Metabolic dynamics of Desulfovibrio vulgaris biofilm grown on a steel surface

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.

The Isolation of Anaerobic and Facultative Anaerobic Sulfate-Reducing Bacteria (SRB) and a Comparison of Related Enzymes in Their Sulfate Reduction Pathways

Sulfate-reducing bacteria (SRB) are an important group of microorganisms that cause microbial corrosion. In this study, culturable SRB were isolated and identified from the inner rust layer of three kinds of steel and from sediments, and a comparison of amino acid sequences encoding related enzymes in the sulfate reduction pathway between anaerobic and facultative anaerobic SRB strains was carried out. The main results are as follows. (1) Seventy-seven strains were isolated, belonging to five genera and seven species, with the majority being Desulfovibrio marinisediminis. For the first time, Holodesulfovibrio spirochaetisodalis and Acinetobacter bereziniae were separated from the inner rust layer of metal, and sulfate reduction by A. bereziniae, Virgibacillus dokdonensis, and Virgibacillus chiguensis, etc., was also demonstrated for the first time. (2) Three strains of strictly anaerobic bacteria and four strains of facultative anaerobic bacteria were screened from seven bacterial strains. (3) Most of the anaerobic SRB only contained enzymes for the dissimilatory sulfate reduction pathway, while those of facultative anaerobic bacteria capable of producing hydrogen sulfide included two possible ways: containing the related enzymes from the dissimilatory pathway only, or containing enzymes from both dissimilatory and assimilation pathways. This study newly discovered that some bacterial genera exhibit sulfate reduction ability and found that there are differences in the distribution of enzymes related to the sulfate reduction pathway between anaerobic and facultative anaerobic SRB type trains, providing a basis for the development and utilization of sulfate-reducing bacterial resources and furthering our understanding of the metabolic mechanisms of SRB.

Antibiofilm assay for antimicrobial peptides combating the sulfate-reducing bacteria Desulfovibrio vulgaris

In medical, environmental, and industrial processes, the accumulation of bacteria in biofilms can disrupt many processes. Antimicrobial peptides (AMPs) are receiving increasing attention in the development of new substances to avoid or reduce biofilm formation. There is a lack of parallel testing of the effect against biofilms in this area, as well as in the testing of other antibiofilm agents. In this paper, a high-throughput screening was developed for the analysis of the antibiofilm activity of AMPs, differentiated into inhibition and removal of a biofilm. The sulfate-reducing bacterium Desulfovibrio vulgaris was used as a model organism. D. vulgaris represents an undesirable bacterium, which is considered one of the major triggers of microbiologically influenced corrosion. The application of a 96-well plate and steel rivets as a growth surface realizes real-life conditions and at the same time establishes a flexible, simple, fast, and cost-effective assay. All peptides tested in this study demonstrated antibiofilm activity, although these peptides should be individually selected depending on the addressed aim. For biofilm inhibition, the peptide DASamP1 is the most suitable, with a sustained effect for up to 21 days. The preferred peptides for biofilm removal are S6L3-33, in regard to bacteria reduction, and Bactenecin, regarding total biomass reduction.

Metabolomic Insights of Biosurfactant Activity from Bacillus niabensis against Planktonic Cells and Biofilm of Pseudomonas stutzeri Involved in Marine Biofouling

In marine environments, biofilm can cause negative impacts, including the biofouling process. In the search for new non-toxic formulations that inhibit biofilm, biosurfactants (BS) produced by the genus Bacillus have demonstrated considerable potential. To elucidate the changes that BS from B. niabensis promote in growth inhibition and biofilm formation, this research performed a nuclear magnetic resonance (NMR) metabolomic profile analysis to compare the metabolic differences between planktonic cells and biofilms of Pseudomonas stutzeri, a pioneer fouling bacteria. The multivariate analysis showed a clear separation between groups with a higher concentration of metabolites in the biofilm than in planktonic cells of P. stutzeri. When planktonic and biofilm stages were treated with BS, some differences were found among them. In planktonic cells, the addition of BS had a minor effect on growth inhibition, but at a metabolic level, NADP+, trehalose, acetone, glucose, and betaine were up-regulated in response to osmotic stress. When the biofilm was treated with the BS, a clear inhibition was observed and metabolites such as glucose, acetic acid, histidine, lactic acid, phenylalanine, uracil, and NADP+ were also up-regulated, while trehalose and histamine were down-regulated in response to the antibacterial effect of the BS.

Desulfovibrio vulgaris as a model microbe for the study of corrosion under sulfate-reducing conditions

Corrosion of iron-containing metals under sulfate-reducing conditions is an economically important problem. Microbial strains now known as Desulfovibrio vulgaris served as the model microbes in many of the foundational studies that developed existing models for the corrosion of iron-containing metals under sulfate-reducing conditions. Proposed mechanisms for corrosion by D. vulgaris include: (1) H2 consumption to accelerate the oxidation of Fe0 coupled to the reduction of protons to H2; (2) production of sulfide that combines with ferrous iron to form iron sulfide coatings that promote H2 production; (3) moribund cells release hydrogenases that catalyze Fe0 oxidation with the production of H2; (4) direct electron transfer from Fe0 to cells; and (5) flavins serving as an electron shuttle for electron transfer between Fe0 and cells. The demonstrated possibility of conducting transcriptomic and proteomic analysis of cells growing on metal surfaces suggests that similar studies on D. vulgaris corrosion biofilms can aid in identifying proteins that play an important role in corrosion. Tools for making targeted gene deletions in D. vulgaris are available for functional genetic studies. These approaches, coupled with instrumentation for the detection of low concentrations of H2, and proven techniques for evaluating putative electron shuttle function, are expected to make it possible to determine which of the proposed mechanisms for D. vulgaris corrosion are most important.

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

Sulfate-reducing bacteria (SRB) have a unique ability to respire under anaerobic conditions using sulfate as a terminal electron acceptor, reducing it to hydrogen sulfide. SRB thrives in many natural environments (freshwater sediments and salty marshes), deep subsurface environments (oil wells and hydrothermal vents), and processing facilities in an industrial setting. Owing to their ability to alter the physicochemical properties of underlying metals, SRB can induce fouling, corrosion, and pipeline clogging challenges. Indigenous SRB causes oil souring and associated product loss and, subsequently, the abandonment of impacted oil wells. The sessile cells in biofilms are 1,000 times more resistant to biocides and induce 100-fold greater corrosion than their planktonic counterparts. To effectively combat the challenges posed by SRB, it is essential to understand their molecular mechanisms of biofilm formation and corrosion. Here, we examine the critical genes involved in biofilm formation and microbiologically influenced corrosion and categorize them into various functional categories. The current effort also discusses chemical and biological methods for controlling the SRB biofilms. Finally, we highlight the importance of surface engineering approaches for controlling biofilm formation on underlying metal surfaces.

Multi-omics tools for studying microbial biofilms: current perspectives and future directions

The advent of omics technologies has greatly improved our understanding of microbial biology, particularly in the last two decades. The field of microbial biofilms is, however, relatively new, consolidated in the 1980s. The morphogenic switching by microbes from planktonic to biofilm phenotype confers numerous survival advantages such as resistance to desiccation, antibiotics, biocides, ultraviolet radiation, and host immune responses, thereby complicating treatment strategies for pathogenic microorganisms. Hence, understanding the mechanisms governing the biofilm phenotype can result in efficient treatment strategies directed specifically against molecular markers mediating this process. The application of omics technologies for studying microbial biofilms is relatively less explored and holds great promise in furthering our understanding of biofilm biology. In this review, we provide an overview of the application of omics tools such as transcriptomics, proteomics, and metabolomics as well as multi-omics approaches for studying microbial biofilms in the current literature. We also highlight how the use of omics tools directed at various stages of the biological information flow, from genes to metabolites, can be integrated via multi-omics platforms to provide a holistic view of biofilm biology. Following this, we propose a future artificial intelligence-based multi-omics platform that can predict the pathways associated with different biofilm phenotypes.

Microbial Communities of Orange Tubercles in Accelerated Low-Water Corrosion

The rapid degradation of marine infrastructure at the low tide level due to accelerated low-water corrosion (ALWC) is a problem encountered worldwide. Despite this, there is limited understanding of the microbial communities involved in this process. We obtained samples of the orange-colored tubercles commonly associated with ALWC from two different types of steel sheet piling, located adjacent to each other but with different levels of localized corrosion, at a seaside harbor. The microbial communities from the outer and inner layers of the orange tubercles and from adjacent seawater were studied by pure culture isolation and metabarcoding of the 16S rRNA genes. A collection of 119 bacterial isolates was obtained from one orange tubercle sample, using a range of media in anaerobic and aerobic conditions. The metabarcoding results showed that sulfur and iron oxidizers were more abundant on the outer sections of the orange tubercles compared to the inner layers, where Deltaproteobacteria (which include many sulfate reducers) were more abundant. The microbial communities varied significantly between the inner and outer layers of the orange tubercles and also with the seawater but overall did not differ significantly between the two steel sheet types. Hence, we saw similar microbial communities in orange tubercles present, but different levels of localized corrosion, for two different types of colocated steel sheet piling. Metallurgical analysis found differences in composition, grain size, ferrite-pearlite ratio, and the extent of inclusions present between the two steel types investigated.IMPORTANCE The presence of orange tubercles on marine steel pilings is often used as an indication that accelerated low-water corrosion is taking place. We studied the microbial communities in attached orange tubercles on two closely located sheet pilings that were of different steel types. The attached orange tubercles were visually similar, but the extents of underlying corrosion on the different steel surfaces were substantially different. No clear difference was found between the microbial communities present on the two different types of sheet piling. However, there were clear differences in the microbial communities in the corrosion layers of tubercles, which were also different from the microbes present in adjacent seawater. The overall results suggest that the presence of orange tubercles, a single measurement of water quality, or the detection of certain general types of microbes (e.g., sulfate-reducing bacteria) should not be taken alone as definitive indications of accelerated corrosion.

The era of 'omics' technologies in the study of microbiologically influenced corrosion

Efforts to elucidate the relationships between microorganisms and metal corrosion were mainly directed to understanding the formation of biofilm structures grown on corroded surfaces. The emergence of high throughput DNA sequencing techniques has helped in the description of microbial species involved directly and indirectly in the corrosion processes of alloys. Coupled with sequencing from environmental samples, other methodologies such as metatranscriptome, metaproteomics and metabolomics have allowed a new horizon to be opened on the understanding of the role of corrosive microbial biofilm. Several groups of bacteria and archaea were identified, showing the dominance of Proteobacteria in several samples analyzed and members of groups that previously received less attention, such as Firmicutes and Bacteroidetes. Our research also shows that metagenomic studies describe the presence of various Archaea domain thermophilic and methanogenic groups associated with metal corrosion. Thus, opening the prospect of describing new microbial groups as possible participants in this current global concern.

Enhanced "contact mechanism" for interaction of extracellular polymeric substances with low-grade copper-bearing sulfide ore in bioleaching by moderately thermophilic Acidithiobacillus caldus

In order to enhance the "contact mechanism" governing the interaction of extracellular polymeric substances (EPS) with low-grade copper-bearing sulfide ore for the bioleaching of copper, moderately thermophilic Acidithiobacillus caldus was subjected to exogenous intervention with iron and sulfur. The enhancement of the contact mechanism was systematically investigated by evaluating the attached cells/EPS dynamics, intracellular adenosine triphosphate (ATP), cell functional groups, gene transcriptional level, and ore characteristics. Confocal laser scanning microscopy (CLSM) revealed that exogenous intervention with iron and sulfur led to the production of a denser EPS layer and faster adsorption of the attached cells to the ore based on differential fluorescence staining, which indicated enhancement of the "contact mechanism". The increased intracellular ATP content of the attached cells in the exogenous substrate system provided the required energy for the adsorption processes associated with the "contact mechanism". Fourier-transform infrared spectroscopic (FTIR) analysis of the attached cells and the ore showed a dramatic shift of the NH and COS peaks (associated with EPS formation), whereas the FTIR peaks of SO and SO₄^2- associated with sulfur metabolism were also significantly influenced. Moreover, reverse transcription polymerase chain reaction (RT-PCR) analysis revealed that the expression of genes related to cellular energy metabolism (nuoB, nuoC, atpE, atpF), sulfur metabolism (sor, sqr, sdo, soxA), biofilm formation (pgaA, pgaB), and cell colonization (acfA, acfB, acfC, acfD) was up-regulated after exogenous intervention, verifying enhancement of the "contact mechanism" at the transcriptional level. In addition, scanning electron microscopy (SEM) indicated more obvious adsorption traces on the ore surface. X-ray diffraction (XRD) indicated the presence of more complex derivatives, such as Fe₃(SO₄)₄, FeSO₄, Fe₂(SO₄)₃, and Cu₂S, which is suggestive of more active iron/sulfur metabolism with addition of the exogenous iron and sulfur. Overall, a model for bioleaching of low-grade copper-bearing sulfide ore by moderately thermophilic A. caldus was constructed. The results of this investigation should provide a guide for similar industrial bioleaching processes.

Analysis of marine microbial communities colonizing various metallic materials and rust layers

High-throughput sequencing was used to visualize microbial biocoenoses on different metallic surfaces and rust layers of highly corroded steels after immersion in coastal marine water for 30 months at Sanya, China. Distinct microbial community compositions were observed on these metallic surfaces. The dominant genus was the copper-tolerant, acid-producing Lactobacillus on copper alloys, the common aerobic surface colonizers Bacillus and Ruegeria on aluminum alloys, and aerobic biofilm-forming Pseudomonas on carbon steel. Most of these are copiotrophic microbes compared to planktonic microbes, which are oligotrophic. Additionally, sulfate-reducing prokaryotes (SRP) were detected in the rust layer, but the dominant genera changed from the outer layer to the inner part. The dominant genera detected in the outer, middle and inner rusts layers were Desulfotomaculum, Desulfonatronum (obligate anaerobe) and Desulfovibiro (electroactive), respectively. Further, the coexistence of methanogens with SRP suggests interspecies interactions.

Analysis of Bacterial Community Composition of Corroded Steel Immersed in Sanya and Xiamen Seawaters in China via Method of Illumina MiSeq Sequencing

Metal corrosion is of worldwide concern because it is the cause of major economic losses, and because it creates significant safety issues. The mechanism of the corrosion process, as influenced by bacteria, has been studied extensively. However, the bacterial communities that create the biofilms that form on metals are complicated, and have not been well studied. This is why we sought to analyze the composition of bacterial communities living on steel structures, together with the influence of ecological factors on these communities. The corrosion samples were collected from rust layers on steel plates that were immersed in seawater for two different periods at Sanya and Xiamen, China. We analyzed the bacterial communities on the samples by targeted 16S rRNA gene (V3–V4 region) sequencing using the Illumina MiSeq. Phylogenetic analysis revealed that the bacteria fell into 13 phylotypes (similarity level = 97%). Proteobacteria, Firmicutes and Bacteroidetes were the dominant phyla, accounting for 88.84% of the total. Deltaproteobacteria, Clostridia and Gammaproteobacteria were the dominant classes, and accounted for 70.90% of the total. Desulfovibrio spp., Desulfobacter spp. and Desulfotomaculum spp. were the dominant genera and accounted for 45.87% of the total. These genera are sulfate-reducing bacteria that are known to corrode steel. Bacterial diversity on the 6 months immersion samples was much higher than that of the samples that had been immersed for 8 years (P < 0.001, Student’s t-test). The average complexity of the biofilms from the 8-years immersion samples from Sanya was greater than those from Xiamen, but not significantly so (P > 0.05, Student’s t-test). Overall, the data showed that the rust layers on the steel plates carried many bacterial species. The bacterial community composition was influenced by the immersion time. The results of our study will be of benefit to the further studies of bacterial corrosion mechanisms and corrosion resistance.