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Liedig C, Neupane P, Lashnits E, Breitschwerdt EB, Maggi RG. Blood Supplementation Enhances Bartonella henselae Growth and Molecular Detection of Bacterial DNA in Liquid Culture. Microbiol Spectr 2023; 11:e0512622. [PMID: 37227273 PMCID: PMC10269525 DOI: 10.1128/spectrum.05126-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 05/07/2023] [Indexed: 05/26/2023] Open
Abstract
Bacteria of the genus Bartonella, a member of the Alphaproteobacteria, are fastidious, Gram-negative, aerobic bacilli that comprise numerous species, subspecies, and genotypes. Bartonella henselae, with a worldwide distribution, infects cats, dogs, horses, humans, and other mammals. Diagnostically, direct detection of Bartonella henselae in patient blood specimens by culture or molecular methods is required to confirm infection with this bacterium. Enrichment blood culture combined with quantitative PCR (qPCR) or ddPCR enhances the sensitivity of direct detection. The addition of sheep blood to liquid culture media increased the Bartonella henselae DNA concentration compared to controls, additionally improving PCR direct detection sensitivity. IMPORTANCE This study aims to improve diagnostic detection of Bartonella henselae. Patient samples are combined with enriched bacterial cultures aimed at growing Bartonella henselae for the best possible chance at detection. However, current Bartonella growth methods could be improved. The DNA extraction method used by most laboratories should also be optimized. Sheep blood was added to increase the growth of Bartonella henselae and multiple DNA extraction methods were to be compared to each other.
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Affiliation(s)
- Chance Liedig
- Intracellular Pathogens Research Laboratory, Department of Clinical Sciences, and the Comparative Medicine Institute, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Pradeep Neupane
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Erin Lashnits
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Edward B. Breitschwerdt
- Intracellular Pathogens Research Laboratory, Department of Clinical Sciences, and the Comparative Medicine Institute, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Ricardo G. Maggi
- Intracellular Pathogens Research Laboratory, Department of Clinical Sciences, and the Comparative Medicine Institute, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
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2
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Dutra J, Gomes R, Yupanqui García GJ, Romero-Cale DX, Santos Cardoso M, Waldow V, Groposo C, Akamine RN, Sousa M, Figueiredo H, Azevedo V, Góes-Neto A. Corrosion-influencing microorganisms in petroliferous regions on a global scale: systematic review, analysis, and scientific synthesis of 16S amplicon metagenomic studies. PeerJ 2023; 11:e14642. [PMID: 36655046 PMCID: PMC9841911 DOI: 10.7717/peerj.14642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 12/05/2022] [Indexed: 01/15/2023] Open
Abstract
The objective of the current systematic review was to evaluate the taxonomic composition and relative abundance of bacteria and archaea associated with the microbiologically influenced corrosion (MIC), and the prediction of their metabolic functions in different sample types from oil production and transport structures worldwide. To accomplish this goal, a total of 552 published studies on the diversity of microbial communities using 16S amplicon metagenomics in oil and gas industry facilities indexed in Scopus, Web of Science, PubMed and OnePetro databases were analyzed on 10th May 2021. The selection of articles was performed following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Only studies that performed amplicon metagenomics to obtain the microbial composition of samples from oil fields were included. Studies that evaluated oil refineries, carried out amplicon metagenomics directly from cultures, and those that used DGGE analysis were removed. Data were thoroughly investigated using multivariate statistics by ordination analysis, bivariate statistics by correlation, and microorganisms' shareability and uniqueness analysis. Additionally, the full deposited databases of 16S rDNA sequences were obtained to perform functional prediction. A total of 69 eligible articles was included for data analysis. The results showed that the sulfidogenic, methanogenic, acid-producing, and nitrate-reducing functional groups were the most expressive, all of which can be directly involved in MIC processes. There were significant positive correlations between microorganisms in the injection water (IW), produced water (PW), and solid deposits (SD) samples, and negative correlations in the PW and SD samples. Only the PW and SD samples displayed genera common to all petroliferous regions, Desulfotomaculum and Thermovirga (PW), and Marinobacter (SD). There was an inferred high microbial activity in the oil fields, with the highest abundances of (i) cofactor, (ii) carrier, and (iii) vitamin biosynthesis, associated with survival metabolism. Additionally, there was the presence of secondary metabolic pathways and defense mechanisms in extreme conditions. Competitive or inhibitory relationships and metabolic patterns were influenced by the physicochemical characteristics of the environments (mainly sulfate concentration) and by human interference (application of biocides and nutrients). Our worldwide baseline study of microbial communities associated with environments of the oil and gas industry will greatly facilitate the establishment of standardized approaches to control MIC.
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Affiliation(s)
- Joyce Dutra
- Graduate Program in Microbiology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Rosimeire Gomes
- Graduate Program in Microbiology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Glen Jasper Yupanqui García
- Graduate Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | - Mariana Santos Cardoso
- Graduate Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Vinicius Waldow
- Petrobras Research and Development Center (CENPES), Petrobras, Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Rubens N. Akamine
- Petrobras Research and Development Center (CENPES), Petrobras, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Maira Sousa
- Petrobras Research and Development Center (CENPES), Petrobras, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Henrique Figueiredo
- Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Vasco Azevedo
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Aristóteles Góes-Neto
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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3
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Kifaro EG, Kim MJ, Jung S, Jang YH, Moon S, Lee DH, Song CS, Misinzo G, Kim SK. Microparticles as Viral RNA Carriers from Stool for Stable and Sensitive Surveillance. Diagnostics (Basel) 2023; 13:diagnostics13020261. [PMID: 36673071 PMCID: PMC9857651 DOI: 10.3390/diagnostics13020261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/29/2022] [Accepted: 01/02/2023] [Indexed: 01/13/2023] Open
Abstract
Since its discovery, polymerase chain reaction (PCR) has emerged as an important technology for the diagnosis and identification of infectious diseases. It is a highly sensitive and reliable nucleic acids (NA) detection tool for various sample types. However, stool, which carries the most abundant micro-organisms and physiological byproducts, remains to be the trickiest clinical specimen for molecular detection of pathogens. Herein, we demonstrate the novel application of hydrogel microparticles as carriers of viral RNA from stool samples without prior RNA purification for real-time polymerase chain reaction (qPCR). In each microparticle of primer-incorporated network (PIN) as a self-sufficient reaction compartment, immobilized reverse transcription (RT) primers capture the viral RNA by hybridization and directly initiate RT of RNA to generate a pool of complementary DNA (PIN-cDNA pool). Through a simple operation with a portable thermostat device, a PIN-cDNA pool for influenza A virus (IAV) was obtained in 20 min. The PIN-cDNA pools can be stored at room temperature, or directly used to deliver cDNA templates for qPCR. The viral cDNA templates were freely released in the subsequent qPCR to allow amplification efficiency of over 91%. The assay displayed good linearity, repeatability, and comparable limit of detection (LoD) with a commercialized viral RNA purification kit. As a proof of concept, this technology carries a huge potential for onsite application to improve human and animal infectious disease surveillance activities using stool samples without the need for a laboratory or centrifuge for sample preparation.
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Affiliation(s)
- Emmanuel George Kifaro
- Molecular Recognition Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- Department of Veterinary Microbiology, Parasitology, and Biotechnology, Sokoine University of Agriculture (SUA), Morogoro P.O. Box 3019, Tanzania
- SACIDS Africa Centre of Excellence for Infectious Diseases, SACIDS Foundation for One Health, Sokoine University of Agriculture (SUA), Morogoro P.O. Box 3297, Tanzania
| | - Mi Jung Kim
- Molecular Recognition Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Seungwon Jung
- Molecular Recognition Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Yoon-ha Jang
- Molecular Recognition Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Sungyeon Moon
- Molecular Recognition Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Dong-Hun Lee
- College of Veterinary Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - Chang-Seon Song
- College of Veterinary Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - Gerald Misinzo
- Department of Veterinary Microbiology, Parasitology, and Biotechnology, Sokoine University of Agriculture (SUA), Morogoro P.O. Box 3019, Tanzania
- SACIDS Africa Centre of Excellence for Infectious Diseases, SACIDS Foundation for One Health, Sokoine University of Agriculture (SUA), Morogoro P.O. Box 3297, Tanzania
| | - Sang Kyung Kim
- Molecular Recognition Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- KHU-KIST Department of Converging Science and Technology, Kyung Hee University, Seoul 02447, Republic of Korea
- Correspondence:
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Doyle DA, Smith PR, Lawson PA, Tanner RS. Clostridium muellerianum sp. nov., a carbon monoxide-oxidizing acetogen isolated from old hay. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005297] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
An acid/alcohol-producing, Gram-stain-positive, obligately anaerobic, rod-shaped, non-motile, non-spore forming acetogen, designated as strain P21T, was isolated from old hay after enrichment with CO as the substrate. Spores not observed even after prolonged incubation (30 days). Phylogenetic analysis of the 16S rRNA gene sequence of strain P21T showed it was closely related to
Clostridium carboxidivorans
DSM 15243T (97.9%),
Clostridium scatologenes
DSM 757T (97.7 %) and
Clostridium drakei
DSM 12750T (97.7 %). The genome is 5.6 Mb and the G+C content is 29.4 mol%. Average nucleotide identity between strain P21T,
C. carboxidivorans
,
C. scatologenes
and
C. drakei
was 87.1, 86.4, 86.4 %, respectively. Strain P21T grew on CO:CO2, H2:CO2, l-arabinose, ribose, xylose, fructose, galactose, glucose, lactose, mannose, cellobiose, sucrose, cellulose, starch, pyruvate, choline, glutamate, histidine, serine, threonine and casamino acids. End products of metabolism were acetate, butyrate, caproate, ethanol and hexanol. Dominant cellular fatty acids (>10 %) were C16 : 0 (41.5 %), C16 : 1 ω7c/C16 : 1 ω6c (10.0 %), and a summed feature containing cyclo C17 : 1/C18 : 0 (17.3 %). Based on the phenotypic, chemotaxonomic, phylogenetic and phylogenomic analyses, strain P21T represents a new species in the genus
Clostridium
, for which the name Clostridium muellerianum sp. nov. is proposed. The type strain is P21T (=DSM 111390T=NCIMB 15261T).
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Affiliation(s)
- D. Annie Doyle
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK 73019, USA
| | - Parker R. Smith
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK 73019, USA
| | - Paul A. Lawson
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK 73019, USA
| | - Ralph S. Tanner
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK 73019, USA
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Shittu OB, Uzairue LI, Ojo OE, Obuotor TM, Folorunso JB, Raheem-Ademola RR, Olanipekun G, Ajose T, Medugu N, Ebruke B, Obaro SK. Antimicrobial resistance and virulence genes in Salmonella enterica serovars isolated from droppings of layer chicken in two farms in Nigeria. J Appl Microbiol 2022; 132:3891-3906. [PMID: 35129256 DOI: 10.1111/jam.15477] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/26/2022] [Accepted: 02/03/2022] [Indexed: 11/28/2022]
Abstract
AIM This study aimed to investigate the isolation rate, antibiotic resistance, and virulence genes of Salmonella enterica serovar from two commercial farms in Nigeria. METHODS AND RESULTS Salmonella isolation was performed according to the United States Food and Drug Agency (USFDA) method. Serotyping, antimicrobial susceptibility testing, detection of resistance and virulence genes were done using the Kauffman-White Scheme, disc diffusion, minimum inhibitory concentration, and real-time polymerase chain reaction techniques. Salmonella serovars were isolated from only farm A at 22/50 (44.0%) while none were isolated from farm B. Salmonella Typhi, 9 (40.9%); Salmonella Typhimurium, 2 (9.1%), Salmonella Enteritidis, 2 (9.1%), Salmonella Pullorum, 1 (4.5%), Salmonella Kentucky, 4 (18.2%) were identified while 4 (18.2%) were untypable. Sixteen isolates (72.7%) showed multiple drug resistance and 17 different resistance profile types with AMP-CHL-TRM-SXT as the most prevalent pattern. Resistance genes (blaTEM, 12/22 (54.5%) and virulence genes (InvA, sopB, mgtC, and spi4D, 22/22 (100.0%), ssaQ, 16/22 (72.7%), and spvC, 13/22 (59.1%) were found, while blaSHV, blaCTX-M, floR, tetA, tetB, tetG, and LJSGI-1 genes were absent. CONCLUSION Pathogenic Salmonella were isolated from the chicken droppings in this study. Most of these strains were resistant to antibiotics and possessed characteristics of virulence. SIGNIFICANCE AND IMPACT OF THE STUDY Chicken droppings from this study area contained pathogenic strains of Salmonella and a rare occurrence of Salmonella Typhi. The study revealed that the environment and the food chain could be at risk of contamination of highly virulent and antimicrobial-resistant strains of Salmonella. These could affect the profitability of the poultry industry and food consumption. There is a need for caution in indiscriminate disposal of poultry waste and the use of uncomposted chicken droppings in soil amendment.
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Affiliation(s)
- Olufunke B Shittu
- Department of Microbiology, Federal University of Agriculture, Abeokuta, Ogun State, Nigeria
| | - Leonard I Uzairue
- Department of Microbiology, Federal University of Agriculture, Abeokuta, Ogun State, Nigeria.,International Foundation Against Infectious Disease in Nigeria(IFAIN), Abuja, Nigeria.,Department of Medical Laboratory Sciences, Federal University Oye Ekiti, Ekiti State, Nigeria
| | - Olufemi E Ojo
- Department of Veterinary Microbiology and Parasitology, Federal University of Agriculture, Abeokuta, Nigeria
| | - Tolulope M Obuotor
- Department of Microbiology, Federal University of Agriculture, Abeokuta, Ogun State, Nigeria
| | - Jamiu B Folorunso
- Department of Microbiology, Federal University of Agriculture, Abeokuta, Ogun State, Nigeria.,Department of Community Medicine, Olabisi Onabanjo Teaching Hospital, Nigeria
| | | | - Grace Olanipekun
- International Foundation Against Infectious Disease in Nigeria(IFAIN), Abuja, Nigeria
| | - Theresa Ajose
- International Foundation Against Infectious Disease in Nigeria(IFAIN), Abuja, Nigeria
| | - Nubwa Medugu
- International Foundation Against Infectious Disease in Nigeria(IFAIN), Abuja, Nigeria.,Department of Microbiology and Parasitology, National Hospital, Abuja, Nigeria
| | - Bernard Ebruke
- International Foundation Against Infectious Disease in Nigeria(IFAIN), Abuja, Nigeria
| | - Stephen K Obaro
- International Foundation Against Infectious Disease in Nigeria(IFAIN), Abuja, Nigeria.,Pediatric Infectious Division, University of Nebraska Medical Center, Omaha, USA
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Patel M, Villa Gómez DK, Pikaar I, Clarke WP. Influence of inoculum selection on the utilisation of volatile fatty acid and glucose in sulfate reducing reactors. ENVIRONMENTAL TECHNOLOGY 2022; 43:225-236. [PMID: 32543310 DOI: 10.1080/09593330.2020.1783371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/19/2020] [Indexed: 06/11/2023]
Abstract
The capacity of three inocula (sewer biofilm, mangrove and estuary sediment) to utilise typical fermentation products of municipal solid waste for biological sulfate reduction was investigated. Each inoculum was used in two reactors, one fed a mixture of volatile fatty acids and another fed glucose to provide a suite of fermentation products via naturally occurring fermentation. Following 228 days of reactor operation, reactors inoculated with mangrove and estuary sediments exhibited higher sulfate reducing efficiencies (80-88%) compared to the biofilm-inoculated reactors (32-49%). Minimal use of acetate and its accumulation in the biofilm-inoculated reactors pointed to the high abundance of incomplete-oxidising sulfate reducing bacteria (SRB), Desulfovibrio and Desulfobulbus (90-96% of the sulfate reducing population). Although Desulfovibrio was also prominent in reactors inoculated with mangrove and estuary sediments, Desulfobacter, a known acetoclastic sulfate reducer, emerged from trace levels in these sediment (0.01% abundance in the estuary sediments and below detection in the mangrove sediments) to comprise 14%-70% of the sulfate reducing population at the end of reactor operation.
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Affiliation(s)
- Miheka Patel
- School of Civil Engineering, The University of Queensland, Brisbane, Australia
- School of Chemical Engineering, University of Queensland, Brisbane, Australia
| | - Denys K Villa Gómez
- School of Civil Engineering, The University of Queensland, Brisbane, Australia
| | - Ilje Pikaar
- School of Civil Engineering, The University of Queensland, Brisbane, Australia
| | - William P Clarke
- School of Civil Engineering, The University of Queensland, Brisbane, Australia
- School of Chemical Engineering, University of Queensland, Brisbane, Australia
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Genome Sequence of Clostridium sp. Strain P21, a CO-Fermenting Acetogen Isolated from Old Hay. Microbiol Resour Announc 2021; 10:10/11/e00864-20. [PMID: 33737364 PMCID: PMC7975882 DOI: 10.1128/mra.00864-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Here, we report the genome sequence of Clostridium sp. strain P21, isolated from old hay from Stillwater, Oklahoma. This announcement describes the generation and annotation of the 5.6-Mb genomic sequence of strain P21, which will aid in studies targeting genes involved in the enhancement of acid-alcohol production. Here, we report the genome sequence of Clostridium sp. strain P21, isolated from old hay from Stillwater, Oklahoma. This announcement describes the generation and annotation of the 5.6-Mb genomic sequence of strain P21, which will aid in studies targeting genes involved in the enhancement of acid-alcohol production.
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8
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Liang R, Davidova I, Hirano SI, Duncan KE, Suflita JM. Community succession in an anaerobic long-chain paraffin-degrading consortium and impact on chemical and electrical microbially influenced iron corrosion. FEMS Microbiol Ecol 2019; 95:5529450. [DOI: 10.1093/femsec/fiz111] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 07/06/2019] [Indexed: 11/12/2022] Open
Abstract
ABSTRACT
Community compositional changes and the corrosion of carbon steel in the presence of different electron donor and acceptor combinations were examined with a methanogenic consortium enriched for its ability to mineralize paraffins. Despite cultivation in the absence of sulfate, metagenomic analysis revealed the persistence of several sulfate-reducing bacterial taxa. Upon sulfate amendment, the consortium was able to couple C28H58 biodegradation with sulfate reduction. Comparative analysis suggested that Desulforhabdus and/or Desulfovibrio likely supplanted methanogens as syntrophic partners needed for C28H58 mineralization. Further enrichment in the absence of a paraffin revealed that the consortium could also utilize carbon steel as a source of electrons. The severity of both general and localized corrosion increased in the presence of sulfate, regardless of the electron donor utilized. With carbon steel as an electron donor, Desulfobulbus dominated in the consortium and electrons from iron accounted for ∼92% of that required for sulfate reduction. An isolated Desulfovibrio spp. was able to extract electrons from iron and accelerate corrosion. Thus, hydrogenotrophic partner microorganisms required for syntrophic paraffin metabolism can be readily substituted depending on the availability of an external electron acceptor and a single paraffin-degrading consortium harbored microbes capable of both chemical and electrical microbially influenced iron corrosion.
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Affiliation(s)
- Renxing Liang
- Department of Microbiology and Plant Biology, Institute for Energy and the Environment, University of Oklahoma, Norman, OK 73019, USA
| | - Irene Davidova
- Department of Microbiology and Plant Biology, Institute for Energy and the Environment, University of Oklahoma, Norman, OK 73019, USA
| | - Shin-ichi Hirano
- Department of Microbiology and Plant Biology, Institute for Energy and the Environment, University of Oklahoma, Norman, OK 73019, USA
| | - Kathleen E Duncan
- Department of Microbiology and Plant Biology, Institute for Energy and the Environment, University of Oklahoma, Norman, OK 73019, USA
| | - Joseph M Suflita
- Department of Microbiology and Plant Biology, Institute for Energy and the Environment, University of Oklahoma, Norman, OK 73019, USA
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Liang R, Aydin E, Le Borgne S, Sunner J, Duncan KE, Suflita JM. Anaerobic biodegradation of biofuels and their impact on the corrosion of a Cu-Ni alloy in marine environments. CHEMOSPHERE 2018; 195:427-436. [PMID: 29274988 DOI: 10.1016/j.chemosphere.2017.12.082] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 12/09/2017] [Accepted: 12/12/2017] [Indexed: 06/07/2023]
Abstract
Fuel biodegradation linked to sulfate reduction can lead to corrosion of the metallic infrastructure in a variety of marine environments. However, the biological stability of emerging biofuels and their potential impact on copper-nickel alloys commonly used in marine systems has not been well documented. Two potential naval biofuels (Camelina-JP5 and Fisher-Tropsch-F76) and their petroleum-derived counterparts (JP5 and F76) were critically assessed in seawater/sediment incubations containing a metal coupon (70/30 Cu-Ni alloy). Relative to a fuel-unamended control (1.2 ± 0.4 μM/d), Camelina-JP5 (86.4 ± 1.6 μM/d) and JP5 (77.6 ± 8.3 μM/d) stimulated much higher rates of sulfate reduction than either FT-F76 (11.4 ± 2.7 μM/d) or F76 (38.4 ± 3.7 μM/d). The general corrosion rate (r2 = 0.91) and pitting corrosion (r2 = 0.92) correlated with sulfate loss in these incubations. Despite differences in microbial community structure on the metal or in the aqueous or sediment phases, sulfate reducing bacteria affiliated with Desulfarculaceae and Desulfobacteraceae became predominant upon fuel amendment. The identification of alkylsuccinates and alkylbenzylsuccinates attested to anaerobic metabolism of fuel hydrocarbons. Sequences related to Desulfobulbaceae were highly enriched (34.2-64.8%) on the Cu-Ni metal surface, regardless of whether the incubation received a fuel amendment. These results demonstrate that the anaerobic metabolism of biofuel linked to sulfate reduction can exacerbate the corrosion of Cu-Ni alloys. Given the relative lability of Camelina-JP5, particular precaution should be taken when incorporating this hydroprocessed biofuel into marine environments serviced by a Cu-Ni metallic infrastructure.
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Affiliation(s)
- Renxing Liang
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, USA
| | - Egemen Aydin
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, USA
| | - Sylvie Le Borgne
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana-Cuajimalpa, Mexico
| | - Jan Sunner
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, USA
| | - Kathleen E Duncan
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, USA
| | - Joseph M Suflita
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, USA.
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10
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Liang R, Duncan KE, Le Borgne S, Davidova I, Yakimov MM, Suflita JM. Microbial activities in hydrocarbon-laden wastewaters: Impact on diesel fuel stability and the biocorrosion of carbon steel. J Biotechnol 2017; 256:68-75. [DOI: 10.1016/j.jbiotec.2017.02.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 02/18/2017] [Accepted: 02/19/2017] [Indexed: 10/20/2022]
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11
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Design features of offshore oil production platforms influence their susceptibility to biocorrosion. Appl Microbiol Biotechnol 2017; 101:6517-6529. [DOI: 10.1007/s00253-017-8356-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 05/18/2017] [Accepted: 05/20/2017] [Indexed: 01/24/2023]
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12
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Oldham AL, Steinberg MK, Duncan KE, Makama Z, Beech I. Molecular methods resolve the bacterial composition of natural marine biofilms on galvanically coupled stainless steel cathodes. J Ind Microbiol Biotechnol 2016; 44:167-180. [PMID: 28013395 DOI: 10.1007/s10295-016-1887-7] [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: 07/15/2016] [Accepted: 12/14/2016] [Indexed: 11/25/2022]
Abstract
Navy vessels consist of various metal alloys and biofilm accumulation at the metal surface is thought to play a role in influencing metal deterioration. To develop better strategies to monitor and control metallic biofilms, it is necessary to resolve the bacterial composition within the biofilm. This study aimed to determine if differences in electrochemical current could influence the composition of dominant bacteria in a metallic biofilm, and if so, determine the level of resolution using metagenomic amplicon sequencing. Current was generated by creating galvanic couples between cathodes made from stainless steel and anodes made from carbon steel, aluminum, or copper nickel and exposing them in the Delaware Bay. Stainless steel cathodes (SSCs) coupled to aluminum or carbon steel generated a higher mean current (0.39 mA) than that coupled to copper nickel (0.17 mA). Following 3 months of exposure, the bacterial composition of biofilms collected from the SSCs was determined and compared. Dominant bacterial taxa from the two higher current SSCs were different from that of the low-current SSC as determined by DGGE and verified by Illumina DNA-seq analysis. These results demonstrate that electrochemical current could influence the composition of dominant bacteria in metallic biofilms and that amplicon sequencing is sufficient to complement current methods used to study metallic biofilms in marine environments.
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Affiliation(s)
- Athenia L Oldham
- Department of Biology, University of Texas of the Permian Basin, 4901 E University, Odessa, TX, 79762, USA.
| | - Mia K Steinberg
- Naval Surface Warfare Center Carderock Division, 9500 Macarthur Blvd, West Bethesda, MD, 20817, USA
| | - Kathleen E Duncan
- Department of Microbiology and Plant Biology, University of Oklahoma, 770 Van Vleet Oval, GLCH #136, Norman, OK, 73019, USA
| | - Zakari Makama
- Department of Microbiology and Plant Biology, University of Oklahoma, 100 E Boyd, Norman, OK, 73019, USA
| | - Iwona Beech
- Department of Microbiology and Plant Biology, University of Oklahoma, 770 Van Vleet Oval, GLCH #136, Norman, OK, 73019, USA
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Liang R, Davidova IA, Marks CR, Stamps BW, Harriman BH, Stevenson BS, Duncan KE, Suflita JM. Metabolic Capability of a Predominant Halanaerobium sp. in Hydraulically Fractured Gas Wells and Its Implication in Pipeline Corrosion. Front Microbiol 2016; 7:988. [PMID: 27446028 PMCID: PMC4916785 DOI: 10.3389/fmicb.2016.00988] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 06/08/2016] [Indexed: 11/13/2022] Open
Abstract
Microbial activity associated with produced water from hydraulic fracturing operations can lead to gas souring and corrosion of carbon-steel equipment. We examined the microbial ecology of produced water and the prospective role of the prevalent microorganisms in corrosion in a gas production field in the Barnett Shale. The microbial community was mainly composed of halophilic, sulfidogenic bacteria within the order Halanaerobiales, which reflected the geochemical conditions of highly saline water containing sulfur species (S2O3 (2-), SO4 (2-), and HS(-)). A predominant, halophilic bacterium (strain DL-01) was subsequently isolated and identified as belonging to the genus Halanaerobium. The isolate could degrade guar gum, a polysaccharide polymer used in fracture fluids, to produce acetate and sulfide in a 10% NaCl medium at 37°C when thiosulfate was available. To mitigate potential deleterious effects of sulfide and acetate, a quaternary ammonium compound was found to be an efficient biocide in inhibiting the growth and metabolic activity of strain DL-01 relative to glutaraldehyde and tetrakis (hydroxymethyl) phosphonium sulfate. Collectively, our findings suggest that predominant halophiles associated with unconventional shale gas extraction could proliferate and produce sulfide and acetate from the metabolism of polysaccharides used in hydraulic fracturing fluids. These metabolic products might be returned to the surface and transported in pipelines to cause pitting corrosion in downstream infrastructure.
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Affiliation(s)
- Renxing Liang
- Department of Microbiology and Plant Biology and OU Biocorrosion Center, University of Oklahoma Norman, OK, USA
| | - Irene A Davidova
- Department of Microbiology and Plant Biology and OU Biocorrosion Center, University of Oklahoma Norman, OK, USA
| | - Christopher R Marks
- Department of Microbiology and Plant Biology and OU Biocorrosion Center, University of Oklahoma Norman, OK, USA
| | - Blake W Stamps
- Department of Microbiology and Plant Biology and OU Biocorrosion Center, University of Oklahoma Norman, OK, USA
| | - Brian H Harriman
- Department of Microbiology and Plant Biology and OU Biocorrosion Center, University of Oklahoma Norman, OK, USA
| | - Bradley S Stevenson
- Department of Microbiology and Plant Biology and OU Biocorrosion Center, University of Oklahoma Norman, OK, USA
| | - Kathleen E Duncan
- Department of Microbiology and Plant Biology and OU Biocorrosion Center, University of Oklahoma Norman, OK, USA
| | - Joseph M Suflita
- Department of Microbiology and Plant Biology and OU Biocorrosion Center, University of Oklahoma Norman, OK, USA
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Glycans affect DNA extraction and induce substantial differences in gut metagenomic studies. Sci Rep 2016; 6:26276. [PMID: 27188959 PMCID: PMC4870698 DOI: 10.1038/srep26276] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 04/25/2016] [Indexed: 01/12/2023] Open
Abstract
Exopolysaccharides produced by bacterial species and present in feces are extremely inhibitory to DNA restriction and can cause discrepancies in metagenomic studies. We determined the effects of different DNA extraction methods on the apparent composition of the gut microbiota using Illumina MiSeq deep sequencing technology. DNA was extracted from the stool from an obese female using 10 different methods and the choice of DNA extraction method affected the proportional abundance at the phylum level, species richness (Chao index, 227 to 2,714) and diversity (non parametric Shannon, 1.37 to 4.4). Moreover DNA was extracted from stools obtained from 83 different individuals by the fastest extraction assay and by an extraction assay that degradated exopolysaccharides. The fastest extraction method was able to detect 68% to 100% genera and 42% to 95% species whereas the glycan degradation extraction method was able to detect 56% to 93% genera and 25% to 87% species. To allow a good liberation of DNA from exopolysaccharides commonly presented in stools, we recommend the mechanical lysis of stools plus glycan degradation, used here for the first time. Caution must be taken in the interpretation of current metagenomic studies, as the efficiency of DNA extraction varies widely among stool samples.
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Stamps BW, Lyles CN, Suflita JM, Masoner JR, Cozzarelli IM, Kolpin DW, Stevenson BS. Municipal Solid Waste Landfills Harbor Distinct Microbiomes. Front Microbiol 2016; 7:534. [PMID: 27148222 PMCID: PMC4837139 DOI: 10.3389/fmicb.2016.00534] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 03/31/2016] [Indexed: 11/16/2022] Open
Abstract
Landfills are the final repository for most of the discarded material from human society and its “built environments.” Microorganisms subsequently degrade this discarded material in the landfill, releasing gases (largely CH4 and CO2) and a complex mixture of soluble chemical compounds in leachate. Characterization of “landfill microbiomes” and their comparison across several landfills should allow the identification of environmental or operational properties that influence the composition of these microbiomes and potentially their biodegradation capabilities. To this end, the composition of landfill microbiomes was characterized as part of an ongoing USGS national survey studying the chemical composition of leachates from 19 non-hazardous landfills across 16 states in the continental U.S. The landfills varied in parameters such as size, waste composition, management strategy, geography, and climate zone. The diversity and composition of bacterial and archaeal populations in leachate samples were characterized by 16S rRNA gene sequence analysis, and compared against a variety of physical and chemical parameters in an attempt to identify their impact on selection. Members of the Epsilonproteobacteria, Gammaproteobacteria, Clostridia, and candidate division OP3 were the most abundant. The distribution of the observed phylogenetic diversity could best be explained by a combination of variables and was correlated most strongly with the concentrations of chloride and barium, rate of evapotranspiration, age of waste, and the number of detected household chemicals. This study illustrates how leachate microbiomes are distinct from those of other natural or built environments, and sheds light on the major selective forces responsible for this microbial diversity.
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Affiliation(s)
- Blake W Stamps
- Department of Microbiology and Plant Biology, University of Oklahoma Norman, OK
| | - Christopher N Lyles
- Department of Microbiology and Plant Biology, University of Oklahoma Norman, OK
| | - Joseph M Suflita
- Department of Microbiology and Plant Biology, University of Oklahoma Norman, OK
| | | | | | | | - Bradley S Stevenson
- Department of Microbiology and Plant Biology, University of Oklahoma Norman, OK
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Abstract
This review summarizes usage of genome-editing technologies for metagenomic studies; these studies are used to retrieve and modify valuable microorganisms for production, particularly in marine metagenomics. Organisms may be cultivable or uncultivable. Metagenomics is providing especially valuable information for uncultivable samples. The novel genes, pathways and genomes can be deducted. Therefore, metagenomics, particularly genome engineering and system biology, allows for the enhancement of biological and chemical producers and the creation of novel bioresources. With natural resources rapidly depleting, genomics may be an effective way to efficiently produce quantities of known and novel foods, livestock feed, fuels, pharmaceuticals and fine or bulk chemicals.
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Affiliation(s)
- Rimantas Kodzius
- Computational Bioscience Research Center (CBRC), Saudi Arabia; Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Saudi Arabia; King Abdullah University of Science and Technology (KAUST), Saudi Arabia.
| | - Takashi Gojobori
- Computational Bioscience Research Center (CBRC), Saudi Arabia; Biological and Environmental Sciences and Engineering Division (BESE), Saudi Arabia; King Abdullah University of Science and Technology (KAUST), Saudi Arabia.
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Lenhart TR, Duncan KE, Beech IB, Sunner JA, Smith W, Bonifay V, Biri B, Suflita JM. Identification and characterization of microbial biofilm communities associated with corroded oil pipeline surfaces. BIOFOULING 2014; 30:823-835. [PMID: 25115517 DOI: 10.1080/08927014.2014.931379] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Microbially influenced corrosion (MIC) has long been implicated in the deterioration of carbon steel in oil and gas pipeline systems. The authors sought to identify and characterize sessile biofilm communities within a high-temperature oil production pipeline, and to compare the profiles of the biofilm community with those of the previously analyzed planktonic communities. Eubacterial and archaeal 16S rRNA sequences of DNA recovered from extracted pipeline pieces, termed 'cookies,' revealed the presence of thermophilic sulfidogenic anaerobes, as well as mesophilic aerobes. Electron microscopy and elemental analysis of cookies confirmed the presence of sessile cells and chemical constituents consistent with corrosive biofilms. Mass spectrometry of cookie acid washes identified putative hydrocarbon metabolites, while surface profiling revealed pitting and general corrosion damage. The results suggest that in an established closed system, the biofilm taxa are representative of the planktonic eubacterial and archaeal community, and that sampling and monitoring of the planktonic bacterial population can offer insight into biocorrosion activity. Additionally, hydrocarbon biodegradation is likely to sustain these communities. The importance of appropriate sample handling and storage procedures to oilfield MIC diagnostics is highlighted.
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Affiliation(s)
- Tiffany R Lenhart
- a Department of Microbiology and Plant Biology , OU Biocorrosion Center, University of Oklahoma , Norman , OK , USA
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