Isolation, identification and diesel-oil biodegradation capacities of indigenous hydrocarbon-degrading strains of Cellulosimicrobium cellulans and Acinetobacter baumannii from tarball at Terengganu beach, Malaysia

Optimizing microbial strain selection for pyrethroid biodegradation in contaminated environments through a TOPSIS-based decision-making system

Improved and contemporary agriculture relies heavily on pesticides, yet some can be quite persistent and have a stable chemical composition, posing a significant threat to the ecology. Removing harmful effects is upon their degradability. Biodegradation must be emphasized to lower pesticide degradation costs, especially in the soil. Here, a decision-making system was used to determine the best microbial strain for the biodegradation of the pyrethroid-contaminated soil. In this system, the criteria chosen as: pH (C1), Temp (C2), RPM (C3), Conc. (C4), Degradation (%) (C5) and Time required for degradation(hrs) (C6); and five alternatives were Bacillus (A1), Acinetobacter (A2), Escherichia (A3), Pseudomonas (A4), and Fusarium (A5). The best alternative was selected by applying the TOPSIS (technique for order performance by similarity to ideal solution) method, which evaluates based on their closeness to the ideal solution and how well they meet specific requirements. Among all the specified criteria, Acinetobacter (A2) was the best and optimal based on the relative closeness value (( R i ∗ ) = 0.740 (A2) > 0.544 (A5) > 0.480 (A1) > 0.403 (A4) > 0.296 (A3)). However, the ranking of the other alternatives is also obtained in the order Fusarium (A5), Bacillus (A1), Pseudomonas (A4), Escherichia (A3). Hence this study suggests Acinetobacter is the best microbial strain for biodegradation of pyrethroids; while least preference should be given to Escherichia. Acinetobacter, versatile metabolic nature with various xenobiotic compounds' degradation ability, is gram-negative, aerobic, coccobacilli, nonmotile, and nonspore forming bacteria. Due to less study about Acinetobacter it is not in that much frame as the other microorganisms. Hence, considering the Acinetobacter strain for the biodegradation study will give more optimal results than the other microbial strains. Novelty of this study, the TOPSIS method is applied first time in selecting the best microbial strain for the biodegradation of pyrethroid-contaminated soil, considering this selection process as multi-criteria decision-making (MCDM) problem.

Fungal diversity associated with Goa's tarballs: Insights from ITS region amplicon sequencing

This study explores the fungal diversity associated with tarballs, weathered crude oil deposits, on Goa's tourist beaches. Despite tarball pollution being a longstanding issue in Goa state in India, comprehensive studies on associated fungi are scarce. Our research based on amplicon sequence analysis of fungal ITS region fills this gap, revealing a dominance of Aspergillus, particularly Aspergillus penicillioides, associated with tarballs from Vagator and Morjim beaches. Other notable species, including Aspergillus sydowii, Aspergillus carbonarius, and Trichoderma species, were identified, all with potential public health and ecosystem implications. A FUNGuild analysis was conducted to investigate the potential ecological roles of these fungi, revealing a diverse range of roles, including nutrient cycling, disease propagation, and symbiotic relationships. The study underscores the need for further research and monitoring, given the potential health risks and contribution of tarball-associated fungi to the bioremediation of crude oil-contaminated beaches.

Construction of Shale Gas Oil-Based Drilling Cuttings Degrading Bacterial Consortium and Their Degradation Characteristics

Oil-based drilling cuttings (OBDCs) contain petroleum hydrocarbons with complex compositions and high concentrations, which have highly carcinogenic, teratogenic, and mutagenic properties. In this study, three highly efficient petroleum hydrocarbon-degrading bacteria were screened from OBDCs of different shale gas wells in Chongqing, China, and identified as Rhodococcus sp. and Dietzia sp. Because of their ability to degrade hydrocarbons of various chain lengths, a new method was proposed for degrading petroleum hydrocarbons in shale gas OBDCs by combining different bacterial species. Results showed that the bacterial consortium, consisting of the three strains, exhibited the highest degradation rate for petroleum hydrocarbons, capable of degrading 74.38% of long-chain alkanes and 93.57% of short-chain alkanes, respectively. Moreover, the petroleum hydrocarbon degradation performance of the bacterial consortium in actual OBDCs could reach 90.60% in the optimal conditions, and the degradation kinetic process followed a first-order kinetic model. This study provides a certain technical reserve for the bioremediation of shale gas OBDCs.

Use of Taguchi design for optimization of diesel-oil biodegradation using consortium of Pseudomonas stutzeri, Cellulosimicrobium cellulans, Acinetobacter baumannii and Pseudomonas balearica isolated from tarball in Terengganu Beach, Malaysia

A consortium of bacteria capable of decomposing oily hydrocarbons was isolated from tarballs on the beaches of Terengganu, Malaysia, and classified as Pseudomonas stutzeri, Cellulosimicrobium cellulans, Acinetobacter baumannii and Pseudomonas balearica. The Taguchi design was used to optimize the biodegradation of diesel using these bacteria as a consortium. The highest biodegradation of diesel-oil in the experimental tests was 93.6%, and the individual n-alkanes decomposed 87.6-97.6% over 30 days. Optimal settings were inoculum size of 2.5 mL (1.248 OD_600nm); 12% (v/v) the initial diesel-oil in a minimal salt medium of pH 7.0, 30.0 gL^-1 NaCl and 2.0 gL^-1 NH₄NO₃ concentration, incubated at 42 °C temperature and 150 rpm agitation speed. Parameters significantly improved diesel-oil removal by consortium as shown by the model determination coefficient (R² = 90.89%; P < 0.001) with a synergistic effect of agitation speed significantly contributing 81.03%. Taguchi design determined the optimal settings for the parameters under study, which significantly improved diesel-oil removal by consortium. This can be used to design a novel bioremediation strategy that can achieve optimal decontamination of oil pollution in a shorter time.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s40201-022-00812-3.

Degradation potential of alkanes by diverse oil-degrading bacteria from deep-sea sediments of Haima cold seep areas, South China Sea

Marine oil spills are a significant concern worldwide, destroying the ecological environment and threatening the survival of marine life. Various oil-degrading bacteria have been widely reported in marine environments in response to marine oil pollution. However, little information is known about culturable oil-degrading bacteria in cold seep of the deep-sea environments, which are rich in hydrocarbons. This study enriched five oil-degrading consortia from sediments collected from the Haima cold seep areas of the South China Sea. Parvibaculum, Erythrobacter, Acinetobacter, Alcanivorax, Pseudomonas, Marinobacter, Halomonas, and Idiomarina were the dominant genera. Further results of bacterial growth and degradation ability tests indicated seven efficient alkane-degrading bacteria belonging to Acinetobacter, Alcanivorax, Kangiella, Limimaricola, Marinobacter, Flavobacterium, and Paracoccus, whose degradation rates were higher in crude oil (70.3–78.0%) than that in diesel oil (62.7–66.3%). From the view of carbon chain length, alkane degradation rates were medium chains > long chains > short chains. In addition, Kangiella aquimarina F7, Acinetobacter venetianus F1, Limimaricola variabilis F8, Marinobacter nauticus J5, Flavobacterium sediminis N3, and Paracoccus sediminilitoris N6 were first identified as oil-degrading bacteria from deep-sea environments. This study will provide insight into the bacterial community structures and oil-degrading bacterial diversity in the Haima cold seep areas, South China Sea, and offer bacterial resources to oil bioremediation applications.

The car tank lid bacteriome: a reservoir of bacteria with potential in bioremediation of fuel

Bioprospecting of microorganisms suitable for bioremediation of fuel or oil spills is often carried out in contaminated environments such as gas stations or polluted coastal areas. Using next-generation sequencing (NGS) we analyzed the microbiota thriving below the lids of the fuel deposits of diesel and gasoline cars. The microbiome colonizing the tank lids differed from the diversity found in other hydrocarbon-polluted environments, with Proteobacteria being the dominant phylum and without clear differences between gasoline or diesel-fueled vehicles. We observed differential growth when samples were inoculated in cultures with gasoline or diesel as the main carbon source, as well as an increase in the relative abundance of the genus Pseudomonas in diesel. A collection of culturable strains was established, mostly Pseudomonas, Stenotrophomonas, Staphylococcus, and Bacillus genera. Strains belonging to Bacillus, Pseudomonas, Achromobacter, and Isoptericola genera showed a clear diesel degradation pattern when analyzed by GC-MS, suggesting their potential use for bioremediation and a possible new species of Isoptericola was further characterized as hydrocarbon degrader.

The diversity of microbes and prediction of their functions in karst caves under the influence of human tourism activities-a case study of Zhijin Cave in Southwest China

Microorganisms, sensitive to the surrounding environment changes, show how the cave environment can be impacted by human activities. Zhijin Cave, featured with the most well-developed karst landform in China, has been open to tourists for more than 30 years. This study explored the microbial diversity in a karst cave and the impacts of tourism activities on the microbial communities and the community structures of bacteria and archaea in three niches in Zhijin Cave, including the mixture of bacteria and cyanobacteria on the rock wall, the aquatic sediments, and the surface sediments, using 16S rRNA high-throughput sequencing technology. It was found that Actinobacteriota and Proteobacteria were the dominant bacteria in the cave and Crenarchaeota and Thermoplasmatota were the dominant archaea. The correlation between microorganisms and environmental variables in the cave showed that archaea were more affected by pH and ORP than bacteria and F^-, Cl^-, NO₃^-, and SO₄^2- were all positively relevant to the distribution of most bacteria and archaea in the cave. PICRUSt's prediction of microbial functions also indicated that abundance of the bacteria's functions was higher than that of the archaea. The intention of this study was to improve the understanding, development, and protection of microbial resources in caves.

Crude Oil Degradation by a Novel Strain Pseudomonas aeruginosa AQNU-1 Isolated from an Oil-Contaminated Lake Wetland

In this study, a novel crude oil degrading bacterium was isolated from an oil-contaminated freshwater lake using crude oil as the sole carbon source. The strain was named Pseudomonas aeruginosa AQNU-1 based on the analyses of its morphological characteristics and 16S rRNA gene sequencing. Gas chromatography-mass spectrometry (GC-MS) was carried out to investigate the degradation of crude oil fractions under dynamic (37 °C, 180 r/min) and static (37 °C, 0 r/min) cultivation over three months of continuous enrichment in the laboratory. It was found that strain AQNU-1 exhibited stronger biodegradation efficiency for n-alkanes of C13–C35 under dynamic cultivation with degradation ratios of 87–100% compared to ratios of 74–100% under static cultivation. Furthermore, this strain could fully utilize alkylcyclohexane (M/Z 82), alkylbenzene (M/Z 92) and alkyltoluene (M/Z 106) in crude oil under both conditions. It also had better biodegradability of partial aromatic compounds in the crude oil, showing differences within compound families of aromatic hydrocarbons. Further, the potential degradation ability of this isolated strain decreased with increasing molecular weight, with the dynamic condition performing better in general. These results suggest that the isolated strain has great potential to assimilate indigestible crude-oil contaminants under different hydrological conditions, providing a valuable microbiological resource for in situ remediation of natural wetlands.

Oil contamination drives the transformation of soil microbial communities: Co-occurrence pattern, metabolic enzymes and culturable hydrocarbon-degrading bacteria

The land-based oil extraction activity has led to serious pollution of the soil. While microbes may play an important role in the remediation of contaminated soils, ecological effects of oil pollution on soil microbial relationships remain poorly understood. Here, typical contaminated soils and undisturbed soils from seven oilfields of China were investigated in terms of their physicochemical characteristics, indigenous microbial assemblages, bacterial co-occurrence patterns, and metabolic enzymes. Network visualization based on k-core decomposition illustrated that oil pollution reduced correlations between co-existing bacteria. The core genera were altered to those related with oil metabolism (Pseudarthrobacter, Alcanivorax, Sphingomonas, Chromohalobacter and Nocardioides). Under oil pollution pressure, the indigenous bacteria Gammaproteobacteria was domesticated as biomarker and the enzyme expression associated with the metabolism of toxic benzene, toluene, ethylbenzene, xylene and polycyclic aromatic hydrocarbons was enhanced. Functional pathways of xenobiotics biodegradation were also stimulated under oil contamination. Finally, twelve culturable hydrocarbon-degrading microbes were isolated from these polluted soils and classified into Stenotrophomonas, Delftia, Pseudomonas and Bacillus. These results show that the soil microbial communities are transformed under oil pollution stress, and also provide useful information for future bioremediation processes.

Bacterial and archaeal diversity in oil fields and reservoirs and their potential role in hydrocarbon recovery and bioprospecting

Hydrocarbon is a primary source of energy in the current urbanized society. Considering the increasing demand, worldwide oil productions are declining due to maturity of oil fields and because of difficulty in discovering new oil fields to substitute the exploited ones. To meet current and future energy demands, further exploitation of oil resources is highly required. Microorganisms inhabiting in these areas exhibit highly diverse catabolic activities to degrade, transform, or accumulate various hydrocarbons. Enrichment of hydrocarbon-utilizing bacteria in oil basin is caused by continuous long duration and low molecular weight hydrocarbon microseepage which plays a very important role as an indicator for petroleum prospecting. The important microbial metabolic processes in most of the oil reservoir are sulfate reduction, fermentation, acetogenesis, methanogenesis, NO3- reduction, and Fe (III) and Mn (IV) reduction. The microorganisms residing in these sites have critical control on petroleum composition, recovery, and production methods. Physical characteristics of heavy oil are altered by microbial biotransformation and biosurfactant production. Considering oil to be one of the most vital energy resources, it is important to have a comprehensive understanding of petroleum microbiology. This manuscript reviews the recent research work referring to the diversity of bacteria in oil field and reservoir sites and their applications for enhancing oil transformation in the target reservoir and geomicrobial prospecting scope for petroleum exploration.

Potential biodegradation of Tapis Light Crude Petroleum Oil, using palm oil mill effluent final discharge as biostimulant for isolated halotolerant Bacillus strains

Petroleum hydrocarbon pollution in marine waters has been an extremely significant environmental and health issue worldwide. This study aims at constructing an efficient indigenous bacterial consortium to biodegrade Tapis Light Crude Petroleum Oil (TLCO). The local agro-industrial wastewater of palm oil mill effluent final discharge (POME FD) was used as biostimulant to enhance the biodegradation efficiency. In this study, three TLCO degrading bacteria were isolated from seawater samples collected. Molecular identification using 16S rRNA genes sequencing was done and results show that these isolated strains belong to: Bacillus tropicus, Bacillus licheniformis and Bacillus subtilis. Bacterial consortium tested using four different concentrations of POME FD (0.1, 0.25, 0.5, and 1%) as biostimulant and TLCO (0.5 and 1.0%) degradation capability was investigated. The residual TLCO in culture medium after 40 days was analysed. The results confirmed that POME FD dosage of 0.25% is optimum for the bacterial consortium and can degrade 99.85% of TLCO at 0.5%. However, TLCO degradation with POME FD dosage (0.25%) in TLCO (1.0%) was found optimum, with biodegradation reaching up to 95.23% in 40 days. This study is a beginning for the future development of a consortium of petroleum hydrocarbon degrading bacteria to mitigate oil spills in the Malaysian shoreline.

Diesel degradation efficiency of Enterobacter sp., Acinetobacter sp., and Cedecea sp. isolated from petroleum waste dumping site: a bioremediation view point

Bioremediation through biodegradation is applied for cleaning up several environmental pollutions including petroleum oil spill containing petrol, diesel, mobil, kerosene, lubricating, etc. which have devastated several endangered terrestrial and aquatic ecosystems. Therefore, the current research was aimed to isolate and identify diesel degrading bacteria from the petroleum waste dumping site and determined their degrading efficiency. The bacterial strains were isolated through a minimum salt medium supplemented with 2% diesel as the sole carbon source. The bacteria were identified by morphological, biochemical characterization, and 16S rRNA gene sequencing. The optimized growth pattern was evaluated by utilization of a wide range of temperatures (25, 30, 35, and 40 °C) and pH (5,6,7 and 8) as well as different concentrations of diesel (2, 3, 5and 7%). Finally, the degradation rate was determined by measuring the residual diesel after 7, 14, and 21 days of incubation. The study isolated Enterobacter ludwigii, Enterobacter mori, Acinetobacter baumannii, and Cedecea davisae where all are gram-negative rod-shaped bacilli. All the bacterial strains utilized the diesel at their best at 30 °C and pH 7, among them, A. baumannii and C. davisae exhibited the best degrading efficiency at all applied concentrations. Finally, the determination of degradation rate (%) through gravimetrical analysis has confirmed the potency of A. Baumannii and C. davisae where the degradation rate was around 61 and 52% respectively after 21 days of incubation period with 10% diesel. The study concludes that all of those isolated bacterial consortiums, especially A. baumannii and C. davisae could be allocated as active agents used for bioremediation to detoxify the diesel-containing contaminated sites in a cost-effective and eco-friendly way.

New insights into the biodegradation of chlorpyrifos by a novel bacterial consortium: Process optimization using general factorial experimental design

Himalayan mountains are subjected to the intensive and unjudicial application of chlorpyrifos (CP) in agricultural practices; hence it has spurred concerns over food safety and environmental consequences. These low-temperature mountainous regions are foremost ecosystems, representing the large-scale distribution of cold trapped CP residues. A bacterial consortium ECO-M was formed by isolating the CP degrading bacterial strains viz Agrobacterium tumefaciens strain ECO1, Cellulosimicrobium funkei strain ECO2, Shinella zoogloeoides strain ECO3 and Bacillus aryabhattai strain ECO4. At an initial concentration of 50 mg L^-1, consortium ECO-M degraded 100% of CP within 6 days. Emergence and subsequent degradation of the two metabolites, 3, 5, 6-trichloro-2-pyridinol (TCP) and 2-hydroxypyridine were confirmed by GC-MS analysis. A degradation pathway of CP by isolated strains has been proposed. A general factorial experimental design was effectuated to prognosticate the optimum biodegradation by manifesting the optimal biological and physicochemical factors. Fitness of the experimental design was affirmed experimentally by employing optimized factors i.e., temperature 30 °C, CP concentration 50 mg L^-1 and an inoculum size of 10% (v/v). The model appropriacy and the rationality of the optimization procedure were appraised by installing an in-situ microcosms experiment using the real contaminated soil collected from the Himalayan mountain ecosystem. The augmentation culture seems to be effectively conspicuous in stimulating maximum degradation up to 94.3% in the CP contaminated soil.

Degradation of petroleum hydrocarbons by embedding immobilized crude oil degrading bacteria

In this study, the removal effect of free and immobilized bacteria on crude oil was determined. Sodium alginate and polyvinyl alcohol were used as embedding agent, and ramie was modified as an adsorbent to immobilize free bacteria. The conditions for preparing immobilized pellets were optimized using the response surface method, and the best combination was simulated and obtained by Design-Expert 8.0. The best degradation rate of immobilized bacteria was 75.52%. The degradation by free bacteria and immobilized bacteria showed that the selected microorganisms had a good degradation effect on petroleum hydrocarbons.

Dehalogenase-producing halophiles and their potential role in bioremediation

This review aims to briefly describe the potential role of dehalogenase-producing halophilic bacteria in decontamination of organohalide pollutants. Hypersaline habitats pose challenges to life because of low water activity (water content) and is considered as the largest and ultimate sink for pollutants due to naturally and anthropogenic activities in which a substantial amount of ecological contaminants are organohalides. Several such environments appear to host and support substantial diversity of extremely halophilic and halotolerant bacteria as well as halophilic archaea. Biodegradation of several toxic inorganic and organic compounds in both aerobic and anaerobic conditions are carried out by halophilic microbes. Therefore, remediation of polluted marine/hypersaline environments are the main scorching issues in the field of biotechnology. Although many microbial species are reported as effective pollutants degrader, but little has been isolated from marine/hypersaline environments. Therefore, more novel microbial species with dehalogenase-producing ability are still desired.

Acinetobacter mesopotamicus sp. nov., Petroleum-degrading Bacterium, Isolated from Petroleum-Contaminated Soil in Diyarbakir, in the Southeast of Turkey

A new petroleum-degrading bacterium, designated strain GC2^T, was isolated from Bozkuş 1 petroleum station in Diyarbakir, located in the southeast of Turkey. Cells were Gram-negative staining, aerobic, coccoid-rods, non-motile, non-spore-forming. The bacterium was found to degrade 100% of n-alkanes ranging from C11 to C34 presented in the 1% crude oil after incubation of 7 days. The membrane phospholipids were 1,2 diacylglycero-3-phosphorylethanolamine (PEA), phosphatidylglycerol (PG), dipalmitoyl-sn-glycerol 1- phosphocholine (PC1), 1,2 dipalmitoyl-sn-glycero-3-phosphocholine monohydrate (PC3), cardiolipin also called diphosphatidylglycerol (CL) and l-α- phosphatidic acid, dipalmitoyl (AP); predominant respiratory ubiquinone was Q-8 and C16:0, C18:1ω9c and C16:1 were the major cellular fatty acids. The 16S rRNA sequence analysis revealed that the strain GC2^T was a member of genus Acinetobacter and was most closely related to Acinetobacter lwoffii DSM 2403 ^T (99.79%), Acinetobacter pseudolwoffii ANC 5318 ^T (98.83%) and Acinetobacter harbinensis HITLi 7 ^T (98.14%). The rpoB and gyrB gene sequence analysis confirmed that the strain GC2^T was a member of genus Acinetobacter and that the closest relative was Acinetobacter lwoffii DSM 2403 ^T (99.08% and 100% similarity, respectively). DNA-DNA hybridization values between GC2^T and its closest relatives ranged from 65.6% (with A. lwoffii) to 5.1% (with A. venetianus). The whole genome sequence of strain GC2^T was obtained. The DNA G + C content of this strain was determined to be 42.9 mol %. ANI indexes, in silico estimations of DDH values and wet lab DDH values demonstrated that strain GC2^T represents an independent genomospecies. On the basis of phenotypic characteristics, chemotaxonomic, phylogenetic data and DNA-DNA hybridization and whole genome analysis, we propose to assign strain GC2^T as a new species of the genus Acinetobacter, for which the name Acinetobacter mesopotamicus sp. nov. is proposed. The type strain of this species is GC2^T (DSM 26953 T = JCM 31073 T). The whole genome of strain GC2^T has been deposited at DDBJ/ENA/GenBank under the accession JAALFF010000000.

Characterization and genomic analysis of a diesel-degrading bacterium, Acinetobacter calcoaceticus CA16, isolated from Canadian soil

Background

With the high demand for diesel across the world, environmental decontamination from its improper usage, storage and accidental spills becomes necessary. One highly environmentally friendly and cost-effective decontamination method is to utilize diesel-degrading microbes as a means for bioremediation. Here, we present a newly isolated and identified strain of Acinetobacter calcoaceticus (‘CA16’) as a candidate for the bioremediation of diesel-contaminated areas.

Results

Acinetobacter calcoaceticus CA16 was able to survive and grow in minimal medium with diesel as the only source of carbon. We determined through metabolomics that A. calcoaceticus CA16 appears to be efficient at diesel degradation. Specifically, CA16 is able to degrade 82 to 92% of aliphatic alkane hydrocarbons (C_nH_n + 2; where n = 12–18) in 28 days. Several diesel-degrading genes (such as alkM and xcpR) that are present in other microbes were also found to be activated in CA16.

Conclusions

The results presented here suggest that Acinetobacter strain CA16 has good potential in the bioremediation of diesel-polluted environments.

Biodegradation of biodiesel-oil by Cellulosimicrobium sp. Isolated from Colombian Caribbean soils

Biodiesel is considered to be a natural substitute for fossil fuel. The comparatively low toxicity of biodiesel and its susceptibility to microbial biodegradation could reduce its environmental impact. Currently, biodiesel is sold previously mixed with petroleum-based hydrocarbons. The aim of this work was to measure the biodegradation potential of commercially available biodiesel, using bacterial strains (BBCOL-001, BBCOL-002, and BBCOL-003) isolated from a tropical forest soils in the Colombian Caribbean. According to nucleotide sequencing of the gene encoding for 16S rRNA, the strains belong to members of the genus Cellulosimicrobium. GC-MS analysis showed that biodiesel-oil alkanes were degraded by an average of 81.5% with optical density reaching 0.2-0.3 in minimal salt media at 37°C for 5 days. Individual diesel-oil alkanes were degraded by the strains at rates between 64.9% to 100%. The increase in bacterial biomass confirmed the use of the substrates by the microorganisms, suggesting these hydrocarbons are a carbon source. Changes in the biochemical behaviour of the strains suggested their capacity to adapt to environmental conditions might be an important resource for bioremediation.

Degradation of tarballs using associated bacterial consortia

Tarballs are semi-solid blobs of crude-oil formed in marine environment. Microbial degradation of tarballs is poorly understood, though there are indications that tarball-associated microbes can degrade recalcitrant hydrocarbons present in tarballs. In this study, 38 tarball-associated bacteria from Betul beach, Goa, India were initially screened for crude oil degradation. Based on preliminary studies and literature survey, four bacterial strains, Alcanivorax sp. Betul-O, Marinobacter sp. Betul-26, Pseudomonas sp. Betul-14, and Pseudomonas sp. Betul-M were selected for bacterial consortia preparation. Eleven bacterial consortia were prepared and studied for degradation of n-alkanes and polycyclic aromatic hydrocarbon compounds (PAHs) of tarballs based on gravimetric and GC-MS-MS analyses. The bacterial consortia depleted 53.69-97.78% and 22.78-61.98% of n-alkanes and PAH compounds, respectively, within 45 days. Bacterial consortium comprising Pseudomonas sp. Betul-14, Pseudomonas sp. Betul-M, and Alcanivorax sp. Betul-O exhibited promising tarball degradation abilities with 97.78% and 61.98% degradation of n-alkanes and PAH, respectively, within 45 days. Further research is required to obtain insights into degradation products and possible pathways involved.

Analysis of petroleum biodegradation by a bacterial consortium isolated from worms of the polychaeta class (Annelida): Implications for NPK fertilizer supplementation

Degradation of petroleum hydrocarbons using bacterial consortia may be a means of optimizing bioremediation techniques. In this study, bacterial strains were isolated from the digestive tract of polychaete worms and evaluated concerning the potential of the bacteria to degrade petroleum compounds (Acinetobacter sp., Bacillus sp., Pantoea sp. and Enterobacter sp.). The strains were separately screened regarding their potential to degrade oil after 24 h. The main experiment was carried out for 30 days with the addition of nitrogen, phosphorus and potassium (NPK) after 15 days (Bact-NPK15) and 28 days (Bact-NPK28) and without NPK (Bact). The Bact treatment biomass remained stable until the 20th day of the experiment. C13-C40 n-alkanes were degraded with all treatments in the following order: Bact>Bact-NPK28>Bact-NPK15. Significant differences were observed between the controls and all treatments (p = 0.00031). Measurement of polycyclic aromatic hydrocarbons (PAHs) indicates a lower contribution of these compounds in the Bact-NPK28 treatment, although no significant difference between groups was observed. Bact-NPK28 was able to remove 40% of naphthalene, while Bact-NPK15 removed 20%; this effect was not observed in Bact. Higher hopane degradation levels were observed in Bact and, to a lesser extent, in Bact-NPK28. NPK application for 28 days mainly favored PAH degradation. The evaluated consortium thus exhibits potential in the bioremediation of petroleum-contaminated areas.

Quantitative evaluation of n-alkanes, PAHs, and petroleum biomarker accumulation in beach-stranded tar balls and coastal surface sediments in the Bushehr Province, Persian Gulf (Iran)

Coastal areas within the Bushehr Province (BP), Persian Gulf, Iran, face great challenges due to the heavy organic contamination caused by rapid industrialization, and the presence of numerous oil fields. In addition, in 2014, a significant number of tar balls are found along the coasts of BP. A total of 96 samples (48 coastal sediments and 48 tar balls) were taken from eight sampling points at the BP coast during the summer of 2014. These samples were analyzed to identify the sources and characteristics of their organic matter using diagnostic ratios and fingerprint analysis based on the distribution of the source-specific biomarkers of n-alkanes, PAHs,¹ hopanes and steranes. Mean concentration of n-alkanes (μg g^-1 dw) and PAHs (ng g^-1 dw) varied respectively from 405 to 220,626, and 267 to 23,568 in coastal sediments, while ranged respectively from 664 to 145,285 and 390 to 46,426 in tar balls. In addition, mean concentration of hopanes and steranes (ng g^-1 dw) were between 18.17 and 3349 and 184.66 to 1578 in coastal sediments, whereas in tar balls were 235-1899 and 520-1504, respectively. Pri/Phy² ratio was 0.25 to 1.51 (0.65) and 0.36 to 1 (0.63) in coastal sediment and tar ball samples, respectively, and the occurrence of UCM³ in both matrices, reflecting the petrogenic OM⁴ inputs and chronic oil contamination, respectively. The C₃₀ and C₂₉ homologues followed Gammacerane were detected in both matrices, in particular those collected from intensive industrial activities, suggesting petrogenic sources of OM. The coastal sediment PAHs profiles were significantly dominated by HMW⁵-PAHs in the Bahregan Beach (BAB) (78% of total PAHs), Bandare-Genaveh (GP) (66%), and Bandare-Bushehr (BUB) (61%) stations, while the Bashi Beach (BSB) (40%), Bandare-Kangan (KP) (57%), and Bandare-Asaluyeh (AP) (51%) stations exhibited higher proportion of LMW⁶-PAHs. PCA⁷ indicated that the tar ball and coastal sediment samples deposited along the Southwest of the BP beaches are most likely originated from the Abuzar oil. Based on the intensity of the anthropogenic activities, NPMDS⁸ analysis revealed that the GP, BAB, NNP, AP, and KP sampling sites had a high concentration of detected organic pollutants. To the best of our knowledge, this is the first study that investigates oil pollution in costal sediments and tar balls in the BP, providing insights in to the fate of oil in the coastal areas of the Persian Gulf, Iran.

Isolation, identification, and characterization of diesel-oil-degrading bacterial strains indigenous to Changqing oil field, China

In the present study, 12 indigenous diesel-oil-degrading bacteria were isolated from the petroleum-contaminated soils of the Changqing oil field (Xi'an, China). Measurement of the diesel-oil degradation rates of these strains by the gravimetric method revealed that they ranged from 42% to 66% within 2 weeks. The highest degradation rates were observed from strains CQ8-1 (66%), CQ8-2 (62.6%), and CQ11 (59%), which were identified as Bacillus thuringiensis, Ochrobactrum anthropi, and Bordetella bronchialis, respectively, based on their 16S rDNA sequences. Moreover, the physiological and biochemical properties of these three strains were analyzed by Gram staining, catalase, oxidase, and Voges-Proskauer tests. Transmission electron microscopy showed that all three strains were rod shaped with flagella. Gas chromatography and mass spectrometric analyses indicated that medium- and long-chain n-alkanes in diesel oil (C11-C29) were degraded to different degrees by B. thuringiensis, O. anthropi, and B. bronchialis, and the degradation rates gradually decreased as the carbon numbers increased. Overall, the results of this study indicate strains CQ8-1, CQ8-2, and CQ11 might be useful for environmentally friendly and cost-effective bioremediation of oil-contaminated soils.

Culturable hydrocarbonoclastic marine bacterial isolates from Indonesian seawater in the Lombok Strait and Indian Ocean

Purpose

The study aims to isolate the culturable marine bacteria and to assess their potential as the bioremediation agent for petroleum hydrocarbons contamination in marine environment.

Methods

Bacteria isolates were obtained by repetitive streaks to obtain purified bacteria on Zobell marine agar plates before further analysis and culture through direct visualization on agar plates. Identification were conducted using 16S rDNA sequence which are compared using NCBI BLAST and, combined with phenotypic and phylogenetic data. The potential use of the selected bacteria was tested by culturing them with two carbon sources i.e., glucose and crude oil.

Result

Fifty-one culturable marine hydrocarbonoclastic bacteria were isolated from the Lombok Strait (LS-3, LS-13, LS-14, LS-15, LS-16 and LS-20) and Indian Ocean (IO-1, IO-6, IO-8, IO-19, IO-24 and IO-25). Twelve isolates were found to degrade crude oil efficiently at a >2% concentration and to grow with crude oil as their sole carbon and energy source. These 12 strains belong to the genus Bacillus, which is well known to produce surface active agents, and the oil displacement assay indicated the production of these agents by these strains. Within the genera Bacillus, five species (Bacillus flexus, B. methylotrophicus, B. aquimaris, B. horikoshii, and B. thioparans) were represented by the 12 identified strains.

Conclusion

Selected strains from the Lombok Strait and Indian Ocean were capable of degrading crude oil (2% v/v) by 43.9-71.9% over 14 days. These results are important for marine bioremediation in Indonesia, which often faces risks of oil spill contamination and disaster.

Metagenomic analysis of tarball-associated bacteria from Goa, India

The beaches of Goa state in India are frequently polluted with tarballs, specifically during pre-monsoon and monsoon seasons. Tarballs contain hydrocarbons, including polycyclic aromatic hydrocarbons, which pose significant environmental risks. Microbes associated with tarballs reportedly possess capabilities to degrade toxic hydrocarbons present in tarballs. In this study, bacterial diversity associated with tarballs from Vagator and Morjim beaches of north Goa was analysed based on V3-V4 regions of 16S rRNA gene sequenced using Illumina Miseq Platform. The Proteobacterial members were dominant in both Vagator (≥85.5%) and Morjim (≥94.0%) samples. Many of the identified taxa have been previously reported as hydrocarbon degraders (e.g. Halomonas, Marinobacter) or possible human pathogens (e.g. Acinetobacter, Klebsiella, Rhodococcus, Staphylococcus, Vibrio). This is the first study reported on a metagenomic analysis of bacteria associated with tarballs from Goa.

Isolation, screening, and crude oil degradation characteristics of hydrocarbons-degrading bacteria for treatment of oily wastewater

The aim of this study was to isolate hydrocarbons-degrading bacteria for treatment of oily wastewater from long-standing petroleum-polluted sediments in Bohai Bay, China. Six hydrocarbons-degrading bacteria were screened and identified as Pseudomonas sp. and Bacillus sp. A new approach using a combination of various bacterial species in petroleum biodegradation was proposed and evaluated for its degradation characteristics. Gas chromatography-flame ionization detection (GC-FID) analysis showed that mixed bacterial agents (YJ01) degraded 80.64% of crude oil and 76.30% of crude oil alkanes, exhibiting good biodegradation effect. Besides, after 14 days of culture, the biodegradation assessment markers, pristane and phytane, showed significant degradation rates of 46.75% and 78.23%, respectively. Kinetic analysis indicated that the degradation trends followed a single first-order kinetics model and the degradation half-life (t_1/2) of 15 g/L crude oil was significantly shorter (5.48 days). These results indicated that YJ01 could degrade a wider range of hydrocarbons as well as some recalcitrant hydrocarbon components, and can be applied for bioremediation and treatment of oil-contaminated environment.

Characteristics of crude oil-degrading bacteria Gordonia iterans isolated from marine coastal in Taean sediment

Crude oil is a major pollutant of marine and coastal ecosystems, and it causes environmental problems more seriously. It is believed ultimate and complete degradation is accomplished mainly by microorganisms. In this study, we aim to search out for bacterial strains with high ability in degrading crude oil. From sediments contaminated by the petroleum spilled in 2007, an accident in Taean, South Korea, we isolated thirty‐one bacterial strains in total with potential application in crude oil contamination remediation. In terms of removal percentage after 7 days, one of the strains, Co17, showed the highest removal efficiency with 84.2% of crude oil in Bushnell‐Haas media. The Co17 strain even exhibited outstanding ability removing crude oil at a high salt concentration. Through the whole genome sequencing annotation results, many genes related with n‐alkane degradation in the genome of Gordonia sp. Co17, revealed alkane‐1‐monooxygenase, alcohol dehydrogenase, and Baeyer–Villiger monooxygenase. Specially, for confirmation of gene‐level, alkB gene encoding alkane hydroxylase (alkane‐1‐monooxygenase) was found in the strain Co17. The expression of alkB upregulated 125‐fold after 18 hr accompany with the removal of n‐alkanes of 48.9%. We therefore propose the strain Gordonia iterans Co17, isolated from crude oil‐contaminated marine sediment, could be used to offer a new strategy for bioremediation with high efficiency.

16S metagenomic analysis reveals adaptability of a mixed-PAH-degrading consortium isolated from crude oil-contaminated seawater to changing environmental conditions

A bacterial consortium, named SWO, was enriched from crude oil-contaminated seawater from Phrao Bay in Rayong Province, Thailand, after a large oil spill in 2013. The bacterial consortium degraded a polycyclic aromatic hydrocarbon (PAH) mixture consisting of phenanthrene, anthracene, fluoranthene, and pyrene (50 mg L^-1 each) by approximately 73%, 69%, 52%, and 48%, respectively, within 21 days. This consortium exhibited excellent adaptation to a wide range of environmental conditions. It could degrade a mixture of four PAHs under a range of pH values (4.0-9.0), temperatures (25 °C-37 °C), and salinities (0-10 g L^-1 with NaCl). In addition, this consortium degraded 20-30% of benzo[a]pyrene and perylene (10 mg L^-1 each), high molecular weight PAHs, in the presence of other PAHs within 35 days, and degraded 40% of 2% (v/v) crude oil within 20 days. The 16S rRNA gene amplicon sequencing analysis demonstrated that Pseudomonas and Methylophaga were the dominant genera of consortium SWO in almost all treatments, while Pseudidiomarina, Thalassospira and Alcanivorax were predominant under higher salt concentrations. Moreover, Pseudomonas and Alcanivorax were dominant in the crude oil-degradation treatment. Our results suggest that the consortium SWO maintained its biodegradation ability by altering the bacterial community profile upon encountering changes in the environmental conditions.

Phylogenetic characterization of culturable bacteria and fungi associated with tarballs from Betul beach, Goa, India

Tarballs are semisolid blobs of crude oil, normally formed due to weathering of crude-oil in the sea after any kind of oil spills. Microorganisms are believed to thrive on hydrocarbon-rich tarballs and possibly assist in biodegradation. The taxonomy of ecologically and economically important tarball-associated microbes, however, needs improvement as DNA-based identification and phylogenetic characterization have been scarcely incorporated into it. In this study, bacteria and fungi associated with tarballs from touristic Betul beach in Goa, India were isolated, followed by phylogenetic analyses of 16S rRNA gene and the ITS sequence-data to decipher their clustering patterns with closely-related taxa. The gene-sequence analyses identified phylogenetically diverse 20 bacterial genera belonging to the phyla Proteobacteria (14), Actinobacteria (3), Firmicutes (2) and Bacteroidetes (1), and 8 fungal genera belonging to the classes Eurotiomycetes (6), Sordariomycetes (1) and Leotiomycetes (1) associated with the Betul tarball samples. Future studies employing a polyphasic approach, including multigene sequence-data, are needed for species-level identification of culturable tarball-associated microbes. This paper also discusses potentials of tarball-associated microbes to degrade hydrocarbons.

Kinetics and Novel Degradation Pathway of Permethrin in Acinetobacter baumannii ZH-14

Persistent use of permethrin has resulted in its ubiquitous presence as a contaminant in surface streams and soils, yet little is known about the kinetics and metabolic behaviors of this pesticide. In this study, a novel bacterial strain Acinetobacter baumannii ZH-14 utilizing permethrin via partial hydrolysis pathways was isolated from sewage sludge. Response surface methodology based on Box-Behnken design of cultural conditions was used for optimization resulting in 100% degradation of permethrin (50 mg·L^-1) within 72 h. Strain ZH-14 degraded permethrin up to a concentration of 800 mg·L^-1. Biodegradation kinetics analysis indicated that permethrin degradation by this strain was concentration dependent, with a maximum specific degradation rate, half-saturation constant, and inhibition constant of 0.0454 h^-1, 4.7912 mg·L^-1, and 367.2165 mg·L^-1, respectively. High-performance liquid chromatography and gas chromatography-mass spectrometry identified 3-phenoxybenzenemethanol and 3-phenoxybenzaldehyde as the major intermediate metabolites of the permethrin degradation pathway. Bioaugmentation of permethrin-contaminated soils with strain ZH-14 significantly enhanced degradation, and over 85% of permethrin was degraded within 9 days with the degradation process following the first-order kinetic model. In addition to degradation of permethrin, strain ZH-14 was capable of degrading a large range of synthetic pyrethroids such as deltamethrin, bifenthrin, fenpropathrin, cyhalothrin, and beta-cypermethrin which are also widely used pesticides with environmental contamination problems, suggesting the promising potentials of A. baumannii ZH-14 in bioremediation of pyrethroid-contaminated terrestrial and aquatic environments.

Microbiota and environmental stress: how pollution affects microbial communities in Manila clams

Given the crucial role of microbiota in host development, health, and environmental interactions, genomic analyses focusing on host-microbiota interactions should certainly be considered in the investigation of the adaptive mechanisms to environmental stress. Recently, several studies suggested that microbiota associated to digestive tract is a key, although still not fully understood, player that must be considered to assess the toxicity of environmental contaminants. Bacteria-dependent metabolism of xenobiotics may indeed modulate the host toxicity. Conversely, environmental variables (including pollution) may alter the microbial community and/or its metabolic activity leading to host physiological alterations that may contribute to their toxicity. Here, 16s rRNA gene amplicon sequencing has been applied to characterize the hepatopancreas microbiota composition of the Manila clam, Ruditapes philippinarum. The animals were collected in the Venice lagoon area, which is subject to different anthropogenic pressures, mainly represented by the industrial activities of Porto Marghera (PM). Seasonal and geographic differences in clam microbiotas were explored and linked to host response to chemical stress identified in a previous study at the transcriptome level, establishing potential interactions among hosts, microbes, and environmental parameters. The obtained results showed the recurrent presence of putatively detoxifying bacterial taxa in PM clams during winter and over-representation of several metabolic pathways involved in xenobiotic degradation, which suggested the potential for host-microbial synergistic detoxifying actions. Strong interaction between seasonal and chemically-induced responses was also observed, which partially obscured such potentially synergistic actions. Seasonal variables and exposure to toxicants were therefore shown to interact and substantially affect clam microbiota, which appeared to mirror host response to environmental variation. It is clear that understanding how animals respond to chemical stress cannot ignore a key component of such response, the microbiota.

Development of tailored indigenous marine consortia for the degradation of naturally weathered polyethylene films

This study investigated the potential of bacterial-mediated polyethylene (PE) degradation in a two-phase microcosm experiment. During phase I, naturally weathered PE films were incubated for 6 months with the indigenous marine community alone as well as bioaugmented with strains able to grow in minimal medium with linear low-density polyethylene (LLDPE) as the sole carbon source. At the end of phase I the developed biofilm was harvested and re-inoculated with naturally weathered PE films. Bacteria from both treatments were able to establish an active population on the PE surfaces as the biofilm community developed in a time dependent way. Moreover, a convergence in the composition of these communities was observed towards an efficient PE degrading microbial network, comprising of indigenous species. In acclimated communities, genera affiliated with synthetic (PE) and natural (cellulose) polymer degraders as well as hydrocarbon degrading bacteria were enriched. The acclimated consortia (indigenous and bioaugmented) reduced more efficiently the weight of PE films in comparison to non-acclimated bacteria. The SEM images revealed a dense and compact biofilm layer and signs of bio-erosion on the surface of the films. Rheological results suggest that the polymers after microbial treatment had wider molecular mass distribution and a marginally smaller average molar mass suggesting biodegradation as opposed to abiotic degradation. Modifications on the surface chemistry were observed throughout phase II while the FTIR profiles of microbially treated films at month 6 were similar to the profiles of virgin PE. Taking into account the results, we can suggest that the tailored indigenous marine community represents an efficient consortium for degrading weathered PE plastics.

Shift in microbial group during remediation by enhanced natural attenuation (RENA) of a crude oil-impacted soil: a case study of Ikarama Community, Bayelsa, Nigeria

Acute and chronic pollution of environments with crude oil does not bode well for biota living within the vicinity of polluted environments. This is due to environmental and public health concerns on the negative impact of crude oil pollution on living organisms. Enhancing microbial activities by adding nutrients and other amendments had proved effective in pollutant removal during bioremediation. This study was carried out to determine how microbial group respond during remediation by enhanced natural attenuation (RENA) during a field-scale bioremediation. Crude oil-polluted soil samples were collected (before, during, and after remediation) from a site undergoing remediation by enhanced natural attenuation (RENA) at Ikarama Community, Bayelsa State, Nigeria, and were analyzed for total petroleum hydrocarbon (TPH), polyaromatic hydrocarbon (PAH), and a shift in microbial community. The gas chromatography-flame ionization detector (GC-FID) results showed that the pollutant concentrations (TPH and PAH) reduced by 98 and 85%, respectively, after the remediation. Culturable hydrocarbon utilizing bacteria (CHUB) was highest (8.3 × 10⁴ cfu/g) for sample collected during the remediation studies, whilst sample collected after remediation had low CHUB (6.1 × 10⁴ cfu/g) compared to that collected before remediation (7.7 × 10⁴ cfu/g). Analysis of 16S rRNA of the isolated CHUB showed they belonged to eight bacterial genera namely: Achromobacter, Alcaligenes, Azospirillus, Bacillus, Lysinibacillus, Ochrobactrum, Proteus, and Pusillimonas, with Alcaligenes as the dominant genus. In this study, it was observed that the bacterial community shifted from mixed group (Gram-positive and -negative) before and during the remediation, to only the latter group after the remediation studies. The betaproteobacteria groups were the dominant isolated bacterial phylotype. This study showed that RENA is an effective method of reducing pollutant concentration in crude oil-polluted sites, and could be applied to other polluted sites in the Niger Delta region of Nigeria to mitigate the devastating effects of crude oil pollution.

Diversity of bacteria and fungi associated with tarballs: Recent developments and future prospects

Tarballs are formed by weathering of crude oil in marine environment. They are transported from open ocean to the shores by sea currents and waves. Tarball pollution is a major concern to global marine ecosystem. Microbes such as bacteria and fungi are known to be associated with tarballs. They presumably play an important role in tarball degradation and some are potential human and animal pathogens. This paper highlights the recent studies on tarball-associated bacteria and fungi. Future perspectives on diversity, ecology and possible applications of tarball-associated microbes in bioremediation of beached tarballs have been discussed.

The ITS-based phylogeny of fungi associated with tarballs

Tarballs, the remnants of crude oil which change into semi-solid phase due to various weathering processes in the sea, are rich in hydrocarbons, including toxic and almost non-degradable hydrocarbons. Certain microorganisms such as fungi are known to utilize hydrocarbons present in tarballs as sole source of carbon for nutrition. Previous studies have reported 53 fungal taxa associated with tarballs. There is apparently no gene sequence-data available for the published taxa so as to verify the fungal identification using modern taxonomic tools. The objective of the present study is to isolate fungi from tarballs collected from Candolim beach in Goa, India and investigate their phylogenetic diversity based on 5.8S rRNA gene and the flanking internal transcribed spacer regions (ITS) sequence analysis. In the ITS-based NJ tree, eight tarball-associated fungal isolates clustered with 3 clades of Dothideomycetes and 2 clades of Saccharomycetes. To the best of our knowledge, this is the first study that has employed ITS-based phylogeny to characterize the fungal diversity associated with tarballs. Further studies are warranted to investigate the role of the tarball-associated fungi in degradation of recalcitrant hydrocarbons present in tarballs and the role of tarballs as carriers of human pathogenic fungi.