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Karnachuk OV, Panova IA, Rusanov II, Schetinina L, Lepokurova OY, Domrocheva EV, Kadnikov VV, Avakyan MR, Lukina AP, Glukhova LB, Pimenov NV, Ravin NV. Coexistence of Psychrophilic, Mesophilic, and Thermophilic Sulfate-Reducing Bacteria in a Deep Subsurface Aquifer Associated with Coal-Bed Methane Production. MICROBIAL ECOLOGY 2023; 86:1934-1946. [PMID: 36821051 DOI: 10.1007/s00248-023-02196-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 02/11/2023] [Indexed: 06/18/2023]
Abstract
The microbial community of subsurface environments remains understudied due to limited access to deep strata and aquifers. Coal-bed methane (CBM) production is associated with a large number of wells pumping water out of coal seams. CBM wells provide access to deep biotopes associated with coal-bed water. Temperature is one of the key constraints for the distribution and activity of subsurface microorganisms, including sulfate-reducing prokaryotes (SRP). The 16S rRNA gene amplicon sequencing coupled with in situ sulfate reduction rate (SRR) measurements with a radioactive tracer and cultivation at various temperatures revealed that the SRP community of the coal bed water of the Kuzbass coal basin is characterized by an overlapping mesophilic-psychrophilic boundary. The genus Desulfovibrio comprised a significant share of the SRP community. The D. psychrotolerans strain 1203, which has a growth optimum below 20 °C, dominated the cultivated SRP. SRR in coal bed water varied from 0.154 ± 0.07 to 2.04 ± 0.048 nmol S cm-3 day-1. Despite the ambient water temperature of ~ 10-20 °C, an active thermophilic SRP community occurred in the fracture water, which reduced sulfate with the rate of 0.159 ± 0.023 to 0.198 ± 0.007 nmol S cm-3 day-1 at 55 °C. A novel moderately thermophilic "Desulforudis audaxviator"-clade SRP has been isolated in pure culture from the coal-bed water.
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Affiliation(s)
- Olga V Karnachuk
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, 634050, Russia.
| | - Inna A Panova
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, 634050, Russia
| | - Igor I Rusanov
- Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | - Lilia Schetinina
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, 634050, Russia
| | - Olesya Y Lepokurova
- Tomsk Branch of the Trofimuk Institute of Petroleum Geology and Geophysics in the Siberian Branch of the Russian Academy of Sciences, Akademicheskiy 4, 634055, Tomsk, Russia
| | - Evgenia V Domrocheva
- Tomsk Branch of the Trofimuk Institute of Petroleum Geology and Geophysics in the Siberian Branch of the Russian Academy of Sciences, Akademicheskiy 4, 634055, Tomsk, Russia
| | - Vitaly V Kadnikov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prosp, Bld. 33‑2, Moscow, Russia, 119071
| | - Marat R Avakyan
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, 634050, Russia
| | - Anstasia P Lukina
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, 634050, Russia
| | - Liubov B Glukhova
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, 634050, Russia
| | - Nikolai V Pimenov
- Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | - Nikolai V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prosp, Bld. 33‑2, Moscow, Russia, 119071
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Evolutionary stasis of a deep subsurface microbial lineage. THE ISME JOURNAL 2021; 15:2830-2842. [PMID: 33824425 PMCID: PMC8443664 DOI: 10.1038/s41396-021-00965-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 02/26/2021] [Accepted: 03/15/2021] [Indexed: 02/01/2023]
Abstract
Sulfate-reducing bacteria Candidatus Desulforudis audaxviator (CDA) were originally discovered in deep fracture fluids accessed via South African gold mines and have since been found in geographically widespread deep subsurface locations. In order to constrain models for subsurface microbial evolution, we compared CDA genomes from Africa, North America and Eurasia using single cell genomics. Unexpectedly, 126 partial single amplified genomes from the three continents, a complete genome from of an isolate from Eurasia, and metagenome-assembled genomes from Africa and Eurasia shared >99.2% average nucleotide identity, low frequency of SNP's, and near-perfectly conserved prophages and CRISPRs. Our analyses reject sample cross-contamination, recent natural dispersal, and unusually strong purifying selection as likely explanations for these unexpected results. We therefore conclude that the analyzed CDA populations underwent only minimal evolution since their physical separation, potentially as far back as the breakup of Pangea between 165 and 55 Ma ago. High-fidelity DNA replication and repair mechanisms are the most plausible explanation for the highly conserved genome of CDA. CDA presents a stark contrast to the current model organisms in microbial evolutionary studies, which often develop adaptive traits over far shorter periods of time.
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Panova IA, Grigoriev MA, Glukhova LB, Avakyan MR, Karnachuk OV. Isolation of a Novel Chemolithothrophic Sulfate-Reducing Firmicute from a Tyumen Thermal Borehole. Microbiology (Reading) 2021. [DOI: 10.1134/s0026261721030097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Lukina AP, Avakyan MR, Danilova EV, Karnachuk OV. Application of Microbial Mats for the Isolation of Spore-Forming Prokaryotes from Deep Biosphere. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720060120] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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5
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Chemical Clogging and Evolution of Head Losses in Steel Slag Filters Used for Phosphorus Removal. WATER 2020. [DOI: 10.3390/w12061517] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The objective of this study was to propose a conceptual model of clogging in alkaline granular filters. Two slag columns were operated for 600 days and monitored using piezometers and tracer tested at regular intervals. The type of influent (organic or inorganic) affected the loss of effective porosity in the filters. Well organized and loose crystal structures were observed by scanning electron microscopy in columns with inorganic and organic influents, respectively. It was postulated that the formation of crystals in unorganized structures results in confined voids that are not accessible for water flow, thus accelerating porosity loss. The effect of the combination of chemical clogging and biofilm on the porosity loss is higher than the effect of these two factors separately. The Kozeny-Carman equation for hydraulic conductivity could not efficiently predict the evolution of head losses in the column fed with an inorganic influent. The crystal structure and connectivity in the presence of homogeneous or heterogeneous precipitation are concepts that could improve predictions of hydraulic conductivity. The results of this study highlighted the importance of the inlet zone on the development of pressure head in alkaline granular filters. Future research on clogging should focus on precipitation mechanisms in the inlet zone and on the design of the feeding system.
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Hamilton-Brehm SD, Stewart LE, Zavarin M, Caldwell M, Lawson PA, Onstott TC, Grzymski J, Neveux I, Lollar BS, Russell CE, Moser DP. Thermoanaerosceptrum fracticalcis gen. nov. sp. nov., a Novel Fumarate-Fermenting Microorganism From a Deep Fractured Carbonate Aquifer of the US Great Basin. Front Microbiol 2019; 10:2224. [PMID: 31611860 PMCID: PMC6776889 DOI: 10.3389/fmicb.2019.02224] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 09/11/2019] [Indexed: 12/16/2022] Open
Abstract
Deep fractured rock ecosystems across most of North America have not been studied extensively. However, the US Great Basin, in particular the Nevada National Security Site (NNSS, formerly the Nevada Test Site), has hosted a number of influential subsurface investigations over the years. This investigation focuses on resident microbiota recovered from a hydrogeologically confined aquifer in fractured Paleozoic carbonate rocks at 863 - 923 meters below land surface. Analysis of the microorganisms living in this oligotrophic environment provides a perspective into microbial metabolic strategies required to endure prolonged hydrogeological isolation deep underground. Here we present a microbiological and physicochemical characterization of a deep continental carbonate ecosystem and describe a bacterial genus isolated from the ecosystem. Strain DRI-13T is a strictly anaerobic, moderately thermophilic, fumarate-respiring member of the phylum Firmicutes. This bacterium grows optimally at 55°C and pH 8.0, can tolerate a concentration of 100 mM NaCl, and appears to obligately metabolize fumarate to acetate and succinate. Culture-independent 16S rRNA gene sequencing indicates a global subsurface distribution, while the closest cultured relatives of DRI-13T are Pelotomaculum thermopropionicum (90.0% similarity) and Desulfotomaculum gibsoniae (88.0% similarity). The predominant fatty acid profile is iso-C15 : 0, C15 : 0, C16 : 0 and C14 : 0. The percentage of the straight-chain fatty acid C15 : 0 is a defining characteristic not present in the other closely related species. The genome is estimated to be 3,649,665 bp, composed of 87.3% coding regions with an overall average of 45.1% G + C content. Strain DRI-13T represents a novel genus of subsurface bacterium isolated from a previously uncharacterized rock-hosted geothermal habitat. The characterization of the bacterium combined with the sequenced genome provides insights into metabolism strategies of the deep subsurface biosphere. Based on our characterization analysis we propose the name Thermoanaerosceptrum fracticalcis (DRI-13T = DSM 100382T = ATCC TSD-12T).
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Affiliation(s)
- Scott D. Hamilton-Brehm
- Division of Earth and Ecosystems Sciences, Desert Research Institute, Las Vegas, NV, United States
- Department of Microbiology, Southern Illinois University Carbondale, Carbondale, IL, United States
| | | | - Mavrik Zavarin
- Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Matt Caldwell
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Paul A. Lawson
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Tullis C. Onstott
- Department of Geosciences, Princeton University, Princeton, NJ, United States
| | - Joseph Grzymski
- Division of Earth and Ecosystems Sciences, Desert Research Institute, Las Vegas, NV, United States
| | - Iva Neveux
- Division of Earth and Ecosystems Sciences, Desert Research Institute, Las Vegas, NV, United States
| | | | - Charles E. Russell
- Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, NV, United States
| | - Duane P. Moser
- Division of Earth and Ecosystems Sciences, Desert Research Institute, Las Vegas, NV, United States
- Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, NV, United States
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Domestication of previously uncultivated Candidatus Desulforudis audaxviator from a deep aquifer in Siberia sheds light on its physiology and evolution. ISME JOURNAL 2019; 13:1947-1959. [PMID: 30899075 DOI: 10.1038/s41396-019-0402-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 02/07/2019] [Accepted: 02/28/2019] [Indexed: 11/09/2022]
Abstract
An enigmatic uncultured member of Firmicutes, Candidatus Desulforudis audaxviator (CDA), is known by its genome retrieved from the deep gold mine in South Africa, where it formed a single-species ecosystem fuelled by hydrogen from water radiolysis. It was believed that in situ conditions CDA relied on scarce energy supply and did not divide for hundreds to thousand years. We have isolated CDA strain BYF from a 2-km-deep aquifer in Western Siberia and obtained a laboratory culture growing with a doubling time of 28.5 h. BYF uses not only H2 but also various organic electron donors for sulfate respiration. Growth required elemental iron, and ferrous iron did not substitute for it. A complex intracellular organization included gas vesicles, internal membranes, and electron-dense structures enriched in phosphorus, iron, and calcium. Genome comparison of BYF with the South African CDA revealed minimal differences mostly related to mobile elements and prophage insertions. Two genomes harbored <800 single-nucleotide polymorphisms and had nearly identical CRISPR loci. We suggest that spores with the gas vesicles may facilitate global distribution of CDA followed by colonization of suitable subsurface environments. Alternatively, a slow evolution rate in the deep subsurface could result in high genetic similarity of CDA populations at two sites spatially separated for hundreds of millions of years.
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Prisilla A, Deena Remin M, Roja B, Chellapandi P. A human-food web-animal interface on the prevalence of food-borne pathogens (Clostridia and Enterococcus) in mixed veterinary farms. Food Sci Biotechnol 2019; 28:1583-1591. [PMID: 31695959 DOI: 10.1007/s10068-019-00595-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 01/25/2019] [Accepted: 02/25/2019] [Indexed: 10/27/2022] Open
Abstract
In the present work, we addressed the impact of a human-food web-animal interface on the prevalence of food-borne pathogens in mixed farms of Tamil Nadu, India. We have isolated and identified six strains of Clostridium sp. and five strains of Enterococcus sp. from food and animal sources disposed near to the veterinary and poultry farms. Phylogenetic relationships of these strains were inferred from their homologies in 16S rDNA sequences and rRNA secondary structures. The strain PCP07 was taxonomically equivalent to C. botulinum confirmed by neurotoxin-specific PCR primers, followed by mouse bioassay. Other Clostridial and Enterococcal isolates have shown a phylogenetic similarity to the C. bifermentans and E. durans isolated from veterinary farms, respectively. Results of our study revealed that a human-food web-animal interface has influenced the disease incidence and prevalence of these isolates in the poultry to veterinary farms, where human food acted as a likely transmittance vehicle for their infections.
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Affiliation(s)
- A Prisilla
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu 620 024 India
| | - M Deena Remin
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu 620 024 India
| | - B Roja
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu 620 024 India
| | - P Chellapandi
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu 620 024 India
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Bhattacharjee AS, Motlagh AM, Gilcrease EB, Islam MI, Casjens SR, Goel R. Complete genome sequence of lytic bacteriophage RG-2014 that infects the multidrug resistant bacterium Delftia tsuruhatensis ARB-1. Stand Genomic Sci 2017; 12:82. [PMID: 29270250 PMCID: PMC5735904 DOI: 10.1186/s40793-017-0290-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 11/24/2017] [Indexed: 01/10/2023] Open
Abstract
A lytic bacteriophage RG-2014 infecting a biofilm forming multidrug resistant bacterium Delftia tsuruhatensis strain ARB-1 as its host was isolated from a full-scale municipal wastewater treatment plant. Lytic phage RG-2014 was isolated for developing phage based therapeutic approaches against Delftia tsuruhatensis strain ARB-1. The strain ARB-1 belongs to the Comamonadaceae family of the Betaproteobacteria class. RG-2014 was characterized for its type, burst size, latent and eclipse time periods of 150 ± 9 PFU/cell, 10-min, <5-min, respectively. The phage was found to be a dsDNA virus belonging to the Podoviridae family. It has an isometric icosahedrally shaped capsid with a diameter of 85 nm. The complete genome of the isolated phage was sequenced and determined to be 73.8 kbp in length with a G + C content of 59.9%. Significant similarities in gene homology and order were observed between Delftia phage RG-2014 and the E. coli phage N4 indicating that it is a member of the N4-like phage group.
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Affiliation(s)
- Ananda Shankar Bhattacharjee
- Department of Civil and Environmental Engineering, University of Utah, Salt Lake City, UT USA.,Bigelow Laboratory for Ocean Science, 60 Bigelow Dr., East Boothbay, ME USA
| | - Amir Mohaghegh Motlagh
- Department of Civil and Environmental Engineering, University of Utah, Salt Lake City, UT USA.,Department of Civil, Environmental, and Construction Engineering, University of Central Florida, 12800 Pegasus Dr., Room 340, Orlando, FL USA
| | - Eddie B Gilcrease
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Md Imdadul Islam
- Department of Civil and Environmental Engineering, University of Utah, Salt Lake City, UT USA
| | - Sherwood R Casjens
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, UT USA.,Department of Biology, University of Utah, Salt Lake City, UT USA
| | - Ramesh Goel
- Department of Civil and Environmental Engineering, University of Utah, Salt Lake City, UT USA
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Li X, Duan J, Xiao H, Li Y, Liu H, Guan F, Zhai X. Analysis of Bacterial Community Composition of Corroded Steel Immersed in Sanya and Xiamen Seawaters in China via Method of Illumina MiSeq Sequencing. Front Microbiol 2017; 8:1737. [PMID: 28955315 PMCID: PMC5601074 DOI: 10.3389/fmicb.2017.01737] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 08/25/2017] [Indexed: 11/23/2022] Open
Abstract
Metal corrosion is of worldwide concern because it is the cause of major economic losses, and because it creates significant safety issues. The mechanism of the corrosion process, as influenced by bacteria, has been studied extensively. However, the bacterial communities that create the biofilms that form on metals are complicated, and have not been well studied. This is why we sought to analyze the composition of bacterial communities living on steel structures, together with the influence of ecological factors on these communities. The corrosion samples were collected from rust layers on steel plates that were immersed in seawater for two different periods at Sanya and Xiamen, China. We analyzed the bacterial communities on the samples by targeted 16S rRNA gene (V3–V4 region) sequencing using the Illumina MiSeq. Phylogenetic analysis revealed that the bacteria fell into 13 phylotypes (similarity level = 97%). Proteobacteria, Firmicutes and Bacteroidetes were the dominant phyla, accounting for 88.84% of the total. Deltaproteobacteria, Clostridia and Gammaproteobacteria were the dominant classes, and accounted for 70.90% of the total. Desulfovibrio spp., Desulfobacter spp. and Desulfotomaculum spp. were the dominant genera and accounted for 45.87% of the total. These genera are sulfate-reducing bacteria that are known to corrode steel. Bacterial diversity on the 6 months immersion samples was much higher than that of the samples that had been immersed for 8 years (P < 0.001, Student’s t-test). The average complexity of the biofilms from the 8-years immersion samples from Sanya was greater than those from Xiamen, but not significantly so (P > 0.05, Student’s t-test). Overall, the data showed that the rust layers on the steel plates carried many bacterial species. The bacterial community composition was influenced by the immersion time. The results of our study will be of benefit to the further studies of bacterial corrosion mechanisms and corrosion resistance.
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Affiliation(s)
- Xiaohong Li
- Key Laboratory of Marine Environmental Corrosion and Biofouling, Institute of Oceanology, Chinese Academy of SciencesQingdao, China.,College of Marine Life Sciences, Ocean University of ChinaQingdao, China
| | - Jizhou Duan
- Key Laboratory of Marine Environmental Corrosion and Biofouling, Institute of Oceanology, Chinese Academy of SciencesQingdao, China
| | - Hui Xiao
- College of Marine Life Sciences, Ocean University of ChinaQingdao, China
| | - Yongqian Li
- Key Laboratory of Marine Environmental Corrosion and Biofouling, Institute of Oceanology, Chinese Academy of SciencesQingdao, China.,College of Marine Life Sciences, Ocean University of ChinaQingdao, China
| | - Haixia Liu
- Key Laboratory of Marine Environmental Corrosion and Biofouling, Institute of Oceanology, Chinese Academy of SciencesQingdao, China
| | - Fang Guan
- Key Laboratory of Marine Environmental Corrosion and Biofouling, Institute of Oceanology, Chinese Academy of SciencesQingdao, China
| | - Xiaofan Zhai
- Key Laboratory of Marine Environmental Corrosion and Biofouling, Institute of Oceanology, Chinese Academy of SciencesQingdao, China
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Chow J, Kovacic F, Dall Antonia Y, Krauss U, Fersini F, Schmeisser C, Lauinger B, Bongen P, Pietruszka J, Schmidt M, Menyes I, Bornscheuer UT, Eckstein M, Thum O, Liese A, Mueller-Dieckmann J, Jaeger KE, Streit WR. The metagenome-derived enzymes LipS and LipT increase the diversity of known lipases. PLoS One 2012; 7:e47665. [PMID: 23112831 PMCID: PMC3480424 DOI: 10.1371/journal.pone.0047665] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 09/13/2012] [Indexed: 11/18/2022] Open
Abstract
Triacylglycerol lipases (EC 3.1.1.3) catalyze both hydrolysis and synthesis reactions with a broad spectrum of substrates rendering them especially suitable for many biotechnological applications. Most lipases used today originate from mesophilic organisms and are susceptible to thermal denaturation whereas only few possess high thermotolerance. Here, we report on the identification and characterization of two novel thermostable bacterial lipases identified by functional metagenomic screenings. Metagenomic libraries were constructed from enrichment cultures maintained at 65 to 75 °C and screened resulting in the identification of initially 10 clones with lipolytic activities. Subsequently, two ORFs were identified encoding lipases, LipS and LipT. Comparative sequence analyses suggested that both enzymes are members of novel lipase families. LipS is a 30.2 kDa protein and revealed a half-life of 48 h at 70 °C. The lipT gene encoded for a multimeric enzyme with a half-life of 3 h at 70 °C. LipS had an optimum temperature at 70 °C and LipT at 75 °C. Both enzymes catalyzed hydrolysis of long-chain (C(12) and C(14)) fatty acid esters and additionally hydrolyzed a number of industry-relevant substrates. LipS was highly specific for (R)-ibuprofen-phenyl ester with an enantiomeric excess (ee) of 99%. Furthermore, LipS was able to synthesize 1-propyl laurate and 1-tetradecyl myristate at 70 °C with rates similar to those of the lipase CalB from Candida antarctica. LipS represents the first example of a thermostable metagenome-derived lipase with significant synthesis activities. Its X-ray structure was solved with a resolution of 1.99 Å revealing an unusually compact lid structure.
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Affiliation(s)
- Jennifer Chow
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, University of Hamburg, Hamburg, Germany
| | - Filip Kovacic
- Institute of Molecular Enzyme Technology, Heinrich Heine University Duesseldorf, Research Center Juelich, Juelich, Germany
| | - Yuliya Dall Antonia
- European Molecular Biology Laboratory (EMBL) Hamburg Outstation, c/o Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Ulrich Krauss
- Institute of Molecular Enzyme Technology, Heinrich Heine University Duesseldorf, Research Center Juelich, Juelich, Germany
| | - Francesco Fersini
- European Molecular Biology Laboratory (EMBL) Hamburg Outstation, c/o Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Christel Schmeisser
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, University of Hamburg, Hamburg, Germany
| | - Benjamin Lauinger
- Institute of Bioorganic Chemistry, Heinrich Heine University Duesseldorf, Research Center Juelich, Juelich, Germany
| | - Patrick Bongen
- Institute of Bioorganic Chemistry, Heinrich Heine University Duesseldorf, Research Center Juelich, Juelich, Germany
| | - Joerg Pietruszka
- Institute of Bioorganic Chemistry, Heinrich Heine University Duesseldorf, Research Center Juelich, Juelich, Germany
| | - Marlen Schmidt
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Greifswald, Germany
| | - Ina Menyes
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Greifswald, Germany
| | - Uwe T. Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Greifswald, Germany
| | - Marrit Eckstein
- Bioprocess Development Consumer Specialties and Biocatalysis Biotechnology, Evonik Industries AG, Essen, Germany
| | - Oliver Thum
- Bioprocess Development Consumer Specialties and Biocatalysis Biotechnology, Evonik Industries AG, Essen, Germany
| | - Andreas Liese
- Institute of Technical Biocatalysis, Hamburg University of Technology, Hamburg, Germany
| | - Jochen Mueller-Dieckmann
- European Molecular Biology Laboratory (EMBL) Hamburg Outstation, c/o Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Duesseldorf, Research Center Juelich, Juelich, Germany
| | - Wolfgang R. Streit
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, University of Hamburg, Hamburg, Germany
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12
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Marty F, Ghiglione JF, Païssé S, Gueuné H, Quillet L, van Loosdrecht MCM, Muyzer G. Evaluation and optimization of nucleic acid extraction methods for the molecular analysis of bacterial communities associated with corroded carbon steel. BIOFOULING 2012; 28:363-380. [PMID: 22500778 DOI: 10.1080/08927014.2012.672644] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Different DNA and RNA extraction approaches were evaluated and protocols optimized on in situ corrosion products from carbon steel in marine environments. Protocols adapted from the PowerSoil DNA/RNA Isolation methods resulted in the best nucleic acid (NA) extraction performances (ie combining high NA yield, quality, purity, representativeness of microbial community and processing time efficiency). The PowerSoil RNA Isolation Kit was the only method which resulted in amplifiable RNA of good quality (ie intact 16S/23S rRNA). Sample homogenization and hot chemical (SDS) cell lysis combined with mechanical (bead-beating) lysis in presence of a DNA competitor (skim milk) contributed to improving substantially (around 23 times) the DNA yield of the PowerSoil DNA Isolation Kit. Apart from presenting NA extraction strategies for optimizing extraction parameters with corrosion samples from carbon steel, this study proposes DNA and RNA extraction procedures suited for comparative molecular analysis of total and active fractions of bacterial communities associated with carbon steel corrosion events, thereby contributing to improved MIC diagnosis and control.
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Affiliation(s)
- Florence Marty
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
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13
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Schleheck D, Weiss M, Pitluck S, Bruce D, Land ML, Han S, Saunders E, Tapia R, Detter C, Brettin T, Han J, Woyke T, Goodwin L, Pennacchio L, Nolan M, Cook AM, Kjelleberg S, Thomas T. Complete genome sequence of Parvibaculum lavamentivorans type strain (DS-1(T)). Stand Genomic Sci 2011; 5:298-310. [PMID: 22675581 PMCID: PMC3368416 DOI: 10.4056/sigs.2215005] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Parvibaculum lavamentivorans DS-1(T) is the type species of the novel genus Parvibaculum in the novel family Rhodobiaceae (formerly Phyllobacteriaceae) of the order Rhizobiales of Alphaproteobacteria. Strain DS-1(T) is a non-pigmented, aerobic, heterotrophic bacterium and represents the first tier member of environmentally important bacterial communities that catalyze the complete degradation of synthetic laundry surfactants. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,914,745 bp long genome with its predicted 3,654 protein coding genes is the first completed genome sequence of the genus Parvibaculum, and the first genome sequence of a representative of the family Rhodobiaceae.
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Affiliation(s)
- David Schleheck
- Department of Biological Sciences and Research School Chemical Biology, University of Konstanz, Germany
| | - Michael Weiss
- Department of Biological Sciences and Research School Chemical Biology, University of Konstanz, Germany
| | - Sam Pitluck
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - David Bruce
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Miriam L. Land
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Shunsheng Han
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Elizabeth Saunders
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Roxanne Tapia
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Chris Detter
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Thomas Brettin
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - James Han
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Lynne Goodwin
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Len Pennacchio
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Matt Nolan
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Alasdair M. Cook
- Department of Biological Sciences and Research School Chemical Biology, University of Konstanz, Germany
| | - Staffan Kjelleberg
- Centre for Marine Bio-Innovation and School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, Australia
| | - Torsten Thomas
- Centre for Marine Bio-Innovation and School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, Australia
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14
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Oliveira VM, Lopes-Oliveira PF, Passarini MRZ, Menezes CBA, Oliveira WRC, Rocha AJ, Sette LD. Molecular analysis of microbial diversity in corrosion samples from energy transmission towers. BIOFOULING 2011; 27:435-447. [PMID: 21563009 DOI: 10.1080/08927014.2011.581751] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Microbial diversity in corrosion samples from energy transmission towers was investigated using molecular methods. Ribosomal DNA fragments were used to assemble gene libraries. Sequence analysis indicated 10 bacterial genera within the phyla Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. In the two libraries generated from corroded screw-derived samples, the genus Acinetobacter was the most abundant. Acinetobacter and Clostridium spp. dominated, with similar percentages, in the libraries derived from corrosion scrapings. Fungal clones were affiliated with 14 genera belonging to the phyla Ascomycota and Basidiomycota; of these, Capnobotryella and Fellomyces were the most abundant fungi observed. Several of the microorganisms had not previously been associated with biofilms and corrosion, reinforcing the need to use molecular techniques to achieve a more comprehensive assessment of microbial diversity in environmental samples.
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Affiliation(s)
- Valéria M Oliveira
- Divisão de Recursos Microbianos, CPQBA/UNICAMP, CP 6171, Campinas, Brazil.
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15
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Schwermer CU, Ferdelman TG, Stief P, Gieseke A, Rezakhani N, van Rijn J, de Beer D, Schramm A. Effect of nitrate on sulfur transformations in sulfidogenic sludge of a marine aquaculture biofilter. FEMS Microbiol Ecol 2010; 72:476-84. [PMID: 20402774 DOI: 10.1111/j.1574-6941.2010.00865.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The effect of NO(3)(-) addition on dissimilatory SO(4)(2-) reduction and sulfide conversion in organic-rich sludge from the digestion basin of a recirculating marine aquaculture system was studied. SO(4)(2-) reduction could only explain a minor fraction (up to 4-9%) of the observed total sulfide production (up to 35 mmol L(-1) day(-1)), indicating that the main source of sulfide in the sludge was not SO(4)(2-) reduction, but desulfuration during the decomposition of organic matter. Although NO(3)(-) inhibited SO(4)(2-) reduction, but not desulfuration, the primary NO(3)(-) mitigation effect was the onset of NO(3)(-)-mediated sulfide oxidation (up to 75 mmol L(-1) day(-1)), partially to elemental sulfur (S(0)). Above NO(3)(-) concentrations of 0.6 mM in the bulk water, the net sulfide production and oxidation zones were moved deeper into flocs and sludge cores, which effectively prevented sulfide from entering the water column. However, the sulfide efflux from the sludge instantly recovered after NO(3)(-) depletion. Thus, the NO(3)(-) level in the water column controls the zonation and magnitude of sulfur transformations in the sludge. The effect of NO(3)(-) relies therefore on its sustained presence in the water column, which in turn depends on a well-functioning nitrification in the mariculture system.
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16
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Gerasimchuk AL, Shatalov AA, Novikov AL, Butorova OP, Pimenov NV, Lein AY, Yanenko AS, Karnachuk OV. The search for sulfate-reducing bacteria in mat samples from the lost city hydrothermal field by molecular cloning. Microbiology (Reading) 2010. [DOI: 10.1134/s0026261710010133] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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17
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Kjellerup BV, Kjeldsen KU, Lopes F, Abildgaard L, Ingvorsen K, Frølund B, Sowers KR, Nielsen PH. Biocorrosion and biofilm formation in a nutrient limited heating system subjected to alternating microaerophilic conditions. BIOFOULING 2009; 25:727-737. [PMID: 20183131 DOI: 10.1080/08927010903114611] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Severe biofilm formation and biocorrosion have been observed in heating systems even when the water quality complied with existing standards. The coupling between water chemistry, biofilm formation, species composition, and biocorrosion in a heating system was investigated by adding low concentrations of nutrients and oxygen under continuous and alternating dosing regimes. Molecular analysis of 16S rRNA gene fragments demonstrated that the amendments did not cause changes in the overall bacterial community composition. The combined alternating dosing of nutrients and oxygen caused increased rates of pitting (bio-) corrosion. Detection of bacteria involved in sulfide production and oxidation by retrieval of the functional dsrAB and apsA genes revealed the presence of Gram-positive sulfate- and sulfite-reducers and an unknown sulfur-oxidizer. Therefore, to control biocorrosion, sources of oxygen and nutrients must be limited, since the effect of the alternating operational conditions apparently is more important than the presence of potentially corrosive biofilm bacteria.
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Affiliation(s)
- B V Kjellerup
- Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Denmark.
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18
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Gittel A, Sørensen KB, Skovhus TL, Ingvorsen K, Schramm A. Prokaryotic community structure and sulfate reducer activity in water from high-temperature oil reservoirs with and without nitrate treatment. Appl Environ Microbiol 2009; 75:7086-96. [PMID: 19801479 PMCID: PMC2786513 DOI: 10.1128/aem.01123-09] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2009] [Accepted: 09/22/2009] [Indexed: 11/20/2022] Open
Abstract
Sulfate-reducing prokaryotes (SRP) cause severe problems like microbial corrosion and reservoir souring in seawater-injected oil production systems. One strategy to control SRP activity is the addition of nitrate to the injection water. Production waters from two adjacent, hot (80 degrees C) oil reservoirs, one with and one without nitrate treatment, were compared for prokaryotic community structure and activity of SRP. Bacterial and archaeal 16S rRNA gene analyses revealed higher prokaryotic abundance but lower diversity for the nitrate-treated field. The 16S rRNA gene clone libraries from both fields were dominated by sequences affiliated with Firmicutes (Bacteria) and Thermococcales (Archaea). Potential heterotrophic nitrate reducers (Deferribacterales) were exclusively found at the nitrate-treated field, possibly stimulated by nitrate addition. Quantitative PCR of dsrAB genes revealed that archaeal SRP (Archaeoglobus) dominated the SRP communities, but with lower relative abundance at the nitrate-treated site. Bacterial SRP were found in only low abundance at both sites and were nearly exclusively affiliated with thermophilic genera (Desulfacinum and Desulfotomaculum). Despite the high abundance of archaeal SRP, no archaeal SRP activity was detected in [(35)S]sulfate incubations at 80 degrees C. Sulfate reduction was found at 60 degrees C in samples from the untreated field and accompanied by the growth of thermophilic bacterial SRP in batch cultures. Samples from the nitrate-treated field generally lacked SRP activity. These results indicate that (i) Archaeoglobus can be a major player in hot oil reservoirs, and (ii) nitrate may act in souring control-not only by inhibiting SRP, but also by changing the overall community structure, including the stimulation of competitive nitrate reducers.
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Affiliation(s)
- Antje Gittel
- Department of Biological Sciences, Microbiology, Aarhus University, Ny Munkegade 114, DK-8000 Aarhus C, Denmark.
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19
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Kjeldsen KU, Tang L, Jørgensen MG, Ingvorsen K. Enumeration and identification of dominant types of sulfate-reducing bacteria in pulp from a paper-recycling plant: a multiphasic approach. FEMS Microbiol Ecol 2009; 69:481-94. [DOI: 10.1111/j.1574-6941.2009.00715.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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20
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Gittel A, Seidel M, Kuever J, Galushko AS, Cypionka H, Könneke M. Desulfopila inferna sp. nov., a sulfate-reducing bacterium isolated from the subsurface of a tidal sand-flat. Int J Syst Evol Microbiol 2009; 60:1626-1630. [PMID: 19717583 DOI: 10.1099/ijs.0.015644-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, rod-shaped, sulfate-reducing bacterium (strain JS_SRB250Lac(T)) was isolated from a tidal sand-flat in the German Wadden Sea. 16S rRNA gene sequence analysis showed that strain JS_SRB250Lac(T) belonged to the Desulfobulbaceae (Deltaproteobacteria), with Desulfopila aestuarii MSL86(T) being the closest recognized relative (94.2 % similarity). Higher similarity (96.6 %) was shared with 'Desulfobacterium corrodens' IS4, but this name has not been validly published. The affiliation of strain JS_SRB250Lac(T) to the genus Desulfopila was further supported by analysis of aprBA gene sequences and shared physiological characteristics, in particular the broad range of organic electron donors used for sulfate reduction. Compared with Desulfopila aestuarii MSL86(T), strain JS_SRB250Lac(T) additionally utilized butyrate and succinate and grew chemolithoautotrophically with hydrogen as an electron donor. CO dehydrogenase activity was demonstrated, indicating that the reductive acetyl-CoA pathway (Wood-Ljungdahl pathway) was used for CO(2) fixation. Results of cellular fatty acid analysis allowed chemotaxonomic differentiation of strain JS_SRB250Lac(T) from Desulfopila aestuarii MSL86(T) by the presence of C(17 : 0) cyclo and the absence of hydroxy and unsaturated branched-chain fatty acids. Based on phylogenetic, physiological and chemotaxonomic characteristics, strain JS_SRB250Lac(T) represents a novel species of the genus Desulfopila, for which the name Desulfopila inferna sp. nov. is proposed. The type strain is JS_SRB250Lac(T) (=DSM 19738(T) =NBRC 103921(T)).
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Affiliation(s)
- Antje Gittel
- Institut für Chemie und Biologie des Meeres, Universität Oldenburg, Carl von Ossietzky-Strasse 9-11, Postfach 2503, D-26111 Oldenburg, Germany
| | - Michael Seidel
- Institut für Chemie und Biologie des Meeres, Universität Oldenburg, Carl von Ossietzky-Strasse 9-11, Postfach 2503, D-26111 Oldenburg, Germany
| | - Jan Kuever
- Bremen Institute for Materials Testing, Paul-Feller-Strasse 1, D-28199 Bremen, Germany
| | - Alexander S Galushko
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany
| | - Heribert Cypionka
- Institut für Chemie und Biologie des Meeres, Universität Oldenburg, Carl von Ossietzky-Strasse 9-11, Postfach 2503, D-26111 Oldenburg, Germany
| | - Martin Könneke
- Institut für Chemie und Biologie des Meeres, Universität Oldenburg, Carl von Ossietzky-Strasse 9-11, Postfach 2503, D-26111 Oldenburg, Germany
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