Gene Sets and Mechanisms of Sulfate-Reducing Bacteria Biofilm Formation and Quorum Sensing With Impact on Corrosion

Genome-Wide Computational Prediction and Analysis of Noncoding RNAs in Oleidesulfovibrio alaskensis G20

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.

Sulfate-reducing bacteria unearthed: ecological functions of the diverse prokaryotic group in terrestrial environments

Sulfate-reducing prokaryotes (SRPs) are essential microorganisms that play crucial roles in various ecological processes. Even though SRPs have been studied for over a century, there are still gaps in our understanding of their biology. In the past two decades, a significant amount of data on SRP ecology has been accumulated. This review aims to consolidate that information, focusing on SRPs in soils, their relation to the rare biosphere, uncultured sulfate reducers, and their interactions with other organisms in terrestrial ecosystems. SRPs in soils form part of the rare biosphere and contribute to various processes as a low-density population. The data reveal a diverse range of sulfate-reducing taxa intricately involved in terrestrial carbon and sulfur cycles. While some taxa like Desulfitobacterium and Desulfosporosinus are well studied, others are more enigmatic. For example, members of the Acidobacteriota phylum appear to hold significant importance for the terrestrial sulfur cycle. Many aspects of SRP ecology remain mysterious, including sulfate reduction in different bacterial phyla, interactions with bacteria and fungi in soils, and the existence of soil sulfate-reducing archaea. Utilizing metagenomic, metatranscriptomic, and culture-dependent approaches will help uncover the diversity, functional potential, and adaptations of SRPs in the global environment.

Superwettable surfaces and factors impacting microbial adherence in microbiologically-influenced corrosion: a review

Microbiologically-influenced corrosion (MIC) is a common operational hazard to many industrial processes. The focus of this review lies on microbial corrosion in the maritime industry. Microbial metal attachment and colonization are the critical steps in MIC initiation. We have outlined the crucial factors influencing corrosion caused by microorganism sulfate-reducing bacteria (SRB), where its adherence on the metal surface leads to Direct Electron Transfer (DET)-MIC. This review thus aims to summarize the recent progress and the lacunae in mitigation of MIC. We further highlight the susceptibility of stainless steel grades to SRB pitting corrosion and have included recent developments in understanding the quorum sensing mechanisms in SRB, which governs the proliferation process of the microbial community. There is a paucity of literature on the utilization of anti-quorum sensing molecules against SRB, indicating that the area of study is in its nascent stage of development. Furthermore, microbial adherence to metal is significantly impacted by surface chemistry and topography. Thus, we have reviewed the application of super wettable surfaces such as superhydrophobic, superhydrophilic, and slippery liquid-infused porous surfaces as "anti-corrosion coatings" in preventing adhesion of SRB, providing a potential avenue for the development of practical and feasible solutions in the prevention of MIC. The emerging field of super wettable surfaces holds significant potential for advancing efficient and practical MIC prevention techniques.

Corrosion of Q235 carbon steel induced by sulfate-reducing bacteria in groundwater: corrosion behavior, corrosion product, and microbial community structure

Microbiologically influenced corrosion (MIC) is one of the reasons leading to the service failure of pipelines buried in the soil. In this work, the effect of sulfate-reducing bacteria (SRB) on the corrosion behavior of Q235 carbon steel in groundwater was investigated by electrochemical methods, surface analysis, and biological analysis. The results show that SRB utilizes iron as electron donor to sustain the vital activities of organic carbon-starved groundwater during the 14-day experimental period. The microbial community composition analysis at the genus level demonstrate that the diversity and richness decrease after corrosion, and the dominant SRB species has changed from Desulfovibrio to Desulfosporosinus. Moreover, the impedance of the carbon steel in the presence of biofilm was 1 order of magnitude higher than that of other periods in the electrochemical test, indicating that the biofilm and formed ferrous sulfide layer impeded the occurrence of corrosion. Although the 3D topography indicated that the surface of carbon steel was more uneven and pits were increased in the presence of SRB, the average weight loss (0.0396 ± 0.0050 g) was much higher than that without SRB (0.0139 ± 0.0007 g). These results implied that the growth of SRB makes the corrosion process of Q235 carbon steel more complicated.

d-tyrosine enhances disoctyl dimethyl ammonium chloride on alleviating SRB corrosion

Microbiologically influenced corrosion (MIC) caused by sulfate reducing bacteria (SRB) is a serious challenge in many industries, but biofilm greatly decreases the toxicity of bactericides to cell inside. d-amino acids are potential enhancers for bactericides due to their excellent performance on biofilm inhibition. However, the mechanism of d-amino acid cooperating with bactericides for MIC inhibition is still unknown. In this study, d-tyrosine（D-Tyr）and disoctyl dimethyl ammonium chloride (DDAC) were selected as the typical d-amino acid and bactericide, respectively, to evaluate their synergetic inhibition on the corrosion caused by Desulfovibrio vulgaris. D-Tyr obviously enhanced the role of DDAC in inhibiting corrosion with high corrosion inhibition efficiency at 77.23 %. The attachment of EPS and live cells on the coupon surface decreased in the presence of D-Try, leading to more cells directly exposed to DDAC. Besides, D-Try decreased the amount of live cells on the surface and thus reduced the utilization of Fe by SRB and corrosion current. Moreover, dead cells settling to the coupon surface may form a protective lay to retard the contact between live SRB and Fe, leading to slow cathode reaction and less corrosion. Therefore, D-Tyr can reduce the coverage of biofilm, thereby reducing its protective effect on SRB and achieving better corrosion inhibition effect. This work provides a new strategy for improving bactericides and inhibiting MIC.

A nanozyme-reinforced injectable photodynamic hydrogel for combating biofilm infection

Bacterial biofilm-associated infectious diseases remain serious menaces to human health. Recently, photodynamic therapy (PDT) has become a prospective strategy for combating biofilm infection. However, anaerobic conditions in a biofilm greatly inhibit its therapeutic efficacy. Here, a nanozyme-reinforced injectable hydrogel is prepared using Ca2+-crosslinked sodium alginate incorporated with photosensitizer-loaded MnO2 nanosheets and CaO2 nanoparticles for O2 self-sufficient PDT to eradicate biofilm infection. In our design, CaO2 reacts with water to produce locally concentrated H2O2, which could be catalyzed by MnO2 nanosheets (catalase-mimic nanozymes) to generate O2 and greatly relieve the hypoxic conditions in the biofilm, thus significantly strengthening PDT efficacy. In vitro assays confirmed that the hybrid hydrogel not only exhibits high-performance bactericidal activity in combating both Gram-positive Staphylococcus aureus and Gram-negative Escherichia coli but also shows great efficacy in eliminating biofilm infection. Moreover, benefiting from its good syringeability, the hybrid hydrogel is prone to fit irregular wounds and exhibits high efficiency in promoting wound healing in a biofilm-infected mice model. Besides, no obvious toxicity is detected in the hybrid hydrogel. Overall, we envision that our designed hydrogel could provide a prospective solution for combating biofilm-associated infections.

Biofilms and beyond: a comprehensive review of the impact of Sulphate Reducing Bacteria on steel corrosion

Sulphate-reducing bacteria (SRB) are known to cause severe corrosion of steel structures in various industries, resulting in significant economic and environmental consequences. This review paper critically examines the impact of SRB-induced corrosion on steel, including the formation of SRB biofilms, the effect on different types of steel, and the various models developed to investigate this phenomenon. The role of environmental factors in SRB-induced corrosion, molecular techniques for studying SRBs, and strategies for mitigating corrosion are discussed. Additionally, the sustainability implications of SRB-induced corrosion and the potential use of alternative materials were explored. By examining the current state of knowledge on this topic, this review aims to provide a comprehensive understanding of the impact of SRB-induced corrosion on steel and identify opportunities for further research and development.

Transcriptome-wide marker gene expression analysis of stress-responsive sulfate-reducing bacteria

Sulfate-reducing bacteria (SRB) are terminal members of any anaerobic food chain. For example, they critically influence the biogeochemical cycling of carbon, nitrogen, sulfur, and metals (natural environment) as well as the corrosion of civil infrastructure (built environment). The United States alone spends nearly $4 billion to address the biocorrosion challenges of SRB. It is important to analyze the genetic mechanisms of these organisms under environmental stresses. The current study uses complementary methodologies, viz., transcriptome-wide marker gene panel mapping and gene clustering analysis to decipher the stress mechanisms in four SRB. Here, the accessible RNA-sequencing data from the public domains were mined to identify the key transcriptional signatures. Crucial transcriptional candidate genes of Desulfovibrio spp. were accomplished and validated the gene cluster prediction. In addition, the unique transcriptional signatures of Oleidesulfovibrio alaskensis (OA-G20) at graphene and copper interfaces were discussed using in-house RNA-sequencing data. Furthermore, the comparative genomic analysis revealed 12,821 genes with translation, among which 10,178 genes were in homolog families and 2643 genes were in singleton families were observed among the 4 genomes studied. The current study paves a path for developing predictive deep learning tools for interpretable and mechanistic learning analysis of the SRB gene regulation.

Convergence research and training in computational bioengineering: a case study on AI/ML driven biofilm-material interaction discovery

Initially, research disciplines operated independently, but the emergence of trans-disciplinary sciences led to convergence research, impacting graduate programs and research laboratories, especially in bioengineering and material engineering as presented here. Current graduate curriculum fails to efficiently prepare students for multidisciplinary and convergence research, thus creating a gap between the students and research laboratory expectations. We present a convergence training framework for graduate students, incorporating problem-based learning under the guidance of senior scientists and collaboration with postdoctoral researchers. This case study serves as a template for transdisciplinary convergent training projects - bridging the expertise gap and fostering successful convergence learning experiences in computational biointerface (material-biology interface). The 18-month Advanced Data Science Workshop, initiated in 2019, involves project-based learning, online training modules, and data collection. A pilot solution utilized Jupyter notebook on Google collaborator and culminated in a face-to-face workshop where project presentations and finalization occurred. The program started with 9 experts in the four diverse fields creating 14 curated projects in data science (Artificial Intelligence/Machine Learning), material science, biofilm engineering, and biointerface. These were integrated into convergence research through webinars by the experts. The experts chose 8 of the 14 projects to be part of an all-day in-person workshop, where over 20 learners formed eight teams that tackled complex problems at the interface of digital image processing, gene expression analysis, and material prediction. Each team was comprised of students and postdoctoral researchers or research scientists from diverse domains including computer science, materials science, and biofilm research. Some projects were selected for presentation at the international IEEE Bioinformatics conference in 2022, with three resulting Machine Learning (ML) models submitted as a journal paper. Students engaged in problem discussions, collaborated with experts from different disciplines, and received guidance in decomposing learning objectives. Based on learner feedback, this successful experience allows for consolidation and integration of convergence research via problem-based learning into the curriculum. Three bioengineering participants, who received training in data science and engineering, have received bioinformatics jobs in biotechnology industries.

Comprehensive Review on the Use of Biocides in Microbiologically Influenced Corrosion

A microbiologically influenced corrosion (MIC) causes huge economic losses and serious environmental damage every year. The prevention and control measures for MIC mainly include physical, chemical, and biological methods. Among them, biocide application is the most cost-effective method. Although various biocides have their own advantages in preventing and treating MIC, most biocides have the problem of polluting the environment and increasing microorganism resistance. Therefore, it has stimulated the exploration of continuously developing new environmentally friendly and efficient biocides. In this review, the application advantages and research progress of various biocides used to prevent and control MIC are discussed. Also, this review provides a resource for the research and rational use of biocides regarding MIC mitigation and prevention.

Electrochemical Assessment of Mitigation of Desulfovibrio ferrophilus IS5 Corrosion against N80 Carbon Steel and 26Cr3Mo Steel Using a Green Biocide Enhanced by a Nature-Mimicking Biofilm-Dispersing Peptide

MIC (microbiologically influenced corrosion) is problematic in many industries, especially in the oil and gas industry. In this work, N80 carbon steel for pipelines was tested with 26Cr3Mo chromium pipeline steel for comparison in SRB (sulfate-reducing bacterium) MIC mitigation using a THPS (tetrakis hydroxymethyl phosphonium sulfate)-based commercial biocide (Biotreat 5475 with 75-80% THPS by mass). Peptide A, a nature-mimicking synthetic cyclic peptide (cys-ser-val-pro-tyr-asp-tyr-asn-trp-tyr-ser-asn-trp-cys) with biofilm dispersal ability was used as a biocide enhancer. Metal coupons covered with 3-d old Desulfovibrio ferrophilus IS5 biofilms were immersed in different biocide solutions. After 1-h treatment, 200 ppm Biotreat 5475, 200 ppm Biotreat 5475 + 200 nM (360 ppb) Peptide A, and 400 ppm Biotreat 5475 achieved 0.5-log, 1.7-log and 1.9-log reductions in sessile cell count on N80, and 0.7-log, 1.7-log, and 1.8-log on 26Cr3Mo, respectively. The addition of 200 nM Peptide A cut the THPS biocide dosage by nearly half. Biocide injection tests in electrochemical glass cells after 1 h exhibited 15%, 70%, and 72% corrosion inhibition efficiency (based on corrosion current density) on N80, and 27%, 79%, 75% on 26Cr3Mo, respectively. Linear polarization resistance and electrochemical impedance spectrometry results also indicated antimicrobial efficacies.

Transformation kinetics of exogenous nickel in a paddy soil during anoxic-oxic alteration: Roles of organic matter and iron oxides

Nickel is generally released from flooded soils; however, the key Ni transformation processes in soils that are freshly contaminated by Ni²⁺ during anoxic-oxic alteration remain unclear. We developed a kinetic model to investigate the Ni transformation in paddy soils under anoxic and oxic conditions based on the results of the seven-step sequential extraction, determination of dissolved and soil organic matter, and surface site quantification, which provide the kinetic data of different Ni fractions, organic matter, and reactive sites for modeling. The dissolved, exchangeable, and specifically adsorbed Ni was gradually transferred to fulvic complex, humic complex, Fe-Mn oxide bound, and sulfide bound Ni after 40 d of anoxic incubation due to the increase in pH and soil surface sites, which were mainly induced by Fe(III) oxide reduction and soil organic matter release. The introduction of oxygen triggered a rapid release of Ni, which was ascribed to the decrease in pH and soil surface sites caused by Fe(II) oxidation and carbon re-immobilization. Kinetic modeling demonstrated that complexation with soil organic matter dominated Ni immobilization under anoxic conditions, while organic matter and Fe-Mn oxides contributed similarly to Ni release under oxic conditions, although the majority of Ni remained complexed with soil organic matter. These findings are important for the evaluation and prediction of Ni behavior in paddy soils with exogenous Ni during flooding-drainage practices.

Enhanced inhibition of HEDP on SRB-mediated corrosion with D-phenylalanine

Microbiologically influenced corrosion (MIC) caused by biofilm is a serious problem in many industries. D-amino acids could be a potential strategy to enhance traditional corrosion inhibitors due to their roles in biofilm reduction. However, the synergistic mechanism of D-amino acids and inhibitors remains unknown. In this study, D-Phenylalanine (D-Phe) and 1-hydroxyethane-1,1-diphosphonic acid (HEDP) were selected as the typical D-amino acid and corrosion inhibitor to evaluate their effect on the corrosion caused by Desulfovibrio vulgaris. The combination of HEDP and D-Phe obviously slowed down the corrosion process by 32.25%, decreased the corrosion pit depth and retarded cathodic reaction. SEM and CLSM analysis indicated that D-Phe reduced the content of extracellular protein and thus inhibited the biofilm formation. The molecular mechanism of D-Phe and HEDP on corrosion inhibition was further explored via transcriptome. The combination of HEDP and D-Phe down-regulated the gene expression of peptidoglycan, flagellum, electron transfer, ferredoxin and quorum sensing (QS) molecules, leading to less peptidoglycan synthesis, weaker electron transfer and stronger QS factor inhibition. This work provides a new strategy for improving traditional corrosion inhibitors, retarding MIC and mitigating subsequent water eutrophication.

Identification of AHL Synthase in Desulfovibrio vulgaris Hildenborough Using an In-Silico Methodology

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.

Text-Mining to Identify Gene Sets Involved in Biocorrosion by Sulfate-Reducing Bacteria: A Semi-Automated Workflow

A significant amount of literature is available on biocorrosion, which makes manual extraction of crucial information such as genes and proteins a laborious task. Despite the fast growth of biology related corrosion studies, there is a limited number of gene collections relating to the corrosion process (biocorrosion). Text mining offers a potential solution by automatically extracting the essential information from unstructured text. We present a text mining workflow that extracts biocorrosion associated genes/proteins in sulfate-reducing bacteria (SRB) from literature databases (e.g., PubMed and PMC). This semi-automatic workflow is built with the Named Entity Recognition (NER) method and Convolutional Neural Network (CNN) model. With PubMed and PMCID as inputs, the workflow identified 227 genes belonging to several Desulfovibrio species. To validate their functions, Gene Ontology (GO) enrichment and biological network analysis was performed using UniprotKB and STRING-DB, respectively. The GO analysis showed that metal ion binding, sulfur binding, and electron transport were among the principal molecular functions. Furthermore, the biological network analysis generated three interlinked clusters containing genes involved in metal ion binding, cellular respiration, and electron transfer, which suggests the involvement of the extracted gene set in biocorrosion. Finally, the dataset was validated through manual curation, yielding a similar set of genes as our workflow; among these, hysB and hydA, and sat and dsrB were identified as the metal ion binding and sulfur metabolism genes, respectively. The identified genes were mapped with the pangenome of 63 SRB genomes that yielded the distribution of these genes across 63 SRB based on the amino acid sequence similarity and were further categorized as core and accessory gene families. SRB's role in biocorrosion involves the transfer of electrons from the metal surface via a hydrogen medium to the sulfate reduction pathway. Therefore, genes encoding hydrogenases and cytochromes might be participating in removing hydrogen from the metals through electron transfer. Moreover, the production of corrosive sulfide from the sulfur metabolism indirectly contributes to the localized pitting of the metals. After the corroboration of text mining results with SRB biocorrosion mechanisms, we suggest that the text mining framework could be utilized for genes/proteins extraction and significantly reduce the manual curation time.

Transcriptomics and Functional Analysis of Copper Stress Response in the Sulfate-Reducing Bacterium Desulfovibrio alaskensis G20

Copper (Cu) is an essential micronutrient required as a co-factor in the catalytic center of many enzymes. However, excess Cu can generate pleiotropic effects in the microbial cell. In addition, leaching of Cu from pipelines results in elevated Cu concentration in the environment, which is of public health concern. Sulfate-reducing bacteria (SRB) have been demonstrated to grow in toxic levels of Cu. However, reports on Cu toxicity towards SRB have primarily focused on the degree of toxicity and subsequent elimination. Here, Cu(II) stress-related effects on a model SRB, Desulfovibrio alaskensis G20, is reported. Cu(II) stress effects were assessed as alterations in the transcriptome through RNA-Seq at varying Cu(II) concentrations (5 µM and 15 µM). In the pairwise comparison of control vs. 5 µM Cu(II), 61.43% of genes were downregulated, and 38.57% were upregulated. In control vs. 15 µM Cu(II), 49.51% of genes were downregulated, and 50.5% were upregulated. The results indicated that the expression of inorganic ion transporters and translation machinery was massively modulated. Moreover, changes in the expression of critical biological processes such as DNA transcription and signal transduction were observed at high Cu(II) concentrations. These results will help us better understand the Cu(II) stress-response mechanism and provide avenues for future research.

Evaluation of trehalase as an enhancer for a green biocide in the mitigation of Desulfovibrio vulgaris biocorrosion of carbon steel

Trehalase can biocatalyze the conversion of trehalose to glucose. It is an enzyme that plays an important role in biofilm formation. Thus, trehalase has been patented as a chemical for preventing and treating biofilms. Sulfate-reducing bacteria (SRB) biofilms are often found responsible for biocorrosion, also known as microbiologically infuenced corrosion (MIC), especially in the oil and gas industries and in water utilities. The MIC treatment process typically requires biocide treatment of biofilms, sometimes together with scrubbing. Owing to environmental concerns, a lower biocide dosage is desired in the treatment process. In this work, trehalase was tested as a green biocide enhancer to enhance tetrakis hydroxymethyl phosphonium sulfate (THPS) in the prevention of Desulfovibrio vulgaris MIC of C1018 carbon steel in ATCC 1249 culture medium at 37 °C. THPS is one of the most popular industrial biocides owing to its broad-spectrum efficacy and green chemical status. After 7 days of incubation in 50 mL anaerobic vials containing 40 mL culture medium at pH 7.0, the sessile cell counts indicated that 50 ppm (w/w) THPS + 30 ppm (w/w) trehalase led to an extra 5.7-fold sessile cell reduction when compared with the 50 ppm THPS alone treatment. As a consequence, the combination treatment also resulted in an extra 54% in pit depth reduction and 30% in weight loss reduction when compared with the 50 ppm THPS alone treatment (with 9.0 μm and 1.0 mg/cm²). The biofilm images corroborated the decreased sessile cell count and pitting corrosion.