potential of AgNPs produced using thermophilic bacteria. How AgNPs cause cell death is different depending on the type of the cell, and the mode of death induced is cell-type specific. Apoptosis, one of the types of regulated cell death, can be extremely useful in the fight against infection because surrounding cells that have phagocytic activity can efficiently absorb the apoptotic bodies formed during apoptosis. In the course of this work, for the first time, comprehensive antifungal studies of AgNPs were performed using thermophilic Geobacillus spp. bacteria against Candida guilliermondii, also with the addition of the model yeast Saccharomyces cerevisiae. The determined minimal inhibitory concentrations (MICs) were 10 µg/mL against C. guilliermondii and 50 µg/mL against S. cerevisiae for Geobacillus sp. strain 25 AgNPs, and for Geobacillus sp. 612 the MICs were 5 µg/mL and 25 µg/mL, respectively. It was shown for the first time that the exposure of the yeast cells leads to caspase activation in both S. cerevisiae and C. guilliermondii after exposure to Geobacillus spp. AgNPs. Also, a statistically significant change in the number of cells with permeable membranes was detected. Moreover, it was shown that the antimicrobial effect of the AgNPs is related to ROS generation and lipid peroxidation in C. guilliermondii yeast.

Characterization and biological activities of a novel exopolysaccharide produced from Geobacillus thermodenitrificans HBB 111 strain.

In this study, EPS production conditions of Geobacillus thermodenitrificans HBB 111, a thermophilic microorganism, were optimized and the amount of produced EPS (EPS 111) was found to be 44.0 mg/L. EPS 111 was purified using ion exchange chromatography and gel filtration chromatography, and a single type of exopolysaccharide was obtained. The structure of the purified EPS 111 was evaluated by TLC, FTIR, NMR, and GC-MS, and it was observed that it contained hexose (glucose, fructose, galactose and mannose) and pentose sugars. From the SEM photographs, it was understood that EPS 111 had an amorphous, rough, and layered structure. It was found that purified EPS 111 had low cytotoxicity (2.3%) and exhibited high antioxidant activity and remarkable antidiabetic, prebiotic and fibrinolytic activities. It is very valuable that the purified EPS 111 in this study offers multiple biological activities compared to the thermophilic EPSs reported in the literature and has a high potential for use in biotechnological and biomedical fields.

Isolation and Characterization of Thermophilic Bacteria from a Hot Spring in the State of Hidalgo, Mexico, and Geochemical Analysis of the Thermal Water.

Hot springs worldwide can be a source of extremophilic microorganisms of biotechnological interest. In this study, samplings of a hot spring in Hidalgo, Mexico, were conducted to isolate, identify, and characterize morphologically, biochemically, and molecularly those bacterial strains with potential industrial applications. In addition, a physicochemical and geochemical examination of the hot spring was conducted to fully understand the study region and its potential connection to the strains discovered. The hot spring was classified as sulfate-calcic according to the Piper Diagram; the hydrogeochemical analysis showed the possible interactions between minerals and water. Eighteen bacterial strains were isolated with optimal growth temperatures from 50 to 55 °C. All strains are Gram-positive, the majority having a rod shape, and one a round shape, and 17 produce endospores. Hydrolysis tests on cellulose, pectin, and xylan agar plates demonstrated enzymatic activity in some of the strains. Molecular identification through the 16S rDNA gene allowed classification of 17 strains within the Phylum Firmicutes and one within Deinococcus-Thermus. The bacterial strains were associated with the genera Anoxybacillus, Bacillus, Anerunibacillus, Paenibacillus, and Deinococcus, indicating a diversity of bacterial strains with potential industrial applications.

Co-occurrence of dominant bacteria and methanogenic archaea and their metabolic traits in a thermophilic anaerobic digester.

Thermophilic anaerobic digestion (TAD) represents a promising biotechnology for both methane energy production and waste stream treatment. However, numerous critical microorganisms and their metabolic characteristics involved in this process remain unidentified due to the limitations of culturable isolates. This study investigated the phylogenetic composition and potential metabolic traits of bacteria and methanogenic archaea in a TAD system using culture-independent metagenomics. Predominant microorganisms identified in the stable phase of TAD included hydrogenotrophic methanogens (Methanothermobacter and Methanosarcina) and hydrogen-producing bacteria (Coprothermobacter, Acetomicrobium, and Defluviitoga). Nine major metagenome-assembled genomes (MAGs) associated with the dominant genera were selected to infer their metabolic potentials. Genes related to thermal resistance were widely found in all nine major MAGs, such as the molecular chaperone genes, Clp protease gene, and RNA polymerase genes, which may contribute to their predominance under thermophilic condition. Thermophilic temperatures may increase the hydrogen partial pressure of Coprothermobacter, Acetomicrobium, and Defluviitoga, subsequently altering the primary methanogenesis pathway from acetoclastic pathway to hydrogenotrophic pathway in the TAD. Consequently, genes encoding the hydrogenotrophic methanogenesis pathway were the most abundant in the recovered archaeal MAGs. The potential interaction between hydrogen-producing bacteria and hydrogenotrophic methanogens may play critical roles in TAD processes.

Genomic and phenotypic characterization of Thermosynechococcus-like strains reveals eight species within the genus Thermosynechococcus and a novel genus Parathermosynechococcus gen. nov.

Thermophilic unicellular cyanobacteria of the family Thermosynechococcaceae are essential primary producers and integral components of many microbial mats found in hot springs of Asia and North America. Historically, based on their simple morphology, these organisms, along with members of taxonomically unrelated thermophilic Thermostichaceae have been described with a generic term, "Synechococcus", used for elongated unicellular cyanobacteria. This has created significant misperception in the scientific literature regarding the taxonomic status of these essential thermophilic primary producers and their relationship with Synechococcus sensu stricto. In this manuscript, we attempted a genome-driven taxonomic reevaluation of the family Thermosynechococcaceae. Application of genomic analyses such as GTDB classification, ANI/AAI and phylogenomics support the delineation of eight species within genus Thermosynechococcus. Two subspecies were further identified within T. taiwanensis by dDDH and phylogenomics. Moreover, the results also suggest the presence of two putative new genera phylogenetically alongside genus Thermosynechococcus, a thermophilic genus Parathermosynechococcus represented by PCC 6715 and a non-thermophilic genus represented by PCC 6312. The proposed genospecies and new genera were further integrated with morphological and/or ecological information. Interestingly, the phylogeny of 16S-23S ITS achieved a better taxonomic relationship than that of 16S rRNA and supported the genome-based classification of Thermosynechococcus spp. Finally, the pan-genome analysis indicated a conserved pattern of genomic core among known members of Thermosynechococcus.