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Wang L, Zhang H, Xu C, Yuan J, Xu X, Wang J, Zhang Y. Long-term nitrogen fertilization and sweetpotato cultivation in the wheat-sweetpotato rotation system decrease alkaline phosphomonoesterase activity by regulating soil phoD-harboring bacteria communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 900:165916. [PMID: 37524185 DOI: 10.1016/j.scitotenv.2023.165916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/02/2023]
Abstract
The alkaline phosphomonoesterase (ALP)-harboring community (phoD-harboring community) plays a crucial role in the conversion of organic phosphorus (P) into available P (AP). However, the response mechanisms of phoD-harboring communities to fertilization strategies, crop types, and their interactions within the wheat-sweetpotato rotation are poorly understood. A nine-year field experiment of different fertilization strategies was established under the wheat-sweetpotato rotation. After harvesting the crop, we collected soil samples without fertilization (CK), inorganic NK fertilization (NK), inorganic NPK fertilization (NPK), and a combined application of inorganic NPK and organic fertilizer (NPKM). We employed high-throughput sequencing and enzymology techniques to analyze the composition and functional activity of phoD-harboring bacterial communities as well as their correlation with soil physicochemical properties. The results showed that long-term nitrogen (N) fertilization, especially inorganic N, significantly reduced soil pH and ALP activity while increasing AP compared with CK. The AP content in sweetpotato season was significantly higher than that in wheat season. Inorganic N fertilization dramatically reshaped the communities of phoD-harboring bacteria and decreased diversity. The phoD-harboring bacterial communities in sweetpotato season were significantly different from those in wheat season. The N fertilization significantly reduced the relative abundance of Acuticoccus, Methylibium, Rhizobacter, and Roseivivax, which was positively correlated with ALP activity. These groups in sweetpotato season decreased significantly compared with wheat season. A structural equation model indicates that pH and AP play a significant role in regulating the phoD-harboring bacteria communities, ALP activity, and their interactions. We demonstrate that fertilization strategies and crop types have a substantial impact on the phoD-harboring bacteria communities and functions, which are closely linked to soil pH and AP levels. Our study highlights the detrimental effects of soil acidification resulting from inorganic N fertilization on P-cycling bacterial communities and functions. However, the combination of inorganic and organic fertilizer can mitigate these adverse effects.
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Affiliation(s)
- Lei Wang
- National Agricultural Experimental Station for Agricultural Environment, Luhe, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Hui Zhang
- National Agricultural Experimental Station for Agricultural Environment, Luhe, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; Jiangsu University, Zhenjiang 212023, China
| | - Cong Xu
- National Agricultural Experimental Station for Agricultural Environment, Luhe, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; Jiangsu University, Zhenjiang 212023, China
| | - Jie Yuan
- National Agricultural Experimental Station for Agricultural Environment, Luhe, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Xianjü Xu
- National Agricultural Experimental Station for Agricultural Environment, Luhe, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Jidong Wang
- National Agricultural Experimental Station for Agricultural Environment, Luhe, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; Jiangsu University, Zhenjiang 212023, China.
| | - Yongchun Zhang
- National Agricultural Experimental Station for Agricultural Environment, Luhe, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; Jiangsu University, Zhenjiang 212023, China.
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Chen Y, Ren H, Kong X, Wu H, Lu Z. A multicomponent propane monooxygenase catalyzes the initial degradation of methyl tert-butyl ether in Mycobacterium vaccae JOB5. Appl Environ Microbiol 2023; 89:e0118723. [PMID: 37823642 PMCID: PMC10617536 DOI: 10.1128/aem.01187-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 08/30/2023] [Indexed: 10/13/2023] Open
Abstract
Methyl tert-butyl ether (MTBE) has been recognized as a groundwater contaminant due to its widespread distribution and potential threat to human health. The limited understanding of the enzymes catalyzing MTBE degradation restricts their application in MTBE bioremediation. In this study, an MTBE-degrading soluble di-iron monooxygenase that clusters phylogenetically with a known propane monooxygenase (PRM) encoded by the prmABCD gene cluster was identified and functionally characterized, revealing their role in MTBE metabolism by Mycobacterium vaccae JOB5. Transcriptome analysis demonstrated that the expression of prmABCD was upregulated when JOB5 was induced by MTBE. Escherichia coli Rosetta heterologously expressing prmABCD from JOB5 could transform MTBE, indicating that the PRM of JOB5 is capable of the initial degradation of MTBE. The loss of the gene encoding the oxygenase α-subunit or β-subunit, the coupling protein, or the reductase disrupted MTBE transformation by the recombinant E. coli Rosetta. In addition, the catalytic capacity of PRM is likely affected by residue G95 in the active site pocket and residues I84, P165, A269, and V270 in the substrate tunnel structure. Mutation of amino acids in the active site and substrate tunnel resulted in inefficiency or inactivation of MTBE degradation, and the activity in 1,4-dioxane (1,4-D) degradation was diminished less than that in MTBE degradation.IMPORTANCEMulticomponent monooxygenases catalyzing the initial hydroxylation of MTBE are important in MTBE biodegradation. Previous studies of MTBE degradation enzymes have focused on P450s, alkane monooxygenase and MTBE monooxygenase, but the vital role of soluble di-iron monooxygenases has rarely been reported. In this study, we deciphered the essential catalytic role of a PRM and revealed the key residues of the PRM in MTBE metabolism. Our findings provide new insight into the MTBE-degrading gene cluster and enzymes in bacteria. This characterization of the PRM associated with MTBE degradation expands our understanding of MTBE-degrading gene diversity and provides a novel candidate enzyme for the bioremediation of MTBE-contaminated sites.
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Affiliation(s)
- Yiyang Chen
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hao Ren
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiangyu Kong
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hao Wu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhenmei Lu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
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Lin WH, Tsai TS. Comparisons of the Oral Microbiota from Seven Species of Wild Venomous Snakes in Taiwan Using the High-Throughput Amplicon Sequencing of the Full-Length 16S rRNA Gene. BIOLOGY 2023; 12:1206. [PMID: 37759605 PMCID: PMC10525742 DOI: 10.3390/biology12091206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/26/2023] [Accepted: 09/02/2023] [Indexed: 09/29/2023]
Abstract
A venomous snake's oral cavity may harbor pathogenic microorganisms that cause secondary infection at the wound site after being bitten. We collected oral samples from 37 individuals belonging to seven species of wild venomous snakes in Taiwan, including Naja atra (Na), Bungarus multicinctus (Bm), Protobothrops mucrosquamatus (Pm), Trimeresurus stejnegeri (Ts), Daboia siamensis (Ds), Deinagkistrodon acutus (Da), and alpine Trimeresurus gracilis (Tg). Bacterial species were identified using full-length 16S rRNA amplicon sequencing analysis, and this is the first study using this technique to investigate the oral microbiota of multiple Taiwanese snake species. Up to 1064 bacterial species were identified from the snake's oral cavities, with 24 pathogenic and 24 non-pathogenic species among the most abundant ones. The most abundant oral bacterial species detected in our study were different from those found in previous studies, which varied by snake species, collection sites, sampling tissues, culture dependence, and analysis methods. Multivariate analysis revealed that the oral bacterial species compositions in Na, Bm, and Pm each were significantly different from the other species, whereas those among Ts, Ds, Da, and Tg showed fewer differences. Herein, we reveal the microbial diversity in multiple species of wild snakes and provide potential therapeutic implications regarding empiric antibiotic selection for wildlife medicine and snakebite management.
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Affiliation(s)
- Wen-Hao Lin
- Institute of Wildlife Conservation, National Pingtung University of Science and Technology, Pingtung 912301, Taiwan;
| | - Tein-Shun Tsai
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung 912301, Taiwan
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DNA stable isotope probing on soil treated by plant biostimulation and flooding revealed the bacterial communities involved in PCB degradation. Sci Rep 2022; 12:19232. [PMID: 36357494 PMCID: PMC9649793 DOI: 10.1038/s41598-022-23728-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 11/04/2022] [Indexed: 11/12/2022] Open
Abstract
Polychlorinated biphenyl (PCB)-contaminated soils represent a major treat for ecosystems health. Plant biostimulation of autochthonous microbial PCB degraders is a way to restore polluted sites where traditional remediation techniques are not sustainable, though its success requires the understanding of site-specific plant-microbe interactions. In an historical PCB contaminated soil, we applied DNA stable isotope probing (SIP) using 13C-labeled 4-chlorobiphenyl (4-CB) and 16S rRNA MiSeq amplicon sequencing to determine how the structure of total and PCB-degrading bacterial populations were affected by different treatments: biostimulation with Phalaris arundinacea subjected (PhalRed) or not (Phal) to a redox cycle and the non-planted controls (Bulk and BulkRed). Phal soils hosted the most diverse community and plant biostimulation induced an enrichment of Actinobacteria. Mineralization of 4-CB in SIP microcosms varied between 10% in Bulk and 39% in PhalRed soil. The most abundant taxa deriving carbon from PCB were Betaproteobacteria and Actinobacteria. Comamonadaceae was the family most represented in Phal soils, Rhodocyclaceae and Nocardiaceae in non-planted soils. Planted soils subjected to redox cycle enriched PCB degraders affiliated to Pseudonocardiaceae, Micromonosporaceae and Nocardioidaceae. Overall, we demonstrated different responses of soil bacterial taxa to specific rhizoremediation treatments and we provided new insights into the populations active in PCB biodegradation.
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Chai G, Wang D, Shan J, Jiang C, Yang Z, Liu E, Meng H, Wang H, Wang Z, Qin L, Xi J, Ma Y, Li H, Qian Y, Li J, Lin Y. Accumulation of high-molecular-weight polycyclic aromatic hydrocarbon impacted the performance and microbial ecology of bioretention systems. CHEMOSPHERE 2022; 298:134314. [PMID: 35292274 DOI: 10.1016/j.chemosphere.2022.134314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 02/13/2022] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
Bioretention has been considered as an effective management practice for urban stormwater in the removal of pollutants including polycyclic aromatic hydrocarbons (PAHs). However, the accumulation of high-molecular-weight (HMW) PAHs in bioretention systems and their potential impact on the pollutants removal performance and microbial ecology are still not fully understood. In this study, comparisons of treatment effectiveness, enzyme activity and microbial community in bioretention systems with different types of media amendments were carried out at different spiking levels of pyrene (PYR). The results showed that the removal efficiencies of chemical oxygen demand (COD) and total nitrogen in the bioretention systems were negatively impacted by the PYR levels. The relative activities of soil dehydrogenase and urease were increasingly inhibited by the elevated PYR level, indicating the declining microbial activity regarding organic matter decomposition. The spiking of PYR negatively affected microbial diversity, and distinct time- and influent-dependent changes in microbial communities were observed. The relative abundance of PAH-degrading microorganisms increased in PYR-spiked systems, while the abundance of nitrifiers decreased. The addition of media amendments was beneficial for the enrichment of microorganisms that are more resistant to PYR-related stress, therefore elevating the COD concentration removal rate by ∼50%. This study gives new insight into the multifaceted impacts of HMW PAH accumulation on microbial fingerprinting and enzyme activities, which may provide guidance on better stormwater management practices via bioretention in terms of improved system longevity and performance.
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Affiliation(s)
- Guodong Chai
- Shaanxi Key Laboratory of Water Resources and Environment, Xi'an University of Technology, Xi'an, Shaanxi 710048, China; Department of Municipal and Environmental Engineering, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China
| | - Dongqi Wang
- Shaanxi Key Laboratory of Water Resources and Environment, Xi'an University of Technology, Xi'an, Shaanxi 710048, China; Department of Municipal and Environmental Engineering, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China; State Key Laboratory of Eco-hydraulics in Northwest Arid Region, Xi'an University of Technology, Xi'an, Shaanxi 710048, China
| | - Jiaqi Shan
- Department of Municipal and Environmental Engineering, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China
| | - Chunbo Jiang
- Department of Municipal and Environmental Engineering, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China
| | - Zhangjie Yang
- Department of Municipal and Environmental Engineering, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China
| | - Enyu Liu
- Department of Municipal and Environmental Engineering, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China
| | - Haiyu Meng
- Department of Municipal and Environmental Engineering, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China
| | - Hui Wang
- Department of Municipal and Environmental Engineering, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China
| | - Zhe Wang
- Department of Municipal and Environmental Engineering, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China
| | - Lu Qin
- Department of Municipal and Environmental Engineering, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China
| | - Jiayao Xi
- Department of Municipal and Environmental Engineering, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China
| | - Yuenan Ma
- Department of Municipal and Environmental Engineering, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China
| | - Huaien Li
- Department of Municipal and Environmental Engineering, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China; State Key Laboratory of Eco-hydraulics in Northwest Arid Region, Xi'an University of Technology, Xi'an, Shaanxi 710048, China
| | - Yishi Qian
- Xi'an Modern Chemistry Research Institute, Xi'an, Shaanxi 710065, China
| | - Jiake Li
- Department of Municipal and Environmental Engineering, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China; State Key Laboratory of Eco-hydraulics in Northwest Arid Region, Xi'an University of Technology, Xi'an, Shaanxi 710048, China.
| | - Yishan Lin
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu, 210023, China.
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Ruen-Pham K, Graham LE, Satjarak A. Spatial Variation of Cladophora Epiphytes in the Nan River, Thailand. PLANTS (BASEL, SWITZERLAND) 2021; 10:2266. [PMID: 34834629 PMCID: PMC8622721 DOI: 10.3390/plants10112266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/19/2021] [Accepted: 10/20/2021] [Indexed: 11/16/2022]
Abstract
Cladophora is an algal genus known to be ecologically important. It provides habitats for microorganisms known to provide ecological services such as biosynthesis of cobalamin (vitamin B12) and nutrient cycling. Most knowledge of microbiomes was obtained from studies of lacustrine Cladophora species. However, whether lotic freshwater Cladophora microbiomes are as complex as the lentic ones or provide similar ecological services is not known. To illuminate these issues, we used amplicons of 16S rDNA, 18S rDNA, and ITS to investigate the taxonomy and diversity of the microorganisms associated with replicate Cladophora samples from three sites along the Nan River, Thailand. Results showed that the diversity of prokaryotic and eukaryotic members of Cladophora microbiomes collected from different sampling sites was statistically different. Fifty percent of the identifiable taxa were shared across sampling sites: these included organisms belonging to different trophic levels, decomposers, and heterotrophic bacteria. These heterogeneous assemblages of bacteria, by functional inference, have the potential to perform various ecological functions, i.e., cellulose degradation, cobalamin biosynthesis, fermentative hydrogen production, ammonium oxidation, amino acid fermentation, dissimilatory reduction of nitrate to ammonium, nitrite reduction, nitrate reduction, sulfur reduction, polyphosphate accumulation, denitrifying phosphorus-accumulation, and degradation of aromatic compounds. Results suggested that river populations of Cladophora provide ecologically important habitat for microorganisms that are key to nutrient cycling in lotic ecosystems.
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Affiliation(s)
- Karnjana Ruen-Pham
- Plants of Thailand Research Unit, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Linda E. Graham
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706, USA;
| | - Anchittha Satjarak
- Plants of Thailand Research Unit, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
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Fodelianakis S, Washburne AD, Bourquin M, Pramateftaki P, Kohler TJ, Styllas M, Tolosano M, De Staercke V, Schön M, Busi SB, Brandani J, Wilmes P, Peter H, Battin TJ. Microdiversity characterizes prevalent phylogenetic clades in the glacier-fed stream microbiome. ISME JOURNAL 2021; 16:666-675. [PMID: 34522009 PMCID: PMC8857233 DOI: 10.1038/s41396-021-01106-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 08/14/2021] [Accepted: 09/02/2021] [Indexed: 02/01/2023]
Abstract
Glacier-fed streams (GFSs) are extreme and rapidly vanishing ecosystems, and yet they harbor diverse microbial communities. Although our understanding of the GFS microbiome has recently increased, we do not know which microbial clades are ecologically successful in these ecosystems, nor do we understand potentially underlying mechanisms. Ecologically successful clades should be more prevalent across GFSs compared to other clades, which should be reflected as clade-wise distinctly low phylogenetic turnover. However, methods to assess such patterns are currently missing. Here we developed and applied a novel analytical framework, “phyloscore analysis”, to identify clades with lower spatial phylogenetic turnover than other clades in the sediment microbiome across twenty GFSs in New Zealand. These clades constituted up to 44% and 64% of community α-diversity and abundance, respectively. Furthermore, both their α-diversity and abundance increased as sediment chlorophyll a decreased, corroborating their ecological success in GFS habitats largely devoid of primary production. These clades also contained elevated levels of putative microdiversity than others, which could potentially explain their high prevalence in GFSs. This hitherto unknown microdiversity may be threatened as glaciers shrink, urging towards further genomic and functional exploration of the GFS microbiome.
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Affiliation(s)
- Stilianos Fodelianakis
- Stream Biofilm & Ecosystem Research Lab, ENAC Division, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland.
| | | | - Massimo Bourquin
- Stream Biofilm & Ecosystem Research Lab, ENAC Division, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Paraskevi Pramateftaki
- Stream Biofilm & Ecosystem Research Lab, ENAC Division, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Tyler J Kohler
- Stream Biofilm & Ecosystem Research Lab, ENAC Division, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Michail Styllas
- Stream Biofilm & Ecosystem Research Lab, ENAC Division, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Matteo Tolosano
- Stream Biofilm & Ecosystem Research Lab, ENAC Division, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Vincent De Staercke
- Stream Biofilm & Ecosystem Research Lab, ENAC Division, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Martina Schön
- Stream Biofilm & Ecosystem Research Lab, ENAC Division, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Susheel Bhanu Busi
- Systems Ecology Research Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Jade Brandani
- Stream Biofilm & Ecosystem Research Lab, ENAC Division, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Paul Wilmes
- Systems Ecology Research Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Hannes Peter
- Stream Biofilm & Ecosystem Research Lab, ENAC Division, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Tom J Battin
- Stream Biofilm & Ecosystem Research Lab, ENAC Division, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland.
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Ares A, Costa J, Joaquim C, Pintado D, Santos D, Messmer MM, Mendes-Moreira PM. Effect of Low-Input Organic and Conventional Farming Systems on Maize Rhizosphere in Two Portuguese Open-Pollinated Varieties (OPV), "Pigarro" (Improved Landrace) and "SinPre" (a Composite Cross Population). Front Microbiol 2021; 12:636009. [PMID: 33717028 PMCID: PMC7953162 DOI: 10.3389/fmicb.2021.636009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/19/2021] [Indexed: 11/13/2022] Open
Abstract
Maize is one of the most important crops worldwide and is the number one arable crop in Portugal. A transition from the conventional farming system to organic agriculture requires optimization of cultivars and management, the interaction of plant-soil rhizosphere microbiota being pivotal. The objectives of this study were to unravel the effect of population genotype and farming system on microbial communities in the rhizosphere of maize. Rhizosphere soil samples of two open-pollinated maize populations ("SinPre" and "Pigarro") cultivated under conventional and organic farming systems were taken during flowering and analyzed by next-generation sequencing (NGS). Phenological data were collected from the replicated field trial. A total of 266 fungi and 317 bacteria genera were identified in "SinPre" and "Pigarro" populations, of which 186 (69.9%) and 277 (87.4%) were shared among them. The microbiota of "Pigarro" showed a significant higher (P < 0.05) average abundance than the microbiota of "SinPre." The farming system had a statistically significant impact (P < 0.05) on the soil rhizosphere microbiota, and several fungal and bacterial taxa were found to be farming system-specific. The rhizosphere microbiota diversity in the organic farming system was higher than that in the conventional system for both varieties. The presence of arbuscular mycorrhizae (Glomeromycota) was mainly detected in the microbiota of the "SinPre" population under the organic farming systems and very rare under conventional systems. A detailed metagenome function prediction was performed. At the fungal level, pathotroph-saprotroph and pathotroph-symbiotroph lifestyles were modified by the farming system. For bacterial microbiota, the main functions altered by the farming system were membrane transport, transcription, translation, cell motility, and signal transduction. This study allowed identifying groups of microorganisms known for their role as plant growth-promoting rhizobacteria (PGPR) and with the capacity to improve crop tolerance for stress conditions, allowing to minimize the use of synthetic fertilizers and pesticides. Arbuscular mycorrhizae (phyla Glomeromycota) were among the most important functional groups in the fungal microbiota and Achromobacter, Burkholderia, Erwinia, Lysinibacillus, Paenibacillus, Pseudomonas, and Stenotrophomonas in the bacterial microbiota. In this perspective, the potential role of these microorganisms will be explored in future research.
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Affiliation(s)
- Aitana Ares
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, Portugal.,Laboratory for Phytopathology, Instituto Pedro Nunes, Coimbra, Portugal
| | - Joana Costa
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, Portugal.,Laboratory for Phytopathology, Instituto Pedro Nunes, Coimbra, Portugal
| | - Carolina Joaquim
- Centro de Recursos Naturais, Ambiente e Sociedade (CERNAS), Coimbra, Portugal
| | - Duarte Pintado
- Centro de Recursos Naturais, Ambiente e Sociedade (CERNAS), Coimbra, Portugal
| | - Daniela Santos
- Centro de Recursos Naturais, Ambiente e Sociedade (CERNAS), Coimbra, Portugal
| | - Monika M Messmer
- Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
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Liang Y, Li M, Pan F, Ma J, Yang Z, Ling T, Qin J, Lu S, Zhong F, Song Z. Alkaline Phosphomonoesterase-Harboring Microorganisms Mediate Soil Phosphorus Transformation With Stand Age in Chinese Pinus massoniana Plantations. Front Microbiol 2020; 11:571209. [PMID: 33329428 PMCID: PMC7728850 DOI: 10.3389/fmicb.2020.571209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 11/04/2020] [Indexed: 12/05/2022] Open
Abstract
phoD-harboring microorganisms facilitate mineralization of organic phosphorus (P), while their role in the regulation of soil P turnover under P-limited conditions in Pinus massoniana plantations is poorly understood. The aim of the present study was to investigate the effects of stand age and season on soil P fractions and phoD-harboring microorganism communities in a chronosequence of Chinese P. massoniana plantations including 3, 19, and 58 years. The soil P fractions (i.e., CaCl2-P, citrate-P, enzyme-P, and HCl-P) varied seasonally, with the higher values observed in the rainy season. The concentrations of the fractions were higher in old plantation (OP) soils and lower in young planation (YP) soils in both seasons. The OTU abundances were negatively correlated with total available P concentration, while were positively correlated with alkaline phosphomonoesterase (ALP) activity at 0–10 cm soil depth. The results indicate that phoD-harboring microorganisms have great potential to mineralize organic P under P-poor conditions and highlights those microorganisms are indicators of P bioavailability in P. massoniana plantations.
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Affiliation(s)
- Yueming Liang
- Key Laboratory of Karst Dynamics, Ministry of Natural and Resources & Guangxi Zhuangzu Autonomy Region, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin, China.,Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, Guangxi Normal University, Guilin, China
| | - Mingjin Li
- Production and Operation Department, Zhenlong Forest Farm of Hengxian County, Nanning, China
| | - Fujing Pan
- College of Environmental and Engineering, Guangxi Key Laboratory of Theory and Technology for Environmental Pollution Control, Guilin University of Technology, Guilin, China
| | - Jiangming Ma
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, Guangxi Normal University, Guilin, China
| | - Zhangqi Yang
- Engineering Research Center of Masson Pine of Guangxi, Guangxi Forestry Research Institute, Nanning, China
| | - Tianwang Ling
- Production and Operation Department, Zhenlong Forest Farm of Hengxian County, Nanning, China
| | - Jiashuang Qin
- Guangxi Institute of Botany, Chinese Academy of Sciences, Guilin, China
| | - Shaohao Lu
- Production and Operation Department, Zhenlong Forest Farm of Hengxian County, Nanning, China
| | - Fengyue Zhong
- Production and Operation Department, Zhenlong Forest Farm of Hengxian County, Nanning, China
| | - Zunrong Song
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, Guangxi Normal University, Guilin, China
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10
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Thornton SF, Nicholls HCG, Rolfe SA, Mallinson HEH, Spence MJ. Biodegradation and fate of ethyl tert-butyl ether (ETBE) in soil and groundwater: A review. JOURNAL OF HAZARDOUS MATERIALS 2020; 391:122046. [PMID: 32145642 DOI: 10.1016/j.jhazmat.2020.122046] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 12/07/2019] [Accepted: 01/07/2020] [Indexed: 06/10/2023]
Abstract
This review summarises the current state of knowledge on the biodegradation and fate of the gasoline ether oxygenate ethyl tert-butyl ether (ETBE) in soil and groundwater. Microorganisms have been identified in soil and groundwater with the ability to degrade ETBE aerobically as a carbon and energy source, or via cometabolism using alkanes as growth substrates. Aerobic biodegradation of ETBE initially occurs via hydroxylation of the ethoxy carbon by a monooxygenase enzyme, with subsequent formation of intermediates which include acetaldehyde, tert-butyl acetate (TBAc), tert-butyl alcohol (TBA), 2-hydroxy-2-methyl-1-propanol (MHP) and 2-hydroxyisobutyric acid (2-HIBA). Slow cell growth and low biomass yields on ETBE are believed to result from the ether structure and slow degradation kinetics, with potential limitations on ETBE metabolism. Genes known to facilitate transformation of ETBE include ethB (within the ethRABCD cluster), encoding a cytochrome P450 monooxygenase, and alkB-encoding alkane hydroxylases. Other genes have been identified in microorganisms but their activity and specificity towards ETBE remains poorly characterised. Microorganisms and pathways supporting anaerobic biodegradation of ETBE have not been identified, although this potential has been demonstrated in limited field and laboratory studies. The presence of co-contaminants (other ether oxygenates, hydrocarbons and organic compounds) in soil and groundwater may limit aerobic biodegradation of ETBE by preferential metabolism and consumption of available dissolved oxygen or enhance ETBE biodegradation through cometabolism. Both ETBE-degrading microorganisms and alkane-oxidising bacteria have been characterised, with potential for use in bioaugmentation and biostimulation of ETBE degradation in groundwater.
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Affiliation(s)
- S F Thornton
- Groundwater Protection and Restoration Group, Dept of Civil and Structural Engineering, University of Sheffield, Sheffield S1 3JD, UK
| | - H C G Nicholls
- Groundwater Protection and Restoration Group, Dept of Civil and Structural Engineering, University of Sheffield, Sheffield S1 3JD, UK
| | - S A Rolfe
- Dept of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, Sheffield S10 2TN, UK
| | - H E H Mallinson
- Groundwater Protection and Restoration Group, Dept of Civil and Structural Engineering, University of Sheffield, Sheffield S1 3JD, UK
| | - M J Spence
- Concawe, Environmental Science for European Refining, Boulevard du Souverain 165, 1160 Brussels, Belgium
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11
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Hashemi SH, Kaykhaii M, Mirmoghaddam M, Boczkaj G. Preconcentration and Analytical Methods for Determination of Methyl Tert-Butyl Ether and Other Fuel Oxygenates and Their Degradation Products in Environment: A Review. Crit Rev Anal Chem 2020; 51:582-608. [PMID: 32312086 DOI: 10.1080/10408347.2020.1753164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Fuel oxygenates (FOs) are mainly ethers or alcohols which are added to gasoline either to boost the octane number or to make the fuel burning process more "cleaner" with increasing the oxygen content, or to obtain a combination of both effects. FOs are water soluble with high mobility in the environment which presence even at very low concentrations lower the quality of water making it unsafe or unpleasant due to their objectionable taste and/or odor. Thus, their determination at trace in environmental samples is of high importance because of their sparingly biodegradability and their biological hazards. Instruments such as gas chromatography, Fourier transform infrared spectroscopy and ion mobility spectrometry are mainly used for the determination of FOs. However, the main challenge for determination of such oxygenates relates to proper sample preparation. Dilute or complex samples often demand a specific treatment to ensure effective enrichment of FOs before their detection. The main techniques used for this purpose are purge and trap, membrane extraction, and solid phase microextraction. This review presents a comprehensive evaluation of extraction/preconcentration techniques and analytical methods for determination of FOs in environmental samples. Advantages and disadvantages of each method are discussed in details along with critical evaluation of currently available methods.
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Affiliation(s)
- Sayyed Hossein Hashemi
- Department of Marine Chemistry, Faculty of Marine Science, Chabahar Maritime University, Chabahar, Iran
| | - Massoud Kaykhaii
- Department of Chemistry, Faculty of Sciences, University of Sistan and Baluchestan, Zahedan, Iran
| | - Majid Mirmoghaddam
- Department of Chemistry, Faculty of Sciences, University of Sistan and Baluchestan, Zahedan, Iran
| | - Grzegorz Boczkaj
- Faculty of Chemistry, Department of Process Engineering and Chemical Technology, Gdansk University of Technology, Gdansk, Poland
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12
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Jiao S, Wang J, Wei G, Chen W, Lu Y. Dominant role of abundant rather than rare bacterial taxa in maintaining agro-soil microbiomes under environmental disturbances. CHEMOSPHERE 2019; 235:248-259. [PMID: 31260865 DOI: 10.1016/j.chemosphere.2019.06.174] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 06/19/2019] [Accepted: 06/23/2019] [Indexed: 06/09/2023]
Abstract
Elucidating the mechanisms underpinning the responses of abundant and rare microbial taxa to environmental disturbances is essential for understanding the biodiversity-stability relationship and maintaining microbial diversity. Here, we explored the response patterns of abundant and rare bacterial taxa to disturbances by invasive plant growth and oil contamination in agricultural soils across a large spatial scale (latitude gradient = 18.62°-46.51°). Our meta-analysis based on existing Illumina sequencing datasets showed that abundant taxa persisted under the disturbances whereas rare taxa were more easily affected, indicating the higher resilience or resistance of abundant taxa to disturbances. The responses of abundant taxa were associated with mean annual temperature at the sampling sites, while rare taxa instead showed stochastic responses. There were significantly negative linear regressions between bacterial α-diversity and community dissimilarities (disturbed vs. undisturbed soils), suggesting stronger resilience or resistance in those bacterial communities with higher α-diversity. This resilience or resistance was mainly associated with the α-diversity of abundant taxa. Our network analysis showed that the disturbances substantially decreased the strength of the connections, loosened the co-occurrence relationships, and reshaped the complex bacterial interactions. In the undisturbed soils, abundant taxa were located in central positions within the network more often than were rare taxa, while these trends were reversed in the disturbed soils. Our results suggest that abundant taxa play a dominant role in the stability and maintenance of agro-soil bacterial communities, while rare taxa could greatly influence local bacterial interactions under environmental disturbances.
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Affiliation(s)
- Shuo Jiao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China; College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
| | - Junman Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Weimin Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Yahai Lu
- College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China.
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13
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Kucharzyk KH, Rectanus HV, Bartling CM, Rosansky S, Minard-Smith A, Mullins LA, Neil K. Use of omic tools to assess methyl tert-butyl ether (MTBE) degradation in groundwater. JOURNAL OF HAZARDOUS MATERIALS 2019; 378:120618. [PMID: 31301927 DOI: 10.1016/j.jhazmat.2019.05.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/03/2019] [Accepted: 05/05/2019] [Indexed: 06/10/2023]
Abstract
This study employed innovative technologies to evaluate multiple lines of evidence for natural attenuation (NA) of methyl tertiary-butyl ether (MTBE) in groundwater at the 22 Area of Marine Corps Base (MCB) Camp Pendleton after decommissioning of a biobarrier system. For comparison, data from the 13 Area Gas Station where active treatment of MTBE is occurring was used to evaluate the effectiveness of omic techniques in assessing biodegradation. Overall, the 22 Area Gas Station appeared to be anoxic. MTBE was detected in large portion of the plume. In comparison, concentrations of MTBE at the 13 Area Gas Station were much higher (42,000 μg/L to 2800 μg/L); however, none of the oxygenates were detected. Metagenomic analysis of the indigenous groundwater microbial community revealed the presence of bacterial strains known to aerobically and anaerobically degrade MTBE at both sites. While proteomic analysis at the 22 Area Gas Station showed the presence of proteins of MTBE degrading microorganisms, the MTBE degradative proteins were only found at the 13 Area Gas Station. Taken together, these results provide evidence for previous NA of MTBE in the groundwater at 22 Area Gas Station and demonstrate the effectiveness of innovative-omic technologies to assist monitored NA assessments.
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Affiliation(s)
| | | | | | - Steve Rosansky
- Battelle Memorial Institute, Columbus, OH, United States
| | | | | | - Kenda Neil
- Naval Facilities Engineering Command (NAVFAC) Engineering and Expeditionary Warfare Center (EXWC), Port Huaneme, CA, United States
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14
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Li S, Wang D, Du D, Qian K, Yan W. Characterization of co-metabolic biodegradation of methyl tert-butyl ether by a Acinetobacter sp. strain. RSC Adv 2019; 9:38962-38972. [PMID: 35540635 PMCID: PMC9076015 DOI: 10.1039/c9ra09507a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 11/20/2019] [Indexed: 11/21/2022] Open
Abstract
Co-metabolic bioremediation is a promising approach for the elimination of methyl tert-butyl ether (MTBE), which is a common pollutant found worldwide in ground water. In this paper, a bacterial strain able to co-metabolically degrade MTBE was isolated and named as Acinetobacter sp. SL3 based on 16S rRNA gene sequencing analysis. Strain SL3 could grow on n-alkanes (C5–C8) accompanied with the co-metabolic degradation of MTBE. The number of carbons present in the n-alkane substrate significantly influenced the degradation rate of MTBE and accumulation of tert-butyl alcohol (TBA), with n-octane resulting in a higher MTBE degradation rate (Vmax = 36.7 nmol min−1 mgprotein−1, Ks = 6.4 mmol L−1) and lower TBA accumulation rate. A degradation experiment in a fed-batch reactor revealed that the efficiency of MTBE degradation by Acinetobacter sp. strain SL3 did not show an obvious decrease after nine rounds of MTBE replenishment ranging from 0.1–0.5 mmol L−1. The results of this paper reveal the preferable properties of Acinetobacter sp. SL3 for the bioremediation of MTBE via co-metabolism and leads towards the development of new MTBE elimination technologies. Acinetobacter sp. SL3 could co-metabolically degrade MTBE when grown on n-alkanes. An extremely low TBA accumulation were achieved on n-octane. The fed-batch reactor degradation revealed continuous MTBE degradation capacity by Acinetobacter sp. SL3.![]()
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Affiliation(s)
- Shanshan Li
- Department of Environmental Science & Engineering
- Xi'an Jiaotong University
- Xi'an
- China
| | - Dan Wang
- Department of Environmental Science & Engineering
- Xi'an Jiaotong University
- Xi'an
- China
| | - Dan Du
- Department of Environmental Science & Engineering
- Xi'an Jiaotong University
- Xi'an
- China
| | - Keke Qian
- Department of Environmental Science & Engineering
- Xi'an Jiaotong University
- Xi'an
- China
| | - Wei Yan
- Department of Environmental Science & Engineering
- Xi'an Jiaotong University
- Xi'an
- China
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15
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Linz AM, He S, Stevens SLR, Anantharaman K, Rohwer RR, Malmstrom RR, Bertilsson S, McMahon KD. Freshwater carbon and nutrient cycles revealed through reconstructed population genomes. PeerJ 2018; 6:e6075. [PMID: 30581671 PMCID: PMC6292386 DOI: 10.7717/peerj.6075] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 11/05/2018] [Indexed: 02/01/2023] Open
Abstract
Although microbes mediate much of the biogeochemical cycling in freshwater, the categories of carbon and nutrients currently used in models of freshwater biogeochemical cycling are too broad to be relevant on a microbial scale. One way to improve these models is to incorporate microbial data. Here, we analyze both genes and genomes from three metagenomic time series and propose specific roles for microbial taxa in freshwater biogeochemical cycles. Our metagenomic time series span multiple years and originate from a eutrophic lake (Lake Mendota) and a humic lake (Trout Bog Lake) with contrasting water chemistry. Our analysis highlights the role of polyamines in the nitrogen cycle, the diversity of diazotrophs between lake types, the balance of assimilatory vs. dissimilatory sulfate reduction in freshwater, the various associations between types of phototrophy and carbon fixation, and the density and diversity of glycoside hydrolases in freshwater microbes. We also investigated aspects of central metabolism such as hydrogen metabolism, oxidative phosphorylation, methylotrophy, and sugar degradation. Finally, by analyzing the dynamics over time in nitrogen fixation genes and Cyanobacteria genomes, we show that the potential for nitrogen fixation is linked to specific populations in Lake Mendota. This work represents an important step towards incorporating microbial data into ecosystem models and provides a better understanding of how microbes may participate in freshwater biogeochemical cycling.
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Affiliation(s)
- Alexandra M Linz
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Shaomei He
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.,Department of Geoscience, University of Wisconsin-Madison, Madison, WI, USA
| | - Sarah L R Stevens
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Robin R Rohwer
- Environmental Chemistry and Technology Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Rex R Malmstrom
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Stefan Bertilsson
- Department of Ecology and Genetics, Limnology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Katherine D McMahon
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.,Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, USA
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16
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Genomic characterization of methylotrophy of Oharaeibacter diazotrophicus strain SM30T. J Biosci Bioeng 2018; 126:667-675. [DOI: 10.1016/j.jbiosc.2018.05.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 05/22/2018] [Accepted: 05/28/2018] [Indexed: 11/21/2022]
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17
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Reyes-Sosa MB, Apodaca-Hernández JE, Arena-Ortiz ML. Bioprospecting for microbes with potential hydrocarbon remediation activity on the northwest coast of the Yucatan Peninsula, Mexico, using DNA sequencing. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 642:1060-1074. [PMID: 30045488 DOI: 10.1016/j.scitotenv.2018.06.097] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 06/05/2018] [Accepted: 06/08/2018] [Indexed: 05/16/2023]
Abstract
Coastal environments harbor diverse microbial communities, which can contain genera with potential bioremediation activity. Next-generation DNA sequencing was used to identify bacteria to the genus level in water and sediment samples collected from the open ocean, shoreline, wetlands and freshwater upwellings on the northwest coast of the Yucatan Peninsula. Supported by an extensive literature review, a phylogenetic investigation of the communities was done using reconstruction of unobserved states software (PICRUSt) to predict metagenome functional content from the sequenced 16S gene in all the samples. Bacterial genera were identified for their potential hydrocarbon bioremediation activity. These included generalist genera commonly reported in hydrocarbon-polluted areas and petroleum reservoirs, as well as specialists such as Alcanivorax and Cycloclasticus. The highest readings for bacteria with potential hydrocarbon bioremediation activity were for the genera Vibrio, Alteromonas, Pseudomonas, Acinetobacter, Burkholderia, Acidovorax and Pseudoalteromonas from different environments in the study area. Some genera were identified only in specific sites; for example, Aquabacterium and Polaromonas were found only in freshwater upwellings. Variation in genera distribution was probably due to differences in environmental conditions in the sampled zones. Bacterial diversity was high in the study area and included numerous genera with known bioremediation activity. Functional prediction of the metagenome indicated that the studied bacterial communities would most probably degrade toluene, naphthalene, chloroalkane and chloroalkene, with lower degradation proportions for aromatic hydrocarbons, fluorobenzoate and xylene. Differences in predicted degradation existed between sediments and water, and between different locations.
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Affiliation(s)
| | | | - María Leticia Arena-Ortiz
- Posgrado en Ciencias del Mar y Limnología UNAM, Mérida, Yucatán, Mexico; Laboratorio de Ecogenonomica Universidad Nacional Autonoma de Mexico.
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18
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Rojas J, Castillo G, Leiva LE, Elgamal S, Orellana O, Ibba M, Katz A. Codon usage revisited: Lack of correlation between codon usage and the number of tRNA genes in enterobacteria. Biochem Biophys Res Commun 2018; 502:450-455. [PMID: 29859934 DOI: 10.1016/j.bbrc.2018.05.168] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 05/25/2018] [Indexed: 01/01/2023]
Abstract
It is widely believed that if a high number of genes are found for any tRNA in a rapidly replicating bacteria, then the cytoplasmic levels of that tRNA will be high and an open reading frame containing a higher frequency of the complementary codon will be translated faster. This idea is based on correlations between the number of tRNA genes, tRNA concentration and the frequency of codon usage observed in a limited number of strains as well as from the fact that artificially changing the number of tRNA genes alters translation efficiency and consequently the amount of properly folded protein synthesized. tRNA gene number may greatly vary in a genome due to duplications, deletions and lateral transfer which in turn would alter the levels and functionality of many proteins. Such changes are potentially deleterious for fitness and as a result it is expected that changes in tRNA gene numbers should be accompanied by a modification of the frequency of codon usage. In contrast to this model, when comparing the number of tRNA genes and the frequency of codon usage of several Salmonella enterica and Escherichia coli strains we found that changes in the number of tRNA genes are not correlated to changes in codon usage. Furthermore, these changes are not correlated with a change in the efficiency of codon translation. These results suggest that once a genome gains or loses tRNA genes, it responds by modulating the concentrations of tRNAs rather than modifying its frequency of codon usage.
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Affiliation(s)
- Joaquín Rojas
- Programa de Biología Celular y Molecular, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, 8380453, Chile
| | - Gabriel Castillo
- Programa de Biología Celular y Molecular, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, 8380453, Chile
| | - Lorenzo Eugenio Leiva
- Programa de Biología Celular y Molecular, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, 8380453, Chile
| | - Sara Elgamal
- Department of Microbiology and The Center for RNA Biology, Ohio State University, Columbus, OH, 43210, USA
| | - Omar Orellana
- Programa de Biología Celular y Molecular, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, 8380453, Chile
| | - Michael Ibba
- Department of Microbiology and The Center for RNA Biology, Ohio State University, Columbus, OH, 43210, USA
| | - Assaf Katz
- Programa de Biología Celular y Molecular, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, 8380453, Chile.
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19
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Suk WA, Heacock ML, Trottier BA, Amolegbe SM, Avakian MD, Henry HF, Carlin DJ, Reed LG. Assessing the Economic and Societal Benefits of SRP-Funded Research. ENVIRONMENTAL HEALTH PERSPECTIVES 2018; 126:065002. [PMID: 29916809 PMCID: PMC6108577 DOI: 10.1289/ehp3534] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 04/17/2018] [Accepted: 04/24/2018] [Indexed: 05/30/2023]
Abstract
BACKGROUND The National Institute of Environmental Health Sciences (NIEHS) Superfund Basic Research and Training Program (SRP) funds a wide range of transdisciplinary research projects spanning the biomedical and environmental sciences and engineering, supporting and promoting the application of that research to solving real-world problems. OBJECTIVES We used a case study approach to identify the economic and societal benefits of SRP-funded research, focusing on the use of potentially hazardous substance remediation and site monitoring tools. We also identified successes and challenges involved in translating SRP grantees' research findings and advances into application. DISCUSSION We identified remediation and detection research projects supported by the SRP with the most potential for economic and societal benefits and selected 36 for analysis. To examine the benefits of these applied technologies, we interviewed 28 SRP-supported researchers and 41 partners. Five case studies emerged with the most complete information on cost savings-total savings estimated at >$100 million. Our analysis identified added societal benefits such as creation of small businesses, land and water reuse, sustainable technologies, exposure reduction, and university-industry partnerships. CONCLUSIONS Research funded by the SRP has yielded significant cost savings while providing additional societal benefits. https://doi.org/10.1289/EHP3534.
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Affiliation(s)
- William A Suk
- Superfund Research Program, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Michelle L Heacock
- Superfund Research Program, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Brittany A Trottier
- Superfund Research Program, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | | | | | - Heather F Henry
- Superfund Research Program, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Danielle J Carlin
- Superfund Research Program, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
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20
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Gonzalez E, Pitre FE, Pagé AP, Marleau J, Guidi Nissim W, St-Arnaud M, Labrecque M, Joly S, Yergeau E, Brereton NJB. Trees, fungi and bacteria: tripartite metatranscriptomics of a root microbiome responding to soil contamination. MICROBIOME 2018; 6:53. [PMID: 29562928 PMCID: PMC5863371 DOI: 10.1186/s40168-018-0432-5] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 03/02/2018] [Indexed: 05/05/2023]
Abstract
BACKGROUND One method for rejuvenating land polluted with anthropogenic contaminants is through phytoremediation, the reclamation of land through the cultivation of specific crops. The capacity for phytoremediation crops, such as Salix spp., to tolerate and even flourish in contaminated soils relies on a highly complex and predominantly cryptic interacting community of microbial life. METHODS Here, Illumina HiSeq 2500 sequencing and de novo transcriptome assembly were used to observe gene expression in washed Salix purpurea cv. 'Fish Creek' roots from trees pot grown in petroleum hydrocarbon-contaminated or non-contaminated soil. All 189,849 assembled contigs were annotated without a priori assumption as to sequence origin and differential expression was assessed. RESULTS The 839 contigs differentially expressed (DE) and annotated from S. purpurea revealed substantial increases in transcripts encoding abiotic stress response equipment, such as glutathione S-transferases, in roots of contaminated trees as well as the hallmarks of fungal interaction, such as SWEET2 (Sugars Will Eventually Be Exported Transporter). A total of 8252 DE transcripts were fungal in origin, with contamination conditions resulting in a community shift from Ascomycota to Basidiomycota genera. In response to contamination, 1745 Basidiomycota transcripts increased in abundance (the majority uniquely expressed in contaminated soil) including major monosaccharide transporter MST1, primary cell wall and lamella CAZy enzymes, and an ectomycorrhiza-upregulated exo-β-1,3-glucanase (GH5). Additionally, 639 DE polycistronic transcripts from an uncharacterised Enterobacteriaceae species were uniformly in higher abundance in contamination conditions and comprised a wide spectrum of genes cryptic under laboratory conditions but considered putatively involved in eukaryotic interaction, biofilm formation and dioxygenase hydrocarbon degradation. CONCLUSIONS Fungal gene expression, representing the majority of contigs assembled, suggests out-competition of white rot Ascomycota genera (dominated by Pyronema), a sometimes ectomycorrhizal (ECM) Ascomycota (Tuber) and ECM Basidiomycota (Hebeloma) by a poorly characterised putative ECM Basidiomycota due to contamination. Root and fungal expression involved transcripts encoding carbohydrate/amino acid (C/N) dialogue whereas bacterial gene expression included the apparatus necessary for biofilm interaction and direct reduction of contamination stress, a potential bacterial currency for a role in tripartite mutualism. Unmistakable within the metatranscriptome is the degree to which the landscape of rhizospheric biology, particularly the important but predominantly uncharacterised fungal genetics, is yet to be discovered.
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Affiliation(s)
- E Gonzalez
- Canadian Center for Computational Genomics, McGill University and Genome Quebec Innovation Center, Montréal, H3A 1A4, Canada
- Department of Human Genetics, McGill University, Montreal, H3A 1B1, Canada
| | - F E Pitre
- Institut de recherche en biologie végétale, University of Montreal, Montreal, QC, H1X 2B2, Canada
- Montreal Botanical Garden, Montreal, QC, H1X 2B2, Canada
| | - A P Pagé
- Aquatic and Crop Resource Development (ACRD), National Research Council Canada, Montréal, QC, H4P 2R2, Canada
| | - J Marleau
- Institut de recherche en biologie végétale, University of Montreal, Montreal, QC, H1X 2B2, Canada
| | - W Guidi Nissim
- Department of Agri-food and Environmental Science, University of Florence, Viale delle Idee, Sesto Fiorentino, FI, Italy
| | - M St-Arnaud
- Institut de recherche en biologie végétale, University of Montreal, Montreal, QC, H1X 2B2, Canada
- Montreal Botanical Garden, Montreal, QC, H1X 2B2, Canada
| | - M Labrecque
- Institut de recherche en biologie végétale, University of Montreal, Montreal, QC, H1X 2B2, Canada
- Montreal Botanical Garden, Montreal, QC, H1X 2B2, Canada
| | - S Joly
- Institut de recherche en biologie végétale, University of Montreal, Montreal, QC, H1X 2B2, Canada
- Montreal Botanical Garden, Montreal, QC, H1X 2B2, Canada
| | - E Yergeau
- Institut National de la Recherche Scientifique, Centre INRS-Institut Armand-Frappier, Laval, QC, Canada
| | - N J B Brereton
- Institut de recherche en biologie végétale, University of Montreal, Montreal, QC, H1X 2B2, Canada.
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21
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Ekimova GA, Fedorov DN, Tani A, Doronina NV, Trotsenko YA. Distribution of 1-aminocyclopropane-1-carboxylate deaminase and d-cysteine desulfhydrase genes among type species of the genus Methylobacterium. Antonie van Leeuwenhoek 2018. [DOI: 10.1007/s10482-018-1061-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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22
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Kou S, Vincent G, Gonzalez E, Pitre FE, Labrecque M, Brereton NJB. The Response of a 16S Ribosomal RNA Gene Fragment Amplified Community to Lead, Zinc, and Copper Pollution in a Shanghai Field Trial. Front Microbiol 2018; 9:366. [PMID: 29545788 PMCID: PMC5838024 DOI: 10.3389/fmicb.2018.00366] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 02/16/2018] [Indexed: 11/27/2022] Open
Abstract
Industrial and agricultural activities have caused extensive metal contamination of land throughout China and across the globe. The pervasive nature of metal pollution can be harmful to human health and can potentially cause substantial negative impact to the biosphere. To investigate the impact of anthropogenic metal pollution found in high concentrations in industrial, agricultural, and urban environments, 16S ribosomal RNA gene amplicon sequencing was used to track change in the amplified microbial community after metal contamination in a large-scale field experiment in Shanghai. A total of 1,566 operational taxonomic units (OTUs) identified from 448,108 sequences gathered from 20 plots treated as controls or with lead, zinc, copper, or all three metals. Constrained Analysis of Principal Coordinates ordination did not separate control and lead treatment but could separate control/lead, zinc, copper, and three metal treatment. DESeq2 was applied to identify 93 significantly differentially abundant OTUs varying in 211 pairwise instances between the treatments. Differentially abundant OTUs representing genera or species belonging to the phyla Chloroflexi, Cyanobacteria, Firmicutes, Latescibacteria, and Planctomycetes were almost universally reduced in abundance due to zinc, copper, or three metal treatment; with three metal treatment abolishing the detection of some OTUs, such as Leptolyngbya, Desmonostoc muscorum, and Microcoleus steenstrupii. The greatest increases due to metal treatment were observed in Bacteroidetes, Actinobacteria, Chlamydiae, Nitrospirae, and Proteobacteria (α, β, δ, and γ); the most (relative) abundant being uncharacterized species within the genera Methylobacillus, Solirubrobacter, and Ohtaekwangia. Three metal treatment alone resulted in identification of 22 OTUs (genera or species) which were not detected in control soil, notably including Yonghaparkia alkaliphila, Pedobacter steynii, Pseudolabrys taiwanensis, Methylophilus methylotrophus, Nitrosospira, and Lysobacter mobilis. The capacity to track alterations of an amplified microbial community at high taxonomic resolution using modern bioinformatic approaches, as well as identifying where that resolution is lost for technical or biological reasons, provides an insight into the complexity of the microbial world resisting anthropogenic pollution. While functional assessment of uncharacterized organisms within environmental samples is technically challenging, an important step is observing those organisms able to tolerate extreme stress and to recognize the extent to which important amplifiable community members still require characterization.
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Affiliation(s)
- Shumeng Kou
- Shanghai Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Gilles Vincent
- Shanghai Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Emmanuel Gonzalez
- Canadian Centre for Computational Genomics, McGill University and Genome Quebec Innovation Centre, Montréal, QC, Canada
| | - Frederic E. Pitre
- Institut de Recherche en Biologie Végétale, Montreal Botanical Garden, Montréal, QC, Canada
| | - Michel Labrecque
- Institut de Recherche en Biologie Végétale, Montreal Botanical Garden, Montréal, QC, Canada
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Lu YZ, Chen GJ, Bai YN, Fu L, Qin LP, Zeng RJ. Chromium isotope fractionation during Cr(VI) reduction in a methane-based hollow-fiber membrane biofilm reactor. WATER RESEARCH 2018; 130:263-270. [PMID: 29241112 DOI: 10.1016/j.watres.2017.11.045] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 10/23/2017] [Accepted: 11/22/2017] [Indexed: 06/07/2023]
Abstract
Chromium (Cr) isotope fractionation analysis is a promising tool for monitoring Cr(VI) reduction in natural aqueous systems. In addition, large amounts of CH4 in natural aqueous sediments are oxidized to CO2 through methanotrophs, thereby mitigating emissions to the atmosphere. However, the investigations on the Cr(VI) reduction process with methanotrophs, and the associated Cr isotope fractionation patterns are scarce. In this study, we have shown that Cr(VI) reduction can occur in the presence of CH4 as the sole electron donor in a hollow-fiber membrane reactor (HfMBR) after direct bacteria enrichment from sediment samples. Products of the methane oxidation by the methanotrophs are used by microbes to reduce Cr(VI) as shown by the progressive increase in δ53Cr with time in the CH4 feed reactor. The isotope fractionation factor (ε) of -2.62 ± 0.20‰ was obtained from the application of the Rayleigh distillation model. The results of Cr isotope fractionation analysis also explained the decrease of Cr(VI) concentration in the N2 feed reactor, where the δ53Cr values remained steady in the first two weeks but significantly increased in the last two weeks, indicating that physical adsorption and subsequent Cr(VI) reduction occurred. This study extended the application of Cr isotope fractionation, showing the suitability of this method for clarifying different Cr(VI) removal processes.
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Affiliation(s)
- Yong-Ze Lu
- CAS Key Laboratory for Urban Pollutant Conversion, Department of Chemistry, University of Science & Technology of China, Hefei 230026, China
| | - Guo-Jun Chen
- CAS Key Laboratory of Crust-Mantle Materials and Environments, School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Ya-Nan Bai
- CAS Key Laboratory for Urban Pollutant Conversion, Department of Chemistry, University of Science & Technology of China, Hefei 230026, China; Advanced Laboratory for Environmental Research and Technology, USTC-CityU, Suzhou 215123, China
| | - Liang Fu
- CAS Key Laboratory for Urban Pollutant Conversion, Department of Chemistry, University of Science & Technology of China, Hefei 230026, China
| | - Li-Ping Qin
- CAS Key Laboratory of Crust-Mantle Materials and Environments, School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Raymond Jianxiong Zeng
- CAS Key Laboratory for Urban Pollutant Conversion, Department of Chemistry, University of Science & Technology of China, Hefei 230026, China; Advanced Laboratory for Environmental Research and Technology, USTC-CityU, Suzhou 215123, China.
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24
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Morlett Chávez JA, Ascacio Martínez JÁ, Haskins WE, Acuña Askar K. Gene Expression during BTEX Biodegradation by a Microbial Consortium Acclimatized to Unleaded Gasoline and a Pseudomonas putida Strain (HM346961) Isolated from It. Pol J Microbiol 2017; 66:189-199. [DOI: 10.5604/01.3001.0010.7836] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Pseudomonas putida strain (HM346961) was isolated from a consortium of bacteria acclimatized to unleaded gasoline-contaminated water. The consortium can efficiently remove benzene, toluene, ethylbenzene and xylene (BTEX) isomers, and a similar capability was observed with the P. putida strain. Proteome of this strain showed certain similarities with that of other strains exposed to the hydrocarbon compounds. Furthermore, the toluene di-oxygenase (tod) gene was up-regulated in P. putida strain when exposed to toluene, ethylbenzene, xylene, and BTEX. In contrast, the tod gene of P. putida F1 (ATCC 700007) was up-regulated only in the presence of toluene and BTEX. Several differences in the nucleotide and protein sequences of these two tod genes were observed. This suggests that tod up-regulation in P. putida strain may partially explain their great capacity to remove aromatic compounds, relative to P. putida F1. Therefore, new tod and P. putida strain are promising for various environmental applications.
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Affiliation(s)
- Jesús A. Morlett Chávez
- Laboratory of Genomics and Bioinformatics, Autonomous University of Nuevo Leon, Monterrey Nuevo León, Mexico; Laboratory of Biotechnology, Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Autonomous University of Nuevo Leon, Monterrey Nuevo León, Mexico
| | - Jorge Á. Ascacio Martínez
- Laboratory of Biotechnology, Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Autonomous University of Nuevo Leon, Monterrey Nuevo León, Mexico
| | - William E. Haskins
- Departments of Biology and Chemistry, University of Texas at San Antonio, San Antonio, TX, USA; RCMI Proteomics, University of Texas at San Antonio, San Antonio, TX, USA; Protein Biomarkers Cores, University of Texas at San Antonio, San Antonio, TX, USA
| | - Karim Acuña Askar
- Laboratory of Environmental Bioremediation, Department of Microbiology, Faculty of Medicine, Autonomous University of Nuevo Leon, Monterrey Nuevo León, Mexico
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25
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Mukherjee A, Chettri B, Langpoklakpam JS, Basak P, Prasad A, Mukherjee AK, Bhattacharyya M, Singh AK, Chattopadhyay D. Bioinformatic Approaches Including Predictive Metagenomic Profiling Reveal Characteristics of Bacterial Response to Petroleum Hydrocarbon Contamination in Diverse Environments. Sci Rep 2017; 7:1108. [PMID: 28439121 PMCID: PMC5430712 DOI: 10.1038/s41598-017-01126-3] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 03/22/2017] [Indexed: 02/01/2023] Open
Abstract
Microbial remediation of oil polluted habitats remains one of the foremost methods for restoration of petroleum hydrocarbon contaminated environments. The development of effective bioremediation strategies however, require an extensive understanding of the resident microbiome of these habitats. Recent developments such as high-throughput sequencing has greatly facilitated the advancement of microbial ecological studies in oil polluted habitats. However, effective interpretation of biological characteristics from these large datasets remain a considerable challenge. In this study, we have implemented recently developed bioinformatic tools for analyzing 65 16S rRNA datasets from 12 diverse hydrocarbon polluted habitats to decipher metagenomic characteristics of the resident bacterial communities. Using metagenomes predicted from 16S rRNA gene sequences through PICRUSt, we have comprehensively described phylogenetic and functional compositions of these habitats and additionally inferred a multitude of metagenomic features including 255 taxa and 414 functional modules which can be used as biomarkers for effective distinction between the 12 oil polluted sites. Additionally, we show that significantly over-represented taxa often contribute to either or both, hydrocarbon degradation and additional important functions. Our findings reveal significant differences between hydrocarbon contaminated sites and establishes the importance of endemic factors in addition to petroleum hydrocarbons as driving factors for sculpting hydrocarbon contaminated bacteriomes.
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Affiliation(s)
- Arghya Mukherjee
- Department of Biotechnology, University of Calcutta, Kolkata, West Bengal, India
| | - Bobby Chettri
- Department of Biochemistry, North-Eastern Hill University, Shillong, India
| | | | - Pijush Basak
- Department of Biochemistry, University of Calcutta, Kolkata, West Bengal, India
| | - Aravind Prasad
- Dr. D.Y.Patil Biotechnology and Bioinformatics Institute, Pune, India
| | - Ashis K Mukherjee
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, India
| | | | - Arvind K Singh
- Department of Biochemistry, North-Eastern Hill University, Shillong, India
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Biodegradation of Methyl tert-Butyl Ether by Co-Metabolism with a Pseudomonas sp. Strain. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2016; 13:ijerph13090883. [PMID: 27608032 PMCID: PMC5036716 DOI: 10.3390/ijerph13090883] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 07/17/2016] [Accepted: 08/30/2016] [Indexed: 11/24/2022]
Abstract
Co-metabolic bioremediation is supposed to be an impressive and promising approach in the elimination technology of methyl tert-butyl ether (MTBE), which was found to be a common pollutant worldwide in the ground or underground water in recent years. In this paper, bacterial strain DZ13 (which can co-metabolically degrade MTBE) was isolated and named as Pseudomonas sp. DZ13 based on the result of 16S rRNA gene sequencing analysis. Strain DZ13 could grow on n-alkanes (C5-C8), accompanied with the co-metabolic degradation of MTBE. Diverse n-alkanes with different carbon number showed a significant influence on the degradation rate of MTBE and accumulation of tert-butyl alcohol (TBA). When Pseudomonas sp. DZ13 co-metabolically degraded MTBE with n-pentane as the growth substrate, a higher MTBE-degrading rate (Vmax = 38.1 nmol/min/mgprotein, Ks = 6.8 mmol/L) and lower TBA-accumulation was observed. In the continuous degradation experiment, the removal efficiency of MTBE by Pseudomonas sp. Strain DZ13 did not show an obvious decrease after five times of continuous addition.
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27
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Joshi G, Schmidt R, Scow KM, Denison MS, Hristova KR. Effect of benzene and ethylbenzene on the transcription of methyl-tert-butyl ether degradation genes of Methylibium petroleiphilum PM1. MICROBIOLOGY-SGM 2016; 162:1563-1571. [PMID: 27450417 DOI: 10.1099/mic.0.000338] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Methyl-tert-butyl ether (MTBE) and its degradation by-product, tert-butyl alcohol (TBA), are widespread contaminants detected frequently in groundwater in California. Since MTBE was used as a fuel oxygenate for almost two decades, leaking underground fuel storage tanks are an important source of contamination. Gasoline components such as BTEX (benzene, toluene, ethylbenzene and xylenes) are often present in mixtures with MTBE and TBA. Investigations of interactions between BTEX and MTBE degradation have not yielded consistent trends, and the molecular mechanisms of BTEX compounds' impact on MTBE degradation are not well understood. We investigated trends in transcription of biodegradation genes in the MTBE-degrading bacterium, Methylibium petroleiphilum PM1 upon exposure to MTBE, TBA, ethylbenzene and benzene as individual compounds or in mixtures. We designed real-time quantitative PCR assays to target functional genes of strain PM1 and provide evidence for induction of genes mdpA (MTBE monooxygenase), mdpJ (TBA hydroxylase) and bmoA (benzene monooxygenase) in response to MTBE, TBA and benzene, respectively. Delayed induction of mdpA and mdpJ transcription occurred with mixtures of benzene and MTBE or TBA, respectively. bmoA transcription was similar in the presence of MTBE or TBA with benzene as in their absence. Our results also indicate that ethylbenzene, previously proposed as an inhibitor of MTBE degradation in some bacteria, inhibits transcription of mdpA, mdpJ and bmoAgenes in strain PM1.
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Affiliation(s)
- Geetika Joshi
- Department of Land, Air and Water Resources, One Shields Avenue, University of California, Davis, CA 95616, USA
| | - Radomir Schmidt
- Department of Land, Air and Water Resources, One Shields Avenue, University of California, Davis, CA 95616, USA
| | - Kate M Scow
- Department of Land, Air and Water Resources, One Shields Avenue, University of California, Davis, CA 95616, USA
| | - Michael S Denison
- Department of Environmental Toxicology, One Shields Avenue, University of California, Davis, CA 95616, USA
| | - Krassimira R Hristova
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, USA.,Department of Land, Air and Water Resources, One Shields Avenue, University of California, Davis, CA 95616, USA
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28
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Hamidat M, Barakat M, Ortet P, Chanéac C, Rose J, Bottero JY, Heulin T, Achouak W, Santaella C. Design Defines the Effects of Nanoceria at a Low Dose on Soil Microbiota and the Potentiation of Impacts by the Canola Plant. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:6892-6901. [PMID: 27243334 DOI: 10.1021/acs.est.6b01056] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Soils act as nanoceria sinks via agricultural spreading and surface waters. Canola plants were grown for one month in soil spiked with nanoceria (1 mg·kg(-1)). To define the role of nanomaterials design on environmental impacts, we studied nanoceria with different sizes (3.5 or 31 nm) and coating (citrate). We measured microbial activities involved in C, N, and P cycling in the rhizosphere and unplanted soil. Bacterial community structure was analyzed in unplanted soil, rhizosphere, and plant roots by 454-pyrosequencing of the 16S rRNA gene. This revealed an impact gradient dependent on nanomaterials design, ranging from decreased microbial enzymatic activities in planted soil to alterations in bacterial community structure in roots. Particle size/aggregation was a key parameter in modulating nanoceria effects on root communities. Citrate coating lowered the impact on microbial enzymatic activities but triggered variability in the bacterial community structure near the plant root. Some nanoceria favored taxa whose closest relatives are hydrocarbon-degrading bacteria and disadvantaged taxa frequently associated in consortia with disease-suppressive activity toward plant pathogens. This work provides a basis to determine outcomes of nanoceria in soil, at a dose close to predicted environmental concentrations, and to design them to minimize these impacts.
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Affiliation(s)
- Mohamed Hamidat
- Laboratory of Microbial Ecology of the Rhizosphere and Extreme Environments (LEMIRE), Aix-Marseille Université, CEA, CNRS, UMR 7265 Biosciences and Biotechnology Institute of Aix-Marseille (BIAM), ECCOREV FR 3098, CEA Cadarache, St-Paul-lez-Durance 13108, France
- GDRi iCEINT, International Consortium for the Environmental Implication of Nanotechnology, CNRS-Duke University , F-13545 Aix-en-Provence, France
| | - Mohamed Barakat
- Laboratory of Microbial Ecology of the Rhizosphere and Extreme Environments (LEMIRE), Aix-Marseille Université, CEA, CNRS, UMR 7265 Biosciences and Biotechnology Institute of Aix-Marseille (BIAM), ECCOREV FR 3098, CEA Cadarache, St-Paul-lez-Durance 13108, France
- GDRi iCEINT, International Consortium for the Environmental Implication of Nanotechnology, CNRS-Duke University , F-13545 Aix-en-Provence, France
| | - Philippe Ortet
- Laboratory of Microbial Ecology of the Rhizosphere and Extreme Environments (LEMIRE), Aix-Marseille Université, CEA, CNRS, UMR 7265 Biosciences and Biotechnology Institute of Aix-Marseille (BIAM), ECCOREV FR 3098, CEA Cadarache, St-Paul-lez-Durance 13108, France
- GDRi iCEINT, International Consortium for the Environmental Implication of Nanotechnology, CNRS-Duke University , F-13545 Aix-en-Provence, France
| | - Corinne Chanéac
- GDRi iCEINT, International Consortium for the Environmental Implication of Nanotechnology, CNRS-Duke University , F-13545 Aix-en-Provence, France
- Chimie de la Matière Condensée, UMR7574, Collège de France, Université de Jussieu , Paris F-75231, France
| | - Jérome Rose
- GDRi iCEINT, International Consortium for the Environmental Implication of Nanotechnology, CNRS-Duke University , F-13545 Aix-en-Provence, France
- CNRS, Aix-Marseille Université, IRD, CEREGE UM34, F-13545 Aix en Provence, France
| | - Jean-Yves Bottero
- GDRi iCEINT, International Consortium for the Environmental Implication of Nanotechnology, CNRS-Duke University , F-13545 Aix-en-Provence, France
- CNRS, Aix-Marseille Université, IRD, CEREGE UM34, F-13545 Aix en Provence, France
| | - Thierry Heulin
- Laboratory of Microbial Ecology of the Rhizosphere and Extreme Environments (LEMIRE), Aix-Marseille Université, CEA, CNRS, UMR 7265 Biosciences and Biotechnology Institute of Aix-Marseille (BIAM), ECCOREV FR 3098, CEA Cadarache, St-Paul-lez-Durance 13108, France
- GDRi iCEINT, International Consortium for the Environmental Implication of Nanotechnology, CNRS-Duke University , F-13545 Aix-en-Provence, France
| | - Wafa Achouak
- Laboratory of Microbial Ecology of the Rhizosphere and Extreme Environments (LEMIRE), Aix-Marseille Université, CEA, CNRS, UMR 7265 Biosciences and Biotechnology Institute of Aix-Marseille (BIAM), ECCOREV FR 3098, CEA Cadarache, St-Paul-lez-Durance 13108, France
- GDRi iCEINT, International Consortium for the Environmental Implication of Nanotechnology, CNRS-Duke University , F-13545 Aix-en-Provence, France
| | - Catherine Santaella
- Laboratory of Microbial Ecology of the Rhizosphere and Extreme Environments (LEMIRE), Aix-Marseille Université, CEA, CNRS, UMR 7265 Biosciences and Biotechnology Institute of Aix-Marseille (BIAM), ECCOREV FR 3098, CEA Cadarache, St-Paul-lez-Durance 13108, France
- GDRi iCEINT, International Consortium for the Environmental Implication of Nanotechnology, CNRS-Duke University , F-13545 Aix-en-Provence, France
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29
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Sun W, Li Y, McGuinness LR, Luo S, Huang W, Kerkhof LJ, Mack EE, Häggblom MM, Fennell DE. Identification of Anaerobic Aniline-Degrading Bacteria at a Contaminated Industrial Site. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:11079-11088. [PMID: 26280684 DOI: 10.1021/acs.est.5b02166] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Anaerobic aniline biodegradation was investigated under different electron-accepting conditions using contaminated canal and groundwater aquifer sediments from an industrial site. Aniline loss was observed in nitrate- and sulfate-amended microcosms and in microcosms established to promote methanogenic conditions. Lag times of 37 days (sulfate amended) to more than 100 days (methanogenic) were observed prior to activity. Time-series DNA-stable isotope probing (SIP) was used to identify bacteria that incorporated (13)C-labeled aniline in the microcosms established to promote methanogenic conditions. In microcosms from heavily contaminated aquifer sediments, a phylotype with 92.7% sequence similarity to Ignavibacterium album was identified as a dominant aniline degrader as indicated by incorporation of (13)C-aniline into its DNA. In microcosms from contaminated canal sediments, a bacterial phylotype within the family Anaerolineaceae, but without a match to any known genus, demonstrated the assimilation of (13)C-aniline. Acidovorax spp. were also identified as putative aniline degraders in both of these two treatments, indicating that these species were present and active in both the canal and aquifer sediments. There were multiple bacterial phylotypes associated with anaerobic degradation of aniline at this complex industrial site, which suggests that anaerobic transformation of aniline is an important process at the site. Furthermore, the aniline degrading phylotypes identified in the current study are not related to any known aniline-degrading bacteria. The identification of novel putative aniline degraders expands current knowledge regarding the potential fate of aniline under anaerobic conditions.
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Affiliation(s)
- Weimin Sun
- Department of Environmental Sciences, Rutgers University , 14 College Farm Road, New Brunswick, New Jersey 08901, United States
| | - Yun Li
- Department of Environmental Sciences, Rutgers University , 14 College Farm Road, New Brunswick, New Jersey 08901, United States
| | | | - Shuai Luo
- Department of Environmental Sciences, Rutgers University , 14 College Farm Road, New Brunswick, New Jersey 08901, United States
| | - Weilin Huang
- Department of Environmental Sciences, Rutgers University , 14 College Farm Road, New Brunswick, New Jersey 08901, United States
| | | | - E Erin Mack
- DuPont, Corporate Remediation Group, Wilmington, Delaware 19714, United States
| | | | - Donna E Fennell
- Department of Environmental Sciences, Rutgers University , 14 College Farm Road, New Brunswick, New Jersey 08901, United States
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30
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Szabó Z, Gyula P, Robotka H, Bató E, Gálik B, Pach P, Pekker P, Papp I, Bihari Z. Draft genome sequence of Methylibium sp. strain T29, a novel fuel oxygenate-degrading bacterial isolate from Hungary. Stand Genomic Sci 2015. [PMID: 26221420 PMCID: PMC4517660 DOI: 10.1186/s40793-015-0023-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Methylibium sp. strain T29 was isolated from a gasoline-contaminated aquifer and proved to have excellent capabilities in degrading some common fuel oxygenates like methyl tert-butyl ether, tert-amyl methyl ether and tert-butyl alcohol along with other organic compounds. Here, we report the draft genome sequence of M. sp. strain T29 together with the description of the genome properties and its annotation. The draft genome consists of 608 contigs with a total size of 4,449,424 bp and an average coverage of 150×. The genome exhibits an average G + C content of 68.7 %, and contains 4754 protein coding and 52 RNA genes, including 48 tRNA genes. 71 % of the protein coding genes could be assigned to COG (Clusters of Orthologous Groups) categories. A formerly unknown circular plasmid designated as pT29A was isolated and sequenced separately and found to be 86,856 bp long.
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Affiliation(s)
- Zsolt Szabó
- Bay Zoltán Nonprofit Ltd. for Applied Research, Budapest, Hungary
| | - Péter Gyula
- Bay Zoltán Nonprofit Ltd. for Applied Research, Budapest, Hungary
| | - Hermina Robotka
- Bay Zoltán Nonprofit Ltd. for Applied Research, Budapest, Hungary
| | - Emese Bató
- Bay Zoltán Nonprofit Ltd. for Applied Research, Budapest, Hungary
| | - Bence Gálik
- Bay Zoltán Nonprofit Ltd. for Applied Research, Budapest, Hungary
| | - Péter Pach
- Bay Zoltán Nonprofit Ltd. for Applied Research, Budapest, Hungary
| | - Péter Pekker
- Materials Science Research Group, Hungarian Academy of Sciences-University of Miskolc, Miskolc, Hungary
| | - Ildikó Papp
- Bay Zoltán Nonprofit Ltd. for Applied Research, Budapest, Hungary
| | - Zoltán Bihari
- Bay Zoltán Nonprofit Ltd. for Applied Research, Budapest, Hungary
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31
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Li S, Li D, Yan W. Cometabolism of methyl tert-butyl ether by a new microbial consortium ERS. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:10196-10205. [PMID: 25697553 DOI: 10.1007/s11356-015-4211-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 02/04/2015] [Indexed: 06/04/2023]
Abstract
The release of methyl tert-butyl-ether (MTBE) into the environment has increased the worldwide concern about the pollution of MTBE. In this paper, a microbial consortium was isolated from the soil sample near an oil station, which can degrade MTBE directly with a low biomass yield and MTBE degrading efficiency. Further research has indicated that this consortium can degrade MTBE efficiently when grown on n-octane as the cometabolic substrate. The results of 16S rDNA based on phylogenetic analysis of the selected operating taxonomic units (OTUs) involved in the consortium revealed that one OTU was related to Pseudomonas putida GPo1, which could cometabolically degrade MTBE on the growth of n-octane. This may help explain why n-octane could be the optimal cometabolic substrate of the consortium for MTBE degradation. Furthermore, the degradation of MTBE was observed along with the consumption of n-octane. Different K s values for MTBE were observed for cells grown with or without n-octane, suggesting that different enzymes are responsible for the oxidation of MTBE in cells grown on n-octane or MTBE. The results are discussed in terms of their impacts on our understanding of MTBE biodegradation and cometabolism.
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Affiliation(s)
- Shanshan Li
- Department of Environmental Science and Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China
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32
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Henriques AC, De Marco P. Methanesulfonate (MSA) Catabolic Genes from Marine and Estuarine Bacteria. PLoS One 2015; 10:e0125735. [PMID: 25978049 PMCID: PMC4433239 DOI: 10.1371/journal.pone.0125735] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 03/26/2015] [Indexed: 11/19/2022] Open
Abstract
Quantitatively, methanesulfonate (MSA) is a very relevant compound in the global biogeochemical sulfur cycle. Its utilization by bacteria as a source of carbon and energy has been described and a specific enzyme, methanesulfonate monooxygenase (MSAMO), has been found to perform the first catabolic step of its oxidation. Other proteins seemingly involved in the import of MSA into bacterial cells have been reported. In this study, we obtained novel sequences of genes msmA and msmE from marine, estuary and soil MSA-degraders (encoding the large subunit of the MSAMO enzyme and the periplasmic component of the import system, respectively). We also obtained whole-genome sequences of two novel marine Filomicrobium strains, Y and W, and annotated two full msm operons in these genomes. Furthermore, msmA and msmE sequences were amplified from North Atlantic seawater and analyzed. Good conservation of the MsmA deduced protein sequence was observed in both cultured strains and metagenomic clones. A long spacer sequence in the Rieske-type [2Fe-2S] cluster-binding motif within MsmA was found to be conserved in all instances, supporting the hypothesis that this feature is specific to the large (α) subunit of the MSAMO enzyme. The msmE gene was more difficult to amplify, from both cultivated isolates and marine metagenomic DNA. However, 3 novel msmE sequences were obtained from isolated strains and one directly from seawater. With both genes, our results combined with previous metagenomic analyses seem to imply that moderate to high-GC strains are somehow favored during enrichment and isolation of MSA-utilizing bacteria, while the majority of msm genes obtained by cultivation-independent methods have low levels of GC%, which is a clear example of the misrepresentation of natural populations that culturing, more often than not, entails. Nevertheless, the data obtained in this work show that MSA-degrading bacteria are abundant in surface seawater, which suggests ecological relevance for this metabolic group of bacteria.
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Affiliation(s)
- Ana C. Henriques
- Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde, CESPU, Rua Central de Gandra 1317, 4585–116 Paredes, Portugal
| | - Paolo De Marco
- Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde, CESPU, Rua Central de Gandra 1317, 4585–116 Paredes, Portugal
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Wu X, Ge T, Wang W, Yuan H, Wegner CE, Zhu Z, Whiteley AS, Wu J. Cropping systems modulate the rate and magnitude of soil microbial autotrophic CO2 fixation in soil. Front Microbiol 2015; 6:379. [PMID: 26005435 PMCID: PMC4424977 DOI: 10.3389/fmicb.2015.00379] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2014] [Accepted: 04/13/2015] [Indexed: 11/26/2022] Open
Abstract
The effect of different cropping systems on CO2 fixation by soil microorganisms was studied by comparing soils from three exemplary cropping systems after 10 years of agricultural practice. Studied cropping systems included: continuous cropping of paddy rice (rice-rice), rotation of paddy rice and rapeseed (rice-rapeseed), and rotated cropping of rapeseed and corn (rapeseed-corn). Soils from different cropping systems were incubated with continuous 14C-CO2 labeling for 110 days. The CO2-fixing bacterial communities were investigated by analyzing the cbbL gene encoding ribulose-1,5-bisphosphate carboxylase oxygenase (RubisCO). Abundance, diversity and activity of cbbL-carrying bacteria were analyzed by quantitative PCR, cbbL clone libraries and enzyme assays. After 110 days incubation, substantial amounts of 14C-CO2 were incorporated into soil organic carbon (14C-SOC) and microbial biomass carbon (14C-MBC). Rice-rice rotated soil showed stronger incorporation rates when looking at 14C-SOC and 14C-MBC contents. These differences in incorporation rates were also reflected by determined RubisCO activities. 14C-MBC, cbbL gene abundances and RubisCO activity were found to correlate significantly with 14C-SOC, indicating cbbL-carrying bacteria to be key players for CO2 fixation in these soils. The analysis of clone libraries revealed distinct cbbL-carrying bacterial communities for the individual soils analyzed. Most of the identified operational taxonomic units (OTU) were related to Nitrobacter hamburgensis, Methylibium petroleiphilum, Rhodoblastus acidophilus, Bradyrhizobium, Cupriavidus metallidurans, Rubrivivax, Burkholderia, Stappia, and Thiobacillus thiophilus. OTUs related to Rubrivivax gelatinosus were specific for rice-rice soil. OTUs linked to Methylibium petroleiphilum were exclusively found in rice-rapeseed soil. Observed differences could be linked to differences in soil parameters such as SOC. We conclude that the long-term application of cropping systems alters underlying soil parameters, which in turn selects for distinct autotrophic communities.
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Affiliation(s)
- Xiaohong Wu
- Key Laboratory of Agro-ecological Processes in Subtropical Region and Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences Changsha, China ; ISA-CAS and UWA Joint Laboratory for Soil Systems Biology Changsha, China
| | - Tida Ge
- Key Laboratory of Agro-ecological Processes in Subtropical Region and Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences Changsha, China ; ISA-CAS and UWA Joint Laboratory for Soil Systems Biology Changsha, China
| | - Wei Wang
- Key Laboratory of Agro-ecological Processes in Subtropical Region and Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences Changsha, China
| | - Hongzhao Yuan
- Key Laboratory of Agro-ecological Processes in Subtropical Region and Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences Changsha, China
| | - Carl-Eric Wegner
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology Marburg, Germany
| | - Zhenke Zhu
- Key Laboratory of Agro-ecological Processes in Subtropical Region and Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences Changsha, China ; ISA-CAS and UWA Joint Laboratory for Soil Systems Biology Changsha, China
| | - Andrew S Whiteley
- ISA-CAS and UWA Joint Laboratory for Soil Systems Biology Changsha, China ; School of Earth and Environment, The University of Western Australia Crawley, WA, Australia
| | - Jinshui Wu
- Key Laboratory of Agro-ecological Processes in Subtropical Region and Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences Changsha, China ; ISA-CAS and UWA Joint Laboratory for Soil Systems Biology Changsha, China
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Careghini A, Saponaro S, Sezenna E, Daghio M, Franzetti A, Gandolfi I, Bestetti G. Lab-scale tests and numerical simulations for in situ treatment of polluted groundwater. JOURNAL OF HAZARDOUS MATERIALS 2015; 287:162-170. [PMID: 25644032 DOI: 10.1016/j.jhazmat.2015.01.028] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 12/23/2014] [Accepted: 01/11/2015] [Indexed: 06/04/2023]
Abstract
Methyl tert-butyl ether (MTBE) is used at significant percentages as an additive of unleaded gasoline. The physical-chemical properties of the substance (water solubility, soil organic carbon-water partition coefficient) cause high mobility and high concentrations in groundwater. Laboratory scale batch and column tests and mathematical modeling were performed to study the feasibility of a biobarrier (BB), that is an in situ permeable biological barrier with or without inoculation, for the remediation of MTBE and other gasoline-derived pollutants (benzene, toluene, ethylbenzene, o-xylene and m+p-xylenes, BTEXs) polluted groundwater and to estimate kinetic constants. The experimental results showed simultaneous biodegradation of MTBE and BTEXs, with similar removals in the uninoculated and the inoculated systems. Ranges for the first order kinetic removal were obtained for MTBE ((0.18±0.02)/(0.28±0.11d(-1))), B ((0.39±0.12)/(0.56±0.12d(-1))), T ((0.51±0.03)/(0.78±0.15d(-1))), E ((0.46±0.18)/(1.57±0.21d(-1))), o-X ((0.24±0.08)/(0.64±0.09d(-1))) and m+p-X ((0.20±0.04)/(1.21±0.04d(-1))). The results of the laboratory tests allowed to improve mathematical modeling in order to design a full-scale BB at a gasoline-contaminated site.
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Affiliation(s)
- A Careghini
- Politecnico di Milano, DICA Sez. Ambientale, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - S Saponaro
- Politecnico di Milano, DICA Sez. Ambientale, Piazza Leonardo da Vinci 32, 20133 Milano, Italy.
| | - E Sezenna
- Politecnico di Milano, DICA Sez. Ambientale, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - M Daghio
- Università degli Studi Milano-Bicocca, Dipartimento di Scienze dell'Ambiente e del Territorio, Piazza della Scienza 1, 20126 Milano, Italy
| | - A Franzetti
- Università degli Studi Milano-Bicocca, Dipartimento di Scienze dell'Ambiente e del Territorio, Piazza della Scienza 1, 20126 Milano, Italy
| | - I Gandolfi
- Università degli Studi Milano-Bicocca, Dipartimento di Scienze dell'Ambiente e del Territorio, Piazza della Scienza 1, 20126 Milano, Italy
| | - G Bestetti
- Università degli Studi Milano-Bicocca, Dipartimento di Scienze dell'Ambiente e del Territorio, Piazza della Scienza 1, 20126 Milano, Italy
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Aleklett K, Leff JW, Fierer N, Hart M. Wild plant species growing closely connected in a subalpine meadow host distinct root-associated bacterial communities. PeerJ 2015; 3:e804. [PMID: 25755932 PMCID: PMC4349149 DOI: 10.7717/peerj.804] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 02/06/2015] [Indexed: 02/01/2023] Open
Abstract
Plant roots are known to harbor large and diverse communities of bacteria. It has been suggested that plant identity can structure these root-associated communities, but few studies have specifically assessed how the composition of root microbiota varies within and between plant species growing under natural conditions. We assessed the community composition of endophytic and epiphytic bacteria through high throughput sequencing using 16S rDNA derived from root tissues collected from a population of a wild, clonal plant (Orange hawkweed-Pilosella aurantiaca) as well as two neighboring plant species (Oxeye daisy-Leucanthemum vulgare and Alsike clover-Trifolium hybridum). Our first goal was to determine if plant species growing in close proximity, under similar environmental conditions, still hosted unique root microbiota. Our results showed that plants of different species host distinct bacterial communities in their roots. In terms of community composition, Betaproteobacteria (especially the family Oxalobacteraceae) were found to dominate in the root microbiota of L. vulgare and T. hybridum samples, whereas the root microbiota of P. aurantiaca had a more heterogeneous distribution of bacterial abundances where Gammaproteobacteria and Acidobacteria occupied a larger portion of the community. We also explored the extent of individual variance within each plant species investigated, and found that in the plant species thought to have the least genetic variance among individuals (P. aurantiaca) still hosted just as diverse microbial communities. Whether all plant species host their own distinct root microbiota and plants more closely related to each other share more similar bacterial communities still remains to be fully explored, but among the plants examined in this experiment there was no trend that the two species belonging to the same family shared more similarities in terms of bacterial community composition.
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Affiliation(s)
- Kristin Aleklett
- Department of Biology, University of British Columbia-Okanagan , Canada
| | - Jonathan W Leff
- Cooperative Institute for Research in Environmental Sciences and the Department of Ecology and Evolutionary Biology, University of Colorado , Boulder, CO , USA
| | - Noah Fierer
- Cooperative Institute for Research in Environmental Sciences and the Department of Ecology and Evolutionary Biology, University of Colorado , Boulder, CO , USA
| | - Miranda Hart
- Department of Biology, University of British Columbia-Okanagan , Canada
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Joshi G, Schmidt R, Scow KM, Denison MS, Hristova KR. Gene mdpC plays a regulatory role in the methyl-tert-butyl ether degradation pathway of Methylibium petroleiphilum strain PM1. FEMS Microbiol Lett 2015; 362:fnv029. [PMID: 25724531 DOI: 10.1093/femsle/fnv029] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Among the few bacteria known to utilize methyl tert-butyl ether (MTBE) as a sole carbon source, Methylibium petroleiphilum PM1 is a well-characterized organism with a sequenced genome; however, knowledge of the genetic regulation of its MTBE degradation pathway is limited. We investigated the role of a putative transcriptional activator gene, mdpC, in the induction of MTBE-degradation genes mdpA (encoding MTBE monooxygenase) and mdpJ (encoding tert-butyl alcohol hydroxylase) of strain PM1 in a gene-knockout mutant mdpC(-). We also utilized quantitative reverse transcriptase PCR assays targeting genes mdpA, mdpJ and mdpC to determine the effects of the mutation on transcription of these genes. Our results indicate that gene mdpC is involved in the induction of both mdpA and mdpJ in response to MTBE and tert-butyl alcohol (TBA) exposure in PM1. An additional independent mechanism may be involved in the induction of mdpJ in the presence of TBA.
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Affiliation(s)
- Geetika Joshi
- Department of Land, Air and Water Resources, University of California, Davis, CA 95616, USA
| | - Radomir Schmidt
- Department of Land, Air and Water Resources, University of California, Davis, CA 95616, USA
| | - Kate M Scow
- Department of Land, Air and Water Resources, University of California, Davis, CA 95616, USA
| | - Michael S Denison
- Department of Environmental Toxicology, University of California, Davis, CA 95616, USA
| | - Krassimira R Hristova
- Department of Land, Air and Water Resources, University of California, Davis, CA 95616, USA Biological Sciences Department, Marquette University, Milwaukee, WI 53201, USA
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Draft Genome Sequence of the Versatile Alkane-Degrading Bacterium Aquabacterium sp. Strain NJ1. GENOME ANNOUNCEMENTS 2014; 2:2/6/e01271-14. [PMID: 25477416 PMCID: PMC4256197 DOI: 10.1128/genomea.01271-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The draft genome sequence of a soil bacterium, Aquabacterium sp. strain NJ1, capable of utilizing both liquid and solid alkanes, was deciphered. This is the first report of an Aquabacterium genome sequence.
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Le Digabel Y, Demanèche S, Benoit Y, Fayolle-Guichard F, Vogel TM. Ethyl tert-butyl ether (ETBE)-degrading microbial communities in enrichments from polluted environments. JOURNAL OF HAZARDOUS MATERIALS 2014; 279:502-510. [PMID: 25108826 DOI: 10.1016/j.jhazmat.2014.07.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 06/06/2014] [Accepted: 07/03/2014] [Indexed: 06/03/2023]
Abstract
The ethyl tert-butyl ether (ETBE) degradation capacity and phylogenetic composition of five aerobic enrichment cultures with ETBE as the sole carbon and energy source were studied. In all cases, ETBE was entirely degraded to biomass and CO2. Clone libraries of the 16S rRNA gene were prepared from each enrichment. The analyses of the DNA sequences obtained showed different taxonomic compositions with a majority of Proteobacteria in three cases. The two other enrichments have different microbiota with an abundance of Acidobacteria in one case, whereas the microbiota in the second was more diverse (majority of Actinobacteria, Chlorobi and Gemmatimonadetes). Actinobacteria were detected in all five enrichments. Several bacterial strains were isolated from the enrichments and five were capable of degrading ETBE and/or tert-butyl alcohol (TBA), a degradation intermediate. The five included three Rhodococcus sp. (IFP 2040, IFP 2041, IFP 2043), one Betaproteobacteria (IFP 2047) belonging to the Rubrivivax/Leptothrix/Ideonella branch, and one Pseudonocardia sp. (IFP 2050). Quantification of these five strains and two other strains, Rhodococcus sp. IFP 2042 and Bradyrhizobium sp. IFP2049, which had been previously isolated from one of the enrichments was carried out on the different enrichments based on quantitative PCR with specific 16S rRNA gene primers and the results were consistent with the hypothesized role of Actinobacteria and Betaproteobacteria in the degradation of ETBE and the possible role of Bradyrhizobium strains in the degradation of TBA.
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Affiliation(s)
- Yoann Le Digabel
- Environmental Microbial Genomics, CNRS UMR 5005, Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, 36 avenue Guy de Collongue, 69134 Ecully, France; Institut Français du Pétrole Energies Nouvelles (IFPEN), Biotechnology Departement, 1-4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France
| | - Sandrine Demanèche
- Environmental Microbial Genomics, CNRS UMR 5005, Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, 36 avenue Guy de Collongue, 69134 Ecully, France
| | - Yves Benoit
- Institut Français du Pétrole Energies Nouvelles (IFPEN), Biotechnology Departement, 1-4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France
| | - Françoise Fayolle-Guichard
- Institut Français du Pétrole Energies Nouvelles (IFPEN), Biotechnology Departement, 1-4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France.
| | - Timothy M Vogel
- Environmental Microbial Genomics, CNRS UMR 5005, Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, 36 avenue Guy de Collongue, 69134 Ecully, France
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Gunasekaran V, Stam L, Constantí M. The effect of BTX compounds on the biodegradation of ETBE by an ETBE degrading bacterial consortium. BIOTECHNOL BIOPROC E 2014. [DOI: 10.1007/s12257-013-0132-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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40
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Enhanced biodegradation of methyl tert-butyl-ether by a microbial consortium. Curr Microbiol 2013; 68:317-23. [PMID: 24162446 DOI: 10.1007/s00284-013-0480-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 09/15/2013] [Indexed: 10/26/2022]
Abstract
The widespread use of Methyl tert-butyl-ether (MTBE) as a gasoline additive has resulted in a higher detection rate of MTBE in groundwater systems. Therefore, the researchers show more concern about the bioremediation of MTBE-impacted aquifers. In this paper, a MTBE-direct-degrading bacterial consortium was enriched (named RS1) and further studied. In order to identify the microbial community of the consortium, 17 and 12 different single strains were isolated from nutrient medium and MSM media (with MTBE as the sole carbon source), respectively. 16S rDNA-based phylogenetic analysis revealed that these diverse bacteria belonged to 14 genera, in which Pseudomonas was dominant. Several strains which can grow with MTBE as the sole carbon and energy source were also identified, such as M1, related to MTBE-degrading Arthrobacter sp. ATCC27778. Furthermore, the appropriate addition of certain single strain in consortium RS1 (M1:RS1 = 1:2) facilitates MTBE degradation by increasing the quantity of efficient MTBE-degrading bacteria. This work will provide microbial source and theoretical fundament for further bioremediation of MTBE-contaminated aquifers, which has applied potential and environmental importance.
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Terrell CR, Burks EA, Whitman CP, Hoffman DW. Structural and kinetic characterization of two 4-oxalocrotonate tautomerases in Methylibium petroleiphilum strain PM1. Arch Biochem Biophys 2013; 537:113-24. [PMID: 23831510 DOI: 10.1016/j.abb.2013.06.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 06/25/2013] [Indexed: 11/26/2022]
Abstract
Methylibium petroleiphilum strain PM1 uses various petroleum products including the fuel additive methyl tert-butyl ether and straight chain and aromatic hydrocarbons as sole carbon and energy sources. It has two operons, dmpI and dmpII, that code for the enzymes in a pair of parallel meta-fission pathways. In order to understand the roles of the pathways, the 4-oxalocrotonate tautomerase (4-OT) isozyme from each pathway was characterized. Tautomerase I and tautomerase II have the lowest pairwise sequence identity (35%) among the isozyme pairs in the parallel pathways, and could offer insight into substrate preferences and pathway functions. The kinetic parameters of tautomerase I and tautomerase II were determined using 2-hydroxymuconate and 5-(methyl)-2-hydroxymuconate. Both tautomerase I and tautomerase II process the substrates, but with different efficiencies. Crystal structures were determined for both tautomerase I and tautomerase II, at 1.57 and 1.64Å resolution, respectively. The backbones of tautomerase I and tautomerase II are highly similar, but have distinct active site environments. The results, in combination with those for other structurally and kinetically characterized 4-OT isozymes, suggest that tautomerase I catalyzes the tautomerization of both 2-hydroxymuconate and alkyl derivatives, whereas tautomerase II might specialize in other aromatic hydrocarbon metabolites.
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Affiliation(s)
- Cassidy R Terrell
- Department of Chemistry and Biochemistry, University of Texas, Austin, 78712, USA
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Hicks KA, Schmidt R, Nickelsen MG, Boyle SL, Baker JM, Tornatore PM, Hristova KR, Scow KM. Successful treatment of an MTBE-impacted aquifer using a bioreactor self-colonized by native aquifer bacteria. Biodegradation 2013; 25:41-53. [PMID: 23613160 DOI: 10.1007/s10532-013-9639-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 04/06/2013] [Indexed: 11/26/2022]
Abstract
A field-scale fixed bed bioreactor was used to successfully treat an MTBE-contaminated aquifer in North Hollywood, CA without requiring inoculation with introduced bacteria. Native bacteria from the MTBE-impacted aquifer rapidly colonized the bioreactor, entering the bioreactor in the contaminated groundwater pumped from the site, and biodegraded MTBE with greater than 99 % removal efficiency. DNA sequencing of the 16S rRNA gene identified MTBE-degrading bacteria Methylibium petroleiphilum in the bioreactor. Quantitative PCR showed M. petroleiphilum enriched by three orders of magnitude in the bioreactor above densities pre-existing in the groundwater. Because treatment was carried out by indigenous rather than introduced organisms, regulatory approval was obtained for implementation of a full-scale bioreactor to continue treatment of the aquifer. In addition, after confirmation of MTBE removal in the bioreactor to below maximum contaminant limit levels (MCL; MTBE = 5 μg L(-1)), treated water was approved for reinjection back into the aquifer rather than requiring discharge to a water treatment system. This is the first treatment system in California to be approved for reinjection of biologically treated effluent into a drinking water aquifer. This study demonstrated the potential for using native microbial communities already present in the aquifer as an inoculum for ex-situ bioreactors, circumventing the need to establish non-native, non-acclimated and potentially costly inoculants. Understanding and harnessing the metabolic potential of native organisms circumvents some of the issues associated with introducing non-native organisms into drinking water aquifers, and can provide a low-cost and efficient remediation technology that can streamline future bioremediation approval processes.
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Affiliation(s)
- Kristin A Hicks
- Department of Land, Air and Water Resources, University of California, One Shields Ave, Davis, CA, 95616, USA
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Ethyl tert-butyl ether (ETBE) biodegradation by a syntrophic association of Rhodococcus sp. IFP 2042 and Bradyrhizobium sp. IFP 2049 isolated from a polluted aquifer. Appl Microbiol Biotechnol 2013; 97:10531-9. [DOI: 10.1007/s00253-013-4803-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 02/20/2013] [Accepted: 02/21/2013] [Indexed: 11/26/2022]
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Constitutive expression of the cytochrome P450 EthABCD monooxygenase system enables degradation of synthetic dialkyl ethers in Aquincola tertiaricarbonis L108. Appl Environ Microbiol 2013; 79:2321-7. [PMID: 23354715 DOI: 10.1128/aem.03348-12] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In Rhodococcus ruber IFP 2001, Rhodococcus zopfii IFP 2005, and Gordonia sp. strain IFP 2009, the cytochrome P450 monooxygenase EthABCD catalyzes hydroxylation of methoxy and ethoxy residues in the fuel oxygenates methyl tert-butyl ether (MTBE), ethyl tert-butyl ether (ETBE), and tert-amyl methyl ether (TAME). The expression of the IS3-type transposase-flanked eth genes is ETBE dependent and controlled by the regulator EthR (C. Malandain et al., FEMS Microbiol. Ecol. 72:289-296, 2010). In contrast, we demonstrated by reverse transcription-quantitative PCR (RT-qPCR) that the betaproteobacterium Aquincola tertiaricarbonis L108, which possesses the ethABCD genes but lacks ethR, constitutively expresses the P450 system at high levels even when growing on nonether substrates, such as glucose. The mutant strain A. tertiaricarbonis L10, which is unable to degrade dialkyl ethers, resulted from a transposition event mediated by a rolling-circle IS91-type element flanking the eth gene cluster in the wild-type strain L108. The constitutive expression of Eth monooxygenase is likely initiated by the housekeeping sigma factor σ(70), as indicated by the presence in strain L108 of characteristic -10 and -35 binding sites upstream of ethA which are lacking in strain IFP 2001. This enables efficient degradation of diethyl ether, diisopropyl ether, MTBE, ETBE, TAME, and tert-amyl ethyl ether (TAEE) without any lag phase in strain L108. However, ethers with larger residues, n-hexyl methyl ether, tetrahydrofuran, and alkyl aryl ethers, were not attacked by the Eth system at significant rates in resting-cell experiments, indicating that the residue in the ether molecule which is not hydroxylated also contributes to the determination of substrate specificity.
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Hyman M. Biodegradation of gasoline ether oxygenates. Curr Opin Biotechnol 2012; 24:443-50. [PMID: 23116604 DOI: 10.1016/j.copbio.2012.10.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 09/17/2012] [Accepted: 10/03/2012] [Indexed: 10/27/2022]
Abstract
Ether oxygenates such as methyl tertiary butyl ether (MTBE) are added to gasoline to improve fuel combustion and decrease exhaust emissions. Ether oxygenates and their tertiary alcohol metabolites are now an important group of groundwater pollutants. This review highlights recent advances in our understanding of the microorganisms, enzymes and pathways involved in both the aerobic and anaerobic biodegradation of these compounds. This review also aims to illustrate how these microbiological and biochemical studies have guided, and have helped refine, molecular and stable isotope-based analytical approaches that are increasingly being used to detect and quantify biodegradation of these compounds in contaminated environments.
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Affiliation(s)
- Michael Hyman
- Department of Microbiology, North Carolina State University, Raleigh, NC 27695, USA.
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Uhlik O, Leewis MC, Strejcek M, Musilova L, Mackova M, Leigh MB, Macek T. Stable isotope probing in the metagenomics era: a bridge towards improved bioremediation. Biotechnol Adv 2012; 31:154-65. [PMID: 23022353 DOI: 10.1016/j.biotechadv.2012.09.003] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 09/17/2012] [Accepted: 09/17/2012] [Indexed: 12/24/2022]
Abstract
Microbial biodegradation and biotransformation reactions are essential to most bioremediation processes, yet the specific organisms, genes, and mechanisms involved are often not well understood. Stable isotope probing (SIP) enables researchers to directly link microbial metabolic capability to phylogenetic and metagenomic information within a community context by tracking isotopically labeled substances into phylogenetically and functionally informative biomarkers. SIP is thus applicable as a tool for the identification of active members of the microbial community and associated genes integral to the community functional potential, such as biodegradative processes. The rapid evolution of SIP over the last decade and integration with metagenomics provide researchers with a much deeper insight into potential biodegradative genes, processes, and applications, thereby enabling an improved mechanistic understanding that can facilitate advances in the field of bioremediation.
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Affiliation(s)
- Ondrej Uhlik
- Institute of Chemical Technology Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Technicka 3, 166 28 Prague, Czech Republic.
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Proteogenomic elucidation of the initial steps in the benzene degradation pathway of a novel halophile, Arhodomonas sp. strain Rozel, isolated from a hypersaline environment. Appl Environ Microbiol 2012; 78:7309-16. [PMID: 22885747 DOI: 10.1128/aem.01327-12] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lately, there has been a special interest in understanding the role of halophilic and halotolerant organisms for their ability to degrade hydrocarbons. The focus of this study was to investigate the genes and enzymes involved in the initial steps of the benzene degradation pathway in halophiles. The extremely halophilic bacteria Arhodomonas sp. strain Seminole and Arhodomonas sp. strain Rozel, which degrade benzene and toluene as the sole carbon source at high salinity (0.5 to 4 M NaCl), were isolated from enrichments developed from contaminated hypersaline environments. To obtain insights into the physiology of this novel group of organisms, a draft genome sequence of the Seminole strain was obtained. A cluster of 13 genes predicted to be functional in the hydrocarbon degradation pathway was identified from the sequence. Two-dimensional (2D) gel electrophoresis and liquid chromatography-mass spectrometry were used to corroborate the role of the predicted open reading frames (ORFs). ORFs 1080 and 1082 were identified as components of a multicomponent phenol hydroxylase complex, and ORF 1086 was identified as catechol 2,3-dioxygenase (2,3-CAT). Based on this analysis, it was hypothesized that benzene is converted to phenol and then to catechol by phenol hydroxylase components. The resulting catechol undergoes ring cleavage via the meta pathway by 2,3-CAT to form 2-hydroxymuconic semialdehyde, which enters the tricarboxylic acid cycle. To substantiate these findings, the Rozel strain was grown on deuterated benzene, and gas chromatography-mass spectrometry detected deuterated phenol as the initial intermediate of benzene degradation. These studies establish the initial steps of the benzene degradation pathway in halophiles.
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Rosell M, Gonzalez-Olmos R, Rohwerder T, Rusevova K, Georgi A, Kopinke FD, Richnow HH. Critical evaluation of the 2D-CSIA scheme for distinguishing fuel oxygenate degradation reaction mechanisms. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2012; 46:4757-4766. [PMID: 22455373 DOI: 10.1021/es2036543] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Although the uniform initial hydroxylation of methyl tert-butyl ether (MTBE) and other oxygenates during aerobic biodegradation has already been proven by molecular tools, variations in carbon and hydrogen enrichment factors (ε(C) and ε(H)) have still been associated with different reaction mechanisms (McKelvie et al. Environ. Sci. Technol. 2009, 43, 2793-2799). Here, we present new laboratory-derived ε(C) and ε(H) data on the initial degradation mechanisms of MTBE, ethyl tert-butyl ether (ETBE), and tert-amyl methyl ether (TAME) by chemical oxidation (permanganate, Fenton reagents), acid hydrolysis, and aerobic bacteria cultures (species of Aquincola, Methylibium, Gordonia, Mycobacterium, Pseudomonas, and Rhodococcus). Plotting of Δδ(2)H/ Δδ(13)C data from chemical oxidation and hydrolysis of ethers resulted in slopes (Λ values) of 22 ± 4 and between 6 and 12, respectively. With A. tertiaricarbonis L108, R. zopfii IFP 2005, and Gordonia sp. IFP 2009, ε(C) was low (<|-1|‰) and ε(H) was insignificant. Fractionation obtained with P. putida GPo1 was similar to acid hydrolysis and M. austroafricanum JOB5 and R. ruber DSM 7511 displayed Λ values previously only ascribed to anaerobic attack. The fractionation patterns rather correlate with the employment of different P450, AlkB, and other monooxygenases, likely catalyzing ether hydroxylation via different transition states. Our data questions the value of 2D-CSIA for a simple distinguishing of oxygenate biotransformation mechanisms, therefore caution and complementary tools are needed for proper interpretation of groundwater plumes at field sites.
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Affiliation(s)
- Mònica Rosell
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany.
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Yaneva N, Schuster J, Schäfer F, Lede V, Przybylski D, Paproth T, Harms H, Müller RH, Rohwerder T. Bacterial acyl-CoA mutase specifically catalyzes coenzyme B12-dependent isomerization of 2-hydroxyisobutyryl-CoA and (S)-3-hydroxybutyryl-CoA. J Biol Chem 2012; 287:15502-11. [PMID: 22433853 DOI: 10.1074/jbc.m111.314690] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Coenzyme B(12)-dependent acyl-CoA mutases are radical enzymes catalyzing reversible carbon skeleton rearrangements in carboxylic acids. Here, we describe 2-hydroxyisobutyryl-CoA mutase (HCM) found in the bacterium Aquincola tertiaricarbonis as a novel member of the mutase family. HCM specifically catalyzes the interconversion of 2-hydroxyisobutyryl- and (S)-3-hydroxybutyryl-CoA. Like isobutyryl-CoA mutase, HCM consists of a large substrate- and a small B(12)-binding subunit, HcmA and HcmB, respectively. However, it is thus far the only acyl-CoA mutase showing substrate specificity for hydroxylated carboxylic acids. Complete loss of 2-hydroxyisobutyric acid degradation capacity in hcmA and hcmB knock-out mutants established the central role of HCM in A. tertiaricarbonis for degrading substrates bearing a tert-butyl moiety, such as the fuel oxygenate methyl tert-butyl ether (MTBE) and its metabolites. Sequence analysis revealed several HCM-like enzymes in other bacterial strains not related to MTBE degradation, indicating that HCM may also be involved in other pathways. In all strains, hcmA and hcmB are associated with genes encoding for a putative acyl-CoA synthetase and a MeaB-like chaperone. Activity and substrate specificity of wild-type enzyme and active site mutants HcmA I90V, I90F, and I90Y clearly demonstrated that HCM belongs to a new subfamily of B(12)-dependent acyl-CoA mutases.
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Affiliation(s)
- Nadya Yaneva
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research (UFZ), 04318 Leipzig, Germany
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Han TH, Han JS, So MH, Seo JW, Ahn CM, Min DH, Yoo YS, Cha DK, Kim CG. The removal of 1,4-dioxane from polyester manufacturing process wastewater using an up-flow Biological Aerated Filter (UBAF) packed with tire chips. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2012; 47:117-129. [PMID: 22217090 DOI: 10.1080/10934529.2012.630291] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
1,4-Dioxane is one of the by-products from the polyester manufacturing process, which has been carelessly discharged into water bodies and is a weak human carcinogen. In this study, a laboratory-scale, up-flow biological aerated filter (UBAF), packed with tire chips, was investigated for the treatment of 1,4-dioxane. The UBAF was fed with effluent, containing an average of 31 mg/L of 1,4-dioxane, discharged from an anaerobic treatment unit at H Co. in the Gumi Industrial Complex, South Korea. In the batch, a maximum of 99.5 % 1,4-dioxane was removed from an influent containing 25.6 mg/L. In the continuous mode, the optimal empty bed contact time (EBCT) and air to liquid flow rate (A:L) were 8.5 hours and 30:1, respectively. It was also found that the removal efficiency of 1,4-dioxane increased with increasing loading rate within the range 0.04 to 0.31 kg 1,4-dioxane/m(3)·day. However, as the COD:1,4-dioxane ratio was increased within the range 3 to 46 (mg/L COD)/(mg/L 1,4-dioxane), the removal efficiency unexpectedly decreased.
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Affiliation(s)
- Thi-Hiep Han
- Department of the Environment Engineering, Inha University, Namgu, Incheon, Korea
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