Bioprospection and selection of bacteria isolated from environments contaminated with petrochemical residues for application in bioremediation

Crude oil degrading efficiency of formulated consortium of bacterial strains isolated from petroleum-contaminated sludge

Crude oil contamination has been widely recognized as a major environmental issue due to its various adverse effects. The use of inhabitant microorganisms (native to the contaminated sites) to detoxify/remove pollutants owing to their diverse metabolic capabilities is an evolving method for the removal/degradation of petroleum industry contaminants. The present study deals with the exploitation of native resident bacteria from crude oil contaminated site (oil exploration field) for bioremediation procedures. Fifteen (out of forty-four) bioremediation-relevant aerobic bacterial strains, belonging to the genera of Bacillus, Stenotrophomonas, Pseudomonas, Paenibacillus, Rhizobium, Burkholderia, and Franconibacter, isolated from crude oil containing sludge, have been selected for the present bioremediation study. Crude oil bioremediation performance of the selected bacterial consortium was assessed using microcosm-based studies. Stimulation of the microbial consortium with nitrogen or phosphorous led to the degradation of 60-70% of total petroleum hydrocarbon (TPH) in 0.25% and 0.5% crude oil experimental sets. CO2 evolution, indicative of crude oil mineralization, was evident with the highest evolution being 28.6 mg mL-1. Ecotoxicity of treated crude oil-containing media was assessed using plant seed germination assay, in which most of the 0.25% and 0.5% treated crude oil sets gave positive results thereby suggesting a reduction in crude oil toxicity.

Bioremediation of Diesel-Contaminated Soil by Fungal Solid-State Fermentation

To address the poor removal of diesel in soil by indigenous microorganisms, we proposed a fungal solid-state fermentation (SSF) method for bioremediation. We screened Pycnoporus sanguineus 5.815, Trametes versicolor 5.996, and Trametes gibbosa 5.952 for their diesel-degrading abilities, with Trametes versicolor 5.996 showing the most promise. The fungal inoculum was obtained through SSF using wood chips and bran. Trametes versicolor 5.996 was applied to two treatments: natural attenuation (NA, diesel-contaminated soil) and bioremediation (BR, 10% SSF added to diesel-contaminated soil). Over 20 days, NA removed 12.9% of the diesel, while BR achieved a significantly higher 38.3% degradation rate. BR also increased CO2 and CH4 emissions but reduced N2O emissions. High-throughput sequencing indicated SSF significantly enriched known diesel-degrading microorganisms like Ascomycota (83.82%), Proteobacteria (46.10%), Actinobacteria (27.88%), Firmicutes (10.35%), and Bacteroidota (4.66%). This study provides theoretical support for the application of fungal remediation technology for diesel and improves understanding of microbiologically mediated diesel degradation and soil greenhouse gas emissions.

New benzo(a)pyrene-degrading strains of the Burkholderia cepacia complex prospected from activated sludge in a petrochemical wastewater treatment plant

The prospection of bacteria that are resistant to polyaromatic hydrocarbons (PAH) of activated sludge from a Petrochemical Wastewater Treatment Plant (WWTP) allows investigating potential biodegraders of PAH. For this purpose, sludge samples were cultured with benzo(a)pyrene and/or naphthalene as carbon sources. The recovered isolates were characterized by biochemical methods and identified based on the analysis of the sequence of three genes: 16S, recA and gyrB. The isolated strains were shown to be capable of producing surfactants, which are important for compound degradation. The ability to reduce benzo(a)pyrene in vitro was tested by gas chromatography. After 20 days of experiment, the consortium that was enriched with 1 mg/L of benzo(a)pyrene was able to reduce 30% of the compound when compared to a control without bacteria. The four isolated strains that significantly reduced benzo(a)pyrene belong to the Burkholderia cepacia complex and were identified within the consortium as the species B. cenocepacia IIIa, B. vietnamiensis, B. cepacia, and B. multivorans. This finding demonstrates the biotechnological potential of the B. cepacia complex strains for use in wastewater treatment and bioremediation. Previous studies on hydrocarbon-degrading strains focused mainly on contaminated soil or marine areas. In this work, the strains were prospected from activated sludge in a WWTP and showed the potential of indigenous samples to be used in both improving treatment systems and bioremediation of areas contaminated with petrochemical waste.

Distinct Changes Occur in the Human Breast Milk Microbiome Between Early and Established Lactation in Breastfeeding Guatemalan Mothers

Human breast milk contains a diverse community of bacteria, but as breast milk microbiome studies have largely focused on mothers from high income countries where few women breastfeed to 6 months, the temporal changes in the breast milk microbiome that occur during later lactation stages have not been explored. For this cross-sectional study, microbiota from breast milk samples of Mam-Mayan mothers living in eight remote rural communities in the Western Highlands of Guatemala were analyzed. All mothers delivered vaginally and breastfed their infants for 6 months. Breast milk from 76 unrelated mothers was used to compare two lactation stages, either “early” (6–46 days post-partum, n = 33) or “late” (109–184 days post-partum, n = 43). Breast milk microbial communities were assessed using 16S ribosomal RNA gene sequencing and lactation stages were compared using DESeq2 differential abundance analysis. A total of 1,505 OTUs were identified, including 287 which could be annotated as putative species. Among several maternal factors, lactation stage explained microbiome variance and inertia in ordination with the most significance (p < 0.001). Differential abundance analysis identified 137 OTUs as significantly higher in either early or late lactation. These included a general shift from Staphylococcus and Streptococcus species in early lactation to Sphingobium and Pseudomonas species in late lactation. Species enriched in early lactation included putative commensal bacteria known to colonize the infant oral and intestinal tracts whereas species enriched in late lactation had a uniform functional trait associated with aromatic compound degradation. Differentially abundant species also included several species which have not previously been reported within breast milk, such as Janthinobacterium agaricidamnosum, Novosphingobium clariflavum, Ottowia beijingensis, and Flavobacterium cucumis. These discoveries describe temporal changes to the breast milk microbiome of healthy Guatemalan mothers from early to late lactation. Collectively, these findings illustrate how studying under-represented human populations might advance our understanding of factors that modulate the human milk microbiome in low and middle income countries (LMIC).

Bioremediation of oily sludge by solid complex bacterial agent with a combined two-step process

In the present research, a bioremediation process was developed using solid complex bacterial agents (SCBA) through a combined two-step biodegradation process. Four isolated strains showed high efficiency for the degradation of total petroleum hydrocarbons (TPH) and the reduction of COD of the oily sludge, at 96.6% and 92.6%, respectively. The mixed strains together with bran prepared in form of SCBA exhibited improved performance compared to individual strains, all of which had an optimal temperature of around 35 °C. The use of SCBA provided advantages over commonly used liquid media for storage and transportation. The two-step process, consisting of firstly biosurfactant-assisted oil recovery and secondly biodegradation of the remaining TPH with SCBA, demonstrated the capability for treating oily sludge with high TPH content (>10 wt%) and short process period (60 days). The large-scale (5 tons oily sludge) field test, achieving a TPH removal efficiency of 93.8% and COD reduction of 91.5%, respectively, confirmed the feasibility and superiority of the technology for industrial applications.

Dynamics and response of microbial diversity to nutritional conditions in denitrifying bioreactor for linear alkylbenzene sulfonate removal

The aim of this study was to evaluate the microbial structure and phylogenetic diversity under the influence of nutritional conditions and hydraulic retention time (HRT) in fluidized bed reactors (FBR), operated in short HRT (8 h - FBR8; 12 h - FBR12) for linear alkylbenzene sulfonate (LAS) removal from laundry wastewater. After each phase, biofilm samples from FBR8 and FBR12 were submitted to microbial sequencing by Mi-Seq Illumina®. Higher LAS removal rates were observed after 313 days, achieving 99 ± 3% in FBR12 (22.5 ± 5.9 mg LAS/L affluent) and 93 ± 12% in FBR8 (20.6 ± 4.4 mg LAS/L affluent). Different modifications involving genera of bacteria were observed throughout the reactors operation. The identified microorganisms were, mostly, related to LAS degradation and nitrogen conversion such as Dechloromonas, Flavobacterium, Pseudomonas, and Zoogloea.

Isolation and characterization of novel bacterial strains for integrated solar-bioelectrokinetic of soil contaminated with heavy petroleum hydrocarbons

This study investigated the isolation and characterization of three novel bacterial strains; Acinetobacter calcoaceticus, Sphingobacterium multivorum, and Sinorhizobium, isolated form agriculture land. From three hundred strains of bacteria, the three isolates were identified for their superior diesel degradation ability by a series of bench-scale tests. The isolates were further investigated in bench tests for their ability to grow in different diesel fuel concentrations, temperature and pH; degrade diesel fuel in vitro; and for the identification of functional genes. Semi-pilot bioelectrokinetic tests were conducted in three electrokinetic cells. An innovative electrode configuration was adopted to stabilize the soil pH and water content during the test. The genes expressed in the diesel degradation process including Lipases enzymes Lip A, LipB, Alk-b2, rubA, P450, and 1698/2041 were detected in the three isolates. The results showed that the solar panel voltage output is in agreement with the trapezoid model. The temperatures in the cells were found to be 5-7 °C higher than the ambient temperature. The electrode configuration succeeded in stabilizing the soil pH and water content, preventing the development of a pH gradient, important progress for the survival of bacteria. The diesel degradation in the soil after bioelectrokinetic tests were 20-30%, compared to 10-12% in the controls. The study succeeded in developing environmentally friendly technology employing novel bacterial strains to degrade diesel fuel and utilizing solar panels to produce renewable energy for bioelectrokinetics during the winter season.

Assessing the efficiency in assisted depuration of coffee processing wastewater from mixed wild microbial selected inoculum

This work evaluated the efficiency of bacterial bio-augmentation to the biological treatment of coffee processing wastewater (CPWW) in a pilot wastewater treatment plant (WTP). Biochemical oxygen demand (BOD) and chemical oxygen demand (COD) values were the basis for the treatment efficiency. Serratia marcescens CCMA 1010 and CCMA 1013, Corynebacterium flavescens CCMA 1006 and Acetobacter indonesiensis CCMA 1002 were previously selected. The microbial cocktail was inoculated and persisted in CPWW during all treatments. The richness of wild species was a little altered over time and up to nine species were found in each sampled season. The microbiota composition presented variation of a total of 13 species, despite the inoculation of the microbial inoculum. The biodegradability index of effluent, close to 0.5, was favourable to biological treatment. The pollution parameters of CPWW were decreased in function of the variation of community composition and microbial activity. The greatest reduction of BOD (~ 33%) and COD (~ 25%) was observed between 72 h and 8 days of the biological treatment. The CPWW toxicity in Allium cepa seeds was lower by up to 60%, and the germination index (GI) exceeded 100% in the treated CPWW. The results of the CPWW biological treatment by bio-augmentation from native micro-organisms in the pilot-scale WTP indicated the greatest efficiency relating to the spontaneous biological treatment of CPWW. After this treatment, the discharge of effluent in the environment would not have toxic effects on the plants.

Mitigation of soil contaminated with diesel fuel using bioelectrokinetics

This study investigated the effectiveness of bioelectrokinetics in rehabilitating a silty clayey sand contaminated with diesel fuel using three novel bacterial strains; Acinetobacter calcoaceticus, Sphingobacterium multivorum, and Sinorhizobium, isolated form agriculture land. Three electrokinetic bioremediation cells were used to conduct the tests and a novel electrode configuration technique was used to stabilize pH and water content in the soil specimen. Solar photovoltaic panels were used to generate sustainable energy for the process. The tests were carried out in outdoors for 55 days. Applied voltage, current passing through the electrokinetic cell, and the temperature of the soil specimen were recorded periodically during the test. The pH, water content, and diesel concentration were determined at the end of the tests. Over the test period, the voltage typically increased from zero before sunrise, remained relatively stabilized for about 4 h, and then started to decrease and dropped to zero by sunset. The temperatures in the cells were found to be 5-7 °C higher than the ambient temperature. The innovative electrode configuration succeeded in keeping the pH of soil to remain the same and thereby prevented the development of a pH gradient in the soil, an important development for survival of the bacteria. The diesel degradation in the soil after bioelectrokinetics were 20-30%, compared to 10-12% in the control test. The study was successful in developing environmentally friendly technology employing novel bacterial strains to degrade diesel fuel and utilizing solar panel to produce renewable energy for bioelectrokinetic during the winter season.

Comparative metagenomics reveals different hydrocarbon degradative abilities from enriched oil-drilling waste

The oil drilling process generates large volumes of waste with inadequate treatments. Here, oil drilling waste (ODW) microbial communities demonstrate different hydrocarbon degradative abilities when exposed to distinct nutrient enrichments as revealed by comparative metagenomics. The ODW was enriched in Luria Broth (LBE) and Potato Dextrose (PDE) media to examine the structure and functional variations of microbial consortia. Two metagenomes were sequenced on Ion Torrent platform and analyzed using MG-RAST. The STAMP software was used to analyze statistically significant differences amongst different attributes of metagenomes. The microbial diversity presented in the different enrichments was distinct and heterogeneous. The metabolic pathways and enzymes were mainly related to the aerobic hydrocarbons degradation. Moreover, our results showed efficient biodegradation after 15 days of treatment for aliphatic hydrocarbons (C8-C33) and polycyclic aromatic hydrocarbons (PAHs), with a total of about 50.5% and 46.4% for LBE and 44.6% and 37.9% for PDE, respectively. The results obtained suggest the idea that the enzymatic apparatus have the potential to degrade petroleum compounds.

Biosurfactant assisted recovery of the C5-C11 hydrocarbon fraction from oily sludge using biosurfactant producing consortium culture of bacteria

A biosurfactant producing culture of bacteria was isolated from an automobile engine oil dump site which was later used as an inoculum in batch and continuous flow oil recovery from oily sludge. Initially, an emulsion of oily sludge was prepared by mixing 5% m/v solids: 21% v/v bituminous sludge: 77% v/v water. The isolated cultures were added to vessels with stable emulsions to facilitate the separation of oil droplets from the sludge matrix. In batches with live cultures, up to 35% oil recovery was achieved after incubation for 10 days. Further investigations were conducted in a semi-continuous feed, fed-batch plug flow reactor (FB-PFR) system. Up to 99.7% was achieved in the FB-PFR after operation for 10 days, much higher than the recovery achieved in the pure batch systems where only 35% oil was recovered after incubation for 10 days. The improved performance in the FB-PFR was attributed to differential separation of particles under variable velocity along the reactor. The culture in the reactor was predominated by Klebsiellae, Enterobacteriaceae and Bacilli throughout the experiment. A crude biosurfactant produced by the cultures was partially purified and analyzed using the liquid chromatograph coupled to a tandem mass spectrometer (LC-MS/MS) which showed that the molecular structure of the biosurfactant produced closely matched the structure of lipopeptides identified in earlier studies. This process is aimed at recovering useful oil from oily waste sludge with the added advantage of degrading aromatic organic impurities in the oil to produce a cleaner oil product. The further advantage of the FB-PFR system was that, the bacteria discharged together with effluent sludge residue further degraded chemical oxygen demand (COD) in the treated sludge thereby reducing the polluting potential of the final disposed sludge.

Brazilian Cerrado soil reveals an untapped microbial potential for unpretreated polyethylene biodegradation

Discarded PE-based products pose a social and environmental threat because of their recalcitrance to degradation, a consequence of the unique set of PE's physicochemical properties. In this study we isolated nine novel PE-degrading bacteria from plastic debris found in soil of the savanna-like Brazilian Cerrado. These bacterial strains from the genera Comamonas, Delftia, and Stenotrophomonas showed metabolic activity and cellular viability after a 90-day incubation with PE as the sole carbon source. ATR/FTIR indicated that biodegraded PE undergone oxidation, vinylene formation, chain scission, among other chemical changes. Considerable nanoroughness shifts and vast damages to the micrometric surface were confirmed by AFM and SEM. Further, phase imaging revealed a 46.7% decrease in the viscous area of biodegraded PE whereas Raman spectroscopy confirmed a loss in its crystalline content, suggesting the assimilation of smaller fragments. Intriguingly, biodegraded PE chemical fingerprint suggests that these strains use novel biochemical strategies in the biodegradation process. Our results indicate that these microbes are capable of degrading unpretreated PE of very high molecular weight (191,000gmol^-1) and survive for long periods under this condition, suggesting not only practical applications in waste management and environmental decontamination, but also future directions to understand the unraveled metabolism of synthetic polymers.

Bacillus spp. Isolated from Puba as a Source of Biosurfactants and Antimicrobial Lipopeptides

Several products of industrial interest are produced by Bacillus, including enzymes, antibiotics, amino acids, insecticides, biosurfactants and bacteriocins. This study aimed to investigate the potential of two bacterial isolates (P5 and C3) from puba, a regional fermentation product from cassava, to produce multiple substances with antimicrobial and surface active properties. Phylogenetic analyses showed close relation of isolates P5 and C3 with Bacillus amyloliquefaciens and Bacillus thuringiensis, respectively. Notably, Bacillus sp. P5 showed antimicrobial activity against pathogens such as Listeria monocytogenes and Bacillus cereus, in addition to antifungal activity. The presence of genes encoding pre-subtilosin (sboA), malonyl CoA transacylase (ituD), and the putative transcriptional terminator of surfactin (sfp) were detected in Bacillus sp. P5, suggesting the production of the bacteriocin subtilosin A and the lipopeptides iturin A and surfactin by this strain. For Bacillus sp. C3 the presence of sboA and spas (subtilin) genes was observed by the first time in members of B. cereus cluster. Bacillus sp. P5 showed emulsifying capability on mineral oil, soybean biodiesel and toluene, while Bacillus sp. C3 showed emulsifying capability only on mineral oil. The reduction of the surface tension in culture medium was also observed for strain P5, confirming the production of surface-active compounds by this bacterium. Monoprotonated molecular species and adducts of sodium and potassium ions of surfactin, iturin, and fengycin were detected in the P5 culture medium. Comparative MS/MS spectra of the peak m/z 1030 (C14 surfactin A or C15 surfactin B [M+Na]⁺) and peak m/z 1079 (C15 iturin [M+Na]⁺) showed the same fragmentation profile of standards, confirming the molecular identification. In conclusion, Bacillus sp. P5 showed the best potential for the production of antifungal, antibacterial, and biosurfactant substances.

Complete Genome Sequence of Bacillus megaterium Myophage Moonbeam

Moonbeam is a newly isolated myophage of Bacillus megaterium, a common Gram-positive bacterium that is routinely used for large-scale protein production. Bacteriophages have potential to be useful tools for industrial applications. Here, we describe the complete genome of Moonbeam and describe its features.

Biosurfactants in agriculture

Agricultural productivity to meet growing demands of human population is a matter of great concern for all countries. Use of green compounds to achieve the sustainable agriculture is the present necessity. This review highlights the enormous use of harsh surfactants in agricultural soil and agrochemical industries. Biosurfactants which are reported to be produced by bacteria, yeasts, and fungi can serve as green surfactants. Biosurfactants are considered to be less toxic and eco-friendly and thus several types of biosurfactants have the potential to be commercially produced for extensive applications in pharmaceutical, cosmetics, and food industries. The biosurfactants synthesized by environmental isolates also has promising role in the agricultural industry. Many rhizosphere and plant associated microbes produce biosurfactant; these biomolecules play vital role in motility, signaling, and biofilm formation, indicating that biosurfactant governs plant–microbe interaction. In agriculture, biosurfactants can be used for plant pathogen elimination and for increasing the bioavailability of nutrient for beneficial plant associated microbes. Biosurfactants can widely be applied for improving the agricultural soil quality by soil remediation. These biomolecules can replace the harsh surfactant presently being used in million dollar pesticide industries. Thus, exploring biosurfactants from environmental isolates for investigating their potential role in plant growth promotion and other related agricultural applications warrants details research. Conventional methods are followed for screening the microbial population for production of biosurfactant. However, molecular methods are fewer in reaching biosurfactants from diverse microbial population and there is need to explore novel biosurfactant from uncultured microbes in soil biosphere by using advanced methodologies like functional metagenomics.