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Kashani M, Engle MA, Kent DB, Gregston T, Cozzarelli IM, Mumford AC, Varonka MS, Harris CR, Akob DM. Illegal dumping of oil and gas wastewater alters arid soil microbial communities. Appl Environ Microbiol 2024; 90:e0149023. [PMID: 38294246 PMCID: PMC10880632 DOI: 10.1128/aem.01490-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 11/27/2023] [Indexed: 02/01/2024] Open
Abstract
The Permian Basin, underlying southeast New Mexico and west Texas, is one of the most productive oil and gas (OG) provinces in the United States. Oil and gas production yields large volumes of wastewater with complex chemistries, and the environmental health risks posed by these OG wastewaters on sensitive desert ecosystems are poorly understood. Starting in November 2017, 39 illegal dumps, as defined by federal and state regulations, of OG wastewater were identified in southeastern New Mexico, releasing ~600,000 L of fluid onto dryland soils. To evaluate the impacts of these releases, we analyzed changes in soil geochemistry and microbial community composition by comparing soils from within OG wastewater dump-affected samples to unaffected zones. We observed significant changes in soil geochemistry for all dump-affected compared with control samples, reflecting the residual salts and hydrocarbons from the OG-wastewater release (e.g., enriched in sodium, chloride, and bromide). Microbial community structure significantly (P < 0.01) differed between dump and control zones, with soils from dump areas having significantly (P < 0.01) lower alpha diversity and differences in phylogenetic composition. Dump-affected soil samples showed an increase in halophilic and halotolerant taxa, including members of the Marinobacteraceae, Halomonadaceae, and Halobacteroidaceae, suggesting that the high salinity of the dumped OG wastewater was exerting a strong selective pressure on microbial community structure. Taxa with high similarity to known hydrocarbon-degrading organisms were also detected in the dump-affected soil samples. Overall, this study demonstrates the potential for OG wastewater exposure to change the geochemistry and microbial community dynamics of arid soils.IMPORTANCEThe long-term environmental health impacts resulting from releases of oil and gas (OG) wastewater, typically brines with varying compositions of ions, hydrocarbons, and other constituents, are understudied. This is especially true for sensitive desert ecosystems, where soil microbes are key primary producers and drivers of nutrient cycling. We found that releases of OG wastewater can lead to shifts in microbial community composition and function toward salt- and hydrocarbon-tolerant taxa that are not typically found in desert soils, thus altering the impacted dryland soil ecosystem. Loss of key microbial taxa, such as those that catalyze organic carbon cycling, increase arid soil fertility, promote plant health, and affect soil moisture retention, could result in cascading effects across the sensitive desert ecosystem. By characterizing environmental changes due to releases of OG wastewater to soils overlying the Permian Basin, we gain further insights into how OG wastewater may alter dryland soil microbial functions and ecosystems.
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Affiliation(s)
- Mitra Kashani
- U.S. Geological Survey, Geology, Energy & Minerals Science Center, Reston, Virginia, USA
| | - Mark A. Engle
- Department of Earth, Environmental and Resource Sciences, University of Texas at El Paso, El Paso, Texas, USA
| | - Douglas B. Kent
- U.S. Geological Survey, Earth Systems Processes Division, Menlo Park, California, USA
| | | | - Isabelle M. Cozzarelli
- U.S. Geological Survey, Geology, Energy & Minerals Science Center, Reston, Virginia, USA
| | - Adam C. Mumford
- U.S. Geological Survey, Maryland-Delaware-D.C. Water Science Center, Baltimore, Maryland, USA
| | - Matthew S. Varonka
- U.S. Geological Survey, Geology, Energy & Minerals Science Center, Reston, Virginia, USA
| | - Cassandra R. Harris
- U.S. Geological Survey, Geology, Energy & Minerals Science Center, Reston, Virginia, USA
| | - Denise M. Akob
- U.S. Geological Survey, Geology, Energy & Minerals Science Center, Reston, Virginia, USA
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2
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Bitencourt JAP, Chequer LPT, Waite CC, Oliveira G, Oliveira AMS, Pereira DC, Crapez MAC. Biomass and enzymatic activities of marine bacteria in the presence of multiple metals. Braz J Microbiol 2023; 54:1523-1532. [PMID: 37212983 PMCID: PMC10485232 DOI: 10.1007/s42770-023-00993-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 04/25/2023] [Indexed: 05/23/2023] Open
Abstract
Marine environments are a repository for metals, and humans have enhanced this phenomenon over the years. Heavy metals are notoriously toxic due to their ability to biomagnify in the food chain and interact with cellular components. Nevertheless, some bacteria have physiological mechanisms that enable them to survive in impacted environments. This characteristic makes them important as biotechnological tools for environmental remediation. Thus, we isolated a bacterial consortium in Guanabara Bay (Brazil), a place with a long metal pollution history. To test the growth efficiency of this consortium in Cu-Zn-Pb-Ni-Cd medium, we measured the activity of key enzymes of microbial activity (esterases and dehydrogenase) under acidic (4.0) and neutral pH conditions, as well as the number of living cells, biopolymer production, and changes in microbial composition during metal exposure. Additionally, we calculated the predicted physiology based on microbial taxonomy. During the assay, a slight modification in bacterial composition was observed, with low abundance changes and little production of carbohydrates. Oceanobacillus chironomi, Halolactibacillus miurensis, and Alkaliphilus oremlandii were predominant in pH 7, despite O. chironomi and Tissierella creatinophila in pH 4, and T. creatinophila in Cu-Zn-Pb-Ni-Cd treatment. The metabolism represented by esterases and dehydrogenase enzymes suggested bacterial investment in esterases to capture nutrients and meet the energy demand in an environment with metal stress. Their metabolism potentially shifted to chemoheterotrophy and recycling nitrogenous compounds. Moreover, concomitantly, bacteria produced more lipids and proteins, suggesting extracellular polymeric substance production and growth in a metal-stressed environment. The isolated consortium showed promise for bioremediation of multimetal contamination and could be a valuable tool in future bioremediation programs.
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Affiliation(s)
| | - L P T Chequer
- Departamento de Biologia Marinha, Programa de Pós-Graduação Em Biologia Marinha E Ambientes Costeiros, Universidade Federal Fluminense, Niterói, RJ, CEP 24020-150, Brazil
| | - C C Waite
- Departamento de Biologia Marinha, Programa de Pós-Graduação Em Biologia Marinha E Ambientes Costeiros, Universidade Federal Fluminense, Niterói, RJ, CEP 24020-150, Brazil
| | - G Oliveira
- Departamento de Biologia Marinha, Programa de Pós-Graduação Em Biologia Marinha E Ambientes Costeiros, Universidade Federal Fluminense, Niterói, RJ, CEP 24020-150, Brazil
- School of Earth and Environmental Sciences, University of Queensland, St. Lucia, Brisbane, QLD, 4072, Australia
| | - A M S Oliveira
- Instituto Tecnológico Vale, Belém, PA, CEP 66055-090, Brazil
| | - D C Pereira
- Departamento de Biologia Marinha, Programa de Pós-Graduação Em Biologia Marinha E Ambientes Costeiros, Universidade Federal Fluminense, Niterói, RJ, CEP 24020-150, Brazil
| | - M A C Crapez
- Departamento de Biologia Marinha, Programa de Pós-Graduação Em Biologia Marinha E Ambientes Costeiros, Universidade Federal Fluminense, Niterói, RJ, CEP 24020-150, Brazil
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3
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Harirchi S, Sar T, Ramezani M, Aliyu H, Etemadifar Z, Nojoumi SA, Yazdian F, Awasthi MK, Taherzadeh MJ. Bacillales: From Taxonomy to Biotechnological and Industrial Perspectives. Microorganisms 2022; 10:2355. [PMID: 36557608 PMCID: PMC9781867 DOI: 10.3390/microorganisms10122355] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 12/02/2022] Open
Abstract
For a long time, the genus Bacillus has been known and considered among the most applicable genera in several fields. Recent taxonomical developments resulted in the identification of more species in Bacillus-related genera, particularly in the order Bacillales (earlier heterotypic synonym: Caryophanales), with potential application for biotechnological and industrial purposes such as biofuels, bioactive agents, biopolymers, and enzymes. Therefore, a thorough understanding of the taxonomy, growth requirements and physiology, genomics, and metabolic pathways in the highly diverse bacterial order, Bacillales, will facilitate a more robust designing and sustainable production of strain lines relevant to a circular economy. This paper is focused principally on less-known genera and their potential in the order Bacillales for promising applications in the industry and addresses the taxonomical complexities of this order. Moreover, it emphasizes the biotechnological usage of some engineered strains of the order Bacillales. The elucidation of novel taxa, their metabolic pathways, and growth conditions would make it possible to drive industrial processes toward an upgraded functionality based on the microbial nature.
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Affiliation(s)
- Sharareh Harirchi
- Swedish Centre for Resource Recovery, University of Borås, 50190 Borås, Sweden
| | - Taner Sar
- Swedish Centre for Resource Recovery, University of Borås, 50190 Borås, Sweden
| | - Mohaddaseh Ramezani
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), Academic Center for Education, Culture and Research (ACECR), Tehran, Iran
| | - Habibu Aliyu
- Institute of Process Engineering in Life Science II: Technical Biology, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Zahra Etemadifar
- Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan 8174673441, Iran
| | - Seyed Ali Nojoumi
- Microbiology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran 1316943551, Iran
| | - Fatemeh Yazdian
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran 1439957131, Iran
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Taicheng Road 3#, Yangling, Xianyang 712100, China
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Dong H, Zhang F, Xu T, Liu Y, Du Y, Wang C, Liu T, Gao J, He Y, Wang X, Sun S, She Y. Culture-dependent and culture-independent methods reveal microbe-clay mineral interactions by dissimilatory iron-reducing bacteria in an integral oilfield. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 840:156577. [PMID: 35688243 DOI: 10.1016/j.scitotenv.2022.156577] [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: 04/05/2022] [Revised: 05/19/2022] [Accepted: 06/05/2022] [Indexed: 06/15/2023]
Abstract
Fe(III) may be reasonably considered as one of the most important electron acceptors in petroleum reservoir ecosystems. The microbial mineralization of clay minerals, especially montmorillonite, is also of great significance to the exploration of petroleum and gas reservoirs. The bioreduction mechanisms of iron-poor minerals in petroleum reservoirs have been poorly investigated. This study investigated the bioreduction of montmorillonite by dissimilatory iron-reducing bacteria (DIRB) in petroleum reservoirs based on culture-independent and culture-dependent methods. Microbial diversity analysis revealed that Halolactibacillus, Bacillus, Alkaliphilus, Shewanella, Clostridium, and Pseudomonas were the key genera involved in the bioreduction of Fe(III). Through the traditional culture-dependent method, most of the key genera were isolated from the samples collected from petroleum reservoirs. Traditional culture-dependent methods can be used to reveal the metabolic characteristics of microorganisms (such as iron-reduction efficiency) to further elucidate the roles of different species (B. subtilis and B. alkalitelluris) in the environment. Moreover, many species with high iron-reduction efficiencies and relatively low abundances in the samples, such as Tessaracoccus and Flaviflexus, were isolated from petroleum reservoirs for the first time. The combination of culture-dependent and culture-independent methods can be used to further the understanding of the microbial communities and the metabolic characteristics of DIRB in petroleum reservoirs. Structural alterations that occurred during the interactions of microorganisms and montmorillonite were revealed through scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FTIR), and X-ray powder diffraction (XRD). The physical and chemical analysis results demonstrated that microorganisms from petroleum reservoirs can dissolve iron-poor montmorillonite and promote the release of interlayer water. The secondary minerals illite and clinoptilolite were observed in bioreduced smectite. The formation of secondary minerals was closely related to the dissolution degrees of minerals based on iron reduction.
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Affiliation(s)
- Hao Dong
- College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou 434023, China.
| | - Fan Zhang
- The Key Laboratory of Marine Reservoir Evolution and Hydrocarbon Accumulation Mechanism, Ministry of Education, College of Energy Resources, China University of Geosciences (Beijing), Beijing 100083, China
| | - Ting Xu
- College of Resources and Environment, Yangtze University, Wuhan 430010, China
| | - Yulong Liu
- Key Laboratory of Drilling and Production Engineering for Oil and Gas, College of Petroleum Engineering, Yangtze University, Wuhan 430010, China
| | - Ying Du
- College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou 434023, China
| | - Chen Wang
- College of Resources and Environment, Yangtze University, Wuhan 430010, China
| | - Tiansheng Liu
- College of Resources and Environment, Yangtze University, Wuhan 430010, China
| | - Ji Gao
- College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou 434023, China
| | - Yanlong He
- College of Petroleum Engineering, Xi'an Shiyou University, Xi'an 710065, China
| | - Xiaotong Wang
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shanshan Sun
- Key Laboratory of Drilling and Production Engineering for Oil and Gas, College of Petroleum Engineering, Yangtze University, Wuhan 430010, China
| | - Yuehui She
- Key Laboratory of Drilling and Production Engineering for Oil and Gas, College of Petroleum Engineering, Yangtze University, Wuhan 430010, China.
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5
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Revealing the bacterial abundance and diversity in brines from started Spanish-style green table olives. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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6
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Suzuki T, Matsutani M, Matsuyama M, Unno R, Matsushita H, Sugiyama M, Yamasato K, Koizumi Y, Ishikawa M. Growth and metabolic properties of halophilic and alkaliphilic lactic acid bacterial strains of Marinilactibacillus psychrotolerans isolated from surface-ripened soft cheese. Int Dairy J 2021. [DOI: 10.1016/j.idairyj.2020.104840] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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7
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Secaira-Morocho H, Castillo JA, Driks A. Diversity and evolutionary dynamics of spore-coat proteins in spore-forming species of Bacillales. Microb Genom 2020; 6. [PMID: 33052805 PMCID: PMC7725329 DOI: 10.1099/mgen.0.000451] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Among members of the Bacillales order, there are several species capable of forming a structure called an endospore. Endospores enable bacteria to survive under unfavourable growth conditions and germinate when environmental conditions are favourable again. Spore-coat proteins are found in a multilayered proteinaceous structure encasing the spore core and the cortex. They are involved in coat assembly, cortex synthesis and germination. Here, we aimed to determine the diversity and evolutionary processes that have influenced spore-coat genes in various spore-forming species of Bacillales using an in silico approach. For this, we used sequence similarity searching algorithms to determine the diversity of coat genes across 161 genomes of Bacillales. The results suggest that among Bacillales, there is a well-conserved core genome, composed mainly by morphogenetic coat proteins and spore-coat proteins involved in germination. However, some spore-coat proteins are taxa-specific. The best-conserved genes among different species may promote adaptation to changeable environmental conditions. Because most of the Bacillus species harbour complete or almost complete sets of spore-coat genes, we focused on this genus in greater depth. Phylogenetic reconstruction revealed eight monophyletic groups in the Bacillus genus, of which three are newly discovered. We estimated the selection pressures acting over spore-coat genes in these monophyletic groups using classical and modern approaches and detected horizontal gene transfer (HGT) events, which have been further confirmed by scanning the genomes to find traces of insertion sequences. Although most of the genes are under purifying selection, there are several cases with individual sites evolving under positive selection. Finally, the HGT results confirm that sporulation is an ancestral feature in Bacillus.
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Affiliation(s)
- Henry Secaira-Morocho
- School of Biological Sciences and Engineering, Yachay Tech University, San Miguel de Urcuquí, Imbabura, Ecuador
| | - José A Castillo
- School of Biological Sciences and Engineering, Yachay Tech University, San Miguel de Urcuquí, Imbabura, Ecuador
| | - Adam Driks
- Department of Microbiology and Immunology, Loyola University Chicago, Chicago, IL, USA
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8
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Lactic acid bacterial diversity in Brie cheese focusing on salt concentration and pH of isolation medium and characterisation of halophilic and alkaliphilic lactic acid bacterial isolates. Int Dairy J 2020. [DOI: 10.1016/j.idairyj.2020.104757] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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9
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Jang GI, Kim G, Hwang CY, Cho BC. Prokaryotic community composition in alkaline-fermented skate ( Raja pulchra ). Food Microbiol 2017; 61:72-82. [DOI: 10.1016/j.fm.2016.08.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 07/15/2016] [Accepted: 08/26/2016] [Indexed: 10/21/2022]
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10
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Navarro RR, Hori T, Inaba T, Matsuo K, Habe H, Ogata A. High-resolution phylogenetic analysis of residual bacterial species of fouled membranes after NaOCl cleaning. WATER RESEARCH 2016; 94:166-175. [PMID: 26945453 DOI: 10.1016/j.watres.2016.02.044] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 02/17/2016] [Accepted: 02/18/2016] [Indexed: 06/05/2023]
Abstract
Biofouling is one of the major problems during wastewater treatment using membrane bioreactors (MBRs). In this regard, sodium hypochlorite (NaOCl) has been widely used to wash fouled membranes for maintenance and recovery purposes. Advanced chemical and biological characterization was conducted in this work to evaluate the performance of aqueous NaOCl solutions during washing of polyacrylonitrile membranes. Fouled membranes from MBR operations supplemented with artificial wastewater were washed with 0.1% and 0.5% aqueous NaOCl solutions for 5, 10 and 30 min. The changes in organics composition on the membrane surface were directly monitored by an attenuated total reflection Fourier transform infrared (ATR-FT-IR) spectrometer. In addition, high-throughput Illumina sequencing of 16S rRNA genes was applied to detect any residual microorganisms. Results from ATR-FT-IR analysis indicated the complete disappearance of functional groups representing different fouling compounds after at least 30 min of treatment with 0.1% NaOCl. However, the biomolecular survey revealed the presence of residual bacteria even after 30 min of treatment with 0.5% NaOCl solution. Evaluation of microbial diversity of treated samples using Chao1, Shannon and Simpson reciprocal indices showed an increase in evenness while no significant decline in richness was observed. These implied that only the population of dominant species was mainly affected. The high-resolution phylogenetic analysis revealed the presence of numerous operational taxonomic units (OTUs) whose close relatives exhibit halotolerance. Some OTUs related to thermophilic and acid-resistant strains were also identified. Finally, the taxonomic analysis of recycled membranes that were previously washed with NaOCl also showed the presence of numerous halotolerant-related OTUs in the early stage of fouling. This further suggested the possible contribution of such chemical tolerance on their survival against NaOCl washing, which in turn affected their re-fouling potential.
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Affiliation(s)
- Ronald R Navarro
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan
| | - Tomoyuki Hori
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan.
| | - Tomohiro Inaba
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan
| | - Kazuyuki Matsuo
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan
| | - Hiroshi Habe
- Research Institute for Sustainable Chemistry, AIST, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Atsushi Ogata
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan
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11
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Abstract
Members of the family Bacillaceae are among the most robust bacteria on Earth, which is mainly due to their ability to form resistant endospores. This trait is believed to be the key factor determining the ecology of these bacteria. However, they also perform fundamental roles in soil ecology (i.e., the cycling of organic matter) and in plant health and growth stimulation (e.g., via suppression of plant pathogens and phosphate solubilization). In this review, we describe the high functional and genetic diversity that is found within the Bacillaceae (a family of low-G+C% Gram-positive spore-forming bacteria), their roles in ecology and in applied sciences related to agriculture. We then pose questions with respect to their ecological behavior, zooming in on the intricate social behavior that is becoming increasingly well characterized for some members of Bacillaceae. Such social behavior, which includes cell-to-cell signaling via quorum sensing or other mechanisms (e.g., the production of extracellular hydrolytic enzymes, toxins, antibiotics and/or surfactants) is a key determinant of their lifestyle and is also believed to drive diversification processes. It is only with a deeper understanding of cell-to-cell interactions that we will be able to understand the ecological and diversification processes of natural populations within the family Bacillaceae. Ultimately, the resulting improvements in understanding will benefit practical efforts to apply representatives of these bacteria in promoting plant growth as well as biological control of plant pathogens.
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12
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Hamdan A, El-Sayed A, Mahmoud M. Effects of a novel marine probiotic, Lactobacillus plantarum
AH 78, on growth performance and immune response of Nile tilapia (Oreochromis niloticus
). J Appl Microbiol 2016; 120:1061-73. [DOI: 10.1111/jam.13081] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 01/01/2016] [Accepted: 01/24/2016] [Indexed: 12/21/2022]
Affiliation(s)
- A.M. Hamdan
- Oceanography Department; Faculty of Science; Alexandria University; Alexandria Egypt
| | - A.F.M. El-Sayed
- Oceanography Department; Faculty of Science; Alexandria University; Alexandria Egypt
| | - M.M. Mahmoud
- Oceanography Department; Faculty of Science; Alexandria University; Alexandria Egypt
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13
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Lucena-Padrós H, Ruiz-Barba JL. Diversity and enumeration of halophilic and alkaliphilic bacteria in Spanish-style green table-olive fermentations. Food Microbiol 2016; 53:53-62. [DOI: 10.1016/j.fm.2015.09.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 08/20/2015] [Accepted: 09/04/2015] [Indexed: 11/29/2022]
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14
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Pelagirhabdus alkalitolerans gen. nov., sp. nov., an alkali-tolerant and thermotolerant bacterium isolated from beach sediment, and reclassification of Amphibacillus fermentum as Pelagirhabdus fermentum comb. nov. Int J Syst Evol Microbiol 2016; 66:84-90. [DOI: 10.1099/ijsem.0.000678] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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15
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Dong Y, Sanford RA, Locke RA, Cann IK, Mackie RI, Fouke BW. Fe-oxide grain coatings support bacterial Fe-reducing metabolisms in 1.7-2.0 km-deep subsurface quartz arenite sandstone reservoirs of the Illinois Basin (USA). Front Microbiol 2014; 5:511. [PMID: 25324834 PMCID: PMC4179719 DOI: 10.3389/fmicb.2014.00511] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 09/11/2014] [Indexed: 02/01/2023] Open
Abstract
The Cambrian-age Mt. Simon Sandstone, deeply buried within the Illinois Basin of the midcontinent of North America, contains quartz sand grains ubiquitously encrusted with iron-oxide cements and dissolved ferrous iron in pore-water. Although microbial iron reduction has previously been documented in the deep terrestrial subsurface, the potential for diagenetic mineral cementation to drive microbial activity has not been well studied. In this study, two subsurface formation water samples were collected at 1.72 and 2.02 km, respectively, from the Mt. Simon Sandstone in Decatur, Illinois. Low-diversity microbial communities were detected from both horizons and were dominated by Halanaerobiales of Phylum Firmicutes. Iron-reducing enrichment cultures fed with ferric citrate were successfully established using the formation water. Phylogenetic classification identified the enriched species to be related to Vulcanibacillus from the 1.72 km depth sample, while Orenia dominated the communities at 2.02 km of burial depth. Species-specific quantitative analyses of the enriched organisms in the microbial communities suggest that they are indigenous to the Mt. Simon Sandstone. Optimal iron reduction by the 1.72 km enrichment culture occurred at a temperature of 40°C (range 20-60°C) and a salinity of 25 parts per thousand (range 25-75 ppt). This culture also mediated fermentation and nitrate reduction. In contrast, the 2.02 km enrichment culture exclusively utilized hydrogen and pyruvate as the electron donors for iron reduction, tolerated a wider range of salinities (25-200 ppt), and exhibited only minimal nitrate- and sulfate-reduction. In addition, the 2.02 km depth community actively reduces the more crystalline ferric iron minerals goethite and hematite. The results suggest evolutionary adaptation of the autochthonous microbial communities to the Mt. Simon Sandstone and carries potentially important implications for future utilization of this reservoir for CO2 injection.
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Affiliation(s)
- Yiran Dong
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign Urbana, IL, USA ; Department of Geology, University of Illinois at Urbana-Champaign Urbana, IL, USA ; Energy Biosciences Institute, University of Illinois at Urbana-Champaign Urbana, IL, USA
| | - Robert A Sanford
- Department of Geology, University of Illinois at Urbana-Champaign Urbana, IL, USA
| | - Randall A Locke
- Illinois State Geological Survey, Urbana-Champaign Urbana, IL, USA
| | - Isaac K Cann
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign Urbana, IL, USA ; Energy Biosciences Institute, University of Illinois at Urbana-Champaign Urbana, IL, USA ; Department of Animal Sciences, University of Illinois at Urbana-Champaign Urbana, IL, USA ; Department of Microbiology, University of Illinois at Urbana-Champaign Urbana, IL, USA
| | - Roderick I Mackie
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign Urbana, IL, USA ; Energy Biosciences Institute, University of Illinois at Urbana-Champaign Urbana, IL, USA ; Department of Animal Sciences, University of Illinois at Urbana-Champaign Urbana, IL, USA
| | - Bruce W Fouke
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign Urbana, IL, USA ; Department of Geology, University of Illinois at Urbana-Champaign Urbana, IL, USA ; Energy Biosciences Institute, University of Illinois at Urbana-Champaign Urbana, IL, USA ; Illinois State Geological Survey, Urbana-Champaign Urbana, IL, USA ; Department of Microbiology, University of Illinois at Urbana-Champaign Urbana, IL, USA
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Abstract
ABSTRACT
The family
Bacillaceae
constitutes a phenotypically diverse and globally ubiquitous assemblage of bacteria. Investigation into how evolution has shaped, and continues to shape, this family has relied on several widely ranging approaches from classical taxonomy, ecological field studies, and evolution in soil microcosms to genomic-scale phylogenetics, laboratory, and directed evolution experiments. One unifying characteristic of the
Bacillaceae
, the endospore, poses unique challenges to answering questions regarding both the calculation of evolutionary rates and claims of extreme longevity in ancient environmental samples.
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17
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Cluff MA, Hartsock A, MacRae JD, Carter K, Mouser PJ. Temporal changes in microbial ecology and geochemistry in produced water from hydraulically fractured Marcellus shale gas wells. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:6508-17. [PMID: 24803059 DOI: 10.1021/es501173p] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Microorganisms play several important roles in unconventional gas recovery, from biodegradation of hydrocarbons to souring of wells and corrosion of equipment. During and after the hydraulic fracturing process, microorganisms are subjected to harsh physicochemical conditions within the kilometer-deep hydrocarbon-bearing shale, including high pressures, elevated temperatures, exposure to chemical additives and biocides, and brine-level salinities. A portion of the injected fluid returns to the surface and may be reused in other fracturing operations, a process that can enrich for certain taxa. This study tracked microbial community dynamics using pyrotag sequencing of 16S rRNA genes in water samples from three hydraulically fractured Marcellus shale wells in Pennsylvania, USA over a 328-day period. There was a reduction in microbial richness and diversity after fracturing, with the lowest diversity at 49 days. Thirty-one taxa dominated injected, flowback, and produced water communities, which took on distinct signatures as injected carbon and electron acceptors were attenuated within the shale. The majority (>90%) of the community in flowback and produced fluids was related to halotolerant bacteria associated with fermentation, hydrocarbon oxidation, and sulfur-cycling metabolisms, including heterotrophic genera Halolactibacillus, Vibrio, Marinobacter, Halanaerobium, and Halomonas, and autotrophs belonging to Arcobacter. Sequences related to halotolerant methanogenic genera Methanohalophilus and Methanolobus were detected at low abundance (<2%) in produced waters several months after hydraulic fracturing. Five taxa were strong indicators of later produced fluids. These results provide insight into the temporal trajectory of subsurface microbial communities after "fracking" and have important implications for the enrichment of microbes potentially detrimental to well infrastructure and natural gas fouling during this process.
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Affiliation(s)
- Maryam A Cluff
- Department of Civil, Environmental and Geodetic Engineering, Ohio State University , Columbus, Ohio 43210, United States
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Yokaryo H, Tokiwa Y. Isolation of alkaliphilic bacteria for production of high optically pure L-(+)-lactic acid. J GEN APPL MICROBIOL 2014; 60:270-5. [DOI: 10.2323/jgam.60.270] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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19
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Chen YS, Wu HC, Lo HY, Hsu WH, Lin WC, Lin BY. Isolation, Identification and Characterization of Lactic Acid Bacteria FromShao-jiou-luo(Fermented Zoned Cerith), a Traditional Fermented Food in Taiwan. JOURNAL OF AQUATIC FOOD PRODUCT TECHNOLOGY 2013. [DOI: 10.1080/10498850.2012.670191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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20
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Ishikawa M, Yamasato K, Kodama K, Yasuda H, Matsuyama M, Okamoto-Kainuma A, Koizumi Y. Alkalibacterium gilvum sp. nov., slightly halophilic and alkaliphilic lactic acid bacterium isolated from soft and semi-hard cheeses. Int J Syst Evol Microbiol 2013; 63:1471-1478. [DOI: 10.1099/ijs.0.042556-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nine novel strains of halophilic and alkaliphilic lactic acid bacteria isolated from European soft and semi-hard cheeses by using a saline, alkaline medium (7 % NaCl, pH 9.5) were taxonomically characterized. The isolates were Gram-stain-positive, non-sporulating and non-motile. They lacked catalase and quinones. Under anaerobic cultivation conditions, lactate was produced from d-glucose with the production of formate, acetate and ethanol with a molar ratio of approximately 2 : 1 : 1. Under aerobic cultivation conditions, acetate and lactate were produced from d-glucose. The isolates were slightly halophilic, highly halotolerant and alkaliphilic. The optimum NaCl concentration for growth ranged between 2.0 % and 5.0 % (w/v), with a growth range of 0–1 % to 15–17.5 %. The optimum pH for growth ranged between 8.5 and 9.5, with a growth range of 7.0–7.5 to 9.5–10.0. Comparative sequence analysis of the 16S rRNA genes revealed that the isolates occupied a phylogenetic position within the genus
Alkalibacterium
, showing the highest sequence similarity (98.2 %) to
Alkalibacterium kapii
T22-1-2T. The isolates constituted a single genomic species with DNA–DNA hybridization values of 79–100 % among the isolates and <29 % between the isolates and other members of the genus
Alkalibacterium
, from which the isolates were different in motility and flagellation, growth responses to NaCl concentrations and pH, and profiles of sugar fermentation. The DNA G+C contents were between 36.0 and 37.6 mol%. The cell-wall peptidoglycan was type A4β, Orn-d-Asp. The major components of cellular fatty acids were C14 : 0, C16 : 0 and C16 : 1ω9c. Based on the phenotypic characteristics and genetic distinctness, the isolates are classified as a novel species within the genus
Alkalibacterium
, for which the name Alkalibacterium gilvum sp. nov. is proposed. The type strain is 3AD-1T ( = DSM 25751T = JCM 18271T).
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Affiliation(s)
- Morio Ishikawa
- Department of Fermentation Science, Faculty of Applied Bio-Science, Tokyo University of Agriculture, 1-1 Sakuragaoka 1-chome, Setagaya-ku, Tokyo 156-8502, Japan
| | - Kazuhide Yamasato
- Department of Fermentation Science, Faculty of Applied Bio-Science, Tokyo University of Agriculture, 1-1 Sakuragaoka 1-chome, Setagaya-ku, Tokyo 156-8502, Japan
| | - Kayo Kodama
- Department of Fermentation Science, Faculty of Applied Bio-Science, Tokyo University of Agriculture, 1-1 Sakuragaoka 1-chome, Setagaya-ku, Tokyo 156-8502, Japan
| | - Hinako Yasuda
- Department of Fermentation Science, Faculty of Applied Bio-Science, Tokyo University of Agriculture, 1-1 Sakuragaoka 1-chome, Setagaya-ku, Tokyo 156-8502, Japan
| | - Mioko Matsuyama
- Department of Fermentation Science, Faculty of Applied Bio-Science, Tokyo University of Agriculture, 1-1 Sakuragaoka 1-chome, Setagaya-ku, Tokyo 156-8502, Japan
| | - Akiko Okamoto-Kainuma
- Department of Fermentation Science, Faculty of Applied Bio-Science, Tokyo University of Agriculture, 1-1 Sakuragaoka 1-chome, Setagaya-ku, Tokyo 156-8502, Japan
| | - Yukimichi Koizumi
- Department of Fermentation Science, Faculty of Applied Bio-Science, Tokyo University of Agriculture, 1-1 Sakuragaoka 1-chome, Setagaya-ku, Tokyo 156-8502, Japan
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Ren B, Yang N, Wang J, Ma XL, Wang Q, Xie F, Guo H, Liu ZH, Pugin B, Zhang LX. Amphibacillus marinus sp. nov., a member of the genus Amphibacillus isolated from marine mud. Int J Syst Evol Microbiol 2013; 63:1485-1491. [DOI: 10.1099/ijs.0.045807-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-positive, spore-forming, rod-shaped bacterium, designated J1T was isolated from deep-sea mud collected from the South China Sea and subjected to polyphasic taxonomic investigation. Phylogenetic analysis based on 16S rRNA gene sequences revealed that J1T clustered with the type strains of
Amphibacillus cookii
,
Amphibacillus sediminis
and
Amphibacillus jilinensis
and exhibited a range of similarity of 93.9–97.0 % to members of the genus
Amphibacillus
. The DNA G+C content was 36.7 mol%. Chemotaxonomic analysis showed no quinones, and the cell wall contained meso-diaminopimelic acid as the diagnostic diamino acid for strain J1T. The major cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0. Strain J1T was positive for catalase activity and negative for oxidase activity. On the basis of phylogenetic position and phenotypic properties, strain J1T represents a novel species of the genus
Amphibacillus
and the name Amphibacillus marinus sp. nov. is proposed. The type strain is J1T ( = CGMCC 1.10434T = JCM 17099T).
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Affiliation(s)
- Biao Ren
- Graduate School of Chinese Academy of Sciences, Beijing, 100049, PR China
- Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Na Yang
- Graduate School of Chinese Academy of Sciences, Beijing, 100049, PR China
- Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Jian Wang
- Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Xiao-Long Ma
- Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Qian Wang
- Graduate School of Chinese Academy of Sciences, Beijing, 100049, PR China
- Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Feng Xie
- Graduate School of Chinese Academy of Sciences, Beijing, 100049, PR China
- Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Hui Guo
- Graduate School of Chinese Academy of Sciences, Beijing, 100049, PR China
- Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Zhi-Heng Liu
- Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Benoît Pugin
- Laboratorio de Microbiología Molecular, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Li-Xin Zhang
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China
- Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
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Enrichment of arsenic transforming and resistant heterotrophic bacteria from sediments of two salt lakes in Northern Chile. Extremophiles 2012; 16:523-38. [PMID: 22555750 DOI: 10.1007/s00792-012-0452-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Accepted: 04/02/2012] [Indexed: 02/07/2023]
Abstract
Microbial populations are involved in the arsenic biogeochemical cycle in catalyzing arsenic transformations and playing indirect roles. To investigate which ecotypes among the diverse microbial communities could have a role in cycling arsenic in salt lakes in Northern Chile and to obtain clues to facilitate their isolation in pure culture, sediment samples from Salar de Ascotán and Salar de Atacama were cultured in diluted LB medium amended with NaCl and arsenic, at different incubation conditions. The samples and the cultures were analyzed by nucleic acid extraction, fingerprinting analysis, and sequencing. Microbial reduction of As was evidenced in all the enrichments carried out in anaerobiosis. The results revealed that the incubation factors were more important for determining the microbial community structure than arsenic species and concentrations. The predominant microorganisms in enrichments from both sediments belonged to the Firmicutes and Proteobacteria phyla, but most of the bacterial ecotypes were confined to only one system. The occurrence of an active arsenic biogeochemical cycle was suggested in the system with the highest arsenic content that included populations compatible with microorganisms able to transform arsenic for energy conservation, accumulate arsenic, produce H(2), H(2)S and acetic acid (potential sources of electrons for arsenic reduction) and tolerate high arsenic levels.
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23
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Schmidt M, Priemé A, Johansen A, Stougaard P. Alkalilactibacillus ikkensis, gen. nov., sp. nov., a novel enzyme-producing bacterium from a cold and alkaline environment in Greenland. Extremophiles 2012; 16:297-305. [PMID: 22297696 DOI: 10.1007/s00792-012-0430-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Accepted: 01/05/2012] [Indexed: 10/14/2022]
Abstract
Three novel Gram-positive, endospore-forming bacteria were isolated from a cold and alkaline environment. Phylogenetic analysis showed that the strains were almost identical, and that they were related to Natronobacillus azotifigens 24KS-1(T) (95.8% identity), Paraliobacillus quinghaiensis YIM-C158(T) (95.1%), Paraliobacillus ryukyuensis O15-7(T) (94.5%), and Halolactibacillus miurensis M23-1(T) (93.9%). The isolates produced amylase, α-galactosidase, β-galactosidase, and β-glucuronidase, and showed optimal growth at pH 10, at 20°C, and at 2-8% (w/v) NaCl. Major fatty acids were C(14:0) (10.6-11.6%), anteiso-C(15:0) (25.7-32.7%), C(16:1) ω11c (12.2-16.0%), and C(16:0) (14.0-20.4%). The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol, and meso-diaminopimelic acid was found in the cell-wall peptidoglycan. The G+C content was 38.4%. DNA-DNA hybridization between strain GCM68(T) and H. miurensis M23-1(T) was 32.4%, while hybridization to N. azotifigens 24KS-1(T), Amphibacillus tropicus Z-7792(T), and Paraliobacillus ryukyuensis O15-7(T) was below 30%. The phylogenetic analysis and G+C content place strain GCM68(T) in relation to species belonging to Bacillus rRNA group 1, but phylogenetic and physiologic data combined with chemotaxonomic analyses support our proposal for a new genus, Alkalilactibacillus, gen. nov., with the novel species Alkalilactibacillus ikkensis, sp. nov. (type strain is GCM68(T) = DSM 19937 = LMG 24405).
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Affiliation(s)
- Mariane Schmidt
- Department of Agriculture and Ecology, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
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Nyanga-Koumou AP, Ouoba LII, Kobawila SC, Louembe D. Response mechanisms of lactic acid bacteria to alkaline environments: a review. Crit Rev Microbiol 2011; 38:185-90. [PMID: 22168378 DOI: 10.3109/1040841x.2011.640978] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Regulation of the cytoplasmic or internal pH (pHin) is a fundamental requirement for the survival and viability of bacteria. The optimum pHin for most bacteria is near the neutral point (pH 7.0). Therefore, bacteria may have some strategies to adapt themselves to the acidity or alkalinity of cytoplasm. As other microorganisms, lactic acid bacteria (LAB) are able to maintain a neutral or near neutral cytoplasmic pH even when the pH of the external medium varies. Mechanisms facilitating survival and growth under alkaline conditions of LAB are reviewed. These mechanisms are: (i) the active potassium extrusion and the potassium-proton antiport system, (ii) the sodium-proton antiport system, (iii) the proton-translocating adenosine triphosphatase (ATPase), (iv) the formation of transmembrane proton gradients (ΔpH) in a reversed direction, and (v) the adaptation, cross-protection, and changes in protein synthesis.
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Affiliation(s)
- Armand P Nyanga-Koumou
- Département de Biologie Cellulaire et Moléculaire, Faculté des Sciences, Université Marien N'Gouabi, Brazzaville, Congo
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25
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Ishikawa M, Nakajima K, Ishizaki S, Kodama K, Okamoto-Kainuma A, Koizumi Y, Yamamoto Y, Yamasato K. Alkalibacterium subtropicum sp. nov., a slightly halophilic and alkaliphilic marine lactic acid bacterium isolated from decaying marine algae. Int J Syst Evol Microbiol 2011; 61:2996-3002. [PMID: 21296925 DOI: 10.1099/ijs.0.027953-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023] Open
Abstract
Two novel strains of marine lactic acid bacteria, isolated from decaying marine algae collected from a subtropical area of Japan, are described. The isolates, designated O24-2(T) and O25-2, were Gram-positive, non-sporulating and non-motile. They lacked catalase and quinones. Under anaerobic cultivation conditions, lactate was produced from glucose with the production of formate, acetate and ethanol in a molar ratio of approximately 2:1:1. Under aerobic cultivation conditions, acetate and lactate were produced from carbohydrates and related compounds. The isolates were slightly halophilic, highly halotolerant and alkaliphilic. They were able to grow in 0-17.0% (w/v) NaCl, with optimum growth of strains O24-2(T) and O25-2 at 1.0-3.0 and 1.0-2.0% (w/v) NaCl, respectively. Growth of strain O24-2(T) was observed at pH 7.5-9.5, with optimum growth at pH 8.0-8.5. Comparative 16S rRNA gene sequence analysis revealed that the isolates occupied a phylogenetic position within the genus Alkalibacterium, showing highest similarity (99.6%) to Alkalibacterium putridalgicola T129-2-1(T). Although sequence similarity was high, the DNA-DNA relatedness value between strain O24-2(T) and A. putridalgicola T129-2-1(T) was 27%, indicating that they are members of distinct species. The DNA G+C contents of O24-2(T) and O25-2 were 43.7 and 44.4 mol%, respectively, and DNA-DNA relatedness between the isolates was 89%. The cell-wall peptidoglycan was type A4β, Orn-d-Asp. The major cellular fatty acid components were C(14:0), C(16:0) and C(16:1)ω9c. Based on phenotypic characteristics and genetic distinctiveness, the isolates were classified as representatives of a novel species within the genus Alkalibacterium, for which the name Alkalibacterium subtropicum sp. nov. is proposed; the type strain is O24-2(T) (=DSM 23664(T)=NBRC 107172(T)).
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Affiliation(s)
- Morio Ishikawa
- Department of Fermentation Science, Faculty of Applied Bio-Science, Tokyo University of Agriculture, 1-1 Sakuragaoka 1-chome, Setagaya-ku, Tokyo 156-8502, Japan
| | - Kazuyuki Nakajima
- Department of Fermentation Science, Faculty of Applied Bio-Science, Tokyo University of Agriculture, 1-1 Sakuragaoka 1-chome, Setagaya-ku, Tokyo 156-8502, Japan
| | - Shihomi Ishizaki
- Department of Fermentation Science, Faculty of Applied Bio-Science, Tokyo University of Agriculture, 1-1 Sakuragaoka 1-chome, Setagaya-ku, Tokyo 156-8502, Japan
| | - Kayo Kodama
- Department of Fermentation Science, Faculty of Applied Bio-Science, Tokyo University of Agriculture, 1-1 Sakuragaoka 1-chome, Setagaya-ku, Tokyo 156-8502, Japan
| | - Akiko Okamoto-Kainuma
- Department of Fermentation Science, Faculty of Applied Bio-Science, Tokyo University of Agriculture, 1-1 Sakuragaoka 1-chome, Setagaya-ku, Tokyo 156-8502, Japan
| | - Yukimichi Koizumi
- Department of Fermentation Science, Faculty of Applied Bio-Science, Tokyo University of Agriculture, 1-1 Sakuragaoka 1-chome, Setagaya-ku, Tokyo 156-8502, Japan
| | - Yasushi Yamamoto
- Department of Fermentation Science, Faculty of Applied Bio-Science, Tokyo University of Agriculture, 1-1 Sakuragaoka 1-chome, Setagaya-ku, Tokyo 156-8502, Japan
| | - Kazuhide Yamasato
- Department of Fermentation Science, Faculty of Applied Bio-Science, Tokyo University of Agriculture, 1-1 Sakuragaoka 1-chome, Setagaya-ku, Tokyo 156-8502, Japan
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Pugin B, Blamey JM, Baxter BK, Wiegel J. Amphibacillus cookii sp. nov., a facultatively aerobic, spore-forming, moderately halophilic, alkalithermotolerant bacterium. Int J Syst Evol Microbiol 2011; 62:2090-2096. [PMID: 22038999 DOI: 10.1099/ijs.0.034629-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Novel strains of facultatively aerobic, moderately alkaliphilic and facultatively halophilic bacteria were isolated from a sediment sample taken from the Southern Arm of Great Salt Lake, Utah. Cells of strain JW/BP-GSL-QD(T) (and related strains JW/BP-GSL-RA and JW/BP-GSL-WB) were rod-shaped, spore-forming, motile bacteria with variable Gram-staining. Strain JW/BP-GSL-QD(T) grew under aerobic conditions between 14.5 and 47 °C (optimum 39 °C), in the pH(37 °C) range 6.5-10.3 (optimum pH(37 °C) 8.0), and between 0.1 and 4.5 M Na(+) (optimum 0.9 M Na(+)). No growth was observed in the absence of supplemented Na(+). Strain JW/BP-GSL-QD(T) utilized L-arabinose, D-fructose, D-galactose, D-glucose, inulin, lactose, maltose, mannitol, D-mannose, pyruvate, D-ribose, D-sorbitol, starch, trehalose, xylitol and D-xylose under both aerobic and anaerobic conditions, and used ethanol and methanol only under aerobic conditions. Strains JW/BP-GSL-WB and JW/BP-GSL-RA had the same profiles except that methanol was not used aerobically. During growth on glucose, the major organic compounds formed under aerobic conditions were acetate and lactate, and under anaerobic conditions, the fermentation products were formate, acetate, lactate and ethanol. Oxidase and catalase activities were not detected and cytochrome was absent. No respiratory quinones were detected. The main cellular fatty acids were iso-C(15 : 0) (39.1 %) and anteiso-C(15 : 0) (36.3 %). Predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unknown phospholipid. Additionally, a small amount of an unknown glycolipid was detected. The DNA G+C content of strain JW/BP-GSL-QD(T) was 35.4 mol% (determined by HPLC). For strain JW/BP-GSL-QD(T) the highest degree of 16S rRNA gene sequence similarity was found with Amphibacillus jilinensis (98.6 %), Amphibacillus sediminis (96.7 %) and Amphibacillus tropicus (95.6 %). The level of DNA-DNA relatedness between strain JW/BP-GSL-QD(T) and A. jilinensis Y1(T) was 58 %. On the basis of physiological, chemotaxonomic and phylogenetic data, strain JW/BP-GSL-QD(T) represents a novel species of the genus Amphibacillus, for which the name Amphibacillus cookii sp. nov. is proposed. The type strain is JW/BP-GSL-QD(T) (= ATCC BAA-2118(T) = DSM 23721(T)).
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Affiliation(s)
- Benoît Pugin
- Fundación Biociencia, José Domingo Cañas 2280, Ñuñoa, Santiago, Chile.,Department of Microbiology, University of Georgia, 1000 Cedar Street, Athens, GA 30602, USA
| | - Jenny M Blamey
- Fundación Biociencia, José Domingo Cañas 2280, Ñuñoa, Santiago, Chile
| | - Bonnie K Baxter
- Great Salt Lake Institute, Westminster College, 1840 South, 1300 East, Salt Lake City, UT 84105, USA
| | - Juergen Wiegel
- Department of Microbiology, University of Georgia, 1000 Cedar Street, Athens, GA 30602, USA
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Calabia BP, Tokiwa Y, Aiba S. Fermentative production of l-(+)-lactic acid by an alkaliphilic marine microorganism. Biotechnol Lett 2011; 33:1429-33. [DOI: 10.1007/s10529-011-0573-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2010] [Accepted: 02/18/2011] [Indexed: 11/24/2022]
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Wang X, Xue Y, Ma Y. Streptohalobacillus salinus gen. nov., sp. nov., a moderately halophilic, Gram-positive, facultative anaerobe isolated from subsurface saline soil. Int J Syst Evol Microbiol 2010; 61:1127-1132. [PMID: 20543154 DOI: 10.1099/ijs.0.025338-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, rod-shaped, non-sporulating, motile and moderately halophilic bacterium, designated strain H96B60(T), was isolated from a saline soil sample of the Qaidam basin, China. The strain was facultatively anaerobic. Major end products formed from glucose fermentation were acetate, ethanol and lactic acid. The cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. The isoprenoid quinone component was menaquinone-6 (MK-6). The predominant cellular fatty acids were C(16: 0), anteiso-C(13 : 0) and anteiso-C(15 : 0). The genomic DNA G+C content of strain H96B60(T) was 36.2 mol%. Phylogenetic analysis based on comparative 16S rRNA gene sequences indicated that strain H96B60(T) represented a novel phyletic lineage within the family Bacillaceae and was related most closely to Halolactibacillus species (96.1-96.4 % similarity). Based on the phenotypic, chemotaxonomic and phylogenetic data presented, strain H96B60(T) is considered to represent a novel species of a new genus, for which the name Streptohalobacillus salinus gen. nov., sp. nov. is proposed. The type strain of Streptohalobacillus salinus is H96B60(T) ( = DSM 22440(T) = CGMCC 1.7733(T)).
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Affiliation(s)
- Xiaowei Wang
- Graduate University of the Chinese Academy of Sciences, Beijing 100049, PR China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yanfen Xue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yanhe Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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30
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Liu W, Jiang L, Guo C, Yang SS. Terribacillus aidingensis sp. nov., a moderately halophilic bacterium. Int J Syst Evol Microbiol 2010; 60:2940-2945. [PMID: 20118295 DOI: 10.1099/ijs.0.017228-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three Gram-positive, moderately halophilic bacteria, designated YI7-61(T), IA7 and DB2, were isolated from sediments of Aiding salt lake in the Xinjiang region of China. Cells of the strains were rod-shaped, motile by means of peritrichous flagella and produced ellipsoidal spores. Colonies were pale yellow in colour. The strains grew optimally at 30-37 °C, pH 6-7 and 3-7 % (w/v) NaCl. The diamino acid in the murein was meso-diaminopimelic acid and the major quinone system was MK-7. The major cellular fatty acids were anteiso-C(15 : 0) and anteiso-C(17 : 0). The DNA G+C content was 44.6-45.0 mol%. 16S rRNA gene sequence analysis revealed that strains YI7-61(T), IA7 and DB2 were closely related to members of the genus Terribacillus and showed 96.8-97.6, 96.4-97.2 and 95.4-95.5 % 16S rRNA gene sequence similarity with Terribacillus halophilus 002-051(T), Terribacillus saccharophilus RB589 and Terribacillus goriensis CL-GR16(T), respectively. DNA-DNA relatedness among the isolates was 88-92 % and strain YI7-61(T) shared 24, 18 and 18 % DNA-DNA relatedness with T. halophilus JCM 21760(T), T. saccharophilus JCM 21759(T) and T. goriensis DSM 18252(T), respectively. On the basis of phenotypic and phylogenetic distinctiveness, the three isolates should be placed in the genus Terribacillus as representatives of a novel species, for which the name Terribacillus aidingensis sp. nov. is proposed. The type strain is YI7-61(T) (=CGMCC 1.8913(T) =NBRC 105790(T)).
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Affiliation(s)
- Wenyan Liu
- National Engineering Laboratory of Biohydrometallurgy, General Research Institute for Nonferrous Metals, Beijing 100088, PR China.,College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, PR China
| | - Linlin Jiang
- Northeast Agricultural University, Haerbin 150030, PR China
| | - Chunjing Guo
- Northeast Agricultural University, Haerbin 150030, PR China
| | - Su Sheng Yang
- Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Key Laboratory for Agro-Microbial Resource and Application, Ministry of Agriculture, Beijing 100193, PR China
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Namwong S, Tanasupawat S, Lee KC, Lee JS. Oceanobacillus kapialis sp. nov., from fermented shrimp paste in Thailand. Int J Syst Evol Microbiol 2009; 59:2254-9. [PMID: 19620352 DOI: 10.1099/ijs.0.007161-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-positive, rod-shaped, strictly aerobic, spore-forming, moderately halophilic bacterium, designated strain SSK2-2T, was isolated from fermented shrimp paste (ka-pi) produced in Thailand. It contained MK-7 as the predominant menaquinone and meso-diaminopimelic acid in the cell-wall peptidoglycan. The isolate grew at 8-43 degrees C, pH 6-9 and in 0.5-24% (w/v) NaCl (optimum, 6-14% NaCl). The major cellular fatty acids were anteiso-C15:0 and anteiso-C17:0. Phosphatidylglycerol and diphosphatidylglycerol were the major polar lipid components. The DNA G+C content was 39.7 mol%. Comparative 16S rRNA gene sequence analyses showed that strain SSK2-2T was most closely related to Oceanobacillus picturae KCTC 3821T with 98.7% sequence similarity. Based on phenotypic and molecular features combined with DNA-DNA hybridization results (<or=24.9% with O. picturae KCTC 3821T), this strain represents a novel species of the genus Oceanobacillus for which the name Oceanobacillus kapialis sp. nov. is proposed; the type strain is SSK2-2T (=KCTC 13177T=PCU 300T=TISTR 1858T).
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Affiliation(s)
- Sirilak Namwong
- Department of Biotechnology, Faculty of Science and Technology, Suan Sunandha Rajabhat University, Bangkok 10300, Thailand
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Arai T, Yanahashi S, Sato J, Sato T, Ishikawa M, Koizumi Y, Kawasaki S, Niimura Y, Nakagawa J. Taxonomical and physiological comparisons of the three species of the genus Amphibacillus. J GEN APPL MICROBIOL 2009; 55:155-62. [PMID: 19436132 DOI: 10.2323/jgam.55.155] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Amphibacillus is a genus for Gram-positive, spore-forming, rod-shaped, facultatively anaerobic bacteria with low-G+C content of DNA, established by Niimura et al. in 1990. Amphibacillus xylanus, the type species of the genus, grows well under both strictly anaerobic and aerobic conditions in spite of lacking any isoprenoid quinones, cytochromes, and catalase. Amphibacillus fermentum and Amphibacillus tropicus were later proposed by Zhilina et al. in 2001 for the isolates from a soda lake. In this paper, we revealed the latter two species also lacked isoprenoid quinones, cytochrome and catalase, and that they grew well under strictly anaerobic and aerobic conditions. The consistent growth of A. xylanus under both conditions is due to the presence of anaerobic and aerobic pathways for glucose metabolism in the organism. Although A. fermentum and A. tropicus are supposed to have a side enzymatic pyruvate pathway to produce lactate under both conditions, the two species have two major pyruvate metabolic pathways as observed in A. xylanus. Analysis data indicated that NADH formed both by the aerobic pyruvate pathway and by the glycolytic pathway was re-oxidized by the NADH oxidase in A. fermentum and A. tropicus as well as A. xylanus, and furthermore that the NADH oxidase-Prx (AhpC) system, i.e., NADH oxidase scavenging hydrogen peroxide with Prx, also functions in A. tropicus as observed with A. xylanus. Not only the taxonomical character of the genus Amphibacillus but also the growth characterization based on the two metabolic pathways and unique oxygen metabolism are distinctive in those traits from other facultative anaerobes.
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Affiliation(s)
- Toshiaki Arai
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
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Ishikawa M, Tanasupawat S, Nakajima K, Kanamori H, Ishizaki S, Kodama K, Okamoto-Kainuma A, Koizumi Y, Yamamoto Y, Yamasato K. Alkalibacterium thalassium sp. nov., Alkalibacterium pelagium sp. nov., Alkalibacterium putridalgicola sp. nov. and Alkalibacterium kapii sp. nov., slightly halophilic and alkaliphilic marine lactic acid bacteria isolated from marine organisms and salted foods collected in Japan and Thailand. Int J Syst Evol Microbiol 2009; 59:1215-26. [DOI: 10.1099/ijs.0.65602-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Chen YG, Cui XL, Zhang YQ, Li WJ, Wang YX, Xu LH, Wen ML, Peng Q, Jiang CL. Paraliobacillus quinghaiensis sp. nov., isolated from salt-lake sediment in China. Int J Syst Evol Microbiol 2009; 59:28-33. [DOI: 10.1099/ijs.0.65735-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Krishnamurthi S, Chakrabarti T. Proposal for transfer of Pelagibacillus goriensis Kim et al. 2007 to the genus Terribacillus as Terribacillus goriensis comb. nov. Int J Syst Evol Microbiol 2008; 58:2287-91. [PMID: 18842842 DOI: 10.1099/ijs.0.65579-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The phenotypic, chemotaxonomic and genotypic characteristics of two recently described genera were compared. Terribacillus saccharophilus and Pelagibacillus goriensis (both type species of their respective genera) are similar in many phenotypic characteristics and in their fatty acid profiles, both have MK-7 as the major menaquinone and they have similar G+C contents. Comparison of the 16S rRNA gene sequence of P. goriensis CL-GR16(T) with those of T. saccharophilus 002-048(T) and Terribacillus halophilus 002-051(T) showed high degrees of sequence similarity, respectively 99.8 and 98.9 %. Phylogenetically, these three taxa are closely related and form a coherent cluster in the phylogenetic tree. The genomic relatedness of P. goriensis DSM 18252(T) with T. saccharophilus JCM 21759(T) and T. halophilus JCM 21760(T) is 51.7 and 35.6 %, respectively, which is well below the value of 70 % recommended for delineation of species. P. goriensis differs from T. saccharophilus in motility, the Voges-Proskauer test and acid production from and utilization of some carbohydrates. Based on these analyses, we conclude that Pelagibacillus should not be considered a separate genus and hence Pelagibacillus goriensis should be transferred to the genus Terribacillus as Terribacillus goriensis comb. nov., with the type strain CL-GR16(T) (=KCCM 42329(T) =DSM 18252(T)).
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Affiliation(s)
- Srinivasan Krishnamurthi
- Microbial Type Culture Collection & Gene Bank (MTCC), Institute of Microbial Technology, Sector 39A, Chandigarh 160 036, India
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Natronobacillus azotifigens gen. nov., sp. nov., an anaerobic diazotrophic haloalkaliphile from soda-rich habitats. Extremophiles 2008; 12:819-27. [PMID: 18769867 DOI: 10.1007/s00792-008-0188-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2008] [Accepted: 08/17/2008] [Indexed: 10/21/2022]
Abstract
Gram-positive bacteria capable of nitrogen fixation were obtained in microoxic enrichments from soda soils in south-western Siberia, north-eastern Mongolia, and the Lybian desert (Egypt). The same organisms were obtained in anoxic enrichments with glucose from soda lake sediments in the Kulunda Steppe (Altai, Russia) using nitrogen-free alkaline medium of pH 10. The isolates were represented by thin motile rods forming terminal round endospores. They are strictly fermentative saccharolytic anaerobes but tolerate high oxygen concentrations, probably due to a high catalase activity. All of the strains are obligately alkaliphilic and highly salt-tolerant natronophiles (chloride-independent sodaphiles). Growth was possible within a pH range from 7.5 to 10.6, with an optimum at 9.5-10, and within a salt range from 0.2 to 4 M Na(+), with an optimum at 0.5-1.5 M for the different strains. The nitrogenase activity in the whole cells also had an alkaline pH optimum but was much more sensitive to high salt concentrations compared to the growing cells. The isolates formed a compact genetic group with a high level of DNA similarity. Phylogenetic analysis based on 16S-rRNA gene sequences placed the isolates into Bacillus rRNA group 1 as a separate lineage with Amphibacillus tropicus as the nearest relative. In all isolates the key functional nitrogenase gene nifH was detected. A new genus and species, Natronobacillus azotifigens gen. nov., sp. nov., is proposed to accommodate the novel diazotrophic haloalkaliphiles.
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Cao SJ, Qu JH, Yang JS, Sun Q, Yuan HL. Halolactibacillus alkaliphilus sp. nov., a moderately alkaliphilic and halophilic bacterium isolated from a soda lake in Inner Mongolia, China, and emended description of the genus Halolactibacillus. Int J Syst Evol Microbiol 2008; 58:2169-73. [DOI: 10.1099/ijs.0.65511-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Lee JC, Li WJ, Xu LH, Jiang CL, Kim CJ. Lentibacillus salis sp. nov., a moderately halophilic bacterium isolated from a salt lake. Int J Syst Evol Microbiol 2008; 58:1838-43. [DOI: 10.1099/ijs.0.65545-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Yumoto I, Hirota K, Nodasaka Y, Tokiwa Y, Nakajima K. Alkalibacterium indicireducens sp. nov., an obligate alkaliphile that reduces indigo dye. Int J Syst Evol Microbiol 2008; 58:901-5. [PMID: 18398191 DOI: 10.1099/ijs.0.64995-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Indigo-reducing, obligately alkaliphilic strains A11T, F11 and F12 were isolated from indigo fermentation liquor obtained from Tokushima Prefecture, Shikoku, Japan. The isolates grew at pH 9.0-12.3, but not at pH 7.0-8.0. The optimum pH range for growth was 9.5-11.5. They were Gram-negative, facultatively anaerobic, rod-shaped strains with peritrichous flagella. The isolates grew in 0-14 % (w/v) NaCl, with optimum growth at 1-11 %. They grew at temperatures of 15-35 degrees C with optimum growth at around 20-30 degrees C. dl-Lactate was the major end product from d-glucose. No quinones were detected. The peptidoglycan type was A4 alpha, l-Lys (l-Orn)-d-Asp. The major cellular fatty acids were C16 : 0, C16 : 17c and C18 : 19c. The DNA G+C contents were 47.0-47.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequence data indicated that the isolates belong to the genus Alkalibacterium. DNA-DNA hybridization revealed low relatedness values between the isolates and the three phylogenetically most closely related species, Alkalibacterium olivapovliticus, Alkalibacterium psychrotolerans and Alkalibacterium iburiense (<41 %). On the basis of phenotypic characteristics, including hydrolysis of cellulose and fermentation of carbohydrates, and chemotaxonomic characteristics, phylogenetic data and DNA-DNA relatedness data, it is concluded that the isolates merit classification as representatives of a novel species of the genus Alkalibacterium, for which the name Alkalibacterium indicireducens sp. nov. is proposed. The type strain of this species is A11T (=JCM 14232T=NCIMB 14253T).
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Affiliation(s)
- Isao Yumoto
- Research Institute of Genome-based Biofactory, National Institute of Advanced Industrial Science and Technology, Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan.
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Tokiwa Y, Calabia BP. Biological production of functional chemicals from renewable resources. CAN J CHEM 2008. [DOI: 10.1139/v08-046] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The development and implementation of renewable feedstocks for the production of multifunctional chemicals has received attention from the food and pharmaceutical industries and also as potential raw materials for the manufacture of biodegradable polymers. A major shift towards renewable resources, however, requires new ways to optimize and evaluate industrial processes. There are several possibilities to replace chemical techniques with biological methods based on renewable resources. This review discusses some examples of process development in which a biotechnological route might be favorable leading to industrial realization. Herein are described the production of biomaterials that can be used as monomers in plastics, such as lactic acid for polylactide (PLA), (R)-3-hydroxybutyric acid (R-3HB) for poly[(R)-3-hydroxybutyrate] (PHB), and succinic acid for poly(butylene succinate) (PBS). Moreover, several species of microorganisms that produce significant quantities of these functional chemicals under specific cultivation conditions from biomass-derived carbohydrates are also reviewed.Key words: functional chemicals, renewable resources, lactic acid, (R)-3-hydroxybutyric acid, succinic acid.
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An SY, Ishikawa S, Kasai H, Goto K, Yokota A. Amphibacillus sediminis sp. nov., an endospore-forming bacterium isolated from lake sediment in Japan. Int J Syst Evol Microbiol 2008; 57:2489-2492. [PMID: 17978206 DOI: 10.1099/ijs.0.64926-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A facultatively anaerobic, moderately alkaliphilic, Gram-positive, spore-forming and rod-shaped bacterial strain, Shu-P-Ggiii25-2T, was isolated from lake sediment in Shizuoka, Japan, and was characterized taxonomically using a polyphasic approach. Analysis of the 16S rRNA gene sequence indicated that the novel isolate clustered with the type strain of Amphibacillus xylanus and it exhibited sequence similarities of 94.9-95.6% to the type strains of species of the genus Amphibacillus. Isoprenoid quinones and oxidase and catalase activities were not detected for strain Shu-P-Ggiii25-2T. The DNA G+C content was 42.3 mol%, the cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid and the major cellular fatty acids were iso-C14:0, iso-C15:0, anteiso-C15:0, C16:0 and iso-C16:0. On the basis of phylogenetic position and phenotypic properties, strain Shu-P-Ggiii25-2T represents a novel species of the genus Amphibacillus, for which the name Amphibacillus sediminis sp. nov. is proposed. The type strain is Shu-P-Ggiii25-2T (=MBIC08269T=IAM 15428T=KCTC 13120T). An emended description of the genus Amphibacillus is also given.
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Affiliation(s)
- Sun-Young An
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Yayoi, 1-1-1, Bunkyo-Ku, Tokyo 113-0032, Japan
| | - Shu Ishikawa
- Marine Biotechnology Institute Co. Ltd, 3-75-1, Heita, Kamaishi, Iwate 026-0001, Japan
| | - Hiroaki Kasai
- Marine Biotechnology Institute Co. Ltd, 3-75-1, Heita, Kamaishi, Iwate 026-0001, Japan
| | - Keiichi Goto
- Microbiological and Analytical Group, Food Research Laboratories, Mitsui Norin Co. Ltd, 223-1, Miyahara, Fujieda, Shizuoka 426-0133, Japan
| | - Akira Yokota
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Yayoi, 1-1-1, Bunkyo-Ku, Tokyo 113-0032, Japan
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Kim YG, Hwang CY, Yoo KW, Moon HT, Yoon JH, Cho BC. Pelagibacillus goriensis gen. nov., sp. nov., a moderately halotolerant bacterium isolated from coastal water off the east coast of Korea. Int J Syst Evol Microbiol 2007; 57:1554-1560. [PMID: 17625193 DOI: 10.1099/ijs.0.64820-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-positive, moderately halotolerant bacterium, designated CL-GR16(T), was isolated from coastal water off the east coast of Korea. The strain was strictly aerobic, rod-shaped, motile by means of peritrichous flagella and produced ellipsoidal spores. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate represented an independent lineage within Bacillus rRNA group 1, showing 93.6-94.6 % similarity with respect to the genus Ornithinibacillus, 94.0 % with respect to Paucisalibacillus, 91.0-93.5 % with respect to Virgibacillus, 93.2-93.3 % with respect to Salinibacillus and 92.8-93.2 % with respect to Oceanobacillus. The optimum temperature and pH for growth were 30 degrees C and pH 7.5. Strain CL-GR16(T) was able to grow at NaCl concentrations from 0 to 14 %, with optimum growth occurring at 0-2 % NaCl. The strain lacked oxidase. The major fatty acids were anteiso-C(15 : 0) (65.6 %), anteiso-C(17 : 0) (11.0 %) and iso-C(15 : 0) (9.1 %). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid. The predominant menaquinone was MK-7. The G+C content of the DNA was 43 mol%. On the basis of the results of the polyphasic analysis, strain CL-GR16(T) represents a novel genus and species, for which the name Pelagibacillus goriensis gen. nov., sp. nov. is proposed. The type strain is strain CL-GR16(T) (=KCCM 42329(T)=DSM 18252(T)).
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MESH Headings
- Aerobiosis
- Anti-Bacterial Agents/pharmacology
- Bacillus/chemistry
- Bacillus/classification
- Bacillus/genetics
- Bacillus/isolation & purification
- Bacterial Typing Techniques
- Base Composition
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Fatty Acids/analysis
- Flagella
- Genes, rRNA
- Hydrogen-Ion Concentration
- Korea
- Locomotion
- Molecular Sequence Data
- Oxidoreductases/analysis
- Phospholipids/analysis
- Phylogeny
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Saline Solution, Hypertonic/pharmacology
- Seawater/microbiology
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Temperature
- Vitamin K 2/analysis
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Affiliation(s)
- Yoon-Gon Kim
- School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, San 56-1 Shillim-dong, Kwanak-gu, Seoul 151-742, Republic of Korea
| | - Chung Yeon Hwang
- School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, San 56-1 Shillim-dong, Kwanak-gu, Seoul 151-742, Republic of Korea
| | - Kwang Woo Yoo
- Safety and Technology Department, Korea Hydro and Nuclear Power Co. Ltd, 167 Samseong-dong, Gangnam-gu, Seoul 135-791, Republic of Korea
| | - Hyung Tae Moon
- Safety and Technology Department, Korea Hydro and Nuclear Power Co. Ltd, 167 Samseong-dong, Gangnam-gu, Seoul 135-791, Republic of Korea
| | - Jung-Hoon Yoon
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Republic of Korea
| | - Byung Cheol Cho
- School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, San 56-1 Shillim-dong, Kwanak-gu, Seoul 151-742, Republic of Korea
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Sawatari Y, Yokota A. Diversity and mechanisms of alkali tolerance in lactobacilli. Appl Environ Microbiol 2007; 73:3909-15. [PMID: 17449704 PMCID: PMC1932741 DOI: 10.1128/aem.02834-06] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We determined the maximum pH that allows growth (pHmax) for 34 strains of lactobacilli. High alkali tolerance was exhibited by strains of Lactobacillus casei, L. paracasei subsp. tolerans, L. paracasei subsp. paracasei, L. curvatus, L. pentosus, and L. plantarum that originated from plant material, with pHmax values between 8.5 and 8.9. Among these, L. casei NRIC 1917 and L. paracasei subsp. tolerans NRIC 1940 showed the highest pHmax, at 8.9. Digestive tract isolates of L. gasseri, L. johnsonii, L. reuteri, L. salivarius subsp. salicinius, and L. salivarius subsp. salivarius exhibited moderate alkali tolerance, with pHmax values between 8.1 and 8.5. Dairy isolates of L. delbrueckii subsp. bulgaricus, L. delbrueckii subsp. lactis, and L. helveticus exhibited no alkali tolerance, with pHmax values between 6.7 and 7.1. Measurement of the internal pH of representative strains revealed the formation of transmembrane proton gradients (DeltapH) in a reversed direction (i.e., acidic interior) at alkaline external-pH ranges, regardless of their degrees of alkali tolerance. Thus, the reversed DeltapH did not determine alkali tolerance diversity. However, the DeltapH contributed to alkali tolerance, as the pHmax values of several strains decreased with the addition of nigericin, which dissipates DeltapH. Although neutral external-pH values resulted in the highest glycolysis activity in the presence of nigericin regardless of alkali tolerance, substantial glucose utilization was still detected in the alkali-tolerant strains, even in a pH range of between 8.0 and 8.5, at which the remaining strains lost most activity. Therefore, the alkali tolerance of glycolysis reactions contributes greatly to the determination of alkali tolerance diversity.
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Affiliation(s)
- Yuki Sawatari
- Laboratory of Microbial Physiology, Division of Applied Bioscience, Research Faculty of Agriculture, Hokkaido University, Kita 9 Nishi 9, Kita-ku, Sapporo, Hokkaido 060-8589, Japan
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Ishikawa M, Kodama K, Yasuda H, Okamoto-Kainuma A, Koizumi K, Yamasato K. Presence of halophilic and alkaliphilic lactic acid bacteria in various cheeses. Lett Appl Microbiol 2007; 44:308-13. [PMID: 17309509 DOI: 10.1111/j.1472-765x.2006.02073.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AIM We sought to confirm the presence of halophilic and alkaliphilic lactic acid bacteria (HALAB) of marine origin in cheeses and thus contribute to the understanding of the roles of LAB flora in cheese ripening. METHODS AND RESULTS We used 7% NaCl glucose-yeast extract-peptone-fish extract broth and agar media (pH 9.5) for pour-plating and enrichment culture for 16 cheese samples produced in six European countries. HALAB were present in 9 of the 16 samples at < 20 --> 10(7) CFU g(-1). In three mould-ripened soft cheeses, HALAB counts ranged from 10(6) to 10(7) CFU g(-1) and were one order (two samples) and six orders (one sample) of magnitude greater than that of nonhaloalkaliphilic, common LAB, as enumerated on lactobacilli MRS agar. The 16S rRNA gene sequences (500 bp) of 51 of the 55 isolates examined were identical or similar to that of Marinilactibacillus psychrotolerans or Alkalibacterium olivapovliticus and related species, all of which are HALAB. CONCLUSIONS HALAB of possible marine origin were present in various soft, semi-hard and semi-soft cheeses and were highly predominant in some mould-ripened cheeses. SIGNIFICANCE AND IMPACT OF THE STUDY HALAB of possible marine origin are members of the microflora of various cheeses and, when dominant, may play a role in the ripening of cheeses. Microbial analysis of LAB flora in cheeses should take into consideration the presence of HALAB.
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Affiliation(s)
- M Ishikawa
- Department of Fermentation Science, Tokyo University of Agriculture, Tokyo, Japan.
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Pakdeeto A, Tanasupawat S, Thawai C, Moonmangmee S, Kudo T, Itoh T. Lentibacillus kapialis sp. nov., from fermented shrimp paste in Thailand. Int J Syst Evol Microbiol 2007; 57:364-369. [PMID: 17267980 DOI: 10.1099/ijs.0.64315-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two strains of strictly aerobic, moderately halophilic Gram-positive rods were isolated from fermented shrimp paste (‘ka-pi’) produced in Thailand. They produced a red pigment and grew optimally in the presence of 5–30 % NaCl. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The predominant menaquinone was MK-7. The major cellular fatty acid was anteiso-C15 : 0. Phosphatidylglycerol, diphosphatidylglycerol and two unidentified glycolipids were found to be the major polar lipid components. The DNA G+C content was 41.2–41.6 mol%. Comparative 16S rRNA gene sequence analyses showed that strain PN7-6T was most closely related to Lentibacillus salarius KCTC 3911T with 96.5 % sequence similarity. On the basis of phenotypic and molecular properties, the two isolates represent a novel species of the genus Lentibacillus, for which the name Lentibacillus kapialis sp. nov. is proposed. The type strain is PN7-6T (=JCM 12580T=PCU 259T=TISTR 1551T).
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MESH Headings
- Animals
- Bacillaceae/classification
- Bacillaceae/isolation & purification
- Bacillaceae/physiology
- Bacterial Typing Techniques
- Base Composition
- Carbohydrate Metabolism
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Decapoda/microbiology
- Diaminopimelic Acid/analysis
- Fatty Acids/analysis
- Fatty Acids/chemistry
- Fermentation
- Food Microbiology
- Genes, rRNA
- Molecular Sequence Data
- Peptidoglycan/chemistry
- Phospholipids/analysis
- Phospholipids/chemistry
- Phylogeny
- Pigments, Biological/biosynthesis
- Quinones/analysis
- Quinones/chemistry
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
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Affiliation(s)
- Amnat Pakdeeto
- Department of Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Somboon Tanasupawat
- Department of Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Chitti Thawai
- Department of Applied Biology, Faculty of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok 10520, Thailand
| | - Somporn Moonmangmee
- Thailand Institute of Scientific and Technological Research, Pathumthani 12120, Thailand
| | - Takuji Kudo
- Japan Collection of Microorganisms, RIKEN BioResource Center, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Takashi Itoh
- Japan Collection of Microorganisms, RIKEN BioResource Center, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
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