Metagenomic Insights into the Bacterial Functions of a Diesel-Degrading Consortium for the Rhizoremediation of Diesel-Polluted Soil

Garrido‐Sanz, Daniel; Redondo‐Nieto, Miguel; Guirado, María; Jiménez, Óscar Pindado; Millán, Rocío; Martín, Marta; Rivilla, Rafael

doi:10.3390/genes10060456

Cited by 92 publications

(48 citation statements)

References 77 publications

(112 reference statements)

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“…Hence, there is a dearth of literature on the effects of contaminant imbibition on seed viability and germination rates—something necessary to complement microcosm studies on phytoremediation of organic contaminants. The aim of the present study is to bridge this gap by examining the effect of exposure to diesel fuel on the seed viability and germination rate of Medicago sativa , a plant with great reclamation potential for soils contaminated with petroleum hydrocarbons [ 9 , 10 , 11 , 12 , 13 , 14 ].…”

Section: Introductionmentioning

confidence: 99%

Assessing the Effect of Diesel Fuel on the Seed Viability and Germination of Medicago sativa Using the Event-Time Model

Eze

Hose

George

2020

Plants

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The remediation of contaminated sites using plant-based techniques has gained increasing attention in recent decades. However, information on the effects of contaminant imbibition on seed viability and germination rates are often lacking in the literature. To this end, our research investigated, by means of an event-time model, the effect of diesel fuel imbibition on the seed viability and germination rate of Medicago sativa, a plant species with great potential for remediation of organic contaminants. The event-time model provided an accurate and biologically relevant method for analysing germination data. Our results reveal that the direct imbibition of diesel fuel by M. sativa seeds for ≤48 h, or their exposure to soil diesel fuel concentrations of 0–10 g/kg diesel fuel, affects their germination rates, as shown by increasing t50 values from 90.6 (±2.78) to 114.2 (±2.67) hours, without significantly affecting seed viability. On the other hand, diesel fuel imbibition of longer duration, or the exposure of M. sativa seeds to ≥20 g/kg diesel fuel-contaminated soils, leads to no further effect on time to seed emergence. Instead, these conditions compromise seed viability, resulting in a decrease in the proportion of germinated seeds from 0.91 (±0.03) in 10 g/kg diesel fuel contaminated soil to 0.84 (±0.04) and 0.70 (±0.05) in 20 and 30 g/kg diesel fuel-contaminated soils, respectively. The fact that low concentrations of diesel fuel and 0–48 h of direct imbibition delayed seed emergence without adversely affecting the percentage of viable seeds suggests that this inhibitory effect on germination at low diesel fuel exposure could be attributed more to physical constraints rather than biological damage on the seeds. The models used in this study provide an accurate and biologically relevant method for the analyses of germination data. This is vital since expensive germination experiments, be it in the field of toxicology or agriculture, deserve to be accurately analysed.

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Section: Introductionmentioning

confidence: 99%

Assessing the Effect of Diesel Fuel on the Seed Viability and Germination of Medicago sativa Using the Event-Time Model

Eze

Hose

George

2020

Plants

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“…Thus, this is evidence that both the enrichment method and randomly picking colonies grown on crude-oil-coated agar plates, apart from yielding hydrocarbon degraders, may produce some unwanted "companions" (e.g., Clostridium sensu stricto 16 and Clostridioides). In this case, cooperation in the metabolic degradation of pollution should have naturally selected the microbial population, as shown recently [46,47]. On the other hand, some of these members might have been considered not necessarily beneficial since some representatives of the Brevundimonas [48] and Enterococcus [49] genera are also known as opportunistic pathogens.…”

Section: Discussionmentioning

confidence: 99%

Hydrocarbon Removal by Two Differently Developed Microbial Inoculants and Comparing Their Actions with Biostimulation Treatment

et al. 2020

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Bioremediation of soils polluted with petroleum compounds is a widely accepted environmental technology. We compared the effects of biostimulation and bioaugmentation of soil historically contaminated with aliphatic and polycyclic aromatic hydrocarbons. The studied bioaugmentation treatments comprised of the introduction of differently developed microbial inoculants, namely: an isolated hydrocarbon-degrading community C1 (undefined—consisting of randomly chosen degraders) and a mixed culture C2 (consisting of seven strains with well-characterized enhanced hydrocarbon-degrading capabilities). Sixty days of remedial treatments resulted in a substantial decrease in total aliphatic hydrocarbon content; however, the action of both inoculants gave a significantly better effect than nutrient amendments (a 69.7% decrease for C1 and 86.8% for C2 vs. 34.9% for biostimulation). The bioaugmentation resulted also in PAH removal, and, again, C2 degraded contaminants more efficiently than C1 (reductions of 85.2% and 64.5%, respectively), while biostimulation itself gave no significant results. Various bioassays applying different organisms (the bacterium Vibrio fischeri, the plants Sorghum saccharatum, Lepidium sativum, and Sinapis alba, and the ostracod Heterocypris incongruens) and Ames test were used to assess, respectively, potential toxicity and mutagenicity risk after bioremediation. Each treatment improved soil quality, however only bioaugmentation with the C2 treatment decreased both toxicity and mutagenicity most efficiently. Illumina high-throughput sequencing revealed the lack of (C1) or limited (C2) ability of the introduced degraders to sustain competition from indigenous microbiota after a 60-day bioremediation process. Thus, bioaugmentation with the bacterial mixed culture C2, made up of identified, hydrocarbon-degrading strains, is clearly a better option for bioremediation purposes when compared to other treatments.

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“…The alcohol dehydrogenase catalyzed step is a very important one in the metabolic processing of aliphatic hydrocarbons and side chain reactions of aromatics, and their derivatives. The enzyme has a broad substrate speci city on various classes of aliphatic, alicyclic, and aromatic alcohols and hydroxyls (van Beilen et al 2003, Hirano et al 2005, Zhou et al 2013Garrido-Sanz et al 2019). It is highly plausible that these genes are involved in the rapid disappearance of short chained aliphatics from the microcosm.…”

Section: Discussionmentioning

confidence: 99%

Remarkable Shift In Structural And Functional Properties of An Animal Charcoal Polluted Soil Accentuated By Inorganic Nutrients Amendment

Salam

Obayori

2020

Preprint

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Abstract The effects of carbon-free mineral medium (CFMM) amendment on hydrocarbon degradation and microbial community structure and function in an animal charcoal polluted soil was monitored for six weeks in field moist microcosms consisting of CFMM treated soil (FN4) and an untreated control (FN1). Gas chromatographic analysis of hydrocarbon fractions revealed the removal 84.02% and 82.38% and 70.09% and 70.14% aliphatic and aromatic fractions in FN4 and FN1 microcosms in 42 days. Shotgun metagenomic analysis of the two metagenomes revealed a remarkable shift in the microbial community structure of FN4 metagenome with 92.97% of the population belonging to the phylum Firmicutes and its dominant representative genera Anoxybacillus (64.58%), Bacillus (21.47%) and Solibacillus (2.39%). In untreated FN1 metagenome, the phyla Proteobacteria (56.12%), Actinobacteria (23.79%), Firmicutes (11.20%); and the genera Xanthobacter (9.73%), Rhizobium (7.49%) and Corynebacterium (7.35%) were preponderant. Functional annotation of putative ORFs from the two metagenomes revealed the detection of degradation genes for benzoate (pcaD, mhpF, aliB, benD-xylL, benC-xylZ, badH, had, dmpD, ligC, CMLE, pcaL, acd), xylene (mhpF, benD-xylL, benC-xylZ, dmpD, cymB, cmtB), chlorocyclohexane/chlorobenzene (dehH, dhaA, linC, linX, pcpC), toluene (bbsG, bbsC, bbsD, tsaC1), and several others in FN1 metagenome. In FN4 metagenome, only seven hydrocarbon degradation genes namely dmpH, mhpD, bphH, nemA and three others were detected. This study has revealed that CFMM amendment negatively impacts the structural and functional properties of the animal charcoal polluted soil. It also revealed that intrinsic bioremediation of the polluted soil could be enhanced via addition of water and aeration.

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Metagenomic Insights into the Bacterial Functions of a Diesel-Degrading Consortium for the Rhizoremediation of Diesel-Polluted Soil

Cited by 92 publications

References 77 publications

Assessing the Effect of Diesel Fuel on the Seed Viability and Germination of Medicago sativa Using the Event-Time Model

Assessing the Effect of Diesel Fuel on the Seed Viability and Germination of Medicago sativa Using the Event-Time Model

Hydrocarbon Removal by Two Differently Developed Microbial Inoculants and Comparing Their Actions with Biostimulation Treatment

Remarkable Shift In Structural And Functional Properties of An Animal Charcoal Polluted Soil Accentuated By Inorganic Nutrients Amendment

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