113 results on '"Van Hamme, Jonathan"'
Search Results
2. Enzyme Catalyzed Formation of CoA Adducts of Fluorinated Hexanoic Acid Analogues using a Long-Chain acyl-CoA Synthetase from Gordonia sp. Strain NB4-1Y.
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Mothersole, Robert G., Mothersole, Mina K., Goddard, Hannah G., Jinxia Liu, and Van Hamme, Jonathan D.
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- 2024
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3. Biotechnological approaches in agriculture and environmental management - bacterium Kocuria rhizophila 14ASP as heavy metal and salt- tolerant plant growth- promoting strain
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Afridi, Muhammad Siddique, Van Hamme, Jonathan d., Bundschuh, Jochen, Sumaira, Khan, Muhammad Nadeem, Salam, Abdul, Waqar, Muhammad, Munis, Muhammad Farooq Hussain, and Chaudhary, Hassan Javed
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- 2021
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4. Transcriptomic response of Gordonia sp. strain NB4-1Y when provided with 6:2 fluorotelomer sulfonamidoalkyl betaine or 6:2 fluorotelomer sulfonate as sole sulfur source
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Bottos, Eric M., AL-shabib, Ebtihal Y., Shaw, Dayton M. J., McAmmond, Breanne M., Sharma, Aditi, Suchan, Danae M., Cameron, Andrew D. S., and Van Hamme, Jonathan D.
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- 2020
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5. Testing microbial pathogens as a cause of early juvenile mortality in wild populations of benthic invertebrates
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Sandee, Samantha D., Van Hamme, Jonathan D., and Gosselin, Louis A.
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- 2016
6. Insights into the κ/ι-carrageenan metabolism pathway of some marine Pseudoalteromonas species
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Hettle, Andrew G., Hobbs, Joanne K., Pluvinage, Benjamin, Vickers, Chelsea, Abe, Kento T., Salama-Alber, Orly, McGuire, Bailey E., Hehemann, Jan-Hendrik, Hui, Joseph P. M., Berrue, Fabrice, Banskota, Arjun, Zhang, Junzeng, Bottos, Eric M., Van Hamme, Jonathan, and Boraston, Alisdair B.
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- 2019
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7. Female mountain bluebirds (Sialia currucoides) paired to more colourful males produce male-biased broods
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Bonderud, Erica S., Flood, Nancy J., Van Hamme, Jonathan D., Boyda, Cameron A. W., and Reudink, Matthew W.
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- 2016
8. First high-quality draft genome of Ochrobactrum haematophilum P6BS-III, a highly glyphosate-tolerant strain isolated from agricultural soil in Argentina
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Massot, Francisco, Gkorezis, Panagiotis, McAmmond, Breanne, d’Haen, Jan, Van Hamme, Jonathan, Merini, Luciano J., Vangronsveld, Jaco, and Thijs, Sofie
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- 2019
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9. Formation of CoA Adducts of Short-Chain Fluorinated Carboxylates Catalyzed by Acyl-CoA Synthetase from Gordonia sp. Strain NB4-1Y.
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Mothersole, Robert G., Wynne, Foster T., Rota, Gaia, Mothersole, Mina K., Liu, Jinxia, and Van Hamme, Jonathan D.
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- 2023
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10. Correspondence on "Defluorination of Perfluorooctanoic Acid (PFOA) and Perfluorooctane Sulfonate (PFOS) by Acidimicrobium sp. Strain A6".
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Liu, Jinxia, Edwards, Elizabeth, Van Hamme, Jonathan, Manefield, Mike, Higgins, Christopher P., Blotevogel, Jens, Liu, Jinyong, and Lee, Linda S.
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- 2023
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11. High Persistence of Novel Polyfluoroalkyl Betaines in Aerobic Soils.
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Liu, Min, Munoz, Gabriel, Hermiston, Juliana, Zhang, Ju, Vo Duy, Sung, Wang, Dan, Sundar Dey, Anindya, Bottos, Eric M., Van Hamme, Jonathan D., Lee, Linda S., Sauvé, Sébastien, and Liu, Jinxia
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- 2023
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12. Accumulation of Black Carbon Particles in Placenta, Cord Blood, and Childhood Urine in Association with the Intestinal Microbiome Diversity and Composition in Four- to Six-Year-Old Children in the ENVIRONAGE Birth Cohort.
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Van Pee, Thessa, Hogervorst, Janneke, Dockx, Yinthe, Witters, Katrien, Thijs, Sofie, Congrong Wang, Bongaerts, Eva, Van Hamme, Jonathan D., Vangronsveld, Jaco, Ameloot, Marcel, Raes, Jeroen, and Nawrot, Tim S.
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RNA analysis ,FECAL analysis ,CARBON analysis ,AIR pollution ,PARTICULATE matter ,STATISTICS ,LIFESTYLES ,MOTHERS ,CONFIDENCE intervals ,SEQUENCE analysis ,GUT microbiome ,MULTIVARIATE analysis ,MULTIPLE regression analysis ,PRENATAL exposure delayed effects ,CORD blood ,SOCIOECONOMIC factors ,ENVIRONMENTAL health ,PLACENTA ,RESEARCH funding ,DESCRIPTIVE statistics ,URINALYSIS ,DATA analysis software ,DATA analysis ,PREGNANCY - Abstract
BACKGROUND: The gut microbiome plays an essential role in human health. Despite the link between air pollution exposure and various diseases, its association with the gut microbiome during susceptible life periods remains scarce. OBJECTIVES: In this study, we examined the association between black carbon particles quantified in prenatal and postnatal biological matrices and bacterial richness and diversity measures, and bacterial families. METHODS: A total of 85 stool samples were collected from 4- to 6-y-old children enrolled in the ENVIRonmental influence ON early AGEing birth cohort. We performed 16S rRNA gene sequencing to calculate bacterial richness and diversity indices (Chao1 richness, Shannon diversity, and Simpson diversity) and the relative abundance of bacterial families. Black carbon particles were quantified via white light generation under femtosecond pulsed laser illumination in placental tissue and cord blood, employed as prenatal exposure biomarkers, and in urine, used as a post-natal exposure biomarker. We used robust multivariable-adjusted linear models to examine the associations between quantified black carbon loads and measures of richness (Chao1 index) and diversity (Shannon and Simpson indices), adjusting for parity, season of delivery, sequencing batch, age, sex, weight and height of the child, and maternal education. Additionally, we performed a differential relative abundance analysis of bacterial families with a correction for sampling fraction bias. Results are expressed as percentage difference for a doubling in black carbon loads with 95% confidence interval (CI). RESULTS: Two diversity indices were negatively associated with placental black carbon [Shannon: -4.38% (95% CI: -8.31%, -0.28%); Simpson: -0.90% (95% CI: -1.76%, -0.04%)], cord blood black carbon [Shannon: -3.38% (95% CI: -5.66%, -0:84%); Simpson: -0.91 (95% CI: -1.66%, -0.16%)], and urinary black carbon [Shannon: -3.39% (95% CI: -5.77%, -0.94%); Simpson: -0.89% (95% CI: -1.37%, -0.40%)]. The explained variance of black carbon on the above indices varied from 6.1% to 16.6%. No statistically significant associations were found between black carbon load and the Chao1 richness index. After multiple testing correction, placental black carbon was negatively associated with relative abundance of the bacterial families Defluviitaleaceae and Marinifilaceae, and urinary black carbon with Christensenellaceae and Coriobacteriaceae; associations with cord blood black carbon were not statistically significant after correction. CONCLUSION: Black carbon particles quantified in prenatal and postnatal biological matrices were associated with the composition and diversity of the childhood intestinal microbiome. These findings address the influential role of exposure to air pollution during pregnancy and early life in human health. [ABSTRACT FROM AUTHOR]
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- 2023
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13. Impacts from Topsoil Stockpile Height on Soil Geochemical Properties in Two Mining Operations in British Columbia: Implications for Restoration Practices.
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Fischer, Ashley M., Van Hamme, Jonathan D., Gardner, Wendy C., and Fraser, Lauchlan H.
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TOPSOIL ,GEOCHEMICAL modeling ,SOIL quality ,GEOCHEMISTRY ,GOLD mining - Abstract
Mining activities are often severely disruptive to the landscape, and a major barrier to reclamation after mining is lack of quality topsoil. This research addresses knowledge gaps in the industry by exploring the compositional nature of topsoil stockpiles and their ability to facilitate post-mining revegetation after long-term storage. To do this, we conducted an extensive profile characterization of two topsoil stockpiles at two mining operations in the interior of British Columbia, where soil geochemical properties were investigated. Both stockpiles showed reduced soil quality and significant changes compared to reference soils. Importantly, there was an accumulation of metals and a reduction in soil nutrients with increasing stockpile depth in one or both stockpiles. These results highlight the important influence of topsoil-stockpile height on soil geochemical properties, which ultimately influences the success of restoration. This research provides insights into the response of soil geochemistry across a depth gradient in severely disturbed mining soils. [ABSTRACT FROM AUTHOR]
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- 2022
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14. Analysis of bacterial communities associated with Mountain Chickadees (Poecile gambeli) across urban and rural habitats.
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Stephens, Colton R.A., McAmmond, Breanne M., Van Hamme, Jonathan D., Otter, Ken A., Reudink, Matthew W., and Bottos, Eric M.
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HABITATS ,CHICKADEES ,MICROBIAL communities ,BACTERIAL communities ,URBAN animals ,PHYLA (Genus) ,URBANIZATION - Abstract
Copyright of Canadian Journal of Microbiology is the property of Canadian Science Publishing and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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- 2021
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15. Community dynamics of a mixed-bacterial culture growing on petroleum hydrocarbons in batch culture
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Ward, Owen P, Van Hamme, Jonathan D, and Odumeru, Joseph A
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- 2000
16. Correlation of Breed, Growth Performance, and Rumen Microbiota in Two Rustic Cattle Breeds Reared Under Different Conditions.
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Daghio, Matteo, Ciucci, Francesca, Buccioni, Arianna, Cappucci, Alice, Casarosa, Laura, Serra, Andrea, Conte, Giuseppe, Viti, Carlo, McAmmond, Breanne M., Van Hamme, Jonathan D., and Mele, Marcello
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CATTLE breeding ,CATTLE breeds ,WEIGHT gain ,BACTERIAL communities ,RUMEN microbiology ,GRAZING ,CATTLE ,RUMEN (Ruminants) - Abstract
The use of rustic cattle is desirable to face challenges brought on by climate change. Maremmana (MA) and Aubrac (AU) are rustic cattle breeds that can be successfully used for sustainable production. In this study, correlations between two rearing systems (feedlot and grazing) and the rumen microbiota, the lipid composition of rumen liquor (RL), and the growth performance of MA and AU steers were investigated. Bacterial community composition was characterized by high-throughput sequencing of 16S rRNA gene amplicons, and the RL lipid composition was determined by measuring fatty acid (FA) and the dimethyl acetal profiles. The main factor influencing bacterial community composition was the cattle breed. Some bacterial groups were positively correlated to average daily weight gain for the two breeds (i.e., Rikenellaceae RC9 gut group, Fibrobacter and Succiniclasticum in the rumen of MA steers, and Succinivibrionaceae UCG-002 in the rumen of AU steers); despite this, animal performance appeared to be influenced by short chain FAs production pathways and by the presence of H
2 sinks that divert the H2 to processes alternative to the methanogenesis. [ABSTRACT FROM AUTHOR]- Published
- 2021
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17. Isolation, Biochemical and Genomic Characterization of Glyphosate Tolerant Bacteria to Perform Microbe-Assisted Phytoremediation.
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Massot, Francisco, Gkorezis, Panagiotis, Van Hamme, Jonathan, Marino, Damian, Trifunovic, Bojana Spirovic, Vukovic, Gorica, d'Haen, Jan, Pintelon, Isabel, Giulietti, Ana María, Merini, Luciano, Vangronsveld, Jaco, and Thijs, Sofie
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GLYPHOSATE ,PHYTOREMEDIATION ,ENDOPHYTIC bacteria ,LOTUS corniculatus ,SOIL pollution ,NUCLEOTIDE sequencing ,HERBICIDES ,RHIZOBIUM - Abstract
The large-scale use of the herbicide glyphosate leads to growing ecotoxicological and human health concerns. Microbe-assisted phytoremediation arises as a good option to remove, contain, or degrade glyphosate from soils and waterbodies, and thus avoid further spreading to non-target areas. To achieve this, availability of plant-colonizing, glyphosate-tolerant and -degrading strains is required and at the same time, it must be linked to plant-microorganism interaction studies focusing on a substantive ability to colonize the roots and degrade or transform the herbicide. In this work, we isolated bacteria from a chronically glyphosate-exposed site in Argentina, evaluated their glyphosate tolerance using the minimum inhibitory concentration assay, their in vitro degradation potential, their plant growth-promotion traits, and performed whole genome sequencing to gain insight into the application of a phytoremediation strategy to remediate glyphosate contaminated agronomic soils. Twenty-four soil and root-associated bacterial strains were isolated. Sixteen could grow using glyphosate as the sole source of phosphorous. As shown in MIC assay, some strains tolerated up to 10000 mg kg
–1 of glyphosate. Most of them also demonstrated a diverse spectrum of in vitro plant growth-promotion traits, confirmed in their genome sequences. Two representative isolates were studied for their root colonization. An isolate of Ochrobactrum haematophilum exhibited different colonization patterns in the rhizoplane compared to an isolate of Rhizobium sp. Both strains were able to metabolize almost 50% of the original glyphosate concentration of 50 mg l–1 in 9 days. In a microcosms experiment with Lotus corniculatus L, O. haematophilum performed better than Rhizobium , with 97% of glyphosate transformed after 20 days. The results suggest that L. corniculatus in combination with to O. haematophilum can be adopted for phytoremediation of glyphosate on agricultural soils. An effective strategy is presented of linking the experimental data from the isolation of tolerant bacteria with performing plant-bacteria interaction tests to demonstrate positive effects on the removal of glyphosate from soils. [ABSTRACT FROM AUTHOR]- Published
- 2021
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18. Erratum: Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range
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Henderson, Gemma, Cox, Faith, Ganesh, Siva, Jonker, Arjan, Young, Wayne, Abecia, Leticia, Angarita, Erika, Aravena, Paula, Nora Arenas, Graciela, Ariza, Claudia, Attwood, Graeme T., Mauricio Avila, Jose, Avila-stagno, Jorge, Bannink, André, Barahona, Rolando, Batistotti, Mariano, Bertelsen, Mads F., Brown-Kav, Aya, Carvajal, Andres M., Cersosimo, Laura, Vieira Chaves, Alexandre, Church, John, Clipson, Nicholas, Cobos-peralta, Mario A., Cookson, Adrian L., Cravero, Silvio, Cristobal Carballo, Omar, Crosley, Katie, Cruz, Gustavo, Cerón Cucchi, María, de la Barra, Rodrigo, de Menezes, Alexandre B., Detmann, Edenio, Dieho, Kasper, Dijkstra, Jan, Dos Reis, William L.S., Dugan, Mike E.R., Hadi Ebrahimi, Seyed, Eythórsdóttir, Emma, Nde Fon, Fabian, Fraga, Martín, Franco, Francisco, Friedeman, Chris, Fukuma, Naoki, Gagić, Dragana, Gangnat, Isabelle, Javier Grilli, Diego, Guan, Le Luo, Heidarian Miri, Vahideh, Hernandez-Sanabria, Emma, Gomez, Alma Ximena Ibarra, Isah, Olubukola A., Ishaq, Suzanne, Jami, Elie, Jelincic, Juan, Kantanen, Juha, Kelly, William J., Kim, Seon-Ho, Klieve, Athol, Kobayashi, Yasuo, Koike, Satoshi, Kopecny, Jan, Nygaard Kristensen, Torsten, Julie Krizsan, Sophie, Lachance, Hannah, Lachman, Medora, Lamberson, William R., Lambie, Suzanne, Lassen, Jan, Leahy, Sinead C., Lee, Sang-Suk, Leiber, Florian, Lewis, Eva, Lin, Bo, Lira, Raúl, Lund, Peter, Macipe, Edgar, Mamuad, Lovelia L., Cuquetto Mantovani, Hilário, Marcoppido, Gisela Ariana, Márquez, Cristian, Martin, Cécile, Martinez, Gonzalo, Eugenia Martinez, Maria, Lucía Mayorga, Olga, McAllister, Tim A., McSweeney, Chris, Mestre, Lorena, Minnee, Elena, Mitsumori, Makoto, Mizrahi, Itzhak, Molina, Isabel, Muenger, Andreas, Muñoz, Camila, Murovec, Bostjan, Newbold, John, Nsereko, Victor, O’donovan, Michael, Okunade, Sunday, O’neill, Brendan, Ospina, Sonia, Ouwerkerk, Diane, Parra, Diana, Pereira, Luiz Gustavo Ribeiro, Pinares-patiño, Cesar, Pope, Phil B., Poulsen, Morten, Rodehutscord, Markus, Rodriguez, Tatiana, Saito, Kunihiko, Sales, Francisco, Sauer, Catherine, Shingfield, Kevin, Shoji, Noriaki, Simunek, Jiri, Stojanović-Radić, Zorica, Stres, Blaz, Sun, Xuezhao, Swartz, Jeffery, Liang Tan, Zhi, Tapio, Ilma, Taxis, Tasia M., Tomkins, Nigel, Ungerfeld, Emilio, Valizadeh, Reza, van Adrichem, Peter, van Hamme, Jonathan, van Hoven, Woulter, Waghorn, Garry, Wallace, John R., Wang, Min, Waters, Sinéad M., Keogh, Kate, Witzig, Maren, Wright, Andre-Denis G., Yamano, Hidehisa, Yan, Tianhai, Yáñez-ruiz, David R., Yeoman, Carl J., Zambrano, Ricardo, Zeitz, Johanna, Zhou, Mi, Wei Zhou, Hua, Xia Zou, Cai, Zunino, Pablo, and Janssen, Peter H.
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Multidisciplinary ,Animal Nutrition ,WIAS ,Life Science ,Laboratorium voor Plantenfysiologie ,Diervoeding ,Laboratory of Plant Physiology - Abstract
Ruminant livestock are important sources of human food and global greenhouse gas emissions. Feed degradation and methane formation by ruminants rely on metabolic interactions between rumen microbes and affect ruminant productivity. Rumen and camelid foregut microbial community composition was determined in 742 samples from 32 animal species and 35 countries, to estimate if this was influenced by diet, host species, or geography. Similar bacteria and archaea dominated in nearly all samples, while protozoal communities were more variable. The dominant bacteria are poorly characterised, but the methanogenic archaea are better known and highly conserved across the world. This universality and limited diversity could make it possible to mitigate methane emissions by developing strategies that target the few dominant methanogens. Differences in microbial community compositions were predominantly attributable to diet, with the host being less influential. There were few strong co-occurrence patterns between microbes, suggesting that major metabolic interactions are non-selective rather than specific.
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- 2016
19. The Interaction between Plants and Bacteria in the Remediation of Petroleum Hydrocarbons: An Environmental Perspective
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Gkorezis, Panagiotis, Daghio, Matte, Franzetti, Andrea, Van Hamme, Jonathan D., Sillen, Wouter, and Vangronsveld, Jaco
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phytoremediation ,bioremediation ,remediation ,petroleum hydrocarbons ,plant-bacteria assisted remediation ,plant–bacteria assisted remediation - Abstract
Widespread pollution of terrestrial ecosystems with petroleum hydrocarbons (PHGs) has generated a need for remediation and, given that many PHCs are biodegradable, bio- and phyto-remediation are often viable approaches for active and passive remediation. This review focuses on phytoremediation with particular interest on the interactions between and use of plant-associated bacteria to restore PHC polluted sites. Plant-associated bacteria include endophytic, phyllospheric, and rhizospheric bacteria, and cooperation between these bacteria and their host plants allows for greater plant survivability and treatment outcomes in contaminated sites. Bacterially driven PHC bioremediation is attributed to the presence of diverse suites of metabolic genes for aliphatic and aromatic hydrocarbons, along with a broader suite of physiological properties including biosurfactant production, biofilm formation, chemotaxis to hydrocarbons, and flexibility in cell-surface hydrophobicity. In soils impacted by PHC contamination, microbial bioremediation generally relies on the addition of high-energy electron acceptors (e.g., oxygen) and fertilization to supply limiting nutrients (e.g., nitrogen, phosphorous, potassium) in the face of excess PHC carbon. As an alternative, the addition of plants can greatly improve bioremediation rates and outcomes as plants provide microbial habitats, improve soil porosity (thereby increasing mass transfer of substrates and electron acceptors), and exchange limiting nutrients with their microbial counterparts. In return, plant-associated microorganisms improve plant growth by reducing soil toxicity through contaminant removal, producing plant growth promoting metabolites, liberating sequestered plant nutrients from soil, fixing nitrogen, and more generally establishing the foundations of soil nutrient cycling. In a practical and applied sense, the collective action of plants and their associated microorganisms is advantageous for remediation of PHC contaminated soil in terms of overall cost and success rates for in situ implementation in a diversity of environments. Mechanistically, there remain biological unknowns that present challenges for applying bio- and phyto-remediation technologies without having a deep prior understanding of individual target sites. In this review, evidence from traditional and modern omics technologies is discussed to provide a framework for plant microbe interactions during PHC remediation. The potential for integrating multiple molecular and computational techniques to evaluate linkages between microbial communities, plant communities and ecosystem processes is explored with an eye on improving phytoremediation of PHC contaminated sites. This work was supported by the Hasselt University BOF project 06G02 and the Methusalem project 08M03VGRJ.
- Published
- 2016
20. Use of a novel fluorinated organosulfur compound to isolate bacteria capable of carbon-sulfur bond cleavage
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Van Hamme, Jonathan D., Fedorak, Phillip, M., Foght, Julia M., Gray, Murray R., and Dettman, Heather D.
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Viscosity -- Research ,Organosulfur compounds -- Properties ,Organosulfur compounds -- Research ,Biological sciences - Abstract
The vacuum residue fraction of heavy crudes contributes to the viscosity of these oils. Screening for microbes that can perform this activity is greatly facilitated by the use of newly synthesized compound, bis- (3- pentafluorophenylpropyl)-sulfide (PFPS), as a novel sulfur source.
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- 2004
21. The Sycamore Maple Bacterial Culture Collection From a TNT Polluted Site Shows Novel Plant-Growth Promoting and Explosives Degrading Bacteria.
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Thijs, Sofie, Sillen, Wouter, Truyens, Sascha, Beckers, Bram, van Hamme, Jonathan, van Dillewijn, Pieter, Samyn, Pieter, Carleer, Robert, Weyens, Nele, and Vangronsveld, Jaco
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ACER pseudoplatanus ,RHIZOSPHERE ,TNT (Chemical) ,PHYTOREMEDIATION ,BIOREMEDIATION - Abstract
Military activities have worldwide introduced toxic explosives into the environment with considerable effects on soil and plant-associated microbiota. Fortunately, these microorganisms, and their collective metabolic activities, can be harnessed for site restoration via in situ phytoremediation. We characterized the bacterial communities inhabiting the bulk soil and rhizosphere of sycamore maple (Acer pseudoplatanus) in two chronically 2,4,6-trinitrotoluene (TNT) polluted soils. Three hundred strains were isolated, purified and characterized, a majority of which showed multiple plant growth promoting (PGP) traits. Several isolates showed high nitroreductase enzyme activity and concurrent TNT-transformation. A 12-member bacterial consortium, comprising selected TNT-detoxifying and rhizobacterial strains, significantly enhanced TNT removal from soil compared to non-inoculated plants, increased root and shoot weight, and the plants were less stressed than the un-inoculated plants as estimated by the responses of antioxidative enzymes. The sycamore maple tree (SYCAM) culture collection is a significant resource of plant-associated strains with multiple PGP and catalytic properties, available for further genetic and phenotypic discovery and use in field applications. [ABSTRACT FROM AUTHOR]
- Published
- 2018
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22. Short-term microbial effects of a large-scale mine-tailing storage facility collapse on the local natural environment.
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Garris, Heath W., Baldwin, Susan A., Taylor, Jon, Gurr, David B., Denesiuk, Daniel R., Van Hamme, Jonathan D., and Fraser, Lauchlan H.
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MICROBIAL communities ,METAL tailings ,RIPARIAN ecology ,COMMUNITY organization ,ENVIRONMENTAL monitoring - Abstract
We investigated the impacts of the Mount Polley tailings impoundment failure on chemical, physical, and microbial properties of substrates within the affected watershed, comprised of 70 hectares of riparian wetlands and 40 km of stream and lake shore. We established a biomonitoring network in October of 2014, two months following the disturbance, and evaluated riparian and wetland substrates for microbial community composition and function via 16S and full metagenome sequencing. A total of 234 samples were collected from substrates at 3 depths and 1,650,752 sequences were recorded in a geodatabase framework. These data revealed a wealth of information regarding watershed-scale distribution of microbial community members, as well as community composition, structure, and response to disturbance. Substrates associated with the impact zone were distinct chemically as indicated by elevated pH, nitrate, and sulphate. The microbial community exhibited elevated metabolic capacity for selenate and sulfate reduction and an abundance of chemolithoautotrophs in the Thiobacillus thiophilus/T. denitrificans/T. thioparus clade that may contribute to nitrate attenuation within the affected watershed. The most impacted area (a 6 km stream connecting two lakes) exhibited 30% lower microbial diversity relative to the remaining sites. The tailings impoundment failure at Mount Polley Mine has provided a unique opportunity to evaluate functional and compositional diversity soon after a major catastrophic disturbance to assess metabolic potential for ecosystem recovery. [ABSTRACT FROM AUTHOR]
- Published
- 2018
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23. Seed Endophyte Microbiome of Crotalaria pumila Unpeeled: Identification of Plant-Beneficial Methylobacteria.
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Sánchez-López, Ariadna S., Pintelon, Isabel, Stevens, Vincent, Imperato, Valeria, Timmermans, Jean-Pierre, González-Chávez, Carmen, Carrillo-González, Rogelio, Van Hamme, Jonathan, Vangronsveld, Jaco, and Thijs, Sofie
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CROTALARIA ,HEAVY-metal tolerant plants ,METHYLOBACTERIUM ,SOIL pollution ,SOIL composition ,HEAVY metals - Abstract
Metal contaminated soils are increasing worldwide. Metal-tolerant plants growing on metalliferous soils are fascinating genetic and microbial resources. Seeds can vertically transmit endophytic microorganisms that can assist next generations to cope with environmental stresses, through yet poorly understood mechanisms. The aims of this study were to identify the core seed endophyte microbiome of the pioneer metallophyte Crotalaria pumila throughout three generations, and to better understand the plant colonisation of the seed endophyte Methylobacterium sp. Cp3. Strain Cp3 was detected in C. pumila seeds across three successive generations and showed the most dominant community member. When inoculated in the soil at the time of flowering, strain Cp3 migrated from soil to seeds. Using confocal microscopy, Cp3-mCherry was demonstrated to colonise the root cortex cells and xylem vessels of the stem under metal stress. Moreover, strain Cp3 showed genetic and in planta potential to promote seed germination and seedling development. We revealed, for the first time, that the seed microbiome of a pioneer plant growing in its natural environment, and the colonisation behaviour of an important plant growth promoting systemic seed endophyte. Future characterization of seed microbiota will lead to a better understanding of their functional contribution and the potential use for seed-fortification applications. [ABSTRACT FROM AUTHOR]
- Published
- 2018
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24. Characterization and degradation potential of diesel-degrading bacterial strains for application in bioremediation.
- Author
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Balseiro-Romero, María, Gkorezis, Panagiotis, Kidd, Petra S., Van Hamme, Jonathan, Weyens, Nele, Monterroso, Carmen, and Vangronsveld, Jaco
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BIOREMEDIATION ,SOIL pollution ,EMISSIONS (Air pollution) ,DIESEL fuels ,HYDROCARBONS ,ACINETOBACTER infections - Abstract
Bioremediation of polluted soils is a promising technique with low environmental impact, which uses soil organisms to degrade soil contaminants. In this study, 19 bacterial strains isolated from a diesel-contaminated soil were screened for their diesel-degrading potential, biosurfactant (BS) production, and biofilm formation abilities, all desirable characteristics when selecting strains for re-inoculation into hydrocarbon-contaminated soils. Diesel-degradation rates were determinedin vitroin minimal medium with diesel as the sole carbon source. The capacity to degrade diesel range organics (DROs) of strains SPG23 (Arthobactersp.) and PF1 (Acinetobacter oleivorans) reached 17–26% of total DROs after 10 days, and 90% for strain GK2 (Acinetobacter calcoaceticus). The amount and rate of alkane degradation decreased significantly with increasing carbon number for strains SPG23 and PF1. Strain GK2, which produced BSs and biofilms, exhibited a greater extent, and faster rate of alkane degradation compared to SPG23 and PF1. Based on the outcomes of degradation experiments, in addition to BS production, biofilm formation capacities, and previous genome characterizations, strain GK2 is a promising candidate for microbial-assisted phytoremediation of diesel-contaminated soils. These results are of particular interest to select suitable strains for bioremediation, not only presenting high diesel-degradation rates, but also other characteristics which could improve rhizosphere colonization. [ABSTRACT FROM PUBLISHER]
- Published
- 2017
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25. Editorial: Petroleum Microbial Biotechnology: Challenges and Prospects.
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Ismai, Wael A., Van Hamme, Jonathan D., Kilbane, John J., and Ji-Dong Gu
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MICROBIAL biotechnology ,BIODEGRADATION of petroleum - Published
- 2017
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26. Comparative Evaluation of Four Bacteria-Specific Primer Pairs for 16S rRNA Gene Surveys.
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Thijs, Sofie, De Beeck, Michiel Op, Beckers, Bram, Truyens, Sascha, Stevens, Vincent, Van Hamme, Jonathan D., Weyens, Nele, and Vangronsveld, Jaco
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RIBOSOMAL RNA ,POLYMERASE chain reaction - Abstract
Bacterial taxonomic community analyses using PCR-amplification of the 16S rRNA gene and high-throughput sequencing has become a cornerstone in microbiology research. To reliably detect the members, or operational taxonomic units (OTUs), that make up bacterial communities, taxonomic surveys rely on the use of the most informative PCR primers to amplify the broad range of phylotypes present in up-to-date reference databases. However, primers specific for the domain Bacteria were often developed some time ago against database versions that are now out of date. Here we evaluated the performance of four bacterial primers for characterizing complex microbial communities in explosives contaminated and non-contaminated forest soil and by in silico evaluation against the current SILVA123 database. Primer pair 341f/785r produced the highest number of bacterial OTUs, phylogenetic richness, Shannon diversity, low non-specificity and most reproducible results, followed by 967f/1391r and 799f/1193r. Primer pair 68f/518r showed overall low coverage and a bias toward Alphaproteobacteria. In silico, primer pair 341f/785r showed the highest coverage of the domain Bacteria (96.1%) with no obvious bias toward the majority of bacterial species. This suggests the high utility of primer pair 341f/785r for soil and plant-associated bacterial microbiome studies. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
27. Fatty acid profile of British Columbia suckler beef.
- Author
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Turner, Tyler D., Hartling, Ivan, Jensen, Jessica, Pilfold, Jessica L., Prema, Dipesh, Van Hamme, Jonathan D., Cinel, Bruno, Donkor, Kingsley K., Church, John S., and Plaizier, J.
- Subjects
FATTY acid content of beef ,GRASSES as feed ,UNSATURATED fatty acids ,GRAIN as feed ,FATTY acid content of milk - Abstract
Copyright of Canadian Journal of Animal Science is the property of Canadian Science Publishing and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
- Published
- 2016
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28. Genomics to assist mine reclamation: a review.
- Author
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Garris, Heath W., Baldwin, Susan A., Van Hamme, Jonathan D., Gardner, Wendy C., and Fraser, Lauchlan H.
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MINES & mineral resources ,GENOMICS ,RECLAMATION of land ,ECOSYSTEMS ,ECOSYSTEM services ,NUCLEOTIDE sequencing - Abstract
Mine reclamation succeeds when healthy, self-sustaining ecosystems develop on previously mined lands. Regulations require reclamation of ecosystem services; however, there are few specified targets, and those that are presented are vague. Sequencing genomic DNA and transcribed RNA from environmental samples may provide critical supportive information for attempts to recreate ecosystem functions from the ground up on disturbed lands. In this review, we highlight the use of genomics to meet mine closure goals, to enhance ecosystem development, and to optimize ecosystem services inherent in self-sustaining reclaimed ecosystems. We address the development of environmental genomics-sequencing and analysis of environmentally derived DNA-to characterize microbial communities on mine sites. We then provide four areas where genomics has proven instrumental for informing management and assisting in reclamation of mine sites in the form of bioreactors, passive treatment systems, novel gene discovery, and DNA barcoding. Finally, we describe how recently developed techniques have transferable value to mine reclamation and provide evidence for future applications of genomics and the necessary steps to integrate these data into comprehensive management of mined sites. [ABSTRACT FROM AUTHOR]
- Published
- 2016
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29. Subsurface Petroleum Microbiology.
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Singh, Ajay, Van Hamme, Jonathan D., Kuhad, Ramesh C., Parmar, Nagina, and Ward, Owen P.
- Published
- 2014
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30. Surfactants in microbiology and biotechnology: Part 2. Application aspects
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Singh, Ajay, Van Hamme, Jonathan D., and Ward, Owen P.
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- *
SURFACE active agents , *BIOSURFACTANTS , *BIOREMEDIATION , *MICROBIOLOGY - Abstract
Abstract: Surfactants are amphiphilic compounds which can reduce surface and interfacial tensions by accumulating at the interface of immiscible fluids and increase the solubility, mobility, bioavailability and subsequent biodegradation of hydrophobic or insoluble organic compounds. Chemically synthesized surfactants are commonly used in the petroleum, food and pharmaceutical industries as emulsifiers and wetting agents. Biosurfactants produced by some microorganisms are becoming important biotechnology products for industrial and medical applications due to their specific modes of action, low toxicity, relative ease of preparation and widespread applicability. They can be used as emulsifiers, de-emulsifiers, wetting and foaming agents, functional food ingredients and as detergents in petroleum, petrochemicals, environmental management, agrochemicals, foods and beverages, cosmetics and pharmaceuticals, and in the mining and metallurgical industries. Addition of a surfactant of chemical or biological origin accelerates or sometimes inhibits the bioremediation of pollutants. Surfactants also play an important role in enhanced oil recovery by increasing the apparent solubility of petroleum components and effectively reducing the interfacial tensions of oil and water in situ. However, the effects of surfactants on bioremediation cannot be predicted in the absence of empirical evidence because surfactants sometimes stimulate bioremediation and sometimes inhibit it. For medical applications, biosurfactants are useful as antimicrobial agents and immunomodulatory molecules. Beneficial applications of chemical surfactants and biosurfactants in various industries are discussed in this review. [Copyright &y& Elsevier]
- Published
- 2007
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31. Physiological aspects: Part 1 in a series of papers devoted to surfactants in microbiology and biotechnology
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Van Hamme, Jonathan D., Singh, Ajay, and Ward, Owen P.
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- *
MICROBIOLOGY , *BIOTECHNOLOGY , *BIOSURFACTANTS , *BIOAVAILABILITY - Abstract
Abstract: Surfactants, both chemical and biological, are amphiphilic compounds which can reduce surface and interfacial tensions by accumulating at the interface of immiscible fluids and increase the solubility, mobility, bioavailability and subsequent biodegradation of hydrophobic or insoluble organic compounds. Investigations on their impacts on microbial activity have generally been limited in scope to the most common and best characterized surfactants. Recently a number of new biosurfactants have been described and accelerated advances in molecular and cellular biology are expected to expand our insights into the diversity of structures and applications of biosurfactants. Biosurfactants play an essential natural role in the swarming motility of microorganisms and participate in cellular physiological processes of signaling and differentiation as well as in biofilm formation. Biosurfactants also exhibit natural physiological roles in increasing bioavailability of hydrophobic molecules and can complex with heavy metals, and some also possess antimicrobial activity. Chemical- and indeed bio-surfactants may also be added exogenously to microbial systems to influence behaviour and/or activity, mimicking the latter effects of biosurfactants. They have been exploited in this way, for example as antimicrobial agents in disease control and to improve degradation of chemical contaminants. Chemical surfactants can interact with microbial proteins and can be manipulated to modify enzyme conformation in a manner that alters enzyme activity, stability and/or specificity. Both chemical- and bio-surfactants are potentially toxic to specific microbes and may be exploited as antimicrobial agents against plant, animal and human microbial pathogens. Because of the widespread use of chemical surfactants, their potential impacts on microbial communities in the environment are receiving considerable attention. [Copyright &y& Elsevier]
- Published
- 2006
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32. Use of Novel Fluorinated Organosulfur Compound To Isolate Bacteria Capable of Carbon-Sulfur Bond Cleavage.
- Author
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Van Hamme, Jonathan D., Fedorak, Phillip M., Foght, Julia M., Gray, Murray R., and Dettman, Heather D.
- Subjects
- *
MICROBIOLOGY , *BACTERIA , *SULFONES , *SULFOXIDES , *ALKYLBENZENE sulfonates , *OXIDATION - Abstract
The vacuum residue fraction of heavy crudes contributes to the viscosity of these oils. Specific microbial cleavage of C—S bonds in alkylsulfide bridges that form linkages in this fraction may result in dramatic viscosity reduction. To date, no bacterial strains have been shown conclusively to cleave C—S bonds within alkyl chains. Screening for microbes that can perform this activity was greatly facilitated by the use of a newly synthesized compound, bis-(3-pentafluorophenylpropyl)-sulfide (PFPS), as a novel sulfur source. The terminal pentafluorinated aromatic rings of PFPS preclude growth of aromatic ring-degrading bacteria but allow for selective enrichment of strains capable of cleaving C—S bonds. A unique bacterial strain, Rhodococcus sp. strain JVH1, that used PFPS as a sole sulfur source was isolated from an oil-contaminated environment. Gas chromatography-mass spectrometry analysis revealed that JVH1 oxidized PFPS to a sulfoxide and then a sulfone prior to cleaving the C—S bond to form an alcohol and, presumably, a sulfinate from which sulfur could be extracted for growth. Four known dibenzothiophene-desuifurizing strains, including Rhodococcus sp. strain IGTS8, were all unable to cleave the C—S bond in PFPS but could oxidize PFPS to the sulfone via the sulfoxide. Conversely, JVH1 was unable to oxidize dibenzothiophene but was able to use a variety of alkyl sulfides, in addition to PFPS, as sole sulfur sources. Overall, PFPS is an excellent tool for isolating bacteria capable of cleaving subterminal C&mdsah;S bonds within alkyl chains. The type of desulfurization displayed by JVH1 differs significantly from previously described reaction results. [ABSTRACT FROM AUTHOR]
- Published
- 2004
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33. Recent Advances in Petroleum Microbiology.
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Van Hamme, Jonathan D., Singh, Ajay, and Ward, Owen P.
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- *
PETROLEUM , *MICROBIOLOGY , *MICROORGANISMS , *PETROLEUM waste , *BIOSENSORS , *BIOLOGY - Abstract
Focuses on developments in petroleum microbiology and in the application of microorganisms in oil bioprocesses and as biosensors. Evaluation of microbial mechanisms that control microbial responses to hydrocarbon substrates; Microbial treatment of petroleum waste; Possible use of biosensors for online monitoring of pollutants.
- Published
- 2003
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34. Dibenzyl Sulfide Metabolism by White Rot Fungi.
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Van Hamme, Jonathan D., Wong, Eddie T., Dettman, Heather, Gray, Murray R., and Pickard, Michael A.
- Subjects
- *
ENZYMES , *OXIDATION , *METABOLITES , *FUNGI - Abstract
Examines the dibenzyl sulfide (DBS) metabolism in white rot fungi. Involvement of extracellular enzymes in DBS oxidation; Accounts on the chemical modifications for increase solvent tolerance; Detection of the major metabolites.
- Published
- 2003
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35. Physical and Metabolic Interactions of Pseudomonas sp. Strain JA5-B45 and Rhodococcus sp. Strain...
- Author
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van Hamme, Jonathan D. and Ward, Owen P.
- Subjects
- *
PSEUDOMONAS , *PETROLEUM microbiology , *SURFACE active agents - Abstract
Studies the physical and metabolic interactions of Pseudomonas sp. strain JA5-B45 and Rhodococcus sp. strain F9-D79 during growth on crude oil. Biodegradation of heterogeneous petroleum waste streams in refinery-based fermentation systems; Effect of a chemical surfactant on Pseudomonas and Rhodococcus; Surface tension and emulsification abilities.
- Published
- 2001
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36. Dissecting the Cofactor-Dependent and Independent Bindings of PDE4 Inhibitors.
- Author
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Liu, Susana, Laliberte, France, Bobechko, Brian, Bartlett, Adrienne, Lario, Paula, Gorseth, Elise, Van Hamme, Jonathan, Gresser, Michael J., and Zheng Huang
- Published
- 2001
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37. Ambient Air Pollution Shapes Bacterial and Fungal Ivy Leaf Communities.
- Author
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Stevens, Vincent, Thijs, Sofie, Bongaerts, Eva, Nawrot, Tim, Marchal, Wouter, Van Hamme, Jonathan, and Vangronsveld, Jaco
- Subjects
AIR pollution ,AIR pollutants ,ENGLISH ivy ,FUNGAL communities ,CARBON-black ,BACTERIAL diversity ,NITROGEN dioxide - Abstract
Ambient air pollution exerts deleterious effects on our environment. Continuously exposed to the atmosphere, diverse communities of microorganisms thrive on leaf surfaces, the phylloplane. The composition of these communities is dynamic, responding to many environmental factors including ambient air pollution. In this field study, over a 2 year period, we sampled Hedera helix (ivy) leaves at six locations exposed to different ambient air pollution conditions. Daily, we monitored ambient black carbon (BC), PM
2.5 , PM10 , nitrogen dioxide, and ozone concentrations and found that ambient air pollution led to a 2–7-fold BC increase on leaves, the phylloplane BC load. Our results further indicated that the phylloplane BC load correlates with the diversity of bacterial and fungal leaf communities, impacting diversity more than seasonal effects. The bacterial genera Novosphingobium, Hymenobacter, and Methylorubrum, and the fungal genus Ampelomyces were indicators for communities exposed to the highest phylloplane BC load. Parallel to this, we present one fungal and two bacterial phylloplane strains isolated from an air-polluted environment able to degrade benzene, toluene, and/or xylene, including a genomics-based description of the degradation pathways involved. The findings of this study suggest that ambient air pollution shapes microbial leaf communities, by affecting diversity and supporting members able to degrade airborne pollutants. [ABSTRACT FROM AUTHOR]- Published
- 2021
- Full Text
- View/download PDF
38. Effluent decontamination by the ibuprofen-mineralizing strain, Sphingopyxis granuli RW412: Metabolic processes.
- Author
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Aguilar-Romero, Inés, De la Torre-Zúñiga, Jesús, Quesada, José Miguel, Haïdour, Ali, O'Connell, Garret, McAmmond, Breanne M., Van Hamme, Jonathan D., Romero, Esperanza, Wittich, Regina-Michaela, and van Dillewijn, Pieter
- Subjects
ENVIRONMENTAL health ,SEWAGE disposal plants ,RIVER sediments ,WASTEWATER treatment ,GENES - Abstract
The high global consumption of ibuprofen and its limited elimination by wastewater treatment plants (WWTPs), has led to the contamination of aquatic systems by this common analgesic and its metabolites. The potentially negative environmental and public health effects of this emerging contaminant have raised concerns, driving the demand for treatment technologies. The implementation of bacteria which mineralize organic contaminants in biopurification systems used to decontaminate water or directly in processes in WWTPs, is a cheap and sustainable means for complete elimination before release into the environment. In this work, an ibuprofen-mineralizing bacterial strain isolated from sediments of the River Elbe was characterized and assayed to remediate different ibuprofen-polluted media. Strain RW412, which was identified as Sphingopyxis granuli , has a 4.48 Mb genome which includes plasmid sequences which harbor the ipf genes that encode the first steps of ibuprofen mineralization. Here, we confirm that these genes encode enzymes which initiate CoA ligation to ibuprofen, followed by aromatic ring activation by a dioxygenase and retroaldol cleavage to unequivocally produce 4-isobutylcatechol and propionyl-CoA which then undergo further degradation. In liquid mineral salts medium, the strain eliminated more than 2 mM ibuprofen within 74 h with a generation time of 16 h. Upon inoculation into biopurification systems, it eliminated repeated doses of ibuprofen within a few days. Furthermore, in these systems the presence of RW412 avoided the accumulation of ibuprofen metabolites. In ibuprofen-spiked effluent from a municipal WWTP, ibuprofen removal by this strain was 7 times faster than by the indigenous microbiota. These results suggest that this strain can persist and remain active under environmentally relevant conditions, and may be a useful innovation to eliminate this emerging contaminant from urban wastewater treatment systems. Image 1 • Sphingopyxis granuli RW412 removes ibuprofen from biopurification systems. • RW412 avoids the accumulation of ibuprofen metabolites in biopurification systems. • RW412 bioaugmentation removes ibuprofen from WWTP effluents. • Structures of intermediates ibuprofenyl-CoA and 4-isobutylcatechol are resolved. Ibuprofen mineralization by Sphingopyxis granuli RW412 was characterized molecularly and the strain assayed to remediate ibuprofen from different artificially polluted media. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
39. Genomic Diversity of Two Hydrocarbon-Degrading and Plant Growth-Promoting Pseudomonas Species Isolated from the Oil Field of Bóbrka (Poland).
- Author
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Imperato, Valeria, Portillo-Estrada, Miguel, McAmmond, Breanne M., Douwen, Yorben, Van Hamme, Jonathan D., Gawronski, Stanislaw W., Vangronsveld, Jaco, and Thijs, Sofie
- Subjects
OPERONS ,OIL fields ,PROTON transfer reactions ,TIME-of-flight mass spectrometry ,PSEUDOMONAS ,ORGANIC acids - Abstract
Hydrocarbon-degrading bacteria are important resources for use in phytoremediation applications. Yet, for many hydrocarbonoclastic strains the genetic information regarding pollutant degradation and detoxification has not been thoroughly revealed. In this study, hydrocarbon-degrading bacteria were isolated from a long-term oil-polluted soil in Bóbrka, Poland. Pseudomonas spp. was the most dominant species. Of all 69 isolated strains tested in the laboratory using qualitative biochemical assays, 61% showed the capability to use diesel as sole carbon source, 33% could produce indole, 19% produced siderophores, 36% produced organic acids, and 54% were capable of producing 1-aminocyclopropane-1-carboxylate (ACC)-deaminase. From all morphologically and genetically different strains, two representative Pseudomonas spp., strain VI4.1 and VI4T1, were selected for genome sequencing. Genomic analyses indicated the presence of the full naphthalene dioxygenase operon (plasmid and chromosomal), of genes involved in the degradation of BTEX compounds (Benzene, Toluene, Ethylbenzene, Xylene) and alkanes (alkB gene) as well as the anthranilate degradation pathway (strain VI4T1) and terephthalate dioxygenase protein (strain VI4.1). Proton transfer reaction time-of-flight mass spectrometry (PTR-TOF-MS) analyses confirmed naphthalene and BTEX degradation within seven days. Motility, resistance to abiotic stresses, high and low temperatures, low pH, and salinity were confirmed at the genetic level and experimentally verified. The presence of multiple degradative and plant growth promotion genes, together with the in vitro experimental evidence, indicates the high value of these two strains and their potential use for sustainable site clean-up. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
40. Whole-Genome Shotgun Sequence of Rhodococcus Species Strain JVH1.
- Author
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Brooks, Shannon L. and Van Hamme, Jonathan D.
- Subjects
- *
RHODOCOCCUS , *BACTERIAL genomes , *NUCLEOTIDE sequence , *ORGANOSULFUR compounds , *OXYGENASES , *MICROBIOLOGY - Abstract
Here we present a whole-genome shotgun sequence of Rhodococcus species strain JVH1, an organism capable of degrading a variety of organosulfur compounds. In particular, JVH1 is able to selectively cleave carbon-sulfur bonds within alkyl chains. A large number of oxygenases were identified, consistent with other members of the genus. [ABSTRACT FROM AUTHOR]
- Published
- 2012
- Full Text
- View/download PDF
41. Degradation and defluorination of 6:2 fluorotelomer sulfonamidoalkyl betaine and 6:2 fluorotelomer sulfonate by Gordonia sp. strain NB4-1Y under sulfur-limiting conditions.
- Author
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Shaw, Dayton M.J., Munoz, Gabriel, Bottos, Eric M., Duy, Sung Vo, Sauvé, Sébastien, Liu, Jinxia, and Van Hamme, Jonathan D.
- Abstract
Abstract 6:2 fluorotelomer sulfonamidoalkyl betaine (6:2 FTAB) is a major component of aqueous film-forming foams (AFFFs) used for firefighting and is frequently detected, along with one of its suspected transformation products, 6:2 fluorotelomer sulfonate (6:2 FTSA), in terrestrial and aquatic ecosystems impacted by AFFF usage. Biochemical processes underlying bacterial biodegradation of these compounds remain poorly understood due to a lack of pure culture studies. Here, we characterized the water-soluble and volatile breakdown products of 6:2 FTSA and 6:2 FTAB produced using Gordonia sp. strain NB4-1Y cultures over seven days under sulfur-limited conditions. After 168 h, 99.9% of 60 μM 6:2 FTSA was degraded into ten major breakdown products, with a mol% recovery of 88.2, while 70.4% of 60 μM 6:2 FTAB was degraded into ten major breakdown products, with a mol% recovery of 84.7. NB4-1Y uses two pathways for 6:2 FTSA metabolism, with 55 mol% of breakdown products assigned to a major pathway and <1.0 mol% assigned to a minor pathway. This work indicates that rapid transformation of 6:2 FTSA and 6:2 FTAB can be achieved under controlled conditions and improves the bacterial metabolism of these compounds. Graphical abstract Unlabelled Image Highlights • Biotransformation of 6:2 FTAB & 6:2 FTSA was studied under sulfur-limiting conditions. • Gordonia sp. NB4-1Y rapidly metabolized 6:2 FTAB (70.4%) & 6:2 FTSA (99.9%). • 16 metabolites were identified using high resolution Orbitrap mass spectrometry. • Two distinct degradation pathways were utilized by Gordonia sp. NB4-1Y. • Major breakdown products included 6:2 FTCA, 6:2 FTUA, and 5:2 fluorotelomer ketone. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
42. Use of plant growth promoting bacterial strains to improve Cytisus striatus and Lupinus luteus development for potential application in phytoremediation.
- Author
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Balseiro-Romero, María, Gkorezis, Panagiotis, Kidd, Petra S., Van Hamme, Jonathan, Weyens, Nele, Monterroso, Carmen, and Vangronsveld, Jaco
- Subjects
- *
PHYTOREMEDIATION , *PLANT growth , *CYTISUS , *LUPINUS luteus , *PLANT development - Abstract
Plant growth promoting (PGP) bacterial strains possess different mechanisms to improve plant development under common environmental stresses, and are therefore often used as inoculants in soil phytoremediation processes. The aims of the present work were to study the effects of a collection of plant growth promoting bacterial strains on plant development, antioxidant enzyme activities and nutritional status of Cytisus striatus and/or Lupinus luteus plants a) growing in perlite under non-stress conditions and b) growing in diesel-contaminated soil. For this, two greenhouse experiments were designed. Firstly, C. striatus and L. luteus plants were grown from seeds in perlite, and periodically inoculated with 6 PGP strains, either individually or in pairs. Secondly, L. luteus seedlings were grown in soil samples of the A and B horizons of a Cambisol contaminated with 1.25% (w/w) of diesel and inoculated with best PGP inoculant selected from the first experiment. The results indicated that the PGP strains tested in perlite significantly improved plant growth. Combination treatments provoked better growth of L. luteus than the respective individual strains, while individual inoculation treatments were more effective for C. striatus . L. luteus growth in diesel-contaminated soil was significantly improved in the presence of PGP strains, presenting a 2-fold or higher increase in plant biomass. Inoculants did not provoke significant changes in plant nutritional status, with the exception of a subset of siderophore-producing and P-solubilising bacterial strains that resulted in significantly modification of Fe or P concentrations in leaf tissues. Inoculants did not cause significant changes in enzyme activities in perlite experiments, however they significantly reduced oxidative stress in contaminated soils suggesting an improvement in plant tolerance to diesel. Some strains were applied to non-host plants, indicating a non-specific performance of their plant growth promotion. The use of PGP strains in phytoremediation may help plants to overcome contaminant and other soil stresses, increasing phytoremediation efficiency. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
43. Differential effect of silver nanoparticles on the microbiome of adult and developing planaria.
- Author
-
Bijnens, Karolien, Thijs, Sofie, Leynen, Nathalie, Stevens, Vincent, McAmmond, Breanne, Van Hamme, Jonathan, Vangronsveld, Jaco, Artois, Tom, and Smeets, Karen
- Subjects
- *
PLANARIA , *BACTERIAL communities , *ESSENTIAL nutrients , *SILVER nanoparticles , *MEDICAL supplies , *AQUATIC organisms , *BACTERIAL diversity - Abstract
• The microbiome of the planarian S. mediterranea consisted mainly of Betaproteobacteriales. • AgNP exposure resulted in a decrease of the genera Curvibacter and Undibacterium. • The AgNP-induced bacterial shift was more pronounced in adult organisms. • A PVP-coating had a limited effect on the planarian microbiome compared to NC-AgNPs. Silver nanoparticles (AgNPs) are widely incorporated in household, consumer and medical products. Their unintentional release via wastewaters raises concerns on their environmental impact, particularly for aquatic organisms and their associated bacterial communities. It is known that the microbiome plays an important role in its host's health and physiology, e.g. by producing essential nutrients and providing protection against pathogens. A thorough understanding of the effects of AgNPs on bacterial communities and on their interactions with the host is crucial to fully assess AgNP toxicity on aquatic organisms. Our results indicate that the microbiome of the invertebrate Schmidtea mediterranea , a freshwater planarian, is affected by AgNP exposure at the tested 10 μg/ml concentration. Using targeted amplification of the bacterial 16S rRNA gene V3–V4 region, two independent experiments on the microbiomes of adult worms revealed a consistent decrease in Betaproteobacteriales after AgNP exposure, mainly attributed to a decrease in Curvibacter and Undibacterium. Although developing tissues and organisms are known to be more sensitive to toxic compounds, three independent experiments in regenerating worms showed a less pronounced effect of AgNP exposure on the microbiome, possibly because underlying bacterial community changes during development mask the AgNP induced effect. The presence of a polyvinyl-pyrrolidone (PVP) coating did not significantly alter the outcome of the experiments compared to those with uncoated particles. The observed variation between the different experiments underlines the highly variable nature of microbiomes and emphasises the need to repeat microbiome experiments, within and between physiological states of the animal. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
44. Comparative Evaluation of Four Bacteria-Specific Primer Pairs for 16S rRNA Gene Surveys
- Author
-
Sascha Truyens, Jonathan D. Van Hamme, Vincent Stevens, Sofie Thijs, Jaco Vangronsveld, Bram Beckers, Michiel Op De Beeck, Nele Weyens, THIJS, Sofie, OP DE BEECK, Michiel, BECKERS, Bram, TRUYENS, Sascha, Van Hamme, Jonathan D., STEVENS, Vincent, WEYENS, Nele, and VANGRONSVELD, Jaco
- Subjects
0301 basic medicine ,Microbiology (medical) ,Genetics ,Phylotype ,biology ,Phylogenetic tree ,Ecology ,030106 microbiology ,Alphaproteobacteria ,microbial communities ,pyrosequencing ,16S rRNA gene sequence primers ,soil ,explosives contamination ,biology.organism_classification ,16S ribosomal RNA ,Microbiology ,03 medical and health sciences ,030104 developmental biology ,Pyrosequencing ,Microbiome ,Primer (molecular biology) ,Bacteria ,Original Research - Abstract
Bacterial taxonomic community analyses using PCR-amplification of the 16S rRNA gene and high-throughput sequencing has become a cornerstone in microbiology research. To reliably detect the members, or operational taxonomic units (OTUs), that make up bacterial communities, taxonomic surveys rely on the use of the most informative PCR primers to amplify the broad range of phylotypes present in up-to-date reference databases. However, primers specific for the domain Bacteria were often developed some time ago against database versions that are now out of date. Here we evaluated the performance of four bacterial primers for characterizing complex microbial communities in explosives contaminated and non-contaminated forest soil and by in silico evaluation against the current SILVA123 database. Primer pair 341f/785r produced the highest number of bacterial OTUs, phylogenetic richness, Shannon diversity, low non-specificity and most reproducible results, followed by 967f/1391r and 799f/1193r. Primer pair 68f/518r showed overall low coverage and a bias toward Alphaproteobacteria. In silico, primer pair 341f/785r showed the highest coverage of the domain Bacteria (96.1%) with no obvious bias toward the majority of bacterial species. This suggests the high utility of primer pair 341f/785r for soil and plant-associated bacterial microbiome studies. This work was financed by the Methusalem project 08M03VGRJ and was also supported by grants to STh and NW from the Fund of Scientific Research Handers. Thanks to Prof. Dr. Geert-Jan Bex for help with setting up the Flemish Supercomputer Centre (VSC) supported by the Research Foundation Handers (FWO) in partnership with the five Flemish university associations.
- Published
- 2017
45. Regulation of competence gene homologs in Salmonella enterica serovar Typhimurium and Escherichia coil
- Author
-
Alshabib, Ebthal Yahya, Cameron, Andrew, Dahms, Tanya, Yost, Christopher, Alexander, David, and Van Hamme, Jonathan
- Abstract
A Thesis Submitted to the Faculty of Graduate Studies and Research In a Partial Fulfilment of the Requirements for degree of Doctor of Philosophy In Biology, University of Regina. XXI, 281 p. Many bacteria have the ability to take up DNA from their environment through a process termed “natural competence”. Even though there are numerous bacterial species that are recognized to be naturally competent, competence is undetected or overlooked in many species such as members of the Enterobacteriaceae. Homologs of competence genes and the main regulator of natural competence, Sxy, are conserved in Salmonella and Escherichia coli; however, these genes were found to be silent under all previously-tested conditions. Thus, I carried out molecular studies to investigate genetic induction and regulation mechanisms of natural competence in Salmonella Typhimurium, and E. coli. Despite decades of work and unsuccessful attempts to induce the cryptic competence genes, our genetic studies in S. Typhimurium show that low temperatures (22 – 25 ᵒC) and growth on semi-solid media to allow for motility induce the expression of competence genes. Nutrient deprivation is hypothesized to be another inducing signal; where the expression of competence genes increased under starvation conditions when using arabinose as a carbon source. We identified Sxy and CRP as positive regulators of competence gene expression, whereas the nucleoid-associated proteins, FIS and H-NS, and the alternate sigma factor, RpoS, repress the expression of competence genes. Bioinformatic analysis of competence gene promoters suggests that DNA supercoiling regulates competence gene expression. However, experimental relaxation of DNA supercoiling did not confirm this. Several competence gene homologs have an evolutionary history of operon and promoter shuffling, nevertheless the transcription of these genes is coordinated and synchronized in different bacterial lineages through coregulated promoters. Altogether these results demonstrate that several environmental signals, transcription factors, and regulatory mechanisms are integrated to regulate competence gene expression in S. Typhimurium. In Haemophilus influenzae, the poorly characterized competence regulator, Sxy, is proposed to be stimulated by starvation for purine nucleotides. In S. Typhimurium, we found that sxy expression is stimulated by temperature, motility on semi-solid media, and nutrient deprivation signals. Further, we found that sxy expression is activated by CRP and repressed by FIS, H-NS, and RpoS. Moreover, it was previously proposed that Sxy assists CRP binding to competence gene promoters. Our phenotypic analysis in E. coli showed that mutations that alter the Sxy C-terminus abolish CRP-S transcriptional activation, and remove the toxic effect characteristic of sxy overexpression. A genome-wide analysis of the Salmonella Sxy regulon using directional RNA-seq revealed that Sxy function is not restricted to the activation of competence genes. Sxy also plays a role in regulating sugar metabolism, DNA replication, nucleotide metabolism, and expression of several small RNAs, transcription factors, and pathogenicity genes. This project is the first to study the genetics of competence in Salmonella, and it is pioneering in identifying novel inducing signals and transcription factors that regulate competence gene expression. The outcomes of this research enhance our understanding of the role of Sxy in regulating competences and other functions. The body of knowledge surrounding regulation of competence genes will greatly inform and guide future research into competence gene regulation and help deduce the ecological role of DNA uptake in gamma-proteobacteria. A Thesis Submitted to the Faculty of Graduate Studies and Research In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy *, University of Regina. *, * p. Student yes
- Published
- 2016
46. Accumulation of Black Carbon Particles in Placenta, Cord Blood, and Childhood Urine in Association with the Intestinal Microbiome Diversity and Composition in Four- to Six-Year-Old Children in the ENVIR ON AGE Birth Cohort.
- Author
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Van Pee T, Hogervorst J, Dockx Y, Witters K, Thijs S, Wang C, Bongaerts E, Van Hamme JD, Vangronsveld J, Ameloot M, Raes J, and Nawrot TS
- Subjects
- Humans, Child, Pregnancy, Female, Child, Preschool, Birth Cohort, Fetal Blood, RNA, Ribosomal, 16S, Bacteria, Carbon, Placenta, Gastrointestinal Microbiome
- Abstract
Background: The gut microbiome plays an essential role in human health. Despite the link between air pollution exposure and various diseases, its association with the gut microbiome during susceptible life periods remains scarce., Objectives: In this study, we examined the association between black carbon particles quantified in prenatal and postnatal biological matrices and bacterial richness and diversity measures, and bacterial families., Methods: A total of 85 stool samples were collected from 4- to 6-y-old children enrolled in the ENVIRonmental influence ON early AGEing birth cohort. We performed 16S rRNA gene sequencing to calculate bacterial richness and diversity indices (Chao1 richness, Shannon diversity, and Simpson diversity) and the relative abundance of bacterial families. Black carbon particles were quantified via white light generation under femtosecond pulsed laser illumination in placental tissue and cord blood, employed as prenatal exposure biomarkers, and in urine, used as a post-natal exposure biomarker. We used robust multivariable-adjusted linear models to examine the associations between quantified black carbon loads and measures of richness (Chao1 index) and diversity (Shannon and Simpson indices), adjusting for parity, season of delivery, sequencing batch, age, sex, weight and height of the child, and maternal education. Additionally, we performed a differential relative abundance analysis of bacterial families with a correction for sampling fraction bias. Results are expressed as percentage difference for a doubling in black carbon loads with 95% confidence interval (CI)., Results: Two diversity indices were negatively associated with placental black carbon [Shannon: - 4.38 % (95% CI: - 8.31 % , - 0.28 % ); Simpson: - 0.90 % (95% CI: - 1.76 % , - 0.04 % )], cord blood black carbon [Shannon: - 3.38 % (95% CI: - 5.66 % , - 0.84 % ); Simpson: - 0.91 (95% CI: - 1.66 % , - 0.16 % )], and urinary black carbon [Shannon: - 3.39 % (95% CI: - 5.77 % , - 0.94 % ); Simpson: - 0.89 % (95% CI: - 1.37 % , - 0.40 % )]. The explained variance of black carbon on the above indices varied from 6.1% to 16.6%. No statistically significant associations were found between black carbon load and the Chao1 richness index. After multiple testing correction, placental black carbon was negatively associated with relative abundance of the bacterial families Defluviitaleaceae and Marinifilaceae , and urinary black carbon with Christensenellaceae and Coriobacteriaceae ; associations with cord blood black carbon were not statistically significant after correction., Conclusion: Black carbon particles quantified in prenatal and postnatal biological matrices were associated with the composition and diversity of the childhood intestinal microbiome. These findings address the influential role of exposure to air pollution during pregnancy and early life in human health. https://doi.org/10.1289/EHP11257.
- Published
- 2023
- Full Text
- View/download PDF
47. Correction for Mukhtar et al., "Draft Genome Sequence of Bacillus safensis SCAL1, an Endophytic Heat-Tolerant Plant Growth-Promoting Bacterium".
- Author
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Mukhtar T, Afridi MS, McArthur R, Van Hamme JD, Rineau F, Mahmood T, Amna, Sumaira, Zahid M, Salam A, Khan MN, Ali F, Mehmood S, Bangash N, and Chaudhary HJ
- Published
- 2019
- Full Text
- View/download PDF
48. Draft Genome Sequence of Bacillus pumilus SCAL1, an Endophytic Heat-Tolerant Plant Growth-Promoting Bacterium.
- Author
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Mukhtar T, Afridi MS, McArthur R, Van Hamme JD, Rineau F, Mahmood T, Amna, Sumaira, Zahid M, Salam A, Khan MN, Ali F, Mehmood S, Bangash N, and Chaudhary HJ
- Abstract
Bacillus pumilus strain SCAL1 is an endophytic, thermophilic plant that was isolated from the leaf of a plant, Solanum lycopersicum L., in Sindh, Pakistan. B. pumilus strain SCAL1 has usually exhibited high resistance to environmental stresses, with a growth temperature ranging from 30 to 60°C. An approximately 3.75-Mb draft genome was assembled into 68 contigs., (Copyright © 2018 Mukhtar et al.)
- Published
- 2018
- Full Text
- View/download PDF
49. Editorial: Petroleum Microbial Biotechnology: Challenges and Prospects.
- Author
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Ismail WA, Van Hamme JD, Kilbane JJ, and Gu JD
- Published
- 2017
- Full Text
- View/download PDF
50. Draft Genome Sequence of Bacillus licheniformis VSD4, a Diesel Fuel-Degrading and Plant Growth-Promoting Phyllospheric Bacterium.
- Author
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Stevens V, Thijs S, McAmmond B, Langill T, Van Hamme J, Weyens N, and Vangronsveld J
- Abstract
We report here the 4.19-Mb draft genome sequence of Bacillus licheniformis VSD4, a Gram-positive bacterium of the Bacillaceae family, isolated from leaves of Hedera helix growing at a high-traffic city center in Belgium. Knowledge about its genome will help to evaluate its potential as an inoculant in phylloremediation applications., (Copyright © 2017 Stevens et al.)
- Published
- 2017
- Full Text
- View/download PDF
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