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Jiang Y, Cui W, Zhang Y, Wang T, Zheng X, Li H, Shang J. FG-4592 relieves diabetic kidney disease severity by influencing metabolic profiles via gut microbiota reconstruction in both human and mouse models. Front Physiol 2023; 14:1195441. [PMID: 37654676 PMCID: PMC10465800 DOI: 10.3389/fphys.2023.1195441] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 07/25/2023] [Indexed: 09/02/2023] Open
Abstract
Objective: Diabetic kidney disease (DKD) is one of the most prevalent complications of diabetes mellitus (DM) and is highly associated with devastating outcomes. Hypoxia-inducible factor (HIF), the main transcription factor that regulates cellular responses to hypoxia, plays an important role in regulating erythropoietin (EPO) synthesis. FG-4592 is the HIF stabilizer that is widely used in patients with renal anemia. We investigated the effect of FG-4592 on DKD phenotypes and the pharmacologic mechanism from the perspective of gut microbiota and systemic metabolism. Design: We collected the clinical data of 73 participants, including 40 DKD patients with combined renal anemia treated with FG-4592, and 33 clinical index-matched DKD patients without FG-4592 treatment from The First Affiliated Hospital of Zhengzhou University at the beginning and after a 3-6-month follow-up period. We established DKD mouse models treated by FG-4592 and performed fecal microbiota transplantation from FG-4592-treated DKD mice to investigate the effects of FG-4592 on DKD and to understand this mechanism from a microbial perspective. Untargeted metabolome-microbiome combined analysis was implemented to globally delineate the mechanism of FG-4592 from both microbial and metabolomic aspects. Result: DKD phenotypes significantly improved after 3-6 months of FG-4592 treatment in DKD patients combined with renal anemia, including a decreased level of systolic blood pressure, serum creatinine, and increased estimated glomerular infiltration rate. Such effects were also achieved in the DKD mouse model treated with FG-4592 and can be also induced by FG-4592-influenced gut microbiota. Untargeted plasma metabolomics-gut microbiota analysis showed that FG-4592 dramatically altered both the microbial and metabolic profiles of DKD mice and relieved DKD phenotypes via upregulating beneficial gut microbiota-associated metabolites. Conclusion: FG-4592 can globally relieve the symptoms of DKD patients combined with renal anemia. In the animal experiment, FG-4592 can reconstruct the intestinal microbial profiles of DKD to further upregulate the production of gut-associated beneficial metabolites, subsequently improving DKD phenotypes.
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Affiliation(s)
- Yumin Jiang
- Department of Emergency Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Wen Cui
- Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Zhengzhou University, Zhengzhou, Henan, China
| | - Yiding Zhang
- Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Zhengzhou University, Zhengzhou, Henan, China
| | - Ting Wang
- Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Zhengzhou University, Zhengzhou, Henan, China
| | - Xuejun Zheng
- Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Zhengzhou University, Zhengzhou, Henan, China
| | - Huangmin Li
- Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Zhengzhou University, Zhengzhou, Henan, China
| | - Jin Shang
- Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Zhengzhou University, Zhengzhou, Henan, China
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Aronson HS, Monteverde DR, Barnes BD, Johnson BR, Zawaski MJ, Speth DR, Wang XT, Wu F, Webb SM, Trower EJ, Magyar JS, Sessions AL, Orphan VJ, Fischer WW. Sulfur cycling at natural hydrocarbon and sulfur seeps in Santa Paula Creek, CA. GEOBIOLOGY 2022; 20:707-725. [PMID: 35894090 DOI: 10.1111/gbi.12512] [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: 12/13/2021] [Revised: 05/31/2022] [Accepted: 06/26/2022] [Indexed: 06/15/2023]
Abstract
Biogeochemical cycling of sulfur is relatively understudied in terrestrial environments compared to marine environments. However, the comparative ease of access, observation, and sampling of terrestrial settings can expand our understanding of organisms and processes important in the modern sulfur cycle. Furthermore, these sites may allow for the discovery of useful process analogs for ancient sulfur-metabolizing microbial communities at times in Earth's past when atmospheric O2 concentrations were lower and sulfide was more prevalent in Earth surface environments. We identified a new site at Santa Paula Creek (SPC) in Ventura County, CA-a remarkable freshwater, gravel-bedded mountain stream charged with a range of oxidized and reduced sulfur species and heavy hydrocarbons from the emergence of subsurface fluids within the underlying sulfur- and organic-rich Miocene-age Monterey Formation. SPC hosts a suite of morphologically distinct microbial biofacies that form in association with the naturally occurring hydrocarbon seeps and sulfur springs. We characterized the geology, stream geochemistry, and microbial facies and diversity of the Santa Paula Creek ecosystem. Using geochemical analyses and 16S rRNA gene sequencing, we found that SPC supports a dynamic sulfur cycle that is largely driven by sulfide-oxidizing microbial taxa, with contributions from smaller populations of sulfate-reducing and sulfur-disproportionating taxa. This preliminary characterization of SPC revealed an intriguing site in which to study geological and geochemical controls on microbial community composition and to expand our understanding of sulfur cycling in terrestrial environments.
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Affiliation(s)
- Heidi S Aronson
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Danielle R Monteverde
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
| | - Ben Davis Barnes
- Department of Geosciences, Pennsylvania State University, Pennsylvania, USA
| | - Brooke R Johnson
- Early Life Traces & Evolution-Astrobiology, University of Liège, Liège, Belgium
- Department of Earth Sciences, Oxford University, Oxford, UK
| | - Mike J Zawaski
- Department of Geological Sciences, University of Colorado Boulder, Boulder, Colorado, USA
| | - Daan R Speth
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Xingchen Tony Wang
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
- Department of Earth and Environmental Sciences, Boston College, Chestnut Hill, Massachusetts, USA
| | - Fenfang Wu
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
| | - Samuel M Webb
- SLAC National Accelerator Laboratory, Stanford Synchrotron Radiation Lightsource, Menlo Park, California, USA
| | | | - John S Magyar
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
| | - Alex L Sessions
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Woodward W Fischer
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
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Zavarzina DG, Prokofeva MI, Pikhtereva VA, Klyukina AA, Maslov AA, Merkel AY, Gavrilov SN. Deferrivibrio essentukiensis sp. nov., gen. nov., a Representative of Deferrivibrionaceae fam. nov., Isolated from the Subsurface Aquifer of Caucasian Mineral Drinking Waters. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722020114] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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Herp S, Durai Raj AC, Salvado Silva M, Woelfel S, Stecher B. The human symbiont Mucispirillum schaedleri: causality in health and disease. Med Microbiol Immunol 2021; 210:173-179. [PMID: 34021796 PMCID: PMC7615636 DOI: 10.1007/s00430-021-00702-9] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 03/16/2021] [Indexed: 12/26/2022]
Abstract
Trillions of bacteria inhabit the mammalian gastrointestinal tract. In the majority of hosts, these symbionts contribute largely to beneficial functions promoting microbe-host homeostasis. However, an increasing number of human diseases is associated with altered microbiota composition and enrichment of certain bacterial species. A well-known example of this is Mucispirillum schaedleri, which has been associated with inflammatory conditions in the intestine. Mucispirillum spp. belong to the phylum Deferribacteres and are prevalent but low abundant members of the rodent, pig and human microbiota. Recently, M. schaedleri was causally linked to the development of Crohn's disease-like colitis in immunodeficient mice. While this study certifies a considerable pathogenic potential, the same organism can also promote health in the immunocompetent host: M. schaedleri protects from Salmonella enterica serovar Typhimurium (S. Tm)-induced colitis by interfering with the expression of the pathogen´s invasion machinery. In this review, we summarize the current knowledge on the mammalian gut symbiont M. schaedleri and its role in intestinal homeostasis and discuss open questions and perspectives for future research.
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Affiliation(s)
- Simone Herp
- Max-Von-Pettenkofer Institute, LMU Munich, Pettenkoferstr. 9a, Munich, Germany.
| | | | - Marta Salvado Silva
- Max-Von-Pettenkofer Institute, LMU Munich, Pettenkoferstr. 9a, Munich, Germany
| | - Simon Woelfel
- Max-Von-Pettenkofer Institute, LMU Munich, Pettenkoferstr. 9a, Munich, Germany
| | - Bärbel Stecher
- Max-Von-Pettenkofer Institute, LMU Munich, Pettenkoferstr. 9a, Munich, Germany
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Ueno A, Tamazawa S, Tamamura S, Murakami T, Kiyama T, Inomata H, Amano Y, Miyakawa K, Tamaki H, Naganuma T, Kaneko K. Desulfovibrio subterraneus sp. nov., a mesophilic sulfate-reducing deltaproteobacterium isolated from a deep siliceous mudstone formation. Int J Syst Evol Microbiol 2021; 71. [PMID: 33588983 DOI: 10.1099/ijsem.0.004683] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel mesophilic sulfate-reducing bacterium, strain HN2T, was isolated from groundwater sampled from the subsurface siliceous mudstone of the Wakkanai Formation located in Horonobe, Hokkaido, Japan. The bacterium was Gram-negative and vibrio-shaped, and its motility was conferred by a single polar flagellum. Cells had desulfoviridin. Catalase and oxidase activities were not detected. It grew in the temperature range of 25-40 °C (optimum, 35 °C) and pH range of 6.3-8.1 (optimum, pH 7.2-7.6). It used sulfate, thiosulfate, dimethyl sulfoxide, anthraquinone-2,6-disulfonate, Fe3+, and manganese oxide, but not elemental sulfur, nitrite, nitrate, or fumarate as electron acceptors. The strain showed weak growth with sulfite as the electron acceptor. Fermentative growth with pyruvate, lactate and cysteine was observed in the absence of sulfate, but not with malate or fumarate. NaCl was not required, but the strain tolerated up to 40 g l-1. Strain HN2T did not require vitamins. The major cellular fatty acids were iso-C15 : 0 (23.8 %), C18 : 1 ω9t (18.4 %), C18 : 0 (15.0 %), C16 : 0 (14.5 %), and anteiso-C17 :0 (10.1 %). The major respiratory quinone was menaquinone MK-6(H2). The G+C content of the genomic DNA was 56.7 mol%. Based on 16S rRNA gene sequence analysis, the closest phylogenetic relative of strain HN2T is Desulfovibrio psychrotolerans JS1T (97.0 %). Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values of the strains HN2T and D. psychrotolerans JS1T were 22.2 and 79.8 %, respectively. Based on the phenotypic and molecular genetic evidence, we propose a novel species, D. subterraneus sp. nov. with the type strain HN2T (=DSM 101010T=NBRC 112213T).
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Affiliation(s)
- Akio Ueno
- Horonobe Research Institute for the Subsurface Environment (H-RISE) Northern Advancement Centre for Science and Technology (NOASTEC), Sakae-machi, Horonobe-cho, Teshio-gun, Hokkaido, Japan
| | - Satoshi Tamazawa
- Horonobe Research Institute for the Subsurface Environment (H-RISE) Northern Advancement Centre for Science and Technology (NOASTEC), Sakae-machi, Horonobe-cho, Teshio-gun, Hokkaido, Japan
| | - Shuji Tamamura
- Horonobe Research Institute for the Subsurface Environment (H-RISE) Northern Advancement Centre for Science and Technology (NOASTEC), Sakae-machi, Horonobe-cho, Teshio-gun, Hokkaido, Japan
| | - Takuma Murakami
- Horonobe Research Institute for the Subsurface Environment (H-RISE) Northern Advancement Centre for Science and Technology (NOASTEC), Sakae-machi, Horonobe-cho, Teshio-gun, Hokkaido, Japan
| | - Tamotsu Kiyama
- Horonobe Research Institute for the Subsurface Environment (H-RISE) Northern Advancement Centre for Science and Technology (NOASTEC), Sakae-machi, Horonobe-cho, Teshio-gun, Hokkaido, Japan
| | - Hidenori Inomata
- Horonobe Research Institute for the Subsurface Environment (H-RISE) Northern Advancement Centre for Science and Technology (NOASTEC), Sakae-machi, Horonobe-cho, Teshio-gun, Hokkaido, Japan
| | - Yuki Amano
- Horonobe Underground Research Center, Japan Atomic Energy Agency (JAEA), Hokushin 432-2, Horonobe-cho, Hokkaido 098-3224, Japan
| | - Kazuya Miyakawa
- Horonobe Underground Research Center, Japan Atomic Energy Agency (JAEA), Hokushin 432-2, Horonobe-cho, Hokkaido 098-3224, Japan
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1, Higashi, Tsukuba 305-856, Japan
| | - Takeshi Naganuma
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4, Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8528, Japan
| | - Katsuhiko Kaneko
- Horonobe Research Institute for the Subsurface Environment (H-RISE) Northern Advancement Centre for Science and Technology (NOASTEC), Sakae-machi, Horonobe-cho, Teshio-gun, Hokkaido, Japan
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Sakamoto S, Nobu MK, Mayumi D, Tamazawa S, Kusada H, Yonebayashi H, Iwama H, Ikarashi M, Wakayama T, Maeda H, Sakata S, Tamura T, Nomura N, Kamagata Y, Tamaki H. Koleobacter methoxysyntrophicus gen. nov., sp. nov., a novel anaerobic bacterium isolated from deep subsurface oil field and proposal of Koleobacteraceae fam. nov. and Koleobacterales ord. nov. within the class Clostridia of the phylum Firmicutes. Syst Appl Microbiol 2020; 44:126154. [PMID: 33227632 DOI: 10.1016/j.syapm.2020.126154] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/28/2020] [Accepted: 11/02/2020] [Indexed: 11/16/2022]
Abstract
An anaerobic thermophilic, rod-shaped bacterium possessing a unique non-lipid sheathed-like structure enveloping a single-membraned cell, designated strain NRmbB1T was isolated from at the deep subsurface oil field located in Yamagata Prefecture, Japan. Growth occurred with 40-60°C (optimum, 55°C), 0-2% (2%), NaCl and pH 6.0-8.5 (8.0). Fermentative growth with various sugars was observed. Glucose-grown cells generated acetate, hydrogen, pyruvate and lactate as the main end products. Syntrophic growth occurred with glucose, pyruvate and 3,4,5-trimethoxybenzoate in the presence of an H2-scavenging partner, and growth on 3,4,5-trimethoxybenzoate was only observed under syntrophic condition. The predominant cellular fatty acids were C16:0, iso-C16:0, anteiso-C15:0, and iso-C14:0. Respiratory quinone was not detected. The genomic G+C content was 40.8mol%. Based on 16S rRNA gene phylogeny, strain NRmbB1T belongs to a distinct order-level clade in the class Clostridia of the phylum Firmicutes, sharing low similarity with other isolated organisms (i.e., 87.5% for top hit Moorella thermoacetica DSM 2955T). In total, chemotaxonomic, phylogenetic and genomic characterization revealed that strain NRmbB1T (=KCTC 25035T, =JCM 39120T) represents a novel species of a new genus. In addition, we also propose the associated family and order as Koleobacteraceae fam. nov and Koleobacterales ord. nov., respectively.
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Affiliation(s)
- Sachiko Sakamoto
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan; JST ERATO Nomura Microbial Community Control Project, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Masaru K Nobu
- Bioproduction Research Institute, AIST, 1-1-1 Higashi, Tsukuba 305-8566, Japan.
| | - Daisuke Mayumi
- Institute for Geo-Resources and Environment, Geological Survey of Japan, AIST, 1-1-1, Higashi, Tsukuba 305-8566, Ibaraki, Japan
| | - Satoshi Tamazawa
- Bioproduction Research Institute, AIST, 1-1-1 Higashi, Tsukuba 305-8566, Japan; Northern Advancement Center for Science & Technology, H-RISE, 5-3 Sakae-machi, Horonobe-cho, Teshio-gun, BPRI, Hokkaido 098-3221, Japan
| | - Hiroyuki Kusada
- JST ERATO Nomura Microbial Community Control Project, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan; Bioproduction Research Institute, AIST, 1-1-1 Higashi, Tsukuba 305-8566, Japan
| | - Hideharu Yonebayashi
- Technical Research Center, INPEX CORPORATION, 9-23-30, Kitakarasuyama, Setagaya, 157-0061, Tokyo, Japan
| | - Hiroki Iwama
- Technical Research Center, INPEX CORPORATION, 9-23-30, Kitakarasuyama, Setagaya, 157-0061, Tokyo, Japan
| | - Masayuki Ikarashi
- Technical Research Center, INPEX CORPORATION, 9-23-30, Kitakarasuyama, Setagaya, 157-0061, Tokyo, Japan
| | - Tatsuki Wakayama
- Technical Research Center, INPEX CORPORATION, 9-23-30, Kitakarasuyama, Setagaya, 157-0061, Tokyo, Japan
| | - Haruo Maeda
- Institute for Geo-Resources and Environment, Geological Survey of Japan, AIST, 1-1-1, Higashi, Tsukuba 305-8566, Ibaraki, Japan; Technical Research Center, INPEX CORPORATION, 9-23-30, Kitakarasuyama, Setagaya, 157-0061, Tokyo, Japan
| | - Susumu Sakata
- Institute for Geo-Resources and Environment, Geological Survey of Japan, AIST, 1-1-1, Higashi, Tsukuba 305-8566, Ibaraki, Japan
| | - Tomohiro Tamura
- Bioproduction Research Institute, AIST, 1-1-1 Higashi, Tsukuba 305-8566, Japan; Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), AIST, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan
| | - Nobuhiko Nomura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan; JST ERATO Nomura Microbial Community Control Project, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Yoichi Kamagata
- Bioproduction Research Institute, AIST, 1-1-1 Higashi, Tsukuba 305-8566, Japan
| | - Hideyuki Tamaki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan; JST ERATO Nomura Microbial Community Control Project, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan; Bioproduction Research Institute, AIST, 1-1-1 Higashi, Tsukuba 305-8566, Japan.
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Tüccar T, Ilhan-Sungur E, Muyzer G. Bacterial Community Composition in Produced Water of Diyarbakır Oil Fields in Turkey : Bacterial communities in produced waters of south-eastern Turkey reported in detail for the first time. JOHNSON MATTHEY TECHNOLOGY REVIEW 2020. [DOI: 10.1595/205651320x15911723486216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Oil fields harbour a wide variety of microorganisms with different metabolic capabilities. To examine the microbial ecology of petroleum reservoirs, a molecular-based approach was used to assess the composition of bacterial communities in produced water of Diyarbakır oil fields
in Turkey. Denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction (PCR)-amplified 16S rRNA gene fragments was performed to characterise the bacterial community structure of produced water samples and to identify predominant community members after sequencing of separated
DGGE bands. The majority of bacterial sequences retrieved from DGGE analysis of produced water samples belonged to unclassified bacteria (50%). Among the classified bacteria, Proteobacteria (29.2%), Firmicutes (8.3%), Bacteroidetes (8.3%) and Actinobacteria (4.2%)
groups were identified. Pseudomonas was the dominant genus detected in the produced water samples. The results of this research provide, for the first time, insight into the complexity of microbial communities in the Diyarbakır oil reservoirs and their dominant constituents.
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Affiliation(s)
- Tuğçe Tüccar
- Department of Biology, Institute of Graduate Studies in Sciences, Istanbul University 34134, Vezneciler Istanbul, Turkey
| | - Esra Ilhan-Sungur
- Department of Biology, Faculty of Science, Istanbul University 34134, Vezneciler Istanbul, Turkey
| | - Gerard Muyzer
- Department of Biotechnology, Delft University of Technology van der Maasweg 9, 2629 HZ Delft The Netherlands
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Price KA, Garrison CE, Richards N, Field EK. A Shallow Water Ferrous-Hulled Shipwreck Reveals a Distinct Microbial Community. Front Microbiol 2020; 11:1897. [PMID: 32973699 PMCID: PMC7466744 DOI: 10.3389/fmicb.2020.01897] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 07/20/2020] [Indexed: 12/12/2022] Open
Abstract
Shipwrecks act as artificial reefs and provide a solid surface in aquatic systems for many different forms of life to attach to, especially microbial communities, making them a hotspot of biogeochemical cycling. Depending on the microbial community and surrounding environment, they may either contribute to the wreck’s preservation or deterioration. Even within a single wreck, preservation and deterioration processes may vary, suggesting that the microbial community may also vary. This study aimed to identify the differences through widespread sampling of the microbial communities associated with the Pappy Lane shipwreck (NC shipwreck site #PAS0001), a shallow water ferrous-hulled shipwreck in Pamlico Sound, North Carolina to determine if there are differences across the wreck as well as from its surrounding environment. Loose shipwreck debris, drilled shipcores, surrounding sediment, and seawater samples were collected from the Pappy Lane shipwreck to characterize the microbial communities on and around the shipwreck. Results indicated that the shipwreck samples were more similar to each other than the surrounding sediment and aquatic environments suggesting they have made a specialized niche associated with the shipwreck. There were differences between the microbial community across the shipwreck, including between visibly corroded and non-corroded shipwreck debris pieces. Relative abundance estimates for neutrophilic iron-oxidizing bacteria (FeOB), an organism that may contribute to deterioration through biocorrosion, revealed they are present across the shipwreck and at highest abundance on the samples containing visible corrosion products. Zetaproteobacteria, a known class of marine iron-oxidizers, were also found in higher abundance on shipwreck samples with visible corrosion. A novel Zetaproteobacteria strain, Mariprofundus ferrooxydans O1, was isolated from one of the shipwreck pieces and its genome analyzed to elucidate the functional potential of the organism. In addition to iron oxidation pathways, the isolate has the genomic potential to perform carbon fixation in both high and low oxygen environments, as well as perform nitrogen fixation, contributing to the overall biogeochemical cycling of nutrients and metals in the shipwreck ecosystem. By understanding the microbial communities associated with shallow water ferrous-hulled shipwrecks, better management strategies and preservation plans can be put into place to preserve these artificial reefs and non-renewable cultural resources.
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Affiliation(s)
- Kyra A Price
- Department of Biology, East Carolina University, Greenville, NC, United States
| | - Cody E Garrison
- Department of Biology, East Carolina University, Greenville, NC, United States
| | - Nathan Richards
- Program in Maritime Studies, Department of History, East Carolina University, Greenville, NC, United States
| | - Erin K Field
- Department of Biology, East Carolina University, Greenville, NC, United States
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Densely Populated Water Droplets in Heavy-Oil Seeps. Appl Environ Microbiol 2020; 86:AEM.00164-20. [PMID: 32220837 PMCID: PMC7237766 DOI: 10.1128/aem.00164-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 03/19/2020] [Indexed: 11/20/2022] Open
Abstract
Most of the microbial degradation in oil reservoirs is believed to take place at the oil-water transition zone (OWTZ). However, a recent study indicates that there is microbial life enclosed in microliter-sized water droplets dispersed in heavy oil of Pitch Lake in Trinidad and Tobago. This life in oil suggests that microbial degradation of oil also takes place in water pockets in the oil-bearing rock of an oil leg independent of the OWTZ. However, it is unknown whether microbial life in water droplets dispersed in oil is a generic property of oil reservoirs rather than an exotic exception. Hence, we took samples from three heavy-oil seeps, Pitch Lake (Trinidad and Tobago), the La Brea Tar Pits (California, USA), and an oil seep on the McKittrick oil field (California, USA). All three tested oil seeps contained dispersed water droplets. Larger droplets between 1 and 10 μl revealed high cell densities of up to 109 cells ml-1 Testing for ATP content and LIVE/DEAD staining showed that these populations consist of active and viable microbial cells with an average of 60% membrane-intact cells and ATP concentrations comparable to those of other subsurface ecosystems. Microbial community analyses based on 16S rRNA gene amplicon sequencing revealed the presence of known anaerobic oil-degrading microorganisms. Surprisingly, the community analyses showed similarities between all three oil seeps, revealing common OTUs, although the sampling sites were thousands of kilometers apart. Our results indicate that small water inclusions are densely populated microhabitats in heavy oil and possibly a generic trait of degraded-oil reservoirs.IMPORTANCE Our results confirmed that small water droplets in oil are densely populated microhabitats containing active microbial communities. Since these microhabitats occurred in three tested oil seeps which are located thousands of kilometers away from each other, such populated water droplets might be a generic trait of biodegraded oil reservoirs and might be involved in the overall oil degradation process. Microbial degradation might thus also take place in water pockets in the oil-bearing oil legs of the reservoir rock rather than only at the oil-water transition zone.
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10
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Tamaki H. Cultivation Renaissance in the Post-Metagenomics Era: Combining the New and Old. Microbes Environ 2019; 34:117-120. [PMID: 31243255 PMCID: PMC6594738 DOI: 10.1264/jsme2.me3402rh] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
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Kato S, Wada K, Kitagawa W, Mayumi D, Ikarashi M, Sone T, Asano K, Kamagata Y. Conductive Iron Oxides Promote Methanogenic Acetate Degradation by Microbial Communities in a High-Temperature Petroleum Reservoir. Microbes Environ 2019; 34:95-98. [PMID: 30773516 PMCID: PMC6440731 DOI: 10.1264/jsme2.me18140] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Supplementation with conductive magnetite particles promoted methanogenic acetate degradation by microbial communities enriched from the production water of a high-temperature petroleum reservoir. A microbial community analysis revealed that Petrothermobacter spp. (phylum Deferribacteres), known as thermophilic Fe(III) reducers, predominated in the magnetite-supplemented enrichment, whereas other types of Fe(III) reducers, such as Thermincola spp. and Thermotoga spp., were dominant under ferrihydrite-reducing conditions. These results suggest that magnetite induced interspecies electron transfer via electric currents through conductive particles between Petrothermobacter spp. and methanogens. This is the first evidence for possible electric syntrophy in high-temperature subsurface environments.
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Affiliation(s)
- Souichiro Kato
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Kaoru Wada
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University
| | - Wataru Kitagawa
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | | | | | - Teruo Sone
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University
| | - Kozo Asano
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University
| | - Yoichi Kamagata
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST).,Bioproduction Research Institute, AIST
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Multidisciplinary involvement and potential of thermophiles. Folia Microbiol (Praha) 2018; 64:389-406. [PMID: 30386965 DOI: 10.1007/s12223-018-0662-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/25/2018] [Indexed: 12/15/2022]
Abstract
The full biotechnological exploitation of thermostable enzymes in industrial processes is necessary for their commercial interest and industrious value. The heat-tolerant and heat-resistant enzymes are a key for efficient and cost-effective translation of substrates into useful products for commercial applications. The thermophilic, hyperthermophilic, and microorganisms adapted to extreme temperatures (i.e., low-temperature lovers or psychrophiles) are a rich source of thermostable enzymes with broad-ranging thermal properties, which have structural and functional stability to underpin a variety of technologies. These enzymes are under scrutiny for their great biotechnological potential. Temperature is one of the most critical parameters that shape microorganisms and their biomolecules for stability under harsh environmental conditions. This review describes in detail the sources of thermophiles and thermostable enzymes from prokaryotes and eukaryotes (microbial cell factories). Furthermore, the review critically examines perspectives to improve modern biocatalysts, its production and performance aiming to increase their value for biotechnology through higher standards, specificity, resistance, lowing costs, etc. These thermostable and thermally adapted extremophilic enzymes have been used in a wide range of industries that span all six enzyme classes. Thus, in particular, target of this review paper is to show the possibility of both high-value-low-volume (e.g., fine-chemical synthesis) and low-value-high-volume by-products (e.g., fuels) by minimizing changes to current industrial processes.
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