Metagenome enrichment approach used for selection of oil-degrading bacteria consortia for drill cutting residue bioremediation

Guerra, Alaine B.; Oliveira, José Santos; Silva-Portela, Rita de Cássia Barreto; Araújo, Wydemberg J.; Carlos, Aline Cardoso; Vasconcelos, Ana Tereza Ribeiro de; Freitas, Ana T.; Domingos, Yldeney Silva; Farias, Mirna Ferreira de; Fernandes, Glauber José Turolla; Agnez-Lima, Lucymara Fassarella

doi:10.1016/j.envpol.2018.01.014

Cited by 103 publications

(55 citation statements)

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“…Quantitative PCR (qPCR) based studies on such functional biomarkers have demonstrated the relationship between the abundance/expression of genes and biodegradation of contaminants [ 3 , 26 , 33 ]. Dombrowski et al, [ 39 ] proposed metabolic linkages amongst different functional groups, like fermentative members of the community which have substrate-level interdependencies with sulfur- and nitrogen-cycling microorganisms.…”

Section: Introductionmentioning

confidence: 99%

“…Extensive research has elucidated microbial communities from a variety of hydrocarbon contaminated environments including deep water horizon spill, oil contaminated soil or sediments, drill cuttings, production and injection water, etc. [ 3 , 19 – 23 , 26 , 27 , 37 , 39 , 40 ]. However, investigation on petroleum refinery waste sludge microbiome remained little explored.…”

Section: Introductionmentioning

confidence: 99%

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Petroleum hydrocarbon rich oil refinery sludge of North-East India harbours anaerobic, fermentative, sulfate-reducing, syntrophic and methanogenic microbial populations

et al. 2018

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BackgroundSustainable management of voluminous and hazardous oily sludge produced by petroleum refineries remains a challenging problem worldwide. Characterization of microbial communities of petroleum contaminated sites has been considered as the essential prerequisite for implementation of suitable bioremediation strategies. Three petroleum refinery sludge samples from North Eastern India were analyzed using next-generation sequencing technology to explore the diversity and functional potential of inhabitant microorganisms and scope for their on-site bioremediation.ResultsAll sludge samples were hydrocarbon rich, anaerobic and reduced with sulfate as major anion and several heavy metals. High throughput sequencing of V3-16S rRNA genes from sludge metagenomes revealed dominance of strictly anaerobic, fermentative, thermophilic, sulfate-reducing bacteria affiliated to Coprothermobacter, Fervidobacterium, Treponema, Syntrophus, Thermodesulfovibrio, Anaerolinea, Syntrophobacter, Anaerostipes, Anaerobaculum, etc., which have been well known for hydrocarbon degradation. Relatively higher proportions of archaea were detected by qPCR. Archaeal 16S rRNA gene sequences showed presence of methanogenic Methanobacterium, Methanosaeta, Thermoplasmatales, etc. Detection of known hydrocarbon utilizing aerobic/facultative anaerobic (Mycobacterium, Pseudomonas, Longilinea, Geobacter, etc.), nitrate reducing (Gordonia, Novosphigobium, etc.) and nitrogen fixing (Azovibrio, Rhodobacter, etc.) bacteria suggested niche specific guilds with aerobic, facultative anaerobic and strict anaerobic populations. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) predicted putative genetic repertoire of sludge microbiomes and their potential for hydrocarbon degradation; lipid-, nitrogen-, sulfur- and methane- metabolism. Methyl coenzyme M reductase A (mcrA) and dissimilatory sulfite reductase beta-subunit (dsrB) genes phylogeny confirmed methanogenic and sulfate-reducing activities within sludge environment endowed by hydrogenotrophic methanogens and sulfate-reducing Deltaproteobacteria and Firmicutes members.ConclusionRefinery sludge microbiomes were comprised of hydrocarbon degrading, fermentative, sulfate-reducing, syntrophic, nitrogen fixing and methanogenic microorganisms, which were in accordance with the prevailing physicochemical nature of the samples. Analysis of functional biomarker genes ascertained the activities of methanogenic and sulfate-reducing organisms within sludge environment. Overall data provided better insights on microbial diversity and activity in oil contaminated environment, which could be exploited suitably for in situ bioremediation of refinery sludge.Electronic supplementary materialThe online version of this article (10.1186/s12866-018-1275-8) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Petroleum hydrocarbon rich oil refinery sludge of North-East India harbours anaerobic, fermentative, sulfate-reducing, syntrophic and methanogenic microbial populations

et al. 2018

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“…Note that it is preferable to obtain microbial consortia with desired functions prior to practical implementation, which can be obtained from naturally occurring microbial communities. But in most cases, this is still not sufficient to reach a desired effective consortium with a low diversity, which can be further used for downstream industrial applications (28, 29). For instance, more than 85 potential strains were detected from KMCG6, although the actual amount may be lower because multi-OTUs could originate from a same single strain due to intrinsic variability amongst multiple copies of 16S rRNA gene (30, 31).…”

Section: Resultsmentioning

confidence: 99%

Construction of simplified microbial consortia to degrade recalcitrant materials based on enrichment and dilution-to-extinction cultures

Kang

Jacquiod

Herschend

et al. 2019

Preprint

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The capacity of microbes degrading recalcitrant materials has been extensively explored from environmental remediation to industrial applications. Although significant achievements were obtained with single strains, focus is now going toward the use of microbial consortia because of advantages in terms of functional stability and efficiency. While consortia assembly attempts were made from several known single strains, another approach consists in obtaining consortia from complex environmental microbial communities in search for novel microbial species, genes and functions. However, assembling efficient microbial consortia from complex environmental communities is far from trivial due to large diversity and biotic interactions at play. Here we propose a strategy containing enrichment and dilution-to-extinction cultures to construct simplified microbial consortia (SMC) for keratinous waste management, from complex environmental communities. Gradual dilutions were performed from a keratinolytic microbial consortium, and dilution 10−9 was selected to construct a SMC library. Further compositional analysis and keratinolytic activity assays demonstrated that microbial consortia were successfully simplified, without impacting their biodegradation capabilities. These SMC possess promising potential for efficient keratinous valorization. More importantly, this reasoning and methodology could be transferred to other topics involving screening for simplified communities for biodegradation, thus considerably broadening its application scope.ImportanceMicrobial consortia have got more and more attention and extensive applications due to their potential advantages. However, a high diversity of microbes is likely to hide uncontrollable risks in practice specific to novel strains and complicated interaction networks. Exploring a convenient and efficient way to construct simplified microbial consortia is able to broaden the applied scope of microbes. This study presents the approach based on enrichment and dilution-to-extinction cultures, which gain abundance microbial consortia including some without losing efficiency from the enriched functional microbial community. The microbial interactions at the strain level were evaluated by using compositional identification and correlation analysis, which contribute to revealing the roles of microbes in the degradation process of recalcitrant materials. Our findings provide a systematic scheme to achieve optimizing microbial consortia for biodegradation from an environmental sample, could be readily applied to a range of recalcitrant materials management from environmental remediation to industrial applications.

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“…The PW sample used in this work was kindly provided by Petrogal Brasil S/A from onshore oil reservoir located in Aracajú, Sergipe, Brazil (Latitude: −10.9111099; Longitude: −37.0716705). Based on protocols adapted from Wu et al (2013) and Guerra et al (2018), the consortia were obtained in Erlenmeyer flasks containing 50 mL of the PW sample and culture medium in a 1:1 (v/v) of volume proportion, and were incubated at 30 • C at 180 rpm for 7 days (1 cycle). After the first incubation cycle, 5% (v/v) of the culture was transferred to a fresh culture medium containing 1% (v/v) sterile petroleum by autoclaving at 135 • C for 30 min.…”

Section: Obtaining Microbial Consortiamentioning

confidence: 99%

Microbial Culture in Minimal Medium With Oil Favors Enrichment of Biosurfactant Producing Genes

Araújo

Oliveira

Araujo

et al. 2020

Front. Bioeng. Biotechnol.

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Culture of Biosurfactant Producing Microbes aromatic hydrocarbons (PAHs). These data suggest that the enrichment of biosurfactant genes in the BH consortium could promote efficient hydrocarbon degradation, despite its lower taxonomical diversity compared to the consortium enriched in YPD medium. Together, these results showed that cultivation in a minimal medium supplemented with oil was an efficient strategy in selecting biosurfactant-producing microorganisms and highlighted the biotechnological potential of these bacterial consortia in waste treatment and bioremediation of impacted areas.

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Metagenome enrichment approach used for selection of oil-degrading bacteria consortia for drill cutting residue bioremediation

Cited by 103 publications

References 54 publications

Petroleum hydrocarbon rich oil refinery sludge of North-East India harbours anaerobic, fermentative, sulfate-reducing, syntrophic and methanogenic microbial populations

Petroleum hydrocarbon rich oil refinery sludge of North-East India harbours anaerobic, fermentative, sulfate-reducing, syntrophic and methanogenic microbial populations

Construction of simplified microbial consortia to degrade recalcitrant materials based on enrichment and dilution-to-extinction cultures

Microbial Culture in Minimal Medium With Oil Favors Enrichment of Biosurfactant Producing Genes

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