Metagenomic and Metatranscriptomic Responses of Chemical Dispersant Application during a Marine Dilbit Spill

The global increase in marine transportation of dilbit (diluted bitumen) can increase the risk of spills, and the application of chemical dispersants remains a common response practice in spill events. To reliably evaluate dispersant effects on dilbit biodegradation over time, we set large-scale (1500 mL) microcosms without nutrients addition using low dilbit concentration (30 ppm). Shotgun metagenomics and metatranscriptomics were deployed to investigate microbial community responses to naturally and chemically dispersed dilbit. We found that the large-scale microcosms could produce more reproducible community trajectories than small-scale (250 mL) ones based on the 16S rRNA gene amplicon sequencing. In the early-stage large-scale microcosms, multiple genera were involved into the biodegradation of dilbit, while dispersant addition enriched primarily Alteromonas and competed for the utilization of dilbit, causing depressed degradation of aromatics. The metatranscriptomic based Metagenome Assembled Genomes (MAG) further elucidated early-stage microbial antioxidation mechanism, which showed dispersant addition triggered the increased expression of the antioxidation process genes of Alteromonas species. Differently, in the late stage, the microbial communities showed high diversity and richness and similar compositions and metabolic functions regardless of dispersant addition, indicating the biotransformation of remaining compounds can occur within the post-oil communities. These findings can guide future microcosm studies and the application of chemical dispersants for responding to a marine dilbit spill. Importance In this study, we employed microcosms to study the effects of marine dilbit spill and dispersant application on microbial community dynamics over time. We evaluated the impacts of microcosm scale and found that increasing the scale is beneficial for reducing community stochasticity, especially in the late stage of biodegradation. We observed that dispersant application suppressed aromatics biodegradation in the early stage (6 days) whereas exerting insignificant effects in the late stage (50 days), from both substances removal and metagenomic/metatranscriptomic perspectives. We further found that Alteromonas species are vital for the early-stage chemically dispersed oil biodegradation, and clarified their degradation and antioxidation mechanisms. The findings would help to better understand microcosm studies and microbial roles for biodegrading dilbit and chemically dispersed dilbit, and suggest that dispersant evaluation in large-scale systems and even through field trails would be more realistic after marine oil spill response.

Microbial Involvement in Carbon Transformation via CH4 and CO2 in Saline Sedimentary Pool

Methane and carbon dioxide are one of the most important greenhouse gases and significant components of the carbon cycle. Biogeochemical methane transformation may occur even in the extreme conditions of deep subsurface ecosystems. This study presents methane-related biological processes in saline sediments of the Miocene Wieliczka Formation, Poland. Rock samples (W2, W3, and W4) differed in lithology (clayey salt with veins of fibrous salt and lenses of gypsum and anhydrite; siltstone and sandstone; siltstone with veins of fibrous salt and lenses of anhydrite) and the accompanying salt type (spiza salts or green salt). Microbial communities present in the Miocene strata were studied using activity measurements and high throughput sequencing. Biological activity (i.e., carbon dioxide and methane production or methane oxidation) occurred in all of the studied clayey salt and siltstone samples but mainly under water-saturated conditions. Microcosm studies performed at elevated moisture created more convenient conditions for the activity of both methanogenic and methanotrophic microorganisms than the intact sediments. This points to the fact that water activity is an important factor regulating microbial activity in saline subsurface sediments. Generally, respiration was higher in anaerobic conditions and ranged from 36 ± 2 (W2200%t.w.c) to 48 ± 4 (W3200%t.w.c) nmol CO2 gdw−1 day−1. Methanogenic activity was the highest in siltstone and sandstone (W3, 0.025 ± 0.018 nmol CH4 gdw−1 day−1), while aerobic methanotrophic activity was the highest in siltstone with salt and anhydrite (W4, 220 ± 66 nmol CH4 gdw−1 day−1). The relative abundance of CH4-utilizing microorganisms (Methylomicrobium, Methylomonas, Methylocystis) constituted 0.7–3.6% of all taxa. Methanogens were represented by Methanobacterium (0.01–0.5%). The methane-related microbes were accompanied by a significant number of unclassified microorganisms (3–64%) and those of the Bacillus genus (4.5–91%). The stable isotope composition of the CO2 and CH4 trapped in the sediments suggests that methane oxidation could have influenced δ13CCH4, especially in W3 and W4.

Distribution of ETBE-degrading microorganisms and functional capability in groundwater, and implications for characterising aquifer ETBE biodegradation potential

Microbes in aquifers are present suspended in groundwater or attached to the aquifer sediment. Groundwater is often sampled at gasoline ether oxygenate (GEO)-impacted sites to assess the potential biodegradation of organic constituents. However, the distribution of GEO-degrading microorganisms between the groundwater and aquifer sediment must be understood to interpret this potential. In this study, the distribution of ethyl tert-butyl ether (ETBE)-degrading organisms and ETBE biodegradation potential was investigated in laboratory microcosm studies and mixed groundwater-aquifer sediment samples obtained from pumped monitoring wells at ETBE-impacted sites. ETBE biodegradation potential (as determined by quantification of the ethB gene) was detected predominantly in the attached microbial communities and was below detection limit in the groundwater communities. The copy number of ethB genes varied with borehole purge volume at the field sites. Members of the Comamonadaceae and Gammaproteobacteria families were identified as responders for ETBE biodegradation. However, the detection of the ethB gene is a more appropriate function-based indicator of ETBE biodegradation potential than taxonomic analysis of the microbial community. The study shows that a mixed groundwater-aquifer sediment (slurry) sample collected from monitoring wells after minimal purging can be used to assess the aquifer ETBE biodegradation potential at ETBE-release sites using this function-based concept.

EFFECT OF THE APPLICATION OF GOAT DUNG ON THE BIOREMEDIATION OF POLLUTED SOIL BY HYDROCARBON DEGRADING BACTERIA: A MICROCOSM STUDY

Biostimulation is an effective means of enhancing bioremediation of toxic compounds. In this study, goat dung was used as an additional source of nutrients to improve the degradation of petroleum hydrocarbons in a heavily contaminated soil. Soil samples collected from a mechanic workshop in Zaria, Nigeria, was subjected to microcosm studies in a screen house and three proportions (2%w/w, 3%w/w, 4%w/w kg-1.soil) of goat dung added to the soil samples. The effect of the addition of nutrients from the goat dung on the hydrocarbon degrading bacterial community in the soil was determined by measuring the hydrocarbon utilizing bacterial counts, percentage degradation of hydrocarbon and biostimulation efficiency. At the end of the seven-week experiment, it was observed that 4% w/w of goat dung had the highest hydrocarbon utilizing bacterial count but, the maximum percentage hydrocarbon degradation occurred in the treatment with 2% w/w goat dung and biostimulation efficiency was optimum with both 2% w/w and 4% w/w goat dung. Nutrient addition can be an effective tool during bioremediation, however, laboratory scale studies should be conducted prior to field studies in order to achieve maximum results

Acetylene-Fueled Trichloroethene Reductive Dechlorination in a Groundwater Enrichment Culture

ABSTRACT In aquifers, acetylene (C2H2) is a product of abiotic degradation of trichloroethene (TCE) catalyzed by in situ minerals. C2H2 can, in turn, inhibit multiple microbial processes including TCE dechlorination and metabolisms that commonly support dechlorination, in addition to supporting the growth of acetylenotrophic microorganisms. Previously, C2H2 was shown to support TCE reductive dechlorination in synthetic, laboratory-constructed cocultures containing the acetylenotroph Pelobacter sp. strain SFB93 and Dehalococcoides mccartyi strain 195 or strain BAV1. In this study, we demonstrate TCE and perchloroethene (PCE) reductive dechlorination by a microbial community enriched from contaminated groundwater and amended with C2H2 as the sole electron donor and organic carbon source. The metagenome of the stable, enriched community was analyzed to elucidate putative community functions. A novel anaerobic acetylenotroph in the phylum Actinobacteria was identified using metagenomic analysis. These results demonstrate that the coupling of acetylenotrophy and reductive dechlorination can occur in the environment with native bacteria and broaden our understanding of biotransformation at contaminated sites containing both TCE and C2H2. IMPORTANCE Understanding the complex metabolisms of microbial communities in contaminated groundwaters is a challenge. PCE and TCE are among the most common groundwater contaminants in the United States that, when exposed to certain minerals, exhibit a unique abiotic degradation pathway in which C2H2 is a product. C2H2 can act as both an inhibitor of TCE dechlorination and of supporting metabolisms and an energy source for acetylenotrophic bacteria. Here, we combine laboratory microcosm studies with computational approaches to enrich and characterize an environmental microbial community that couples two uncommon metabolisms, demonstrating unique metabolic interactions only yet reported in synthetic, laboratory-constructed settings. Using this comprehensive approach, we have identified the first reported anaerobic acetylenotroph in the phylum Actinobacteria, demonstrating the yet-undescribed diversity of this metabolism that is widely considered to be uncommon.

Role of nematodes in the food web: nematodes as predator and prey.

This chapter provides information on the role of nematodes in the food web, including their participation in matter and energy fluxes within ecosystems. It highlights that nematodes are both predators and prey for organisms ranging from protozoans to vertebrates, based on gut analyses and direct observations. Functional response experiments, microcosm studies, and enclosures/exclosures in the field can be used to investigate the intensity of these trophic interactions and their impact on individual species as well as entire communities.

Interactions with freshwater biofilms cause rapid removal of common herbicides through degradation – evidence from microcosm studies

We found that biofilms drive the removal of bentazone, metazachlor and metribuzin from water through rapid mineralization of these herbicides, rather than by their sorption and accumulation.

Aqueous Mercury Removal with Carbonaceous and Iron Sulfide Sorbents and Their Applicability as Thin-Layer Caps in Mercury-Contaminated Estuary Sediment

This study aimed to investigate the Hg removal efficiency of iron sulfide (FeS), sulfurized activated carbon (SAC), and raw activated carbon (AC) sorbents influenced by salinity and dissolved organic matter (DOM), and the effectiveness of these sorbents as thin layer caps on Hg-contaminated sediment remediation via microcosm experiments to decrease the risk of release. In the batch adsorption experiments, FeS showed the greatest Hg2+ removal efficiencies, followed by SAC and AC. The effect of salinity levels on FeS was insignificant. In contrast, the Hg2+ removal efficiency of AC and SAC increased as increasing the salinity levels. The presence of DOM tended to decrease Hg removal efficiency of sorbents. Microcosm studies also showed that FeS had the greatest Hg sorption in both freshwater and estuary water; furthermore, the methylmercury (MeHg) removal ability of sorbents was greater in the freshwater than that in the estuary water. Notably, for the microcosms without capping, the overlying water MeHg in the estuary microcosm (0.14−1.01 ng/L) was far lesser than that in the freshwater microcosms (2.26−11.35 ng/L). Therefore, Hg compounds in the freshwater may be more bioavailable to microorganisms in methylated phase as compared to those in the estuary water. Overall, FeS showed the best Hg removal efficiency, resistance to salinity, and only slightly affected by DOM in aqueous adsorption experiments. Additionally, in the microcosms, AC showed as the best MeHg adsorber that help inhibiting the release of MeHg into overlying and decreasing the risk to the aqueous system.