Biodegradation of pyrene and catabolic genes in contaminated soils cultivated with Lolium multiflorum L

Five polycyclic aromatic hydrocarbon (PAH) degrading bacterial strains, Pseudomonas putida 34, Pseudomonas fluorescens 62, Pseudomonas aeruginosa 57, Sphingomonas sp. strain 107, and the unidentified strain PL1, were isolated from two contaminated soils and characterized for specific features regarding PAH degradation. Degradation efficiency was determined by the rapidity to form clearing zones around colonies when sprayed with different PAH solutions and the growth in liquid medium with different PAHs as sole source of carbon and energy. The presence of plasmids, the production of biosurfactants, the effect of salicylate on PAH degradation, the transformation of indole to indigo indicating the presence of an aromatic ring dioxygenase activity, and the hybridization with the SphAb probe representing a sequence highly homologous to the naphthalene dioxygenase ferredoxin gene nahAb were examined. The most efficient strain in terms of substrate specificity and rapidity to degrade different PAHs was Sphingomonas sp. strain 107, followed by strain PL1 and P. aeruginosa 57. The less efficient strains were P. putida 34 and P. fluorescens 62. Each strain transformed indole to indigo, except strain PL1. Biosurfactants were produced by P. aeruginosa 57 and P. putida 34, and a bioemulsifier was produced by Sphingomonas sp. strain 107. The presence of salicylate in solid medium has accelerated the formation of clearing zones and the transformation of indole by Sphingomonas sp. strain 107 and P. aeruginosa 57 colonies. Plasmids were found in Sphingomonas sp. strain 107 and strain PL1. The SphAb probe hybridized with DNA extracted from each strain. However, hybridization signals were detected only in the plasmidic fraction of Sphingomonas sp. strain 107 and strain PL1. Using a polymerase chain reaction (PCR) approach, we determined that several genes encoding enzymes involved in the upper catabolic pathway of naphthalene were present in each strain. Sequencing of PCR DNA fragments revealed that, for all the five strains, these genes are highly homologous with respective genes found in the pah, dox, and nah opérons, and are arranged in a polycistronic operon. Results suggest that these genes are ordered in the five selected strains like the pah, nah, and dox opérons.Key words: polycyclic aromatic hydrocarbons, biodegradation, polymerase chain reaction, naphthalene catabolic genes.

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Influence of tea saponin on enhancing accessibility of pyrene and cadmium phytoremediated with Lolium multiflorum in co-contaminated soils

Environmental Science and Pollution Research ◽

10.1007/s11356-015-5784-9 ◽

2015 ◽

Vol 23 (6) ◽

pp. 5705-5711 ◽

Cited By ~ 18

Author(s):

Qian Wang ◽

Xiaoyan Liu ◽

Xinying Zhang ◽

Yunyun Hou ◽

Xiaoxin Hu ◽

...

Keyword(s):

Contaminated Soils ◽

Lolium Multiflorum ◽

Tea Saponin

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Assessment of the Number of Catabolic Genes of Oil-Contaminated Soils

Uchenye Zapiski Kazanskogo Universiteta. Seriya Estestvennye Nauki ◽

10.26907/2542-064x.2019.2.255-274 ◽

2019 ◽

Vol 161 (2) ◽

pp. 255-274

Author(s):

L.R. Biktasheva ◽

◽

A.A. Saveliev ◽

P.A. Kuryntseva ◽

S.Y. Selivanovskaya ◽

...

Keyword(s):

Contaminated Soils ◽

Catabolic Genes

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Effects of different fertilizers on growth and nutrient uptake of Lolium multiflorum grown in Cd-contaminated soils

Environmental Science and Pollution Research ◽

10.1007/s11356-017-9706-x ◽

2017 ◽

Vol 24 (29) ◽

pp. 23363-23370 ◽

Cited By ~ 6

Author(s):

Mohan Liu ◽

Yang Li ◽

Yeye Che ◽

Shaojun Deng ◽

Yan Xiao

Keyword(s):

Nutrient Uptake ◽

Contaminated Soils ◽

Lolium Multiflorum

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Effects of chelates (EDTA, EDDS, NTA) on Phytoavailability of HMs (As, Cd, Cu, Pb, Zn) using Ryegrass (Lolium multiflorum)

10.21203/rs.3.rs-521306/v1 ◽

2021 ◽

Author(s):

Ngoc Son Hai Nguyen ◽

Peter Sanderson ◽

Fangjie Qi ◽

Jianhua Du ◽

Ngoc Nong Nguyen ◽

...

Keyword(s):

Contaminated Soils ◽

Plant Biomass ◽

Ethylenediaminetetraacetic Acid ◽

Lolium Multiflorum ◽

Split Dose ◽

Mining Sites ◽

Maximum Decrease ◽

Sequential Addition ◽

Single Addition ◽

Chelate Treatment

Abstract This paper summarises a study of the application of the synthetic chelate ethylenediaminetetraacetic acid (EDTA), and the natural chelates ethylenediamine-N,N-disuccinic acid (EDDS) and nitrilotriacetate (NTA) to enhance ryegrass uptake of the heavy metal(oid)s (HMs) (As, Cd, Cu, Pb and Zn) from contaminated soils in mining sites. The study compares the effects of these chelates (EDTA, EDDS and NTA) on the phytoavailability of HMs (As, Cd, Cu, Pb, Zn) using ryegrass (Lolium multiflorum) through the single addition and sequential addition methods. The results show that application of EDTA, EDDS and NTA significantly increases ryegrass’s (Lolium multiflorum) shoot uptake of some HMs when compared with no EDTA, EDDS or NTA application, particularly through sequential chelate treatment (EDTA 0.5:1 + 0.5:1; NTA 0.5:1 + 0.5:1; EDDS 0.5:1 + 0.5:1). EDTA 0.5:1 + 0.5:1 was more effective at increasing the concentration of Pb in shoots than were the other chelates (EDDS and NTA) and controls. Moreover, the concentrations of Zn in the shoots of ryegrass in LH significantly increased with the application of split dose (0.5:1 + 0.5:1). The plants displayed symptoms of toxicity including yellow and necrotic leaves at the end of the experiment. The selected chelates (EDTA, EDDS and NTA) led to a significant decrease in plant biomass (yield) 28 days after transfer with a maximum decrease in EDTA treatment (0.5:1 + 0.5:1) soils. This decrease was 3.43-fold in HT, 3-fold in LH and 1.59-fold, respectively, relative to the control. HM concentration and dissolved organic carbon (DOC) in pore water, provided an explanation for why fresh weight was significantly reduced with application of chelates in sequential dose (EDTA 0.5:1 + 0.5:1 and NTA 0.5:1 + 0.5:1).

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Selection of Specific Endophytic Bacterial Genotypes by Plants in Response to Soil Contamination

Applied and Environmental Microbiology ◽

10.1128/aem.67.6.2469-2475.2001 ◽

2001 ◽

Vol 67 (6) ◽

pp. 2469-2475 ◽

Cited By ~ 256

Author(s):

Steven D. Siciliano ◽

Nathalie Fortin ◽

Anca Mihoc ◽

Gesine Wisse ◽

Suzanne Labelle ◽

...

Keyword(s):

Contaminated Soils ◽

Festuca Arundinacea ◽

Bulk Soil ◽

Contaminated Sites ◽

Associated Bacteria ◽

Contaminant Degradation ◽

Catabolic Genes ◽

Genes Encoding ◽

Bacterial Genotypes ◽

Selection Of

ABSTRACT Plant-bacterial combinations can increase contaminant degradation in the rhizosphere, but the role played by indigenous root-associated bacteria during plant growth in contaminated soils is unclear. The purpose of this study was to determine if plants had the ability to selectively enhance the prevalence of endophytes containing pollutant catabolic genes in unrelated environments contaminated with different pollutants. At petroleum hydrocarbon contaminated sites, two genes encoding hydrocarbon degradation, alkane monooxygenase (alkB) and naphthalene dioxygenase (ndoB), were two and four times more prevalent in bacteria extracted from the root interior (endophytic) than from the bulk soil and sediment, respectively. In field sites contaminated with nitroaromatics, two genes encoding nitrotoluene degradation, 2-nitrotoluene reductase (ntdAa) and nitrotoluene monooxygenase (ntnM), were 7 to 14 times more prevalent in endophytic bacteria. The addition of petroleum to sediment doubled the prevalence ofndoB-positive endophytes in Scirpus pungens, indicating that the numbers of endophytes containing catabolic genotypes were dependent on the presence and concentration of contaminants. Similarly, the numbers of alkB- orndoB-positive endophytes in Festuca arundinaceawere correlated with the concentration of creosote in the soil but not with the numbers of alkB- or ndoB-positive bacteria in the bulk soil. Our results indicate that the enrichment of catabolic genotypes in the root interior is both plant and contaminant dependent.

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Identification of essential β-oxidation genes and corresponding metabolites for estrogen degradation by actinobacteria

10.1101/2021.04.22.440886 ◽

2021 ◽

Author(s):

Tsun-Hsien Hsiao ◽

Tzong-Huei Lee ◽

Meng-Rong Chuang ◽

Po-Hsiang Wang ◽

Menghsiao Meng ◽

...

Keyword(s):

Mass Spectrometry ◽

Contaminated Soils ◽

Profile Analysis ◽

Cost Effective ◽

Metabolite Profile ◽

Estuarine Sediments ◽

Mass Spectrometry Analysis ◽

Time Saving ◽

Spectrometry Analysis ◽

Catabolic Genes

SummarySteroidal estrogens (C18) are contaminants receiving increasing attention due to their endocrine-disrupting activities at sub-nanomolar concentrations. Although estrogens can be eliminated through photodegradation, microbial function is critical for removing estrogens from ecosystems devoid of sunlight exposure including activated sludge, soils, and aquatic sediments. Actinobacteria were found to be key estrogen degraders in manure-contaminated soils and estuarine sediments. Previously, we used the actinobacterium Rhodococcus sp. strain B50 as a model microorganism to identify two oxygenase genes, aedA and aedB, involved in the activation and subsequent cleavage of the estrogenic A-ring, respectively. However, genes responsible for the downstream degradation of estrogen A/B-rings remained completely unknown. In this study, we employed tiered comparative transcriptomics, gene disruption experiments, and mass spectrometry–based metabolite profile analysis to identify estrogen catabolic genes. We observed the up-regulation of thiolase-encoding aedF and aedK in the transcriptome of strain B50 grown with estrone. Consistently, two downstream estrogenic metabolites, 5-oxo-4-norestrogenic acid (C17) and 2,3,4-trinorestrogenic acid (C15), were accumulated in aedF- and aedK-disrupted strain B50 cultures. Disruption of fadD3 [3aα-H-4α(3’-propanoate)-7aβ-methylhexahydro-1,5-indanedione (HIP)-coenzyme A ligase gene] in strain B50 resulted in apparent HIP accumulation in estrone-fed cultures, indicating the essential role of fadD3 in actinobacterial estrogen degradation. In addition, we detected a unique meta-cleavage product, 4,5-seco-estrogenic acid (C18), during actinobacterial estrogen degradation. Differentiating the estrogenic metabolite profile and degradation genes of actinobacteria and proteobacteria enables the cost-effective and time-saving identification of potential estrogen degraders in various ecosystems through liquid chromatography–mass spectrometry analysis and polymerase chain reaction–based functional assays.

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Mechanistic insights into the success of xenobiotic degraders resolved from metagenomes of microbial enrichment cultures

10.1101/2021.03.03.433815 ◽

2021 ◽

Author(s):

Junhui Li ◽

Chongjian Jia ◽

Qihong Lu ◽

Bruce A Hungate ◽

Paul Dijkstra ◽

...

Keyword(s):

Microbial Communities ◽

Contaminated Soils ◽

Microbial Processes ◽

Positive Interactions ◽

Ecological Strategies ◽

Catabolic Enzymes ◽

Catabolic Genes ◽

Genes Encoding ◽

Micro Organisms ◽

Xenobiotic Biodegradation

Even though microbial communities can be more effective at degrading xenobiotics than cultured micro-organisms, yet little is known about the microbial strategies that underpin xenobiotic biodegradation by microbial communities. Here, we employ metagenomic community sequencing to explore the mechanisms that drive the development of 49 xenobiotic-degrading microbial communities, which were enriched from 7 contaminated soils or sediments with a range of xenobiotic compounds. We show that multiple microbial strategies likely co-drive the development of xenobiotic degrading communities, notably (i) presence of genes encoding catabolic enzymes to degrade xenobiotics; (ii) presence of genes encoding efflux pumps; (iii) auxiliary catabolic genes on plasmids; and (iv) positive interactions dominate microbial communities with efficient degradation. Overall, the integrated analyses of microbial ecological strategies advance our understanding of microbial processes driving the biodegradation of xenobiotics and promote the design of bioremediation systems.

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