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.

Artificial Intelligence-Driven Image Analysis of Bacterial Cells and Biofilms.

The current study explores an artificial intelligence framework for measuring the structural features from microscopy images of the bacterial biofilms. Desulfovibrio alaskensis G20 (DA-G20) grown on mild steel surfaces is used as a model for sulfate reducing bacteria that are implicated in microbiologically influenced corrosion problems. Our goal is to automate the process of extracting the geometrical properties of the DA-G20 cells from the scanning electron microscopy (SEM) images, which is otherwise a laborious and costly process. These geometric properties are a biofilm phenotype that allow us to understand how the biofilm structurally adapts to the surface properties of the underlying metals, which can lead to better corrosion prevention solutions. We adapt two deep learning models: (a) a deep convolutional neural network (DCNN) model to achieve semantic segmentation of the cells, (d) a mask region-convolutional neural network (Mask R-CNN) model to achieve instance segmentation of the cells. These models are then integrated with moment invariants approach to measure the geometric characteristics of the segmented cells. Our numerical studies confirm that the Mask-RCNN and DCNN methods are 227x and 70x faster respectively, compared to the traditional method of manual identification and measurement of the cell geometric properties by the domain experts.

Photosynthetic microbial fuel cells for methanol treatment using graphene electrodes.

Photosynthetic microbial fuel cells (pMFC) represent a promising approach for treating methanol (CH3OH) wastewater. However, their use is constrained by a lack of knowledge on the extracellular electron transfer capabilities of photosynthetic methylotrophs, especially when coupled with metal electrodes. This study assessed the CH3OH oxidation capabilities of Rhodobacter sphaeroides 2.4.1 in two-compartment pMFCs. A 3D nickel (Ni) foam modified with plasma-grown graphene (Gr) was used as an anode, nitrate mineral salts media (NMS) supplemented with 0.1% CH3OH as anolyte, carbon brush as cathode, and 50 mM ferricyanide as catholyte. Two simultaneous pMFCs that used bare Ni foam and carbon felt served as controls. The Ni/Gr electrode registered a two-fold lower charge transfer resistance (0.005 kΩ cm2) and correspondingly 16-fold higher power density (141 mW/m2) compared to controls. The underlying reasons for the enhanced performance of R. sphaeroides at the graphene interface were discerned. The real-time polymerase chain reaction (PCR) analysis revealed the upregulation of cytochrome c oxidase, aa3 type, subunit I gene, and Flp pilus assembly protein genes in the sessile cells compared to their planktonic counterparts. The key EET pathways used for sustaining CH3OH oxidation were discussed.

A cheap two-step cultivation of Phaeodactylum tricornutum for increased TAG production and differential expression of TAG biosynthesis associated genes.

A cheap cultivation of microalgae greatly reduces the biodiesel production cost. Subsequently in this study, citric acid and effluents from sugar and tannery industries were used as the nutritional supplements for the improvement of biomass and TAG production in Phaeodactylum tricornutum using two-step cultivation. When compared to control (media without supplementation), a considerable increase in biomass and chlorophyll a was obtained with citric acid (CA) and sugar industry effluent (SIE) supplemented media. In the two-step cultivation method, biomass raised from CA (100 mg·L-1) and SIE (1.5 mL·L-1) supplementations in the first step, viz. biomass production (BP) step was allowed for lipid accumulation in the second step, viz. lipid production (LP) step, and thus yielded enhanced lipids of 11.5 ± 0.7 mg·L-1·day-1 and 13.5 ± 1.9 mg·L-1·day-1 respectively, with improved TAG synthesis. Further, differential expression analysis of TAG biosynthetic genes of P. tricornutum under single-step and two-step cultivation modes were performed, and the gene expression patterns were studied.

Enhanced biohydrogen production with low graphene oxide content using thermophilic bioreactors.

Modern society envisions hydrogen (H2) fuel to drive the transportation, industrial, and domestic sectors. Here, we explore use of graphene oxide nanoparticles (GO NPs) for greatly enhancing bio-H2 production by a consortium based on Thermoanaerobacterium thermosaccharolyticum spp. Thermophilic batch bioreactors were set up at 60 OC and initial pH of 8.5 to assess the effects of GO NPs supplements on biohydrogen production. Under optimal GO NPs loading of 10 mg/L, the supplemented system yielded âˆ¼ 300% higher H2 yield (6.78 mol H2/mol sucrose) than control. Such an optimized system offered 73% H2 purity and 85% conversion efficiency by promoted the desirable acetate fermentation pathway. Miseq Illumina sequencing tests revealed that the optimal levels of GO NPs did not alter the microbial composition of consortium.

Review on integrated biofuel production from microalgal biomass through the outset of transesterification route: a cascade approach for sustainable bioenergy.

In recent years, microalgal feedstocks have gained immense potential for sustainable biofuel production. Thermochemical, biochemical conversions and transesterification processes are employed for biofuel production. Especially, the transesterification process of lipid molecules to fatty acid alkyl esters (FAAE) is being widely employed for biodiesel production. In the case of the extractive transesterification process, biodiesel is produced from the extracted microalgal oil. Whereas In-situ (reactive) transesterification allows the direct conversion of microalgae to biodiesel avoiding the sequential steps, which subsequently reduces the production cost. Though microalgae have the highest potential to be an alternate renewable feedstock, the minimization of biofuel production cost is still a challenge. The biorefinery approaches that rely on simple cascade processes involving cost-effective technologies are the need of an hour for sustainable bioenergy production using microalgae. At the same time, combining the biorefineries for both (i) high value-low volume (food and health supplements) and (ii) low value- high volume (waste remediation, bioenergy) from microalgae involves regulatory and technical problems. Waste-remediation and algal biorefinery were extensively reviewed in many previous reports. On the other hand, this review focuses on the cascade processes for efficient utilization of microalgae for integrated bioenergy production through the transesterification. Microalgal biomass remnants after the transesterification process, comprising carbohydrates as a major component (process flow A) or the carbohydrate fraction after bio-separation of pretreated microalgae (process flow B) can be utilized for bioethanol production. Therefore, this review concentrates on the cascade flow of integrated bioprocessing methods for biodiesel and bioethanol production through the transesterification and biochemical routes. The review also sheds light on the recent combinatorial approaches of transesterification of microalgae. The applicability of spent microalgal biomass residue for biogas and other applications to bring about zero-waste residue are discussed. Furthermore, techno-economic analysis (TEA), life cycle assessment (LCA) and challenges of microalgal biorefineries are discussed.

Electricity from methane by Methylococcus capsulatus (Bath) and Methylosinus trichosporium OB3b.

Given the difficulties valorizing methane (CH4) via catalytic routes, this study explores use of CH4-oxidizing bacteria ("methanotrophs") for generating electricity directly from CH4. A preconditioned methanotrophic biofilm on 3D nickel foam with reduced graphene oxide (rGO/Ni) was used as the anode in two-compartment microbial fuel cells (MFCs). This study demonstrates a proof of concept for turning CH4 into electricity by two model methanotrophs including Methylosinus trichosposium OB3b and Methylococcus capsulatus (Bath). Both OB3b (205 mW.m-2) and Bath (110 mW.m-2) strains yielded a higher electricity from CH4 when grown on rGO/Ni compared to graphite felt electrodes. Based on electrochemistry tests, molecular dynamics simulations, genome annotations and interaction analysis, a mechanistic understanding of reasons behind enhanced performance of methanotrophs grown on rGO/Ni are presented.

Anaerobic wastewater treatment and reuse enabled by thermophilic bioprocessing integrated with a bioelectrochemical/ultrafiltration module.

The current study aimed to develop an anaerobic wastewater treatment and reuse module enabled by thermophilic bioprocessing, a microbial fuel cell (MFC) and ultrafiltration (UF) treatment. A previously unexplored consortium based on Thermoanaerobacterium thermosaccharolyticum and Arcobacter sp. was used to remove ~73% of chemical oxygen demand (COD) from wastewater under anaerobic conditions (CODi = 200 mg/L). The subsequent MFC and UF treatment removed the COD remnants to meet the secondary treatment standards and reuse criteria. The energy efficiency of polyethersulfone UF membranes was improved by modifying their surfaces with coatings based on self-polymerized dopamine, mixtures of dopamine and poly(2-dimethylamino) ethyl methacrylate methyl, and dopamine analog norepinephrine. The resulting hydrophilic, anti-fouling layers were found to reduce interactions between rejected species and the membrane surface. Finally, this study presents a comparative treatment performance and energy efficiency of the wastewater treatment and reuse modules arranged in six different configurations.

Hexagonal Boron Nitride for Sulfur Corrosion Inhibition.

Corrosion by sulfur compounds is a long-standing challenge in many engineering applications. Specifically, designing a coating that protects metals from both abiotic and biotic forms of sulfur corrosion remains an elusive goal. Here we report that atomically thin layers (∼4) of hexagonal boron nitride (hBN) act as a protective coating to inhibit corrosion of the underlying copper (Cu) surfaces (∼6-7-fold lower corrosion than bare Cu) in abiotic (sulfuric acid and sodium sulfide) and biotic (sulfate-reducing bacteria medium) environments. The corrosion resistance of hBN is attributed to its outstanding barrier properties to the corrosive species in diverse environments of sulfur compounds. Increasing the number of atomic layers did not necessarily improve the corrosion protection mechanisms. Instead, multilayers of hBN were found to upregulate the adhesion genes in Desulfovibrio alaskensis G20 cells, promote cell adhesion and biofilm growth, and lower the protection against biogenic sulfide attack when compared to the few layers of hBN. Our findings confirm hBN as the thinnest coating to resist diverse forms of sulfur corrosion.

Valorization of methane from environmental engineering applications: A critical review.

Wastewater and waste management sectors alone account for 18% of the anthropogenic methane (CH4) emissions. This study presents a critical overview of methanotrophs ("methane oxidizing microorganisms") for valorizing typically discarded CH4 from environmental engineering applications, focusing on wastewater treatment plants. Methanotrophs can convert CH4 into valuable bioproducts including chemicals, biodiesel, DC electricity, polymers, and S-layers, all under ambient conditions. As discarded CH4 and its oxidation products can also be used as a carbon source in nitrification and annamox processes. Here we discuss modes of CH4 assimilation by methanotrophs in both natural and engineered systems. We also highlight the technical challenges and technological breakthroughs needed to enable targeted CH4 oxidation in wastewater treatment plants.

Electricity from methanol using indigenous methylotrophs from hydraulic fracturing flowback water.

Methanol solvents that are used in hydraulic fracturing often return back to the surface in the form of recalcitrant flowback water. Here, the indigenous methylotrophic bacteria from flowback water were enriched and used to generate electricity from methanol in a two-compartment microbial fuel cell (CH3OH-MFC). An identical MFC based on a tryptone-yeast extract (TY-MFC) was used as a control. CH3OH-MFC yielded a 2.7-fold thicker biofilm dominated by electrogenic species (81%) and higher power density (76 mW/m2) compared with TY-MFC (50 mW/m2). Illumina MiSeq sequencing of the 16S rRNA gene in TY-MFC revealed classes from Actinobacteria, Bacteroidia and γ-proteobacteria. The CH3OH-MFC yielded α-proteobacteria, ß-proteobacteria, γ-proteobacteria and Bacteroidia, with a dominant fraction of Rhodobacter sphaeroides (~29%). We discuss the potential pathways used by R. sphaeroides to maintain syntrophic cooperation with other bacterial and archaeal members to sustain CH3OH oxidation. Finally, we establish that a pure culture of R. sphaeroides 2.4.1 generates electricity directly from methanol.

Vitamin-C-enabled reduced graphene oxide chemistry for tuning biofilm phenotypes of methylotrophs on nickel electrodes in microbial fuel cells.

This study reports the use of multi-layered reduced graphene oxide (rGO) coating on porous nickel foam (NF) electrodes for enhancing biofilm growth of Rhodobacter Sphaeroides spp fed with methanol in microbial fuel cells (CH3OH-MFCs). Electrochemical methods were used to assess the methylotrophic activity on rGO/NF electrodes. The power density and current density offered by rGO/NF (1200 mW m-2 and 680 mA m-2) were 220-fold and 540-fold higher compared to bare NF (5.50 mW m-2 and 1.26 mA m-2), respectively. Electrochemical impedance spectroscopy results show that rGO/NF suppresses charge transfer resistance to CH3OH oxidation by 40-fold compared to the control. This improved performance is due to the ability of rGO coatings to decrease the wetting contact angle (improve the hydrophilicity) of NF from 1280 to 00. A preliminary cost analysis was carried out to assess the viability of rGO/NF electrodes via vitamin-C-enabled graphene oxide chemistry for CH3OH-MFCs applications.

Improved biomass and lipid production in Synechocystis sp. NN using industrial wastes and nano-catalyst coupled transesterification for biodiesel production.

In this study, the improved biomass (1.6 folds) and lipid (1.3 folds) productivities in Synechocystis sp. NN using agro-industrial wastes supplementation through hybrid response surface methodology-genetic algorithm (RSM-GA) for cost-effective methodologies for biodiesel production was achieved. Besides, efficient harvesting in Synechocystis sp. NN was achieved by electroflocculation (flocculation efficiency 97.8±1.2%) in 10min when compared to other methods. Furthermore, different pretreatment methods were employed for lipid extraction and maximum lipid content of 19.3±0.2% by Synechocystis sp. NN was attained by ultrasonication than microwave and liquid nitrogen assisted pretreatment methods. The highest FAME (fatty acid methyl ester) conversion of 36.5±8.3mg FAME/g biomass was obtained using titanium oxide as heterogeneous nano-catalyst coupled whole-cell transesterification based method. Conclusively, Synechocystis sp. NN may be used as a biodiesel feedstock and its fuel production can be enriched by hybrid RSM-GA and nano-catalyst technologies.