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

2001 ◽  
Vol 67 (6) ◽  
pp. 2469-2475 ◽  
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.

scholarly journals Changes in Microbial Community Composition and Function during a Polyaromatic Hydrocarbon Phytoremediation Field Trial

2003 ◽  
Vol 69 (1) ◽  
pp. 483-489 ◽  
Author(s):  
Steven D. Siciliano ◽  
James J. Germida ◽  
Kathy Banks ◽  
Charles W. Greer
Keyword(s):  
Microbial Community ◽  
Festuca Arundinacea ◽  
Rhizosphere Soil ◽  
Microbial Community Composition ◽  
Hydrocarbon Degradation ◽  
Bulk Soil ◽  
Catabolic Gene ◽  
Soil Microbial ◽  
Catabolic Genes ◽  
And Function

ABSTRACT The purpose of this study was to investigate the mechanism by which phytoremediation systems promote hydrocarbon degradation in soil. The composition and degradation capacity of the bulk soil microbial community during the phytoremediation of soil contaminated with aged hydrocarbons was assessed. In the bulk soil, the level of catabolic genes involved in hydrocarbon degradation (ndoB, alkB, and xylE) as well as the mineralization of hexadecane and phenanthrene was higher in planted treatment cells than in treatment cells with no plants. There was no detectable shift in the 16S ribosomal DNA (rDNA) composition of the bulk soil community between treatments, but there were plant-specific and -selective effects on specific catabolic gene prevalence. Tall Fescue (Festuca arundinacea) increased the prevalence of ndoB, alkB, and xylE as well as naphthalene mineralization in rhizosphere soil compared to that in bulk soil. In contrast, Rose Clover (Trifolium hirtum) decreased catabolic gene prevalence and naphthalene mineralization in rhizosphere soil. The results demonstrated that phytoremediation systems increase the catabolic potential of rhizosphere soil by altering the functional composition of the microbial community. This change in composition was not detectable by 16S rDNA but was linked to specific functional genotypes with relevance to petroleum hydrocarbon degradation.

scholarly journals Soil characteristics constrain the response of bacterial and fungal communities and hydrocarbon degradation genes to phenanthrene soil contamination and phytoremediation with poplars

2020 ◽  
Author(s):  
Sara Correa-García ◽  
Karelle Rheault ◽  
Julien Tremblay ◽  
Armand Séguin ◽  
Etienne Yergeau
Keyword(s):  
Soil Type ◽  
Contaminated Soils ◽  
Agricultural Soils ◽  
Its Region ◽  
Physicochemical Characteristics ◽  
Soil Microbial ◽  
Contaminant Degradation ◽  
Real Time Quantitative Pcr ◽  
Genes Encoding ◽  
Bacterial Genes

AbstractRhizodegradation is a promising cleanup technology where microorganisms degrade soil contaminants in the rhizosphere. A symbiotic relationship is expected to occur between plant roots and soil microorganisms in contaminated soils that enhance natural microbial degradation in soils. However, little is known about how this initial microbiota influences the rhizodegradation outcome in a context of different soil microbiotas. Recent studies have hinted that soil initial diversity has a determining effect on the outcome of contaminant degradation. To test this hypothesis, we planted (P) or not (NP) balsam poplars (Populus balsamifera) in two soils of contrasting diversity (agricultural and forest) that were contaminated or not with 50 mg kg-1 of phenanthrene (PHE). The DNA from the rhizosphere of the P and the bulk soil of the NP pots was extracted and the bacterial genes encoding for the 16S rRNA, the PAH ring-hydroxylating dioxygenase alpha subunits (PAH-RHDα) of gram-positive (GP) and gram-negative (GN) bacteria, and the fungal ITS region were sequenced to characterize the microbial communities. and the abundance of the PAH-RHDα genes were also quantified by real-time quantitative PCR. Plant presence had a significant effect on PHE degradation only in the forest soil, whereas both NP and P agricultural soils degraded the same amount of PHE. Bacterial communities were principally affected by the soil type, and upon contamination the dominant PAH degrading community was similarly constrained by soil type. Our results highlight the crucial importance of soil microbial and physicochemical characteristics in the outcome of rhizoremediation.

Mercury concentrations, redox state, and isotope ratios in consecutive water extracts of Hg(II)-chloride contaminated soils

2020 ◽  
Author(s):  
Alina Kleindienst ◽  
Lorenz Schwab ◽  
David McLagan ◽  
Stephan M. Krämer ◽  
Harald Biester ◽  
...  
Keyword(s):  
Contaminated Soils ◽  
Isotope Fractionation ◽  
Water Solubility ◽  
Solid Phase ◽  
Isotope Ratios ◽  
Water Soluble ◽  
Bulk Soil ◽  
Contaminated Sites ◽  
Water Extracts ◽  
Chloride Contaminated

<p>Mercury (Hg) leaching from contaminated soils into groundwater or surface waters represents a serious environmental problem at industrial legacy sites, whereby Hg mobility strongly depends on its chemical form. For example, the water solubility of potentially relevant Hg compounds ranges over several orders of magnitude (HgCl<sub>2</sub>>HgO>Hg<sub>2</sub>Cl<sub>2</sub>>Hg<sup>(0)</sup>>>HgS). Water leaching experiments may provide important information on Hg mobility and help assess its fate at contaminated sites. However, single extraction steps are often not sufficient to extract the entire water-soluble Hg pool. Performing multiple consecutive water extracts on the same sample allows investigating the relative importance of kinetic and thermodynamic controls on Hg mobilization. Moreover, differences between the Hg isotope composition of water extracts and the bulk soil may offer novel insights into the transformation dynamics of Hg species as well as the evolution of Hg isotope signatures at contaminated sites [1].</p><p>Here, we present results of consecutive water extractions performed on three soil samples and one artificially-contaminated aquifer material from former industrial sites in Germany contaminated with highly soluble HgCl<sub>2</sub> using three extraction solutions (oxygenated water, oxygen-depleted water, 2 mM CaCl<sub>2</sub>). Batch extractions were conducted with up to nine consecutive steps over timescales of up to three months. Aliquots of selected extracts were purged with argon to remove Hg<sup>(0)</sup> and to quantify the Hg<sup>(0)</sup>/Hg<sup>(II)</sup> ratio by comparison with unpurged extracts. Hg concentrations were measured by CV-AAS/AFS and Hg isotope ratios were determined using CV-MC-ICP-MS. Pyrolytic thermodesorption analysis was used on selected samples to investigate changes in the solid phase speciation.</p><p>Total Hg concentrations in extracts decreased after the first step (range: 17 to 1270 μg L<sup>−1</sup>) but remained surprisingly high until the ninth step (range: 3 to 263 μg L<sup>−</sup><sup>1</sup>) illustrating continuous slow Hg release from the contaminated soils in contact with water. The fraction of total soil Hg mobilized at the end of the experiments ranged from 5.6% to 30%. The extracts exhibited large δ<sup>202</sup>Hg variations from –0.75‰ to +0.94‰ relative to bulk soil indicating preferential mobilization of either light or heavy Hg isotopes for different samples and extraction conditions. Lower Hg concentrations in the purged extracts provided evidence for the presence of Hg<sup>(0)</sup> approaching its solubility in some extracts, particularly under oxygen-depleted conditions with up to 85% of total dissolved Hg, which is produced by reduction from Hg<sup>(II)</sup> in our HgCl<sub>2</sub>-contaminated samples. The isotopic mass balance between purged and unpurged extracts revealed an important control of the Hg<sup>(0)</sup>/Hg<sup>(II)</sup> ratio on δ<sup>202</sup>Hg extract values of some samples with Hg<sup>(0)</sup> being about 2‰ lighter than Hg<sup>(II)</sup>, consistent with theoretical predictions for equilibrium isotope fractionation. Our results demonstrate that consecutive water extracts can leach large amounts of Hg from contaminated soils accompanied by significant Hg isotope fractionation during the mobilization from solid to solution phase, which is at least partly controlled by equilibrium isotope effects between Hg redox states in solution.</p><p>[1] Brocza FM, Biester H, Richard J-H, Kraemer SM, Wiederhold, JG (2019) Mercury isotope fractionation in the subsurface of a Hg(II) chloride-contaminated industrial legacy site. Environ. Sci. Technol. 53, 7296-7305.</p>

scholarly journals Selection of clc, cba, andfcb Chlorobenzoate-Catabolic Genotypes from Groundwater and Surface Waters Adjacent to the Hyde Park, Niagara Falls, Chemical Landfill

1999 ◽  
Vol 65 (4) ◽  
pp. 1627-1635 ◽  
Author(s):  
Michelle C. Peel ◽  
R. Campbell Wyndham
Keyword(s):  
Surface Waters ◽  
Contaminated Sites ◽  
Carbon Source Utilization ◽  
Microb Ecol ◽  
Contaminant Exposure ◽  
Niagara Falls ◽  
Catabolic Genes ◽  
High Level ◽  
Type Strains ◽  
Selection Of

ABSTRACT The frequency of isolation of three nonhomologous chlorobenzoate catabolic genotypes (clc, cba, andfcb) was determined for 464 isolates from freshwater sediments and groundwater in the vicinity of the Hyde Park industrial landfill site in the Niagara watershed. Samples were collected from both contaminated and noncontaminated sites during spring, summer, and fall and enriched at 4, 22, or 32°C with micromolar to millimolar concentrations of chlorobenzoates and 3-chlorobiphenyl (M. C. Peel and R. C. Wyndham, Microb. Ecol: 33:59–68, 1997). Hybridization at moderate stringency to restriction-digested genomic DNA with DNA probes revealed the chlorocatechol 1,2-dioxygenase operon (clcABD), the 3-chlorobenzoate 3,4-(4,5)-dioxygenase operon (cbaABC), and the 4-chlorobenzoate dehalogenase (fcbB) gene in isolates enriched from all contaminated sites in the vicinity of the industrial landfill. Nevertheless, the known genes were found in less than 10% of the isolates from the contaminated sites, indicating a high level of genetic diversity in the microbial community. The known genotypes were not enriched from the noncontaminated control sites nearby. The clc,cba, and fcb isolates were distributed across five phenotypically distinct groups based on Biolog carbon source utilization, with the breadth of the host range decreasing in the orderclc > cba > fcb. Restriction fragment length polymorphism (RFLP) patterns showed that the cba genes were conserved in all isolates whereas the clc andfcb genes exhibited variation in RFLP patterns. These observations are consistent with the recent spread of thecba genes by horizontal transfer as part of transposon Tn5271 in response to contaminant exposure at Hyde Park. Consistent with this hypothesis, IS1071, the flanking element in Tn5271, was found in all isolates that carried the cba genes. Interestingly, IS1071 was also found in a high proportion of isolates from Hyde Park carrying theclc and fcb genes, as well as in type strains carrying the clcABD operon and the biphenyl (bph) catabolic genes.

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

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.

THE PERFORMANCE OF S170 TALL FESCUE IN CANTERBURY

1974 ◽  
pp. 214-215
Author(s):  
B.R. Watkin
Keyword(s):  
New Zealand ◽  
White Clover ◽  
Tall Fescue ◽  
Trifolium Repens ◽  
Festuca Arundinacea ◽  
Sheep Grazing ◽  
Selection Of

AN Aberystwyth selection of tall fescue (Festuca arundinacea Schreb.), known as S170, was sown with certified New Zealand white clover (Trifolium repens) and re' clover (T. pratense) and compared under sheep grazing with other grass/clover pastures at the Grasslands Division Regional Station at Lincoln (Watkin, 1975) .

scholarly journals Screening of Neutrophil Activating Factors from a Metagenome Library of Sponge-Associated Bacteria

Marine Drugs ◽  
2021 ◽  
Vol 19 (8) ◽  
pp. 427
Author(s):  
Yoshiko Okamura ◽  
Hirokazu Takahashi ◽  
Atsuyuki Shiida ◽  
Yuto Hirata ◽  
Haruko Takeyama ◽  
...  
Keyword(s):  
Immune System ◽  
Genomic Sequence ◽  
Maximum Activity ◽  
Associated Bacteria ◽  
Metagenome Library ◽  
Peptide Synthetase ◽  
Sponge Associated Bacteria ◽  
Genes Encoding ◽  
Chemotactic Factors ◽  
By Products

Marine sponge-associated bacteria are known as bio-active compound produce. We have constructed metagenome libraries of the bacteria and developed a metagenomic screening approach. Activity-based screening successfully identified novel genes and novel enzymes; however, the efficiency was only in 1 out of 104 clones. Therefore, in this study, we thought that bioinformatics could help to reduce screening efforts, and combined activity-based screening with database search. Neutrophils play an important role for the immune system to recognize excreted bacterial by-products as chemotactic factors and are recruited to infection sites to kill pathogens via phagocytosis. These excreted by-products are considered critical triggers that engage the immune system to mount a defense against infection, and identifying these factors may guide developments in medicine and diagnostics. We focused on genes encoding amino acid ligase and peptide synthetase and selected from an in-house sponge metagenome database. Cell-free culture medium of each was used in a neutrophil chemiluminescence assay in luminol reaction. The clone showing maximum activity had a genomic sequence expected to produce a molecule like a phospho-N-acetylmuramyl pentapeptide by the metagenome fragment analysis.

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

2009 ◽  
Vol 9 (5) ◽  
pp. 482-491 ◽  
Author(s):  
Sardar Khan ◽  
Abd El-Latif Hesham ◽  
Gu Qing ◽  
Liu Shuang ◽  
Jizheng He
Keyword(s):  
Contaminated Soils ◽  
Lolium Multiflorum ◽  
Catabolic Genes

scholarly journals Insights into functional and evolutionary analysis of carbaryl metabolic pathway from Pseudomonas sp. strain C5pp

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Vikas D. Trivedi ◽  
Pramod Kumar Jangir ◽  
Rakesh Sharma ◽  
Prashant S. Phale
Keyword(s):  
Draft Genome ◽  
Degradation Pathway ◽  
Evolutionary Analysis ◽  
Extradiol Dioxygenase ◽  
Transfer Event ◽  
New Family ◽  
New Genes ◽  
Catabolic Genes ◽  
Soil Isolate ◽  
Genes Encoding

Abstract Carbaryl (1-naphthyl N-methylcarbamate) is a most widely used carbamate pesticide in the agriculture field. Soil isolate, Pseudomonas sp. strain C5pp mineralizes carbaryl via 1-naphthol, salicylate and gentisate, however the genetic organization and evolutionary events of acquisition and assembly of pathway have not yet been studied. The draft genome analysis of strain C5pp reveals that the carbaryl catabolic genes are organized into three putative operons, ‘upper’, ‘middle’ and ‘lower’. The sequence and functional analysis led to identification of new genes encoding: i) hitherto unidentified 1-naphthol 2-hydroxylase, sharing a common ancestry with 2,4-dichlorophenol monooxygenase; ii) carbaryl hydrolase, a member of a new family of esterase; and iii) 1,2-dihydroxy naphthalene dioxygenase, uncharacterized type-II extradiol dioxygenase. The ‘upper’ pathway genes were present as a part of a integron while the ‘middle’ and ‘lower’ pathway genes were present as two distinct class-I composite transposons. These findings suggest the role of horizontal gene transfer event(s) in the acquisition and evolution of the carbaryl degradation pathway in strain C5pp. The study presents an example of assembly of degradation pathway for carbaryl.

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