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Bottos EM, Al-Shabib EY, Shaw DMJ, McAmmond BM, Sharma A, Suchan DM, Cameron ADS, Van Hamme JD. Transcriptomic response of Gordonia sp. strain NB4-1Y when provided with 6:2 fluorotelomer sulfonamidoalkyl betaine or 6:2 fluorotelomer sulfonate as sole sulfur source. Biodegradation 2020; 31:407-422. [PMID: 33150552 PMCID: PMC7661421 DOI: 10.1007/s10532-020-09917-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/27/2020] [Indexed: 02/06/2023]
Abstract
Abstract Perfluoroalkyl and polyfluoroalkyl substances (PFAS) are environmental contaminants of concern. We previously described biodegradation of two PFAS that represent components and transformation products of aqueous film-forming foams (AFFF), 6:2 fluorotelomer sulfonamidoalkyl betaine (6:2 FTAB) and 6:2 fluorotelomer sulfonate (6:2 FTSA), by Gordonia sp. strain NB4-1Y. To identify genes involved in the breakdown of these compounds, the transcriptomic response of NB4-1Y was examined when grown on 6:2 FTAB, 6:2 FTSA, a non-fluorinated analog of 6:2 FTSA (1-octanesulfonate), or MgSO4, as sole sulfur source. Differentially expressed genes were identified as those with ± 1.5 log2-fold-differences (± 1.5 log2FD) in transcript abundances in pairwise comparisons. Transcriptomes of cells grown on 6:2 FTAB and 6:2 FTSA were most similar (7.9% of genes expressed ± 1.5 log2FD); however, several genes that were expressed in greater abundance in 6:2 FTAB treated cells compared to 6:2 FTSA treated cells were noted for their potential role in carbon–nitrogen bond cleavage in 6:2 FTAB. Responses to sulfur limitation were observed in 6:2 FTAB, 6:2 FTSA, and 1-octanesulfonate treatments, as 20 genes relating to global sulfate stress response were more highly expressed under these conditions compared to the MgSO4 treatment. More highly expressed oxygenase genes in 6:2 FTAB, 6:2 FTSA, and 1-octanesulfonate treatments were found to code for proteins with lower percent sulfur-containing amino acids compared to both the total proteome and to oxygenases showing decreased expression. This work identifies genetic targets for further characterization and will inform studies aimed at evaluating the biodegradation potential of environmental samples through applied genomics. Graphic Abstract ![]()
Electronic supplementary material The online version of this article (10.1007/s10532-020-09917-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Eric M Bottos
- Department of Biological Sciences, Thompson Rivers University, Kamloops, BC, V2C 0C8, Canada
| | - Ebtihal Y Al-Shabib
- Department of Biology, University of Regina, Regina, SK, S4S 0A2, Canada
- Faculty of Science, Institute for Microbial Systems and Society, University of Regina, Regina, SK, S4S 0A2, Canada
| | - Dayton M J Shaw
- Department of Biological Sciences, Thompson Rivers University, Kamloops, BC, V2C 0C8, Canada
| | - Breanne M McAmmond
- Department of Biological Sciences, Thompson Rivers University, Kamloops, BC, V2C 0C8, Canada
| | - Aditi Sharma
- Department of Biology, University of Regina, Regina, SK, S4S 0A2, Canada
- Faculty of Science, Institute for Microbial Systems and Society, University of Regina, Regina, SK, S4S 0A2, Canada
| | - Danae M Suchan
- Department of Biology, University of Regina, Regina, SK, S4S 0A2, Canada
- Faculty of Science, Institute for Microbial Systems and Society, University of Regina, Regina, SK, S4S 0A2, Canada
| | - Andrew D S Cameron
- Department of Biology, University of Regina, Regina, SK, S4S 0A2, Canada
- Faculty of Science, Institute for Microbial Systems and Society, University of Regina, Regina, SK, S4S 0A2, Canada
| | - Jonathan D Van Hamme
- Department of Biological Sciences, Thompson Rivers University, Kamloops, BC, V2C 0C8, Canada.
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Ma Q, Liu S, Li S, Hu J, Tang M, Sun Y. Removal of malodorant skatole by two enriched microbial consortia: Performance, dynamic, function prediction and bacteria isolation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 725:138416. [PMID: 32302841 DOI: 10.1016/j.scitotenv.2020.138416] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/26/2020] [Accepted: 04/01/2020] [Indexed: 06/11/2023]
Abstract
Malodor emission has become one of the major challenges in animal husbandry. Skatole, one of the most offensive odorous compounds, can cause several diseases to organisms and is resistant to biodegradation. However, the microbial community information for skatole degradation has yet to be reported. In this study, the aerobic sequencing batch reactors with two different inocula were constructed. Both Group N (sample from cattle house) and Group E (sample from goose house) could efficiently degrade skatole after 70 days operation under conditions of pH 7.0-9.0 and temperature 20-40 °C. High-throughput sequencing results showed that the α-diversity in Group N was higher than that in Group E, while neither of them changed during the whole operation process. Bacterial community structures in both groups shifted. Generally, Lactococcus, Pseudomonas and Flavobacterium remarkably reduced, while Arthrobacter became the dominant population. Function prediction results indicated that the xenobiotics biodegradation and metabolism category was significantly up-regulated in Group E but remained unchanged in Group N. On the other hand, culture-dependent technique was applied and ten bacteria were obtained from the sludges. Two strains belonged to Rhodococcus, a minor genus in the communities, were firstly proven to harbor excellent skatole-degrading capacity. This study proved that skatole could be effectively removed by activated sludges, and the non-core bacteria Rhodococcus would be functionally important in the degradation process. These findings provide new insights into our understanding of skatole biotransformation process, and offer valuable bacterial resources for bioremediation application.
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Affiliation(s)
- Qiao Ma
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China.
| | - Shengwei Liu
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Shuzhen Li
- School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Jiabao Hu
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Minyi Tang
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Yeqing Sun
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
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Benedek T, Szentgyörgyi F, Szabó I, Farkas M, Duran R, Kriszt B, Táncsics A. Aerobic and oxygen-limited naphthalene-amended enrichments induced the dominance of Pseudomonas spp. from a groundwater bacterial biofilm. Appl Microbiol Biotechnol 2020; 104:6023-6043. [PMID: 32415320 PMCID: PMC7306034 DOI: 10.1007/s00253-020-10668-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 04/29/2020] [Accepted: 05/04/2020] [Indexed: 12/20/2022]
Abstract
In this study, we aimed at determining the impact of naphthalene and different oxygen levels on a biofilm bacterial community originated from a petroleum hydrocarbon-contaminated groundwater. By using cultivation-dependent and cultivation-independent approaches, the enrichment, identification, and isolation of aerobic and oxygen-limited naphthalene degraders was possible. Results indicated that, regardless of the oxygenation conditions, Pseudomonas spp. became the most dominant in the naphthalene-amended selective enrichment cultures. Under low-oxygen conditions, P. veronii/P. extremaustralis lineage affiliating bacteria, and under full aerobic conditions P. laurentiana-related isolates were most probably capable of naphthalene biodegradation. A molecular biological tool has been developed for the detection of naphthalene 1,2-dioxygenase-related 2Fe-2S reductase genes of Gram-negative bacteria. The newly developed COnsensus DEgenerate Hybrid Oligonucleotide Primers (CODEHOP-PCR) technique may be used in the monitoring of the natural attenuation capacity of PAH-contaminated sites. A bacterial strain collection with prolific biofilm-producing and effective naphthalene-degrading organisms was established. The obtained strain collection may be applicable in the future for the development of biofilm-based bioremediation systems for the elimination of PAHs from groundwater (e.g., biofilm-based biobarriers).
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Affiliation(s)
- Tibor Benedek
- Regional University Centre of Excellence in Environmental Industry, Szent István University, Páter K. u. 1, Gödöllő, H-2100, Hungary.
| | - Flóra Szentgyörgyi
- Department of Environmental Protection and Safety, Szent István University, Páter K. u. 1, Gödöllő, H-2100, Hungary
| | - István Szabó
- Department of Environmental Protection and Safety, Szent István University, Páter K. u. 1, Gödöllő, H-2100, Hungary
| | - Milán Farkas
- Department of Environmental Protection and Safety, Szent István University, Páter K. u. 1, Gödöllő, H-2100, Hungary
| | - Robert Duran
- IPREM UMR CNRS 5254, Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l'Adour, Pau, France
| | - Balázs Kriszt
- Department of Environmental Protection and Safety, Szent István University, Páter K. u. 1, Gödöllő, H-2100, Hungary
| | - András Táncsics
- Regional University Centre of Excellence in Environmental Industry, Szent István University, Páter K. u. 1, Gödöllő, H-2100, Hungary
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54
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Pigoleva SV, Zakharchenko NS, Furs OV, Tarlachkov SV, Funtikova TV, Filonov AE, Aripovskii AV, Dyachenko OV, Buryanov YI, Shevchuk TV. Effects of Associative Microorganisms on Plant Growth and Resistance to Xenobiotics and Phytopathogens. APPL BIOCHEM MICRO+ 2020. [DOI: 10.1134/s0003683820040134] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Sandhu M, Jha P, Paul AT, Singh RP, Jha PN. Evaluation of biphenyl- and polychlorinated-biphenyl (PCB) degrading Rhodococcus sp. MAPN-1 on growth of Morus alba by pot study. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2020; 22:1487-1496. [PMID: 32602350 DOI: 10.1080/15226514.2020.1784088] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
This study focused on isolation of bacteria with biphenyl/polychlorinated biphenyl (PCB) degrading ability from the rhizosphere of Morus alba (mulberry plant). Repetitive enrichment of rhizospheric soil samples with biphenyl resulted in the isolation of Rhodococcus sp. MAPN-1, identified by 16S rRNA gene sequence analysis. The bacterium showed growth on five different aromatic compounds (naphthalene, salicylic acid, benzoic acid, dibenzofuran and anthracene). Benzoic acid was detected as the major metabolite during biphenyl degradation using high-performance thin-layer chromatography (HPTLC) with Rf 0.42 at 254 nm. Further GC-MS/MS study showed 95% and 15% degradation of biphenyl and dichlorobiphenyl, respectively. A pot study was conducted to evaluate the effect of presence of biphenyl on M. alba and the role of biphenyl degrader Rhodococcus sp. MAPN-1 in relation to phytoremediation. Morus alba twigs in biphenyl spiked soil (100 mg/kg and 300 mg/kg) inoculated with Rhodococcus sp. MAPN-1 showed growth, whereas, growth of plants (control) was adversely affected in biphenyl-spiked uninoculated soil. It is the first report of isolation of Rhodococcus sp. MAPN-1 from the rhizosphere of Morus alba, its capability to degrade biphenyl, thereby showing a positive effect on the plant growth grown in biphenyl spiked soil.
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Affiliation(s)
- Monika Sandhu
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India
| | - Prameela Jha
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India
| | - Atish T Paul
- Department of Pharmacy, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India
| | - Rajnish P Singh
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India
| | - Prabhat N Jha
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India
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56
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Effects of cadmium perturbation on the microbial community structure and heavy metal resistome of a tropical agricultural soil. BIORESOUR BIOPROCESS 2020. [DOI: 10.1186/s40643-020-00314-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
AbstractThe effects of cadmium (Cd) contamination on the microbial community structure, soil physicochemistry and heavy metal resistome of a tropical agricultural soil were evaluated in field-moist soil microcosms. A Cd-contaminated agricultural soil (SL5) and an untreated control (SL4) were compared over a period of 5 weeks. Analysis of the physicochemical properties and heavy metals content of the two microcosms revealed a statistically significant decrease in value of the soil physicochemical parameters (P < 0.05) and concentration of heavy metals (Cd, Pb, Cr, Zn, Fe, Cu, Se) content of the agricultural soil in SL5 microcosm. Illumina shotgun sequencing of the DNA extracted from the two microcosms showed the predominance of the phyla, classes, genera and species of Proteobacteria (37.38%), Actinobacteria (35.02%), Prevotella (6.93%), and Conexibacter woesei (8.93%) in SL4, and Proteobacteria (50.50%), Alphaproteobacteria (22.28%), Methylobacterium (9.14%), and Methylobacterium radiotolerans (12,80%) in SL5, respectively. Statistically significant (P < 0.05) difference between the metagenomes was observed at genus and species delineations. Functional annotation of the two metagenomes revealed diverse heavy metal resistome for the uptake, transport, efflux and detoxification of various heavy metals. It also revealed the exclusive detection in SL5 metagenome of members of RND (resistance nodulation division) protein czcCBA efflux system (czcA, czrA, czrB), CDF (cation diffusion facilitator) transporters (czcD), and genes for enzymes that protect the microbial cells against cadmium stress (sodA, sodB, ahpC). The results obtained in this study showed that Cd contamination significantly affects the soil microbial community structure and function, modifies the heavy metal resistome, alters the soil physicochemistry and results in massive loss of some autochthonous members of the community not adapted to the Cd stress.
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57
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Sharma M, Nandy A, Taylor N, Venkatesan SV, Ozhukil Kollath V, Karan K, Thangadurai V, Tsesmetzis N, Gieg LM. Bioelectrochemical remediation of phenanthrene in a microbial fuel cell using an anaerobic consortium enriched from a hydrocarbon-contaminated site. JOURNAL OF HAZARDOUS MATERIALS 2020; 389:121845. [PMID: 31862354 DOI: 10.1016/j.jhazmat.2019.121845] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 11/15/2019] [Accepted: 12/06/2019] [Indexed: 06/10/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAH) are organic pollutants that require remediation due to their detrimental impact on human and environmental health. In this study, we used a novel approach of sequestering a model PAH, phenanthrene, onto a solid carbon matrix bioanode in a microbial fuel cell (MFC) to assess its biodegradation coupled with power generation. Here, the bioanode serves as a site for enrichment of electroactive and hydrocarbon-degrading microorganisms, which can simultaneously act to biodegrade a pollutant and generate power. Carbon cloth electrodes loaded with two rates of phenanthrene (2 and 20 mg cm-2) were compared using dual chamber MFCs that were operated for 50 days. The lower loading rate of 2 mg cm-2 was most efficient in the degradation of phenanthrene and had higher power production capacities (37 mW m-2) as compared to the higher loading rate of 20 mg cm-2 (power production of 19.2 mW m-2). FTIR (Fourier-Transform Infrared Spectroscopy) analyses showed a depletion in absorbance peak signals associated with phenanthrene. Microbes known to have electroactive properties or phenanthrene biodegradation abilities like Pseudomonas, Rhodococcus, Thauera and Ralstonia were enriched over time in the MFCs, substantiating the electrochemical and FTIR analyses. The MFC approach taken here thus offers great promise towards PAH bioelectroremediation.
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Affiliation(s)
- Mohita Sharma
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Arpita Nandy
- Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Nicole Taylor
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Senthil Velan Venkatesan
- Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Vinayaraj Ozhukil Kollath
- Department of Chemical & Petroleum Engineering, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Kunal Karan
- Department of Chemical & Petroleum Engineering, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Venkataraman Thangadurai
- Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Nicolas Tsesmetzis
- Shell International Exploration and Production Inc., 3333 Highway 6 South, Houston, Texas, 77251-7171, USA
| | - Lisa M Gieg
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada.
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Horizontal Spread of Rhodococcus equi Macrolide Resistance Plasmid pRErm46 across Environmental Actinobacteria. Appl Environ Microbiol 2020; 86:AEM.00108-20. [PMID: 32169935 DOI: 10.1128/aem.00108-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 02/27/2020] [Indexed: 12/26/2022] Open
Abstract
Conjugation is one of the main mechanisms involved in the spread and maintenance of antibiotic resistance in bacterial populations. We recently showed that the emerging macrolide resistance in the soilborne equine and zoonotic pathogen Rhodococcus equi is conferred by the erm(46) gene carried on the 87-kb conjugative plasmid pRErm46. Here, we investigated the conjugal transferability of pRErm46 to 14 representative bacteria likely encountered by R. equi in the environmental habitat. In vitro mating experiments demonstrated conjugation to different members of the genus Rhodococcus as well as to Nocardia and Arthrobacter spp. at frequencies ranging from ∼10-2 to 10-6 pRErm46 transfer was also observed in mating experiments in soil and horse manure, albeit at a low frequency and after prolonged incubation at 22 to 30°C (environmental temperatures), not 37°C. All transconjugants were able to transfer pRErm46 back to R. equi Conjugation could not be detected with Mycobacterium or Corynebacterium spp. or several members of the more distant phylum Firmicutes such as Enterococcus, Streptococcus, or Staphylococcus Thus, the pRErm46 host range appears to span several actinobacterial orders with certain host restriction within the Corynebacteriales All bacterial species that acquired pRErm46 expressed increased macrolide resistance with no significant deleterious impact on fitness, except in the case of Rhodococcus rhodnii Our results indicate that actinobacterial members of the environmental microbiota can both acquire and transmit the R. equi pRErm46 plasmid and thus potentially contribute to the maintenance and spread of erm(46)-mediated macrolide resistance in equine farms.IMPORTANCE This study demonstrates the efficient horizontal transfer of the Rhodococcus equi conjugative plasmid pRErm46, recently identified as the cause of the emerging macrolide resistance among equine isolates of this pathogen, to and from different environmental Actinobacteria, including a variety of rhodococci as well as Nocardia and Arthrobacter spp. The reported data support the notion that environmental microbiotas may act as reservoirs for the endemic maintenance of antimicrobial resistance in an antibiotic pressurized farm habitat.
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Garrido-Sanz D, Sansegundo-Lobato P, Redondo-Nieto M, Suman J, Cajthaml T, Blanco-Romero E, Martin M, Uhlik O, Rivilla R. Analysis of the biodegradative and adaptive potential of the novel polychlorinated biphenyl degrader Rhodococcus sp. WAY2 revealed by its complete genome sequence. Microb Genom 2020; 6. [PMID: 32238227 PMCID: PMC7276702 DOI: 10.1099/mgen.0.000363] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The complete genome sequence of Rhodococcus sp. WAY2 (WAY2) consists of a circular chromosome, three linear replicons and a small circular plasmid. The linear replicons contain typical actinobacterial invertron-type telomeres with the central CGTXCGC motif. Comparative phylogenetic analysis of the 16S rRNA gene along with phylogenomic analysis based on the genome-to-genome blast distance phylogeny (GBDP) algorithm and digital DNA–DNA hybridization (dDDH) with other Rhodococcus type strains resulted in a clear differentiation of WAY2, which is likely a new species. The genome of WAY2 contains five distinct clusters of bph, etb and nah genes, putatively involved in the degradation of several aromatic compounds. These clusters are distributed throughout the linear plasmids. The high sequence homology of the ring-hydroxylating subunits of these systems with other known enzymes has allowed us to model the range of aromatic substrates they could degrade. Further functional characterization revealed that WAY2 was able to grow with biphenyl, naphthalene and xylene as sole carbon and energy sources, and could oxidize multiple aromatic compounds, including ethylbenzene, phenanthrene, dibenzofuran and toluene. In addition, WAY2 was able to co-metabolize 23 polychlorinated biphenyl congeners, consistent with the five different ring-hydroxylating systems encoded by its genome. WAY2 could also use n-alkanes of various chain-lengths as a sole carbon source, probably due to the presence of alkB and ladA gene copies, which are only found in its chromosome. These results show that WAY2 has a potential to be used for the biodegradation of multiple organic compounds.
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Affiliation(s)
- Daniel Garrido-Sanz
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, C/ Darwin 2, 28049 Madrid, Spain
| | - Paula Sansegundo-Lobato
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, C/ Darwin 2, 28049 Madrid, Spain
| | - Miguel Redondo-Nieto
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, C/ Darwin 2, 28049 Madrid, Spain
| | - Jachym Suman
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Technika 3, 16628 Prague, Czech Republic
| | - Tomas Cajthaml
- Laboratory of Environmental Biotechnology, Institute of Microbiology, Czech Academy of Sciences v.v.i., Vídeňská 1083, 14200 Prague, Czech Republic
| | - Esther Blanco-Romero
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, C/ Darwin 2, 28049 Madrid, Spain
| | - Marta Martin
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, C/ Darwin 2, 28049 Madrid, Spain
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Technika 3, 16628 Prague, Czech Republic
| | - Rafael Rivilla
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, C/ Darwin 2, 28049 Madrid, Spain
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Coimbra NDR, Goes-Neto A, Azevedo V, Ouangraoua A. Reconstructing the Phylogeny of Corynebacteriales while Accounting for Horizontal Gene Transfer. Genome Biol Evol 2020; 12:381-395. [PMID: 32186700 PMCID: PMC7186787 DOI: 10.1093/gbe/evaa058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/17/2020] [Indexed: 12/25/2022] Open
Abstract
Horizontal gene transfer is a common mechanism in Bacteria that has contributed to the genomic content of existing organisms. Traditional methods for estimating bacterial phylogeny, however, assume only vertical inheritance in the evolution of homologous genes, which may result in errors in the estimated phylogenies. We present a new method for estimating bacterial phylogeny that accounts for the presence of genes acquired by horizontal gene transfer between genomes. The method identifies and corrects putative transferred genes in gene families, before applying a gene tree-based summary method to estimate bacterial species trees. The method was applied to estimate the phylogeny of the order Corynebacteriales, which is the largest clade in the phylum Actinobacteria. We report a collection of 14 phylogenetic trees on 360 Corynebacteriales genomes. All estimated trees display each genus as a monophyletic clade. The trees also display several relationships proposed by past studies, as well as new relevant relationships between and within the main genera of Corynebacteriales: Corynebacterium, Mycobacterium, Nocardia, Rhodococcus, and Gordonia. An implementation of the method in Python is available on GitHub at https://github.com/UdeS-CoBIUS/EXECT (last accessed April 2, 2020).
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Affiliation(s)
- Nilson Da Rocha Coimbra
- Department of Computer Science, University of Sherbrooke, Quebec, Canada
- Programa Interunidades de Pós-graduação em Bioinformática, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Aristoteles Goes-Neto
- Programa Interunidades de Pós-graduação em Bioinformática, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Vasco Azevedo
- Programa Interunidades de Pós-graduação em Bioinformática, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Aïda Ouangraoua
- Department of Computer Science, University of Sherbrooke, Quebec, Canada
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Anokhina TO, Esikova TZ, Gafarov AB, Polivtseva VN, Baskunov BP, Solyanikova IP. Alternative Naphthalene Metabolic Pathway Includes Formation of ortho-Phthalic Acid and Cinnamic Acid Derivatives in the Rhodococcus opacus Strain 3D. BIOCHEMISTRY (MOSCOW) 2020; 85:355-368. [DOI: 10.1134/s0006297920030116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Ma Q, Gao X, Bi X, Tu L, Xia M, Shen Y, Wang M. Isolation, characterisation, and genome sequencing of Rhodococcus equi: a novel strain producing chitin deacetylase. Sci Rep 2020; 10:4329. [PMID: 32152368 PMCID: PMC7062688 DOI: 10.1038/s41598-020-61349-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 02/24/2020] [Indexed: 11/19/2022] Open
Abstract
Chitin deacetylase (CDA) can hydrolyse the acetamido group of chitin polymers to produce chitosans, which are used in various fields including the biomedical and pharmaceutical industries, food production, agriculture, and water treatment. CDA represents a more environmentally-friendly and easier to control alternative to the chemical methods currently utilised to produce chitosans from chitin; however, the majority of identified CDAs display activity toward low-molecular-weight oligomers and are essentially inactive toward polymeric chitin or chitosans. Therefore, it is important to identify novel CDAs with activity toward polymeric chitin and chitosans. In this study, we isolated the bacterium Rhodococcus equi F6 from a soil sample and showed that it expresses a novel CDA (ReCDA), whose activity toward 4-nitroacetanilide reached 19.20 U/mL/h during fermentation and was able to deacetylate polymeric chitin, colloidal chitin, glycol-chitin, and chitosan. Whole genome sequencing revealed that ReCDA is unique to the R. equi F6 genome, while phylogenetic analysis indicated that ReCDA is evolutionarily distant from other CDAs. In conclusion, ReCDA isolated from the R. equi F6 strain expands the known repertoire of CDAs and could be used to deacetylate polymeric chitosans and chitin in industrial applications.
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Affiliation(s)
- Qinyuan Ma
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science & Technology), Ministry of Education, Tianjin Key Lab of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, P.R. China
| | - Xiuzhen Gao
- School of Life Science, Shandong University of Technology, Zibo, 255049, China
| | - Xinyu Bi
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science & Technology), Ministry of Education, Tianjin Key Lab of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, P.R. China
| | - Linna Tu
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science & Technology), Ministry of Education, Tianjin Key Lab of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, P.R. China
| | - Menglei Xia
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science & Technology), Ministry of Education, Tianjin Key Lab of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, P.R. China
| | - Yanbing Shen
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science & Technology), Ministry of Education, Tianjin Key Lab of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, P.R. China.
| | - Min Wang
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science & Technology), Ministry of Education, Tianjin Key Lab of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, P.R. China.
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63
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Kumar S, Paul D, Shouche Y, Suryavanshi M. Data on genome sequencing, assembly, annotation and genomic analysis of Rhodococcus rhodochrous strain SPC17 isolated from Lonar Lake. Data Brief 2020; 29:105336. [PMID: 32154356 PMCID: PMC7058525 DOI: 10.1016/j.dib.2020.105336] [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: 01/27/2020] [Revised: 02/17/2020] [Accepted: 02/18/2020] [Indexed: 11/26/2022] Open
Abstract
The bacterial isolates of genus Rhodococcus are best known for their significant biodegradation abilities. Here, we report the data related to draft genome sequencing of Rhodococcus rhodochrous strain SPC17 isolated from sediments of Lonar Lake. The de novo assembly of 1598096 Illumina's paired-end sequencing reads resulted in 51 contigs for an overall genome assembly size of 4.98Mb. A total of 4546 genes were predicted using the National Center for Biotechnology Information- Prokaryotic Genome Annotation Pipeline (NCBI-PGAP). RAST server-based annotation of the Rhodococcus strain SPC17 genome resulted in a total of 295 subsystems with 25% subsystem coverage. The data on the draft genome shotgun project are accessible at NCBI-GenBank under the accession number WUUR00000000. Our data resource will facilitate further molecular and genomic studies of diverse hydrocarbon catabolizing genes present in Rhodococcus rhodochrous strain SPC17.
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Affiliation(s)
- Satish Kumar
- National Centre for Cell Science, Savitribai Phule Pune University Campus, Pune, MH, India
- ICAR-National Institute of Abiotic Stress Management, Baramati, Pune, MH, India
- Corresponding author. National Centre for Microbial resource, National Centre for Cell Science, Savitribai Phule Pune University Campus, Pune, 411007, Maharashtra State, India.
| | - Dhiraj Paul
- National Centre for Cell Science, Savitribai Phule Pune University Campus, Pune, MH, India
- Corresponding author. National Centre for Cell Science, Savitribai Phule Pune University Campus, Pune, 411007, Maharashtra State, India.
| | - Yogesh Shouche
- National Centre for Cell Science, Savitribai Phule Pune University Campus, Pune, MH, India
- Corresponding author. National Centre for Cell Science, Savitribai Phule Pune University Campus, Pune, 411007, Maharashtra State, India.
| | - Mangesh Suryavanshi
- Yenepoya Research Centre, Yenepoya Deemed to be University, Mangalore, 575018, Karnataka, India
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64
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Viesser JA, Sugai-Guerios MH, Malucelli LC, Pincerati MR, Karp SG, Maranho LT. Petroleum-Tolerant Rhizospheric Bacteria: Isolation, Characterization and Bioremediation Potential. Sci Rep 2020; 10:2060. [PMID: 32029873 PMCID: PMC7005311 DOI: 10.1038/s41598-020-59029-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 12/19/2019] [Indexed: 11/09/2022] Open
Abstract
Petroleum is an important energy source. Due to its intensive exploration, accidents resulting in oil spills on soil are frequent, which creates consequences to ecosystems and human health. Rhizodegradation is an efficient technique that promotes the decontamination of polluted environments through the selection and use of rhizosphere microorganisms from phytoremediation plants. The aim of this study was to isolate, identify and characterize bacteria capable of degrading petroleum from the rhizosphere of Panicum aquaticum Poir., a plant that grows in petroleum contaminated soils. Three bacteria were isolated and characterized at the morphological (Gram staining), molecular (16S rRNA gene sequence analysis) and biochemical level. These bacteria were identified as new strains of Bacillus thurigiensis, Bacillus pumilus and Rhodococcus hoagii, which have been reported as potential bioremediators in the literature. All three bacteria were able to use petroleum hydrocarbons as the sole carbon source during in vitro degradation assays. Gas chromatography analysis of these assays indicated reductions of petroleum hydrocarbons between 23% and 96% within 48 h. Among the isolated bacteria, Rhodococcus hoagii presented the highest efficiency of petroleum consumption, reaching 87% of degradation after only 24 h of cultivation, which corresponds to a higher and faster degradation than previously reported, confirming the potential use of Rhodococcus hoagii for petroleum biodegradation.
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Affiliation(s)
- Jéssica Aparecida Viesser
- PhD Program in Industrial Biotechnology, Universidade Positivo (UP), Av. Pedro Prof. Viriato Parigot de Souza, 5300, CEP 81280-330, Curitiba, PR, Brazil
| | - Maura Harumi Sugai-Guerios
- PhD Program in Industrial Biotechnology, Universidade Positivo (UP), Av. Pedro Prof. Viriato Parigot de Souza, 5300, CEP 81280-330, Curitiba, PR, Brazil
| | - Lucca Centa Malucelli
- PhD Program in Environmental Management, Universidade Positivo (UP), Av. Pedro Prof. Viriato Parigot de Souza, 5300, CEP 81280-330, Curitiba, PR, Brazil
| | - Marcia Regina Pincerati
- PhD Program in Industrial Biotechnology, Universidade Positivo (UP), Av. Pedro Prof. Viriato Parigot de Souza, 5300, CEP 81280-330, Curitiba, PR, Brazil
| | - Susan Grace Karp
- PhD Program in Industrial Biotechnology, Universidade Positivo (UP), Av. Pedro Prof. Viriato Parigot de Souza, 5300, CEP 81280-330, Curitiba, PR, Brazil.,PhD Program in Bioprocess Engineering and Biotechnology, Universidade Federal do Paraná, Caixa Postal 19011 - ACF Centro Politécnico, CEP 81531-980, Curitiba, PR, Brazil
| | - Leila Teresinha Maranho
- PhD Program in Industrial Biotechnology, Universidade Positivo (UP), Av. Pedro Prof. Viriato Parigot de Souza, 5300, CEP 81280-330, Curitiba, PR, Brazil.
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65
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Kan J, Peng T, Huang T, Xiong G, Hu Z. NarL, a Novel Repressor for CYP108j1 Expression during PAHs Degradation in Rhodococcus sp. P14. Int J Mol Sci 2020; 21:ijms21030983. [PMID: 32024188 PMCID: PMC7037279 DOI: 10.3390/ijms21030983] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 01/27/2020] [Accepted: 01/30/2020] [Indexed: 12/18/2022] Open
Abstract
Rhodococcus sp. P14 was isolated from crude-oil-contaminated sediments, and a wide range of polycyclic aromatic hydrocarbons (PAHs) could be used as the sole source of carbon and energy. A key CYP450 gene, designated as cyp108j1 and involved in the degradation of PAHs, was identified and was able to hydroxylate various PAHs. However, the regulatory mechanism of the expression of cyp108j1 remains unknown. In this study, we found that the expression of cyp108j1 is negatively regulated by a LuxR (helix-turn-helix transcription factors in acyl-homoserine lactones-mediated quorum sensing) family regulator, NarL (nitrate-dependent two-component regulatory factor), which is located upstream of cyp108j1. Further analysis revealed that NarL can directly bind to the promoter region of cyp108j1. Mutational experiments demonstrated that the binding site between NarL and the cyp108j1 promoter was the palindromic sequence GAAAGTTG-CAACTTTC. Together, the finding reveal that NarL is a novel repressor for the expression of cyp108j1 during PAHs degradation.
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Affiliation(s)
- Jie Kan
- Department of Biology, Shantou University, Shantou 515063, China; (J.K.); (T.P.); (T.H.)
| | - Tao Peng
- Department of Biology, Shantou University, Shantou 515063, China; (J.K.); (T.P.); (T.H.)
| | - Tongwang Huang
- Department of Biology, Shantou University, Shantou 515063, China; (J.K.); (T.P.); (T.H.)
| | - Guangming Xiong
- Institute of Toxicology and Pharmacology for Natural Scientists, University Medical School Schleswig-Holstein, 24103 Kiel, Germany;
| | - Zhong Hu
- Department of Biology, Shantou University, Shantou 515063, China; (J.K.); (T.P.); (T.H.)
- Correspondence:
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66
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Draft Genome Sequence of Rhodococcus aetherivorans JCM 14343 T, a Bacterium Capable of Degrading Recalcitrant Noncyclic and Cyclic Ethers. Microbiol Resour Announc 2020; 9:9/3/e01345-19. [PMID: 31948959 PMCID: PMC6965577 DOI: 10.1128/mra.01345-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here, we report the draft genome sequence of Rhodococcus aetherivorans JCM 14343T, which possesses the versatile ability to degrade recalcitrant noncyclic and cyclic ether compounds. The 4.2-Mbp genome of this bacterium contains alkane hydroxylase and propane monooxygenase genes involved in the degradation of noncyclic and cyclic ethers, respectively. Here, we report the draft genome sequence of Rhodococcus aetherivorans JCM 14343T, which possesses the versatile ability to degrade recalcitrant noncyclic and cyclic ether compounds. The 4.2-Mbp genome of this bacterium contains alkane hydroxylase and propane monooxygenase genes involved in the degradation of noncyclic and cyclic ethers, respectively.
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67
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Complete Genome Sequence of Rhodococcus ruber R1, a Novel Strain Showing a Broad Catabolic Potential toward Lignin-Derived Aromatics. Microbiol Resour Announc 2020; 9:9/2/e00905-19. [PMID: 31919154 PMCID: PMC6952640 DOI: 10.1128/mra.00905-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rhodococcus ruber R1 was isolated from a pulp mill wastewater treatment plant because of its ability to use methoxylated aromatics as growth substrates. We report the 5.56-Mb genome sequence of strain R1, which can provide insights into the biodegradation of lignin-derived phenolic monomers and potentially support processes for lignocellulose conversion. Rhodococcus ruber R1 was isolated from a pulp mill wastewater treatment plant because of its ability to use methoxylated aromatics as growth substrates. We report the 5.56-Mb genome sequence of strain R1, which can provide insights into the biodegradation of lignin-derived phenolic monomers and potentially support processes for lignocellulose conversion.
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68
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Wang C, Chen Y, Zhou H, Li X, Tan Z. Adaptation mechanisms of Rhodococcus sp. CNS16 under different temperature gradients: Physiological and transcriptome. CHEMOSPHERE 2020; 238:124571. [PMID: 31472351 DOI: 10.1016/j.chemosphere.2019.124571] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 08/06/2019] [Accepted: 08/09/2019] [Indexed: 06/10/2023]
Abstract
Rhodococcus exhibits strong adaptability to environmental stressors and plays a crucial role in environmental bioremediation. However, seasonal changes in ambient temperature, especially rapid temperature drops exert an adverse effect on in situ bioremediation. In this paper, we studied the cell morphology and fatty acid composition of an aniline-degrading strain Rhodococcus sp. CNS16 at temperatures of 30 °C, 20 °C, and 10 °C. At suboptimal temperatures, cell morphology of CNS16 changed from short rod-shaped to long rod or irregular shaped, and the proportion of unsaturated fatty acids was upregulated. Transcriptomic technologies were then utilized to gain detailed insights into the adaptive mechanisms of CNS16 subjected to suboptimal temperatures. The results showed that the number of gene responses was significantly higher at 10 °C than that at 20 °C. The inhibition of peptidoglycan synthase expression and up-regulation of Filamentous Temperature Sensitive as well as unsaturated fatty acid synthesis genes at suboptimal temperatures might be closely related to corresponding changes in cell morphology and fatty acids composition. Strain CNS16 showed loss of catalase and superoxide dismutase activity, and utilized thioredoxin-dependent thiol peroxidase to resist oxidative stress. The up-regulation of carotenoid and Vitamin B2 synthesis at 10 °C might also be involved in the resistance to oxidative stress. Amino acid metabolism, coenzyme and vitamin metabolism, ABC transport, and energy metabolism are essential for peptidoglycan synthesis and regulation of cellular metabolism; therefore, synergistically resisting environmental stress. This study provides a mechanistic basis for the regulation of aniline degradation in Rhodococcus sp. CNS16 at low temperatures.
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Affiliation(s)
- Chen Wang
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, China; University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yangwu Chen
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, China
| | - Houzhen Zhou
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, China
| | - Xudong Li
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, China
| | - Zhouliang Tan
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, China.
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69
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Wang H, Lu L, Chen X, Bian Y, Ren ZJ. Geochemical and microbial characterizations of flowback and produced water in three shale oil and gas plays in the central and western United States. WATER RESEARCH 2019; 164:114942. [PMID: 31401327 DOI: 10.1016/j.watres.2019.114942] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 07/30/2019] [Accepted: 07/31/2019] [Indexed: 06/10/2023]
Abstract
Limited understanding of wastewater streams produced from shale oil and gas wells impedes best practices of wastewater treatment and reuse. This study provides a comprehensive and comparative analysis of flowback and produced water from three major and newly developed shale plays (the Bakken shale, North Dakota; the Barnett shale, Texas; and the Denver-Julesburg (DJ) basin, Colorado) in central and western United States. Geochemical features that included more than 10 water quality parameters, dissolved organic matter, as well as microbial community structures were characterized and compared. Results showed that wastewater from Bakken and Barnett shales has extremely high salinity (∼295 g/L total dissolved solids (TDS)) and low organic concentration (80-252 mg/L dissolved organic carbon (DOC)). In contrast, DJ basin showed an opposite trend with low TDS (∼30 g/L) and high organic content (644 mg/L DOC). Excitation-emission matrix (EEM) fluorescence spectra demonstrated that more humic acid and fluvic acid-like organics with higher aromaticity existed in Bakken wastewater than that in Barnett and DJ basin. Microbial communities of Bakken samples were dominated by Fe (III)-reducing bacteria Geobacter, lactic acid bacteria Lactococcus and Enterococcus, and Bradyrhizobium, while DJ basin water showed higher abundance of Rhodococcus, Thermovirga, and sulfate reducing bacteria Thermotoga and Petrotoga. All these bacteria are capable of hydrocarbon degradation. Hydrogenotrophic methanogens dominated the archaeal communities in all samples.
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Affiliation(s)
- Huan Wang
- Department of Civil and Environmental Engineering and Andlinger Center for Energy and the Environment, Princeton University, Princeton, NJ, 08544, United States; Department of Civil, Environmental, and Architectural Engineering, University of Colorado Boulder, Boulder, CO, 80309, United States.
| | - Lu Lu
- Department of Civil and Environmental Engineering and Andlinger Center for Energy and the Environment, Princeton University, Princeton, NJ, 08544, United States.
| | - Xi Chen
- Department of Civil and Environmental Engineering and Andlinger Center for Energy and the Environment, Princeton University, Princeton, NJ, 08544, United States.
| | - Yanhong Bian
- Department of Civil and Environmental Engineering and Andlinger Center for Energy and the Environment, Princeton University, Princeton, NJ, 08544, United States.
| | - Zhiyong Jason Ren
- Department of Civil and Environmental Engineering and Andlinger Center for Energy and the Environment, Princeton University, Princeton, NJ, 08544, United States; Department of Civil, Environmental, and Architectural Engineering, University of Colorado Boulder, Boulder, CO, 80309, United States.
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70
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Microaerobic conditions caused the overwhelming dominance of Acinetobacter spp. and the marginalization of Rhodococcus spp. in diesel fuel/crude oil mixture-amended enrichment cultures. Arch Microbiol 2019; 202:329-342. [PMID: 31664492 PMCID: PMC7012980 DOI: 10.1007/s00203-019-01749-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 10/02/2019] [Accepted: 10/10/2019] [Indexed: 02/03/2023]
Abstract
The aim of the present study was to reveal how different microbial communities evolve in diesel fuel/crude oil-contaminated environments under aerobic and microaerobic conditions. To investigate this question, aerobic and microaerobic bacterial enrichments amended with a diesel fuel/crude oil mixture were established and analysed. The representative aerobic enrichment community was dominated by Gammaproteobacteria (64.5%) with high an abundance of Betaproteobacteriales (36.5%), followed by Alphaproteobacteria (8.7%), Actinobacteria (5.6%), and Candidatus Saccharibacteria (4.5%). The most abundant alkane monooxygenase (alkB) genotypes in this enrichment could be linked to members of the genus Rhodococcus and to a novel Gammaproteobacterium, for which we generated a high-quality draft genome using genome-resolved metagenomics of the enrichment culture. Contrarily, in the microaerobic enrichment, Gammaproteobacteria (99%) overwhelmingly dominated the microbial community with a high abundance of the genera Acinetobacter (66.3%), Pseudomonas (11%) and Acidovorax (11%). Under microaerobic conditions, the vast majority of alkB gene sequences could be linked to Pseudomonas veronii. Consequently, results shed light on the fact that the excellent aliphatic hydrocarbon degrading Rhodococcus species favour clear aerobic conditions, while oxygen-limited conditions can facilitate the high abundance of Acinetobacter species in aliphatic hydrocarbon-contaminated subsurface environments.
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71
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Busch H, Hagedoorn PL, Hanefeld U. Rhodococcus as A Versatile Biocatalyst in Organic Synthesis. Int J Mol Sci 2019; 20:E4787. [PMID: 31561555 PMCID: PMC6801914 DOI: 10.3390/ijms20194787] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 09/23/2019] [Accepted: 09/24/2019] [Indexed: 12/11/2022] Open
Abstract
The application of purified enzymes as well as whole-cell biocatalysts in synthetic organic chemistry is becoming more and more popular, and both academia and industry are keen on finding and developing novel enzymes capable of performing otherwise impossible or challenging reactions. The diverse genus Rhodococcus offers a multitude of promising enzymes, which therefore makes it one of the key bacterial hosts in many areas of research. This review focused on the broad utilization potential of the genus Rhodococcus in organic chemistry, thereby particularly highlighting the specific enzyme classes exploited and the reactions they catalyze. Additionally, close attention was paid to the substrate scope that each enzyme class covers. Overall, a comprehensive overview of the applicability of the genus Rhodococcus is provided, which puts this versatile microorganism in the spotlight of further research.
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Affiliation(s)
- Hanna Busch
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
| | - Peter-Leon Hagedoorn
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
| | - Ulf Hanefeld
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
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72
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Vázquez-Boland JA, Meijer WG. The pathogenic actinobacterium Rhodococcus equi: what's in a name? Mol Microbiol 2019; 112:1-15. [PMID: 31099908 PMCID: PMC6852188 DOI: 10.1111/mmi.14267] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2019] [Indexed: 12/17/2022]
Abstract
Rhodococcus equi is the only recognized animal pathogenic species within an extended genus of metabolically versatile Actinobacteria of considerable biotechnological interest. Best known as a horse pathogen, R. equi is commonly isolated from other animal species, particularly pigs and ruminants, and causes severe opportunistic infections in people. As typical in the rhodococci, R. equi niche specialization is extrachromosomally determined, via a conjugative virulence plasmid that promotes intramacrophage survival. Progress in the molecular understanding of R. equi and its recent rise as a novel paradigm of multihost adaptation has been accompanied by an unusual nomenclatural instability, with a confusing succession of names: "Prescottia equi", "Prescotella equi", Corynebacterium hoagii and Rhodococcus hoagii. This article reviews current advances in the genomics, biology and virulence of this pathogenic actinobacterium with a unique mechanism of plasmid‐transferable animal host tropism. It also discusses the taxonomic and nomenclatural issues around R. equi in the light of recent phylogenomic evidence that confirms its membership as a bona fide Rhodococcus.
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Affiliation(s)
- José A Vázquez-Boland
- Microbial Pathogenesis Group, Edinburgh Medical School (Biomedical Sciences - Infection Medicine), University of Edinburgh, Chancellor's Building, Little France campus, Edinburgh, EH16 4SB, UK
| | - Wim G Meijer
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
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73
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Luo D, Chen J, Xie G, Yue L, Wang Y. Enzyme characterization and biological activities of a resuscitation promoting factor from an oil degrading bacterium Rhodococcus erythropolis KB1. PeerJ 2019; 7:e6951. [PMID: 31149404 PMCID: PMC6534110 DOI: 10.7717/peerj.6951] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 04/14/2019] [Indexed: 01/28/2023] Open
Abstract
Resuscitation-promoting factors (Rpf) are a class of muralytic enzymes, which participate in recovery of dormant cells and promoting bacteria growth in poor media. In the present study the expression vector of the rpf-1 gene from an oil-degrading bacterium Rhodococcus erythropolis KB1 was constructed and expressed in Escherichia coli. The expressed protein was purified by Ni2+-affinity chromatography, and showed muralytic activity when measured with 4-methylumbelliferyl-β-D-N,N′,N″-triacetyl chitotrioside as substrate. Addition of purified Rpf-1 to R. erythropolis culture efficiently improved bacterial cell growth. The purified protein also increased resuscitation of viable but nonculturable cells of R. erythropolis to culturable state. The conserved amino acid residues including Asp45, Glu51, Cys50, Thr60, Gln69, Thr74, Trp75 and Cys114 of the Rpf-1 were replaced with different amino acids. The mutant proteins were also expressed and purified with Ni2+-affinity chromatography. The muralytic activities of the mutant proteins decreased to different extents when compared with that of the wild type Rpf-1. Gln69 was found to play the most important role in the enzyme activity, substitution of Gln69 with lysine (Q69K) resulted in the greatest decrease of muralytic activity. The other amino acid residues such as Asp45, Glu51, Cys50 and Cys114 were also found to be very important in maintaining muralytic activity and biological function of the Rpf-1. Our results indicated that Rpf-1 from R. erythropolis showed muralytic activities and weak protease activity, but the muralytic activity was responsible for its growth promotion and resuscitation activity.
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Affiliation(s)
- Dan Luo
- School of Petrochemical Engineering, Lanzhou University of Technology, Lan Zhou, China
| | - Jixiang Chen
- School of Petrochemical Engineering, Lanzhou University of Technology, Lan Zhou, China
| | - Gang Xie
- School of Petrochemical Engineering, Lanzhou University of Technology, Lan Zhou, China
| | - Liang Yue
- School of Petrochemical Engineering, Lanzhou University of Technology, Lan Zhou, China
| | - Yonggang Wang
- School of Life science and Engineering, Lanzhou University of Technology, Lan Zhou, China
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Aburto-Medina A, Shahsavari E, Salzman SA, Kramer A, Ball AS, Allinson G. Elucidation of the microbial diversity in rivers in south-west Victoria, Australia impacted by rural agricultural contamination (dairy farming). ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 172:356-363. [PMID: 30731266 DOI: 10.1016/j.ecoenv.2019.01.112] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 01/24/2019] [Accepted: 01/31/2019] [Indexed: 06/09/2023]
Abstract
We assessed the water quality of south-west Victorian rivers impacted by the dairy industry using traditional water quality assessment together with culture-dependent (colilert/enterolert) and also culture-independent (next generation sequencing) microbial methods. The aim of the study was to identify relationships/associations between dairy farming intensity and water contamination. Water samples with high total and faecal coliforms (>1000 MPN cfu/100 ml), and with high nitrogen levels (TN) were observed in zones with a high proportion of dairy farming. Members of the genus Nitrospira, Rhodobacter and Rhodoplanes were predominant in such high cattle density zones. Samples from sites in zones with lower dairy farming activities registered faecal coliform numbers within the permissible limits (<1000 MPN cfu/100 ml) and showed the presence of a wide variety of microorganisms. However, no bacterial pathogens were found in the river waters regardless of the proportion of cattle. The data suggests that using the spatially weighted proportion of land used for dairy farming is a useful way to target at-risk sub-catchments across south west Victoria; further work is required to confirm that this approach is applicable in other regions.
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Affiliation(s)
- Arturo Aburto-Medina
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Bundoora, Victoria 3083, Australia.
| | - Esmaeil Shahsavari
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Bundoora, Victoria 3083, Australia
| | - Scott A Salzman
- Department of Information Systems and Business Analytics, Deakin University, Warrnambool, Victoria 3280 Australia
| | - Andrew Kramer
- Environment Protection Authority Victoria, Centre for Applied Sciences, Ernest Jones Drive, Macleod, Victoria 3085 Australia; Waikato Regional Council, Private Bag 3038, Waikato Mail Centre, Hamilton 3240, New Zealand
| | - Andrew S Ball
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Bundoora, Victoria 3083, Australia
| | - Graeme Allinson
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Melbourne, Victoria 3001, Australia
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75
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Kuyukina MS, Ivshina IB. Bioremediation of Contaminated Environments Using Rhodococcus. ACTA ACUST UNITED AC 2019. [DOI: 10.1007/978-3-030-11461-9_9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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76
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Abstract
The review is devoted to biocatalysts based on actinobacteria of the genus Rhodococcus, which are promising for environmental biotechnologies. In the review, biotechnological advantages of Rhodococcus bacteria are evaluated, approaches used to develop robust and efficient biocatalysts are discussed, and their relevant applications are given. We focus on Rhodococcus cell immobilization in detail (methods of immobilization, criteria for strains and carriers, and optimization of process parameters) as the most efficient approach for stabilizing biocatalysts. It is shown that advanced Rhodococcus biocatalysts with improved working characteristics, enhanced stress tolerance, high catalytic activities, human and environment friendly, and commercially viable are developed, which are suitable for wastewater treatment, bioremediation, and biofuel production.
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77
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Bianco A, Fancello F, Balmas V, Dettori M, Motroni A, Zara G, Budroni M. Microbial communities and malt quality of durum wheat used in brewing. JOURNAL OF THE INSTITUTE OF BREWING 2019. [DOI: 10.1002/jib.555] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Angela Bianco
- Department of Agricultural Science; University of Sassari; Sassari Sardinia Italy
| | - Francesco Fancello
- Department of Agricultural Science; University of Sassari; Sassari Sardinia Italy
| | - Virgilio Balmas
- Department of Agricultural Science; University of Sassari; Sassari Sardinia Italy
| | - Marco Dettori
- Agricultural Research Agency of Sardinia (Agris); Cagliari Sardinia Italy
| | - Andrea Motroni
- Hydro-Meteo-Climate Department, Sardinian Regional Agency for Environmental Protection; Sassari Italy
| | - Giacomo Zara
- Department of Agricultural Science; University of Sassari; Sassari Sardinia Italy
| | - Marilena Budroni
- Department of Agricultural Science; University of Sassari; Sassari Sardinia Italy
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78
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Salam LB, Ishaq A. Biostimulation potentials of corn steep liquor in enhanced hydrocarbon degradation in chronically polluted soil. 3 Biotech 2019; 9:46. [PMID: 30729070 DOI: 10.1007/s13205-019-1580-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 01/17/2019] [Indexed: 12/16/2022] Open
Abstract
The effects of corn steep liquor (CSL) on hydrocarbon degradation and microbial community structure and function was evaluated in field-moist soil microcosms. Chronically polluted soil treated with CSL (AB4) and an untreated control (3S) was compared over a period of 6 weeks. Gas chromatographic fingerprints of residual hydrocarbons revealed removal of 95.95% and 94.60% aliphatic and aromatic hydrocarbon fractions in AB4 system with complete disappearance of nC1-nC8, nC10, nC15, nC20-nC23 aliphatics and aromatics such as naphthalene, acenaphthylene, fluorene, phenanthrene, pyrene, benzo(a)anthracene, and indeno(123-cd)pyrene in 42 days. In 3S system, there is removal of 61.27% and 66.58% aliphatic and aromatic fractions with complete disappearance of nC2 and nC21 aliphatics and naphthalene, acenaphthylene, fluorene, phenanthrene, pyrene, and benzo(a)anthracene aromatics in 42 days. Illumina shotgun sequencing of the DNA extracted from the two systems showed the preponderance of Actinobacteria (31.46%) and Proteobacteria (38.95%) phyla in 3S and AB4 with the dominance of Verticillium (22.88%) and Microbacterium (8.16%) in 3S, and Laceyella (24.23%), Methylosinus (8.93%) and Pedobacter (7.73%) in AB4. Functional characterization of the metagenomic reads revealed diverse metabolic potentials and adaptive traits of the microbial communities in the two systems to various environmental stressors. It also revealed the exclusive detection of catabolic enzymes in AB4 system belonging to the aldehyde dehydrogenase superfamily. The results obtained in this study showed that CSL is a potential resource for bioremediation of hydrocarbon-polluted soils.
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Affiliation(s)
- Lateef B Salam
- Department of Biological Sciences, Microbiology Unit Al-Hikmah University, Ilorin, Kwara Nigeria
| | - Aisha Ishaq
- Department of Biological Sciences, Microbiology Unit Al-Hikmah University, Ilorin, Kwara Nigeria
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79
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Sengupta K, Swain MT, Livingstone PG, Whitworth DE, Saha P. Genome Sequencing and Comparative Transcriptomics Provide a Holistic View of 4-Nitrophenol Degradation and Concurrent Fatty Acid Catabolism by Rhodococcus sp. Strain BUPNP1. Front Microbiol 2019; 9:3209. [PMID: 30662435 PMCID: PMC6328493 DOI: 10.3389/fmicb.2018.03209] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 12/11/2018] [Indexed: 12/03/2022] Open
Abstract
Rhodococcus sp.strain BUPNP1 can utilize the priority environmental pollutant 4-nitrophenol (4-NP) as its sole source of carbon and energy. In this study, genome and transcriptome sequencing were used to gain mechanistic insights into 4-NP degradation. The draft BUPNP1 genome is 5.56 Mbp and encodes 4,963 proteins, which are significantly enriched in hypothetical proteins compared to other Rhodococcus sp. A novel 4-NP catabolic 43 gene cluster “nph” was identified that encodes all the genes required for the conversion of 4-NP into acetyl-CoA and succinate, via 4-nitrocatechol. The cluster also encodes pathways for the catabolism of other diverse aromatic compounds. Comparisons between BUPN1 growing on either 4-NP or glucose resulted in significant changes in the expression of many nph cluster genes, and, during 4-NP growth, a loss of lipid inclusions. Moreover, fatty acid degradation/synthesis genes were found within the nph cluster, suggesting fatty acids may be concurrently catabolised with 4-NP. A holistic model for the action of the nph gene cluster is proposed which incorporates genetic architecture, uptake and metabolism of aromatic compounds, enzymatic activities and transcriptional regulation. The model provides testable hypotheses for further biochemical investigations into the genes of the nph cluster, for potential exploitation in bioremediation.
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Affiliation(s)
- Kriti Sengupta
- Department of Microbiology, Burdwan University, Bardhaman, India
| | - Martin T Swain
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Paul G Livingstone
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - David E Whitworth
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Pradipta Saha
- Department of Microbiology, Burdwan University, Bardhaman, India
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80
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Anthony WE, Carr RR, DeLorenzo DM, Campbell TP, Shang Z, Foston M, Moon TS, Dantas G. Development of Rhodococcus opacus as a chassis for lignin valorization and bioproduction of high-value compounds. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:192. [PMID: 31404385 PMCID: PMC6683499 DOI: 10.1186/s13068-019-1535-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 07/24/2019] [Indexed: 05/09/2023]
Abstract
The current extraction and use of fossil fuels has been linked to extensive negative health and environmental outcomes. Lignocellulosic biomass-derived biofuels and bioproducts are being actively considered as renewable alternatives to the fuels, chemicals, and materials produced from fossil fuels. A major challenge limiting large-scale, economic deployment of second-generation biorefineries is the insufficient product yield, diversity, and value that current conversion technologies can extract from lignocellulose, in particular from the underutilized lignin fraction. Rhodococcus opacus PD630 is an oleaginous gram-positive bacterium with innate catabolic pathways and tolerance mechanisms for the inhibitory aromatic compounds found in depolymerized lignin, as well as native or engineered pathways for hexose and pentose sugars found in the carbohydrate fractions of biomass. As a result, R. opacus holds potential as a biological chassis for the conversion of lignocellulosic biomass into biodiesel precursors and other value-added products. This review begins by examining the important role that lignin utilization will play in the future of biorefineries and by providing a concise survey of the current lignin conversion technologies. The genetic machinery and capabilities of R. opacus that allow the bacterium to tolerate and metabolize aromatic compounds and depolymerized lignin are also discussed, along with a synopsis of the genetic toolbox and synthetic biology methods now available for engineering this organism. Finally, we summarize the different feedstocks that R. opacus has been demonstrated to consume, and the high-value products that it has been shown to produce. Engineered R. opacus will enable lignin valorization over the coming years, leading to cost-effective conversion of lignocellulose into fuels, chemicals, and materials.
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Affiliation(s)
- Winston E. Anthony
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA
| | - Rhiannon R. Carr
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130 USA
| | - Drew M. DeLorenzo
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130 USA
| | - Tayte P. Campbell
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA
| | - Zeyu Shang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130 USA
| | - Marcus Foston
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130 USA
| | - Tae Seok Moon
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130 USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63108 USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130 USA
- Department of Molecular Microbiology, Washington University in St. Louis School of Medicine, St. Louis, MO 63108 USA
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81
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82
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Francis IM, Vereecke D. Plant-Associated Rhodococcus Species, for Better and for Worse. BIOLOGY OF RHODOCOCCUS 2019. [DOI: 10.1007/978-3-030-11461-9_13] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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83
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Zhou H, Yang Y, You S, Liu B, Ren N, Xing D. Oxygen reduction reaction activity and the microbial community in response to magnetite coordinating nitrogen-doped carbon catalysts in bioelectrochemical systems. Biosens Bioelectron 2018; 122:113-120. [DOI: 10.1016/j.bios.2018.09.044] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 09/11/2018] [Accepted: 09/12/2018] [Indexed: 10/28/2022]
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84
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Barbey C, Chane A, Burini JF, Maillot O, Merieau A, Gallique M, Beury-Cirou A, Konto-Ghiorghi Y, Feuilloley M, Gobert V, Latour X. A Rhodococcal Transcriptional Regulatory Mechanism Detects the Common Lactone Ring of AHL Quorum-Sensing Signals and Triggers the Quorum-Quenching Response. Front Microbiol 2018; 9:2800. [PMID: 30524404 PMCID: PMC6262395 DOI: 10.3389/fmicb.2018.02800] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 10/31/2018] [Indexed: 01/08/2023] Open
Abstract
The biocontrol agent Rhodococcus erythropolis disrupts virulence of plant and human Gram-negative pathogens by catabolizing their N-acyl-homoserine lactones. This quorum-quenching activity requires the expression of the qsd (quorum-sensing signal degradation) operon, which encodes the lactonase QsdA and the fatty acyl-CoA ligase QsdC, involved in the catabolism of lactone ring and acyl chain moieties of signaling molecules, respectively. Here, we demonstrate the regulation of qsd operon expression by a TetR-like family repressor, QsdR. This repression was lifted by adding the pathogen quorum signal or by deleting the qsdR gene, resulting in enhanced lactone degrading activity. Using interactomic approaches and transcriptional fusion strategy, the qsd operon derepression was elucidated: it is operated by the binding of the common part of signaling molecules, the homoserine lactone ring, to the effector-receiving domain of QsdR, preventing a physical binding of QsdR to the qsd promoter region. To our knowledge, this is the first evidence revealing quorum signals as inducers of the suitable quorum-quenching pathway, confirming this TetR-like protein as a lactone sensor. This regulatory mechanism designates the qsd operon as encoding a global disrupting pathway for degrading a wide range of signal substrates, allowing a broad spectrum anti-virulence activity mediated by the rhodococcal biocontrol agent. Understanding the regulation mechanisms of qsd operon expression led also to the development of biosensors useful to monitor in situ the presence of exogenous signals and quorum-quenching activity.
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Affiliation(s)
- Corinne Barbey
- Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM EA 4312) - Normandie Université - LMSM, Évreux, France.,Structure Fédérative de Recherche Normandie Végétal 4277 (NORVEGE), Mont-Saint-Aignan, France.,Seeds Innovation Protection Research and Environment, Achicourt, France.,Seeds Innovation Protection Research and Environment, Bretteville du Grand-Caux, France
| | - Andrea Chane
- Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM EA 4312) - Normandie Université - LMSM, Évreux, France.,Structure Fédérative de Recherche Normandie Végétal 4277 (NORVEGE), Mont-Saint-Aignan, France
| | - Jean-François Burini
- Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM EA 4312) - Normandie Université - LMSM, Évreux, France.,Structure Fédérative de Recherche Normandie Végétal 4277 (NORVEGE), Mont-Saint-Aignan, France
| | - Olivier Maillot
- Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM EA 4312) - Normandie Université - LMSM, Évreux, France.,Structure Fédérative de Recherche Normandie Végétal 4277 (NORVEGE), Mont-Saint-Aignan, France
| | - Annabelle Merieau
- Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM EA 4312) - Normandie Université - LMSM, Évreux, France.,Structure Fédérative de Recherche Normandie Végétal 4277 (NORVEGE), Mont-Saint-Aignan, France
| | - Mathias Gallique
- Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM EA 4312) - Normandie Université - LMSM, Évreux, France.,Structure Fédérative de Recherche Normandie Végétal 4277 (NORVEGE), Mont-Saint-Aignan, France
| | - Amélie Beury-Cirou
- Seeds Innovation Protection Research and Environment, Achicourt, France.,Seeds Innovation Protection Research and Environment, Bretteville du Grand-Caux, France.,French Federation of Seed Potato Growers (FN3PT/RD3PT), Paris, France
| | - Yoan Konto-Ghiorghi
- Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM EA 4312) - Normandie Université - LMSM, Évreux, France.,Structure Fédérative de Recherche Normandie Végétal 4277 (NORVEGE), Mont-Saint-Aignan, France
| | - Marc Feuilloley
- Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM EA 4312) - Normandie Université - LMSM, Évreux, France.,Structure Fédérative de Recherche Normandie Végétal 4277 (NORVEGE), Mont-Saint-Aignan, France
| | - Virginie Gobert
- Seeds Innovation Protection Research and Environment, Achicourt, France.,Seeds Innovation Protection Research and Environment, Bretteville du Grand-Caux, France.,French Federation of Seed Potato Growers (FN3PT/RD3PT), Paris, France
| | - Xavier Latour
- Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM EA 4312) - Normandie Université - LMSM, Évreux, France.,Structure Fédérative de Recherche Normandie Végétal 4277 (NORVEGE), Mont-Saint-Aignan, France
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85
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Ito K, Harada M, Nakajima N, Yamamura S, Tomita M, Suzuki H, Amachi S. Genomic Analysis of Rhodococcus sp. Br-6, a Bromate Reducing Bacterium Isolated From Soil in Chiba, Japan. J Genomics 2018; 6:122-126. [PMID: 30510597 PMCID: PMC6275400 DOI: 10.7150/jgen.27741] [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: 06/08/2018] [Accepted: 07/26/2018] [Indexed: 11/06/2022] Open
Abstract
Bromate is a byproduct of the ozone disinfection of drinking water. It is a genotoxic carcinogen and causes renal cell tumors in rats. Physicochemical removal of bromate is very difficult, making microbial reduction of bromate to bromide a promising approach to eliminate bromate from water. Rhodococcus sp. Br-6, isolated from soil, can efficiently reduce bromate by using acetate as an electron donor. We determined the draft genome sequence of Rhodococcus sp. Br-6 for the potential practical application of the bromate-reducing bacterium. Core genome phylogeny suggests that the Br-6 strain is most closely related to R. equi. The Br-6 genome contains genes encoding multiple isoforms of diaphorase, previously found to be involved in Br-6-mediated bromate reduction. The genes identified in the present study could be effective targets for experimental studies of microbial bromate reduction in the future.
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Affiliation(s)
- Kohei Ito
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan.,Faculty of Environment and Information Studies, Keio University, Fujisawa, Kanagawa, Japan
| | - Masafumi Harada
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan.,Faculty of Environment and Information Studies, Keio University, Fujisawa, Kanagawa, Japan
| | - Nobuyoshi Nakajima
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan
| | - Shigeki Yamamura
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan.,Center for Regional Environmental Research, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan.,Faculty of Environment and Information Studies, Keio University, Fujisawa, Kanagawa, Japan
| | - Haruo Suzuki
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan.,Faculty of Environment and Information Studies, Keio University, Fujisawa, Kanagawa, Japan
| | - Seigo Amachi
- Graduate School of Horticulture, Chiba University, Matsudo City, Chiba, Japan
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86
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Castro AR, Silva PTS, Castro PJG, Alves E, Domingues MRM, Pereira MA. Tuning culturing conditions towards the production of neutral lipids from lubricant-based wastewater in open mixed bacterial communities. WATER RESEARCH 2018; 144:532-542. [PMID: 30081335 DOI: 10.1016/j.watres.2018.07.068] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 07/26/2018] [Accepted: 07/28/2018] [Indexed: 06/08/2023]
Abstract
Production of bacterial lipid-based biofuels using inexpensive substrates, as wastes, is an emerging approach. In this work, a selective process using carbon feast-famine cycles was applied to obtain an indigenous microbial community of hydrocarbon-degrading and lipid-accumulating bacteria, using a real lubricant-based wastewater as carbon source. In the conditions applied, the enriched bacterial community, dominated by members of the genus Rhodococcus, Pseudomonas and Acinetobacter, was able to degrade almost all hydrocarbons present in the wastewater within 24 h' incubation and to accumulate, although in low levels, triacylglycerol (TAG) (<5% of cell dry weight (CDW)) and polyhydroxyalkanoates (PHA) (3.8% ± 1.1% of the CDW) as well as an unknown lipid (29% ± 6% of CDW), presumably a wax ester-like compound. The influence of culture conditions, namely carbon and nitrogen concentrations (and C/N ratio) and cultivation time, on the amount and profile of produced storage compounds was further assessed using a statistical approach based on a central composite circumscribed design and surface response methodology. The regression analysis of the experimental design revealed that only nitrogen concentration and C/N ratio are significant for neutral lipid biosynthesis (p < 0.05). Maximum neutral lipid content, i.e. 33% (CDW basis), was achieved for the lowest carbon and nitrogen concentrations evaluated (10 g COD L-1 and 0.02 g N L-1). PHA accounted for less than 5% of CDW. In these conditions, neutral lipid content was mainly composed by TAG, about 70% (w/w). TAG precursors, namely monoacylglycerols (MAG), diacylglycerols (DAG) and fatty acids (FA), accounted for 22% of total neutral lipids and WE for about 7%. Nevertheless, according to the applied response surface model, further improvement of neutral lipids content is still possible if even lower nitrogen concentrations are used. The fatty acids detected in TAG extracts ranged from myristic acid (C14:0) to linoleic acid (C18:2), being the most abundant palmitic acid (C16:0), stearic acid (C18:0) and oleic acid (C18:1). This study shows the feasibility of combining treatment of hydrocarbon contaminated wastewater, herein demonstrated for lubricant-based wastewater, with the production of bacterial neutral lipids using open mixed bacterial communities. This approach can decrease the costs associated to both processes and contribute to a more sustainable waste management and production of lipid-based biofuels.
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Affiliation(s)
- Ana Rita Castro
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-57 Braga, Portugal
| | - Pedro T S Silva
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-57 Braga, Portugal
| | - Paulo J G Castro
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-57 Braga, Portugal
| | - Eliana Alves
- Mass Spectrometry Centre, Department of Chemistry & QOPNA, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - M Rosário M Domingues
- Mass Spectrometry Centre, Department of Chemistry & QOPNA, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Maria Alcina Pereira
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-57 Braga, Portugal.
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87
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Ní Chadhain SM, Miller JL, Dustin JP, Trethewey JP, Jones SH, Launen LA. An assessment of the microbial community in an urban fringing tidal marsh with an emphasis on petroleum hydrocarbon degradative genes. MARINE POLLUTION BULLETIN 2018; 136:351-364. [PMID: 30509817 PMCID: PMC6281173 DOI: 10.1016/j.marpolbul.2018.09.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 08/26/2018] [Accepted: 09/02/2018] [Indexed: 06/09/2023]
Abstract
Small fringing marshes are ecologically important habitats often impacted by petroleum. We characterized the phylogenetic structure (16S rRNA) and petroleum hydrocarbon degrading alkane hydroxylase genes (alkB and CYP 153A1) in a sediment microbial community from a New Hampshire fringing marsh, using alkane-exposed dilution cultures to enrich for petroleum degrading bacteria. 16S rRNA and alkB analysis demonstrated that the initial sediment community was dominated by Betaproteobacteria (mainly Comamonadaceae) and Gammaproteobacteria (mainly Pseudomonas), while CYP 153A1 sequences predominantly matched Rhizobiales. 24 h of exposure to n-hexane, gasoline, dodecane, or dilution culture alone reduced functional and phylogenetic diversity, enriching for Gammaproteobacteria, especially Pseudomonas. Gammaproteobacteria continued to dominate for 10 days in the n-hexane and no alkane exposed samples, while dodecane and gasoline exposure selected for gram-positive bacteria. The data demonstrate that small fringing marshes in New England harbor petroleum-degrading bacteria, suggesting that petroleum degradation may be an important fringing marsh ecosystem function.
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Affiliation(s)
- Sinéad M Ní Chadhain
- Department of Biology, LSCB 217, University of South Alabama, 5871 USA Drive N., Mobile, AL 36688, USA
| | - Jarett L Miller
- Department of Biology, Keene State College, 246 Main St., Keene, NH 03435, USA
| | - John P Dustin
- Department of Biology, Keene State College, 246 Main St., Keene, NH 03435, USA
| | - Jeff P Trethewey
- Department of Biology, Keene State College, 246 Main St., Keene, NH 03435, USA
| | - Stephen H Jones
- Department of Natural Resources and the Environment, University of New Hampshire, 285 Rudman Hall, 46 College Rd., Durham, NH 03824, USA
| | - Loren A Launen
- Department of Biology, Keene State College, 246 Main St., Keene, NH 03435, USA.
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88
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Microbial Degradation of Epoxy. MATERIALS 2018; 11:ma11112123. [PMID: 30380643 PMCID: PMC6267298 DOI: 10.3390/ma11112123] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 09/24/2018] [Accepted: 10/26/2018] [Indexed: 11/17/2022]
Abstract
Epoxy resins have a wide range of applications, including in corrosion protection of metals, electronics, structural adhesives, and composites. The consumption of epoxy resins is predicted to keep growing in the coming years. Unfortunately, thermoset resins cannot be recycled, and are typically not biodegradable. Hence, they pose environmental pollution risk. Here, we report degradation of epoxy resin by two bacteria that are capable of using epoxy resin as a sole carbon source. These bacteria were isolated from soil samples collected from areas around an epoxy and polyurethanes manufacturing plant. Using an array of molecular, biochemical, analytical, and microscopic techniques, they were identified as Rhodococcus rhodochrous and Ochrobactrum anthropi. As epoxy was the only carbon source available for these bacteria, their measured growth rate reflected their ability to degrade epoxy resin. Bacterial growth took place only when the two bacteria were grown together, indicating a synergistic effect. The surface morphology of the epoxy droplets changed significantly due to the biodegradation process. The metabolic pathway of epoxy by these two microbes was investigated by liquid chromatography mass spectrometry. Bisphenol A, 3,3′-((propane-2,2-diylbis(4,1-phenylene))bis(oxy))bis(propane-1,2-diol) and some other constituents were identified as being consumed by the bacteria.
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89
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Charniauskaya MI, Bukliarevich AA, Delegan YA, Akhremchuk AE, Filonov AE, Titok MA. Biodiversity of Hydrocarbon-Oxidizing Soil Bacteria from Various Climatic Zones. Microbiology (Reading) 2018. [DOI: 10.1134/s0026261718050065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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90
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Li G, Gao P, Zhi B, Fu B, Gao G, Chen Z, Gao M, Wu M, Ma T. The relative abundance of alkane-degrading bacteria oscillated similarly to a sinusoidal curve in an artificial ecosystem model from oil-well products. Environ Microbiol 2018; 20:3772-3783. [DOI: 10.1111/1462-2920.14382] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/19/2018] [Accepted: 08/10/2018] [Indexed: 12/21/2022]
Affiliation(s)
- Guoqiang Li
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education; College of Life Sciences, Nankai University; Tianjin People's Republic of China
- Department of Microbiology and Plant Biology; University of Oklahoma; Norman OK USA
| | - Peike Gao
- College of Life Sciences; Qufu Normal University; Qufu People's Repubic of China
| | - Bo Zhi
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education; College of Life Sciences, Nankai University; Tianjin People's Republic of China
| | - Bing Fu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education; College of Life Sciences, Nankai University; Tianjin People's Republic of China
| | - Ge Gao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education; College of Life Sciences, Nankai University; Tianjin People's Republic of China
| | - Zhaohui Chen
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education; College of Life Sciences, Nankai University; Tianjin People's Republic of China
| | - Mengli Gao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education; College of Life Sciences, Nankai University; Tianjin People's Republic of China
| | - Mengmeng Wu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education; College of Life Sciences, Nankai University; Tianjin People's Republic of China
| | - Ting Ma
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education; College of Life Sciences, Nankai University; Tianjin People's Republic of China
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91
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Improving stress tolerance and cell integrity of Rhodococcus ruber by overexpressing small-shock-protein Hsp16 of Rhodococcus. ACTA ACUST UNITED AC 2018; 45:929-938. [DOI: 10.1007/s10295-018-2066-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 07/27/2018] [Indexed: 01/10/2023]
Abstract
Abstract
Rhodococcus species have been successfully used as cell catalysts for valuable chemicals production due to their well-characterized resistance to harmful factors. An understanding of how they respond to stress is of great interest, which will enable the identification of engineering strategies for further improving their resistance and maintaining cell integrity and viability. Here, we assessed the transcriptome response of R. ruber TH3 to heat shock. Approximately, 376 genes were up-regulated in heat-shocked TH3. Among all the up-regulated functional genes, the small heat-shock-protein (Hsp16) with maximal enhanced transcript (463-fold) was identified, and its function was investigated. Results showed that overexpressed Hsp16 has no significant promotive effect on stress tolerance of in-cell enzyme. Interestingly, compared to the control TH3, a little fewer pores and folds on the surface of TH3(Hsp16) and more intact TH3(Hsp-GFP) cells under AM treatment were observed by SEM and LCSM, respectively. Moreover, survival test showed that more (about 501–700) TH3(Hsp16) colonies were observed while only 1–100 TH3 colonies after 50% AM treatment, and this trend is also found in high-temperature cultivation experiments. These results indicate that Hsp16 does great contributions to preventing cell leakage, maintaining cell integrity and viability of R. ruber under stress conditions.
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92
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Rahpeyma SS, Dilmaghani A, Raheb J. Evaluation of desulfurization activity of SPION nanoparticle-coated bacteria in the presence of magnetic field. APPLIED NANOSCIENCE 2018. [DOI: 10.1007/s13204-018-0876-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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93
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Current taxonomy of Rhodococcus species and their role in infections. Eur J Clin Microbiol Infect Dis 2018; 37:2045-2062. [PMID: 30159693 DOI: 10.1007/s10096-018-3364-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 08/20/2018] [Indexed: 10/28/2022]
Abstract
Rhodococcus is a genus of obligate aerobic, Gram-positive, partially acid-fast, catalase-positive, non-motile, and none-endospore bacteria. The genus Rhodococcus was first introduced by Zopf. This bacterium can be isolated from various sources of the environment and can grow well in non-selective medium. A large number of phenotypic characterizations are used to compare different species of the genus Rhodococcus, and these tests are not suitable for accurate identification at the genus and species level. Among nucleic acid-based methods, the most powerful target gene for revealing reliable phylogenetic relationships is 16S ribosomal RNA gene (16S rRNA gene) sequence analysis, but this gene is unable to differentiation some of Rhodococcus species. To date, whole genome sequencing analysis has solved taxonomic complexities in this genus. Rhodococcus equi is the major cause of foal pneumonia, and its implication in human health is related to cases in immunocompromised patients. Macrolide family together with rifampicin is one of the most effective antibiotic agents for treatment rhodococcal infections.
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94
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Shields-Menard SA, Amirsadeghi M, French WT, Boopathy R. A review on microbial lipids as a potential biofuel. BIORESOURCE TECHNOLOGY 2018; 259:451-460. [PMID: 29580729 DOI: 10.1016/j.biortech.2018.03.080] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 03/15/2018] [Accepted: 03/16/2018] [Indexed: 05/24/2023]
Abstract
Energy security, environmental concerns, and unstable oil prices have been the driving trifecta of demand for alternative fuels in the United States. The United States' dependence on energy resources, often from unstable oil-producing countries has created political insecurities and concerns. As we try to gain energy security, unconventional oil becomes more common, flooding the market, and causing the major downshift of the usual unstable oil prices. Meanwhile, consumption of fossil fuels and the consequent CO2 emissions have driven disruptions in the Earth's atmosphere and are recognized to be responsible for global climate change. While the significance of each of these three factors may fluctuate with global politics or new technologies, transportation energy will remain the prominent focus of multi-disciplined research. Bioenergy future depends on the price of oil. Current energy policy of the United States heavily favors petroleum industry. In this review, the current trend in microbial lipids as a potential biofuel is discussed.
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Affiliation(s)
- Sara A Shields-Menard
- Department of Biological Sciences, Nicholls State University, Thibodaux, LA 70310, USA
| | - Marta Amirsadeghi
- Department of Chemical and Materials Engineering, California State Polytechnic University, Pomona, CA 91768, USA
| | - W Todd French
- Dave C. Swalm School of Chemical Engineering, Mississippi State University, Mississippi State 39762, USA
| | - Raj Boopathy
- Department of Biological Sciences, Nicholls State University, Thibodaux, LA 70310, USA.
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95
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Chaudhary DK, Kim J. Rhodococcus olei sp. nov., with the ability to degrade petroleum oil, isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2018; 68:1749-1756. [DOI: 10.1099/ijsem.0.002750] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Dhiraj Kumar Chaudhary
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Gyeonggi-Do 16227, Republic of Korea
| | - Jaisoo Kim
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Gyeonggi-Do 16227, Republic of Korea
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96
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Cho HU, Park JM. Biodiesel production by various oleaginous microorganisms from organic wastes. BIORESOURCE TECHNOLOGY 2018; 256:502-508. [PMID: 29478783 DOI: 10.1016/j.biortech.2018.02.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 02/01/2018] [Accepted: 02/02/2018] [Indexed: 05/23/2023]
Abstract
Biodiesel is a biodegradable and renewable fuel. A large amount of research has considered microbial oil production using oleaginous microorganisms, but the commercialization of microbial lipids produced in this way remains uncertain due to the high cost of feedstock or low lipid yield. Microbial lipids can be typically produced by microalgae, yeasts, and bacteria; the lipid yields of these microorganisms can be improved by using sufficient concentrations of organic carbon sources. Therefore, combining low-cost organic compounds contained in organic wastes with cultivation of oleaginous microorganisms can be a promising approach to obtain commercial viability. However, to achieve effective bioconversion of low-cost substrates to microbial lipids, the characteristics of each microorganism and each substrate should be considered simultaneously. This article discusses recent approaches to developing cost-effective microbial lipid production processes that use various oleaginous microorganisms and organic wastes.
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Affiliation(s)
- Hyun Uk Cho
- School of Environmental Science and Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea; Bioenergy Research Center, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Jong Moon Park
- School of Environmental Science and Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea; Bioenergy Research Center, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea; Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea; Division of Advanced Nuclear Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea.
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97
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Eyheraguibel B, Leremboure M, Traikia M, Sancelme M, Bonhomme S, Fromageot D, Lemaire J, Lacoste J, Delort AM. Environmental scenarii for the degradation of oxo-polymers. CHEMOSPHERE 2018; 198:182-190. [PMID: 29421728 DOI: 10.1016/j.chemosphere.2018.01.153] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 01/18/2018] [Accepted: 01/28/2018] [Indexed: 06/08/2023]
Abstract
The fate of oxo-polymers in nature is strongly dependent on environmental conditions, mainly on the intensity and duration of sunshine, which vary with the season and the climate. In this work, we report the effect of different scenarii on the production and the molecular composition of oligomers released from oxo-biodegradable HDPE films. Under our experimental conditions, the duration of accelerated weathering corresponded to a period of 3 months to 3 years of exposure to outside conditions under temperate climate. In addition, the oligomers were extracted in three different solvents: i) water to mimics the natural environment; ii) acetone and chloroform to identify oligomers trapped in the polymer matrix. The combination of high-resolution mass spectrometry and 1H NMR spectroscopy gives an extensive picture of the relative concentrations and the structural compositions of the extracted oligomers in the different tested conditions. In particular, the masses, the number of oxygen and carbon atoms could be determined for up to 2283 molecules. Globally the concentration and the size of oligomers increased with the duration of extraction, the level of aging of the polymer and the use of non-polar solvents. Surprisingly, the presence of highly oxidized molecules in acetone and chloroform extract, suggested an important swelling of HPDE films in these solvents and a better diffusion of these oligomers in the matrix. In nature, the biodegradability of oligomers could result from processes occurring both at the molecular (oxidation) and the macromolecular (diffusion and release) levels.
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Affiliation(s)
- B Eyheraguibel
- Université Clermont Auvergne, CNRS, Sigma, Institut de Chimie de Clermont-Ferrand, F-63000, Clermont-Ferrand, France.
| | - M Leremboure
- Université Clermont Auvergne, CNRS, Sigma, Institut de Chimie de Clermont-Ferrand, F-63000, Clermont-Ferrand, France
| | - M Traikia
- Université Clermont Auvergne, CNRS, Sigma, Institut de Chimie de Clermont-Ferrand, F-63000, Clermont-Ferrand, France
| | - M Sancelme
- Université Clermont Auvergne, CNRS, Sigma, Institut de Chimie de Clermont-Ferrand, F-63000, Clermont-Ferrand, France
| | - S Bonhomme
- Centre National d'Evaluation de Photoprotection, 25 Avenue Blaise Pascal, 63178, Aubière Cedex, France
| | - D Fromageot
- Centre National d'Evaluation de Photoprotection, 25 Avenue Blaise Pascal, 63178, Aubière Cedex, France
| | - J Lemaire
- Centre National d'Evaluation de Photoprotection, 25 Avenue Blaise Pascal, 63178, Aubière Cedex, France
| | - J Lacoste
- Université Clermont Auvergne, CNRS, Sigma, Institut de Chimie de Clermont-Ferrand, F-63000, Clermont-Ferrand, France; Centre National d'Evaluation de Photoprotection, 25 Avenue Blaise Pascal, 63178, Aubière Cedex, France
| | - A M Delort
- Université Clermont Auvergne, CNRS, Sigma, Institut de Chimie de Clermont-Ferrand, F-63000, Clermont-Ferrand, France
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98
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Chen BS, Médici R, van der Helm MP, van Zwet Y, Gjonaj L, van der Geest R, Otten LG, Hanefeld U. Rhodococcus strains as source for ene-reductase activity. Appl Microbiol Biotechnol 2018; 102:5545-5556. [PMID: 29705954 PMCID: PMC5999131 DOI: 10.1007/s00253-018-8984-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 03/28/2018] [Accepted: 04/02/2018] [Indexed: 11/30/2022]
Abstract
Rhodococcus strains are ubiquitous in nature and known to metabolise a wide variety of compounds. At the same time, asymmetric reduction of C=C bonds is important in the production of high-valued chiral building blocks. In order to evaluate if Rhodococci can be used for this task, we have probed several Rhodococcus rhodochrous and R. erythropolis strains for ene-reductase activity. A series of substrates including activated ketones, an aldehyde, an imide and nitro-compound were screened using whole cells of seven Rhodococcus strains. This revealed that whole cells of all Rhodococcus strains showed apparent (S)-selectivity towards ketoisophorone, while most other organisms show (R)-selectivity for this compound. Three putative ene-reductases from R. rhodochrous ATCC 17895 were heterologously expressed in Escherichia coli. One protein was purified and its biocatalytic and biochemical properties were characterised, showing typical (enantioselective) properties for class 3 ene-reductases of the old yellow enzyme family.
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Affiliation(s)
- Bi-Shuang Chen
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands.,School of Marine Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Rosario Médici
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Michelle P van der Helm
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Ymke van Zwet
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Lorina Gjonaj
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands.,Department of Chemical Immunology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Roelien van der Geest
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Linda G Otten
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Ulf Hanefeld
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands.
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99
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Gao L, Zhou W, Wu S, He S, Huang J, Zhang X. Nitrogen removal by thiosulfate-driven denitrification and plant uptake in enhanced floating treatment wetland. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 621:1550-1558. [PMID: 29054632 DOI: 10.1016/j.scitotenv.2017.10.073] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 09/30/2017] [Accepted: 10/09/2017] [Indexed: 06/07/2023]
Abstract
This study investigated the potential of thiosulfate-driven autotrophic enhanced floating treatment wetland (AEFTW) in removing nitrogen from the secondary effluent at the relatively short hydraulic retention times and low S/N ratios. Simultaneous autotrophic and heterotrophic denitrification was observed in AEFTW. The peak TN removal rate (15.3gm-2d-1) exceeded most of the reported floating treatment wetlands. Based on the kinetic model results, low mean temperature coefficient and high k20 verified that the excellent performance in AEFTW diminished the microbial dependence on temperature. Nitrogen removal performance of enhanced floating treatment wetland (EFTW) and floating treatment wetland (FTW) were similar and highly sensitive to temperature. The interaction of sulfur transformation on the nitrogen, carbon uptake of plants was studied. Thiosulfate addition significantly raised sulfur content in the shoots and further enhanced the uptake of nitrogen and carbon, and increased the plant biomass at the same time. Higher composition of autotrophic and heterotrophic denitrifiers in AEFTW interpreted the occurrence of mixotrophic denitrification during summer. Thiosulfate induced mutual promotion of nitrogen removal by plant uptake and microbial denitrification in AEFTW.
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Affiliation(s)
- Lei Gao
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Weili Zhou
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Suqing Wu
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shengbing He
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Jungchen Huang
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xu Zhang
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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100
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Salam LB, Ilori MO, Amund OO, LiiMien Y, Nojiri H. Characterization of bacterial community structure in a hydrocarbon-contaminated tropical African soil. ENVIRONMENTAL TECHNOLOGY 2018; 39:939-951. [PMID: 28393681 DOI: 10.1080/09593330.2017.1317838] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 04/03/2017] [Indexed: 06/07/2023]
Abstract
The bacterial community structure in a hydrocarbon-contaminated Mechanical Engineering Workshop (MWO) soil was deciphered using 16S rRNA gene clone library analysis. Four hundred and thirty-seven clones cutting across 13 bacterial phyla were recovered from the soil. The representative bacterial phyla identified from MWO soil are Proteobacteria, Bacteroidetes, Chloroflexi, Acidobacteria, Firmicutes, Actinobacteria, Verrucomicrobia, Planctomycetes, Ignavibacteriae, Spirochaetes, Chlamydiae, Candidatus Saccharibacteria and Parcubacteria. Proteobacteria is preponderant in the contaminated soil (51.2%) with all classes except Epsilonproteobacteria duly represented. Rarefaction analysis indicates 42%, 52% and 77% of the clone library is covered at the species, genus and family/class delineations with Shannon diversity (H') and Chao1 richness indices of 5.59 and 1126, respectively. A sizeable number of bacterial phylotypes in the clone library shared high similarities with strains previously described to be involved in hydrocarbon biodegradation. Novel uncultured genera were identified that have not been previously reported from tropical African soil to be associated with natural attenuation of hydrocarbon pollutants. This study establishes the involvement of a wide array of physiologically diverse bacterial groups in natural attenuation of hydrocarbon pollutants in soil.
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Affiliation(s)
- Lateef B Salam
- a Department of Microbiology , University of Lagos , Akoka , Lagos , Nigeria
- b Microbiology Unit, Department of Biological Sciences , Al-Hikmah University , Ilorin , Kwara , Nigeria
| | - Mathew O Ilori
- a Department of Microbiology , University of Lagos , Akoka , Lagos , Nigeria
| | - Olukayode O Amund
- a Department of Microbiology , University of Lagos , Akoka , Lagos , Nigeria
| | - Yee LiiMien
- c Biotechnology Research Center , The University of Tokyo , Tokyo , Japan
| | - Hideaki Nojiri
- c Biotechnology Research Center , The University of Tokyo , Tokyo , Japan
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