Novel anaerobe obtained from a hexadecane-degrading consortium

Background: Aliphatic hydrocarbons (AHC) are abundant in crude oil and fuels, and are frequent contaminants of water, soil and sediments. There is potential for AHC bioremediation using sulfate as electron acceptor, due to its abundance in marine environments and natural presence in soils and groundwater. Objectives: In this work sulfate-reducing anaerobic microorganisms involved in AHC biodegradation were studied. Methods: Anaerobic sludge was incubated at 37ºC with hexadecane (1mM) and sulfate (20mM) in serum vials. Cultures were successively transferred to fresh medium until a stable enrichment was obtained (monitored by microscopy and PCR-DGGE of 16S rRNA gene). For isolation of AHC-degrading bacteria, serial dilutions and successive transfers are now running using palmitate (1mM) as an easier substrate. Conclusions: Cultures growing on palmitate show two main bacterial cell types: a rod-shaped bacterium closely related to Desulfomonile limimaris (94% identity) was predominant in the first 30 days of incubation, when 83% of the added palmitate was degraded coupled to 4 mM sulfate reduction (suggesting stoichiometric palmitate conversion to acetate); and an oval-shaped bacterium related to Desulforhabdus amnigena (99% identity) that mainly developed when incubations where extended and a total of 11.5 mM sulfate was reduced. Growth of Desulforhabdus was stimulated when incubated with acetate. The role of the Desulfomonile in AHC degradation will be further discussed in the presentation, as well as its halorespiring ability, a characteristic of the Desulfomonile genera. Further characterization of this novel bacterium is important due to its high potential for bioremediation of hydrocarbons, fats and halogenated pollutants

Bioremediation of petroleum-contaminated soils: mathematical modelling as a tool for the simulation of alternative strategies

POCI-01-0145-FEDER-016575; ERC Grant n.º 323009; UID/BIO/04469/2013; POCI -01-0145-FEDER-006684; NORTE-01-0145-FEDER-000004; FCOMP-01-0124- FEDER-027462; SFRH/BPD/80528/2011info:eu-repo/semantics/publishedVersio

Who is who in anaerobic oil biodegradation?

[Excerpt] Anaerobic bioremediation is an important alternative for the common aerobic cleanup of subsurface petroleum-contaminated soil and water. Microbial communities involved in anaerobic oil biodegradation are scarcely studied, and only few mechanisms of anaerobic hydrocarbons degradation are described. In this work, microbial degradation of aliphatic hydrocarbons (AHC) was studied by using culture-dependent and culture-independent approaches. Hexadecane and hexadecene-degrading microbial communities were enriched under sulfate-reducing and methanogenic conditions. The microorganisms present in the enriched cultures were identified by 16S rRNA gene sequencing. (...

Facts and challenges on hydrocarbons bioremediation

Book of Abstracts of CEB Annual Meeting 2017[Excerpt] The intense activity of the oil industry generates substantial amounts of contaminated wastes and wastewaters. Moreover, accidental oil spills occur frequently, causing severe damages in the marine environment and in the soil. Subsurface soil contamination is generally caused by oil leakages from underground storage tanks and transport pipelines that can further lead to groundwater contamination. To date, common techniques for remediation of petroleum-contaminated environments include physical removal, washing by cosolvents or surfactants, thermal desorption, electrokinetic movement of contaminants and oxidation/reduction via chemical agents. Biological technologies can be an alternative to the more aggressive physicochemical methods, as bioremediation exploits the metabolic diversity of microorganisms and their ability to degrade organic contaminants. Aerobic bioremediation is frequently preferred over anaerobic processes, due to faster rates of hydrocarbons activation and biodegradation [1]. However, in subsurface environments oxygen is generally scarce and anoxic conditions prevail. Anaerobic microorganisms can biodegrade hydrocarbons coupled to the reduction of nitrate, iron(III), sulfate or under methanogenic conditions [2]. In situ bioremediation of hydrocarbons at anoxic conditions has not been extensively studied, despite the broad occurrence of these contaminants in the subsurface. Reduced knowledge on the catabolic mechanisms and microbial communities involved in anaerobic hydrocarbons biodegradation has limited this approach, and needs further research. [...]info:eu-repo/semantics/publishedVersio

Multi-walled carbon nanotubes enhance methanogenesis from diverse organic compounds in anaerobic sludge and river sediments

Conductive nanomaterials affect anaerobic digestion (AD) processes usually by improving methane production. Nevertheless, their effect on anaerobic communities, and particularly on specific trophic groups such as syntrophic bacteria or methanogens, is not extensively reported. In this work, we evaluate the effect of multi-walled carbon nanotubes (MWCNT) on the activity of two different anaerobic microbial communities: an anaerobic sludge and a river sediment. Methane production by anaerobic sludge was assessed in the presence of different MWCNT concentrations, with direct methanogenic substrates (acetate, hydrogen) and with typical syntrophic substrates (ethanol, butyrate). MWCNT accelerated the initial specific methane production rate (SMPR) from all compounds, with a more pronounced effect on the assays with acetate and butyrate, i.e., 2.1 and 2.6 times, respectively. In the incubations with hydrogen and ethanol, SMPR increased 1.1 and 1.2 times. Experiments with the river sediment were performed in the presence of MWCNT and MWCNT impregnated with 2% iron (MWCNT-Fe). Cumulative methane production was 10.2 and 4.5 times higher in the assays with MWCNT-Fe and MWCNT, respectively, than in the assays without MWCNT. This shows the high potential of MWCNT toward bioenergy production, in waste/wastewater treatment or ex situ bioremediation in anaerobic digesters.This research was funded by the Portuguese Foundation for Science and Technology(FCT) under the scope of project MORE (POCI-01-0145-FEDER-016575), of the strategic funding of UIDB/04469/2020 unit and BioTecNorte operation (NORTE-01-0145-FEDER-000004) funded by the European Regional Development Fund under the scope of Norte2020-Programa Operacional Regional do Norte, as well as FCT/MCTES trough national funds (PIDDAC) and Base Funding-UIDB/50020/20 of the Associate Laboratory LSRE-LCM-funded by national funds rough FCT/MCTES (PIDDAC). Research of O.S.G.P.S. was funded by FCT under the Scientific Employment Stimulus-Institutional Call EECINST/00049/2018.info:eu-repo/semantics/publishedVersio

Genome analysis and physiological comparison of Alicycliphilus denitrificans strains BC and K601T

The genomes of the Betaproteobacteria Alicycliphilus denitrificans strains BC and K601T have been sequenced to get insight into the physiology of the two strains. Strain BC degrades benzene with chlorate as electron acceptor. The cyclohexanol-degrading denitrifying strain K601T is not able to use chlorate as electron acceptor, while strain BC cannot degrade cyclohexanol. The 16S rRNA sequences of strains BC and K601T are identical and the fatty acid methyl ester patterns of the strains are similar. Basic Local Alignment Search Tool (BLAST) analysis of predicted open reading frames of both strains showed most hits with Acidovorax sp. JS42, a bacterium that degrades nitro-aromatics. The genomes include strain-specific plasmids (pAlide201 in strain K601T and pAlide01 and pAlide02 in strain BC). Key genes of chlorate reduction in strain BC were located on a 120 kb megaplasmid (pAlide01), which was absent in strain K601T. Genes involved in cyclohexanol degradation were only found in strain K601T. Benzene and toluene are degraded via oxygenase-mediated pathways in both strains. Genes involved in the meta-cleavage pathway of catechol are present in the genomes of both strains. Strain BC also contains all genes of the ortho-cleavage pathway. The large number of mono- and dioxygenase genes in the genomes suggests that the two strains have a broader substrate range than known thus far.This research was supported by the Technology Foundation, the Applied Science Division (STW) of the Netherlands Organization for Scientific Research (NWO), project number 08053, the graduate school WIMEK (Wageningen Institute for Environment and Climate Research, which is part of SENSE Research School for Socio-Economic and Natural Sciences of the Environment, www.wimek-new.wur.nl and www.sense.nl), SKB (Dutch Centre for Soil Quality Management and Knowledge Transfer, www.skbodem.nl) and the Consolider project CSD-2007-00055. The research was incorporated in the TRIAS (TRIpartite Approaches 469 toward Soil systems processes) program (http://www.nwo.nl/en/research-and-results/programmes/alw/trias-tripartite-approach-to-soil-system-processes/index. html). Flávia Talarico Saia was supported by a FAPESP (the State of São Paulo Research Foundation) scholarship (2006-01997/5). The work conducted by the DOE JGI is supported by the Office of Science of the United States Department of Energy under contract number DE-AC02-05CH11231. Alfons Stams acknowledges support by an ERC (European Research Counsil) advanced grant (project 323009). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Aerobic nonylphenol degradation and nitro-nonylphenol formation by microbial cultures from sediments

Nonylphenol (NP) is an estrogenic pollutant which is widely present in the aquatic environment. Biodegradation of NP can reduce the toxicological risk. In this study, aerobic biodegradation of NP in river sediment was investigated. The sediment used for the microcosm experiments was aged polluted with NP. The biodegradation of NP in the sediment occurred within 8 days with a lag phase of 2 days at 30°C. During the biodegradation, nitro-nonylphenol metabolites were formed, which were further degraded to unknown compounds. The attached nitro-group originated from the ammonium in the medium. Five subsequent transfers were performed from original sediment and yielded a final stable population. In this NP-degrading culture, the microorganisms possibly involved in the biotransformation of NP to nitro-nonylphenol were related to ammonium-oxidizing bacteria. Besides the degradation of NP via nitro-nonylphenol, bacteria related to phenol-degrading species, which degrade phenol via ring cleavage, are abundantly present

A benzene-degrading nitrate-reducing microbial consortium displays aerobic and anaerobic benzene degradation pathways

All sequence data from this study were deposited at the European Bioinformatics Institute under the accession numbers ERS1670018 to ERS1670023. Further, all assigned genes, taxonomy, function, sequences of contigs, genes and proteins can be found in Table S3.In this study, we report transcription of genes involved in aerobic and anaerobic benzene degradation pathways in a benzene-degrading denitrifying continuous culture. Transcripts associated with the family Peptococcaceae dominated all samples (2136% relative abundance) indicating their key role in the community. We found a highly transcribed gene cluster encoding a presumed anaerobic benzene carboxylase (AbcA and AbcD) and a benzoate-coenzyme A ligase (BzlA). Predicted gene products showed >96% amino acid identity and similar gene order to the corresponding benzene degradation gene cluster described previously, providing further evidence for anaerobic benzene activation via carboxylation. For subsequent benzoyl-CoA dearomatization, bam-like genes analogous to the ones found in other strict anaerobes were transcribed, whereas gene transcripts involved in downstream benzoyl-CoA degradation were mostly analogous to the ones described in facultative anaerobes. The concurrent transcription of genes encoding enzymes involved in oxygenase-mediated aerobic benzene degradation suggested oxygen presence in the culture, possibly formed via a recently identified nitric oxide dismutase (Nod). Although we were unable to detect transcription of Nod-encoding genes, addition of nitrite and formate to the continuous culture showed indication for oxygen production. Such an oxygen production would enable aerobic microbes to thrive in oxygen-depleted and nitrate-containing subsurface environments contaminated with hydrocarbons.This study was supported by a grant of BE-Basic-FES funds from the Dutch Ministry of Economic Affairs. The research of A.J.M. Stams is supported by an ERC grant (project 323009) and the gravitation grant “Microbes for Health and Environment” (project 024.002.002) of the Netherlands Ministry of Education, Culture and Science. F. Hugenholtz was supported by the same gravitation grant (project 024.002.002). B. Hornung is supported by Wageningen University and the Wageningen Institute for Environment and Climate Research (WIMEK) through the IP/OP program Systems Biology (project KB-17-003.02-023).info:eu-repo/semantics/publishedVersio