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Arthi R, Parameswari E, Dhevagi P, Janaki P, Parimaladevi R. Microbial alchemists: unveiling the hidden potentials of halophilic organisms for soil restoration. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024:10.1007/s11356-024-33949-9. [PMID: 38877191 DOI: 10.1007/s11356-024-33949-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 06/05/2024] [Indexed: 06/16/2024]
Abstract
Salinity, resulting from various contaminants, is a major concern to global crop cultivation. Soil salinity results in increased osmotic stress, oxidative stress, specific ion toxicity, nutrient deficiency in plants, groundwater contamination, and negative impacts on biogeochemical cycles. Leaching, the prevailing remediation method, is expensive, energy-intensive, demands more fresh water, and also causes nutrient loss which leads to infertile cropland and eutrophication of water bodies. Moreover, in soils co-contaminated with persistent organic pollutants, heavy metals, and textile dyes, leaching techniques may not be effective. It promotes the adoption of microbial remediation as an effective and eco-friendly method. Common microbes such as Pseudomonas, Trichoderma, and Bacillus often struggle to survive in high-saline conditions due to osmotic stress, ion imbalance, and protein denaturation. Halophiles, capable of withstanding high-saline conditions, exhibit a remarkable ability to utilize a broad spectrum of organic pollutants as carbon sources and restore the polluted environment. Furthermore, halophiles can enhance plant growth under stress conditions and produce vital bio-enzymes. Halophilic microorganisms can contribute to increasing soil microbial diversity, pollutant degradation, stabilizing soil structure, participating in nutrient dynamics, bio-geochemical cycles, enhancing soil fertility, and crop growth. This review provides an in-depth analysis of pollutant degradation, salt-tolerating mechanisms, and plant-soil-microbe interaction and offers a holistic perspective on their potential for soil restoration.
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Affiliation(s)
- Ravichandran Arthi
- Department of Environmental Science, Tamil Nadu Agricultural University, Coimbatore, India
| | | | - Periyasamy Dhevagi
- Department of Environmental Science, Tamil Nadu Agricultural University, Coimbatore, India
| | - Ponnusamy Janaki
- Nammazhvar Organic Farming Research Centre, Tamil Nadu Agricultural University, Coimbatore, India
| | - Rathinasamy Parimaladevi
- Department of Bioenergy, Agrl. Engineering College & Research Institute, Tamil Nadu Agricultural University, Coimbatore, India
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Shao X, Wang YN, Zhang YF, Meng D, Su JY, Yu B, Sun ML, Li Y. Marinobacter qingdaonensis sp. nov., a moderately halotolerant bacterium isolated from intertidal sediment. Int J Syst Evol Microbiol 2024; 74. [PMID: 38591775 DOI: 10.1099/ijsem.0.006327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2024] Open
Abstract
A Gram-stain-negative, aerobic, rod-shaped and halotolerant bacterium, designated as strain ASW11-75T, was isolated from intertidal sediments in Qingdao, PR China, and identified using a polyphasic taxonomic approach. Growth of strain ASW11-75T occurred at 10-45 °C (optimum, 37 °C), pH 6.5-9.0 (optimum, pH 8.0) and 0.5-18.0 % NaCl concentrations (optimum, 2.5 %). Phylogenetic analyses based on 16S rRNA gene sequences and 1179 single-copy orthologous clusters indicated that strain ASW11-75T is affiliated with the genus Marinobacter. Strain ASW11-75T showed highest 16S rRNA gene sequence similarity to 'Marinobacter arenosus' CAU 1620T (98.5 %). The digital DNA-DNA hybridization and average nucleotide identity values between strain ASW11-75T and its closely related strains (Marinobacter salarius R9SW1T, Marinobacter similis A3d10T, 'Marinobacter arenosus' CAU 1620T, Marinobacter sediminum R65T, Marinobacter salinus Hb8T, Marinobacter alexandrii LZ-8T and Marinobacter nauticus ATCC 49840T) were 19.8-24.5 % and 76.6-80.7 %, respectively. The predominant cellular fatty acids were C16 : 0, C18 : 1 ω9c and C16 : 0 N alcohol. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified aminophospholipid and two unidentified lipids. The major isoprenoid quinone was ubiquinone-9. The genomic DNA G+C content was 62.2 mol%. Based on genomic and gene function analysis, strain ASW11-75T had lower protein isoelectric points with higher ratios of acidic residues to basic residues and possessed genes related to ion transport and organic osmoprotectant uptake, implying its potential tolerance to salt. The results of polyphasic characterization indicated strain ASW11-75T represents a novel Marinobacter species, for which the name Marinobacter qingdaonensis sp. nov. with the type strain ASW11-75T is proposed. The type strain is ASW11-75T (=KCTC 82497T=MCCC 1K05587T).
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Affiliation(s)
- Xuan Shao
- Henan Provincial Engineering Research Center for Development and Application of Characteristic Microorganism Resources, Engineering Technology Research Center of Biomass Degradation and Gasification, Key Laboratory on Agricultural Microorganism Resources Development of Shangqiu, Shangqiu Normal University, Shangqiu 476000, PR China
| | - Ya-Nan Wang
- College of Life Sciences, Shanxi Agricultural University, Taigu 030801, PR China
| | - Ya-Fei Zhang
- College of Life Sciences, Shanxi Agricultural University, Taigu 030801, PR China
| | - Di Meng
- Henan Provincial Engineering Research Center for Development and Application of Characteristic Microorganism Resources, Engineering Technology Research Center of Biomass Degradation and Gasification, Key Laboratory on Agricultural Microorganism Resources Development of Shangqiu, Shangqiu Normal University, Shangqiu 476000, PR China
| | - Jing-Yun Su
- College of Life Sciences, Shanxi Agricultural University, Taigu 030801, PR China
| | - Bing Yu
- College of Life Sciences, Shanxi Agricultural University, Taigu 030801, PR China
| | - Mei-Ling Sun
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266000, PR China
| | - Yi Li
- College of Life Sciences, Shanxi Agricultural University, Taigu 030801, PR China
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Cheng J, Xing D, Wang P, Tang S, Cai Z, Zhou J, Zhu X. Enrichment of antibiotic resistant genes and pathogens in face masks from coastal environments. JOURNAL OF HAZARDOUS MATERIALS 2023; 449:131038. [PMID: 36821901 PMCID: PMC9938759 DOI: 10.1016/j.jhazmat.2023.131038] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 02/12/2023] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
Face masks (FMs) are essential to limit the spread of the coronavirus during pandemic, a considerable of which are accumulated on the coast. However, limited is known about the microbial profile in the biofilm of the face masks (so-called plastisphere) and the impacts of face masks on the surrounding environments. We herein performed face mask exposures to coastal sediments and characterized the microbial community and the antibiotic resistome. We detected 64 antibiotic-resistance genes (ARGs) and 12 mobile gene elements (MGEs) in the plastisphere. Significant enrichments were found in the relative abundance of total ARGs in the plastisphere compared to the sediments. In detail, the relative abundance of tetracycline, multidrug, macrolide-lincosamide-streptogramin B (MLSB), and phenicol-resistant genes had increased by 5-10 times. Moreover, the relative abundance of specific hydrocarbonoclastic bacteria (e.g., Polycyclovorans sp.), pathogens (e.g., Pseudomonas oleovorans), and total MGEs significantly increased in the sediments after face mask exposure, which was congruent with the alteration of pH value and metal concentrations in the microcosms. Our study demonstrated the negative impacts of FMs on coastal environments regardless of the profiles of ARGs or pathogens. These findings improved the understanding of the ecological risks of face masks and underlined the importance of beach cleaning.
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Affiliation(s)
- Jingguang Cheng
- Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China
| | - Daochao Xing
- Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China
| | - Pu Wang
- Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China
| | - Si Tang
- Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China
| | - Zhonghua Cai
- Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China
| | - Jin Zhou
- Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China.
| | - Xiaoshan Zhu
- Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China; College of Ecology and Environment, Hainan University, Haikou 570228, PR China.
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Bird LJ, Mickol RL, Eddie BJ, Thakur M, Yates MD, Glaven SM. Marinobacter: A case study in bioelectrochemical chassis evaluation. Microb Biotechnol 2023; 16:494-506. [PMID: 36464922 PMCID: PMC9948230 DOI: 10.1111/1751-7915.14170] [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: 06/20/2022] [Revised: 10/28/2022] [Accepted: 11/03/2022] [Indexed: 12/08/2022] Open
Abstract
The junction of bioelectrochemical systems and synthetic biology opens the door to many potentially groundbreaking technologies. When developing these possibilities, choosing the correct chassis organism can save a great deal of engineering effort and, indeed, can mean the difference between success and failure. Choosing the correct chassis for a specific application requires a knowledge of the metabolic potential of the candidate organisms, as well as a clear delineation of the traits, required in the application. In this review, we will explore the metabolic and electrochemical potential of a single genus, Marinobacter. We will cover its strengths, (salt tolerance, biofilm formation and electrochemical potential) and weaknesses (insufficient characterization of many strains and a less developed toolbox for genetic manipulation) in potential synthetic electromicrobiology applications. In doing so, we will provide a roadmap for choosing a chassis organism for bioelectrochemical systems.
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Affiliation(s)
- Lina J Bird
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, District of Columbia, USA
| | - Rebecca L Mickol
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, District of Columbia, USA
| | - Brian J Eddie
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, District of Columbia, USA
| | - Meghna Thakur
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, District of Columbia, USA.,College of Science, George Mason University, Fairfax, Virginia, USA
| | - Matthew D Yates
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, District of Columbia, USA
| | - Sarah M Glaven
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, District of Columbia, USA
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Tourova TP, Sokolova DS, Semenova EM, Ershov AP, Grouzdev DS, Nazina TN. Genomic and Physiological Characterization of Halophilic Bacteria of the Genera Halomonas and Marinobacter from Petroleum Reservoirs. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722300038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Settanni L, Busetta G, Puccio V, Licitra G, Franciosi E, Botta L, Di Gerlando R, Todaro M, Gaglio R. In-Depth Investigation of the Safety of Wooden Shelves Used for Traditional Cheese Ripening. Appl Environ Microbiol 2021; 87:e0152421. [PMID: 34550766 PMCID: PMC8579974 DOI: 10.1128/aem.01524-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/13/2021] [Indexed: 01/04/2023] Open
Abstract
The main goal of this research was to characterize the bacterial diversity of the wooden boards used for aging traditional Sicilian cheeses and to evaluate whether pathogenic bacteria are associated with these surfaces. Eighteen cheese dairy factories producing three traditional cheese typologies (PDO Pecorino Siciliano, PDO Piacentinu Ennese, and Caciocavallo Palermitano) were selected within the region of Sicily. The wooden shelf surfaces were sampled by a destructive method to detach wood splinters as well as by a nondestructive brushing to collect microbial cells. Scanning electron microscopy showed the presence of almost continuous bacterial formations on the majority of the shelves analyzed. Yeasts and fungal hyphae were also visualized, indicating the complexity of the plank communities. The amplicon library of the 16S rRNA gene V3-V4 region was paired-end sequenced using the Illumina MiSeq system, allowing the identification of 14 phyla, 32 classes, 52 orders, 93 families, and 137 genera. Staphylococcus equorum was identified from all wooden surfaces, with a maximum abundance of 64.75%. Among cheese-surface-ripening bacteria, Brevibacterium and Corynebacterium were detected in almost all samples. Several halophilic (Halomonas, Tetragenococcus halophilus, Chromohalobacter, Salimicrobium, Marinococcus, Salegentibacter, Haererehalobacter, Marinobacter, and Idiomarinaceae) and moderately halophilic (Salinicoccus, Psychrobacter, and Salinisphaera) bacteria were frequently identified. Lactic acid bacteria (LAB) were present at low percentages in the genera Leuconostoc, Lactococcus, Lactobacillus, Pediococcus, and Streptococcus. The levels of viable microorganisms on the wooden shelves ranged between 2.4 and 7.8 log CFU/cm2. In some cases, LAB were counted at very high levels (8.2 log CFU/cm2). Members of the Enterobacteriaceae family were detected in a viable state for only six samples. Coagulase-positive staphylococci, Salmonella spp., and Listeria monocytogenes were not detected. Seventy-five strains belonged to the genera Leuconostoc, Lactococcus, Pediococcus, Enterococcus, Lactobacillus, and Weissella. IMPORTANCE This study provides evidence for the lack of pathogenic bacteria on the wooden shelves used to ripen internal bacterially ripened semihard and hard cheeses produced in Sicily. These three cheeses are not inoculated on their surfaces, and surface ripening is not considered to occur or, at least, does not occur at the same extent as surface-inoculated smear cheeses. Several bacterial groups identified from the wooden shelves are typically associated with smear cheeses, strongly suggesting that PDO Pecorino Siciliano, PDO Piacentinu Ennese, and Caciocavallo Palermitano cheese rind contributes to their final organoleptic profiles.
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Affiliation(s)
- Luca Settanni
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Palermo, Italy
| | - Gabriele Busetta
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Palermo, Italy
| | - Valeria Puccio
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Palermo, Italy
| | - Giuseppe Licitra
- Dipartimento di Agricoltura, Alimentazione e Ambiente (Di3A), Università degli Studi di Catania, Catania, Italy
| | - Elena Franciosi
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all’Adige, Italy
| | - Luigi Botta
- Dipartimento di Ingegneria, UdR INSTM di Palermo, Università degli Studi di Palermo, Palermo, Italy
| | - Rosalia Di Gerlando
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Palermo, Italy
| | - Massimo Todaro
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Palermo, Italy
| | - Raimondo Gaglio
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Palermo, Italy
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Vaishnavi J, Devanesan S, AlSalhi MS, Rajasekar A, Selvi A, Srinivasan P, Govarthanan M. Biosurfactant mediated bioelectrokinetic remediation of diesel contaminated environment. CHEMOSPHERE 2021; 264:128377. [PMID: 33017706 DOI: 10.1016/j.chemosphere.2020.128377] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/06/2020] [Accepted: 09/15/2020] [Indexed: 06/11/2023]
Abstract
The present study integrated the electrokinetic (EK) with bioremediation (Bioelectrokinetic -BEK) of diesel hydrocarbon by Staphylococcus epidermidis EVR4. It was identified as efficient biosurfactant producing bacteria and growth parameters was optimized using response surface methodology. Upon degradation, there is a complete disappearance of peaks from nonane (C9) to tricosane (C23) and 85%, 47% of degradation of pentacosane and octacosane respectively. Marine bacterial strain, EVR4 was found to be potential to degrade the diesel with a maximum degradation efficiency of 96% within 4 d, which was due to its synergistic role of biosurfactant and catabolic enzymes (dehydrogenase, catalase and cytochrome C). The application of integrated BEK was an effective insitu method for the remediation of diesel contaminated soil by BEK (84%) than EK (67%). EVR4 as an effective strain can be employed for BIO-EK method to clean the diesel hydrocarbon polluted environment.
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Affiliation(s)
- Jeevanandam Vaishnavi
- Environmental Molecular Microbiology Research Laboratory, Department of Biotechnology, Thiruvalluvar University, Serkadu, Vellore, 632115, Tamilnadu, India
| | - Sandhanasamy Devanesan
- Research Chair in Laser Diagnosis of Cancers, Department of Physics and Astronomy, College of Science, King Saud University, Riyadh KSA, P.O. Box -2455, Riyadh, 11451, Saudi Arabia
| | - Mohamad S AlSalhi
- Research Chair in Laser Diagnosis of Cancers, Department of Physics and Astronomy, College of Science, King Saud University, Riyadh KSA, P.O. Box -2455, Riyadh, 11451, Saudi Arabia.
| | - Aruliah Rajasekar
- Environmental Molecular Microbiology Research Laboratory, Department of Biotechnology, Thiruvalluvar University, Serkadu, Vellore, 632115, Tamilnadu, India.
| | - Adikesavan Selvi
- Environmental Molecular Microbiology Research Laboratory, Department of Biotechnology, Thiruvalluvar University, Serkadu, Vellore, 632115, Tamilnadu, India
| | - Palanisamy Srinivasan
- PG & Research Department of Biotechnology, Mahendra Arts and Science College, Kalipatti, 637501, Tamil Nadu, India
| | - Muthusamy Govarthanan
- Department of Environmental Engineering, Kyungpook National University, Daegu, South Korea.
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Loss of Motility as a Non-Lethal Mechanism for Intercolony Inhibition ("Sibling Rivalry") in Marinobacter. Microorganisms 2021; 9:microorganisms9010103. [PMID: 33466273 PMCID: PMC7824750 DOI: 10.3390/microorganisms9010103] [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: 11/19/2020] [Revised: 12/23/2020] [Accepted: 12/30/2020] [Indexed: 11/17/2022] Open
Abstract
Bacteria from the genus Marinobacter are ubiquitous throughout the worlds' oceans as "opportunitrophs" capable of surviving a wide range of conditions, including colonization of surfaces of marine snow and algae. To prevent too many bacteria from occupying this ecological niche simultaneously, some sort of population dependent control must be operative. Here, we show that while Marinobacter do not produce or utilize an acylhomoserine lactone (AHL)-based quorum sensing system, "sibling" colonies of many species of Marinobacter exhibit a form of non-lethal chemical communication that prevents colonies from overrunning each other's niche space. Evidence suggests that this inhibition is the result of a loss in motility for cells at the colony interfaces. Although not the signal itself, we have identified a protein, glycerophosphoryl diester phosphodiesterase, that is enriched in the inhibition zone between the spreading colonies that may be part of the overall response.
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9
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Lijewski AM, Knutson CM, Lenneman EM, Barney BM. Evaluation of two thioesterases from Marinobacter aquaeolei VT8: Relationship to wax ester production. FEMS Microbiol Lett 2020; 368:fnaa206. [PMID: 33301558 DOI: 10.1093/femsle/fnaa206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The biosynthesis of lipid-based biofuels is an important aspect of developing sustainable alternatives to conventional oils derived from fossil fuel reserves. Many biosynthetic approaches to biodiesel fuels and oils involve fatty acid derivatives as a precursor, and thioesterases have been employed in various strategies to increase fatty acid pools. Thioesterases liberate fatty acids from fatty acyl-coenzyme A or fatty acyl-acyl carrier protein substrates. The role played by thioesterases has not been extensively studied in model bacteria that accumulate elevated levels of biological oils based on fatty acid precursors. In this report, two primary thioesterases from the wax ester accumulating bacterium Marinobacter aquaeolei VT8 were heterologously expressed, isolated and characterized. These genes were further analyzed at the transcriptional level in the native bacterium during wax ester accumulation, and their genes were disrupted to determine the effect these changes had on wax ester levels. Combined, these results indicate that these two thioesterases do not play an integral role in wax ester accumulation in this natural lipid-accumulating model bacterium.
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Affiliation(s)
- Amelia M Lijewski
- Department of Bioproducts and Biosystems Engineering and Biotechnology Institute, University of Minnesota, 1390 Eckles Avenue, St. Paul, MN 55108
| | - Carolann M Knutson
- Department of Bioproducts and Biosystems Engineering and Biotechnology Institute, University of Minnesota, 1390 Eckles Avenue, St. Paul, MN 55108
| | - Eric M Lenneman
- Department of Bioproducts and Biosystems Engineering and Biotechnology Institute, University of Minnesota, 1390 Eckles Avenue, St. Paul, MN 55108
| | - Brett M Barney
- Department of Bioproducts and Biosystems Engineering and Biotechnology Institute, University of Minnesota, 1390 Eckles Avenue, St. Paul, MN 55108
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Chernikova TN, Bargiela R, Toshchakov SV, Shivaraman V, Lunev EA, Yakimov MM, Thomas DN, Golyshin PN. Hydrocarbon-Degrading Bacteria Alcanivorax and Marinobacter Associated With Microalgae Pavlova lutheri and Nannochloropsis oculata. Front Microbiol 2020; 11:572931. [PMID: 33193176 PMCID: PMC7655873 DOI: 10.3389/fmicb.2020.572931] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/01/2020] [Indexed: 12/26/2022] Open
Abstract
Marine hydrocarbon-degrading bacteria play an important role in natural petroleum biodegradation processes and were initially associated with man-made oil spills or natural seeps. There is no full clarity though on what, in the absence of petroleum, their natural niches are. Few studies pointed at some marine microalgae that produce oleophilic compounds (alkanes, long-chain fatty acids, and alcohols) as potential natural hosts of these bacteria. We established Dansk crude oil-based enrichment cultures with photobioreactor-grown marine microalgae cultures Pavlova lutheri and Nannochloropsis oculata and analyzed the microbial succession using cultivation and SSU (16S) rRNA amplicon sequencing. We found that petroleum enforced a strong selection for members of Alpha- and Gamma-proteobacteria in both enrichment cultures with the prevalence of Alcanivorax and Marinobacter spp., well-known hydrocarbonoclastic bacteria. In total, 48 non-redundant bacterial strains were isolated and identified to represent genera Alcanivorax, Marinobacter, Thalassospira, Hyphomonas, Halomonas, Marinovum, Roseovarius, and Oleibacter, which were abundant in sequencing reads in both crude oil enrichments. Our assessment of public databases demonstrated some overlaps of geographical sites of isolation of Nannochloropsis and Pavlova with places of molecular detection and isolation of Alcanivorax and Marinobacter spp. Our study suggests that these globally important hydrocarbon-degrading bacteria are associated with P. lutheri and N. oculata.
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Affiliation(s)
- Tatyana N Chernikova
- School of Natural Sciences, Bangor University, Bangor, United Kingdom.,CEB-Centre for Environmental Biotechnology, Bangor University, Bangor, United Kingdom
| | - Rafael Bargiela
- School of Natural Sciences, Bangor University, Bangor, United Kingdom
| | | | | | - Evgenii A Lunev
- Institute of Living Systems, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Michail M Yakimov
- Institute for Marine Biological Resources and Biotechnology of the National Research Council, IRBIM-CNR, Messina, Italy
| | - David N Thomas
- School of Ocean Sciences, Bangor University, Menai Bridge, United Kingdom
| | - Peter N Golyshin
- School of Natural Sciences, Bangor University, Bangor, United Kingdom.,CEB-Centre for Environmental Biotechnology, Bangor University, Bangor, United Kingdom
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Chen Q, Zhu B, Sun D, Liu W, Sun X, Duan S. The effect of protocatechuic acid on the phycosphere in harmful algal bloom species Scrippsiella trochoidea. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2020; 227:105591. [PMID: 32853898 DOI: 10.1016/j.aquatox.2020.105591] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 07/27/2020] [Accepted: 08/03/2020] [Indexed: 06/11/2023]
Abstract
The effects of allelopathy and the potential harm of several isolated allelochemicals have been studied in detail. Microorganisms in the phycosphere play an important role in algal growth, decay and nutrient cycling. However, it is unknown and often neglected whether allelochemicals affect the phycosphere. The present study selected a phenolic acid protocatechuic acid (PA) - previously shown to be an allelochemical. We studied PA at a half maximal effective concentration of 0.20 mM (30 mg L-1) against Scrippsiella trochoidea to assess the effect of PA on its phycosphere in an acute time period (48 h). The results showed that: 1) OTUs (operational taxonomic units) in the treatment groups (31.4 ± 0.55) exceeded those of the control groups (28.2 ± 1.30) and the Shannon and Simpson indices were lower than the control groups (3.31 ± 0.08 and 0.84 ± 0.02, 3.45 ± 0.09 and 0.88 ± 0.01); 2) Gammaproteobacteria predominated in the treatment groups (44.71 ± 2.13 %) while Alphaproteobacteria dominated in the controls (67.17 ± 3.87 %); 3) Gammaproteobacteria and Alphaproteobacteria were important biomarkers in the treatment and control groups respectively (LDA > 4.0). PA improved the relative abundance of Alteromonas significantly and decreased the one of Rhodobacteraceae. PICRUSt analysis showed that the decrease of Rhodobacterceae was closely related with the decline of most functional genes in metabolism such as amino acid, carbohydrate, xenobiotics, cofactors and vitamins metabolism after PA-treated.
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Affiliation(s)
- Qi Chen
- Department of Ecology, Jinan University, Guangzhou 510632, China
| | - Bo Zhu
- School of Life Science and Engineering, State Defense Key Laboratory of the Nuclear Waste and Environmental Security, Southwest University of Science and Technology, Mianyang 621010, China
| | - Dong Sun
- Department of Ecology, Jinan University, Guangzhou 510632, China
| | - Weijie Liu
- South China Institute of Environmental Science, Ministry of Ecology and Environment of the People's Republic of China, Guangzhou 510530, China
| | - Xian Sun
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai Key Laboratory of Marine Bioresources and Environment, Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Guangzhou 510275, China.
| | - Shunshan Duan
- Department of Ecology, Jinan University, Guangzhou 510632, China.
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12
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Survival of the Halophilic Archaeon Halovarius luteus after Desiccation, Simulated Martian UV Radiation and Vacuum in Comparison to Bacillus atrophaeus. ORIGINS LIFE EVOL B 2020; 50:157-173. [PMID: 32617792 DOI: 10.1007/s11084-020-09597-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 05/20/2020] [Indexed: 02/03/2023]
Abstract
Extraterrestrial environments influence the biochemistry of organisms through a variety of factors, including high levels of radiation and vacuum, temperature extremes and a lack of water and nutrients. A wide variety of terrestrial microorganisms, including those counted amongst the most ancient inhabitants of Earth, can cope with high levels of salinity, extreme temperatures, desiccation and high levels of radiation. Key among these are the haloarchaea, considered particularly relevant for astrobiological studies due to their ability to thrive in hypersaline environments. In this study, a novel haloarchaea isolated from Urmia Salt Lake, Iran, Halovarius luteus strain DA50T, was exposed to varying levels of simulated extraterrestrial conditions and compared to that of the bacteria Bacillus atrophaeus. Bacillus atrophaeus was selected for comparison due to its well-described resistance to extreme conditions and its ability to produce strong spore structures. Thin films were produced to investigate viability without the protective influence of cell multi-layers. Late exponential phase cultures of Hvr. luteus and B. atrophaeus were placed in brine and phosphate buffered saline media, respectively. The solutions were allowed to evaporate and cells were encapsulated and exposed to radiation, desiccation and vacuum conditions, and their post-exposure viability was studied by the Most Probable Number method. The protein profile using High Performance Liquid Chromatography and Matrix Assisted Laser Desorption/Ionization bench top reflector time-of-flight are explored after vacuum and UV-radiation exposure. Results showed that the change in viability of the spore-forming bacteria B. atrophaeus was only minor whereas Hvr. luteus demonstrated a range of viability under different conditions. At the peak radiation flux of 105 J/m2 under nitrogen flow and after two weeks of desiccation, Hvr. luteus demonstrated the greatest decrease in viability. This study further expands our understanding of the boundary conditions of astrobiologically relevant organisms in the harsh space environment.
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Zhong ZP, Rapp JZ, Wainaina JM, Solonenko NE, Maughan H, Carpenter SD, Cooper ZS, Jang HB, Bolduc B, Deming JW, Sullivan MB. Viral Ecogenomics of Arctic Cryopeg Brine and Sea Ice. mSystems 2020; 5:e00246-20. [PMID: 32546670 PMCID: PMC7300359 DOI: 10.1128/msystems.00246-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 05/24/2020] [Indexed: 01/09/2023] Open
Abstract
Arctic regions, which are changing rapidly as they warm 2 to 3 times faster than the global average, still retain microbial habitats that serve as natural laboratories for understanding mechanisms of microbial adaptation to extreme conditions. Seawater-derived brines within both sea ice (sea-ice brine) and ancient layers of permafrost (cryopeg brine) support diverse microbes adapted to subzero temperatures and high salinities, yet little is known about viruses in these extreme environments, which, if analogous to other systems, could play important evolutionary and ecosystem roles. Here, we characterized viral communities and their functions in samples of cryopeg brine, sea-ice brine, and melted sea ice. Viral abundance was high in cryopeg brine (1.2 × 108 ml-1) and much lower in sea-ice brine (1.3 × 105 to 2.1 × 105 ml-1), which roughly paralleled the differences in cell concentrations in these samples. Five low-input, quantitative viral metagenomes were sequenced to yield 476 viral populations (i.e., species level; ≥10 kb), only 12% of which could be assigned taxonomy by traditional database approaches, indicating a high degree of novelty. Additional analyses revealed that these viruses: (i) formed communities that differed between sample type and vertically with sea-ice depth; (ii) infected hosts that dominated these extreme ecosystems, including Marinobacter, Glaciecola, and Colwellia; and (iii) encoded fatty acid desaturase (FAD) genes that likely helped their hosts overcome cold and salt stress during infection, as well as mediated horizontal gene transfer of FAD genes between microbes. Together, these findings contribute to understanding viral abundances and communities and how viruses impact their microbial hosts in subzero brines and sea ice.IMPORTANCE This study explores viral community structure and function in remote and extreme Arctic environments, including subzero brines within marine layers of permafrost and sea ice, using a modern viral ecogenomics toolkit for the first time. In addition to providing foundational data sets for these climate-threatened habitats, we found evidence that the viruses had habitat specificity, infected dominant microbial hosts, encoded host-derived metabolic genes, and mediated horizontal gene transfer among hosts. These results advance our understanding of the virosphere and how viruses influence extreme ecosystems. More broadly, the evidence that virally mediated gene transfers may be limited by host range in these extreme habitats contributes to a mechanistic understanding of genetic exchange among microbes under stressful conditions in other systems.
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Affiliation(s)
- Zhi-Ping Zhong
- Byrd Polar and Climate Research Center, The Ohio State University, Columbus, Ohio, USA
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Josephine Z Rapp
- School of Oceanography, University of Washington, Seattle, Washington, USA
| | - James M Wainaina
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | | | | | - Shelly D Carpenter
- School of Oceanography, University of Washington, Seattle, Washington, USA
| | - Zachary S Cooper
- School of Oceanography, University of Washington, Seattle, Washington, USA
| | - Ho Bin Jang
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Benjamin Bolduc
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Jody W Deming
- School of Oceanography, University of Washington, Seattle, Washington, USA
| | - Matthew B Sullivan
- Byrd Polar and Climate Research Center, The Ohio State University, Columbus, Ohio, USA
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, Ohio, USA
- Center of Microbiome Science, The Ohio State University, Columbus, Ohio, USA
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Viggor S, Jõesaar M, Soares-Castro P, Ilmjärv T, Santos PM, Kapley A, Kivisaar M. Microbial Metabolic Potential of Phenol Degradation in Wastewater Treatment Plant of Crude Oil Refinery: Analysis of Metagenomes and Characterization of Isolates. Microorganisms 2020; 8:E652. [PMID: 32365784 PMCID: PMC7285258 DOI: 10.3390/microorganisms8050652] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/24/2020] [Accepted: 04/28/2020] [Indexed: 01/30/2023] Open
Abstract
The drilling, processing and transportation of oil are the main sources of pollution in water and soil. The current work analyzes the microbial diversity and aromatic compounds degradation potential in the metagenomes of communities in the wastewater treatment plant (WWTP) of a crude oil refinery. By focusing on the degradation of phenol, we observed the involvement of diverse indigenous microbial communities at different steps of the WWTP. The anaerobic bacterial and archaeal genera were replaced by aerobic and facultative anaerobic bacteria through the biological treatment processes. The phyla Proteobacteria, Bacteroidetes and Planctomycetes were dominating at different stages of the treatment. Most of the established protein sequences of the phenol degradation key enzymes belonged to bacteria from the class Alphaproteobacteria. From 35 isolated strains, 14 were able to grow on aromatic compounds, whereas several phenolic compound-degrading strains also degraded aliphatic hydrocarbons. Two strains, Acinetobacter venetianus ICP1 and Pseudomonas oleovorans ICTN13, were able to degrade various aromatic and aliphatic pollutants and were further characterized by whole genome sequencing and cultivation experiments in the presence of phenol to ascertain their metabolic capacity in phenol degradation. When grown alone, the intermediates of catechol degradation, the meta or ortho pathways, accumulated into the growth environment of these strains. In the mixed cultures of the strains ICP1 and ICTN13, phenol was degraded via cooperation, in which the strain ICP1 was responsible for the adherence of cells and ICTN13 diminished the accumulation of toxic intermediates.
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Affiliation(s)
- Signe Viggor
- Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Street, 51010 Tartu, Estonia; (M.J.); (T.I.); (M.K.)
| | - Merike Jõesaar
- Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Street, 51010 Tartu, Estonia; (M.J.); (T.I.); (M.K.)
| | - Pedro Soares-Castro
- Centre of Molecular and Environmental Biology (CBMA), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; (P.S.-C.); (P.M.S.)
| | - Tanel Ilmjärv
- Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Street, 51010 Tartu, Estonia; (M.J.); (T.I.); (M.K.)
| | - Pedro M. Santos
- Centre of Molecular and Environmental Biology (CBMA), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; (P.S.-C.); (P.M.S.)
| | - Atya Kapley
- Director’s Research Division, CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur 440 020, India;
| | - Maia Kivisaar
- Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Street, 51010 Tartu, Estonia; (M.J.); (T.I.); (M.K.)
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15
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Li G, Wang S, Gai Y, Liu X, Lai Q, Shao Z. Marinobacter changyiensis, sp. nov., isolated from offshore sediment. Int J Syst Evol Microbiol 2020; 70:3004-3011. [PMID: 32320379 DOI: 10.1099/ijsem.0.004118] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An aerobic, Gram-stain-negative bacterium, designated CLL7-20T, was isolated from a marine sediment sample from offshore of Changyi, Shandong Province, China. Cells of strain CLL7-20T were rod-shaped, motile with one or more polar flagella, and grew optimally at pH 7.0, at 28 °C and with 3 % (w/v) NaCl. The principal fatty acids of strain CLL7-20T were C16 : 0 and summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c). The main polar lipids of strain CLL7-20T were phosphatidylethanolamine (PE), phosphatidylglycerol (PG), diphosphatidylglycerol (DPG) and an unidentified aminolipid (AL). Strain CLL7-20T contained Q-9 as the major respiratory quinone. The G+C content of its genomic DNA was 56.2 mol%. Phylogenetically, strain CLL7-20T branched within the genus Marinobacter, with M. daqiaonensis YCSA40T being its closest phylogenetic relative (96.7 % 16S rRNA gene sequence similarity), followed by M. sediminum R65T (96.6 %). Average nucleotide identity and in silico DNA-DNA hybridization values between strain CLL7-20T and the closest related reference strains were 73.2% and 19.8 %, respectively. On the basis of its phenotypic, phylogenetic and chemotaxonomic characteristics, we suggest that strain CLL7-20T (=MCCC 1A14855T=KCTC 72664T) is the type strain of a novel species in the genus Marinobacter, for which the name Marinobacter changyiensis sp. nov. is proposed. Based on the genomic analysis, siderophore genes were found from strain CLL7-20T, which indicate its potential as a promising alternative to chemical fertilizers in iron-limitated environments such as saline soils.
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Affiliation(s)
- Guangyu Li
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, PR China
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen, PR China
| | - Shanshan Wang
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen, PR China
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, PR China
| | - Yingbao Gai
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen, PR China
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, PR China
| | - Xiupian Liu
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen, PR China
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, PR China
| | - Qiliang Lai
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen, PR China
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, PR China
| | - Zongze Shao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, PR China
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen, PR China
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Insights into the metabolism pathway and functional genes of long-chain aliphatic alkane degradation in haloarchaea. Extremophiles 2020; 24:475-483. [DOI: 10.1007/s00792-020-01167-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Accepted: 03/24/2020] [Indexed: 12/22/2022]
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Aparna S, Parvathi A, Kaniyassery A. Isolation and characterization of a moderately halophilic Marinobacter phage-host system from the Arabian Sea. ENVIRONMENTAL MONITORING AND ASSESSMENT 2020; 192:199. [PMID: 32107642 DOI: 10.1007/s10661-020-8166-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 02/18/2020] [Indexed: 06/10/2023]
Abstract
Marinobacter is an ecologically important genus of Gammaproteobacteria found in diverse marine habitats, many species of which are capable of degrading hydrocarbons. In this study, we isolated a Marinobacter phage-host system from the surface waters of the Arabian Sea using enrichment culture methods, studied their growth characteristics and investigated the effect of salinity and nitrate concentrations on phage-host interactions. The bacterial isolate had maximum identity to Marinobacter salsuginis based on 16S rRNA similarities and was termed as Marinobacter sp., strain D1S9. It could tolerate up to 14% of NaCl with maximum growth at 11% NaCl. The host grew optimally between 35 and 40 °C and at pH 8. It had a generation time of 3.7 h with a mean growth rate of 0.27 h-1. The phage infected the host forming clear, round plaques of 1-2 mm diameter. It had a narrow host range restricted to the strain Marinobacter D1S9. The latent period and burst size of the phage were estimated to be 30 min and 106 phages per infected cell, respectively. The phage had an adsorption rate of 3.4 × 10-8 ml min-1 and retained 40.4% of its adsorption efficiency at 16% NaCl with a maximum at 4% NaCl (76.1%). Inorganic nitrate was found to have a direct role in controlling host growth and phage burst size.
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Affiliation(s)
- Sreekumar Aparna
- CSIR-National Institute of Oceanography, Regional Centre (CSIR), Kochi, 682 018, India
| | - Ammini Parvathi
- CSIR-National Institute of Oceanography, Regional Centre (CSIR), Kochi, 682 018, India.
| | - Arya Kaniyassery
- CSIR-National Institute of Oceanography, Regional Centre (CSIR), Kochi, 682 018, India
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18
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Thakur N, Sharma N, Kumar V, Bhalla TC. Computational Analysis of the Primary and Secondary Structure of Amidases in Relation to their pH Adaptation. CURR PROTEOMICS 2020. [DOI: 10.2174/1570164616666190718150627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Amidases are ubiquitous enzymes and biological functions of these enzymes
vary widely. They are considered to be synergistically involved in the synthesis of a wide variety of
carboxylic acids, hydroxamic acids and hydrazides, which find applications in commodity chemicals
synthesis, pharmaceuticals agrochemicals and wastewater treatments.
Methods:
They hydrolyse a wide variety of amides (short-chain aliphatic amides, mid-chain amides,
arylamides, α-aminoamides and α-hydroxyamides) and can be grouped on the basis of their catalytic
site and preferred substrate. Despite their economic importance, we lack knowledge as to how these
amidases withstand elevated pH and temperature whereas others cannot.
Results:
The present study focuses on the statistical comparison between the acid-tolerant, alkali tolerant
and neutrophilic organisms. In silico analysis of amidases of acid-tolerant, alkali tolerant and neutrophilic
organisms revealed some striking trends as to how amino acid composition varies significantly.
Statistical analysis of primary and secondary structure revealed amino acid trends in amidases of
these three groups of bacteria. The abundance of isoleucine (Ile, I) in acid-tolerant and leucine (Leu, L)
in alkali tolerant showed the aliphatic amino acid dominance in extreme conditions of pH in acidtolerant
and alkali tolerant amidases.
Conclusion:
The present investigation insights physiochemical properties and dominance of some crucial
amino acid residues in the primary and secondary structure of some amidases from acid-tolerant,
alkali tolerant and neutrophilic microorganisms.
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Affiliation(s)
- Neerja Thakur
- Bioinformatics Centre, Himachal Pradesh University, Summer Hill, Shimla, Himachal Pradesh 171005, India
| | - Nikhil Sharma
- Bioinformatics Centre, Himachal Pradesh University, Summer Hill, Shimla, Himachal Pradesh 171005, India
| | - Vijay Kumar
- Department of Biotechnology, Himachal Pradesh University, Summer Hill, Shimla, Himachal Pradesh 171005, India
| | - Tek Chand Bhalla
- Department of Biotechnology, Himachal Pradesh University, Summer Hill, Shimla, Himachal Pradesh 171005, India
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19
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Nikolova C, Gutierrez T. Use of Microorganisms in the Recovery of Oil From Recalcitrant Oil Reservoirs: Current State of Knowledge, Technological Advances and Future Perspectives. Front Microbiol 2020; 10:2996. [PMID: 32010082 PMCID: PMC6978736 DOI: 10.3389/fmicb.2019.02996] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 12/11/2019] [Indexed: 11/26/2022] Open
Abstract
The depletion of oil resources, increasing global energy demand, the current low, yet unpredictable, price of oil, and increasing maturity of major oil fields has driven the need for the development of oil recovery technologies that are less costly and, where possible, environmentally compatible. Using current technologies, between 20 and 40% of the original oil in a reservoir can be extracted by conventional production operations (e.g., vertical drilling), with secondary recovery methods yielding a further 15-25%. Hence, up to 55% of the original oil can remain unrecovered in a reservoir. Enhanced oil recovery (EOR) is a tertiary recovery process that involves application of different thermal, chemical, and microbial processes to recover an additional 7-15% of the original oil in place (OOIP) at an economically feasible production rate from poor-performing and depleted oil wells. EOR can significantly impact oil production, as increase in the recovery rate of oil by even a small margin could bring significant revenues without developing unconventional resources. Microbial enhanced oil recovery (MEOR) is an attractive, alternative oil recovery approach, which is claimed to potentially recover up to 50% of residual oil. The in situ production of biological surface-active compounds (e.g., biosurfactants) during the MEOR process does not require vast energy inputs and are not affected by global crude oil prices. Compared to other EOR methods, MEOR can be an economically and more environmentally friendly alternative. In this review, the current state of knowledge of MEOR, with insights from discussions with the industry and other stakeholders, is presented and in addition to the future outlook for this technology.
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Affiliation(s)
| | - Tony Gutierrez
- Institute of Mechanical, Process and Energy Engineering, School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, United Kingdom
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20
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Marinobacter nauticus (Baumann et al. 1972) comb. nov. arising from instances of synonymy and the incorrect interpretation of the International Code of Nomenclature of Prokaryotes. Arch Microbiol 2019; 202:657-663. [DOI: 10.1007/s00203-019-01761-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/13/2019] [Accepted: 10/30/2019] [Indexed: 10/25/2022]
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21
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Complete Genome Sequence of Marinobacter sp. Strain JH2, Isolated from Seawater of the Kiel Fjord. Microbiol Resour Announc 2019; 8:8/30/e00596-19. [PMID: 31346022 PMCID: PMC6658692 DOI: 10.1128/mra.00596-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here, we present the genome sequence of the Gram-negative and rod-shaped Marinobacter sp. strain JH2, which was isolated from seawater of the Kiel Fjord in Germany. The draft genome consists of two replicons, including one chromosome (3.6 Mb) and a circular plasmid (36.7 kb). The genome harbors 3,347 protein-coding genes. Here, we present the genome sequence of the Gram-negative and rod-shaped Marinobacter sp. strain JH2, which was isolated from seawater of the Kiel Fjord in Germany. The draft genome consists of two replicons, including one chromosome (3.6 Mb) and a circular plasmid (36.7 kb). The genome harbors 3,347 protein-coding genes.
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22
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Culbreath K, Melanson S, Gale J, Baker J, Li F, Saebo O, Kommedal O, Contreras D, Garner OB, Yang S. Validation and Retrospective Clinical Evaluation of a Quantitative 16S rRNA Gene Metagenomic Sequencing Assay for Bacterial Pathogen Detection in Body Fluids. J Mol Diagn 2019; 21:913-923. [PMID: 31229651 DOI: 10.1016/j.jmoldx.2019.05.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 03/03/2019] [Accepted: 05/24/2019] [Indexed: 02/07/2023] Open
Abstract
Next-generation sequencing-based 16S rRNA gene metagenomic sequencing (16S MG) technology has tremendous potential for improving diagnosis of bacterial infections given its quantitative capability and culture-independent approach. We validated and used a quantitative 16S MG assay to identify and quantify bacterial species in clinical samples from a wide spectrum of infections, including meningitis, septic arthritis, brain abscess, intra-abdominal abscess, soft tissue abscess, and pneumonia. Twenty clinical samples were tested, and 16S MG identified a total of 34 species, compared with 22 species and three descriptive findings identified by culture. 16S MG results matched culture results in 75% (15/20) of the samples but detected at least one more species in five samples, including one culture-negative cerebrospinal fluid sample that was found to contain Streptococcus intermedius. Shotgun metagenomic sequencing verified the presence of all additional species. The 16S MG assay is highly sensitive, with a limit of detection of 10 to 100 colony-forming units/mL. Other performance characteristics, including linearity, precision, and specificity, all met the requirements for a clinical test. This assay showed the advantages of accurate identification and quantification of bacteria in culture-negative and polymicrobial infections for which conventional microbiology methods are limited. It also showed promises to serve unmet clinical needs for solving difficult infectious diseases cases.
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Affiliation(s)
- Karissa Culbreath
- Department of Pathlogy, University of New Mexico Health Sciences Center, Albuquerque, New Mexico; TriCore Reference Laboratories, Albuquerque, New Mexico
| | | | - James Gale
- TriCore Reference Laboratories, Albuquerque, New Mexico
| | - Justin Baker
- TriCore Reference Laboratories, Albuquerque, New Mexico
| | - Fan Li
- Department of Pediatrics, University of California Los Angeles, Los Angeles, California
| | | | - Oyvind Kommedal
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Deisy Contreras
- Clinical Microbiology Laboratory, Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California
| | - Omai B Garner
- Clinical Microbiology Laboratory, Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California
| | - Shangxin Yang
- Department of Pathlogy, University of New Mexico Health Sciences Center, Albuquerque, New Mexico; Clinical Microbiology Laboratory, Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California.
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23
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Chua MJ, Campen RL, Wahl L, Grzymski JJ, Mikucki JA. Genomic and physiological characterization and description of Marinobacter gelidimuriae sp. nov., a psychrophilic, moderate halophile from Blood Falls, an antarctic subglacial brine. FEMS Microbiol Ecol 2019; 94:4850642. [PMID: 29444218 DOI: 10.1093/femsec/fiy021] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 02/08/2018] [Indexed: 11/12/2022] Open
Abstract
Antarctic subice environments are diverse, underexplored microbial habitats. Here, we describe the ecophysiology and annotated genome of a Marinobacter strain isolated from a cold, saline, iron-rich subglacial outflow of the Taylor Glacier, Antarctica. This strain (BF04_CF4) grows fastest at neutral pH (range 6-10), is psychrophilic (range: 0°C-20°C), moderately halophilic (range: 0.8%-15% NaCl) and hosts genes encoding potential low temperature and high salt adaptations. The predicted proteome suggests it utilizes fewer charged amino acids than a mesophilic Marinobacter strain. BF04_CF4 has increased concentrations of membrane unsaturated fatty acids including palmitoleic (33%) and oleic (27.5%) acids that may help maintain cell membrane fluidity at low temperatures. The genome encodes proteins for compatible solute biosynthesis and transport, which are known to be important for growth in saline environments. Physiological verification of predicted metabolic functions demonstrate BF04_CF4 is capable of denitrification and may facilitate iron oxidation. Our data indicate that strain BF04_CF4 represents a new Marinobacter species, Marinobacter gelidimuriae sp. nov., that appears well suited for the subglacial environment it was isolated from. Marinobacter species have been isolated from other cold, saline environments in the McMurdo Dry Valleys and permanently cold environments globally suggesting that this lineage is cosmopolitan and ecologically relevant in icy brines.
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Affiliation(s)
- Michelle J Chua
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Richard L Campen
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Lindsay Wahl
- Department of Environmental Studies, Dartmouth College, Hanover, NH, 03755, USA
| | - Joseph J Grzymski
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, 89512, USA
| | - Jill A Mikucki
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37996, USA
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24
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Evans MV, Panescu J, Hanson AJ, Welch SA, Sheets JM, Nastasi N, Daly RA, Cole DR, Darrah TH, Wilkins MJ, Wrighton KC, Mouser PJ. Members of Marinobacter and Arcobacter Influence System Biogeochemistry During Early Production of Hydraulically Fractured Natural Gas Wells in the Appalachian Basin. Front Microbiol 2018; 9:2646. [PMID: 30498478 PMCID: PMC6249378 DOI: 10.3389/fmicb.2018.02646] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 10/17/2018] [Indexed: 11/17/2022] Open
Abstract
Hydraulic fracturing is the prevailing method for enhancing recovery of hydrocarbon resources from unconventional shale formations, yet little is understood regarding the microbial impact on biogeochemical cycling in natural-gas wells. Although the metabolisms of certain fermentative bacteria and methanogenic archaea that dominate in later produced fluids have been well studied, few details have been reported on microorganisms prevelant during the early flowback period, when oxygen and other surface-derived oxyanions and nutrients become depleted. Here, we report the isolation, genomic and phenotypic characterization of Marinobacter and Arcobacter bacterial species from natural-gas wells in the Utica-Point Pleasant and Marcellus Formations coupled to supporting geochemical and metagenomic analyses of produced fluid samples. These unconventional hydrocarbon system-derived Marinobacter sp. are capable of utilizing a diversity of organic carbon sources including aliphatic and aromatic hydrocarbons, amino acids, and carboxylic acids. Marinobacter and Arcobacter can metabolize organic nitrogen sources and have the capacity for denitrification and dissimilatory nitrate reduction to ammonia (DNRA) respectively; with DNRA and ammonification processes partially explaining high concentrations of ammonia measured in produced fluids. Arcobacter is capable of chemosynthetic sulfur oxidation, which could fuel metabolic processes for other heterotrophic, fermentative, or sulfate-reducing community members. Our analysis revealed mechanisms for growth of these taxa across a broad range of salinities (up to 15% salt), which explains their enrichment during early natural-gas production. These results demonstrate the prevalence of Marinobacter and Arcobacter during a key maturation phase of hydraulically fractured natural-gas wells, and highlight the significant role these genera play in biogeochemical cycling for this economically important energy system.
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Affiliation(s)
- Morgan V Evans
- Department of Civil, Environmental, and Geodetic Engineering, The Ohio State University, Columbus, OH, United States
| | - Jenny Panescu
- Department of Civil, Environmental, and Geodetic Engineering, The Ohio State University, Columbus, OH, United States
| | - Andrea J Hanson
- Department of Civil and Environmental Engineering, Colorado State University, Fort Collins, CO, United States
| | - Susan A Welch
- School of Earth Sciences, The Ohio State University, Columbus, OH, United States
| | - Julia M Sheets
- School of Earth Sciences, The Ohio State University, Columbus, OH, United States
| | - Nicholas Nastasi
- Department of Civil, Environmental, and Geodetic Engineering, The Ohio State University, Columbus, OH, United States
| | - Rebecca A Daly
- Department of Microbiology, The Ohio State University, Columbus, OH, United States
| | - David R Cole
- School of Earth Sciences, The Ohio State University, Columbus, OH, United States
| | - Thomas H Darrah
- School of Earth Sciences, The Ohio State University, Columbus, OH, United States
| | - Michael J Wilkins
- School of Earth Sciences, The Ohio State University, Columbus, OH, United States.,Department of Microbiology, The Ohio State University, Columbus, OH, United States
| | - Kelly C Wrighton
- Department of Microbiology, The Ohio State University, Columbus, OH, United States
| | - Paula J Mouser
- Department of Civil, Environmental, and Geodetic Engineering, The Ohio State University, Columbus, OH, United States.,Department of Civil and Environmental Engineering, University of New Hampshire, Durham, NH, United States
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O’Brien PA, Smith HA, Fallon S, Fabricius K, Willis BL, Morrow KM, Bourne DG. Elevated CO 2 Has Little Influence on the Bacterial Communities Associated With the pH-Tolerant Coral, Massive Porites spp. Front Microbiol 2018; 9:2621. [PMID: 30443242 PMCID: PMC6221987 DOI: 10.3389/fmicb.2018.02621] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 10/12/2018] [Indexed: 12/21/2022] Open
Abstract
Ocean acidification (OA) as a result of increased anthropogenic CO2 input into the atmosphere carries consequences for all ocean life. Low pH can cause a shift in coral-associated microbial communities of pCO2-sensitive corals, however, it remains unknown whether the microbial community is also influenced in corals known to be more tolerant to high pCO2/low pH. This study profiles the bacterial communities associated with the tissues of the pCO2-tolerant coral, massive Porites spp., from two natural CO2 seep sites in Papua New Guinea. Amplicon sequencing of the hypervariable V3-V4 regions of the 16S rRNA gene revealed that microbial communities remained stable across CO2 seep sites (pH = 7.44-7.85) and adjacent control sites (ambient pH = 8.0-8.1). Microbial communities were more significantly influenced by reef location than pH, with the relative abundance of dominant microbial taxa differing between reefs. These results directly contrast with previous findings that increased CO2 has a strong effect on structuring microbial communities. The stable structure of microbial communities associated with the tissues of massive Porites spp. under high pCO2/low pH conditions confirms a high degree of tolerance by the whole Porites holobiont to OA, and suggest that pH tolerant corals such as Porites may dominate reef assemblages in an increasingly acidic ocean.
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Affiliation(s)
- Paul A. O’Brien
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
- Australian Institute of Marine Science, Townsville, QLD, Australia
- AIMS@JCU, Townsville, QLD, Australia
| | - Hillary A. Smith
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia
| | - Stewart Fallon
- Research School of Earth Sciences, The Australian National University, Canberra, ACT, Australia
| | | | - Bette L. Willis
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
- AIMS@JCU, Townsville, QLD, Australia
| | - Kathleen M. Morrow
- Department of Environmental Science and Policy, George Mason University, Fairfax, VA, United States
| | - David G. Bourne
- Department of Environmental Science and Policy, George Mason University, Fairfax, VA, United States
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Xu S, Wang D, Wei Y, Cui Q, Li W. Marinobacter bohaiensis sp. nov., a moderate halophile isolated from benthic sediment of the Bohai Sea. Int J Syst Evol Microbiol 2018; 68:3534-3539. [PMID: 30231958 DOI: 10.1099/ijsem.0.003025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, motile, aerobic and rod-shaped bacterial strain, designated T17T, was isolated from benthic sediment sampled at Jiaozhou Bay, Bohai Sea, China, and its taxonomic position was investigated. The 16S rRNA gene sequence of strain T17T exhibited the highest similarity values to those of the type strain Marinobacter lacisalsi FP2.5 (96.2 %) and Marinobacter koreensis DD-M3T (96.2 %). Strain T17T grew optimally at 35 °C, pH 7.0-8.0 and in the presence of 6.0-10.0 % (w/v) NaCl. The predominant ubiquinone in strain T17T was identified as Q-9. The major fatty acids of strain T17T were C12 : 0, C16 : 0 and C16 : 0 10-CH3. The major polar lipids of strain T17T were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidglycerol, an unidentified aminolipid and an unidentified phospholipid. The DNA G+C content of strain T17T was 63.0 mol%. The draft genome sequence of strain T17T includes 4 755 891 bp in total (N50=2 856 325 bp) with a medium read coverage of 100.0x and 11 scaffolds. In silico DNA-DNA hybridization with the three type strains showed 20.3, 19.7 and 19.9 % relatedness to Marinobacter santoriniensis NKSG1T, Marinobacter segnicrescens SS11B1-4T and Marinobacter daqiaonensis CGMCC 1.9167T, respectively. On the basis of the phenotypic, phylogenetic, genomic and chemotaxonomic properties, strain T17T is considered to represent a novel species within the genus Marinobacter, for which the name Marinobacterbohaiensis sp. nov. is proposed. The type strain is T17T (=KCTC 52710T=MCCC 1K03282T).
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Affiliation(s)
- Shanshan Xu
- 1Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, PR China
| | - Dandan Wang
- 1Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, PR China.,2Life Science College, Qingdao University, Qingdao 266071, PR China
| | - Yuxi Wei
- 2Life Science College, Qingdao University, Qingdao 266071, PR China
| | - Qiu Cui
- 3Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Science, Qingdao 266101, PR China
| | - Wenli Li
- 1Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, PR China.,4Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, PR China
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Tin HS, Palaniveloo K, Anilik J, Vickneswaran M, Tashiro Y, Vairappan CS, Sakai K. Impact of Land-use Change on Vertical Soil Bacterial Communities in Sabah. MICROBIAL ECOLOGY 2018; 75:459-467. [PMID: 28779295 DOI: 10.1007/s00248-017-1043-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 07/10/2017] [Indexed: 06/07/2023]
Abstract
Decline in forest productivity due to forest conversion is defining the Bornean landscape. Responses of bacterial communities due to land-use changes are vital and could define our understanding of ecosystem functions. This study reports the changes in bacterial community structure in organic soil (0-5 cm; O-Horizon) and organic-mineral soil (5-15 cm; A-Horizon) across Maliau Basin Conservation Area old growth forest (MBOG), Fragment E logged forest (FELF) located in Kalabakan Forest Reserve to Benta Wawasan oil palm plantation (BWOP) using two-step PCR amplicon analysis of bacteria DNA on Illumina Miseq next generation sequencing. A total of 30 soil samples yielded 893,752-OTU reads at ≥97% similarity from 5,446,512 good quality sequences. Soil from BWOP plantation showed highest unshared OTUs for organic (49.2%) and organic-mineral (50.9%) soil. MBOG soil showed a drop in unshared OTUs between organic (48.6%) and organic-mineral (33.9%). At phylum level, Proteobacteria dominated MBOG but shifted to Actinobacteria in logged and plantation soil. Present findings also indicated that only FELF exhibited change in bacterial communities along the soil depth, moving from the organic to the organic-mineral layer. Both layers of BWOP plantation soils deviated from other forests' soil in β-diversity analysis. To our knowledge, this is the first report on transitions of bacterial community structures with different soil horizons in the tropical rainforest including Borneo, Sabah. Borneo tropical soils form a large reservoir for soil bacteria and future exploration is needed for fully understanding the diversity structure and their bacterial functional properties.
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Affiliation(s)
- Hoe Seng Tin
- Laboratory of Natural Products Chemistry, Institute for Tropical Biology and Conservation, Universiti Malaysia Sabah, Jalan UMS, 88450, Kota Kinabalu, Sabah, Malaysia
| | - Kishneth Palaniveloo
- Laboratory of Natural Products Chemistry, Institute for Tropical Biology and Conservation, Universiti Malaysia Sabah, Jalan UMS, 88450, Kota Kinabalu, Sabah, Malaysia
| | - Junia Anilik
- Laboratory of Natural Products Chemistry, Institute for Tropical Biology and Conservation, Universiti Malaysia Sabah, Jalan UMS, 88450, Kota Kinabalu, Sabah, Malaysia
| | - Mathavan Vickneswaran
- Laboratory of Natural Products Chemistry, Institute for Tropical Biology and Conservation, Universiti Malaysia Sabah, Jalan UMS, 88450, Kota Kinabalu, Sabah, Malaysia
| | - Yukihiro Tashiro
- Laboratory of Soil and Environmental Microbiology, Division of Systems Bioengineering, Department of Biosciences and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 6-10-1 Hakozaki, Higasi-ku, Fukuoka, 812-8581, Japan
- Laboratory of Microbial Environmental Protection, Tropical Microbiology Unit, Center for International Education and Research of Agriculture, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, 812-8581, Japan
| | - Charles S Vairappan
- Laboratory of Natural Products Chemistry, Institute for Tropical Biology and Conservation, Universiti Malaysia Sabah, Jalan UMS, 88450, Kota Kinabalu, Sabah, Malaysia.
| | - Kenji Sakai
- Laboratory of Soil and Environmental Microbiology, Division of Systems Bioengineering, Department of Biosciences and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 6-10-1 Hakozaki, Higasi-ku, Fukuoka, 812-8581, Japan
- Laboratory of Microbial Environmental Protection, Tropical Microbiology Unit, Center for International Education and Research of Agriculture, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, 812-8581, Japan
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Mahmoud GAE, Bagy MMK. Microbial Degradation of Petroleum Hydrocarbons. MICROBIAL ACTION ON HYDROCARBONS 2018:299-320. [DOI: 10.1007/978-981-13-1840-5_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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29
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Genomic potential of Marinobacter salinus Hb8T as sulfur oxidizing and aromatic hydrocarbon degrading bacterium. Mar Genomics 2017. [DOI: 10.1016/j.margen.2017.02.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Five Fatty Aldehyde Dehydrogenase Enzymes from Marinobacter and Acinetobacter spp. and Structural Insights into the Aldehyde Binding Pocket. Appl Environ Microbiol 2017; 83:AEM.00018-17. [PMID: 28389542 DOI: 10.1128/aem.00018-17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 04/03/2017] [Indexed: 12/15/2022] Open
Abstract
Enzymes involved in lipid biosynthesis and metabolism play an important role in energy conversion and storage and in the function of structural components such as cell membranes. The fatty aldehyde dehydrogenase (FAldDH) plays a central function in the metabolism of lipid intermediates, oxidizing fatty aldehydes to the corresponding fatty acid and competing with pathways that would further reduce the fatty aldehydes to fatty alcohols or require the fatty aldehydes to produce alkanes. In this report, the genes for four putative FAldDH enzymes from Marinobacter aquaeolei VT8 and an additional enzyme from Acinetobacter baylyi were heterologously expressed in Escherichia coli and shown to display FAldDH activity. Five enzymes (Maqu_0438, Maqu_3316, Maqu_3410, Maqu_3572, and the enzyme reported under RefSeq accession no. WP_004927398) were found to act on aldehydes ranging from acetaldehyde to hexadecanal and also acted on the unsaturated long-chain palmitoleyl and oleyl aldehydes. A comparison of the specificities of these enzymes with various aldehydes is presented. Crystallization trials yielded diffraction-quality crystals of one particular FAldDH (Maqu_3316) from M. aquaeolei VT8. Crystals were independently treated with both the NAD+ cofactor and the aldehyde substrate decanal, revealing specific details of the likely substrate binding pocket for this class of enzymes. A likely model for how catalysis by the enzyme is accomplished is also provided.IMPORTANCE This study provides a comparison of multiple enzymes with the ability to oxidize fatty aldehydes to fatty acids and provides a likely picture of how the fatty aldehyde and NAD+ are bound to the enzyme to facilitate catalysis. Based on the information obtained from this structural analysis and comparisons of specificities for the five enzymes that were characterized, correlations to the potential roles played by specific residues within the structure may be drawn.
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31
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Rani S, Koh HW, Kim H, Rhee SK, Park SJ. Marinobacter salinus sp. nov., a moderately halophilic bacterium isolated from a tidal flat environment. Int J Syst Evol Microbiol 2017; 67:205-211. [PMID: 27902222 DOI: 10.1099/ijsem.0.001587] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Sundas Rani
- Department of Biology, Jeju National University, Jejudaehak-ro 102, Jeju 63243, Republic of Korea
| | - Hyeon-Woo Koh
- Department of Biology, Jeju National University, Jejudaehak-ro 102, Jeju 63243, Republic of Korea
| | - Hongik Kim
- R&D Division, VITABIO, Inc., Daejeon 34025, Republic of Korea
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, Chungdae-ro 1, Cheongju 28644, Republic of Korea
| | - Soo-Je Park
- Department of Biology, Jeju National University, Jejudaehak-ro 102, Jeju 63243, Republic of Korea
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32
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Halophiles: biology, adaptation, and their role in decontamination of hypersaline environments. World J Microbiol Biotechnol 2016; 32:135. [PMID: 27344438 DOI: 10.1007/s11274-016-2081-9] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/07/2016] [Indexed: 10/21/2022]
Abstract
The unique cellular enzymatic machinery of halophilic microbes allows them to thrive in extreme saline environments. That these microorganisms can prosper in hypersaline environments has been correlated with the elevated acidic amino acid content in their proteins, which increase the negative protein surface potential. Because these microorganisms effectively use hydrocarbons as their sole carbon and energy sources, they may prove to be valuable bioremediation agents for the treatment of saline effluents and hypersaline waters contaminated with toxic compounds that are resistant to degradation. This review highlights the various strategies adopted by halophiles to compensate for their saline surroundings and includes descriptions of recent studies that have used these microorganisms for bioremediation of environments contaminated by petroleum hydrocarbons. The known halotolerant dehalogenase-producing microbes, their dehalogenation mechanisms, and how their proteins are stabilized is also reviewed. In view of their robustness in saline environments, efforts to document their full potential regarding remediation of contaminated hypersaline ecosystems merits further exploration.
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33
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Zhang X, Feng X, Wang F. Diversity and Metabolic Potentials of Subsurface Crustal Microorganisms from the Western Flank of the Mid-Atlantic Ridge. Front Microbiol 2016; 7:363. [PMID: 27047476 PMCID: PMC4797314 DOI: 10.3389/fmicb.2016.00363] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Accepted: 03/07/2016] [Indexed: 02/01/2023] Open
Abstract
Deep-sea oceanic crust constitutes the largest region of the earth’s surface. Accumulating evidence suggests that unique microbial communities are supported by iron cycling processes, particularly in the young (<10 million-year old), cool (<25°C) subsurface oceanic crust. To test this hypothesis, we investigated the microbial abundance, diversity, and metabolic potentials in the sediment-buried crust from “North Pond” on western flank of the Mid-Atlantic Ridge. Three lithologic units along basement Hole U1383C were found, which typically hosted ∼104 cells cm-3 of basaltic rock, with higher cell densities occurring between 115 and 145 m below seafloor. Similar bacterial community structures, which are dominated by Gammaproteobacterial and Sphingobacterial species closely related to iron oxidizers, were detected regardless of variations in sampling depth. The metabolic potentials of the crust microbiota were assayed by metagenomic analysis of two basalt enrichments which showed similar bacterial structure with the original sample. Genes coding for energy metabolism involved in hydrocarbon degradation, dissimilatory nitrate reduction to ammonium, denitrification and hydrogen oxidation were identified. Compared with other marine environments, the metagenomes from the basalt-hosted environments were enriched in pathways for Fe3+ uptake, siderophore synthesis and uptake, and Fe transport, suggesting that iron metabolism is an important energy production and conservation mechanism in this system. Overall, we provide evidence that the North Pond crustal biosphere is dominated by unique bacterial groups with the potential for iron-related biogeochemical cycles.
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Affiliation(s)
- Xinxu Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityShanghai, China; State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong UniversityShanghai, China
| | - Xiaoyuan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityShanghai, China; State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong UniversityShanghai, China
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34
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Cui Z, Gao W, Xu G, Luan X, Li Q, Yin X, Huang D, Zheng L. Marinobacter aromaticivorans sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from sea sediment. Int J Syst Evol Microbiol 2016; 66:353-359. [DOI: 10.1099/ijsem.0.000722] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Zhisong Cui
- Marine Ecology Research Center, First Institute of Oceanography, State Oceanic Administration of China, Qingdao, PR China
| | - Wei Gao
- Marine Ecology Research Center, First Institute of Oceanography, State Oceanic Administration of China, Qingdao, PR China
- College of Marine life, Ocean University of China, Qingdao, PR China
| | - Guangfei Xu
- Marine Ecology Research Center, First Institute of Oceanography, State Oceanic Administration of China, Qingdao, PR China
| | - Xiao Luan
- Marine Ecology Research Center, First Institute of Oceanography, State Oceanic Administration of China, Qingdao, PR China
| | - Qian Li
- Marine Ecology Research Center, First Institute of Oceanography, State Oceanic Administration of China, Qingdao, PR China
| | - Xiaofei Yin
- Marine Ecology Research Center, First Institute of Oceanography, State Oceanic Administration of China, Qingdao, PR China
| | - Deming Huang
- Marine Ecology Research Center, First Institute of Oceanography, State Oceanic Administration of China, Qingdao, PR China
| | - Li Zheng
- Marine Ecology Research Center, First Institute of Oceanography, State Oceanic Administration of China, Qingdao, PR China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology
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35
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Masilamani R, Natarajan S. Molecular cloning, overexpression and characterization of a new thiol-dependent, alkaline serine protease with destaining function and fibrinolytic potential from Marinobacter aquaeolei MS2-1. Biologia (Bratisl) 2015. [DOI: 10.1515/biolog-2015-0144] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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36
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Kleindienst S, Seidel M, Ziervogel K, Grim S, Loftis K, Harrison S, Malkin SY, Perkins MJ, Field J, Sogin ML, Dittmar T, Passow U, Medeiros PM, Joye SB. Chemical dispersants can suppress the activity of natural oil-degrading microorganisms. Proc Natl Acad Sci U S A 2015; 112:14900-5. [PMID: 26553985 PMCID: PMC4672791 DOI: 10.1073/pnas.1507380112] [Citation(s) in RCA: 151] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During the Deepwater Horizon oil well blowout in the Gulf of Mexico, the application of 7 million liters of chemical dispersants aimed to stimulate microbial crude oil degradation by increasing the bioavailability of oil compounds. However, the effects of dispersants on oil biodegradation rates are debated. In laboratory experiments, we simulated environmental conditions comparable to the hydrocarbon-rich, 1,100 m deep plume that formed during the Deepwater Horizon discharge. The presence of dispersant significantly altered the microbial community composition through selection for potential dispersant-degrading Colwellia, which also bloomed in situ in Gulf deep waters during the discharge. In contrast, oil addition to deepwater samples in the absence of dispersant stimulated growth of natural hydrocarbon-degrading Marinobacter. In these deepwater microcosm experiments, dispersants did not enhance heterotrophic microbial activity or hydrocarbon oxidation rates. An experiment with surface seawater from an anthropogenically derived oil slick corroborated the deepwater microcosm results as inhibition of hydrocarbon turnover was observed in the presence of dispersants, suggesting that the microcosm findings are broadly applicable across marine habitats. Extrapolating this comprehensive dataset to real world scenarios questions whether dispersants stimulate microbial oil degradation in deep ocean waters and instead highlights that dispersants can exert a negative effect on microbial hydrocarbon degradation rates.
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Affiliation(s)
- Sara Kleindienst
- Department of Marine Sciences, University of Georgia, Athens, GA 30602
| | - Michael Seidel
- Department of Marine Sciences, University of Georgia, Athens, GA 30602
| | - Kai Ziervogel
- Department of Marine Sciences, University of North Carolina, Chapel Hill, NC 27599
| | - Sharon Grim
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA 02543
| | - Kathy Loftis
- Department of Marine Sciences, University of Georgia, Athens, GA 30602
| | - Sarah Harrison
- Department of Marine Sciences, University of Georgia, Athens, GA 30602
| | - Sairah Y Malkin
- Department of Marine Sciences, University of Georgia, Athens, GA 30602
| | - Matthew J Perkins
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331
| | - Jennifer Field
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331
| | - Mitchell L Sogin
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA 02543
| | - Thorsten Dittmar
- Research Group for Marine Geochemistry, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University, 26129 Oldenburg, Germany; Max Planck Institute for Marine Microbiology (MPI), 28359 Bremen, Germany
| | - Uta Passow
- Marine Science Institute, University of California, Santa Barbara, CA 93106
| | | | - Samantha B Joye
- Department of Marine Sciences, University of Georgia, Athens, GA 30602;
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Turner WJ, Dunlop MJ. Trade-Offs in Improving Biofuel Tolerance Using Combinations of Efflux Pumps. ACS Synth Biol 2015; 4:1056-63. [PMID: 25496359 DOI: 10.1021/sb500307w] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Microbes can be engineered to produce next-generation biofuels; however, the accumulation of toxic biofuels can limit yields. Previous studies have shown that efflux pumps can increase biofuel tolerance and improve production. Here, we asked whether expressing multiple pumps in combination could further increase biofuel tolerance. Pump overexpression inhibits cell growth, suggesting a trade-off between biofuel and pump toxicity. With multiple pumps, it is unclear how the fitness landscape is impacted. To address this, we measured tolerance of Escherichia coli to the biojet fuel precursor α-pinene in one-pump and two-pump strains. To support our experiments, we developed a mathematical model describing toxicity due to biofuel and overexpression of pumps. We found that data from one-pump strains can accurately predict the performance of two-pump strains. This result suggests that it may be possible to dramatically reduce the number of experiments required for characterizing the effects of combined biofuel tolerance mechanisms.
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Affiliation(s)
- William J. Turner
- School
of Engineering, University of Vermont, Burlington, Vermont 05405, United States
| | - Mary J. Dunlop
- School
of Engineering, University of Vermont, Burlington, Vermont 05405, United States
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38
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Tomko TA, Dunlop MJ. Engineering improved bio-jet fuel tolerance in Escherichia coli using a transgenic library from the hydrocarbon-degrader Marinobacter aquaeolei. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:165. [PMID: 26448785 PMCID: PMC4596283 DOI: 10.1186/s13068-015-0347-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 09/22/2015] [Indexed: 06/05/2023]
Abstract
BACKGROUND Recent metabolic engineering efforts have generated microorganisms that can produce biofuels, including bio-jet fuels, however these fuels are often toxic to cells, limiting production yields. There are natural examples of microorganisms that have evolved mechanisms for tolerating hydrocarbon-rich environments, such as those that thrive near natural oil seeps and in oil-polluted waters. RESULTS Using genomic DNA from the hydrocarbon-degrading microbe Marinobacter aquaeolei, we constructed a transgenic library that we expressed in Escherichia coli. We exposed cells to inhibitory levels of pinene, a monoterpene that can serve as a jet fuel precursor with chemical properties similar to existing tactical fuels. Using a sequential strategy with a fosmid library followed by a plasmid library, we were able to isolate a region of DNA from the M. aquaeolei genome that conferred pinene tolerance when expressed in E. coli. We determined that a single gene, yceI, was responsible for the tolerance improvements. Overexpression of this gene placed no additional burden on the host. We also tested tolerance to other monoterpenes and showed that yceI selectively improves tolerance. CONCLUSIONS The genomes of hydrocarbon-tolerant microbes represent a rich resource for tolerance engineering. Using a transgenic library, we were able to identify a single gene that improves E. coli's tolerance to the bio-jet fuel precursor pinene.
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Affiliation(s)
- Timothy A. Tomko
- School of Engineering, University of Vermont, 33 Colchester Ave, Burlington, VT 05405 USA
| | - Mary J. Dunlop
- School of Engineering, University of Vermont, 33 Colchester Ave, Burlington, VT 05405 USA
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39
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Contribution of cyanobacterial alkane production to the ocean hydrocarbon cycle. Proc Natl Acad Sci U S A 2015; 112:13591-6. [PMID: 26438854 DOI: 10.1073/pnas.1507274112] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Hydrocarbons are ubiquitous in the ocean, where alkanes such as pentadecane and heptadecane can be found even in waters minimally polluted with crude oil. Populations of hydrocarbon-degrading bacteria, which are responsible for the turnover of these compounds, are also found throughout marine systems, including in unpolluted waters. These observations suggest the existence of an unknown and widespread source of hydrocarbons in the oceans. Here, we report that strains of the two most abundant marine cyanobacteria, Prochlorococcus and Synechococcus, produce and accumulate hydrocarbons, predominantly C15 and C17 alkanes, between 0.022 and 0.368% of dry cell weight. Based on global population sizes and turnover rates, we estimate that these species have the capacity to produce 2-540 pg alkanes per mL per day, which translates into a global ocean yield of ∼ 308-771 million tons of hydrocarbons annually. We also demonstrate that both obligate and facultative marine hydrocarbon-degrading bacteria can consume cyanobacterial alkanes, which likely prevents these hydrocarbons from accumulating in the environment. Our findings implicate cyanobacteria and hydrocarbon degraders as key players in a notable internal hydrocarbon cycle within the upper ocean, where alkanes are continually produced and subsequently consumed within days. Furthermore we show that cyanobacterial alkane production is likely sufficient to sustain populations of hydrocarbon-degrading bacteria, whose abundances can rapidly expand upon localized release of crude oil from natural seepage and human activities.
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Bonin P, Vieira C, Grimaud R, Militon C, Cuny P, Lima O, Guasco S, Brussaard CPD, Michotey V. Substrates specialization in lipid compounds and hydrocarbons of Marinobacter genus. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:15347-15359. [PMID: 25561256 DOI: 10.1007/s11356-014-4009-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 12/15/2014] [Indexed: 06/04/2023]
Abstract
The impact of petroleum contamination and of burrowing macrofauna on abundances of Marinobacter and denitrifiers was tested in marine sediment mesocoms after 3 months incubation. Quantification of this genus by qPCR with a new primer set showed that the main factor favoring Marinobacter abundance was hydrocarbon amendment followed by macrofauna presence. In parallel, proportion of nosZ-harboring bacteria increased in the presence of marcrofauna. Quantitative finding were explained by physiological data from a set of 34 strains and by genomic analysis of 16 genomes spanning 15 different Marinobacter-validated species (Marinobacter hydrocarbonoclasticus, Marinobacter daeopensis, Marinobacter santoriniensis, Marinobacter pelagius, Marinobacter flavimaris, Marinobacter adhaerens, Marinobacter xestospongiae, Marinobacter algicola, Marinobacter vinifirmus, Marinobacter maritimus, Marinobacter psychrophilus, Marinobacter lipoliticus, Marinobacter manganoxydans, Marinobacter excellens, Marinobacter nanhaiticus) and 4 potential novel ones. Among the 105 organic electron donors tested in physiological analysis, Marinobacter pattern appeared narrow for almost all kinds of organic compounds except lipid ones. Strains of this set could oxidize a very large spectrum of lipids belonging to glycerolipids, branched, fatty acyls, and aromatic hydrocarbon classes. Physiological data were comforted by genomic analysis, and genes of alkane 1-monooxygenase, haloalkane dehalogenase, and flavin-binding monooxygenase were detected in most genomes. Denitrification was assessed for several strains belonging to M. hydrocarbonoclasticus, M. vinifirmus, Marinobacter maritinus, and M. pelagius species indicating the possibility to use nitrate as alternative electron acceptor. Higher occurrence of Marinobacter in the presence of petroleum appeared to be the result of a broader physiological trait allowing this genus to use lipids including hydrocarbon as principal electron donors.
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Affiliation(s)
- Patricia Bonin
- Aix Marseille Université, UM110, MIO CNRS IRD, campus de Luminy, case 901, 13288, Marseille, France
| | - Christophe Vieira
- Aix Marseille Université, UM110, MIO CNRS IRD, campus de Luminy, case 901, 13288, Marseille, France
- Sorbonne Universités, UPMC Univ Paris 06, IFD, 4 Place Jussieu, 75252, Paris cedex 05, France
| | - Régis Grimaud
- Institut Pluridisciplinaire de Recherche en Environnement et Matériaux, Equipe Environnement et Microbiologie, UMR 5254, CNRS, IBEAS, Université de Pau et des Pays de l'Adour, Pau, France
| | - Cécile Militon
- Aix Marseille Université, UM110, MIO CNRS IRD, campus de Luminy, case 901, 13288, Marseille, France
| | - Philippe Cuny
- Aix Marseille Université, UM110, MIO CNRS IRD, campus de Luminy, case 901, 13288, Marseille, France
| | - Oscar Lima
- Aix Marseille Université, UM110, MIO CNRS IRD, campus de Luminy, case 901, 13288, Marseille, France
- Ecosystèmes, Biodiversité, Evolution (ECOBIO), CNRS : UMR6553 - Université de Rennes 1 - INEE - Observatoire des Sciences de l'Univers de Rennes, Rennes, France
| | - Sophie Guasco
- Aix Marseille Université, UM110, MIO CNRS IRD, campus de Luminy, case 901, 13288, Marseille, France
| | - Corina P D Brussaard
- Department of Biological Oceanography, Royal Netherlands Institute for Sea Research, NL-1790, Den Burg, AB, Netherlands
| | - Valérie Michotey
- Aix Marseille Université, UM110, MIO CNRS IRD, campus de Luminy, case 901, 13288, Marseille, France.
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Vaidya B, Kumar R, Korpole S, Tanuku NRS, Pinnaka AK. Marinobacter nitratireducens sp. nov., a halophilic and lipolytic bacterium isolated from coastal surface sea water. Int J Syst Evol Microbiol 2015; 65:2056-2063. [DOI: 10.1099/ijs.0.000218] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-negative, rod-shaped, motile bacterium, designated strain AK21T, was isolated from coastal surface sea water at Visakhapatnam, India. The strain was positive for oxidase, catalase, lipase, l-proline arylamidase and tyrosine arylamidase activities. The predominant fatty acids were C12:0, C12:0 3-OH, C16:0, C16:1ω9c, C18:1ω9c and summed feature 3 (C16:1ω7c and/or iso-C15:0 2-OH). The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, one unidentified aminophospholipid, two unidentified phospholipids and one unidentified lipid. Q-10 was the predominant respiratory quinone. The DNA G+C content of the strain was 54.6 mol%. 16S rRNA gene sequence analysis indicated that strain AK21T was a member of the genus Marinobacter and was closely related to Marinobacter xestospongiae, with pairwise sequence similarity of 97.2 % to the type strain, with similarity to other members of the genus of 94.0–96.8 %. The mean DNA–DNA relatedness of strain AK21T with M. xestospongiae JCM 17469T was 34.5 %, and relatedness with Marinobacter mobilis JCM 15154T was 40.5 %. Phylogenetic analysis showed that strain AK21T clustered with the type strains of M. xestospongiae and M. mobilis at distances of 2.9 and 2.8 % (97.1 and 97.2 % similarity), respectively. Based on the phenotypic characteristics and on phylogenetic inference, it appears that strain AK21T represents a novel species of the genus Marinobacter, for which the name Marinobacter nitratireducens sp. nov. is proposed. The type strain of Marinobacter nitratireducens is AK21T ( = MTCC 11704T = JCM 18428T).
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Affiliation(s)
- Bhumika Vaidya
- MTCC – Microbial Type Culture Collection & Gene Bank, CSIR – Institute of Microbial Technology, Chandigarh – 160036, India
| | - Ravinder Kumar
- MTCC – Microbial Type Culture Collection & Gene Bank, CSIR – Institute of Microbial Technology, Chandigarh – 160036, India
| | - Suresh Korpole
- MTCC – Microbial Type Culture Collection & Gene Bank, CSIR – Institute of Microbial Technology, Chandigarh – 160036, India
| | - Naga Radha Srinivas Tanuku
- CSIR – National Institute of Oceanography, Regional Centre, 176, Lawsons Bay Colony, Visakhapatnam – 530017, India
| | - Anil Kumar Pinnaka
- MTCC – Microbial Type Culture Collection & Gene Bank, CSIR – Institute of Microbial Technology, Chandigarh – 160036, India
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Zhong ZP, Liu Y, Liu HC, Wang F, Zhou YG, Liu ZP. Marinobacter halophilus sp. nov., a halophilic bacterium isolated from a salt lake. Int J Syst Evol Microbiol 2015; 65:2838-2845. [PMID: 25985830 DOI: 10.1099/ijs.0.000338] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-negative bacterium, strain XCD-X12(T), was isolated from Xiaochaidan Lake, a salt lake (salinity 9.9%, w/w) in Qaidam basin, Qinghai Province, China. Its taxonomic position was determined by using a polyphasic approach. Cells of strain XCD-X12(T) were non-spore-forming rods, 0.4-0.7 μm wide, 2.1-3.2 μm long and motile with a single polar flagellum. Strain XCD-X12(T) was strictly aerobic and catalase- and oxidase-positive. Growth was observed in the presence of 0-20.0% (w/v) NaCl (optimum, 4.0-8.0%), at 4-35 °C (optimum, 30 °C) and at pH 6.5-10.5 (optimum, pH 8.5). It contained Q-9 as the predominant respiratory quinone. The major fatty acids (>10.0%) were C16 : 0, C16 : 1ω9c and C18 : 1ω9c. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, two unknown phospholipids and an uncharacterized aminophospholipid. The DNA G+C content was 55.6 mol% (Tm). Phylogenetic trees based on 16S rRNA gene sequences showed that strain XCD-X12(T) was associated with the genus Marinobacter, and showed the highest 16S rRNA gene sequence similarity to Marinobacter hydrocarbonoclasticus ATCC 49840(T) (97.4%), M. vinifirmus FB1(T) (96.8%), M. excellens KMM 3809(T) (96.8%) and M. antarcticus ZS2-30(T) (96.7%). DNA-DNA relatedness of strain XCD-X12(T) to M. hydrocarbonoclasticus CGMCC 1.7683(T) was 34 ± 5%. Based on these data, it is concluded that strain XCD-X12(T) represents a novel species of the genus Marinobacter, for which the name Marinobacter halophilus sp. nov. is proposed. The type strain is XCD-X12(T) ( = CGMCC 1.12481(T)= JCM 30472(T)).
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Affiliation(s)
- Zhi-Ping Zhong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China.,University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Ying Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Hong-Can Liu
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Fang Wang
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing 100089, PR China
| | - Yu-Guang Zhou
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Zhi-Pei Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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Foong CP, Lau NS, Deguchi S, Toyofuku T, Taylor TD, Sudesh K, Matsui M. Whole genome amplification approach reveals novel polyhydroxyalkanoate synthases (PhaCs) from Japan Trench and Nankai Trough seawater. BMC Microbiol 2014; 14:318. [PMID: 25539583 PMCID: PMC4326521 DOI: 10.1186/s12866-014-0318-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 12/10/2014] [Indexed: 11/16/2022] Open
Abstract
Background Special features of the Japanese ocean include its ranges of latitude and depth. This study is the first to examine the diversity of Class I and II PHA synthases (PhaC) in DNA samples from pelagic seawater taken from the Japan Trench and Nankai Trough from a range of depths from 24 m to 5373 m. PhaC is the key enzyme in microorganisms that determines the types of monomer units that are polymerized into polyhydroxyalkanoate (PHA) and thus affects the physicochemical properties of this thermoplastic polymer. Complete putative PhaC sequences were determined via genome walking, and the activities of newly discovered PhaCs were evaluated in a heterologous host. Results A total of 76 putative phaC PCR fragments were amplified from the whole genome amplified seawater DNA. Of these 55 clones contained conserved PhaC domains and were classified into 20 genetic groups depending on their sequence similarity. Eleven genetic groups have undisclosed PhaC activity based on their distinct phylogenetic lineages from known PHA producers. Three complete DNA coding sequences were determined by IAN-PCR, and one PhaC was able to produce poly(3-hydroxybutyrate) in recombinant Cupriavidus necator PHBˉ4 (PHB-negative mutant). Conclusions A new functional PhaC that has close identity to Marinobacter sp. was discovered in this study. Phylogenetic classification for all the phaC genes isolated from uncultured bacteria has revealed that seawater and other environmental resources harbor a great diversity of PhaCs with activities that have not yet been investigated. Functional evaluation of these in silico-based PhaCs via genome walking has provided new insights into the polymerizing ability of these enzymes. Electronic supplementary material The online version of this article (doi:10.1186/s12866-014-0318-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Choon Pin Foong
- Synthetic Genomics Research Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, 230-0045, Japan. .,Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800, Gelugor, Penang, Malaysia.
| | - Nyok-Sean Lau
- Synthetic Genomics Research Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, 230-0045, Japan. .,Centre for Chemical Biology, Universiti Sains Malaysia, 11800, Gelugor, Penang, Malaysia.
| | - Shigeru Deguchi
- R&D Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan.
| | - Takashi Toyofuku
- R&D Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan.
| | - Todd D Taylor
- Laboratory for Integrated Bioinformatics, Core for Precise Measuring and Modeling, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, 230-0045, Japan.
| | - Kumar Sudesh
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800, Gelugor, Penang, Malaysia. .,Centre for Chemical Biology, Universiti Sains Malaysia, 11800, Gelugor, Penang, Malaysia.
| | - Minami Matsui
- Synthetic Genomics Research Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, 230-0045, Japan.
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Ng HJ, López-Pérez M, Webb HK, Gomez D, Sawabe T, Ryan J, Vyssotski M, Bizet C, Malherbe F, Mikhailov VV, Crawford RJ, Ivanova EP. Marinobacter salarius sp. nov. and Marinobacter similis sp. nov., isolated from sea water. PLoS One 2014; 9:e106514. [PMID: 25198502 PMCID: PMC4157798 DOI: 10.1371/journal.pone.0106514] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 07/31/2014] [Indexed: 11/18/2022] Open
Abstract
Two non-pigmented, motile, Gram-negative marine bacteria designated R9SW1T and A3d10T were isolated from sea water samples collected from Chazhma Bay, Gulf of Peter the Great, Sea of Japan, Pacific Ocean, Russia and St. Kilda Beach, Port Phillip Bay, the Tasman Sea, Pacific Ocean, respectively. Both organisms were found to grow between 4 °C and 40 °C, between pH 6 to 9, and are moderately halophilic, tolerating up to 20% (w/v) NaCl. Both strains were found to be able to degrade Tween 40 and 80, but only strain R9SW1T was found to be able to degrade starch. The major fatty acids were characteristic for the genus Marinobacter including C16:0, C16:1ω7c, C18:1ω9c and C18:1ω7c. The G+C content of the DNA for strains R9SW1T and A3d10T were determined to be 57.1 mol% and 57.6 mol%, respectively. The two new strains share 97.6% of their 16S rRNA gene sequences, with 82.3% similarity in the average nucleotide identity (ANI), 19.8% similarity in the in silico genome-to-genome distance (GGD), 68.1% similarity in the average amino acid identity (AAI) of all conserved protein-coding genes, and 31 of the Karlin's genomic signature dissimilarity. A phylogenetic analysis showed that R9SW1T clusters with M. algicola DG893T sharing 99.40%, and A3d10T clusters with M. sediminum R65T sharing 99.53% of 16S rRNA gene sequence similarities. The results of the genomic and polyphasic taxonomic study, including genomic, genetic, phenotypic, chemotaxonomic and phylogenetic analyses based on the 16S rRNA, gyrB and rpoD gene sequence similarities, the analysis of the protein profiles generated using MALDI-TOF mass spectrometry, and DNA-DNA relatedness data, indicated that strains R9SW1T and A3d10(T) represent two novel species of the genus Marinobacter. The names Marinobacter salarius sp. nov., with the type strain R9SW1(T) ( = LMG 27497(T) = JCM 19399(T) = CIP 110588(T) = KMM 7502(T)) and Marinobacter similis sp. nov., with the type strain A3d10(T) ( = JCM 19398(T) = CIP 110589(T) = KMM 7501T), are proposed.
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Affiliation(s)
- Hooi Jun Ng
- Faculty of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, Victoria, Australia
| | | | - Hayden K. Webb
- Faculty of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, Victoria, Australia
| | - Daniela Gomez
- Faculty of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, Victoria, Australia
| | - Tomoo Sawabe
- Laboratory of Microbiology, Faculty of Fisheries, Hokkaido University, Minato-cho, Hakodate, Japan
| | - Jason Ryan
- Callaghan Innovation, Lower Hutt, Wellington, New Zealand
| | | | - Chantal Bizet
- Collection de 1’Institut Pasteur, Institut Pasteur, Paris, France
| | - François Malherbe
- Faculty of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, Victoria, Australia
| | - Valery V. Mikhailov
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry of the Far-Eastern Branch of the Russian Academy of Sciences, Vladivostok, Primorski Krai, Russian Federation
| | - Russell J. Crawford
- Faculty of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, Victoria, Australia
| | - Elena P. Ivanova
- Faculty of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, Victoria, Australia
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Liebensteiner MG, Tsesmetzis N, Stams AJM, Lomans BP. Microbial redox processes in deep subsurface environments and the potential application of (per)chlorate in oil reservoirs. Front Microbiol 2014; 5:428. [PMID: 25225493 PMCID: PMC4150442 DOI: 10.3389/fmicb.2014.00428] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Accepted: 07/29/2014] [Indexed: 12/15/2022] Open
Abstract
The ability of microorganisms to thrive under oxygen-free conditions in subsurface environments relies on the enzymatic reduction of oxidized elements, such as sulfate, ferric iron, or CO2, coupled to the oxidation of inorganic or organic compounds. A broad phylogenetic and functional diversity of microorganisms from subsurface environments has been described using isolation-based and advanced molecular ecological techniques. The physiological groups reviewed here comprise iron-, manganese-, and nitrate-reducing microorganisms. In the context of recent findings also the potential of chlorate and perchlorate [jointly termed (per)chlorate] reduction in oil reservoirs will be discussed. Special attention is given to elevated temperatures that are predominant in the deep subsurface. Microbial reduction of (per)chlorate is a thermodynamically favorable redox process, also at high temperature. However, knowledge about (per)chlorate reduction at elevated temperatures is still scarce and restricted to members of the Firmicutes and the archaeon Archaeoglobus fulgidus. By analyzing the diversity and phylogenetic distribution of functional genes in (meta)genome databases and combining this knowledge with extrapolations to earlier-made physiological observations we speculate on the potential of (per)chlorate reduction in the subsurface and more precisely oil fields. In addition, the application of (per)chlorate for bioremediation, souring control, and microbial enhanced oil recovery are addressed.
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Affiliation(s)
| | | | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University Wageningen, Netherlands ; Center of Biological Engineering, University of Minho Braga, Portugal
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Subramanian M, Srinivasan T, Sudarsanam D. Examining the Gm18 and m(1)G Modification Positions in tRNA Sequences. Genomics Inform 2014; 12:71-5. [PMID: 25031570 PMCID: PMC4099351 DOI: 10.5808/gi.2014.12.2.71] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Revised: 03/20/2014] [Accepted: 03/26/2014] [Indexed: 12/30/2022] Open
Abstract
The tRNA structure contains conserved modifications that are responsible for its stability and are involved in the initiation and accuracy of the translation process. tRNA modification enzymes are prevalent in bacteria, archaea, and eukaryotes. tRNA Gm18 methyltransferase (TrmH) and tRNA m1G37 methyltransferase (TrmD) are prevalent and essential enzymes in bacterial populations. TrmH involves itself in methylation process at the 2'-OH group of ribose at the 18th position of guanosine (G) in tRNAs. TrmD methylates the G residue next to the anticodon in selected tRNA subsets. Initially, m1G37 modification was reported to take place on three conserved tRNA subsets (tRNAArg, tRNALeu, tRNAPro); later on, few archaea and eukaryotes organisms revealed that other tRNAs also have the m1G37 modification. The present study reveals Gm18, m1G37 modification, and positions of m1G that take place next to the anticodon in tRNA sequences. We selected extremophile organisms and attempted to retrieve the m1G and Gm18 modification bases in tRNA sequences. Results showed that the Gm18 modification G residue occurs in all tRNA subsets except three tRNAs (tRNAMet, tRNAPro, tRNAVal). Whereas the m1G37 modification base G is formed only on tRNAArg, tRNALeu, tRNAPro, and tRNAHis, the rest of the tRNAs contain adenine (A) next to the anticodon. Thus, we hypothesize that Gm18 modification and m1G modification occur irrespective of a G residue in tRNAs.
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Affiliation(s)
- Mayavan Subramanian
- Synthetic Biology and Biofuel Group, International Center for Genetic Engineering and Biotechnology (ICGEB), New Delhi 110 067, India
| | - Thangavelu Srinivasan
- DST-FIST Bioinformatics and Principal Investigator, School of Genomics and Bioinformatics, Department of Advanced Zoology and Biotechnology, Loyola College, Chennai 600 034, India
| | - Dorairaj Sudarsanam
- DST-FIST Bioinformatics and Principal Investigator, School of Genomics and Bioinformatics, Department of Advanced Zoology and Biotechnology, Loyola College, Chennai 600 034, India
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Todorova NH, Mironova RS, Karamfilov VK. Comparative molecular analysis of bacterial communities inhabiting pristine and polluted with polycyclic aromatic hydrocarbons Black Sea coastal sediments. MARINE POLLUTION BULLETIN 2014; 83:231-240. [PMID: 24759506 DOI: 10.1016/j.marpolbul.2014.03.047] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 03/13/2014] [Accepted: 03/29/2014] [Indexed: 06/03/2023]
Abstract
Molecular analysis was applied to characterize bacterial community structure in sediment samples collected from pristine site and oil-polluted Black Sea harbor. Amplified Ribosomal DNA Restriction Analysis (ARDRA) revealed a high similarity in the restriction patterns of both samples thus not demonstrating the effect of the pollutant on the structure of the bacterial communities. Constructed 16S rRNA gene libraries gave more detailed assessment of members. Results showed that α- and γ-Proteobacteria were dominant in the oil polluted site, whereas the pristine site was characterized by prevalence of Actinobacteria. The biodegradative potential of the adapted bacterial community in the oil-polluted sediments was demonstrated by the presence of the aromatic ring hydroxylating dioxygenase genes.
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Affiliation(s)
- Nadezhda H Todorova
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Y. Gagarin 2 str., 1113 Sofia, Bulgaria.
| | - Roumyana S Mironova
- Institute of Molecular Biology "Roumen Tsanev", Bulgarian Academy of Sciences, G. Bonchev str., bl. 21, 1113 Sofia, Bulgaria.
| | - Ventzislav K Karamfilov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Y. Gagarin 2 str., 1113 Sofia, Bulgaria.
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Fathepure BZ. Recent studies in microbial degradation of petroleum hydrocarbons in hypersaline environments. Front Microbiol 2014; 5:173. [PMID: 24795705 PMCID: PMC4005966 DOI: 10.3389/fmicb.2014.00173] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 03/30/2014] [Indexed: 12/29/2022] Open
Abstract
Many hypersaline environments are often contaminated with petroleum compounds. Among these, oil and natural gas production sites all over the world and hundreds of kilometers of coastlines in the more arid regions of Gulf countries are of major concern due to the extent and magnitude of contamination. Because conventional microbiological processes do not function well at elevated salinities, bioremediation of hypersaline environments can only be accomplished using high salt-tolerant microorganisms capable of degrading petroleum compounds. In the last two decades, there have been many reports on the biodegradation of hydrocarbons in moderate to high salinity environments. Numerous microorganisms belonging to the domain Bacteria and Archaea have been isolated and their phylogeny and metabolic capacity to degrade a variety of aliphatic and aromatic hydrocarbons in varying salinities have been demonstrated. This article focuses on our growing understanding of bacteria and archaea responsible for the degradation of hydrocarbons under aerobic conditions in moderate to high salinity conditions. Even though organisms belonging to various genera have been shown to degrade hydrocarbons, members of the genera Halomonas Alcanivorax, Marinobacter, Haloferax, Haloarcula, and Halobacterium dominate the published literature. Despite rapid advances in understanding microbial taxa that degrade hydrocarbons under aerobic conditions, not much is known about organisms that carry out similar processes in anaerobic conditions. Also, information on molecular mechanisms and pathways of hydrocarbon degradation in high salinity is scarce and only recently there have been a few reports describing genes, enzymes and breakdown steps for some hydrocarbons. These limited studies have clearly revealed that degradation of oxygenated and non-oxygenated hydrocarbons by halophilic and halotolerant microorganisms occur by pathways similar to those found in non-halophiles.
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Affiliation(s)
- Babu Z Fathepure
- Department of Microbiology and Molecular Genetics, Oklahoma State University Stillwater, OK, USA
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Lamendella R, Strutt S, Borglin S, Chakraborty R, Tas N, Mason OU, Hultman J, Prestat E, Hazen TC, Jansson JK. Assessment of the Deepwater Horizon oil spill impact on Gulf coast microbial communities. Front Microbiol 2014; 5:130. [PMID: 24772107 PMCID: PMC3982105 DOI: 10.3389/fmicb.2014.00130] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 03/13/2014] [Indexed: 02/01/2023] Open
Abstract
One of the major environmental concerns of the Deepwater Horizon oil spill in the Gulf of Mexico was the ecological impact of the oil that reached shorelines of the Gulf Coast. Here we investigated the impact of the oil on the microbial composition in beach samples collected in June 2010 along a heavily impacted shoreline near Grand Isle, Louisiana. Successional changes in the microbial community structure due to the oil contamination were determined by deep sequencing of 16S rRNA genes. Metatranscriptomics was used to determine expression of functional genes involved in hydrocarbon degradation processes. In addition, potential hydrocarbon-degrading Bacteria were obtained in culture. The 16S data revealed that highly contaminated samples had higher abundances of Alpha- and Gammaproteobacteria sequences. Successional changes in these classes were observed over time, during which the oil was partially degraded. The metatranscriptome data revealed that PAH, n-alkane, and toluene degradation genes were expressed in the contaminated samples, with high homology to genes from Alteromonadales, Rhodobacterales, and Pseudomonales. Notably, Marinobacter (Gammaproteobacteria) had the highest representation of expressed genes in the samples. A Marinobacter isolated from this beach was shown to have potential for transformation of hydrocarbons in incubation experiments with oil obtained from the Mississippi Canyon Block 252 (MC252) well; collected during the Deepwater Horizon spill. The combined data revealed a response of the beach microbial community to oil contaminants, including prevalence of Bacteria endowed with the functional capacity to degrade oil.
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Affiliation(s)
- Regina Lamendella
- Lawrence Berkeley National Laboratory, Earth Sciences Division, Ecology Department Berkeley, CA, USA ; Biology Department, Juniata College Huntingdon, PA, USA
| | - Steven Strutt
- Biology Department, Juniata College Huntingdon, PA, USA
| | - Sharon Borglin
- Lawrence Berkeley National Laboratory, Earth Sciences Division, Ecology Department Berkeley, CA, USA
| | - Romy Chakraborty
- Lawrence Berkeley National Laboratory, Earth Sciences Division, Ecology Department Berkeley, CA, USA
| | - Neslihan Tas
- Lawrence Berkeley National Laboratory, Earth Sciences Division, Ecology Department Berkeley, CA, USA
| | - Olivia U Mason
- Lawrence Berkeley National Laboratory, Earth Sciences Division, Ecology Department Berkeley, CA, USA ; Department of Earth, Ocean and Atmospheric Science, Florida State University Tallahassee, FL, USA
| | - Jenni Hultman
- Lawrence Berkeley National Laboratory, Earth Sciences Division, Ecology Department Berkeley, CA, USA ; Department of Food Hygiene and Environmental Health, University of Helsinki Helsinki, Finland
| | - Emmanuel Prestat
- Lawrence Berkeley National Laboratory, Earth Sciences Division, Ecology Department Berkeley, CA, USA
| | - Terry C Hazen
- Lawrence Berkeley National Laboratory, Earth Sciences Division, Ecology Department Berkeley, CA, USA ; Department of Civil and Environmental Engineering, University of Tennessee Knoxville, TN, USA ; Oak Ridge National Laboratory, Biosciences Division Oak Ridge, TN, USA
| | - Janet K Jansson
- Lawrence Berkeley National Laboratory, Earth Sciences Division, Ecology Department Berkeley, CA, USA ; Department of Energy, Joint Genome Institute Walnut Creek, CA, USA
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Statistical Optimization of Crude Oil Biodegradation by Marinobacter sp. Isolated from Qeshm Island, Iran. IRANIAN JOURNAL OF BIOTECHNOLOGY 2014. [DOI: 10.5812/ijb.15392] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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