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ABSTRACT A comprehensive pangenomic approach was employed to analyze the genomes of 75 type II methylotrophs spanning various genera. Our investigation revealed 256 exact core gene families shared by all 75 organisms, emphasizing their crucial role in the survival and adaptability of these organisms. Additionally, we predicted the functionality of 12 hypothetical proteins. The analysis unveiled a diverse array of genes associated with key metabolic pathways, including methane, serine, glyoxylate, and ethylmalonyl-CoA (EMC) metabolic pathways. While all selected organisms possessed essential genes for the serine pathway,Methylooceanibacter marginalislacked serine hydroxymethyltransferase (SHMT), andMethylobacterium variabileexhibited both isozymes of SHMT, suggesting its potential to utilize a broader range of carbon sources. Notably,Methylobrevissp. displayed a unique serine-glyoxylate transaminase isozyme not found in other organisms. Only nine organisms featured anaplerotic enzymes (isocitrate lyase and malate synthase) for the glyoxylate pathway, with the rest following the EMC pathway.Methylovirgulasp. 4MZ18 stood out by acquiring genes from both glyoxylate and EMC pathways, andMethylocapsasp. S129 featured an A-form malate synthase, unlike the G-form found in the remaining organisms. Our findings also revealed distinct phylogenetic relationships and clustering patterns among type II methylotrophs, leading to the proposal of a separate genus forMethylovirgulasp. 4M-Z18 andMethylocapsasp. S129. This pangenomic study unveils remarkable metabolic diversity, unique gene characteristics, and distinct clustering patterns of type II methylotrophs, providing valuable insights for future carbon sequestration and biotechnological applications. IMPORTANCEMethylotrophs have played a significant role in methane-based product production for many years. However, a comprehensive investigation into the diverse genetic architectures across different genera of methylotrophs has been lacking. This study fills this knowledge gap by enhancing our understanding of core hypothetical proteins and unique enzymes involved in methane oxidation, serine, glyoxylate, and ethylmalonyl-CoA pathways. These findings provide a valuable reference for researchers working with other methylotrophic species. Furthermore, this study not only unveils distinctive gene characteristics and phylogenetic relationships but also suggests a reclassification forMethylovirgulasp. 4M-Z18 andMethylocapsasp. S129 into separate genera due to their unique attributes within their respective genus. Leveraging the synergies among various methylotrophic organisms, the scientific community can potentially optimize metabolite production, increasing the yield of desired end products and overall productivity. 

The investigation aimed to determine whether altering metal microstructure by introducing special grain boundaries through annealing could reduce the corrosion damage observed in the presence of pyruvate. Oxygen-free pure copper coupons were annealed at 325°C, 475°C and 950°C for varying durations to optimize the formation of ∑3 special boundaries. Samples annealed at 475°C for 30 min had the highest yield of such boundaries, thus, were selected for testing. Annealed and as-received, untreated, copper specimens were exposed under stagnant conditions to an aqueous oxic solution of sodium pyruvate for 30 days. Microscopy, spectroscopy, and electrochemical methods were employed to characterize the specimens prior to and following pyruvate exposure. Pyruvate caused localized corrosion of copper seen as micro pitting, irrespective of the specimen treatment. Reduced pitting severity and a decrease in the corrosion rate by 32 % were recorded for annealed coupons when compared to as-received ones. It is proposed that the difference in thickness and morphology of the oxide layer between annealed and as-received coupons, evidenced through electrochemical techniques, is the likely contributor to the improved corrosion resistance of annealed coupons. 

Abstract Despite decades of research, metallic corrosion remains a long‐standing challenge in many engineering applications. Specifically, designing a material that can resist corrosion both in abiotic as well as biotic environments remains elusive. Here a lightweight sulfur–selenium (S–Se) alloy is designed with high stiffness and ductility that can serve as an excellent corrosion‐resistant coating with protection efficiency of ≈99.9% for steel in a wide range of diverse environments. S–Se coated mild steel shows a corrosion rate that is 6–7 orders of magnitude lower than bare metal in abiotic (simulated seawater and sodium sulfate solution) and biotic (sulfate‐reducing bacterial medium) environments. The coating is strongly adhesive, mechanically robust, and demonstrates excellent damage/deformation recovery properties, which provide the added advantage of significantly reducing the probability of a defect being generated and sustained in the coating, thus improving its longevity. The high corrosion resistance of the alloy is attributed in diverse environments to its semicrystalline, nonporous, antimicrobial, and viscoelastic nature with superior mechanical performance, enabling it to successfully block a variety of diffusing species. 

The effect of varying surface roughness on microbiologically influenced corrosion by a model sulfate reducing bacteriumOleidesulfovibrio alaskensisG20 culture on copper 101 coupons was investigated using microscopic, spectroscopic and surface characterization techniques. After 7-day of anoxic exposure abundant biodeposits consisting of sessile cells and copper sulfide minerals were found and pitting attack was observed upon their removal. Results showed that the distribution and thickness of the biodeposits as well as the pitting severity were affected by the varying surface roughness. A direct relationship between surface roughness and microbial activity was not observed. However, a statistically significant reduction in the corrosion rate was recorded when the surface roughness was decreased from ∼2.71 μm to ∼0.006 μm. 

Noncoding RNAs (ncRNAs) play key roles in the regulation of important pathways, including cellular growth, stress management, signaling, and biofilm formation. Sulfate-reducing bacteria (SRB) contribute to huge economic losses causing microbial-induced corrosion through biofilms on metal surfaces. To effectively combat the challenges posed by SRB, it is essential to understand their molecular mechanisms of biofilm formation. This study aimed to identify ncRNAs in the genome of a model SRB, Oleidesulfovibrio alaskensis G20 (OA G20). Three in silico approaches revealed genome-wide distribution of 37 ncRNAs excluding tRNAs in the OA G20. These ncRNAs belonged to 18 different Rfam families. This study identified riboswitches, sRNAs, RNP, and SRP. The analysis revealed that these ncRNAs could play key roles in the regulation of several pathways of biosynthesis and transport involved in biofilm formation by OA G20. Three sRNAs, Pseudomonas P10, Hammerhead type II, and sX4, which were found in OA G20, are rare and their roles have not been determined in SRB. These results suggest that applying various computational methods could enrich the results and lead to the discovery of additional novel ncRNAs, which could lead to understanding the “rules of life of OA G20” during biofilm formation. 

In the present study, a thermophilic strain designated CamBx3 was isolated from the Campanario hot spring, Chile. Based on 16S rRNA gene sequence, phylogenomic, and average nucleotide identity analysis the strain CamBx3 was identified asBacillus paralicheniformis. Genome analysis ofB. paralicheniformisCamBx3 revealed the presence of genes related to heat tolerance, exopolysaccharides (EPS), dissimilatory nitrate reduction, and assimilatory sulfate reduction. The pangenome analysis of strain CamBx3 with eightBacillusspp. resulted in 26,562 gene clusters, 7,002 shell genes, and 19,484 cloud genes. The EPS produced byB. paralicheniformisCamBx3 was extracted, partially purified, and evaluated for its functional activities.B. paralicheniformisCamBx3 EPS with concentration 5 mg mL⁻¹showed an optimum 92 mM ferrous equivalent FRAP activity, while the same concentration showed a maximum 91% of Fe²⁺chelating activity.B. paralicheniformisCamBx3 EPS (0.2 mg mL⁻¹) demonstratedβ-glucosidase inhibition. The EPS formed a viscoelastic gel at 45°C with a maximum instantaneous viscosity of 315 Pa.s at acidic pH 5. The present study suggests thatB. paralicheniformisCamBx3 could be a valuable resource for biopolymers and bioactive molecules for industrial applications. 

Over the past decade, copper (Cu) has been recognized as a crucial metal in the differential expression of soluble (sMMO) and particulate (pMMO) forms of methane monooxygenase (MMO) through a mechanism referred to as the “Cu switch”. In this study, we used Methylosinus trichosporium OB3b as a model bacterium to investigate the range of Cu concentrations that trigger the expression of sMMO to pMMO and its effect on growth and methane oxidation. The Cu switch was found to be regulated within Cu concentrations from 3 to 5 µM, with a strict increase in the methane consumption rates from 3.09 to 3.85 µM occurring on the 6th day. Our findings indicate that there was a decrease in the fold changes in the expression of methanobactin (Mbn) synthesis gene (mbnA) with a higher Cu concentration, whereas the Ton-B siderophore receptor gene (mbnT) showed upregulation at all Cu concentrations. Furthermore, the upregulation of the di-heme enzyme at concentrations above 5 µM Cu may play a crucial role in the copper switch by increasing oxygen consumption; however, the role has yet not been elucidated. We developed a quantitative assay based on the naphthalene–Molisch principle to distinguish between the sMMO- and pMMO-expressing cells, which coincided with the regulation profile of the sMMO and pMMO genes. At 0 and 3 µM Cu, the naphthol concentration was higher (8.1 and 4.2 µM, respectively) and gradually decreased to 0 µM naphthol when pMMO was expressed and acted as the sole methane oxidizer at concentrations above 5 µM Cu. Using physical protein–protein interaction, we identified seven transporters, three cell wall biosynthesis or degradation proteins, Cu resistance operon proteins, and 18 hypothetical proteins that may be involved in Cu toxicity and homeostasis. These findings shed light on the key regulatory genes of the Cu switch that will have potential implications for bioremediation and biotechnology applications. 

The growth and survival of an organism in a particular environment is highly depends on the certain indispensable genes, termed as essential genes. Sulfate-reducing bacteria (SRB) are obligate anaerobes which thrives on sulfate reduction for its energy requirements. The present study usedOleidesulfovibrio alaskensisG20 (OA G20) as a model SRB to categorize the essential genes based on their key metabolic pathways. Herein, we reported a feedback loop framework for gene of interest discovery, from bio-problem to gene set of interest, leveraging expert annotation with computational prediction. Defined bio-problem was applied to retrieve the genes of SRB from literature databases (PubMed, and PubMed Central) and annotated them to the genome of OA G20. Retrieved gene list was further used to enrich protein–protein interaction and was corroborated to the pangenome analysis, to categorize the enriched gene sets and the respective pathways under essential and non-essential. Interestingly, thesatgene (dde_2265) from the sulfur metabolism was the bridging gene between all the enriched pathways. Gene clusters involved in essential pathways were linked with the genes from seleno-compound metabolism, amino acid metabolism, secondary metabolite synthesis, and cofactor biosynthesis. Furthermore, pangenome analysis demonstrated the gene distribution, where 69.83% of the 116 enriched genes were mapped under “persistent,” inferring the essentiality of these genes. Likewise, 21.55% of the enriched genes, which involves specially the formate dehydrogenases and metallic hydrogenases, appeared under “shell.” Our methodology suggested that semi-automated text mining and network analysis may play a crucial role in deciphering the previously unexplored genes and key mechanisms which can help to generate a baseline prior to perform any experimental studies. 

Sulfate-reducing bacteria (SRB) are anaerobic bacteria that form biofilm and induce corrosion on various material surfaces. The quorum sensing (QS) system that employs acyl homoserine lactone (AHL)-type QS molecules primarily govern biofilm formation. Studies on SRB have reported the presence of AHL, but no AHL synthase have been annotated in SRB so far. In this computational study, we used a combination of data mining, multiple sequence alignment (MSA), homology modeling and docking to decode a putative AHL synthase in the model SRB, Desulfovibrio vulgaris Hildenborough (DvH). Through data mining, we shortlisted 111 AHL synthase genes. Conserved domain analysis of 111 AHL synthase genes generated a consensus sequence. Subsequent MSA of the consensus sequence with DvH genome indicated that DVU_2486 (previously uncharacterized protein from acetyltransferase family) is the gene encoding for AHL synthase. Homology modeling revealed the existence of seven α-helices and six β sheets in the DvH AHL synthase. The amalgamated study of hydrophobicity, binding energy, and tunnels and cavities revealed that Leu99, Trp104, Arg139, Trp97, and Tyr36 are the crucial amino acids that govern the catalytic center of this putative synthase. Identifying AHL synthase in DvH would provide more comprehensive knowledge on QS mechanism and help design strategies to control biofilm formation.