1
|
Ramdass AC, Rampersad SN. Genome features of a novel hydrocarbonoclastic Chryseobacterium oranimense strain and its comparison to bacterial oil-degraders and to other C. oranimense strains. DNA Res 2023; 30:dsad025. [PMID: 37952165 PMCID: PMC10710014 DOI: 10.1093/dnares/dsad025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/29/2023] [Accepted: 11/09/2023] [Indexed: 11/14/2023] Open
Abstract
For the first time, we report the whole genome sequence of a hydrocarbonoclastic Chryseobacterium oranimense strain isolated from Trinidad and Tobago (COTT) and its genes involved in the biotransformation of hydrocarbons and xenobiotics through functional annotation. The assembly consisted of 11 contigs with 2,794 predicted protein-coding genes which included a diverse group of gene families involved in aliphatic and polycyclic hydrocarbon degradation. Comparative genomic analyses with 18 crude-oil degrading bacteria in addition to two C. oranimense strains not associated with oil were carried out. The data revealed important differences in terms of annotated genes involved in the hydrocarbon degradation process that may explain the molecular mechanisms of hydrocarbon and xenobiotic biotransformation. Notably, many gene families were expanded to explain COTT's competitive ability to manage habitat-specific stressors. Gene-based evidence of the metabolic potential of COTT supports the application of indigenous microbes for the remediation of polluted terrestrial environments and provides a genomic resource for improving our understanding of how to optimize these characteristics for more effective bioremediation.
Collapse
Affiliation(s)
- Amanda Christine Ramdass
- Biochemistry Research Lab (Rm216), Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago, West Indies
| | - Sephra Nalini Rampersad
- Biochemistry Research Lab (Rm216), Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago, West Indies
| |
Collapse
|
2
|
Sazonova OI, Ivanova AA, Delegan YA, Streletskii RA, Vershinina DD, Sokolov SL, Vetrova AA. Characterization and Genomic Analysis of the Naphthalene-Degrading Delftia tsuruhatensis ULwDis3 Isolated from Seawater. Microorganisms 2023; 11:microorganisms11041092. [PMID: 37110515 PMCID: PMC10146988 DOI: 10.3390/microorganisms11041092] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/11/2023] [Accepted: 04/19/2023] [Indexed: 04/29/2023] Open
Abstract
Strains of the genus Delftia are poorly studied microorganisms. In this work, the complete genome of the naphthalene-degrading Delftia tsuruhatensis strain ULwDis3 isolated from seawater of the Gulf of Finland of the Baltic Sea was assembled. For the first time, genes encoding naphthalene cleavage pathways via salicylate and gentisate were identified in a strain of the genus Delftia. The genes are part of one operon (nag genes). Three open reading frames (ORFs) were found in the genome of D. tsuruhatensis strain ULwDis3 that encode gentisate 1.2-dioxygenase. One of the ORFs is part of the nag operon. The physiological and biochemical characteristics of the strain ULwDis3 when cultured in mineral medium with naphthalene as the sole source of carbon and energy were also studied. It was found that after 22 h of growth, the strain stopped consuming naphthalene, and at the same time, naphthalene 1.2-dioxygenase and salicylate 5-hydroxylase activities were not detected. Later, a decrease in the number of living cells and the death of the culture were observed. Gentisate 1.2-dioxygenase activity was detected from the time of gentisate formation until culture death.
Collapse
Affiliation(s)
- Olesya I Sazonova
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", 142290 Pushchino, Russia
| | - Anastasia A Ivanova
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", 142290 Pushchino, Russia
| | - Yanina A Delegan
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", 142290 Pushchino, Russia
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Russia
| | - Rostislav A Streletskii
- Laboratory of Ecological Soil Science, Faculty of Soil Science, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Diana D Vershinina
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", 142290 Pushchino, Russia
- Federal State Budgetary Educational Institution of Higher Education Pushchino State Natural Science Institute, 142290 Pushchino, Russia
| | - Sergei L Sokolov
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", 142290 Pushchino, Russia
| | - Anna A Vetrova
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", 142290 Pushchino, Russia
| |
Collapse
|
3
|
Hirose J. Diversity and Evolution of Integrative and Conjugative Elements Involved in Bacterial Aromatic Compound Degradation and Their Utility in Environmental Remediation. Microorganisms 2023; 11:microorganisms11020438. [PMID: 36838403 PMCID: PMC9960961 DOI: 10.3390/microorganisms11020438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/01/2023] [Accepted: 02/03/2023] [Indexed: 02/12/2023] Open
Abstract
Integrative and conjugative elements (ICEs) are mobile DNA molecules that can be transferred through excision, conjugation, and integration into chromosomes. They contribute to the horizontal transfer of genomic islands across bacterial species. ICEs carrying genes encoding aromatic compound degradation pathways are of interest because of their contribution to environmental remediation. Recent advances in DNA sequencing technology have increased the number of newly discovered ICEs in bacterial genomes and have enabled comparative analysis of their evolution. The two different families of ICEs carry various aromatic compound degradation pathway genes. ICEclc and its related ICEs contain a number of members with diverse catabolic capabilities. In addition, the Tn4371 family, which includes ICEs that carry the chlorinated biphenyl catabolic pathway, has been identified. It is apparent that they underwent evolution through the acquisition, deletion, or exchange of modules to adapt to an environmental niche. ICEs have the property of both stability and mobility in the chromosome. Perspectives on the use of ICEs in environmental remediation are also discussed.
Collapse
Affiliation(s)
- Jun Hirose
- Department of Applied Chemistry, Faculty of Engineering, University of Miyazaki, Miyazaki 889-2192, Japan
| |
Collapse
|
4
|
Whole-Genome Sequencing of a Multidrug-Resistant Strain: Delftia acidovorans B408. Biochem Genet 2022; 61:1086-1096. [DOI: 10.1007/s10528-022-10306-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 11/21/2022] [Indexed: 12/03/2022]
|
5
|
Co-biomass degradation of fluoranthene by marine-derived fungi; Aspergillus aculeatus and Mucor irregularis: Comprehensive process optimization, enzyme induction and metabolic analyses. ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2022.104036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
|
6
|
Potential for Natural Attenuation of Domestic and Agricultural Pollution in Karst Groundwater Environments. WATER 2022. [DOI: 10.3390/w14101597] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In karst areas, anthropogenic contaminants reach the subsurface with detrimental effects on the groundwater ecosystem and downstream springs, which often serve as drinking water sources for the local human communities. We analyzed the water chemistry and microbial community composition in upstream and downstream locations of five hydrokarst systems (HKS) during four seasons. Conductivity and nitrates were higher in the downstream springs than in the pre-karst waters, whereas the concentration of organic matter, considered here as a pollution indicator, was lower. The microbial community composition varied largely between upstream and downstream locations, with multiple species of potentially pathogenic bacteria decreasing in the HKS. Bacteria indicative of pollution decreased as well when passing through the HKS, but potential biodegraders increased. This suggests that the HKS can filter out part of the polluting organic matter and, with it, part of the associated microorganisms. Nevertheless, the water quality, including the presence of pathogens in downstream springs, must be further monitored to control whether the water is appropriate for consumption. In parallel, the human populations located upstream must be advised of the risks resulting from their daily activities, improper stocking of their various wastes and dumping of their refuse in surface streams.
Collapse
|
7
|
Muller LAH, Ballhausen MB, Andrade-Linares DR, Pinek L, Golubeva P, Rillig MC. Fungus-bacterium associations are widespread in fungal cultures isolated from a semi-arid natural grassland in Germany. FEMS Microbiol Ecol 2021; 97:6228834. [PMID: 33861336 DOI: 10.1093/femsec/fiab059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 04/14/2021] [Indexed: 01/18/2023] Open
Abstract
We report on a study that aimed at establishing a large soil-fungal culture collection spanning a wide taxonomic diversity and systematically screening the collection for bacterial associations. Fungal cultures were isolated from soil samples obtained from a natural grassland in eastern Germany and bacterial associations were assessed by PCR-amplification and sequencing of bacterial 16S rRNA. In addition, intraspecies genetic diversities of a subset of the isolated species were estimated by double-digest restriction associated DNA sequencing. A total of 688 fungal cultures, representing at least 106 fungal species from 36 different families, were obtained and even though clonal isolates were identified in almost all fungal species subjected to ddRAD-seq, relatively high genetic diversities could be observed in some of the isolated species. A total of 69% of the fungal isolates in our collection were found to be associated with bacteria and the most commonly identified bacterial genera were Pelomonas, Enterobacter and Burkholderia. Our results indicate that bacterial associations commonly occur in soil fungi, even if antibiotics are being applied during the isolation process, and provide a basis for the use of our culture collection in ecological experiments that want to acknowledge the importance of intraspecies genetic diversity.
Collapse
Affiliation(s)
- L A H Muller
- Institut für Biologie - Ökologie der Pflanzen, Freie Universität Berlin, Altensteinstr. 6, 14195 Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 6, 14195 Berlin, Germany
| | - M-B Ballhausen
- Institut für Biologie - Ökologie der Pflanzen, Freie Universität Berlin, Altensteinstr. 6, 14195 Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 6, 14195 Berlin, Germany
| | - D R Andrade-Linares
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - L Pinek
- Institut für Biologie - Ökologie der Pflanzen, Freie Universität Berlin, Altensteinstr. 6, 14195 Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 6, 14195 Berlin, Germany
| | - P Golubeva
- Institut für Biologie - Ökologie der Pflanzen, Freie Universität Berlin, Altensteinstr. 6, 14195 Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 6, 14195 Berlin, Germany
| | - M C Rillig
- Institut für Biologie - Ökologie der Pflanzen, Freie Universität Berlin, Altensteinstr. 6, 14195 Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 6, 14195 Berlin, Germany
| |
Collapse
|
8
|
Lyu Y, Yang T, Liu H, Qi Z, Li P, Shi Z, Xiang Z, Gong D, Li N, Zhang Y. Enrichment and characterization of an effective hexavalent chromium-reducing microbial community YEM001. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:19866-19877. [PMID: 33410044 DOI: 10.1007/s11356-020-11863-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 11/27/2020] [Indexed: 06/12/2023]
Abstract
Chromium (Cr) is one of the most widely used heavy metals in industrial processes, resulting in water and soil pollution that seriously threaten environmental safety. In this paper, we have directionally enriched a Cr(VI)-reducing bacterial community YEM001 from no-Cr(VI) polluted pond sedimental sludge by selectively growing it in Cr(VI)-containing media. This community could effectively reduce Cr(VI) in laboratory rich media containing different concentrations of Cr(VI), such as 61% reduction at 435 mg/L Cr(VI), 85% reduction at 355 mg/L Cr(VI), and complete reduction at 269 mg/L Cr(VI) in 93.5 h. It was also able to completely reduce 100 mg/L and 300 mg/L Cr(VI) in landfill leachate and natural sludge in 48 h, respectively. Optimal pH for Cr(VI) reduction of the YEM001 is between 7 and 8 and the best efficiency for Cr(VI) reduction occurs at 30 °C. Metagenomic data demonstrated that the YEM001 community was composed of multiple bacteria, including well-known Cr(VI)-reducing bacteria and non-Cr(VI)-reducing bacteria. Delftia, Comamonas, Alicycliphilus, Acidovorax, Bacillus, and Clostridioides account for 83% of total community abundance. The stability of the composition of the YEM001 community and its Cr(VI)-reducing activity allows for its application in bioremediation of environmental Cr(VI) pollution.
Collapse
Affiliation(s)
- Yucai Lyu
- Hubei Engineering Research Center for Biological Jiaosu, China Three Gorges University, Yichang, 443002, China.
- Hubei Engineering Technology Research Center for Farmland Environmental Monitoring, China Three Gorges University, Yichang, 443002, China.
- Key Laboratory of Functional Yeast, China National Light Industry, China Three Gorges University, Yichang, 443002, China.
| | - Tao Yang
- Hubei Engineering Research Center for Biological Jiaosu, China Three Gorges University, Yichang, 443002, China
| | - Herong Liu
- Hubei Engineering Research Center for Biological Jiaosu, China Three Gorges University, Yichang, 443002, China
| | - Zheng Qi
- Hubei Engineering Research Center for Biological Jiaosu, China Three Gorges University, Yichang, 443002, China
| | - Ping Li
- Hubei Engineering Research Center for Biological Jiaosu, China Three Gorges University, Yichang, 443002, China
| | - Ziyao Shi
- College of Hydraulic and Environmental Engineering, China Three Gorges University, Yichang, 443002, China
| | - Zhen Xiang
- College of Hydraulic and Environmental Engineering, China Three Gorges University, Yichang, 443002, China
| | - Dachun Gong
- Hubei Engineering Research Center for Biological Jiaosu, China Three Gorges University, Yichang, 443002, China
- Hubei Engineering Technology Research Center for Farmland Environmental Monitoring, China Three Gorges University, Yichang, 443002, China
- Key Laboratory of Functional Yeast, China National Light Industry, China Three Gorges University, Yichang, 443002, China
| | - Ning Li
- College of Hydraulic and Environmental Engineering, China Three Gorges University, Yichang, 443002, China
| | - Yaoping Zhang
- Hubei Engineering Research Center for Biological Jiaosu, China Three Gorges University, Yichang, 443002, China.
- DOE-Great Lakes Bioenergy Research Center (GLBRC), University of Wisconsin-Madison, Madison, WI, USA.
| |
Collapse
|
9
|
Analysis of column reactor results with organic decay by native organic microbiota and varying permeability. Sci Rep 2021; 11:5069. [PMID: 33658586 PMCID: PMC7930145 DOI: 10.1038/s41598-021-84530-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 02/16/2021] [Indexed: 11/25/2022] Open
Abstract
Field bio-remediation techniques (FBRT) can be a low cost method to avoid the removal of top layers of soil which are rich in organic matter and bio diversity. The use of native microorganisms in FBRT is preferable because non-indigenous species can transfer their genetic material to the environment with negative impacts on the local ecological equilibrium. Petroleum Produced Water (PPW) is an important pollutant source in onshore production areas. However, due to high sodium concentrations in PPW and the occurrence of organic matter in dissolved and dispersed forms, obtaining pollutant transport parameters may be a difficult task. Results of column tests performed using a natural soil permeated by PPW are presented. All the samples presented a permeability decrease over time and the total hydrocarbon petroleum (TPH) breakthrough curves presented evidence of biological decay. Soil samples underwent biological characterization after tests (Metagenomic analyses and cultural media tests). Curves were modelled in an incremental way using a non-constant decay rate to better simulate the growing process of the microorganisms and consider the occurrence of varying velocity/permeability. Biological characterization results indicate the native organisms that are potentially more able to degrade PPW, including four bacteria (Bacillus and Lysinibacillus genus) and two fungi species (Malassezia and Talaromyces genus) that have not previously been mentioned in the consulted literature. The obtained results contribute to the development of more sustainable FBRTs focusing on native microorganisms, already adapted to the local environmental conditions.
Collapse
|
10
|
Mishra A, Rathour R, Singh R, Kumari T, Thakur IS. Degradation and detoxification of phenanthrene by actinobacterium Zhihengliuella sp. ISTPL4. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:27256-27267. [PMID: 31172432 DOI: 10.1007/s11356-019-05478-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 05/14/2019] [Indexed: 06/09/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are universal environmental contaminants of great concern with regard to their potential exposure and deleterious effect on human health. The current study is the first report of phenanthrene degradation by a psychrotolerant (15 °C), halophilic (5% NaCl), and alkalophilic (pH 8) bacterial strain Zhihengliuella sp. ISTPL4, isolated from the sediment sample of the Pangong Lake, Ladakh, Jammu and Kashmir, India. Degradation studies revealed that the optimum specific growth rate was observed at 250 ppm of phenanthrene with 81% and 87% removal of phenanthrene in 72 h and 168 h, respectively. During the degradation of phenanthrene; 9,10-dihydrophenanthrene; 1-phenanthrenecarboxylic acid; and phthalic acid were detected as intermediates. Whole-genome sequencing of strain ISTPL4 has predicted phenanthrene; 9,10-monooxygense; and epoxide hydrolase B that are involved in the phenanthrene metabolism. Phenanthrene cytotoxicity was evaluated with human hepatic carcinoma cell line (HepG2) and it was observed that the cytotoxicity decreased with increased duration of bacterial incubation and maximum cell viability was observed at 168 h (89.92%). Our results suggest, Zhihengliuella sp. ISTPL4 may promise a great potential for environmental remediation applications.
Collapse
Affiliation(s)
- Arti Mishra
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Rashmi Rathour
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Rashmi Singh
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Taruna Kumari
- Department of Statistics, University of Delhi, New Delhi, 110007, India
| | - Indu Shekhar Thakur
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
| |
Collapse
|
11
|
Sakshi, Haritash AK. A comprehensive review of metabolic and genomic aspects of PAH-degradation. Arch Microbiol 2020; 202:2033-2058. [DOI: 10.1007/s00203-020-01929-5] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 05/14/2020] [Accepted: 05/26/2020] [Indexed: 01/01/2023]
|
12
|
Remizovschi A, Carpa R, Forray FL, Chiriac C, Roba CA, Beldean-Galea S, Andrei AȘ, Szekeres E, Baricz A, Lupan I, Rudi K, Coman C. Mud volcanoes and the presence of PAHs. Sci Rep 2020; 10:1253. [PMID: 31988316 PMCID: PMC6985136 DOI: 10.1038/s41598-020-58282-2] [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: 04/08/2019] [Accepted: 01/08/2020] [Indexed: 02/01/2023] Open
Abstract
A mud volcano (MV) is a naturally hydrocarbon-spiked environment, as indicated by the presence of various quantities of PAHs and aromatic isotopic shifts in its sediments. Recurrent expulsion of various hydrocarbons consolidates the growth of hydrocarbonoclastic bacterial communities in the areas around MVs. In addition to the widely-known availability of biologically malleable alkanes, MVs can represent hotbeds of polyaromatic hydrocarbons (PAHs), as well - an aspect that has not been previously explored. This study measured the availability of highly recalcitrant PAHs and the isotopic signature of MV sediments both by GC-MS and δ13C analyses. Subsequently, this study highlighted both the occurrence and distribution of putative PAH-degrading bacterial OTUs using a metabarcoding technique. The putative hydrocarbonoclastic taxa incidence are the following: Enterobacteriaceae (31.5%), Methylobacteriaceae (19.9%), Bradyrhizobiaceae (16.9%), Oxalobacteraceae (10.2%), Comamonadaceae (7.6%) and Sphingomonadaceae (5.5%). Cumulatively, the results of this study indicate that MVs represent polyaromatic hydrocarbonoclastic hotbeds, as defined by both natural PAH input and high incidence of putative PAH-degrading bacterial OTUs.
Collapse
Affiliation(s)
- Alexei Remizovschi
- Babeş-Bolyai University, Faculty of Biology and Geology, Department of Molecular Biology and Biotechnology, 1, M. Kogalniceanu Street, 400084, Cluj-Napoca, Cluj, Romania
| | - Rahela Carpa
- Babeş-Bolyai University, Faculty of Biology and Geology, Department of Molecular Biology and Biotechnology, 1, M. Kogalniceanu Street, 400084, Cluj-Napoca, Cluj, Romania.
| | - Ferenc L Forray
- Babeş-Bolyai University, Faculty of Biology and Geology, Department of Geology, 1, M. Kogalniceanu Street, 400084, Cluj-Napoca, Cluj, Romania
| | - Cecilia Chiriac
- NIRDBS, Institute of Biological Research, 48 Republicii Street, 400015, Cluj-Napoca, Romania
| | - Carmen-Andreea Roba
- Babeş-Bolyai University, Faculty of Environmental Science and Engineering, 30 Fântânele Street, 400294, Cluj-Napoca, Romania
| | - Simion Beldean-Galea
- Babeş-Bolyai University, Faculty of Environmental Science and Engineering, 30 Fântânele Street, 400294, Cluj-Napoca, Romania
| | - Adrian-Ștefan Andrei
- Institute of Hydrobiology, Department of Aquatic Microbial Ecology, Biology Center of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic
| | - Edina Szekeres
- NIRDBS, Institute of Biological Research, 48 Republicii Street, 400015, Cluj-Napoca, Romania
| | - Andreea Baricz
- NIRDBS, Institute of Biological Research, 48 Republicii Street, 400015, Cluj-Napoca, Romania
| | - Iulia Lupan
- Babeş-Bolyai University, Faculty of Biology and Geology, Department of Molecular Biology and Biotechnology, 1, M. Kogalniceanu Street, 400084, Cluj-Napoca, Cluj, Romania
| | - Knut Rudi
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, As, Norway
| | - Cristian Coman
- NIRDBS, Institute of Biological Research, 48 Republicii Street, 400015, Cluj-Napoca, Romania
| |
Collapse
|
13
|
He C, Li Y, Huang C, Chen F, Ma Y. Genome Sequence and Metabolic Analysis of a Fluoranthene-Degrading Strain Pseudomonas aeruginosa DN1. Front Microbiol 2018; 9:2595. [PMID: 30429835 PMCID: PMC6220107 DOI: 10.3389/fmicb.2018.02595] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 10/11/2018] [Indexed: 11/28/2022] Open
Abstract
Pseudomonas aeruginosa DN1, isolated from petroleum-contaminated soil, showed excellent degradation ability toward diverse polycyclic aromatic hydrocarbons (PAHs). Many studies have been done to improve its degradation ability. However, the molecular mechanisms of PAHs degradation in DN1 strain are unclear. In this study, the whole genome of DN1 strain was sequenced and analyzed. Its genome contains 6,641,902 bp and encodes 6,684 putative open reading frames (ORFs), which has the largest genome in almost all the comparative Pseudomonas strains. Results of gene annotation showed that this strain harbored over 100 candidate genes involved in PAHs degradation, including those encoding 25 dioxygenases, four ring-hydroxylating dioxygenases, five ring-cleaving dioxygenases, and various catabolic enzymes, transcriptional regulators, and transporters in the degradation pathways. In addition, gene knockout experiments revealed that the disruption of some key PAHs degradation genes in DN1 strain, such as catA, pcaG, pcaH, and rhdA, did not completely inhibit fluoranthene degradation, even though their degradative rate reduced to some extent. Three intermediate metabolites, including 9-hydroxyfluorene, 1-acenaphthenone, and 1, 8-naphthalic anhydride, were identified as the dominating intermediates in presence of 50 μg/mL fluoranthene as the sole carbon source according to gas chromatography mass spectrometry analysis. Taken together, the genomic and metabolic analysis indicated that the fluoranthene degradation by DN1 strain was initiated by dioxygenation at the C-1, 2-, C-2, 3-, and C-7, 8- positions. These results provide new insights into the genomic plasticity and environmental adaptation of DN1 strain.
Collapse
Affiliation(s)
- Chunqiu He
- Shaanxi Provincial Key Laboratory of Biotechnology, Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an, China
| | - Yanpeng Li
- Shaanxi Provincial Key Laboratory of Biotechnology, Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an, China
| | - Chao Huang
- Shaanxi Provincial Key Laboratory of Biotechnology, Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an, China
| | - Fulin Chen
- Shaanxi Provincial Key Laboratory of Biotechnology, Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an, China
| | - Yanling Ma
- Shaanxi Provincial Key Laboratory of Biotechnology, Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an, China
| |
Collapse
|
14
|
Kotoky R, Rajkumari J, Pandey P. The rhizosphere microbiome: Significance in rhizoremediation of polyaromatic hydrocarbon contaminated soil. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2018; 217:858-870. [PMID: 29660711 DOI: 10.1016/j.jenvman.2018.04.022] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 03/22/2018] [Accepted: 04/05/2018] [Indexed: 06/08/2023]
Abstract
Microbial communities are an essential part of plant rhizosphere and participate in the functioning of plants, including rhizoremediation of petroleum contaminants. Rhizoremediation is a promising technology for removal of polyaromatic hydrocarbons based on interactions between plants and microbiome in the rhizosphere. Root exudation in the rhizosphere provides better nutrient uptake for rhizosphere microbiome, and therefore it is considered to be one of the major factors of microbial community function in the rhizosphere that plays a key role in the enhanced PAH biodegradation. Although the importance of the rhizosphere microbiome for plant growth has been widely recognized, the interactions between microbiome and plant roots in the process of rhizosphere mediated remediation of PAH still needs attention. Most of the current researches target PAH degradation by plant or single microorganism, separately, whereas the interactions between plants and whole microbiome are overlooked and its role has been ignored. This review summarizes recent knowledge of PAH degradation in the rhizosphere in the process of plant-microbiome interactions based on emerging omics approaches such as metagenomics, metatranscriptomics, metabolomics and metaproteomics. These omics approaches with combinations to bioinformatics tools provide us a better understanding in integrated activity patterns between plants and rhizosphere microbes, and insight into the biochemical and molecular modification of the meta-organisms (plant-microbiome) to maximize rhizoremediation activity. Moreover, a better understanding of the interactions could lead to the development of techniques to engineer rhizosphere microbiome for better hydrocarbon degradation.
Collapse
Affiliation(s)
- Rhitu Kotoky
- Department of Microbiology, Assam University, Silchar, 788011, India
| | - Jina Rajkumari
- Department of Microbiology, Assam University, Silchar, 788011, India
| | - Piyush Pandey
- Department of Microbiology, Assam University, Silchar, 788011, India.
| |
Collapse
|
15
|
Martin MS, Santos IC, Carlton DD, Stigler-Granados P, Hildenbrand ZL, Schug KA. Characterization of bacterial diversity in contaminated groundwater using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 622-623:1562-1571. [PMID: 29054663 DOI: 10.1016/j.scitotenv.2017.10.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 10/04/2017] [Accepted: 10/04/2017] [Indexed: 06/07/2023]
Abstract
Groundwater is a major source for drinking water in the United States, and therefore, its quality and quantity is of extreme importance. One major concern that has emerged is the possible contamination of groundwater due to the unconventional oil and gas extraction activities. As such, the impacts of exogenous contaminants on microbial ecology is an area to be explored to understand what are the chemical and physical conditions that allow the proliferation of pathogenic bacteria and to find alternatives for water treatment by identifying organic-degrading bacteria. In this work, we assess the interplay between groundwater quality and the microbiome in contaminated groundwaters rich in hydrocarbon gases, volatile organic and inorganic compounds, and various metals. Opportunistic pathogenic bacteria, such as Aeromonas hydrophila, Bacillus cereus, Pseudomonas aeruginosa, and Stenotrophomonas maltophilia, were identified, increasing the risk for consumption of and exposure to these contaminated groundwaters. Additionally, antimicrobial tests revealed that many of the identified bacteria were resistant to different antibiotics. The MALDI-TOF MS results were successfully confirmed with 16S rRNA gene sequencing, proving the accuracy of this high-throughput method. Collectively, these data provide a seminal understanding of the microbial populations in contaminated groundwater overlying anthropogenic activities like unconventional oil and gas development.
Collapse
Affiliation(s)
- Misty S Martin
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX, USA
| | - Inês C Santos
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX, USA; Collaborative Laboratories for Environmental Analysis and Remediation, The University of Texas at Arlington, Arlington, TX, USA
| | - Doug D Carlton
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX, USA; Collaborative Laboratories for Environmental Analysis and Remediation, The University of Texas at Arlington, Arlington, TX, USA
| | | | - Zacariah L Hildenbrand
- Collaborative Laboratories for Environmental Analysis and Remediation, The University of Texas at Arlington, Arlington, TX, USA; Inform Environmental, LLC, Dallas, TX, USA.
| | - Kevin A Schug
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX, USA; Collaborative Laboratories for Environmental Analysis and Remediation, The University of Texas at Arlington, Arlington, TX, USA.
| |
Collapse
|
16
|
Hickey WJ, Shetty AR, Massey RJ, Toso DB, Austin J. Three-dimensional bright-field scanning transmission electron microscopy elucidate novel nanostructure in microbial biofilms. J Microsc 2016; 265:3-10. [PMID: 27519057 DOI: 10.1111/jmi.12455] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Revised: 05/17/2016] [Accepted: 07/18/2016] [Indexed: 01/03/2023]
Abstract
Bacterial biofilms play key roles in environmental and biomedical processes, and understanding their activities requires comprehension of their nanoarchitectural characteristics. Electron microscopy (EM) is an essential tool for nanostructural analysis, but conventional EM methods are limited in that they either provide topographical information alone, or are suitable for imaging only relatively thin (<300 nm) sample volumes. For biofilm investigations, these are significant restrictions. Understanding structural relations between cells requires imaging of a sample volume sufficiently large to encompass multiple cells and the capture of both external and internal details of cell structure. An emerging EM technique with such capabilities is bright-field scanning transmission electron microscopy (BF-STEM) and in the present report BF-STEM was coupled with tomography to elucidate nanostructure in biofilms formed by the polycyclic aromatic hydrocarbon-degrading soil bacterium, Delftia acidovorans Cs1-4. Dual-axis BF-STEM enabled high-resolution 3-D tomographic recontructions (6-10 nm) visualization of thick (1250 and 1500 nm) sections. The 3-D data revealed that novel extracellular structures, termed nanopods, were polymorphic and formed complex networks within cell clusters. BF-STEM tomography enabled visualization of conduits formed by nanopods that could enable intercellular movement of outer membrane vesicles, and thereby enable direct communication between cells. This report is the first to document application of dual-axis BF-STEM tomography to obtain high-resolution 3-D images of novel nanostructures in bacterial biofilms. Future work with dual-axis BF-STEM tomography combined with correlative light electron microscopy may provide deeper insights into physiological functions associated with nanopods as well as other nanostructures.
Collapse
Affiliation(s)
- William J Hickey
- O.N. Allen Laboratory for Soil Microbiology, Department Soil Science, University of Wisconsin-Madison, Madison, Wisconsin, U.S.A
| | - Ameesha R Shetty
- O.N. Allen Laboratory for Soil Microbiology, Department Soil Science, University of Wisconsin-Madison, Madison, Wisconsin, U.S.A
| | - Randall J Massey
- Electron Microscope Facility, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, U.S.A
| | - Daniel B Toso
- O.N. Allen Laboratory for Soil Microbiology, Department Soil Science, University of Wisconsin-Madison, Madison, Wisconsin, U.S.A
| | - Jotham Austin
- Department Molecular Genetics and Cell Biology and Advanced Electron Microscopy Facility, University of Chicago, Chicago, Illinois, U.S.A
| |
Collapse
|
17
|
A. Morel M, Iriarte A, Jara E, Musto H, Castro-Sowinski S. Revealing the biotechnological potential of Delftia sp. JD2 by a genomic approach. AIMS BIOENGINEERING 2016. [DOI: 10.3934/bioeng.2016.2.156] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|