Alkane biodegradation and dynamics of phylogenetic subgroups of sulfate-reducing bacteria in an anoxic coastal marine sediment artificially contaminated with oil

Microbial remediation of oil-contaminated shorelines: a review

Frequent marine oil spills have led to increasingly serious oil pollution along shorelines. Microbial remediation has become a research hotspot of intertidal oil pollution remediation because of its high efficiency, low cost, environmental friendliness, and simple operation. Many microorganisms are able to convert oil pollutants into non-toxic substances through their growth and metabolism. Microorganisms use enzymes' catalytic activities to degrade oil pollutants. However, microbial remediation efficiency is affected by the properties of the oil pollutants, microbial community, and environmental conditions. Feasible field microbial remediation technologies for oil spill pollution in the shorelines mainly include the addition of high-efficiency oil degrading bacteria (immobilized bacteria), nutrients, biosurfactants, and enzymes. Limitations to the field application of microbial remediation technology mainly include slow start-up, rapid failure, long remediation time, and uncontrolled environmental impact. Improving the environmental adaptability of microbial remediation technology and developing sustainable microbial remediation technology will be the focus of future research. The feasibility of microbial remediation techniques should also be evaluated comprehensively.

Impacts of Nutrients on Alkene Biodegradation Rates and Microbial Community Composition in Enriched Consortia from Natural Inocula

There is a growing need for biological and chemical methods for upcycling plastic waste streams. Pyrolysis processes can accelerate plastic depolymerization by breaking polyethylene into smaller alkene components which may be more biodegradable than the initial polymer. While the biodegradation of alkanes has been extensively studied, the role microorganisms play in alkene breakdown is not well understood. Alkene biodegradation holds the potential to contribute to the coupling of chemical and biological processing of polyethylene plastics. In addition, nutrient levels are known to impact rates of hydrocarbon degradation. Model alkenes were used (C6, C10, C16, and C20) to follow the breakdown capability of microbial communities from three environmental inocula in three nutrient levels over the course of 5 days. Higher-nutrient cultures were anticipated to exhibit enhanced biodegradation capabilities. Alkene mineralization was assessed by measuring CO2 production in the culture headspace using GC-FID (gas chromatography-flame ionization detection), and alkene breakdown was directly quantified by measuring extracted residual hydrocarbons using gas chromatography-mass spectrometry (GC/MS). Here, the efficacy of enriched consortia derived from the microbial communities of three inoculum sources (farm compost, Caspian Sea sediment, and an iron-rich sediment) at alkene breakdown was investigated over the course of 5 days across three nutrient treatments. No significant differences in CO2 production across nutrient levels or inoculum types were found. A high extent of biodegradation was observed in all sample types, with most samples achieving 60% to 95% biodegradation of all quantified compounds. Here, our findings indicate that alkene biodegradation is a common metabolic process in diverse environments and that nutrient levels common to culture media can support the growth of alkene-biodegrading consortia, primarily from the families Xanthamonadaceae, Nocardiaceae, and Beijerinkiaceae. IMPORTANCE Excess plastic waste poses a major environmental problem. Microorganisms can metabolize many of the breakdown products (alkenes) of plastics. While microbial degradation of plastics is typically slow, coupling chemical and biological processing of plastics has the potential to lead to novel methods for the upcycling of plastic wastes. Here, we explored how microbial consortia derived from diverse environments metabolize alkenes, which are produced by the pyrolysis of polyolefin plastics such as HDPE, and PP. We found that microbial consortia from diverse environments can rapidly metabolize alkenes of different chain lengths. We also explored how nutrients affect the rates of alkene breakdown and the microbial diversity of the consortia. Here, the findings indicate that alkene biodegradation is a common metabolism in diverse environments (farm compost, Caspian sediment, and iron-rich sediment) and that nutrient levels common to culture medium can support growth of alkene-biodegrading consortia, primarily from families Xanthamonadaceae, Nocardiaceae, and Beijerinkiaceae.

Microbial bioremediation of produced water under different redox conditions in marine sediments

The discharge of produced water from offshore oil platforms is an emerging concern due to its potential adverse effects on marine ecosystems. In this study, we investigated the feasibility and capability of using marine sediments for the bioremediation of produced water. We utilized a combination of porewater and solid phase analysis in a series of sediment batch incubations amended with produced water and synthetic produced water to determine the biodegradation of hydrocarbons under different redox conditions. Significant removal of benzene, toluene, ethylbenzene and xylene (BTEX) compounds was observed under different redox conditions, with biodegradation efficiencies of 93-97% in oxic incubations and 45-93% in anoxic incubations with nitrate, iron oxide or sulfate as the electron acceptor. Higher biodegradation rates of BTEX were obtained by incubations dominated by nitrate reduction (104-149 nmolC/cm³/d) and oxygen respiration (52-57 nmolC/cm³/d), followed by sulfate reduction (14-76 nmolC/cm³/d) and iron reduction (29-39 nmolC/cm³/d). Chemical fingerprint analysis showed that hydrocarbons were biodegraded to smaller alcohols/acids under oxic conditions compared to anoxic conditions with nitrate, indicating that the presence of oxygen facilitated a more complete biodegradation process. Toxicity of treated produced water to the marine copepod Acartia tonsa was reduced by half after sediment incubations with oxygen and nitrate. Our study emphasizes the possibility to use marine sediment as a biofilter for treating produced water at sea without extending the oil and gas platform or implementing a large-scale construction.

A Structural View of Alkyl-Coenzyme M Reductases, the First Step of Alkane Anaerobic Oxidation Catalyzed by Archaea

Microbial anaerobic oxidation of alkanes intrigues the scientific community by way of its impact on the global carbon cycle, and its biotechnological applications. Archaea are proposed to degrade short- and long-chain alkanes to CO₂ by reversing methanogenesis, a theoretically reversible process. The pathway would start with alkane activation, an endergonic step catalyzed by methyl-coenzyme M reductase (MCR) homologues that would generate alkyl-thiols carried by coenzyme M. While the methane-generating MCR found in methanogens has been well characterized, the enzymatic activity of the putative alkane-fixing counterparts has not been validated so far. Such an absence of biochemical investigations contrasts with the current explosion of metagenomics data, which draws new potential alkane-oxidizing pathways in various archaeal phyla. Therefore, validating the physiological function of these putative alkane-fixing machines and investigating how their structures, catalytic mechanisms, and cofactors vary depending on the targeted alkane have become urgent needs. The first structural insights into the methane- and ethane-capturing MCRs highlighted unsuspected differences and proposed some explanations for their substrate specificity. This Perspective reviews the current physiological, biochemical, and structural knowledge of alkyl-CoM reductases and offers fresh ideas about the expected mechanistic and chemical differences among members of this broad family. We conclude with the challenges of the investigation of these particular enzymes, which might one day generate biofuels for our modern society.

Biostimulation of sulfate-reducing bacteria used for treatment of hydrometallurgical waste by secondary metabolites of urea decomposition by Ochrobactrum sp. POC9: From genome to microbiome analysis

Sulfate-reducing bacteria (SRB) are key players in many passive and active systems dedicated to the treatment of hydrometallurgical leachates. One of the main factors reducing the efficiency and activity of SRB is the low pH and poor nutrients in leachates. We propose an innovative solution utilizing biogenic ammonia (B-NH₃), produced by urea degrading bacteria, as a pretreatment agent for increasing the pH of the leachate and spontaneously stimulating SRB activity via bacterial secondary metabolites. The selected strain, Ochrobactrum sp. POC9, generated 984.7 mg/L of ammonia in 24 h and promotes an effective neutralization of B-NH₃. The inferred metabolic traits indicated that the Ochrobactrum sp. POC9 can synthesize a group of vitamins B, and the production of various organic metabolites was confirmed by GC-MS analysis. These metabolites comprise alcohols, organic acids, and unsaturated hydrocarbons that may stimulate biological sulfate reduction. With the pretreatment of B-NH₃, sulfate removal efficiency reached ~92.3% after 14 days of incubation, whereas SRB cell count and abundance were boosted (~10⁷ cell counts and 88 OTUs of SRB) compared to synthetic ammonia (S-NH₃) (~10³ cell counts and 40 OTUs of SRB). The dominant SRB is Desulfovibrio in both S-NH₃ and B-NH₃ pretreated leachate, however, it belonged to two different clades. By reconstructing the ecological network, we found that B-NH₃ not only directly increases SRB performance but also promotes other strains with positive correlations with SRB.

Accelerated bioremediation of a complexly contaminated river sediment through ZVI-electrode combined stimulation

Complexly contaminated river sediment caused by reducible and oxidizable organic pollutants is a growing global concern due to the adverse influence on ecosystem safety and planetary health. How to strengthen indigenous microbial metabolic activity to enhance biodegradation and mineralization efficiency of refractory composite pollutants is critical but poorly understood in environmental biotechnology. Here, a synergetic biostimulation coupling electrode with zero-valent iron (ZVI) was investigated for the bioremediation of river sediments contaminated by 2,4,6-tribromophenol (TBP, reducible pollutant) and hydrocarbons (oxidizable pollutants). The bioremediation efficiency of ZVI based biostimulation coupling electrode against TBP debromination and hydrocarbons degradation were 1.1-3 times higher than the electrode used solely, which was attributed to the shape of distinctive microbial communities and the enrichment of potential dehalogenators (like Desulfovibrio, Desulfomicrobium etc.). The sediment microbial communities were significantly positively correlated with the enhanced degradation efficiencies of TBP and hydrocarbons (P < 0.05). Moreover, the coupled system predominately increased positive microbial interactions in the ecological networks. The possible mutual relationship between microbes i.e., Thiobacillus (iron-oxidizing bacteria) and Desulfovibrio (dehalogenator) as well as Pseudomonas (electroactive bacteria) and Clostridium (hydrocarbons degraders) were revealed. This study proposed a promising approach for efficient bioremediation of complexly contaminated river sediments.

Horizontal and vertical gene transfer drive sediment antibiotic resistome in an urban lagoon system

Rapid urbanization has resulted in pervasive occurrence of antibiotic resistance genes (ARGs) in urban aquatic ecosystems. However, limited information is available concerning the ARG profiles and the forces responsible for their assembly in urban landscape lagoon systems. Here, we employed high-throughput quantitative PCR (HT-qPCR) to characterize the spatial variations of ARGs in surface and core sediments of Yundang Lagoon, China. The results indicated that the average richness and absolute abundance of ARGs were 11 and 53 times higher in the lagoon sediments as compared to pristine reference Tibetan lake sediments, highlighting the role of anthropogenic activities in ARG pollution. Co-occurrence network analysis indicated that various anaerobic prokaryotic genera belonging to Alpha-, Deltaproteobacteria, Bacteroidetes, Euryarchaeota, Firmicutes and Synergistetes were the potential hosts of ARGs. The partial least squares-path modeling (PLS-PM) analysis revealed positive and negative indirect effects of physicochemical factors and heavy metals on the lagoon ARG profiles, via biotic factors, respectively. The horizontal (mediated by mobile genetic elements) and vertical (mediated by prokaryotic communities) gene transfer may directly contribute the most to drive the abundance and composition of ARGs, respectively. Furthermore, the neutral community model demonstrated that the assembly of sediment ARG communities was jointly governed by deterministic and stochastic processes. Overall, this study provides novel insights into the diversity and distribution of ARGs in the benthic habitat of urban lagoon systems and underlying mechanisms for the spread and proliferation of ARGs.

Anaerobic biodegradation of fluoxetine using a high-performance bacterial community

Fluoxetine (FLX), an antidepressant extensively used worldwide is considered an emerging pollutant. The present work intends to investigate for the first time the capacity of a bacterial community containing sulphate-reducing bacteria (SRB) enriched from an anaerobic sludge to biodegrade and use FLX as sole carbon source, since current literature suggests that this drug is poorly biodegraded being mainly removed by adsorption to sediments, where it persists. FLX was biodegraded under sulphate reducing conditions until reaching its lowest and reliably detectable concentration, when 20 mg/L of the drug was used as sole carbon source, while 66 ± 9% of 50 mg/L FLX was removed, after 31 days. The initial bacterial population was mainly constituted by Desulfomicrobium and Desulfovibrio whereas during the experiments using FLX as unique carbon source a clear shift occurred with the increase of vadinBC27 wastewater-sludge group, Macellibacteroidetes, Dethiosulfovibrio, Bacteroides, Tolumonas, Sulfuricurvum, f_Enterobacteriaceae_OTU_18 that are assumed for the first time as FLX degrading bacteria. Although the main mechanism of FLX removal described in literature is by adsorption, in the results herein presented anaerobic biodegradation appears to play the main role in the removal of the FLX, thus demonstrating the potentialities that the anaerobic processes can play in wastewater treatment aiming the removal of new emerging compounds.

Evaluation of rhizoremediation and methane emission in diesel-contaminated soil cultivated with tall fescue (Festuca arundinacea)

Rhizoremediation, CH₄ emission, and bacterial community dynamics were evaluated in diesel-contaminated soil cultivated with tall fescue via a pot experiment. At the beginning of the experiment, total petroleum hydrocarbons (TPHs) removal efficiency was 30.2% in tall fescue-cultivated soil, which was significantly higher than that of unplanted soil (19.4%). However, when compost was added as a soil amendment, TPHs removal efficiency increased to 39.2% in tall fescue-cultivated soil. Interestingly, potential CH₄ emissions were more affected by the initial diesel concentration than by compost addition or tall fescue planting. Specifically, the potential CH₄ emission was approximately 3.8 times higher in the treatment with the highest initial diesel concentration (T-WC38) than that of the treatment with the lowest initial diesel concentration (T-WC5). Functional gene analysis revealed that TPHs removal had a linear correlation with the alkB/16S gene ratio, whereas potential CH₄ emission had a linear correlation with pmoA gene copy numbers. Initial diesel concentrations in soil also affected bacterial community structures and the genera Rhizobium, Halothiobacillus, and Geobacter were found to be positively linked to diesel-contaminated soil rhizoremediation. Therefore, this study provides useful insights into the development of strategies to enhance rhizoremediation efficiency and CH₄ emission mitigation in diesel-contaminated soils.

Diverse Profiles of AI-1 Type Quorum Sensing Molecules in Cultivable Bacteria from the Mangrove (Kandelia obovata) Rhizosphere Environment

Mangrove rhizosphere environment harbors diverse populations of microbes, and some evidence showed that rhizobacteria behavior was regulated by quorum sensing (QS). Investigating the diverse profiles of QS molecules in mangrove ecosystems may shed light on the bacterial roles and lead to a better understanding of the symbiotic interactions between plants and microbes. The aims of the current study focus on identifying AI-1 type QS signals, i.e., acyl homoserine lactones (AHLs), in Kandelia obovata rhizosphere environment. Approximately 1200 rhizobacteria were screened and 184 strains (15.3%) tested were positive. Subsequent 16s rRNA gene sequencing and dereplication analyses identified 24 species from the positive isolates, which were affiliated to three different phyla, including Proteobacteria, Firmicutes, and Actinobacteria. Thin-layer chromatography separation of extracts revealed diverse AHL profiles and detected at least one active compound in the supernatant of these 24 cultivable AHL-producers. The active extracts from these bacterial isolates were further evaluated by ultra performance liquid chromatography-mass spectrometry, and the carbon side chain length ranged from C4 to C14. This is the first report on the diversity of AI-1 type auto-inducers in the mangrove plant K. obovata, and it is imperative to expand our knowledge of plant-bacteria interactions with respect to the maintenance of wetland ecosystem health.

Rhizosphere Microbiomes of European + Seagrasses Are Selected by the Plant, But Are Not Species Specific

Seagrasses are marine flowering plants growing in soft-body sediments of intertidal and shallow sub-tidal zones. They play an important role in coastal ecosystems by stabilizing sediments, providing food and shelter for animals, and recycling nutrients. Like other plants, seagrasses live intimately with both beneficial and unfavorable microorganisms. Although much is known about the microbiomes of terrestrial plants, little is known about the microbiomes of seagrasses. Here we present the results of a detailed study on the rhizosphere microbiome of seagrass species across the North-eastern Atlantic Ocean: Zostera marina, Zostera noltii, and Cymodocea nodosa. High-resolution amplicon sequencing of 16S rRNA genes showed that the rhizobiomes were significantly different from the bacterial communities of surrounding bulk sediment and seawater. Although we found no significant differences between the rhizobiomes of different seagrass species within the same region, those of seagrasses in different geographical locations differed strongly. These results strongly suggest that the seagrass rhizobiomes are shaped by plant metabolism, but not coevolved with their host. The core rhizobiome of seagrasses includes mostly bacteria involved in the sulfur cycle, thereby highlighting the importance of sulfur-related processes in seagrass ecosystems.

Anaerobic biodegradation of surrogate naphthenic acids

Surface bitumen extraction from the Alberta's oil sands region generates large settling basins known as tailings ponds. The oil sands process-affected water (OSPW) stored in these ponds contain solid and residual bitumen-associated compounds including naphthenic acids (NAs) that can potentially be biodedgraded by indigenous tailings microorganisms. While the biodegradation of some NAs is known to occur under aerobic conditions, little is understood about anaerobic NA biodegradation even though tailings ponds are mainly anoxic. Here, we investigated the potential for anaerobic NA biodegradation by indigenous tailings microorganisms. Enrichment cultures were established from anoxic tailings that were amended with 5 single-ringed surrogate NAs or acid-extractable organics (AEO) from OSPW and incubated under nitrate-, sulfate-, iron-reducing, and methanogenic conditions. Surrogate NA depletion was observed under all anaerobic conditions tested to varying extents, correlating to losses in the respective electron acceptor (sulfate or nitrate) or the production of predicted products (Fe(II) or methane). Tailings-containing cultures incubated under the different electron-accepting conditions resulted in the enrichment and putative identification of microbial community members that may function in metabolizing surrogate NAs under the various anoxic conditions. In addition, more complex NAs (in the form of AEO) was observed to drive sulfate and iron reduction relative to controls. Overall, this study has shown that simple surrogate NAs can be biodegraded under a variety of anoxic conditions, a key first step in understanding the potential anaerobic metabolism of NAs in oil sands tailings ponds and other industrial wastewaters.

Application of nitrate to enhance biodegradation of gasoline components in soil by indigenous microorganisms under anoxic condition

Anaerobic/anoxic biodegradation of hydrocarbons offers an attractive approach to the removal of these compounds from polluted environments such as aquifers, aquatic sediments, submerged soils and subsurface soils. The application of nitrate was investigated to accelerate the degradation of gasoline components such as mono-aromatic hydrocarbons and total petroleum hydrocarbons (TPH) in soil by indigenous microorganisms under anoxic condition. The addition of nitrate had little effect on the degradation of mono-aromatic hydrocarbons m- & p-xylene, o-xylene, sec-butylbenzene and 1,2,4-trimethylbenzene, but facilitated the degradation of TPH (C6-C12) and mono-aromatic hydrocarbons toluene and ethylbenzene markedly. Furthermore, the more nitrate added, the higher the percentage of toluene, ethylbenzene and TPH (C6-C12) degraded after 180 days of anoxic incubation. Microorganisms capable of degrading toluene, ethylbenzene and TPH (C6-C12) with nitrate as the electron acceptor under anaerobic/anoxic condition are composed predominantly of Alpha-, Beta-, Gamma- or Delta-proteobacteria. Beta- and Gamma-proteobacteria were the main components of indigenous microorganisms, and accounted for 83-100% of the total amount of indigenous microorganisms in soil used in this study. Furthermore, the total amount of indigenous microorganisms increased with nitrate added. The addition of nitrate stimulated the growth of indigenous microorganisms, and therefore facilitated the degradation of toluene, ethylbenzene and TPH (C6-C12).

An integrated bioremediation process for petroleum hydrocarbons removal and odor mitigation from contaminated marine sediment

This study developed a novel integrated bioremediation process for the removal of petroleum hydrocarbons and the mitigation of odor induced by reduced sulfur from contaminated marine sediment. The bioremediation process consisted of two phases. In Phase I, acetate was dosed into the sediment as co-substrate to facilitate the sulfate reduction process. Meanwhile, akaganeite (β-FeOOH) was dosed in the surface layer of the sediment to prevent S(2-) release into the overlying seawater. In Phase II, NO3(-) was injected into the sediment as an electron acceptor to facilitate the denitrification process. After 20 weeks of treatment, the sequential integration of the sulfate reduction and denitrification processes led to effective biodegradation of total petroleum hydrocarbons (TPH), in which about 72% of TPH was removed. In Phase I, the release of S(2-) was effectively controlled by the addition of akaganeite. The oxidation of S(2-) by Fe(3+) and the precipitation of S(2-) by Fe(2+) were the main mechanisms for S(2-) removal. In Phase II, the injection of NO3(-) completely inhibited the sulfate reduction process. Most of residual AVS and S(0) were removed within 4 weeks after NO3(-) injection. The 16S rRNA clone library-based analysis revealed a distinct shift of bacterial community structure in the sediment over different treatment phases. The clones affiliated with Desulfobacterales and Desulfuromonadales were the most abundant in Phase I, while the clones related to Thioalkalivibrio sulfidophilus, Thiohalomonas nitratireducens and Sulfurimonas denitrificans predominated in Phase II.

Dynamic of sulphate-reducing microorganisms in petroleum-contaminated marine sediments inhabited by the polychaete Hediste diversicolor

The behaviour of sulphate-reducing microbial community was investigated at the oxic-anoxic interface (0-2 cm) of marine sediments when submitted to oil and enhanced bioturbation activities by the addition of Hediste diversicolor. Although total hydrocarbon removal was not improved by the addition of H. diversicolor, terminal restriction fragment length polymorphism (T-RFLP) analyses based on dsrAB (dissimilatory sulphite reductase) genes and transcripts showed different patterns according to the presence of H. diversicolor which favoured the abundance of dsrB genes during the early stages of incubation. Complementary DNA (cDNA) dsrAB libraries revealed that in presence of H. diversicolor, most dsrAB sequences belonged to hydrocarbonoclastic Desulfobacteraceae, suggesting that sulphate-reducing microorganisms (SRMs) may play an active role in hydrocarbon biodegradation in sediments where the reworking activity is enhanced. Furthermore, the presence of dsrAB sequences related to sequences found associated to environments with high dinitrogen fixation activity suggested potential N2 fixation by SRMs in bioturbated-polluted sediments.

Dynamics of bacterial assemblages and removal of polycyclic aromatic hydrocarbons in oil-contaminated coastal marine sediments subjected to contrasted oxygen regimes

To study the impact of oxygen regimes on the removal of polycylic aromatic hydrocarbons (PAHs) in oil-spill-affected coastal marine sediments, we used a thin-layer incubation method to ensure that the incubated sediment was fully oxic, anoxic, or was influenced by oxic-anoxic switches without sediment stirring. Hydrocarbon content and microbial assemblages were followed during 60 days to determine PAH degradation kinetics and microbial community dynamics according to the oxygenation regimes. The highest PAH removal, with 69 % reduction, was obtained at the end of the experiment under oxic conditions, whereas weaker removals were obtained under oscillating and anoxic conditions (18 and 12 %, respectively). Bacterial community structure during the experiment was determined using a dual 16S rRNA genes/16S rRNA transcripts approach, allowing the characterization of metabolically active bacteria responsible for the functioning of the bacterial community in the contaminated sediment. The shift of the metabolically active bacterial communities showed that the selection of first responders belonged to Pseudomonas spp. and Labrenzia sp. and included an unidentified Deltaproteobacteria-irrespective of the oxygen regime-followed by the selection of late responders adapted to the oxygen regime. A novel unaffiliated phylotype (B38) was highly active during the last stage of the experiment, at which time, the low-molecular-weight (LMW) PAH biodegradation rates were significant for permanent oxic- and oxygen-oscillating conditions, suggesting that this novel phylotype plays an active role during the restoration phase of the studied ecosystem.

Oil spill effects on macrofaunal communities and bioturbation of pristine marine sediments (Caleta Valdés, Patagonia, Argentina): experimental evidence of low resistance capacities of benthic systems without history of pollution

The Patagonian coast is characterized by the existence of pristine ecosystems which may be particularly sensitive to oil contamination. In this study, a simulated oil spill at acute and chronic input levels was carried out to assess the effects of contamination on the macrobenthic community structure and the bioturbation activity of sediments sampled in Caleta Valdés creek. Superficial sediments were either noncontaminated or contaminated by Escalante crude oil and incubated in the laboratory for 30 days. Oil contamination induced adverse effects on macrobenthic community at both concentrations with, for the highest concentration, a marked decrease of approximately 40 and 55 % of density and specific richness, respectively. Besides the disappearance of sensitive species, some other species like Oligochaeta sp. 1, Paranebalia sp., and Ostracoda sp. 2 species have a higher resistance to oil contamination. Sediment reworking activity was also affected by oil addition. At the highest level of contamination, nearly no activity was observed due to the high mortality of macroorganisms. The results strongly suggest that an oil spill in this protected marine area with no previous history of contamination would have a deep impact on the non-adapted macrobenthic community.

Optimization of biostimulant for bioremediation of contaminated coastal sediment by response surface methodology (RSM) and evaluation of microbial diversity by pyrosequencing

The present study aims to optimize the slow release biostimulant ball (BSB) for bioremediation of contaminated coastal sediment using response surface methodology (RSM). Different bacterial communities were evaluated using a pyrosequencing-based approach in contaminated coastal sediments. The effects of BSB size (1-5cm), distance (1-10cm) and time (1-4months) on changes in chemical oxygen demand (COD) and volatile solid (VS) reduction were determined. Maximum reductions of COD and VS, 89.7% and 78.8%, respectively, were observed at a 3cm ball size, 5.5cm distance and 4months; these values are the optimum conditions for effective treatment of contaminated coastal sediment. Most of the variance in COD and VS (0.9291 and 0.9369, respectively) was explained in our chosen models. BSB is a promising method for COD and VS reduction and enhancement of SRB diversity.

Concentrations of viable oil-degrading microorganisms are increased in feces from Calanus finmarchicus feeding in petroleum oil dispersions

Zooplankton are suggested to be biotic contributors to the transport and weathering of oil in marine environments due to their ingestion of oil. In the present experiment, feeding activity and microbial communities in feces from Calanus finmarchicus feeding in oil dispersions were characterized. Feeding activity was significantly reduced in oil dispersions. The microbial communities in clean and oil-containing copepod feces were dominated by Rhodobacteraceae family bacteria (Lesingera, Phaeobacter, Rugeria, and Sulfitobacter), which were suggested to be indigenous to copepod feces. The results also indicated that these bacteria were metabolizing oil compounds, as a significant increase in the concentrations of viable oil degrading microorganisms was observed in oil-containing feces. This study shows that bacteria in feces from copepods feeding in dilute oil dispersions have capacity for degradation of oil. Zooplankton may therefore contribute to weathering of oil by excreting feces with microbial communities already adapted to degradation of oil.

Oil Biodegradation and Oil-Degrading Microbial Populations in Marsh Sediments Impacted by Oil from the Deepwater Horizon Well Blowout

To study hydrocarbon biodegradation in marsh sediments impacted by Macondo oil from the Deepwater Horizon well blowout, we collected sediment cores 18-36 months after the accident at the marshes in Bay Jimmy (Upper Barataria Bay), Louisiana, United States. The highest concentrations of oil were found in the top 2 cm of sediment nearest the waterline at the shorelines known to have been heavily oiled. Although petroleum hydrocarbons were detectable, Macondo oil could not be identified below 8 cm in 19 of the 20 surveyed sites. At the one site where oil was detected below 8 cm, concentrations were low. Residual Macondo oil was already highly weathered at the start of the study, and the concentrations of individual saturated hydrocarbons and polycyclic aromatic hydrocarbons continued to decrease over the course of the study due to biodegradation. Desulfococcus oleovorans, Marinobacter hydrocarbonoclasticus, Mycobacterium vanbaalenii, and related mycobacteria were the most abundant oil-degrading microorganisms detected in the top 2 cm at the oiled sites. Relative populations of these taxa declined as oil concentrations declined. The diversity of the microbial community was low at heavily oiled sites compared to that of the unoiled reference sites. As oil concentrations decreased over time, microbial diversity increased and approached the diversity levels of the reference sites. These trends show that the oil continues to be biodegraded, and microbial diversity continues to increase, indicating ongoing overall ecological recovery.

A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes

Dissimilatory sulphate reduction is the unifying and defining trait of sulphate-reducing prokaryotes (SRP). In their predominant habitats, sulphate-rich marine sediments, SRP have long been recognized to be major players in the carbon and sulphur cycles. Other, more recently appreciated, ecophysiological roles include activity in the deep biosphere, symbiotic relations, syntrophic associations, human microbiome/health and long-distance electron transfer. SRP include a high diversity of organisms, with large nutritional versatility and broad metabolic capacities, including anaerobic degradation of aromatic compounds and hydrocarbons. Elucidation of novel catabolic capacities as well as progress in the understanding of metabolic and regulatory networks, energy metabolism, evolutionary processes and adaptation to changing environmental conditions has greatly benefited from genomics, functional OMICS approaches and advances in genetic accessibility and biochemical studies. Important biotechnological roles of SRP range from (i) wastewater and off gas treatment, (ii) bioremediation of metals and hydrocarbons and (iii) bioelectrochemistry, to undesired impacts such as (iv) souring in oil reservoirs and other environments, and (v) corrosion of iron and concrete. Here we review recent advances in our understanding of SRPs focusing mainly on works published after 2000. The wealth of publications in this period, covering many diverse areas, is a testimony to the large environmental, biogeochemical and technological relevance of these organisms and how much the field has progressed in these years, although many important questions and applications remain to be explored.

Investigation of intertidal wetland sediment as a novel inoculation source for anaerobic saline wastewater treatment

Biological treatment of saline wastewater is considered unfavorable due to salinity inhibition on microbial activity. In this study, intertidal wetland sediment (IWS) collected from a high saline environment was investigated as a novel inoculation source for anaerobic treatment of saline pharmaceutical wastewater. Two parallel lab-scale anaerobic sequencing batch reactors (AnSBR) were set up to compare the organic removal potential of IWS with conventional anaerobic digested sludge (ADS). Under steady-state condition, IWS reactor (R(i)) showed organic reduction performance significantly superior to that of ADS reactor (R(a)), achieving COD removal efficiency of 71.4 ± 3.7 and 32.3 ± 6.1%, respectively. In addition, as revealed by fluorescent in situ hybridization (FISH) analysis, a higher relative abundance of methanogenic populations was detected in R(i). A further 16S rRNA gene pyrosequencing test was conducted to understand both the bacterial and archaeal community populations in the two AnSBRs. A predominance of halophilic/tolerant microorganisms (class Clostridia of bacteria, genera Methanosarcina, and Methanohalophilus of archaea) in R(i) enhanced its organic removal efficiency. Moreover, several microbial groups related with degradation of hardly biodegradable compounds (PAHs, n-alkenes, aliphatic hydrocarbons, and alkanes, etc.) were detected in the IWS. All these findings indicated that IWS is a promising inoculation source for anaerobic treatment of saline wastewater.

Biostimulation of petroleum-hydrocarbon-contaminated marine sediment with co-substrate: involved metabolic process and microbial community

This study investigated the effect of acetate and methanol as co-substrates on anaerobic biodegradation of total petroleum hydrocarbons (TPHs, C10-C40) in marine sediment. The findings evidenced that the degradation of TPH can be enhanced by adding acetate or methanol. The addition of acetate was generally more favorable than the addition of methanol for the TPH degradation. Both sulfate reduction and methanogenesis occurred in the acetate-treated sediment. However, the depletion of SO4 (2-) inhibited sulfate reduction over the incubation period. Only methanogenesis was prevalent in the methanol-treated sediment within the whole incubation period. The degradation of TPH fractions with higher carbon number ranges (C31-C40) was speculated to be more favored under sulfate-reducing condition, while TPH fractions with lower carbon number ranges (C10-C20) were preferentially degraded under methanogenic condition. The 16S rRNA clone library-based analysis revealed that the addition of different co-substrates led to distinct structures of the microbial community. Clones related to sulfate-reducing Desulfobacterales were the most abundant in the sediment dosed with acetate. Clones related to Clostridiales predominated in the sediment dosed with methanol. Acetoclastic methanogens were found to be the predominant archaeal species in the sediment dosed with acetate, while both acetoclastic methanogens and hydrogenotrophic methanogens accounted for large proportions in the sediment dosed with methanol. The results obtained in this study will contribute to more comprehensive knowledge on the role of acetate and methanol as co-substrates in biostimulation of petroleum-hydrocarbon-contaminated marine sediment.

Diversity of bacterial communities along a petroleum contamination gradient in desert soils

Microbial communities in oil-polluted desert soils have been rarely studied compared to their counterparts from freshwater and marine environments. We investigated bacterial diversity and changes therein in five desert soils exposed to different levels of oil pollution. Automated rRNA intergenic spacer (ARISA) analysis profiles showed that the bacterial communities of the five soils were profoundly different (analysis of similarities (ANOSIM), R = 0.45, P < 0.0001) and shared less than 20 % of their operational taxonomic units (OTUs). OTU richness was relatively higher in the soils with the higher oil pollution levels. Multivariate analyses of ARISA profiles revealed that the microbial communities in the S soil, which contains the highest level of contamination, were different from the other soils and formed a completely separate cluster. A total of 16,657 ribosomal sequences were obtained, with 42-89 % of these sequences belonging to the phylum Proteobacteria. While sequences belonging to Betaproteobacteria, Gammaproteobacteria, Bacilli, and Actinobacteria were encountered in all soils, sequences belonging to anaerobic bacteria from the classes Deltaproteobacteria, Clostridia, and Anaerolineae were only detected in the S soil. Sequences belonging to the genus Terriglobus of the class Acidobacteria were only detected in the B3 soil with the lowest level of contamination. Redundancy analysis (RDA) showed that oil contamination level was the most determinant factor that explained variations in the microbial communities. We conclude that the exposure to different levels of oil contamination exerts a strong selective pressure on bacterial communities and that desert soils are rich in aerobic and anaerobic bacteria that could potentially contribute to the degradation of hydrocarbons.

Differential distribution and abundance of diazotrophic bacterial communities across different soil niches using a gene-targeted clone library approach

Diazotrophs are key players of the globally important biogeochemical nitrogen cycle, having a significant role in maintaining ecosystem sustainability. Saline soils are pristine and unexplored habitats representing intriguing ecosystems expected to harbour potential diazotrophs capable of adapting in extreme conditions, and these implicated organisms are largely obscure. Differential occurrence of diazotrophs was studied by the nifH gene-targeted clone library approach. Four nifH gene clone libraries were constructed from different soil niches, that is saline soils (low and high salinity; EC 3.8 and 7.1 ds m(-1) ), and agricultural and rhizosphere soil. Additionally, the abundance of diazotrophic community members was assessed using quantitative PCR. Results showed environment-dependent metabolic versatility and the presence of nitrogen-fixing bacteria affiliated with a range of taxa, encompassing members of the Alphaproteobacteria, Betaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, Cyanobacteria and Firmicutes. The analyses unveiled the dominance of Alphaproteobacteria and Gammaproteobacteria (Pseudomonas, Halorhodospira, Ectothiorhodospira, Bradyrhizobium, Agrobacterium, Amorphomonas) as nitrogen fixers in coastal-saline soil ecosystems, and Alphaproteobacteria and Betaproteobacteria (Bradyrhizobium, Azohydromonas, Azospirillum, Ideonella) in agricultural/rhizosphere ecosystems. The results revealed a repertoire of novel nitrogen-fixing bacterial guilds particularly in saline soil ecosystems.

High sulfate reduction efficiency in a UASB using an alternative source of sulfidogenic sludge derived from hydrothermal vent sediments

Sulfidogenesis in reactors is mostly achieved through adaptation of predominantly methanogenic granular sludge to sulfidogenesis. In this work, an upflow anaerobic sludge blanket (UASB) reactor operated under sulfate-reducing conditions was inoculated with hydrothermal vent sediments to carry out sulfate reduction using volatile fatty acids (VFAs) as substrate and chemical oxygen demand (COD)/SO4 (-2) ratios between 0.49 and 0.64. After a short period of adaptation, a robust non-granular sludge was capable of achieving high sulfate reduction efficiencies while avoiding competence with methanogens and toxicity to the microorganisms due to high sulfide concentration. The highest sulfide concentration (2,552 mg/L) was obtained with acetate/butyrate, and sulfate reduction efficiencies were up to 98 %. A mixture of acetate/butyrate, which produced a higher yielding of HS(-), was preferred over acetate/propionate/butyrate since the consumption of COD was minimized during the process. Sludge was analyzed, and some of the microorganisms identified in the sludge belong to the genera Desulfobacterium, Marinobacter, and Clostridium. The tolerance of the sludge to sulfide may be attributed to the syntrophy among these microorganisms, some of which have been reported to tolerate high concentrations of sulfide. To the best of our knowledge, this is the first report on the analysis of the direct utilization of hydrothermal vent sediments as an alternate source of sludge for sulfate reduction under high sulfide concentrations.

Resolving biodegradation patterns of persistent saturated hydrocarbons in weathered oil samples from the Deepwater Horizon disaster

Biodegradation plays a major role in the natural attenuation of oil spills. However, limited information is available about biodegradation of different saturated hydrocarbon classes in surface environments, despite that oils are composed mostly of saturates, due to the limited ability of conventional gas chromatography (GC) to resolve this compound group. We studied eight weathered oil samples collected from four Gulf of Mexico beaches 12-19 months after the Deepwater Horizon disaster. Using comprehensive two-dimensional gas chromatography (GC × GC), we successfully separated, identified, and quantified several distinct saturates classes in these samples. We find that saturated hydrocarbons eluting after n-C22 dominate the GC-amenable fraction of these weathered samples. This compound group represented 8-10%, or 38-68 thousand metric tons, of the oil originally released from Macondo well. Saturates in the n-C22 to n-C29 elution range were found to be partly biodegraded, but to different relative extents, with ease of biodegradation decreasing in the following order: n-alkanes > methylalkanes and alkylcyclopentanes+alkylcyclohexanes > cyclic and acyclic isoprenoids. We developed a new quantitative index designed to characterize biodegradation of >n-C22 saturates. These results shed new light onto the environmental fate of these persistent, hydrophobic, and mostly overlooked compounds in the unresolved complex mixtures (UCM) of weathered oils.

Richness and composition of sediment bacterial assemblages in an Atlantic port environment

In the present study, we assessed the bacterial richness and composition of sediment samples collected in and around the port of Aveiro, on the Atlantic coast of mainland Portugal. Sediment samples were collected in five locations: two within the port harbor, two in port areas along a channel adjacent to the harbor and one in a relatively undisturbed reference location. These areas were characterized as under high, medium and no port activity, respectively. In-depth, barcoded-pyrosequencing analysis indicated that port activity affects the composition and abundance of bacterial communities colonizing surface sediments. Sampling sites under the influence of port activities (channel and harbor) were associated with higher relative abundances of Desulfobacterales and a marked decline in the abundance of Flavobacteriia. In addition, there was a pronounced prevalence of operational taxonomic units (OTUs) in the port area that were closely related to hydrocarbon-degrading bacteria (Desulfococcus spp.), antifouling paint (bacterium strain WH6-7) and copper rich sediments (bacterium strain CanalPD16A). Here we provide evidence that specific phylotypes detected have the potential to be used as biomarkers and should be evaluated in future studies as proxies for sediment disturbance associated with port activity.

High bacterial biodiversity increases degradation performance of hydrocarbons during bioremediation of contaminated harbor marine sediments

We investigated changes of bacterial abundance and biodiversity during bioremediation experiments carried out on oxic and anoxic marine harbor sediments contaminated with hydrocarbons. Oxic sediments, supplied with inorganic nutrients, were incubated in aerobic conditions at 20 °C and 35 °C for 30 days, whereas anoxic sediments, amended with organic substrates, were incubated in anaerobic conditions at the same temperatures for 60 days. Results reported here indicate that temperature exerted the main effect on bacterial abundance, diversity and assemblage composition. At higher temperature bacterial diversity and evenness increased significantly in aerobic conditions, whilst decreased in anaerobic conditions. In both aerobic and anaerobic conditions, biodegradation efficiencies of hydrocarbons were significantly and positively related with bacterial richness and evenness. Overall results presented here suggest that bioremediation strategies, which can sustain high levels of bacterial diversity rather than the selection of specific taxa, may significantly increase the efficiency of hydrocarbon degradation in contaminated marine sediments.

Increment in anaerobic hydrocarbon degradation activity of Halic Bay sediments via nutrient amendment

In this study, hydrocarbon (HC) degradation activity of a HC-rich marine sediment was assessed in anaerobic microcosms during a 224 days incubation period. Natural TOC/N/P ratio of the sediment porewater (1,000/5/1) was gradually decreased to 1,000/40/6 which resulted in approximately ninefold increase in gas production (CH(4)+CO(2)) and HC removal. Addition of external HCs to the microcosms was also resulted in approximately twofold higher gas production and HC removal. A high proportion (92%) of aromatic HCs and all n-alkanes were removed from the microcosms under unlimited nutrient supply conditions without external HC addition. The microorganisms of the sediment degraded a wide range of aliphatic (n-C(9-31) alkanes and acyclic isoprenoids) and aromatic (18 different one- to five-ring aromatics) HCs. Monitoring functional gene and transcript abundances revealed that methanogenesis and dissimilatory sulfate reduction took place simultaneously during the first 126 days, afterwards, only the syntrophic methanogenic consortium was active. Genes and transcripts related to initial activation of HCs were highly abundant throughout the incubation period showing that fumarate addition was the main pathway of anaerobic HC degradation. In conclusion, biostimulation of highly polluted anoxic marine sediments via nutrient amendment is effective and may constitute a suitable and cost-effective field-scale bioremediation strategy.

STITCH: algorithm to splice, trim, identify, track, and capture the uniqueness of 16S rRNAs sequence pairs using public or in-house database

A comparison of variable regions within the 16S rRNA gene is widely used to characterize relationships between bacteria and to identify phylogenetic affiliation of unknown bacteria. In environmental studies, polymerase chain reaction amplification of 16S rRNA followed by cloning and sequencing of numerous individual clones is an extensively used molecular method for elucidating microbial diversity. The sequencing process typically utilizes a forward and reverse primer pair to produce two partial reads (~700 to 800 base pairs each) that overlap and in total cover a large region of the full 16S rRNA sequence (~1.5 k base). In a typical application, this approach rapidly generates very large numbers of 16S rRNA datasets that can overwhelm manual processing efforts leading to both delays and errors. In particular, the approach presents two computational challenges: (1) the assembly of a composite sequence from the two partial reads and (2) the subsequent appropriate identification of the organism represented by the newly sequenced clones. Herein, we describe a software package, search, trim, identify, track, and capture the uniqueness of 16S rRNAs using public and in-house database (STITCH), which offers automated sequence pair splicing and genetic identification, thus simplifying the computationally intensive analysis of large sequencing libraries. The STITCH software is freely accessible over the Internet at: http://prion.bchs.uh.edu/stitch/.

Microbial community response to a simulated hydrocarbon spill in mangrove sediments

In this study, we examined the hypothesis that the microbial communities in mangrove sediments with different chemical and historical characteristics respond differently to the disturbance of a hydrocarbon spill. Two different mangrove sediments were sampled, one close to an oil refinery that had suffered a recent oil spill and another that had not been in contact with oil. Based on the sampled sediment, two sets of mesocosms were built, and oil was added to one of them. They were subjected to mimicked mangrove conditions and monitored for 75 days. Archaeal and bacterial communities were evaluated through PCR-DGGE. Both communities showed the emergence of small numbers of novel bands in response to oil pollution. 16S rRNA gene clone libraries were constructed from both mesocosms before the addition of oil and at day 75 after oil addition. LIBSHUFF analysis showed that both mangrove-based mesocosms contained similar communities at the start of the experiment and that they were different from the initial one, as well as from each other, after 75 days. These results hint at a role of environmental history that is not obvious from community diversity indicators, but is apparent from the response to the applied stress.

Diversity and identification of methanogenic archaea and sulphate-reducing bacteria in sediments from a pristine tropical mangrove

Mangrove sediments are anaerobic ecosystems rich in organic matter. This environment is optimal for anaerobic microorganisms, such as sulphate-reducing bacteria and methanogenic archaea, which are responsible for nutrient cycling. In this study, the diversity of these two functional guilds was evaluated in a pristine mangrove forest using denaturing gradient gel electrophoresis (DGGE) and clone library sequencing in a 50 cm vertical profile sampled every 5.0 cm. DGGE profiles indicated that both groups presented higher richness in shallow samples (0-30 cm) with a steep decrease in richness beyond that depth. According to redundancy analysis, this alteration significantly correlated with a decrease in the amount of organic matter. Clone library sequencing indicated that depth had a strong effect on the selection of dissimilatory sulphate reductase (dsrB) operational taxonomic units (OTUs), as indicated by the small number of shared OTUs found in shallow (0.0 cm) and deep (40.0 cm) libraries. On the other hand, methyl coenzyme-M reductase (mcrA) libraries indicated that most of the OTUs found in the shallow library were present in the deep library. These results show that these two guilds co-exist in these mangrove sediments and indicate important roles for these organisms in nutrient cycling within this ecosystem.

Bioremediation of petroleum hydrocarbons in anoxic marine sediments: consequences on the speciation of heavy metals

We investigated the effects of biostimulation and bioagumentation strategies applied to harbor sediments displaying reducing conditions and high concentrations of petroleum hydrocarbons and heavy metals. We compared the microbial efficiency of hydrocarbon removal from sediments maintained for 60 days in anoxic conditions and inoculated with acetate, sulfate-reducing bacterial strains and acetate and sulfate-reducing bacteria. All treatments determined a significant increase in the microbial growth and significant decreases of hydrocarbon contents and of redox potential values. The addition of sulfate-reducing bacterial strains to the sediment was the most efficient treatment for the hydrocarbon removal. In all experiments, significant changes of the heavy metals' phase repartition were observed. The results reported here suggest that the biodegradation of petroleum hydrocarbons in anoxic marine sediments may be enhanced by stimulating microbial anaerobic metabolism, but care should be applied to monitor the potential changes in the mobility and bioavailability of heavy metals induced by bio-treatments.

Novel alkane hydroxylase gene (alkB) diversity in sediments associated with hydrocarbon seeps in the Timor Sea, Australia

Hydrocarbon seeps provide inputs of petroleum hydrocarbons to widespread areas of the Timor Sea. Alkanes constitute the largest proportion of chemical components found in crude oils, and therefore genes involved in the biodegradation of these compounds may act as bioindicators for this ecosystem's response to seepage. To assess alkane biodegradation potential, the diversity and distribution of alkane hydroxylase (alkB) genes in sediments of the Timor Sea were studied. Deduced AlkB protein sequences derived from clone libraries identified sequences only distantly related to previously identified AlkB sequences, suggesting that the Timor Sea maybe a rich reservoir for novel alkane hydroxylase enzymes. Most sequences clustered with AlkB sequences previously identified from marine Gammaproteobacteria though protein sequence identities averaged only 73% (with a range of 60% to 94% sequence identities). AlkB sequence diversity was lower in deep water (>400 m) samples off the continental slope than in shallow water (<100 m) samples on the continental shelf but not significantly different in response to levels of alkanes. Real-time PCR assays targeting Timor Sea alkB genes were designed and used to quantify alkB gene targets. No correlation was found between gene copy numbers and levels of hydrocarbons measured in sediments using sensitive gas chromatography-mass spectrometry techniques, probably due to the very low levels of hydrocarbons found in most sediment samples. Interestingly, however, copy numbers of alkB genes increased substantially in sediments exposed directly to active seepage even though only low or undetectable concentrations of hydrocarbons were measured in these sediments in complementary geochemical analyses due to efficient biodegradation.

Biogeographical distribution and diversity of bacterial and archaeal communities within highly polluted anoxic marine sediments from the Marmara Sea

Physicochemical and microbiological characterization of anoxic sediments taken from seven highly polluted sites of the Marmara Sea was carried out. The 16S rRNA based microbial community structure analyses were performed using domain-specific PCR followed by denaturant gradient gel electrophoresis (DGGE) and sequencing of characteristic bands. The results showed that the microbial communities in these sediments were diverse and evenly distributed. Relating the prokaryotic and geochemical variables through statistical tools revealed that the microbial diversity in the sediments significantly related to depth, and S, Mn and Fe content of the sediments. Fermentative bacteria, denitrifying bacteria and hydrogenotrophic methanogens were dominant whereas sulfate reducing bacteria were absent in the DGGE patterns. This unusual microbial community structure implied that the newly discovered anaerobic methane oxidation coupled to denitrification process may occur in these subseafloor environments.