Bacterial community response to petroleum hydrocarbon amendments in freshwater, marine, and hypersaline water-containing microcosms

Factors that affect water column hydrocarbon concentrations have minor impacts on microbial responses following simulated diesel fuel spills

Effects of season and mixing on hydrocarbon concentrations and the microbial community response was explored in a series of mesocosm experiments simulating surface spills of diesel into coastal waters. Mixing of any amount contributed to hydrocarbons entering the water column, but diesel fuel composition had a significant effect on hydrocarbon concentrations. Higher initial concentrations of aromatic hydrocarbons resulted in higher water column concentrations, with minimal differences among seasons due to high variability. Regardless of the concentrations of hydrocarbons, prokaryotes increased and there were higher relative abundances of hydrocarbon affiliated bacteria with indications of biodegradation within 4 d of exposure. As concentrations decreased over time, the eukaryote community shifted from the initial community to one which appeared to be composed of organisms with some resilience to hydrocarbons. This series of experiments demonstrates the wide range of conditions under which natural attenuation of diesel fuel is an effective response.

Influence of Extremely High Pressure and Oxygen on Hydrocarbon-Enriched Microbial Communities in Sediments from the Challenger Deep, Mariana Trench

Recent studies reported that highly abundant alkane content exists in the ~11,000 m sediment of the Mariana Trench, and a few key alkane-degrading bacteria were identified in the Mariana Trench. At present, most of the studies on microbes for degrading hydrocarbons were performed mainly at atmospheric pressure (0.1 MPa) and room temperature; little is known about which microbes could be enriched with the addition of n-alkanes under in-situ environmental pressure and temperature conditions in the hadal zone. In this study, we conducted microbial enrichments of sediment from the Mariana Trench with short-chain (SCAs, C7–C17) or long-chain (LCAs, C18–C36) n-alkanes and incubated them at 0.1 MPa/100 MPa and 4 °C under aerobic or anaerobic conditions for 150 days. Microbial diversity analysis showed that a higher microbial diversity was observed at 100 MPa than at 0.1 MPa, irrespective of whether SCAs or LCAs were added. Non-metric multidimensional scaling (nMDS) and hierarchical cluster analysis revealed that different microbial clusters were formed according to hydrostatic pressure and oxygen. Significantly different microbial communities were formed according to pressure or oxygen (p < 0.05). For example, Gammaproteobacteria (Thalassolituus) were the most abundant anaerobic n-alkanes-enriched microbes at 0.1 MPa, whereas the microbial communities shifted to dominance by Gammaproteobacteria (Idiomarina, Halomonas, and Methylophaga) and Bacteroidetes (Arenibacter) at 100 MPa. Compared to the anaerobic treatments, Actinobacteria (Microbacterium) and Alphaproteobacteria (Sulfitobacter and Phenylobacterium) were the most abundant groups with the addition of hydrocarbon under aerobic conditions at 100 MPa. Our results revealed that unique n-alkane-enriched microorganisms were present in the deepest sediment of the Mariana Trench, which may imply that extremely high hydrostatic pressure (100 MPa) and oxygen dramatically affected the processes of microbial-mediated alkane utilization.

Characterization of new diesel-degrading bacteria isolated from freshwater sediments

As the result of diesel's extensive production and use as fuel for transportation, pollution with such complex mixtures of hydrocarbons is a major concern worldwide. The present study's focus was to investigate the presence of diesel-degrading bacteria in different Danube Delta freshwater sediments. Ten bacterial strains capable to grow in a minimal medium with diesel as the sole carbon source were isolated and characterized in this study. Based on the phenotypic and molecular characteristics, the ten strains belong to four genera and seven species, such as Pseudomonas (P. aeruginosa, P. nitroreducens, P. resinovorans, P. multiresinivorans), Acinetobacter (A. tandoii), Bacillus (B. marisflavi), and Stenotrophomonas (S. maltophilia). All these bacteria were excellent biosurfactant producers, and they were able to tolerate saturated hydrocarbons, like n-heptane, n-decane, n-pentadecane, and n-hexadecane. The ten strains possess at least one alkane hydroxylase gene in their genome, and they were also able to tolerate and degrade diesel. Higher biodegradation rates of diesel were acquired for the strains from the genera Pseudomonas, Acinetobacter, and Stenotrophomonas, compared with that obtained for the Bacillus strain. Due to their remarkable potential to degrade diesel and produce biosurfactants, the ten isolated bacteria are attractive candidates for bioremediation of diesel-polluted environments.

Deep mining decreases the microbial taxonomic and functional diversity of subsurface oil reservoirs

Microbes in subsurface oil reservoirs play important roles in elemental cycles and biogeochemical processes. However, the community assembly pattern of indigenous microbiome and their succession under long-term human activity remain poorly understood. Here we studied the microbial community assembly in underground sandstone cores from 190 to 2050 m in northeast China and their response to long-term oil recovery (10-50 years). Indigenous microbiome in subsurface petroleum reservoirs were dominated by Gammaproteobacteria, Firmicutes, Alphaproteobacteria, Bacteroidetes, and Actinobacteria, which exhibited a higher contribution of homogenizing dispersal assembly and different taxonomy distinct ecological modules when compared with perturbed samples. Specifically, the long-term oil recovery reduced the bacterial taxonomic- and functional-diversity, and increased the community co-occurrence associations in subsurface oil reservoirs. Moreover, distinguished from the perturbed samples, both variation partition analysis and structural equation model revealed that the contents of quartz, NO₃^- and Cl^- significantly structured the α- and β-diversity in indigenous subsurface bacterial communities. These findings first provide the holistic picture of microbiome in the deep oil reservoirs, which demonstrate the significant impact of human activity on microbiome in deep continental subsurface.

Chronic Environmental Perturbation Influences Microbial Community Assembly Patterns

Acute environmental perturbations are reported to induce deterministic microbial community assembly, while it is hypothesized that chronic perturbations promote development of alternative stable states. Such acute or chronic perturbations strongly impact on the pre-adaptation capacity to the perturbation. To determine the importance of the level of microbial pre-adaptation and the community assembly processes following acute or chronic perturbations in the context of hydrocarbon contamination, a model system of pristine and polluted (hydrocarbon-contaminated) sediments was incubated in the absence or presence (discrete or repeated) of hydrocarbon amendment. The community structure of the pristine sediments changed significantly following acute perturbation, with selection of different phylotypes not initially detectable. Conversely, historically polluted sediments maintained the initial community structure, and the historical legacy effect of chronic pollution likely facilitated community stability. An alternative stable state was also reached in the pristine sediments following chronic perturbation, further demonstrating the existence of a legacy effect. Finally, ecosystem functional resilience was demonstrated through occurrence of hydrocarbon degradation by different communities in the tested sites, but the legacy effect of perturbation also strongly influenced the biotic response. This study therefore demonstrates the importance of perturbation chronicity on microbial community assembly processes and reveals ecosystem functional resilience following environmental perturbation.

Plastisphere in freshwaters: An emerging concern

Plastisphere, an ecosystem of microbes thriving on floating plastic debris, has been extensively studied in marine waters since 2013. Currently, very little is known about the freshwater plastisphere. This review seeks to provide a broad insight into the freshwater science of plastisphere in the light of marine plastisphere, including research gaps, suggestions, and rising concerns, which would be of interest to the public, policymakers, and stakeholders. Given that freshwaters are endangered ecosystems, it is imperative to understand the role and impact of plastisphere on freshwaters. Plastic debris, especially microplastics (size <5 mm) in freshwater ecosystems, provide a stable, persistent, and buoyant substrate for microbes. Although current evidence suggests that freshwater environmental conditions and microplastics' physical and chemical properties significantly influence microbial colonisation, its role and integration in the aquatic ecosystems are unknown. Considering that the plastisphere biodiversity is unique, we seek to establish why and how many species co-exist in the plastisphere. Evaluating such fundamental questions should advance our basic understanding of the resilience of plastisphere to the changing environment. Plastisphere microbes, including the pathogenic bacteria, were found in both systems demonstrating their ability to survive on the plastic fragments from one ecosystem to another. A significant concern regarding plastisphere is the potential freshwater dispersal of anthropogenic pollutants and invasive or pathogenic species. Notably, microplastics aggregates may serve as a food source for grazers, which opens the question of the extent to which it can impact freshwater food webs. To gain a thorough understanding of the interplay between microplastics and the biogeochemical cycle, further insight into plastisphere microbes' functional role is needed. This would shed light on the unconsidered freshwater elemental cycling pathways. Given the complexity and universal nature of the plastisphere, strong interdisciplinary global research initiatives or networks are required to address the emerging concerns of plastisphere in freshwaters.

Sulphate-reducing bacterial community structure from produced water of the Periquito and Galo de Campina onshore oilfields in Brazil

Sulphate-reducing bacteria (SRB) cause fouling, souring, corrosion and produce H2S during oil and gas production. Produced water obtained from Periquito (PQO) and Galo de Campina (GC) onshore oilfields in Brazil was investigated for SRB. Produced water with Postgate B, Postgate C and Baars media was incubated anaerobically for 20 days. DNA was extracted, 16S rDNA PCR amplified and fragments were sequenced using Illumina TruSeq. 4.2 million sequence reads were analysed and deposited at NCBI SAR accession number SRP149784. No significant differences in microbial community composition could be attributed to the different media but significant differences in the SRB were observed between the two oil fields. The dominant bacterial orders detected from both oilfields were Desulfovibrionales, Pseudomonadales and Enterobacteriales. The genus Pseudomonas was found predominantly in the GC oilfield and Pleomorphominas and Shewanella were features of the PQO oilfield. 11% and 7.6% of the sequences at GC and PQO were not classified at the genus level but could be partially identified at the order level. Relative abundances changed for Desulfovibrio from 29.8% at PQO to 16.1% at GC. Clostridium varied from 2.8% at PQO and 2.4% at GC. These data provide the first description of SRB from onshore produced water in Brazil and reinforce the importance of Desulfovibrionales, Pseudomonadales, and Enterobacteriales in produced water globally. Identifying potentially harmful microbes is an important first step in developing microbial solutions that prevent their proliferation.

Application of integrated extremophilic (halo-alkalo-thermophilic) bacterial consortium in the degradation of petroleum hydrocarbons and treatment of petroleum refinery wastewater under extreme condition

Degradation of petroleum hydrocarbon under extreme conditions such as high salinity, temperature and pH was difficult due to unavailability of potential bacterial strains. The present study details the efficiency of extremophilic bacterial consortium in biodegradation of different petroleum hydrocarbons and treatment of petroleum refinery wastewater under extreme condition. Extreme condition for the degradation of petroleum hydrocarbons was optimized at 8% salinity, pH-10 and temperature-60 °C. The consortium recorded complete degradation of low molecular weight (LMW) petroleum hydrocarbons (200 ppm) such as anthracene, phenanthrene, fluorene and naphthalene in 8 days under optimized extreme condition. High molecular weight (HMW) hydrocarbons such as pyrene (100 ppm), benzo(e)pyrene (20 ppm), benzo(k)fluoranthene (20 ppm) and benzo(a)pyrene (20 ppm), revealed 93%, 60%, 55% and 51% degradation by the extremophilic consortium under optimized extreme condition. The extremophilic consortium mineralized fluorene (61%) at high saline condition up to 24%. Addition of yeast extract potently accelerated the biodegradation under extreme condition. Treatment of petroleum refinery wastewater in continuous stirred tank reactor recorded 92% COD removal with complete removal of LMW hydrocarbons in 16 days and 91% of HMW hydrocarbons in 32 days under extreme condition. The hydrocarbons degrading extremophilic consortium possessed Ochrobactrum, Bacillus, Marinobacter, Pseudomonas, Martelella, Stenotrophomonas and Rhodococcus.

The role of gut microbial community and metabolomic shifts in adaptive resistance of Atlantic killifish (Fundulus heteroclitus) to polycyclic aromatic hydrocarbons

Altered gut microbiomes may play a role in rapid evolution to anthropogenic change but remain poorly understood. Atlantic killifish (Fundulus heteroclitus) in the Elizabeth River, VA have evolved resistance to polycyclic aromatic hydrocarbons (PAHs) and provide a unique opportunity to examine the links between shifts in the commensal microbiome and organismal physiology associated with evolved resistance. Here, 16S rRNA sequence libraries derived from fish guts and sediments sampled from a highly PAH contaminated site revealed significant differences collected at similar samples from an uncontaminated site. Phylogenetic groups enriched in the libraries derived from PAH-resistant fish were dissimilar to their associated sediment libraries, suggesting the specific environment within the PAH-resistant fish intestine influence the gut microbiome composition. Gut metabolite analysis revealed shifts between PAH-resistant and non-resistant subpopulations. Notably, PAH-resistant fish exhibited reduced levels of tryptophan and increased levels of sphingolipids. Exposure to PAHs appears to impact several bacterial in the gut microbiome, particularly sphingolipid containing bacteria. Bacterial phylotypes known to include species containing sphingolipids were generally lower in the intestines of fish subpopulations exposed to high concentrations of PAHs, inferring a complex host-microbiome relationship. Overall, killifish microbial community shifts appear to be related to a suppression of overall metabolite level, indicating a potential role of the gut in organismal response to anthropogenic environmental change. These results on microbial and metabolomics shifts are potentially linked to altered bioenergetic phenotype observed in the same PAH-resistant killifish populations in other studies.

Impact of sample collection on prokaryotic and eukaryotic diversity of niche environments of the oil-sand mining impacted Athabasca River

Microbial communities are an important aspect of overall riverine ecology; however, appreciation of the effects of anthropogenic activities on unique riverine microbial niches, and how the collection of these samples affects the observed diversity and community profile is lacking. We analyzed prokaryotic and eukaryotic communities from surface water, biofilm, suspended load niches along a gradient of oil sands-related contamination in the Athabasca River (Alberta, Canada), with suspended load or particle-associated communities collected either via Kenney Sampler or centrifugation manifold. At the level of phyla, different niche communities were highly similar to one another and across locations. However, there were significant differences in the abundance of specific genera amongst different niches and across sampling locations. A generalized linear model revealed that use of the Kenney Sampler resulted in more diverse bacterial and eukaryotic suspended load community than centrifugal collection, though "suspended load" communities collected by any means remained stably diverse across locations. Though there was influence of water quality parameters on community composition, all sampled sites support diverse bacterial and eukaryotic communities regardless of the degree of contamination, highlighting the need to look beyond ecological diversity as means of assessing ecological perturbations, and consider collecting samples from multiple niche environments.

Dissimilatory Iron-Reducing Microorganisms Are Present and Active in the Sediments of the Doce River and Tributaries Impacted by Iron Mine Tailings from the Collapsed Fundão Dam (Mariana, MG, Brazil)

On 5 November 2015, a large tailing deposit failed in Brazil, releasing an estimated 32.6 to 62 million m3 of iron mining tailings into the environment. Tailings from the Fundão Dam flowed down through the Gualaxo do Norte and Carmo riverbeds and floodplains and reached the Doce River. Since then, bottom sediments have become enriched in Fe(III) oxyhydroxides. Dissimilatory iron-reducing microorganisms (DIRMs) are anaerobes able to couple organic matter oxidation to Fe(III) reduction, producing CO2 and Fe(II), which can precipitate as magnetite (FeO·Fe2O3) and other Fe(II) minerals. In this work, we investigated the presence of DIRMs in affected and non-affected bottom sediments of the Gualaxo do Norte and Doce Rivers. The increase in Fe(II) concentrations in culture media over time indicated the presence of Fe(III)-reducing microorganisms in all sediments tested, which could reduce Fe(III) from both tailings and amorphous ferric oxyhydroxide. Half of our enrichment cultures converted amorphous Fe(III) oxyhydroxide into magnetite, which was characterized by X-ray diffraction, transmission electron microscopy, and magnetic measurements. The conversion of solid Fe(III) phases to soluble Fe(II) and/or magnetite is characteristic of DIRM cultures. The presence of DIRMs in the sediments of the Doce River and tributaries points to the possibility of reductive dissolution of goethite (α-FeOOH) and/or hematite (α-Fe2O3) from sediments, along with the consumption of organics, release of trace elements, and impairment of water quality.

Effect of natural microbiome and culturable biosurfactants-producing bacterial consortia of freshwater lake on petroleum-hydrocarbon degradation

Freshwater lake ecosystem is a reservior of valuable microbial diversity. It needs to be explored for addressing key environmental issues like petroleum-hydrocarbon contamination. In this work, the microbial communities (pre and post enriched with petroleum-hydrocarbons) from different layers of freshwater lake, i.e. surface water, sediments and deepwater, were explored through metagenomic and culture-dependent approaches. A total of 41 bacterial phyla were retrieved from pre-enriched samples, which were significantly reduced in enriched samples where Proteobacteria were dominant (87% to 100%) followed by Bacteroidetes (7.37%) and Verrucomicrobia (3.06%). The most dominant hydrocarbon-degrading genera were extensively verified as Pseudomonas (48.65%), Acinetobacter (45.38%), Stenotrophomonas (3.16%) and Brevundimonas (2.07%) in surface water (S1WCC); Acinetobacter (62.46%), Aeromonas (10.7%), Sphingobacterium (5.20%) and Pseudomonas (4.23%) in sediment (S2MCC); and Acinetobacter (46.57%), Pseudomonas (13.10%), Comamonas (12.93%), Flavobacterium (12.18%) and Enterobacter (9.62%) in deep water (S4WCC). Additionally, the maximum biodegradation of petroleum-hydrocarbons (i.e. used engine oil or UEO) was achieved by microbiome of S2MCC (67.60 ± 0.08%) followed by S4WCC (59.70 ± 0.12%), whereas only 36.80 ± 0.10% degradation was achieved by S1WCC microbiome. On the other hand, UEO degradation by cultivable biosurfactant-producing single cultures such as Pseudomonas sp. S2WE, Pseudomonas sp. S2WG, Pseudomonas sp. S2MS, Ochrobactrum sp. S1MM and Bacillus nealsonii S2MT showed 31.10 ± 0.08% to 40.50 ± 0.11% biodegradation. Comparatively, the biodegradation efficiency was found higher (i.e. 42.20 ± 0.12% to 56.10 ± 0.12%) in each consortia comprising of two, three, four, and five bacterial cultures. Conclusively, the isolated culturable biosurfactants-producing bacterial consortium of freshwater lake demonstrated >80% contribution in the total petroleum-hydrocarbons degradation by the natural microbiome of the ecosystem.

Toxic mechanism of pyrene to catalase and protective effects of vitamin C: Studies at the molecular and cell levels

Polycyclic aromatic hydrocarbons, distributing extensively in the soil, would potentially threaten the soil organisms (Eisenia fetida) by triggering oxidative stress. As a ubiquitous antioxidant enzyme, catalase can protect organisms from oxidative damage. To reveal the potential impact of polycyclic aromatic hydrocarbon pyrene (Pyr) on catalase (CAT) and the possible protective effect of Ascorbic acid (vitamin C), multi-spectral and molecular docking techniques were used to investigate the influence of structure and function of catalase by pyrene. Fluorescence and circular dichroism analysis showed that pyrene would induce the microenvironmental changes of CAT amino acid residues and increase the α-helix in the secondary structure. Molecular simulation results indicated that the main binding force of pyrene around the active center of CAT is hydrogen bonding force. Furthermore, pyrene inhibited catalase activity to 69.9% compared with the blank group, but the degree of inhibition was significantly weakened after vitamin C added into the research group. Cell level experiments showed that pyrene can increase the level of ROS in the body cavity cell of earthworms, and put the cells under the threat of potential oxidative damage. Antioxidants-vitamin C has a protective effect on catalase and maintains the stability of intracellular ROS levels to a certain extent.

Optimization of an Autochthonous Bacterial Consortium Obtained from Beach Sediments for Bioremediation of Petroleum Hydrocarbons

Oil spill pollution remains a serious concern in marine environments and the development of effective oil bioremediation techniques are vital. This work is aimed at developing an autochthonous hydrocarbon-degrading consortium with bacterial strains with high potential for hydrocarbons degradation, optimizing first the growth conditions for the consortium, and then testing its hydrocarbon-degrading performance in microcosm bioremediation experiments. Bacterial strains, previously isolated from a sediment and cryopreserved in a georeferenced microbial bank, belonged to the genera Pseudomonas, Rhodococcus and Acinetobacter. Microcosms were assembled with natural seawater and petroleum, for testing: natural attenuation (NA); biostimulation (BS) (nutrients addition); bioaugmentation with inoculum pre-grown in petroleum (BA/P) and bioaugmentation with inoculum pre-grown in acetate (BA/A). After 15 days, a clear blending of petroleum with seawater was observed in BS, BA/P and BA/A but not in NA. Acetate was the best substrate for consortium growth. BA/A showed the highest hydrocarbons degradation (66%). All bacterial strains added as inoculum were recovered at the end of the experiment. This study provides an insight into the capacity of autochthonous communities to degrade hydrocarbons and on the use of alternative carbon sources for bacterial biomass growth for the development of bioremediation products to respond to oil spills.

Changes in Soil Health with Remediation of Petroleum Hydrocarbon Contaminated Soils Using Two Different Remediation Technologies

For sustainable soil management, there is an increasing demand for soil quality, resilience, and health assessment. After remediation of petroleum hydrocarbon (PHC)-contaminated soils, changes in the physicochemical and ecological characteristics of the soil were investigated. Two kinds of remediation technologies were applied to contaminated soils: land farming (LF) and high temperature thermal desorption (HTTD). As a result of total petroleum hydrocarbons (TPH), PHC-contaminated soils were efficiently remediated by LF and HTTD. The soil health could not be completely recovered after the removal of pollutants due to adverse changes in the soil properties, especially in soil enzyme activities. Therefore, monitoring is necessary for accurate estimation of soil ecotoxicity and effective remediation, and additional soil management, such as fertilizer application or organic amendments, is needed to restore soil heath. In the case of HTTD, soil ecological properties are severely changed during the remediation process. The decision to reuse or recycle remediated soils should reflect changes in soil quality. HTTD is a harsh remediation method that results in deterioration of soil fertility and ecological functions. Alternatives, such as low-temperature thermal desorption or additional soil management using fertilizer or organic amendments, for example, are needed.

Diversity and Dynamics of Seaweed Associated Microbial Communities Inhabiting the Lagoon of Venice

Seaweeds are a group of essential photosynthetic organisms that harbor a rich diversity of associated microbial communities with substantial functions related to host health and defense. Environmental and anthropogenic stressors may disrupt the microbial communities and their metabolic activity, leading to host physiological alterations that negatively affect seaweeds’ performance and survival. Here, the bacterial communities associated with one of the most common seaweed, Ulva laetevirens Areshough, were sampled over a year at three sites of the lagoon of Venice affected by different environmental and anthropogenic stressors. Bacterial communities were characterized through Illumina sequencing of the V4 hypervariable region of 16S rRNA genes. The study demonstrated that the seaweed associated bacterial communities at sites impacted by environmental stressors were host-specific and differed significantly from the less affected site. Furthermore, these communities were significantly distinct from those of the surrounding seawater. The bacterial communities’ composition was significantly correlated with environmental parameters (nutrient concentrations, dissolved oxygen saturation, and pH) across sites. This study showed that several more abundant bacteria on U. laetevirens at stressed sites belonged to taxa related to the host response to the stressors. Overall, environmental parameters and anthropogenic stressors were shown to substantially affect seaweed associated bacterial communities, which reflect the host response to environmental variations.

Microbial eco-physiological strategies for salinity-mediated crude oil biodegradation

Salinity variability strongly affects the behaviors of oil degrading bacteria for spilled oil biodegradation in the marine environment. However, limited studies explored the strategies of microbes on salinity-mediated crude oil biodegradation. In this study, a halotolerant bio-emulsifier producer, Exiguobacterium sp. N41P, was examined as a model strain for Alaska North Slope (ANS) crude oil (0.5%, v/v) biodegradation. Results indicated that Exiguobacterium sp. N41P could tolerant a wide range of salinity (0-120 g/L NaCl) and achieve the highest degradation efficiency under the salinity of 15 g/L NaCl due to the highest biofilm formation ability. Moreover, increased salinity induced decreased cell surface hydrophobicity and a migration of microbial growth from oil phase to aqueous phase, leading to limited bio-emulsifier productivity and depressed degradation of insoluble long-chain n-alkanes while enhancing the degradation of relative soluble naphthalene. Research findings illustrated the microbial eco-physiological mechanism for spilled oil biodegradation under diverse salinities and advanced the understanding of sophisticated marine crude oil biodegradation process.

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.

Evaluation of fatty acid derivatives in the remediation of aged PAH-contaminated soil and microbial community and degradation gene response

In this study, derivatives of two common fatty acids in plant root exudates, sodium palmitate and sodium linoleate (sodium aliphatates), were added to an aged Polycyclic aromatic hydrocarbons (PAHs) contaminated soil to estimate their effectiveness in the removal of PAHs. Sodium linoleate was more effective in lowering PAHs and especially high-molecular-weight (4-6 ring) PAHs (HMW-PAHs). Principal coordinates analysis (PCoA) indicates that both amendments led to a shift in the soil bacterial community. Moreover, linear discriminant effect size (LEfSe) analysis demonstrates that the specific PAHs degraders Pseudomonas, Arenimonas, Pseudoxanthomonas and Lysobacter belonging to the γ-proteobacteria and Nocardia and Rhodococcus belonging to the Actinobacteria were the biomarkers of, respectively, sodium linoleate and sodium palmitate amendments. Correlation analysis suggests that four biomarkers in the sodium linoleate amendment treatment from γ-proteobacteria were all highly linearly negatively related to HMW-PAHs residues (p < 0.01) while two biomarkers in the sodium palmitate amendment treatment from Actinobacteria were highly linearly negatively related to LMW-PAHs residues (p < 0.01). Higher removal efficiency of PAHs (especially HMW-PAHs) in the sodium linoleate amendment treatment than in the sodium palmitate amendment treatment might be ascribed to the specific enrichment of microbes from the γ-proteobacteria. The bacterial functional KEGG orthologs (KOs) assigned to PAHs metabolism and functional C23O and C12O genes related to cleavage of the benzene ring were both up-regulated. These results provide new insight into the mechanisms of the two sodium aliphatate amendments in accelerating PAHs biodegradation and have implications for practical application in the remediation of PAHs-contaminated soils.

Changes in microbial community in the presence of oil and chemical dispersant and their effects on the corrosion of API 5L steel coupons in a marine-simulated microcosm

The influence of crude oil and chemical dispersant was evaluated over planktonic bacteria and biofilms grown on API 5L steel surfaces in microcosm systems. Three conditions were simulated, an untreated marine environment and a marine environment with the presence of crude oil and a containing crude oil and chemical dispersant. The results of coupon corrosion rates indicated that in the oil microcosm, there was a high corrosion rate when compared with the other two systems. Analysis of bacterial communities by 16S rRNA gene sequencing described a clear difference between the different treatments. In plankton communities, the Bacilli and Gammaproteobacteria classes were the most present in numbers of operational taxonomic unit (OTUs). The Vibrionales, Oceanospirillales, and Alteromonadales orders were predominant in the treatment with crude oil, whereas in the microcosm containing oil and chemical dispersant, mainly members of Bacillales order were detected. In the communities analyzed from biofilms attached to the coupons, the most preponderant class was Alphaproteobacteria, followed by Gammaproteobacteria. In the control microcosm, there was a prevalence of the orders Rhodobacterales, Aeromonadales, and Alteromonadales, whereas in the dispersed oil and oil systems, the members of the order Rhodobacterales were present in a larger number of OTUs. These results demonstrate how the presence of a chemical dispersant and oil influence the corrosion rate and bacterial community structures present in the water column and biofilms grown on API 5L steel surfaces in a marine environment. KEY POINTS: • Evaluation of the effects of oil and chemical surfactants on the corrosion of API 5L. • Changes in microbial communities do not present corrosive biofilm on API 5L coupons.

Sustainable remediation of diesel-contaminated soil by low temperature thermal treatment: Improved energy efficiency and soil reusability

Thermal treatment can effectively remediate diesel-contaminated soil, but is considered unsustainable because of its energy-intensive nature and potential to damage soil properties. Here, we used low temperature thermal treatment (LTTT) as an energy-efficient technique to remediate diesel-contaminated soil. The impacts of LTTT on the physiochemical and ecological properties of soils were investigated to evaluate the reusability of heated soil. Heating at 250 °C for 10 min reduced the concentration of the total petroleum hydrocarbons from 6271 mg/kg to 359  mg/kg, which is lower than the Chinese risk screening level of 826 mg/kg. After LTTT, most soil physiochemical properties were nearly unchanged, and the NO₃^--N and NH₄⁺-N contents increased. Moreover, LTTT-remediated soil was favorable for the germination and early growth of wheat. The microbial community changed substantially, but recovered after being mixed with uncontaminated soil. Finally, exploration of the mechanisms of LTTT revealed that pyrolysis was the dominant mechanism of diesel removal. A biochar-like pyrolytic carbon was formed, which improved the soil reusability.

Biological response to dissolved versus dispersed oil

The water-soluble compounds of oil (e.g. low molecular weight PAHs) dissolve as a function of their physicochemical properties and environmental conditions, while the non-soluble compounds exist as dispersed droplets. Both the chemical and physical form of oil will affect the biological response. We present data from a mesocosm study comparing the microbial response to the water-soluble fraction (WSF), versus a water-accommodated fraction of oil (WAF), which contains both dispersed and dissolved oil components. WAF and WSF contained similar concentrations of low molecular weight PAHs, but concentrations of 4- and 5-ring PAHs were higher in WAF compared to WSF. Microbial communities were significantly different between WSF and WAF treatments, primary productivity was reduced more in WSF than in WAF, and concentrations of transparent exopolymeric particles were highest in WSF and lowest in the controls. These differences highlight the importance of dosing strategy for mesocosm and toxicity tests.

Spatial and temporal heterogeneity in the structure and function of sediment bacterial communities of a tropical mangrove forest

Bacterial communities of mangrove sediments are well appreciated for their role in nutrient cycling. However, spatiotemporal variability in these communities over large geographical scale remains understudied. We investigated sediment bacterial communities and their metabolic potential in an intertidal mangrove forest of India, Bhitarkanika, using high-throughput sequencing of 16S rRNA genes and community-level physiological profiling. Bulk surface sediments from five different locations representing riverine and bay sites were collected over three seasons. Seasonality largely explained the variation in the structural and metabolic patterns of the sediment bacterial communities. Freshwater Actinobacteria were more abundant in monsoon, whereas γ-Proteobacteria demonstrated higher abundance in summer. Distinct differences in the bacterial community composition were noted between riverine and bay sites. For example, salt-loving marine bacteria affiliated to Oceanospirillales were more prominent in the bay sites than the riverine sites. L-asparagine, N-acetyl-D-glucosamine, and D-mannitol were the preferentially utilized carbon sources by bacterial communities. Bacterial community composition was largely governed by salinity and organic carbon content of the sediments. Modeling analysis revealed that the abundance of δ-Proteobacteria increased with salinity, whereas β-Proteobacteria displayed an opposite trend. Metabolic mapping of taxonomic data predicted biogeochemical functions such as xylan and chitin degradation, ammonia oxidation, nitrite reduction, and sulfate reduction in the bacterial communities suggesting their role in carbon, nitrogen, and sulfur cycling in mangrove sediments. This study has provided valuable clues about spatiotemporal heterogeneity in the structural and metabolic patterns of bacterial communities and their environmental determinants in a tropical mangrove forest.

Water Quality and Microbial Community Changes in an Urban River after Micro-Nano Bubble Technology in Situ Treatment

Currently, black-odor river has received great attention in China. In this study, the micro-nano bubble technology (MBT) was used to mitigate the water pollution rapidly and continuously by increasing the concentration of dissolved oxygen (DO) in water. During treatment, the concentration of DO increased from 0.60 mg/L to over 5.00 mg/L, and the oxidation reduction potential (ORP) also changed from a negative value to over 100.00 mV after only five days aeration. High throughput pyrosequencing technology was employed to identify the microbial community structure. At genus level, the dominant bacteria were anaerobic and nutrient-loving microbes (e.g., Arcobacter sp., Azonexus sp., and Citrobacter sp.) before, and the relative abundances of aerobic and functional microbes (e.g., Perlucidibaca sp., Pseudarcicella sp., Rhodoluna sp., and Sediminibacterium sp.) were increased after treatment. Meanwhile, the water quality was significantly improved with about 50% removal ratios of chemical oxygen demand (CODCr) and ammonia nitrogen (NH4+-N). Canonical correspondence analysis (CCA) results showed that microbial community structure shaped by COD, DO, NH4+-N, and TP, CCA1 and CCA2 explained 41.94% and 24.56% of total variances, respectively. Overall, the MBT could improve the water quality of urban black-odor river by raising the DO and activate the aerobic microbes.

Responses and roles of roots, microbes, and degrading genes in rhizosphere during phytoremediation of petroleum hydrocarbons contaminated soil

Rhizodegradation performed by plant roots and the associated bacteria is one of the major mechanisms that contribute to removal of petroleum hydrocarbons (PHCs) during phytoremediation. In this study, the pot-culture experiment using wild ornamental Hylotelephium spectabile (Boreau) H. Ohba was designed to explore responses and roles of roots, microbes, and degrading genes in the rhizodegradation process. Results showed that PHCs degradation rate by phytoremediation was up to 37.6-53.3% while phytoaccumulation accounted for a low proportion, just at 0.3-13.3%. A total of 37 phyla were classified through the high throughput sequencing, among which Proteobacteria, Actinobacteria, and Acidobacteria were the three most dominant phyla, accounting for >60% of the phylum frequency. The selective enrichment of PHC degraders with high salt-tolerance, including Alcanivorax and Bacteroidetes, was induced. Generally, relative abundance of the PHC degrading genes increased significantly with an increase in PHCs concentrations, and the gene copy number in the phytoremediation group was 1.46-14.44 times as much as that in the unplanted controls. Overall, the presence of PHCs and plant roots showed a stimulating effect on the development of specific degraders containing PHC degrading genes, and correspondingly, a biodegradation-beneficial community structure had been constructed to contribute to PHCs degradation in the rhizosphere.

Aquatic Bacterial Communities Associated With Land Use and Environmental Factors in Agricultural Landscapes Using a Metabarcoding Approach

This study applied a 16S rRNA gene metabarcoding approach to characterize bacterial community compositional and functional attributes for surface water samples collected within, primarily, agriculturally dominated watersheds in Ontario and Québec, Canada. Compositional heterogeneity was best explained by stream order, season, and watercourse discharge. Generally, community diversity was higher at agriculturally dominated lower order streams, compared to larger stream order systems such as small to large rivers. However, during times of lower relative water flow and cumulative 2-day rainfall, modestly higher relative diversity was found in the larger watercourses. Bacterial community assemblages were more sensitive to environmental/land use changes in the smaller watercourses, relative to small-to-large river systems, where the proximity of the sampled water column to bacteria reservoirs in the sediments and adjacent terrestrial environment was greater. Stream discharge was the environmental variable most significantly correlated (all positive) with bacterial functional groups, such as C/N cycling and plant pathogens. Comparison of the community structural similarity via network analyses helped to discriminate sources of bacteria in freshwater derived from, for example, wastewater treatment plant effluent and intensity and type of agricultural land uses (e.g., intensive swine production vs. dairy dominated cash/livestock cropping systems). When using metabarcoding approaches, bacterial community composition and coexisting pattern rather than individual taxonomic lineages, were better indicators of environmental/land use conditions (e.g., upstream land use) and bacterial sources in watershed settings. Overall, monitoring changes and differences in aquatic microbial communities at regional and local watershed scales has promise for enhancing environmental footprinting and for better understanding nutrient cycling and ecological function of aquatic systems impacted by a multitude of stressors and land uses.

Biochemical and molecular alterations in freshwater mollusks as biomarkers for petroleum product, domestic heating oil

To investigate the effect one of the oil products, domestic heating oil (DHO), on freshwater mollusks, Unio tigridis and Viviparous bengalensis were exposed to three DHO concentrations for each species (5.8, 8.7, and 17.4 ml L^-1 for mussels; 6.5, 9.7, and 19.5 mlL^-1 for snails, respectively). Antioxidant enzymes (superoxide dismutase, catalase), malondialdehyde, acetylcholinesterase and DNA damage in both species tissues were monitored over 21 days. The results showed that both antioxidant enzymes concentration (SOD and CAT) increased in the lowest DHO concentrations (5.8, and 8.7 ml L^-1), and then decreased in the highest concentration (17.4 ml L^-1) as the same pattern for Unio tigridis, but this not occurred for Viviparous bengalensis. MDA values recorded significantly increased compared to control. No reduction was observed in AChE concentrations in soft tissues of both mollusks may due to that DHO was a non-neurotoxicant to Unio tigridis and Viviparous bengalensis. The results of DNA damage parameters were showed significant differences (p≤ 0.05) between control and DHO concentrations except lowest concentration for each parameter measured in digestive gland of Unio tigridis. As well as, these significant differences were recorded between control and three concentrations of DHO exposure for comet length, and tail length parameters, and between control and highest oil concentration for tail moment in Viviparous bengalensis. DHO has the ability to prevent the reproduction of Viviparous bengalensis snail relation to control, that is what we considered strong evidence of the toxicity properties of DHO on the reproductive status of this species of snails. SOD, CAT, and MDA were useful biomarkers for evaluating the toxicity of DHO in mussel and snails, and comet assay was a good tool to assess the potential genotoxicity of DHO.

Potential microbial consortium involved in the biodegradation of diesel, hexadecane and phenanthrene in mangrove sediment explored by metagenomics analysis

Hydrocarbon contamination is a serious problem that degrades the quality of mangrove ecosystems, and bioremediation using autochthonous bacteria is a promising technology to recover an impacted environment. This research investigates the biodegradation rates of diesel, hexadecane and phenanthrene, by conducting a microcosm study and survey of the autochthonous microbial community in contaminated mangrove sediment, using an Illumina MiSeq platform. The biodegradation rates of diesel, hexadecane and phenanthrene were 82, 86 and 8 mg kg^-1 sediment day^-1, respectively. The removal efficiencies of hexadecane and phenanthrene were >99%, whereas the removal efficiency of diesel was 88%. A 16S rRNA gene amplicon sequence analysis revealed that the major bacterial assemblages detected were Gammaproteobacteria, Deltaproteobacteria, Alphaproteobacteria. The bacterial compositions were relatively constant, while reductions of the supplemented hydrocarbons were observed. The results imply that the autochthonous microorganisms in the mangrove sediment were responsible for the degradation of the respective hydrocarbons. Diesel-, hexadecane- and phenanthrene-degrading bacteria, namely Bacillus sp., Pseudomonas sp., Acinetobacter sp. and Staphylococcus sp., were also isolated from the mangrove sediment. The mangrove sediment provides a potential resource of effective hydrocarbon-degrading bacteria that can be used as an inoculum or further developed as a ready-to-use microbial consortium for the purpose of bioremediation.

Risk factors for periodic fever, aphthous stomatitis, pharyngitis, and adenitis (PFAPA) syndrome: a case-control study

The etiology and pathogenesis of periodic fever, aphthous stomatitis, pharyngitis, and adenitis (PFAPA) syndrome are unclear. We performed a case-control study to evaluate potential environmental or lifestyle factors associated with PFAPA morbidity. We enrolled 119 patients with PFAPA syndrome who had undergone tonsillectomy in Oulu University Hospital between 1987 and 2007. We recruited 230 controls, matched for sex, birth date, and place from the database of the Population Register Center of Finland. All the patients and controls completed a questionnaire regarding exposure to environmental triggers during early childhood. Maternal smoking was more common among PFAPA syndrome patients than controls (23 vs. 14%; P = 0.005). PFAPA patients had lower breastfeeding rates than controls (94 vs. 99%; P = 0.006). No other environmental factors were associated with PFAPA syndrome, except having an aquarium at home (P = 0.007). The patient group also used natural or herbal medicines more often than the controls (P = 0.01).

CONCLUSION

Maternal smoking and lack of breastfeeding, known risk factors for common childhood infections, were more common in patients with PFAPA syndrome than in matched controls. Environmental factors may be important in the pathogenesis of PFAPA syndrome and should be evaluated in future studies. What is Known: • The pathogenesis and genetics of periodic fever, aphthous stomatitis, pharyngitis, and adenitis (PFAPA) syndrome remain unsolved. • PFAPA syndrome has been shown to cluster in families. What is New: • Maternal smoking and lack of breastfeeding are more common in patients with PFAPA syndrome than in the controls. • Environmental risk factors may be important in the pathogenesis of the syndrome.

Microbial degradation of Cold Lake Blend and Western Canadian select dilbits by freshwater enrichments

Treatability experiments were conducted to determine the biodegradation of diluted bitumen (dilbit) at 5 and 25 °C for 72 and 60 days, respectively. Microbial consortia obtained from the Kalamazoo River Enbridge Energy spill site were enriched on dilbit at both 5 (cryo) and 25 (meso) ºC. On every sampling day, triplicates were sacrificed and residual hydrocarbon concentrations (alkanes and polycyclic aromatic hydrocarbons) were determined by GCMS/MS. The composition and relative abundance of different bacterial groups were identified by 16S rRNA gene sequencing analysis. While some physicochemical differences were observed between the two dilbits, their biodegradation profiles were similar. The rates and extent of degradation were greater at 25 °C. Both consortia metabolized 99.9% of alkanes; however, the meso consortium was more effective at removing aromatics than the cryo consortium (97.5 vs 70%). Known hydrocarbon-degrading bacteria were present in both consortia (Pseudomonas, Rhodococcus, Hydrogenophaga, Parvibaculum, Arthrobacter, Acidovorax), although their relative abundances depended on the temperatures at which they were enriched. Regardless of the dilbit type, the microbial community structure significantly changed as a response to the diminishing hydrocarbon load. Our results demonstrate that dilbit can be effectively degraded by autochthonous microbial consortia from sites with recent exposure to dilbit contamination.

Response of marine bacteria to oil contamination and to high pressure and low temperature deep sea conditions

The effect of pressure and temperature on microbial communities of marine environments contaminated with petroleum hydrocarbons is understudied. This study aims to reveal the responses of marine bacterial communities to low temperature, high pressure, and contamination with petroleum hydrocarbons using seawater samples collected near an offshore Brazilian platform. Microcosms containing only seawater and those containing seawater contaminated with 1% crude oil were subjected to three different treatments of temperature and pressure as follows: (1) 22°C/0.1 MPa; (2) 4°C/0.1 MPa; and (3) 4°C/22 MPa. The effect of depressurization followed by repressurization on bacterial communities was also evaluated (4°C/22 MPaD). The structure and composition of the bacterial communities in the different microcosms were analyzed by PCR-DGGE and DNA sequencing, respectively. Contamination with oil influenced the structure of the bacterial communities in microcosms incubated either at 4°C or 22°C and at low pressure. Incubation at low temperature and high pressure greatly influenced the structure of bacterial communities even in the absence of oil contamination. The 4°C/22 MPa and 4°C/22 MPaD treatments resulted in similar DGGE profiles. DNA sequencing (after 40 days of incubation) revealed that the diversity and relative abundance of bacterial genera were related to the presence or absence of oil contamination in the nonpressurized treatments. In contrast, the variation in the relative abundances of bacterial genera in the 4°C/22 MPa-microcosms either contaminated or not with crude oil was less evident. The highest relative abundance of the phylum Bacteroidetes was observed in the 4°C/22 MPa treatment.

Distribution of Anaerobic Hydrocarbon-Degrading Bacteria in Soils from King George Island, Maritime Antarctica

Anaerobic diesel fuel Arctic (DFA) degradation has already been demonstrated in Antarctic soils. However, studies comparing the distribution of anaerobic bacterial groups and of anaerobic hydrocarbon-degrading bacteria in Antarctic soils containing different concentrations of DFA are scarce. In this study, functional genes were used to study the diversity and distribution of anaerobic hydrocarbon-degrading bacteria (bamA, assA, and bssA) and of sulfate-reducing bacteria (SRB-apsR) in highly, intermediate, and non-DFA-contaminated soils collected during the summers of 2009, 2010, and 2011 from King George Island, Antarctica. Signatures of bamA genes were detected in all soils analyzed, whereas bssA and assA were found in only 4 of 10 soils. The concentration of DFA was the main factor influencing the distribution of bamA-containing bacteria and of SRB in the analyzed soils, as shown by PCR-DGGE results. bamA sequences related to genes previously described in Desulfuromonas, Lautropia, Magnetospirillum, Sulfuritalea, Rhodovolum, Rhodomicrobium, Azoarcus, Geobacter, Ramlibacter, and Gemmatimonas genera were dominant in King George Island soils. Although DFA modulated the distribution of bamA-hosting bacteria, DFA concentration was not related to bamA abundance in the soils studied here. This result suggests that King George Island soils show functional redundancy for aromatic hydrocarbon degradation. The results obtained in this study support the hypothesis that specialized anaerobic hydrocarbon-degrading bacteria have been selected by hydrocarbon concentrations present in King George Island soils.

Accelerated biodegradation of BPA in water-sediment microcosms with Bacillus sp. GZB and the associated bacterial community structure

Bisphenol A (BPA) is a synthetic chemical primarily used to produce polycarbonate plastics and epoxy resins. Significant industrial and consumer's consumption of BPA-containing products has contributed to extensive contamination in different environmental matrices. In this study, microcosms bioaugmented with Bacillus sp. GZB were constructed to investigate BPA biodegradation, identify the main bacterial community, and evaluate bacterial community responses in the microcosms. Under aerobic conditions, BPA was quickly depleted as a result of bioaugmentation with Bacillus sp. GZB in water-sediment contaminated with pollutants. The pollutants used were generally associated with the electronic wastes (mobile phones, computers, televisions) dismantling process. Adding BPA affected the bacterial community composition in the water-sediment. Furthermore, BPA biodegradation was enhanced by adding electron donors/co-substrates: humic acid, NaCl, glucose, and yeast extract. Metagenomic analysis of the total 16S rRNA genes from the BPA-degrading microcosms with bioaugmentation illustrated that the genera Bacillus, Thiobacillus, Phenylobacterium, and Cloacibacterium were dominant after a 7-week incubation period. A consortium of microorganisms from different bacterial genera may be involved in BPA biodegradation in electronic waste contaminated water-sediment. This study provides new insights about BPA bioaugmentation and bacterial ecology in the BPA-degrading environment.

The Deep-Sea Microbial Community from the Amazonian Basin Associated with Oil Degradation

One consequence of oil production is the possibility of unplanned accidental oil spills; therefore, it is important to evaluate the potential of indigenous microorganisms (both prokaryotes and eukaryotes) from different oceanic basins to degrade oil. The aim of this study was to characterize the microbial response during the biodegradation process of Brazilian crude oil, both with and without the addition of the dispersant Corexit 9500, using deep-sea water samples from the Amazon equatorial margin basins, Foz do Amazonas and Barreirinhas, in the dark and at low temperatures (4°C). We collected deep-sea samples in the field (about 2570 m below the sea surface), transported the samples back to the laboratory under controlled environmental conditions (5°C in the dark) and subsequently performed two laboratory biodegradation experiments that used metagenomics supported by classical microbiological methods and chemical analysis to elucidate both taxonomic and functional microbial diversity. We also analyzed several physical–chemical and biological parameters related to oil biodegradation. The concomitant depletion of dissolved oxygen levels, oil droplet density characteristic to oil biodegradation, and BTEX concentration with an increase in microbial counts revealed that oil can be degraded by the autochthonous deep-sea microbial communities. Indigenous bacteria (e.g., Alteromonadaceae, Colwelliaceae, and Alcanivoracaceae), archaea (e.g., Halobacteriaceae, Desulfurococcaceae, and Methanobacteriaceae), and eukaryotic microbes (e.g., Microsporidia, Ascomycota, and Basidiomycota) from the Amazonian margin deep-sea water were involved in biodegradation of Brazilian crude oil within less than 48-days in both treatments, with and without dispersant, possibly transforming oil into microbial biomass that may fuel the marine food web.

Bacterial interactions and implications for oil biodegradation process in mangrove sediments

Mangrove sediment harbors a unique microbiome and is a hospitable environment for a diverse group of bacteria capable of oil biodegradation. Our goal was to understand bacterial community dynamics from mangrove sediments contaminated with heavy-oil and to evaluate patterns potentially associated with oil biodegradation is such environments. We tested the previously proposed hypothesis of a two-phase pattern of petroleum biodegradation, under which key events in the degradation process take place in the first three weeks after contamination. Two sample sites with different oil pollution histories were compared through T-RFLP analyses and using a pragmatic approach based on the Microbial Resource Management Framework. Our data corroborated the already reported two-phase pattern of oil biodegradation, although the original proposed explanation related to the biophysical properties of the soil is questioned, opening the possibility to consider other plausible hypotheses of microbial interactions as the main drivers of this pattern.

Biostimulation of indigenous microorganisms for bioremediation of oily hypersaline microcosms from the Arabian Gulf Kuwaiti coasts

Hypersaline soil and water samples were collected in summer and winter from the "sabkha" area at the Kuwaiti shore of the Arabian Gulf. Physicochemical parameters were analyzed, and found suitable for microbial oil-removal. Summer- and winter-microcosms were treated with individual cation (K⁺, Ca²⁺, Mg²⁺, Fe³⁺) salts, and with animal blood and commercial yeast, as cost-effective vitamin sources. Those microcosms were exposed to the open environment for six winter and six summer months, and analyzed for their hydrocarbonoclastic microorganisms at time zero and in two month intervals. The hydrocarbonoclastic microbial communities in the microcosms consisted of halophilic bacteria and haloarchaea. The constituent bacterial species varied according to the season. Three species, Dietzia kunjamensis, Marinobacter lacisalsi and Halomonas oxialensis consistently occurred both in summer- and winter-samples, but the remaining species were different. On the other hand, the haloarchaeal communities in summer and winter were quite similar, and consisted mainly of Haloferax spp and Halobacterium spp. Treating the microcosms with cations and with vitamin-containing natural products enhanced microbial numbers and oil-removal. The effectiveness of the cations in oil-removal was in the order; Fe³⁺ (94%) > Ca²⁺ (89%) > Mg²⁺ (85%) > K⁺ (82%). Thus, oily microcosms amended with trivalent and divalent cations lost most of the oil, and those amended with commercial yeast and with animal blood, as vitamin sources, lost 78% and 72% oil, respectively.

Comparative Study on Rate of Biodegradation of Diluted Bitumen and Conventional Oil in Fresh Water

In recent years, diluted bitumen (or dilbit) has become an important source of hydrocarbon-based fuel. While information on the degradation of crude oils has been well researched, dilbit degradation has been studied at a much lesser extent. The objective of this study was to compare biodegradation of dilbit with a conventional crude oil (CCO) under various conditions. Two different microcosm experiments were set up, one containing a mixed culture acclimated to dilbit (Kalamazoo River Enrichment, KRC) and the other having a mixed culture enriched on soil contaminated with hydrocarbons (Anderson Ferry Enrichment, AFC). The microcosms were run for 60 d at 25 °C and for 72 days at 5 °C in flasks containing sterile Bushnell Hass broth and naturally dispersed oil. Each flask was inoculated with the KRC and AFC mixed cultures, and rotated on an orbital shaker (200 rpm) at the above stated temperatures. On each sampling day, triplicates were sacrificed to determine the residual hydrocarbon concentration. Additionally, some samples were used to determine the bacterial composition using 16S rRNA gene sequencing analysis. Hydrocarbon analysis (alkanes and PAHs) was performed by gas chromatography/mass spectrometry (GC/MS/MS). Higher degradation rates were achieved at 25 °C as compared to 5 °C. All the enrichments metabolized CCO as well dilbit, but the nature and extent of the degradation was distinct. KRC meso culture was the most effective among all, as it completely removed alkanes and most of the PAHs. AFC enrichment performed differently at the two temperatures; an acclimation period (8 d) was observed at 5 °C while there was no lag at 25 °C. KRC cryo culture as well as AFC culture at both temperatures degraded alkanes completely while they were not able to metabolize heavier fractions of the oil (C2–4 homologues of 3- and 4-ring compounds). All cultures showed the presence of diverse oil degrading bacteria and the differences in their compositions affected the biodegradation. Although dilbit was biodegraded, for all the treatments except AFC at 5 °C, the rate of degradation and the extent of degradation was greater for CCO owing to the higher concentrations of lighter hydrocarbons.

Metagenomic insights into effects of spent engine oil perturbation on the microbial community composition and function in a tropical agricultural soil

Analyzing the microbial community structure and functions become imperative for ecological processes. To understand the impact of spent engine oil (SEO) contamination on microbial community structure of an agricultural soil, soil microcosms designated 1S (agricultural soil) and AB1 (agricultural soil polluted with SEO) were set up. Metagenomic DNA extracted from the soil microcosms and sequenced using Miseq Illumina sequencing were analyzed for their taxonomic and functional properties. Taxonomic profiling of the two microcosms by MG-RAST revealed the dominance of Actinobacteria (23.36%) and Proteobacteria (52.46%) phyla in 1S and AB1 with preponderance of Streptomyces (12.83%) and Gemmatimonas (10.20%) in 1S and Geodermatophilus (26.24%), Burkholderia (15.40%), and Pseudomonas (12.72%) in AB1, respectively. Our results showed that soil microbial diversity significantly decreased in AB1. Further assignment of the metagenomic reads to MG-RAST, Cluster of Orthologous Groups (COG) of proteins, Kyoto Encyclopedia of Genes and Genomes (KEGG), GhostKOALA, and NCBI's CDD hits revealed diverse metabolic potentials of the autochthonous microbial community. It also revealed the adaptation of the community to various environmental stressors such as hydrocarbon hydrophobicity, heavy metal toxicity, oxidative stress, nutrient starvation, and C/N/P imbalance. To the best of our knowledge, this is the first study that investigates the effect of SEO perturbation on soil microbial communities through Illumina sequencing. The results indicated that SEO contamination significantly affects soil microbial community structure and functions leading to massive loss of nonhydrocarbon degrading indigenous microbiota and enrichment of hydrocarbonoclastic organisms such as members of Proteobacteria and Actinobacteria.

Fate of Eight Different Polymers under Uncontrolled Composting Conditions: Relationships Between Deterioration, Biofilm Formation, and the Material Surface Properties

With the ever-increasing volume of polymer wastes and their associated detrimental impacts on the environment, the plastic life cycle has drawn increasing attention. Here, eight commercial polymers selected from biodegradable to environmentally persistent materials, all formulated under a credit card format, were incubated in an outdoor compost to evaluate their fate over time and to profile the microbial communities colonizing their surfaces. After 450 days in compost, the samples were all colonized by multispecies biofilms, these latest displaying different amounts of adhered microbial biomass and significantly distinct bacterial and fungal community compositions depending on the substrate. Interestingly, colonization experiments on the eight polymers revealed a large core of shared microbial taxa, predominantly composed of microorganisms previously reported from environments contaminated with petroleum hydrocarbons or plastics debris. These observations suggest that biofilms may contribute to the alteration process of all the polymers studied. Actually, four substrates, independently of their assignment to a polymer group, displayed a significant deterioration, which might be attributed to biologically mediated mechanisms. Relevantly, the deterioration appears strongly associated with the formation of a high-cell density biofilm onto the polymer surfaces. The analysis of various surface properties revealed that roughness and hydrophilicity are likely prominent parameters for driving the biological interactions with the polymers.

Occurrence and Potential Biological Effects of Amphetamine on Stream Communities

The presence of pharmaceuticals, including illicit drugs in aquatic systems, is a topic of environmental significance because of their global occurrence and potential effects on aquatic ecosystems and human health, but few studies have examined the ecological effects of illicit drugs. We conducted a survey of several drug residues, including the potentially illicit drug amphetamine, at 6 stream sites along an urban to rural gradient in Baltimore, Maryland, U.S.A. We detected numerous drugs, including amphetamine (3 to 630 ng L(-1)), in all stream sites. We examined the fate and ecological effects of amphetamine on biofilm, seston, and aquatic insect communities in artificial streams exposed to an environmentally relevant concentration (1 μg L(-1)) of amphetamine. The amphetamine parent compound decreased in the artificial streams from less than 1 μg L(-1) on day 1 to 0.11 μg L(-1) on day 22. In artificial streams treated with amphetamine, there was up to 45% lower biofilm chlorophyll a per ash-free dry mass, 85% lower biofilm gross primary production, 24% greater seston ash-free dry mass, and 30% lower seston community respiration compared to control streams. Exposing streams to amphetamine also changed the composition of bacterial and diatom communities in biofilms at day 21 and increased cumulative dipteran emergence by 65% and 89% during the first and third weeks of the experiment, respectively. This study demonstrates that amphetamine and other biologically active drugs are present in urban streams and have the potential to affect both structure and function of stream communities.

Salt secretion is linked to acid-base regulation of ionocytes in seawater-acclimated medaka: new insights into the salt-secreting mechanism

Ionocytes in the skin and gills of seawater (SW) teleosts are responsible for both salt and acid secretion. However, the mechanism through which ionocytes secrete acid is still unclear. Here, we hypothesized that apical Na⁺/H⁺ exchangers (NHE2/3), carbonic anhydrase (CA2-like), and basolateral HCO₃⁻/Cl⁻ exchanger (AE1) are involved in acid secretion. In addition, the hypothesized involvement of basolateral AE1 suggested that acid secretion may be linked to Cl⁻ secretion by ionocytes. The scanning ion-selective electrode technique (SIET) was used to measure H⁺ and Cl⁻ secretion by ionocytes in the skin of medaka larvae acclimated to SW. Treatment with inhibitors of NHE, CA, and AE suppressed both H⁺ and Cl⁻ secretion by ionocytes. Short-term exposure to hypercapnic SW stimulated both H⁺ and Cl⁻ secretion. mRNA of CA2-like and AE1 were localized to ionocytes in the skin. Branchial mRNA levels of NKCC1a, CA2-like, and AE1a increased together with the salinity to which fish were acclimated. In addition, both AE1a and AE1b mRNA increased in fish acclimated to acidified (pH 7) SW; NKCC1a mRNA increased in fish acclimated to pH 9 SW. This study reveals the mechanism of H⁺ secretion by ionocytes, and refines our understanding of the well-established mechanism of Cl⁻ secretion by ionocytes of SW fish.

Bioremediation of petroleum contaminated soil to combat toxicity on Withania somnifera through seed priming with biosurfactant producing plant growth promoting rhizobacteria

Soil contaminated by Petroleum oil cannot be utilized for agricultural purposes due to hydrocarbon toxicity. Oil contaminated soil induces toxicity affecting germination, growth and productivity. Several technologies have been proposed for bioremediation of oil contaminated sites, but remediation through biosurfactant producing plant growth promontory rhizobacteria (PGPR) is considered to be most promising methods. In the present study the efficacy of seed priming on growth and pigment of Withania somnifera under petroleum toxicity is explored. Seeds of W. somnifera were primed with biosurfactant producing Pseudomonas sp. AJ15 with plant growth promoting traits having potentiality to utilized petroleum as carbon source. Results indicates that plant arose from priming seeds under various petroleum concentration expressed high values for all the parameters studied namely germination, shoot length, root length, fresh and dry weight and pigments (chlorophyll and carotenoid) as compared to non primed seed. Hence, the present study signifies that petroleum degrarding biosurfactant producing PGPR could be further used for management and detoxification of petroleum contaminated soils for growing economically important crops.

Macroscale distribution of virioplankton and heterotrophic bacteria in the Bohai Sea

In light of limited research into the relationship between the macroscale distribution and dynamic changes of microplankton in the shallow Bohai Sea, here we used flow cytometry to analyse samples collected from the Bohai Sea channel in winter and summer. Results showed that the average of both viral abundance (VA) and bacterial abundance (BA) were lower in winter (3.61 × 10(7) and 1.84 × 10(6) cells/mL, respectively) than in summer (7.47 × 10(7) and 5.05 × 10(6) cells/mL, respectively). At all 16 stations, VA was one order of magnitude greater than BA, with a positive relationship between one another. In the horizontal distribution, variations in VA and BA followed a similar trend, and both were obviously higher near-shore than offshore. In the vertical distribution, variations in both VA and BA did not show a clear relationship with water depth. VA and BA in summer were 2.1 and 2.7 times those in winter, respectively. Spearman correlation analysis showed that both VA and BA were correlated with the concentration of PO4-P in winter (positive) and NO3-N in summer (negative). Additionally, BA showed a negative correlation with salinity. It is clear that the macroscale distribution of these two kinds of microbes in the Bohai Sea is related to seasonal variation and nutrient availability.