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Gagnon JC, Beauregard-Tousignant S, Marcil JS, Lazar CS. Deep Isolated Aquifer Brines Harbor Atypical Halophilic Microbial Communities in Quebec, Canada. Genes (Basel) 2023; 14:1529. [PMID: 37628582 PMCID: PMC10454208 DOI: 10.3390/genes14081529] [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: 06/15/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
The deep terrestrial subsurface, hundreds of meters to kilometers below the surface, is characterized by oligotrophic conditions, dark and often anoxic settings, with fluctuating pH, salinity, and water availability. Despite this, microbial populations are detected and active, contributing to biogeochemical cycles over geological time. Because it is extremely difficult to access the deep biosphere, little is known about the identity and metabolisms of these communities, although they likely possess unknown pathways and might interfere with deep waste deposits. Therefore, we analyzed rock and groundwater microbial communities from deep, isolated brine aquifers in two regions dating back to the Ordovician and Devonian, using amplicon and whole genome sequencing. We observed significant differences in diversity and community structure between both regions, suggesting an impact of site age and composition. The deep hypersaline groundwater did not contain typical halophilic bacteria, and genomes suggested pathways involved in protein and hydrocarbon degradation, and carbon fixation. We identified mainly one strategy to cope with osmotic stress: compatible solute uptake and biosynthesis. Finally, we detected many bacteriophage families, potentially indicating that bacteria are infected. However, we also found auxiliary metabolic genes in the viral genomes, probably conferring an advantage to the infected hosts.
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Affiliation(s)
- Jean-Christophe Gagnon
- Department of Biological Sciences, University of Québec at Montréal (UQAM), C.P. 8888, Succ. Centre-Ville, Montréal, QC H3C 3P8, Canada; (J.-C.G.); (S.B.-T.)
- Interuniversity Research Group in Limnology/Groupe de Recherche Interuniversitaire en Limnologie (GRIL), Montréal, QC H3C 3P8, Canada
| | - Samuel Beauregard-Tousignant
- Department of Biological Sciences, University of Québec at Montréal (UQAM), C.P. 8888, Succ. Centre-Ville, Montréal, QC H3C 3P8, Canada; (J.-C.G.); (S.B.-T.)
| | - Jean-Sébastien Marcil
- Derena Geosciences, Quebec, QC G7A 3Y5, Canada;
- Ressources Utica Inc., Quebec, QC G1V 4M7, Canada
| | - Cassandre Sara Lazar
- Department of Biological Sciences, University of Québec at Montréal (UQAM), C.P. 8888, Succ. Centre-Ville, Montréal, QC H3C 3P8, Canada; (J.-C.G.); (S.B.-T.)
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2
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Farjana N, Tu Z, Furukawa H, Yumoto I. Environmental factors contributing to the convergence of bacterial community structure during indigo reduction. Front Microbiol 2023; 14:1097595. [PMID: 36876097 PMCID: PMC9978934 DOI: 10.3389/fmicb.2023.1097595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/16/2023] [Indexed: 02/11/2023] Open
Abstract
Indigo is solubilized through the reducing action of the microbiota that occurs during alkaline fermentation of composted leaves of Polygonum tinctorium L. (sukumo). However, the environmental effects on the microbiota during this treatment, as well as the mechanisms underlying the microbial succession toward stable state remain unknown. In this study, physicochemical analyses and Illumina metagenomic sequencing was used to determine the impact pretreatment conditions on the subsequent initiation of bacterial community transition and their convergence, dyeing capacity and the environmental factors critical for indigo reducing state during aging of sukumo. The initial pretreatment conditions analyzed included 60°C tap water (heat treatment: batch 1), 25°C tap water (control; batch 2), 25°C wood ash extract (high pH; batch 3) and hot wood ash extract (heat and high pH; batch 4), coupled with successive addition of wheat bran from days 5 to 194. High pH had larger impact than heat treatment on the microbiota, producing more rapid transitional changes from days 1 to 2. Although the initial bacterial community composition and dyeing intensity differed during days 2-5, the microbiota appropriately converged to facilitate indigo reduction from day 7 in all the batches, with Alkaliphilus oremalandii, Amphibacillus, Alkalicella caledoniensis, Atopostipes suicloalis and Tissierellaceae core taxa contributing to the improvement of when the dyeing intensity. This convergence is attributed to the continuous maintenance of high pH (day 1 ~) and low redox potential (day 2~), along with the introduction of wheat bran at day 5 (day 5~). PICRUSt2 predictive function profiling revealed the enrichment of phosphotransferease system (PTS) and starch and sucrose metabolism subpathways key toward indigo reduction. Seven NAD(P)-dependent oxidoreductases KEGG orthologs correlating to the dyeing intensity was also identified, with Alkalihalobacillus macyae, Alkalicella caledoniensis, and Atopostipes suicloalis contributing significantly toward the initiation of indigo reduction in batch 3. During the ripening period, the staining intensity was maintained by continuous addition of wheat bran and the successive emergence of indigo-reducing bacteria that also contributed to material circulation in the system. The above results provide insight into the interaction of microbial system and environmental factors in sukumo fermentation.
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Affiliation(s)
- Nowshin Farjana
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan.,Laboratory of Environmental Microbiology, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Zhihao Tu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan.,Laboratory of Environmental Microbiology, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Hiromitsu Furukawa
- Sensing System Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan
| | - Isao Yumoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan.,Laboratory of Environmental Microbiology, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
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3
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Li S, Shi Y, Huang H, Tong Y, Wu S, Wang Y. Fermentation Blues: Analyzing the Microbiota of Traditional Indigo Vat Dyeing in Hunan, China. Microbiol Spectr 2022; 10:e0166322. [PMID: 35708341 PMCID: PMC9430710 DOI: 10.1128/spectrum.01663-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 05/25/2022] [Indexed: 11/21/2022] Open
Abstract
Traditional indigo dyeing through anaerobic fermentation has recently gained worldwide attention in efforts to address concerns regarding the sustainability of industrial indigo dyeing and the impact of toxic reducing agents such as sodium dithionite (Na2S2O4) on human health and the ecological environment. Intriguingly, changes in the microbiota during indigo fermentation are known to potently affect the onset of indigo reduction, and thus elucidation of the microbial community transitions could help develop methods to control the initiation of indigo reduction. Here, we investigated the microbiota associated with the traditional indigo dyeing practiced in Hunan, China. Specifically, we identified the bacterial and fungal components of the microbiota at distinct stages in the indigo fermentation process by analyzing 16S rRNA gene and internal transcribed spacer sequences. Our analyses revealed two substantial changes in the microbiota during the traditional indigo fermentation process. The first change, which was probably caused by the introduction of Chinese liquor (featuring a high alcohol concentration), resulted in decreased bacterial diversity and increased proportions of Pseudomonas, Stenotrophomonas, and Bacillaceae family members. The second change, which could be attributed to the addition of specific plant species, led to an increase in the abundance of Alkalibacterium, Amphibacillus, the obligate anaerobe Turicibacter, the facultative anaerobe Enterococcus, and ZOR0006, as well as to a decrease in the pH and redox potential values. Our results indicate that the specific plant mixture included in the procedure here could be used as an effective additive to accelerate the initiation of indigo reduction during the fermentation process. To the best of our knowledge, this is the first report revealing the fungal diversity during the indigo fermentation process and, furthermore, showing that the fungal diversity has remained in transition despite the relatively stable bacterial diversity in the proper indigo fermentation process. Although traditional indigo fermentation in China is challenging to manage, we can benefit from local knowledge of the fermentation process, and understanding the scientific bases of traditional indigo fermentation will facilitate the development of environmentally friendly procedures. IMPORTANCE Chemical reducing agents included in modern indigo dyeing to initiate indigo reduction can be harmful to both human health and the environment. Given that traditional indigo dyeing involves natural fermentation in a dye vat using natural organic additives without the use of toxic chemicals and that changes in the microbiota during traditional indigo fermentation potently affect the onset of indigo reduction, elucidation of these microbial community transitions could help develop methods to control the initiation of indigo reduction. This study on the microbiota associated with the traditional indigo dyeing practiced in Hunan, China, has identified the bacterial and fungal communities at distinct stages of the indigo fermentation process. Notably, the addition of specific plant species might yield the desired microbial communities and appropriate fermentation conditions, which could be used as an effective additive to accelerate the initiation of indigo reduction. This study has also revealed the fungal diversity during the indigo fermentation process for the first time and shown that the fungal diversity has remained in transition despite the relatively stable bacterial diversity. Thus, this work provides new insights into the traditional indigo fermentation process used in China and substantially enhances current efforts devoted to designing environmentally friendly methods for industrial indigo dyeing.
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Affiliation(s)
- Shan Li
- Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, China
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Yuru Shi
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Hui Huang
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Yan Tong
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Shaohua Wu
- Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, China
| | - Yuhua Wang
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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4
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Solubility enhancement of indigo dye through biochemical reduction and structural modification. KOREAN J CHEM ENG 2022. [DOI: 10.1007/s11814-022-1165-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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5
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Tu Z, Lopes HDFS, Yumoto I. Fundicoccus fermenti sp. nov., an indigo-reducing facultative anaerobic alkaliphile isolated from indigo fermentation liquor used for dyeing. Int J Syst Evol Microbiol 2022; 72. [PMID: 35156919 DOI: 10.1099/ijsem.0.005239] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two facultative anaerobic and facultative alkaliphilic indigo-reducing strains, designated F-1T and F-2, were isolated from indigo fermentation liquor produced from couched woad fermentation-based Indian indigo fermentation fluid. The 16S rRNA gene phylogeny showed that Fundicoccus ignavus WS4937T (99.5%) was the closest neighbour of F-1T. The isolated bacterial cells were Gram-stain-positive and facultative anaerobic coccoids. Strain F-1T grew at between 5 and 37 °C with optimum growth between 28‒32 °C. The isolate grew in a pH range of 7.0‒10.5, with optimum growth between pH 9.0‒10.5. The DNA G+C content was 37.6 mol% (HPLC). The whole-cell fatty acid profile mainly consisted (>10 %) of C16 : 0, C16 : 1 ω9c, C18 : 0 and C18 : 1 ω9c. The digital DNA-DNA hybridization value between strain F-1T and F. ignavus WS4937T was 52.9 %. Based on their physiological and biochemical characteristics, and phylogenetic and genomic data, the isolates can be discriminated from F. ignavus WS4937T. The name Fundicoccus fermenti sp. nov. is proposed. The type strain of this species is F-1T (JCM 34140T=NCIMB 15255T).
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Affiliation(s)
- Zhihao Tu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan.,Laboratory of Environmental Microbiology, Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo 060-8589, Japan
| | - Helena de Fátima Silva Lopes
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan.,Laboratory of Environmental Microbiology, Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo 060-8589, Japan
| | - Isao Yumoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan.,Laboratory of Environmental Microbiology, Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo 060-8589, Japan
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6
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Nakagawa K, Takeuchi M, Tada M, Matsunaga M, Kugo M, Kiyofuji S, Kikuchi M, Yomota K, Sakamoto T, Kenji K, Ogawa J, Sakuradani E. Isolation and characterization of indigo-reducing bacteria and analysis of microbiota from indigo fermentation suspensions. Biosci Biotechnol Biochem 2021; 86:273-281. [PMID: 34864880 DOI: 10.1093/bbb/zbab209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 11/23/2021] [Indexed: 11/14/2022]
Abstract
In natural indigo dyeing, the water-insoluble indigo included in the composted indigo leaves called sukumo is converted to water-soluble leuco-indigo through the reduction activities of microorganisms under alkaline conditions. To understand the relationship between indigo reduction and microorganisms in indigo-fermentation suspensions, we isolated and identified the microorganisms that reduce indigo and analyzed the microbiota in indigo-fermentation suspensions. Indigo-reducing microorganisms, which were not isolated by means of a conventional indigo carmine-reduction assay method, were isolated by using indigo as a direct substrate and further identified and characterized. We succeeded in isolating bacteria closely related to Corynebacterium glutamicum, Chryseomicrobium aureum, Enterococcus sp. for the first time. Anthraquinone was found to be an effective mediator that facilitated the indigo-reduction activity of the isolated strains. On analysis of the microbiota in indigo-fermentation suspensions, the ratio of indigo-reducing bacteria and others was found to be important for maintaining the indigo-reduction activity.
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Affiliation(s)
- Kasumi Nakagawa
- Graduate School of Advanced Technology and Science, Tokushima University, 2-1 Minamijosanjima-cho, Tokushima 770-8513, Japan
| | - Michiki Takeuchi
- Industrial Microbiology, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Manami Tada
- Graduate School of Advanced Technology and Science, Tokushima University, 2-1 Minamijosanjima-cho, Tokushima 770-8513, Japan
| | - Momoka Matsunaga
- Faculty of Bioscience and Bioindustry, Tokushima University, 2-1 Minamijosanjima-cho, Tokushima 770-8513, Japan
| | - Masami Kugo
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Suzuna Kiyofuji
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Mayu Kikuchi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kazuya Yomota
- Graduate School of Advanced Technology and Science, Tokushima University, 2-1 Minamijosanjima-cho, Tokushima 770-8513, Japan
| | - Takaiku Sakamoto
- Graduate School of Advanced Technology and Science, Tokushima University, 2-1 Minamijosanjima-cho, Tokushima 770-8513, Japan.,Faculty of Bioscience and Bioindustry, Tokushima University, 2-1 Minamijosanjima-cho, Tokushima 770-8513, Japan.,Graduate School of Technology, Industrial and Social Sciences, Tokushima University, 2-1 Minamijosanjima-cho, Tokushima 770-8513, Japan
| | - Kano Kenji
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Jun Ogawa
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Eiji Sakuradani
- Graduate School of Advanced Technology and Science, Tokushima University, 2-1 Minamijosanjima-cho, Tokushima 770-8513, Japan.,Faculty of Bioscience and Bioindustry, Tokushima University, 2-1 Minamijosanjima-cho, Tokushima 770-8513, Japan.,Graduate School of Technology, Industrial and Social Sciences, Tokushima University, 2-1 Minamijosanjima-cho, Tokushima 770-8513, Japan
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7
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de Fátima Silva Lopes H, Tu Z, Sumi H, Furukawa H, Yumoto I. Indigofera tinctoria leaf powder as a promising additive to improve indigo fermentation prepared with sukumo (composted Polygonum tinctorium leaves). World J Microbiol Biotechnol 2021; 37:179. [PMID: 34562162 DOI: 10.1007/s11274-021-03142-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 08/09/2021] [Indexed: 01/04/2023]
Abstract
Being insoluble in the oxidize form, indigo dye must be solubilized by reduction for it to penetrate textile. One of the procedures is the reduction by natural bacterial fermentation. Sukumo, composted leaves of Polygonum tinctorium, is a natural source of indigo in Japan. Although sukumo has an intrinsic bacterial seed, the onset of indigo reduction with this material may vary greatly. Certain additives improve indigo fermentation. Here, we studied the effects of Indigofera tinctoria leaf powder (LP) on the initiation of indigo reduction, bacterial community, redox potential (ORP), and dyeing intensity in the initial stages and in aged fermentation fluids prepared with sukumo. I. tinctoria LP markedly decreased ORP at day 1 and stabilised it during early fermentation. These effects could be explained by the phytochemicals present in I. tinctoria LP that act as oxygen scavengers and electron mediators. Using next generation sequencing results, we observed differences in the bacterial community in sukumo fermentation treated with I. tinctoria LP, which was not influenced by the bacterial community in I. tinctoria LP per se. The concomitant decrease in Bacillaceae and increase in Proteinivoraceae at the onset of fermentation, increase in the ratio of facultative to obligate anaerobes (F/O ratio), or the total abundance of facultative anaerobes (F) or obligate anaerobes (O) (designated F + O) are vital for the initiation and maintenance of indigo reduction. Hence, I. tinctoria LP improved early indigo reduction by decreasing the ORP and hasten the appropriate transitions in the bacterial community in sukumo fermentation.
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Affiliation(s)
- Helena de Fátima Silva Lopes
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo, 062-8517, Japan.,Laboratory of Environmental Microbiology, Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo, 060-8589, Japan
| | - Zhihao Tu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo, 062-8517, Japan
| | - Hisako Sumi
- North-Indigo Textile Arts Studio 2-3-9, Matsugae, Otaru, 047-1470, Japan
| | - Hiromitsu Furukawa
- Sensing System Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Higashi, Tsukuba, Ibaraki, 305-8565, Japan
| | - Isao Yumoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo, 062-8517, Japan. .,Laboratory of Environmental Microbiology, Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo, 060-8589, Japan.
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8
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Tu Z, Lopes HDFS, Narihiro T, Yumoto I. The Mechanism Underlying of Long-Term Stable Indigo Reduction State in Indigo Fermentation Using Sukumo (Composted Polygonum tinctorium Leaves). Front Microbiol 2021; 12:698674. [PMID: 34367099 PMCID: PMC8342947 DOI: 10.3389/fmicb.2021.698674] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/30/2021] [Indexed: 01/04/2023] Open
Abstract
Indigo fermentation fluid maintains its indigo-reducing state for more than 6 months under open-air. To elucidate the mechanism underlying the sustainability of this indigo reduction state, three indigo fermentation batches with different durations for the indigo reduction state were compared. The three examined batches exhibited different microbiota and consisted of two phases. In the initial phase, oxygen-metabolizing-bacteria derived from sukumo established an initial network. With decreasing redox potential (ORP), the initial bacterial community was replaced by obligate anaerobes (mainly Proteinivoraceae; phase 1). Approximately 1 month after the beginning of fermentation, the predominating obligate anaerobes were decreased, and Amphibacillus and Polygonibacillus, which can decompose macromolecules derived from wheat bran, were predominantly observed, and the transition of microbiota became slow (phase 2). Considering the substrate utilization ability of the dominated bacterial taxa, the transitional change from phase 1 to phase 2 suggests that this changed from the bacterial flora that utilizes substrates derived from sukumo, including intrinsic substrates in sukumo and weakened or dead bacterial cells derived from early events (heat and alkaline treatment and reduction of ORP) to that of wheat bran-utilizers. This succession was directly related to the change in the major substrate sustaining the corresponding community and the turning point was approximately 1 month after the start of fermentation. As a result, we understand that the role of sukumo includes changes in the microbial flora immediately after the start of fermentation, which has an important function in the start-up phase of fermentation, whereas the ecosystem comprised of the microbiota utilizing wheat bran underpins the subsequent long-term indigo reduction.
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Affiliation(s)
- Zhihao Tu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan.,Laboratory of Environmental Microbiology, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Helena de Fátima Silva Lopes
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan.,Laboratory of Environmental Microbiology, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan
| | - Isao Yumoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan.,Laboratory of Environmental Microbiology, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
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9
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Ezzat SM, Ewida AYI. Smart soil grouting using innovative urease-producing bacteria and low cost materials. J Appl Microbiol 2021; 131:2294-2307. [PMID: 33900669 DOI: 10.1111/jam.15117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/15/2021] [Accepted: 04/21/2021] [Indexed: 11/27/2022]
Abstract
AIMS Calcium carbonate is a biomineral whose precipitation could be mediated by ureolytic bacteria and contributes in strengthening of sandy soils. The type of bacteria and grade of reagents have significant influence on microbially induced calcite precipitation (MICP). In the present study, factorial experiments based on these two factors were designed to determine their potential on MICP process, taking into consideration the economic advantages while giving quality results as well. METHODS AND RESULTS For the first time, Alkalibacterium iburiense strain EE1 (GenBank accession no. MF355369.1) is reported for its biogrouting activity. Optimum growth conditions for MICP treatments were pH (9·56 ± 0·021), EC (44·7 ± 0·057 mS cm-1 ), OD600 (2·04 ± 0·015), NH4 + concentration (487·06 ± 1·021 mmol l-1 ), and urease activity (20·0 ± 0·75 mmol l-1 urea hydrolysed min-1 ) after 72-h incubation. Statistical analysis comparing the growth in technical-grade medium prepared in tap water and analytical-grade medium prepared in deionized water showed no significant differences (P = 1·0) in biomass and urease activity. In contrast to previous studies, the current approach could reduce the bacterial culture and cementation solution ratio by about 50%, using a simple surface percolation method with staged injection instead of parallel injection to treat different sand columns. Using fixation solution could immobilize the bacteria over the full length of columns for better strength improvement. The unconfined compressive strength ranged between 0·64 to 2·11 kg cm-2 , and the corresponding CaCO3 contents 5·7-38·5%. The scanning electron microscope images indicated that the precipitated CaCO3 by bacteria was stable calcite. CONCLUSIONS Alkalibacterium iburiense and technical-grade reagents under nonsterile conditions are satisfactory consolidating agents for sandy soils. SIGNIFICANCE AND IMPACT OF THE STUDY This approach is considered eco-friendly and cost-effective for future scale-up applications in various geotechnical engineering.
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Affiliation(s)
- S M Ezzat
- Microbiology Department, Central Laboratory for Environmental Quality Monitoring (CLEQM), National Water Research Center (NWRC), Cairo, Egypt
| | - A Y I Ewida
- Microbiology Department, Central Laboratory for Environmental Quality Monitoring (CLEQM), National Water Research Center (NWRC), Cairo, Egypt
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10
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NAKAGAWA K, TAKEUCHI M, KIKUCHI M, KIYOFUJI S, KUGO M, SAKAMOTO T, KANO K, OGAWA J, SAKURADANI E. Mechanistic Insights into Indigo Reduction in Indigo Fermentation: A Voltammetric Study. ELECTROCHEMISTRY 2021. [DOI: 10.5796/electrochemistry.20-00123] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Kasumi NAKAGAWA
- Graduate School of Advanced Technology and Science, Tokushima University
| | - Michiki TAKEUCHI
- Industrial Microbiology, Graduate School of Agriculture, Kyoto University
| | - Mayu KIKUCHI
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University
| | - Suzuna KIYOFUJI
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University
| | - Masami KUGO
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University
| | - Takaiku SAKAMOTO
- Graduate School of Advanced Technology and Science, Tokushima University
- Graduate School of Technology, Industrial and Social Sciences, Tokushima University
| | - Kenji KANO
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University
| | - Jun OGAWA
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University
| | - Eiji SAKURADANI
- Graduate School of Advanced Technology and Science, Tokushima University
- Graduate School of Technology, Industrial and Social Sciences, Tokushima University
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11
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Mamo G, Mattiasson B. Alkaliphiles: The Versatile Tools in Biotechnology. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2020; 172:1-51. [PMID: 32342125 DOI: 10.1007/10_2020_126] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The extreme environments within the biosphere are inhabited by organisms known as extremophiles. Lately, these organisms are attracting a great deal of interest from researchers and industrialists. The motive behind this attraction is mainly related to the desire for new and efficient products of biotechnological importance and human curiosity of understanding nature. Organisms living in common "human-friendly" environments have served humanity for a very long time, and this has led to exhaustion of the low-hanging "fruits," a phenomenon witnessed by the diminishing rate of new discoveries. For example, acquiring novel products such as drugs from the traditional sources has become difficult and expensive. Such challenges together with the basic research interest have brought the exploration of previously neglected or unknown groups of organisms. Extremophiles are among these groups which have been brought to focus and garnering a growing importance in biotechnology. In the last few decades, numerous extremophiles and their products have got their ways into industrial, agricultural, environmental, pharmaceutical, and other biotechnological applications.Alkaliphiles, organisms which thrive optimally at or above pH 9, are one of the most important classes of extremophiles. To flourish in their extreme habitats, alkaliphiles evolved impressive structural and functional adaptations. The high pH adaptation gave unique biocatalysts that are operationally stable at elevated pH and several other novel products with immense biotechnological application potential. Advances in the cultivation techniques, success in gene cloning and expression, metabolic engineering, metagenomics, and other related techniques are significantly contributing to expand the application horizon of these remarkable organisms of the 'bizarre' world. Studies have shown the enormous potential of alkaliphiles in numerous biotechnological applications. Although it seems just the beginning, some fantastic strides are already made in tapping this potential. This work tries to review some of the prominent applications of alkaliphiles by focusing such as on their enzymes, metabolites, exopolysaccharides, and biosurfactants. Moreover, the chapter strives to assesses the whole-cell applications of alkaliphiles including in biomining, food and feed supplementation, bioconstruction, microbial fuel cell, biofuel production, and bioremediation.
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Affiliation(s)
| | - Bo Mattiasson
- Department of Biotechnology, Lund University, Lund, Sweden
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12
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Tu Z, de Fátima Silva Lopes H, Igarashi K, Yumoto I. Characterization of the microbiota in long- and short-term natural indigo fermentation. ACTA ACUST UNITED AC 2019; 46:1657-1667. [DOI: 10.1007/s10295-019-02223-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 08/07/2019] [Indexed: 12/12/2022]
Abstract
Abstract
The duration for which the indigo-reducing state maintenance in indigo natural fermentation in batch dependent. The microbiota was analyzed in two batches of sukumo fermentation fluids that lasted for different durations (Batch 1: less than 2 months; Batch 2: nearly 1 year) to understand the mechanisms underlying the sustainability and deterioration of this natural fermentation process. The transformation of the microbiota suggested that the deterioration of the fermentation fluid is associated with the relative abundance of Alcaligenaceae. Principal coordinates analysis (PCoA) showed that the microbial community maintained a very stable state in only the long-term Batch 2. Therefore, entry of the microbiota into a stable state under alkaline anaerobic condition is an important factor for maintenance of indigo fermentation for long duration. This is the first report on the total transformation of the microbiota for investigation of long-term maintenance mechanisms and to address the problem of deterioration in indigo fermentation.
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Affiliation(s)
- Zhihao Tu
- grid.39158.36 0000 0001 2173 7691 Graduate School of Agriculture Hokkaido University Sapporo Japan
- grid.208504.b 0000 0001 2230 7538 Bioproduction Research Institute National Institute of Advanced Industrial Science and Technology Sapporo Japan
| | - Helena de Fátima Silva Lopes
- grid.39158.36 0000 0001 2173 7691 Graduate School of Agriculture Hokkaido University Sapporo Japan
- grid.208504.b 0000 0001 2230 7538 Bioproduction Research Institute National Institute of Advanced Industrial Science and Technology Sapporo Japan
| | - Kensuke Igarashi
- grid.208504.b 0000 0001 2230 7538 Bioproduction Research Institute National Institute of Advanced Industrial Science and Technology Sapporo Japan
| | - Isao Yumoto
- grid.39158.36 0000 0001 2173 7691 Graduate School of Agriculture Hokkaido University Sapporo Japan
- grid.208504.b 0000 0001 2230 7538 Bioproduction Research Institute National Institute of Advanced Industrial Science and Technology Sapporo Japan
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13
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Analysis of the microbiota involved in the early changes associated with indigo reduction in the natural fermentation of indigo. World J Microbiol Biotechnol 2019; 35:123. [DOI: 10.1007/s11274-019-2699-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 07/17/2019] [Indexed: 01/01/2023]
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14
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Martynov VO, Brygadyrenko VV. The influence of the synthetic food colourings tartrazine, allura red and indigo carmine on the body weight of Tenebrio molitor (Coleoptera, Tenebrionidae) larvae. REGULATORY MECHANISMS IN BIOSYSTEMS 2018. [DOI: 10.15421/021871] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Substances for protecting plants often contain colourings, the impact of which on invertebrates has been studied insufficiently. The addition of food colourings in different concentrations to the diet of saprophage beetles can affect their metabolism, causing loss of body weight. In the experiment, we determined the impact of tartrazine, allura red and indigo carmine on the body weight of Tenebrio molitor Linnaeus, 1758 larvae. The substances were added to their fodder at five concentrations (1, 0.1, 0.01, 0.001 and 0.0001 g/kg of dry fodder) during a 21-day experiment. Statistically significant data on changes in the body weight of T. molitor larvae were received after adding 1 g/kg concentration of indigo carmine and 0.1 and 1 g/kg concentrations of tartrazine. In the other variants of the experiment, no statistically significant differences were determined. Tartrazine, allura red and indigo carmine cause decrease in the body weight of T. molitor larvae, depending on the concentration of the colouring. The toxic effect of synthetic food colourings on living organisms and the low number of studies devoted to such impact on insects indicate the relevance and necessity for further research in this sphere.
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15
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Aino K, Hirota K, Okamoto T, Tu Z, Matsuyama H, Yumoto I. Microbial Communities Associated With Indigo Fermentation That Thrive in Anaerobic Alkaline Environments. Front Microbiol 2018; 9:2196. [PMID: 30279681 PMCID: PMC6153312 DOI: 10.3389/fmicb.2018.02196] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/28/2018] [Indexed: 12/31/2022] Open
Abstract
Indigo fermentation, which depends on the indigo-reducing action of microorganisms, has traditionally been performed to dye textiles blue in Asia as well as in Europe. This fermentation process is carried out by naturally occurring microbial communities and occurs under alkaline, anaerobic conditions. Therefore, there is uncertainty regarding the fermentation process, and many unknown microorganisms thrive in this unique fermentation environment. Until recently, there was limited information available on bacteria associated with this fermentation process. Indigo reduction normally occurs from 4 days to 2 weeks after initiation of fermentation. However, the changes in the microbiota that occur during the transition to an indigo-reducing state have not been elucidated. Here, the structural changes in the bacterial community were estimated by PCR-based methods. On the second day of fermentation, a large change in the redox potential occurred. On the fourth day, distinct substitution of the genus Halomonas with the aerotolerant genus Amphibacillus was observed, corresponding to marked changes in indigo reduction. Under open-air conditions, indigo reduction during the fermentation process continued for 6 months on average. The microbiota, including indigo-reducing bacteria, was continuously replaced with other microbial communities that consisted of other types of indigo-reducing bacteria. A stable state consisting mainly of the genus Anaerobacillus was also observed in a long-term fermentation sample. The stability of the microbiota, proportion of indigo-reducing microorganisms, and appropriate diversity and microbiota within the fluid may play key factors in the maintenance of a reducing state during long-term indigo fermentation. Although more than 10 species of indigo-reducing bacteria were identified, the reduction mechanism of indigo particle is riddle. It can be predicted that the mechanism involves electrons, as byproducts of metabolism, being discarded by analogs mechanisms reported in bacterial extracellular solid Fe3+ reduction under alkaline anaerobic condition.
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Affiliation(s)
- Keiichi Aino
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Sapporo, Japan
- Department of Bioscience and Technology, School of Biological Science and Engineering, Tokai University, Hiratsuka-shi, Japan
| | - Kikue Hirota
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Sapporo, Japan
| | - Takahiro Okamoto
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Zhihao Tu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Sapporo, Japan
- Department of Bioscience and Technology, School of Biological Science and Engineering, Tokai University, Hiratsuka-shi, Japan
| | | | - Isao Yumoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Sapporo, Japan
- Department of Bioscience and Technology, School of Biological Science and Engineering, Tokai University, Hiratsuka-shi, Japan
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16
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Suzuki H, Abe T, Doi K, Ohshima T. Azoreductase from alkaliphilic Bacillus sp. AO1 catalyzes indigo reduction. Appl Microbiol Biotechnol 2018; 102:9171-9181. [PMID: 30105570 DOI: 10.1007/s00253-018-9284-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 07/27/2018] [Accepted: 07/30/2018] [Indexed: 10/28/2022]
Abstract
Indigo is an insoluble blue dye historically used for dyeing textiles. A traditional approach for indigo dyeing involves microbial reduction of polygonum indigo to solubilize it under alkaline conditions; however, the mechanism by which microorganisms reduce indigo remains poorly understood. Here, we aimed to identify an enzyme that catalyzes indigo reduction; for this purpose, from alkaline liquor that performed microbial reduction of polygonum indigo, we isolated indigo carmine-reducing microorganisms. All isolates were facultative anaerobic and alkali-tolerant Bacillus spp. An isolate termed AO1 was found to be an alkaliphile that preferentially grows at pH 9.0-11.0 and at 30-35 °C. We focused on flavin-dependent azoreductase as a possible enzyme for indigo carmine reduction and identified its gene (azoA) in Bacillus sp. AO1 using homology-based strategies. azoA was monocistronic but clustered with ABC transporter genes. Primary sequence identities were < 50% between the azoA product (AzoA) and previously characterized flavin-dependent azoreductases. AzoA was heterologously produced as a flavoprotein tolerant to alkaline and organic solvents. The enzyme efficiently reduced indigo carmine in an NADH-dependent manner and showed strict specificity for electron acceptors. Notably, AzoA oxidized NADH in the presence, but not the absence, of indigo. The reaction rate was enhanced by adding organic solvents to solubilize indigo. Absorption spectrum analysis showed that indigo absorption decreased during the reaction. These observations suggest that AzoA can reduce indigo in vitro and potentially in Bacillus sp. AO1. This is the first study that identified an indigo reductase, providing a new insight into a traditional approach for indigo dyeing.
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Affiliation(s)
- Hirokazu Suzuki
- Functional Genomics of Extremophiles, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka, 812-8581, Japan. .,Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, 4-101 Koyama-Minami, Tottori, 680-8550, Japan. .,Centre for Research on Green Sustainable Chemistry, Tottori University, 4-101 Koyama-Minami, Tottori, 680-8550, Japan.
| | - Tomoaki Abe
- Microbial Genetic Division, Institute of Genetic Resources, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka, 812-8581, Japan
| | - Katsumi Doi
- Microbial Genetic Division, Institute of Genetic Resources, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka, 812-8581, Japan
| | - Toshihisa Ohshima
- Microbial Genetic Division, Institute of Genetic Resources, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka, 812-8581, Japan.,Faculty of Engineering, Osaka Institute of Technology, Osaka, 535-8585, Japan
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17
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Ling HL, Rahmat Z, Bakar FDA, Murad AMA, Illias RM. Secretome analysis of alkaliphilic bacterium Bacillus lehensis G1 in response to pH changes. Microbiol Res 2018; 215:46-54. [PMID: 30172308 DOI: 10.1016/j.micres.2018.06.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 04/18/2018] [Accepted: 06/16/2018] [Indexed: 12/27/2022]
Abstract
Bacillus lehensis G1 is an alkaliphilic bacterium that is capable of surviving in environments up to pH 11. Secretome related to bacterial acclimation in alkaline environment has been less studied compared to cytoplasmic and membrane proteome. The aim of this study was to gain better understanding of bacterial acclimation to alkaline media through analyzing extracellular proteins of B. lehensis. The pH range for B. lehensis growth was conducted, and two-dimensional electrophoresis and MALDI-TOF/TOF MS analysis were conducted to characterize changes in protein profiling in B. lehensis cultured at pH 8 and pH 11 when compared with those cultured at pH 10 (optimal growth pH). B. lehensis could grow well at pH ranging from 8 to 11 in which the bacteria showed to posses thinner flagella at pH 11. Proteomic analyses demonstrated that five proteins were up-regulated and 13 proteins were down-regulated at pH 8, whereas at pH 11, 14 proteins were up-regulated and 8 were down-regulated. Majority of the differentially expressed proteins were involved in the cell wall, main glycolytic pathways, the metabolism of amino acids and related molecules and some proteins of unknown function. A total of 40 differentially expressed protein spots corresponding to 33 proteins were identified; including GlcNAc-binding protein A, chitinase, endopeptidase lytE, flagellar hook-associated proteins and enolase. These proteins may play important roles in acclimation to alkaline media via reallocation of cell wall structure and changes to cell surface glycolytic enzymes, amino acid metabolism, flagellar hook-associated proteins and chaperones to sustain life under pH-stressed conditions.
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Affiliation(s)
- How Lie Ling
- Department of Bioprocess and Polymer Engineering, Faculty of Chemical and Energy Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| | - Zaidah Rahmat
- Department of Biotechnology and Medical Engineering, Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| | - Farah Diba Abu Bakar
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - Abdul Munir Abdul Murad
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - Rosli Md Illias
- Department of Bioprocess and Polymer Engineering, Faculty of Chemical and Energy Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia.
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18
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Bacillus fermenti sp. nov., an indigo-reducing obligate alkaliphile isolated from indigo fermentation liquor for dyeing. Int J Syst Evol Microbiol 2018; 68:1123-1129. [DOI: 10.1099/ijsem.0.002636] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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19
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Hirota K, Nishita M, Matsuyama H, Yumoto I. Paralkalibacillus indicireducens gen., nov., sp. nov., an indigo-reducing obligate alkaliphile isolated from indigo fermentation liquor used for dyeing. Int J Syst Evol Microbiol 2017; 67:4050-4056. [DOI: 10.1099/ijsem.0.002248] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Kikue Hirota
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8571, Japan
| | - Masatoshi Nishita
- School of Biological Science and Engineering, Tokai University, Minamisawa, Minami-ku, Sapporo 005-8601, Japan
| | - Hidetoshi Matsuyama
- School of Biological Science and Engineering, Tokai University, Minamisawa, Minami-ku, Sapporo 005-8601, Japan
| | - Isao Yumoto
- Laboratory of Molecular Environmental Microbiology, Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo 060-8589, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8571, Japan
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20
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Bang-Andreasen T, Nielsen JT, Voriskova J, Heise J, Rønn R, Kjøller R, Hansen HCB, Jacobsen CS. Wood Ash Induced pH Changes Strongly Affect Soil Bacterial Numbers and Community Composition. Front Microbiol 2017; 8:1400. [PMID: 28804476 PMCID: PMC5532396 DOI: 10.3389/fmicb.2017.01400] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 07/11/2017] [Indexed: 02/01/2023] Open
Abstract
Recirculation of wood ash from energy production to forest soil improves the sustainability of this energy production form as recycled wood ash contains nutrients that otherwise would be lost at harvest. In addition, wood-ash is beneficial to many soils due to its inherent acid-neutralizing capabilities. However, wood ash has several ecosystem-perturbing effects like increased soil pH and pore water electrical conductivity both known to strongly impact soil bacterial numbers and community composition. Studies investigating soil bacterial community responses to wood ash application remain sparse and the available results are ambiguous and remain at a general taxonomic level. Here we investigate the response of bacterial communities in a spruce forest soil to wood ash addition corresponding to 0, 5, 22, and 167 t wood ash ha-1. We used culture-based enumerations of general bacteria, Pseudomonas and sporeforming bacteria combined with 16S rRNA gene amplicon sequencing to valuate soil bacterial responses to wood ash application. Results showed that wood ash addition strongly increased soil pH and electrical conductivity. Soil pH increased from acidic through neutral at 22 t ha-1 to alkaline at 167 t ha-1. Bacterial numbers significantly increased up to a wood ash dose of 22 t ha-1 followed by significant decrease at 167 t ha-1 wood ash. The soil bacterial community composition changed after wood ash application with copiotrophic bacteria responding positively up to a wood ash dose of 22 t ha-1 while the adverse effect was seen for oligotrophic bacteria. Marked changes in bacterial community composition occurred at a wood ash dose of 167 t ha-1 with a single alkaliphilic genus dominating. Additionally, spore-formers became abundant at an ash dose of 167 t ha-1 whereas this was not the case at lower ash doses. Lastly, bacterial richness and diversity strongly decreased with increasing amount of wood ash applied. All of the observed bacterial responses can be directly explained by the wood ash induced changes in pH, electrical conductivity and the addition of wood ash inherent nutrients.
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Affiliation(s)
- Toke Bang-Andreasen
- Department of Environmental Science, Aarhus UniversityRoskilde, Denmark.,Department of Biology, University of CopenhagenCopenhagen, Denmark.,Department of Geochemistry, Geological Survey of Denmark and Greenland (GEUS)Copenhagen, Denmark
| | - Jeppe T Nielsen
- Department of Geochemistry, Geological Survey of Denmark and Greenland (GEUS)Copenhagen, Denmark.,Department of Plant and Environmental Sciences, University of CopenhagenFrederiksberg, Denmark
| | - Jana Voriskova
- Department of Geochemistry, Geological Survey of Denmark and Greenland (GEUS)Copenhagen, Denmark.,Ecology Department, Climate and Ecosystem Sciences, Lawrence Berkeley National Laboratory, BerkeleyCA, United States.,Center for Permafrost (CENPERM), University of CopenhagenCopenhagen, Denmark
| | - Janine Heise
- Section for Geomicrobiology, GFZ German Research Centre for GeosciencesPotsdam, Germany
| | - Regin Rønn
- Department of Biology, University of CopenhagenCopenhagen, Denmark.,Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of SciencesXiamen, China.,Arctic Station, University of CopenhagenQeqertarsuaq, Greenland
| | - Rasmus Kjøller
- Department of Biology, University of CopenhagenCopenhagen, Denmark
| | - Hans C B Hansen
- Department of Plant and Environmental Sciences, University of CopenhagenFrederiksberg, Denmark
| | - Carsten S Jacobsen
- Department of Environmental Science, Aarhus UniversityRoskilde, Denmark.,Department of Geochemistry, Geological Survey of Denmark and Greenland (GEUS)Copenhagen, Denmark.,Center for Permafrost (CENPERM), University of CopenhagenCopenhagen, Denmark
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21
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Milanović V, Osimani A, Taccari M, Garofalo C, Butta A, Clementi F, Aquilanti L. Insight into the bacterial diversity of fermentation woad dye vats as revealed by PCR-DGGE and pyrosequencing. ACTA ACUST UNITED AC 2017; 44:997-1004. [DOI: 10.1007/s10295-017-1921-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 02/05/2017] [Indexed: 01/18/2023]
Abstract
Abstract
The bacterial diversity in fermenting dye vats with woad (Isatis tinctoria L.) prepared and maintained in a functional state for approximately 12 months was examined using a combination of culture-dependent and -independent PCR-DGGE analyses and next-generation sequencing of 16S rRNA amplicons. An extremely complex ecosystem including taxa potentially contributing to both indigo reduction and formation, as well as indigo degradation was found. PCR-DGGE analyses revealed the presence of Paenibacillus lactis, Sporosarcina koreensis, Bacillus licheniformis, and Bacillus thermoamylovorans, while Bacillus thermolactis, Bacillus pumilus and Bacillus megaterium were also identified but with sequence identities lower than 97%. Dominant operational taxonomic units (OTUs) identified by pyrosequencing included Clostridium ultunense, Tissierella spp., Alcaligenes faecalis, Erysipelothrix spp., Enterococcus spp., Virgibacillus spp. and Virgibacillus panthothenicus, while sub-dominant OTUs included clostridia, alkaliphiles, halophiles, bacilli, moderately thermophilic bacteria, lactic acid bacteria, Enterobacteriaceae, aerobes, and even photosynthetic bacteria. Based on the current knowledge of indigo-reducing bacteria, it is considered that indigo-reducing bacteria constituted only a small fraction in the unique microcosm detected in the natural indigo dye vats.
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Affiliation(s)
- Vesna Milanović
- 0000 0001 1017 3210 grid.7010.6 Dipartimento di Scienze Agrarie, Alimentari, ed Ambientali (D3A) Università Politecnica delle Marche via Brecce Bianche 60131 Ancona Italy
| | - Andrea Osimani
- 0000 0001 1017 3210 grid.7010.6 Dipartimento di Scienze Agrarie, Alimentari, ed Ambientali (D3A) Università Politecnica delle Marche via Brecce Bianche 60131 Ancona Italy
| | - Manuela Taccari
- 0000 0001 1017 3210 grid.7010.6 Dipartimento di Scienze Agrarie, Alimentari, ed Ambientali (D3A) Università Politecnica delle Marche via Brecce Bianche 60131 Ancona Italy
| | - Cristiana Garofalo
- 0000 0001 1017 3210 grid.7010.6 Dipartimento di Scienze Agrarie, Alimentari, ed Ambientali (D3A) Università Politecnica delle Marche via Brecce Bianche 60131 Ancona Italy
| | - Alessandro Butta
- La Campana Soc. Coop. Agricola Montefiore dell’Aso Ascoli Piceno Italy
| | - Francesca Clementi
- 0000 0001 1017 3210 grid.7010.6 Dipartimento di Scienze Agrarie, Alimentari, ed Ambientali (D3A) Università Politecnica delle Marche via Brecce Bianche 60131 Ancona Italy
| | - Lucia Aquilanti
- 0000 0001 1017 3210 grid.7010.6 Dipartimento di Scienze Agrarie, Alimentari, ed Ambientali (D3A) Università Politecnica delle Marche via Brecce Bianche 60131 Ancona Italy
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22
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Nishita M, Hirota K, Matsuyama H, Yumoto I. Development of media to accelerate the isolation of indigo-reducing bacteria, which are difficult to isolate using conventional media. World J Microbiol Biotechnol 2017; 33:133. [PMID: 28585166 DOI: 10.1007/s11274-017-2300-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 05/23/2017] [Indexed: 11/26/2022]
Abstract
Indigo-reducing bacteria perform natural fermentation in indigo fermentation fluid. Owing to the stochastic nature of the process, the constituent in indigo fermentation fluid differ depending on the prepared batch and fermentation period. To identify new indigo-reducing bacteria, isolation of the bacteria is indispensable. However, isolation of indigo-reducing bacteria is difficult because conventional media are often unsuitable to isolate these slow-growing bacteria that also exist in low numbers. Hydrolysates of polysaccharides and mixtures of plant base constituents are candidates to accelerate the isolation of indigo-reducing bacteria that cannot be isolated using conventional media. In this current study, wheat bran hydrolysate and composted indigo leaves (sukumo) were used as ingredients in the fermentation fluid in the selective medium for indigo-reducing bacteria in anaerobic culture. The results suggested that obligate and oxygen-non-metabolizing facultative anaerobes are difficult to isolate using conventional media, whereas oxygen-metabolizing facultative anaerobes, relatively rapid-growing and major bacterial strains are relatively easy to isolate. Media containing sukumo hydrolysate facilitated the isolation of novel species of Bacillus pseudofirmus-related strains, whereas media containing wheat bran hydrolysate facilitated the isolation of Amphibacillus spp. (including new species). Seven species (including two new species) of indigo-reducing bacteria were isolated using wheat bran hydrolysate-containing media, whereas six species (including three new species) of indigo-reducing bacteria were isolated using media containing both wheat bran and sukumo hydrolysates. These newly developed culture media will facilitate the isolation of unknown bacteria in indigo fermentation and in environments similar to indigo fermentation fluid.
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Affiliation(s)
- Masatoshi Nishita
- School of Biological Science and Engineering, Tokai University, Minamisawa, Minami-ku, Sapporo, 005-8601, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo, 062-8517, Japan
| | - Kikue Hirota
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo, 062-8517, Japan
| | - Hidetoshi Matsuyama
- School of Biological Science and Engineering, Tokai University, Minamisawa, Minami-ku, Sapporo, 005-8601, Japan
| | - Isao Yumoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo, 062-8517, Japan.
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23
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Okamoto T, Aino K, Narihiro T, Matsuyama H, Yumoto I. Analysis of microbiota involved in the aged natural fermentation of indigo. World J Microbiol Biotechnol 2017; 33:70. [DOI: 10.1007/s11274-017-2238-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 03/03/2017] [Indexed: 10/20/2022]
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24
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Hirota K, Okamoto T, Matsuyama H, Yumoto I. Polygonibacillus indicireducens gen. nov., sp. nov., an indigo-reducing and obligate alkaliphile isolated from indigo fermentation liquor for dyeing. Int J Syst Evol Microbiol 2016; 66:4650-4656. [DOI: 10.1099/ijsem.0.001405] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Kikue Hirota
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
| | - Takahiro Okamoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
- School of Biological Science and Engineering, Tokai University, Minamisawa, Minami-ku, Sapporo 005-8601, Japan
| | - Hidetoshi Matsuyama
- School of Biological Science and Engineering, Tokai University, Minamisawa, Minami-ku, Sapporo 005-8601, Japan
| | - Isao Yumoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
- Laboratory of Molecular Environmental Microbiology, Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo 060-8589, Japan
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Hirota K, Aino K, Yumoto I. Fermentibacillus polygoni gen. nov., sp. nov., an alkaliphile that reduces indigo dye. Int J Syst Evol Microbiol 2016; 66:2247-2253. [DOI: 10.1099/ijsem.0.001015] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Kikue Hirota
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo, Hokkaido 062-8517, Japan
| | - Kenichi Aino
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo, Hokkaido 062-8517, Japan
- Laboratory of Environmental Microbiology, Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo, Hokkaido 060-8589, Japan
| | - Isao Yumoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo, Hokkaido 062-8517, Japan
- Laboratory of Environmental Microbiology, Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo, Hokkaido 060-8589, Japan
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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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Vaidya B, Kumar R, Sharma G, Srinivas TNR, Anil Kumar P. Xanthomarina gelatinilytica gen. nov., sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2015; 65:3926-3932. [PMID: 26956595 DOI: 10.1099/ijsem.0.000515] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023] Open
Abstract
A novel Gram-stain-negative, rod-shaped, yellow-pigmented, non-sporulating, non-motile bacterium, designated strain AK20T, was isolated from seawater collected from Kochi city, Kerala state, India. Colonies on marine agar were circular, yellow, shiny, translucent, 2-3 mm in diameter, convex and with entire margin. Flexirubin-type pigment was present. The fatty acids were dominated by iso-branched units with a high abundance of iso-C15:0, iso-C15:1 G, iso-C17:0 3-OH, summed feature 3 (C16:1ω7c and/or iso-C15:0 2-OH) and iso-C15:0 3-OH. Polar lipids included phosphatidylethanolamine, two unidentified aminophospholipids, two unidentified phospholipids and four unidentified lipids. Menaquinone 6 (MK-6) was the predominant respiratory quinone. The DNA G+C content of strain AK20T was 38.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain AK20T was closely related to Formosa spongicola A2T and Bizionia paragorgiae KMM 6029T (pair-wise sequence similarities of 95.9 and 95.7%, respectively), forming a distinct branch within the family Flavobacteriaceae and clustering with the clade comprising species of the genus Bizionia. Based on phenotypic and chemotaxonomic characteristics and phylogenetic analysis, strain AK20T is different from the existing genera in the family Flavobacteriaceae, and is therefore considered to represent a novel species of a new genus, for which the name Xanthomarina gelatinilytica gen. nov., sp. nov. is proposed. The type strain of Xanthomarina gelatinilytica is AK20T ( = MTCC 11705T = JCM 18821T).
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Affiliation(s)
- Bhumika Vaidya
- MTCC - Microbial Type Culture Collection & Gene Bank, CSIR - Institute of Microbial Technology, Chandigarh -160036, India
| | - Ravinder Kumar
- MTCC - Microbial Type Culture Collection & Gene Bank, CSIR - Institute of Microbial Technology, Chandigarh -160036, India
| | - Gunjan Sharma
- MTCC - Microbial Type Culture Collection & Gene Bank, CSIR - Institute of Microbial Technology, Chandigarh -160036, India
| | - Tanuku Naga Radha Srinivas
- CSIR - National Institute of Oceanography, Regional Centre, 176, Lawsons Bay Colony, Visakhapatnam -530017, India
| | - Pinnaka Anil Kumar
- MTCC - Microbial Type Culture Collection & Gene Bank, CSIR - Institute of Microbial Technology, Chandigarh -160036, India
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Hirota K, Hanaoka Y, Nodasaka Y, Yumoto I. Gracilibacillus alcaliphilus sp. nov., a facultative alkaliphile isolated from indigo fermentation liquor for dyeing. Int J Syst Evol Microbiol 2014; 64:3174-3180. [DOI: 10.1099/ijs.0.060871-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A facultatively alkaliphilic, lactic-acid-producing and halophilic strain, designated SG103T, was isolated from a fermented Polygonum indigo (Polygonum tinctorium Lour.) liquor sample for dyeing prepared in a laboratory. 16S rRNA gene sequence phylogeny suggested that SG103T is a member of the genus
Gracilibacillus
with the closest relatives being ‘Gracilibacillus
xinjiangensis’ J2 (similarity: 97.06 %),
Gracilibacillus thailandensis
TP2-8T (97.06 %) and
Gracilibacillus halotolerans
NNT (96.87 %). Cells of the isolate stained Gram-positive and were facultatively anaerobic straight rods that were motile by peritrichous flagella. The strain grew at temperatures between 13 and 48 °C with the optimum at 39 °C. It grew in the range pH 7–10 with the optimum at pH 9. The isoprenoid quinone detected was menaquinone-7 (MK-7) and the DNA G+C content was 41.3 mol%. The whole-cell fatty acid profile mainly (>10 %) consisted of iso-C15 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. Unlike other reported species of the genus
Gracilibacillus
, the strain lacked diphosphatidylglycerol as a major polar lipid. DNA–DNA hybridization experiments with strains exhibiting greater than 96.87 % 16S rRNA gene sequence similarity, ‘G. xinjiangensis’ J2,
G. thailandensis
TP2-8T and
G. halotolerans
NNT, revealed 2±4 %, 4±9 % and 3±2 % relatedness, respectively. On the basis of the differences in phenotypic and chemotaxonomic characteristics, and the results of phylogenetic analyses based on 16S rRNA gene sequences and DNA–DNA relatedness data from reported species of the genus
Gracilibacillus
, strain SG103T merits classification as a members of a novel species, for which the name Gracilibacillus
alcaliphilus sp. nov. is proposed. The type strain is SG103T ( = JCM 17253T = NCIMB 14683T).
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Affiliation(s)
- Kikue Hirota
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
| | - Yoshiko Hanaoka
- Laboratory of Environmental Microbiology, Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo 060-8589, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
| | - Yoshinobu Nodasaka
- Laboratory of Electron Microscopy, Graduate School of Dentistry, Hokkaido University, Kita-ku, Sapporo 060-8586, Japan
| | - Isao Yumoto
- Laboratory of Environmental Microbiology, Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo 060-8589, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
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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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Hirota K, Aino K, Yumoto I. Amphibacillus iburiensis sp. nov., an alkaliphile that reduces an indigo dye. Int J Syst Evol Microbiol 2013; 63:4303-4308. [DOI: 10.1099/ijs.0.048009-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An indigo-reducing alkaliphilic strain, designated strain N314T, was isolated from a fermented polygonum indigo (Polygonum tinctorium Lour.) liquor sample, aged for 10 months, that was obtained from Date City, Iburi Branch, Hokkaido, Japan. The 16S rRNA gene sequence phylogeny suggested that strain N314T is a member of the genus
Amphibacillus
, with the closest relatives being
Amphibacillus indicireducens
(98.9 % similarity to the type strain) and
Amphibacillus xylanus
(98.0 % similarity to the type strain), the only species with 16S rRNA gene sequence similarities higher than 97 % to strain N314T. The cells of the isolate stained Gram-positive and were facultatively anaerobic, straight rods that were motile by means of peritrichous flagella. The strain grew at 26–39 °C with optimum growth at 36 °C. It grew at pH 8.0–9.1, with optimum growth at pH 8.9–9.1. No isoprenoid quinone was detected, and the DNA G+C content was 38.4 mol%. The whole-cell fatty acid profile consisted mainly of iso-C15 : 0 and anteiso-C15 : 0. Analysis of DNA–DNA hybridization with the type strains of
A. indicireducens
and
A. xylanus
revealed 29±2 % and 10±2 % relatedness, respectively. Owing to differences in phenotypic characteristics from reported species of the genus
A.
and results of phylogenetic analyses based on 16S rRNA gene sequences and DNA–DNA relatedness data, the isolate merits classification within a novel species, for which the name Amphibacillus iburiensis sp. nov. is proposed. The type strain is N314T ( = JCM 18529T = NCIMB 14823T).
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Affiliation(s)
- Kikue Hirota
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
| | - Kenichi Aino
- Laboratory of Environmental Microbiology, Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo 060-8589, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
| | - Isao Yumoto
- Laboratory of Environmental Microbiology, Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo 060-8589, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
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Hirota K, Hanaoka Y, Nodasaka Y, Yumoto I. Oceanobacillus
polygoni sp. nov., a facultatively alkaliphile isolated from indigo fermentation fluid. Int J Syst Evol Microbiol 2013; 63:3307-3312. [DOI: 10.1099/ijs.0.048595-0] [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
A facultatively alkaliphilic, lactic-acid-producing and halophilic strain, designated SA9T, was isolated from a fermented Polygonum indigo (Polygonum tinctorium Lour.) liquor sample prepared in a laboratory. The 16S rRNA gene sequence phylogeny suggested that strain SA9T was a member of the genus
Oceanobacillus
with the closest relative being
Oceanobacillus profundus
KCCM 42318T (99.3 % 16S rRNA gene sequence similarity). Cells of strain SA9T stained Gram-positive and were facultative anaerobic straight rods that were motile by peritrichous flagella. The strain grew between 5 and 48 °C (optimum, 35 °C) and at pH 7–12 (optimum, pH 9). The isoprenoid quinone detected was menaquinone-7 (MK-7) and the DNA G+C content was 40.6±0.9 mol%. The whole-cell fatty acid profile mainly consisted of iso-C15 : 0, anteiso-C15 : 0, C16 : 0 and anteiso-C17 : 0. DNA–DNA hybridization with
Oceanobacillus profundus
DSM 18246T revealed a DNA–DNA relatedness value of 23±2 %. On the basis of the differences in phenotypic and chemotaxonomic characteristics, and the results of phylogenetic analyses based on 16S rRNA gene sequences and DNA–DNA relatedness data from recognized species of the genus
Oceanobacillus
, strain SA9T merits classification as a representative of a novel species of the genus
Oceanobacillus
, for which the name
Oceanobacillus
polygoni sp. nov. is proposed. The type strain is SA9T ( = JCM 17252T = NCIMB 14684T). An emended description of the genus
Oceanobacillus
is also provided.
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Affiliation(s)
- Kikue Hirota
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
| | - Yoshiko Hanaoka
- Laboratory of Environmental Microbiology, Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo 060-8589, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
| | - Yoshinobu Nodasaka
- Laboratory of Electron Microscopy, Graduate School of Dentistry, Hokkaido University, Kita-ku, Sapporo 060-8586, Japan
| | - Isao Yumoto
- Laboratory of Environmental Microbiology, Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo 060-8589, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
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Hirota K, Aino K, Nodasaka Y, Yumoto I. Oceanobacillus indicireducens sp. nov., a facultative alkaliphile that reduces an indigo dye. Int J Syst Evol Microbiol 2013; 63:1437-1442. [DOI: 10.1099/ijs.0.034579-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An indigo-reducing facultatively alkaliphilic and halophilic strain, designated strain A21T, was isolated from a fermented Polygonum indigo (Polygonum tinctorium Lour.) liquor sample aged for 4 days prepared in a laboratory. 16S rRNA gene sequence phylogeny suggested that strain A21T was a member of the genus
Oceanobacillus
with the closest relative being the type strain of
Oceanobacillus chironomi
(similarity: 96.0 %). The cells of the isolate stained Gram-positive and were facultatively anaerobic straight rods that were motile by peritrichous flagella. The strain grew between 18 and 48 °C with optimum growth at 39 °C. It grew in the pH range of 7–12. It hydrolysed casein, gelatin and Tween 20 but not Tweens 40, 60 and 80, starch or DNA. No isoprenoid quinone was detected and the DNA G+C content was 39.7 mol%. The whole-cell fatty acid profile mainly consisted of iso-C15 : 0, anteiso-C15 : 0 and C16 : 0. DNA–DNA hybridization experiments with
O. chironomi
revealed 13 % relatedness. Owing to the differences in phenotypic and chemotaxonomic characteristics, and phylogenetic analyses based on 16S rRNA gene sequences and DNA–DNA relatedness data from reported
Oceanobacillus
species, the isolate merits classification as a representative of a novel species, for which the name Oceanobacillus indicireducens sp. nov. is proposed. The type strain is A21T ( = JCM 17251T = NCIMB 14685T). The description of the genus
Oceanobacillus
is also emended.
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Affiliation(s)
- Kikue Hirota
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
| | - Kenichi Aino
- Laboratory of Environmental Microbiology, Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo 060-8589, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
| | - Yoshinobu Nodasaka
- Laboratory of Electron Microscopy, Graduate School of Dentistry, Hokkaido University, Kita-ku, Sapporo 060-8586, Japan
| | - Isao Yumoto
- Laboratory of Environmental Microbiology, Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo 060-8589, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
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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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Hirota K, Aino K, Nodasaka Y, Morita N, Yumoto I. Amphibacillus indicireducens sp. nov., an alkaliphile that reduces an indigo dye. Int J Syst Evol Microbiol 2013; 63:464-469. [DOI: 10.1099/ijs.0.037622-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two indigo-reducing alkaliphilic strains, designated strain C40T and strain N214, were isolated from a fermented Polygonum Indigo (Polygonum tinctorium Lour.) liquor sample aged for 10 months and obtained from Date City, Hokkaido, Japan. 16S rRNA gene sequence phylogeny suggested that strains C40T and N214 were members of the genus
Amphibacillus
with the closest relative being
Amphibacillus xylanus
JCM 7361T (97.5 % 16S rRNA gene sequence similarity with strain C40T), which is the only strain having a 16S rRNA gene sequence similarity higher than 97 % with strain C40T. Cells of strain C40T were Gram-stain-positive, facultatively anaerobic, straight rods that were motile by means of peritrichous flagella. The strains grew between 17 and 39 °C (optimum, 35 °C) and in the pH range of 9.0–12.0. No isoprenoid quinone was detected and the DNA G+C content was 37.5–37.7 mol%. The whole-cell fatty acid profile mainly consisted of iso-C15 : 0 and anteiso-C15 : 0. DNA–DNA hybridization of strain C40T with
Amphibacillus xylanus
JCM 7361T revealed a DNA–DNA relatedness value of 10±3 %. Owing to the differences in phenotypic characteristics and phylogenetic analyses based on 16S rRNA gene sequences, as well as DNA–DNA relatedness data from reported species of the genus
Amphibacillus
, the isolates merit classification as a novel species in the genus
Amphibacillus
, for which the name Amphibacillus indicireducens sp. nov. is proposed. The type strain is C40T ( = JCM 17250T = NCIMB 14686T). An additional strain of the species is N214. An emended description of the genus
Amphibacillus
is provided.
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Affiliation(s)
- Kikue Hirota
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
| | - Kenichi Aino
- Laboratory of Environmental Microbiology, Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo 060-8589, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
| | - Yoshinobu Nodasaka
- Laboratory of Electron Microscopy, Graduate School of Dentistry, Hokkaido University, Kita-ku, Sapporo 060-8586, Japan
| | - Naoki Morita
- Laboratory of Environmental Microbiology, Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo 060-8589, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
| | - Isao Yumoto
- Laboratory of Environmental Microbiology, Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo 060-8589, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
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Surendra V, Bhawana P, Suresh K, Srinivas TNR, Anil Kumar P. Imtechella halotolerans gen. nov., sp. nov., a member of the family
Flavobacteriaceae
isolated from estuarine water. Int J Syst Evol Microbiol 2012; 62:2624-2630. [DOI: 10.1099/ijs.0.038356-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-negative, rod-shaped, non-motile, non-sporulating bacterium, designated strain K1T, was isolated from an estuarine water sample collected from Kochi, Kerala, India. Colonies on marine agar were circular, 2.0–2.5 mm in diameter, shiny, yellow, translucent and convex with entire margins. Strain K1T was negative for ornithine decarboxylase, lysine decarboxylase, nitrate reduction and H2S production. The fatty acids were dominated by iso-branched components with a high abundance of iso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH; MK-6 (64 %) and MK-7 (34 %) were found as major respiratory quinones; and phosphatidylethanolamine, two unidentified aminolipids, four unidentified phospholipids and two unidentified lipids were major polar lipids. The DNA G+C content of strain K1T was 46.1 mol%. 16S rRNA gene sequence analysis indicated that strain K1T was related most closely to the type strain of
Zhouia amylolytica
(pairwise sequence similarity of 93.0 %). Phylogenetic analysis showed that strain K1T formed a distinct branch within the family
Flavobacteriaceae
and clustered with the clade comprising species of the genera
Zhouia
,
Coenonia
and
Capnocytophaga
, being phylogenetically most closely related to the type strain of
Zhouia amylolytica
at a distance of 9.2 % (90.8 % similarity). Other species of the genera within the same clade were related to strain K1T at distances of 15.0–23.1 %. Based on phenotypic and chemotaxonomic characteristics and on phylogenetic inference, strain K1T is considered to represent a novel species of a new genus in the family
Flavobacteriaceae
, for which the name Imtechella halotolerans gen. nov., sp. nov. is proposed. The type strain of Imtechella halotolerans is K1T ( = MTCC 11055T = JCM 17677T).
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Affiliation(s)
- Vikram Surendra
- CSIR–Microbial Type Culture Collection and Gene bank, Institute of Microbial Technology, Sector 39A, Chandigarh 160 036, India
| | - Pant Bhawana
- CSIR–Microbial Type Culture Collection and Gene bank, Institute of Microbial Technology, Sector 39A, Chandigarh 160 036, India
| | - Korpole Suresh
- CSIR–Microbial Type Culture Collection and Gene bank, Institute of Microbial Technology, Sector 39A, Chandigarh 160 036, India
| | - T. N. R. Srinivas
- CSIR–National Institute of Oceanography, Regional Centre, PB No. 1913, Dr Salim Ali Road, Kochi 682018 (Kerala), India
| | - Pinnaka Anil Kumar
- CSIR–Microbial Type Culture Collection and Gene bank, Institute of Microbial Technology, Sector 39A, Chandigarh 160 036, India
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Implementation of a biotechnological process for vat dyeing with woad. ACTA ACUST UNITED AC 2012; 39:1309-19. [DOI: 10.1007/s10295-012-1139-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Accepted: 04/18/2012] [Indexed: 11/26/2022]
Abstract
Abstract
The traditional process for vat dyeing with woad (Isatis tinctoria L.) basically relies on microbial reduction of indigo to its soluble form, leucoindigo, through a complex fermentative process. In the 19th century, cultivation of woad went into decline and use of synthetic indigo dye and chemical reduction agents was established, with a consequent negative impact on the environment due to the release of polluting wastewaters by the synthetic dyeing industry. Recently, the ever-growing demand for environmentally friendly dyeing technologies has led to renewed interest in ecological textile traditions. In this context, this study aims at developing an environmentally friendly biotechnological process for vat dyeing with woad to replace use of polluting chemical reduction agents. Two simple broth media, containing yeast extract or corn steep liquor (CSL), were comparatively evaluated for their capacity to sustain the growth and reducing activity of the strain Clostridium isatidis DSM 15098T. Subsequently, the dyeing capacity of the CSL medium added with 140 g L−1 of woad powder, providing 2.4 g L−1 of indigo dye, was evaluated after fermentation in laboratory bioreactors under anaerobic or microaerophilic conditions. In all fermentations, a sufficiently negative oxidation/reduction potential for reduction of indigo was reached as early as 24 h and maintained up to the end of the monitoring period. However, clearly faster indigo dye reduction was seen in the broth cultures fermented under strict anaerobiosis, thus suggesting the suitability of the N2 flushing strategy for enhancement of bacterial-driven indigo reduction.
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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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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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Aino K, Narihiro T, Minamida K, Kamagata Y, Yoshimune K, Yumoto I. Bacterial community characterization and dynamics of indigo fermentation. FEMS Microbiol Ecol 2010; 74:174-83. [DOI: 10.1111/j.1574-6941.2010.00946.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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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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Iino T, Suzuki KI, Harayama S. Lacticigenium naphtae gen. nov., sp. nov., a halotolerant and motile lactic acid bacterium isolated from crude oil. Int J Syst Evol Microbiol 2009; 59:775-80. [DOI: 10.1099/ijs.0.003293-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [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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Abstract
Prokaryotic extremophiles were the first representatives of life on Earth and they are responsible for the genesis of geological structures during the evolution and creation of all currently known ecosystems. Flexibility of the genome probably allowed life to adapt to a wide spectrum of extreme environments. As a result, modern prokaryotic diversity formed in a framework of physico-chemical factors, and it is composed of: thermophilic, psychrophilic, acidophilic, alkaliphilic, halophilic, barophilic, and radioresistant species. This artificial systematics cannot reflect the multiple actions of different environmental factors since one organism could unite characteristics of several extreme-groups. In this review we show the current status of studies in all fields of extremophiles and summarize the limits of life for different species of microbial extremophiles. We also discuss the finding of extremophiles from unusual places such as soils, and briefly review recent studies of microfossils in meteorites in the context of the significance of microbial extremophiles to Astrobiology.
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Affiliation(s)
- Elena V Pikuta
- National Space Sciences and Technology Center, NASA, Astrobiology Laboratory, Huntsville, Alabama 35805, USA.
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Ramya M, Anusha B, Kalavathy S. Decolorization and biodegradation of Indigo carmine by a textile soil isolate Paenibacillus larvae. Biodegradation 2007; 19:283-91. [PMID: 17554499 DOI: 10.1007/s10532-007-9134-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2007] [Accepted: 05/11/2007] [Indexed: 11/26/2022]
Abstract
The potential of recently isolated bacteria Paenibacillus larvae for the effective decolorization of Indigo carmine was evaluated. The effects of operational parameters (temperature, pH, dye concentration, shaking/non shaking) were tested. Maximum extent of decolorization was observed when the medium was incorporated with 10 g/l of yeast extract and peptone. Decolorization was strongly inhibited at non-shaken conditions as well as incorporation of inorganic sources (sodium nitrite and ammonium chloride) in the medium. Maximum decolorization was observed at 30 degrees C (100%) and 40 degrees C (92%) at 8 h of incubation. The LC-MS and NMR analysis confirms the oxidation of Indigo carmine . The primary degradation products were found to be Isatin sulfonic acid and anthranilicacid.
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Affiliation(s)
- Mohandass Ramya
- Biotechnology Department, Bishop Heber College, Vyalur Road, Tiruchirapalli 620017 Tamilnadu, India.
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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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Di Giacomo M, Paolino M, Silvestro D, Vigliotta G, Imperi F, Visca P, Alifano P, Parente D. Microbial community structure and dynamics of dark fire-cured tobacco fermentation. Appl Environ Microbiol 2007; 73:825-37. [PMID: 17142368 PMCID: PMC1800767 DOI: 10.1128/aem.02378-06] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2006] [Accepted: 11/20/2006] [Indexed: 11/20/2022] Open
Abstract
The Italian Toscano cigar production includes a fermentation step that starts when dark fire-cured tobacco leaves are moistened and mixed with ca. 20% prefermented tobacco to form a 500-kg bulk. The dynamics of the process, lasting ca. 18 days, has never been investigated in detail, and limited information is available on microbiota involved. Here we show that Toscano fermentation is invariably associated with the following: (i) an increase in temperature, pH, and total microbial population; (ii) a decrease in reducing sugars, citric and malic acids, and nitrate content; and (iii) an increase in oxalic acid, nitrite, and tobacco-specific nitrosamine content. The microbial community structure and dynamics were investigated by culture-based and culture-independent approaches, including denaturing gradient gel electrophoresis and single-strand conformational polymorphism. Results demonstrate that fermentation is assisted by a complex microbial community, changing in structure and composition during the process. During the early phase, the moderately acidic and mesophilic environment supports the rapid growth of a yeast population predominated by Debaryomyces hansenii. At this stage, Staphylococcaceae (Jeotgalicoccus and Staphylococcus) and Lactobacillales (Aerococcus, Lactobacillus, and Weissella) are the most commonly detected bacteria. When temperature and pH increase, endospore-forming low-G+C content gram-positive bacilli (Bacillus spp.) become evident. This leads to a further pH increase and promotes growth of moderately halotolerant and alkaliphilic Actinomycetales (Corynebacterium and Yania) during the late phase. To postulate a functional role for individual microbial species assisting the fermentation process, a preliminary physiological and biochemical characterization of representative isolates was performed.
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Ghosh A, Bhardwaj M, Satyanarayana T, Khurana M, Mayilraj S, Jain RK. Bacillus lehensis sp. nov., an alkalitolerant bacterium isolated from soil. Int J Syst Evol Microbiol 2007; 57:238-242. [PMID: 17267957 DOI: 10.1099/ijs.0.64617-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-positive, endospore-forming, alkalitolerant bacterial strain, designated MLB2T, was isolated from soil from Leh, India, and was subjected to a polyphasic taxonomic study. The strain exhibited phenotypic properties that included chemotaxonomic characteristics consistent with its classification in the genusBacillus. Growth was observed at pH 7.0–11.0, but not at pH 6.0. The DNA G+C content was 41.4 mol%. The highest level of 16S rRNA gene sequence similarity was withBacillus oshimensisJCM 12663T(98.8 %). However, DNA–DNA hybridization experiments indicated low levels of genomic relatedness with the type strains ofB. oshimensis(62 %),Bacillus patagoniensis(55 %),Bacillus clausii(51 %) andBacillus gibsonii(34 %), the species with which strain MLB2Tformed a coherent cluster (based on the results of the phylogenetic analysis). On the basis of the phenotypic characteristics and genotypic distinctiveness of strain MLB2T, it should be classified within a novel species ofBacillus, for which the nameBacillus lehensissp. nov. is proposed. The type strain is MLB2T(=MTCC 7633T=JCM 13820T).
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MESH Headings
- Alkalies/pharmacology
- Anti-Bacterial Agents/pharmacology
- Bacillus/classification
- Bacillus/cytology
- Bacillus/isolation & purification
- Bacillus/physiology
- Bacterial Typing Techniques
- Base Composition
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Drug Resistance, Bacterial
- Genes, rRNA/genetics
- Hydrogen-Ion Concentration
- India
- Molecular Sequence Data
- Nucleic Acid Hybridization
- Phylogeny
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Soil Microbiology
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Affiliation(s)
- A Ghosh
- Microbial Type Culture Collection and Gene Bank (MTCC), Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India
| | - M Bhardwaj
- Microbiology, University of Delhi, South Campus, Benito Juarez Road, New Delhi 110021, India
| | - T Satyanarayana
- Microbiology, University of Delhi, South Campus, Benito Juarez Road, New Delhi 110021, India
| | - M Khurana
- Microbial Type Culture Collection and Gene Bank (MTCC), Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India
| | - S Mayilraj
- Microbial Type Culture Collection and Gene Bank (MTCC), Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India
| | - R K Jain
- Microbial Type Culture Collection and Gene Bank (MTCC), Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India
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Goto T, Matsuno T, Hishinuma-Narisawa M, Yamazaki K, Matsuyama H, Inoue N, Yumoto I. Cytochrome c and bioenergetic hypothetical model for alkaliphilic Bacillus spp. J Biosci Bioeng 2005; 100:365-79. [PMID: 16310725 DOI: 10.1263/jbb.100.365] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2005] [Accepted: 07/05/2005] [Indexed: 11/17/2022]
Abstract
Although a bioenergetic parameter is unfavorable for production of ATP (DeltapH<0), the growth rate and yield of alkaliphilic Bacillus strains are higher than those of neutralophilic Bacillus subtilis. This finding suggests that alkaliphiles possess a unique energy-producing machinery taking advantage of the alkaline environment. Expected bioenergetic parameters for the production of ATP (DeltapH and DeltaPsi) do not reflect the actual parameters for energy production. Certain strains of alkaliphilic Bacillus spp. possess large amounts of cytochrome c when grown at a high pH. The growth rate and yield are higher at pH 10 than at pH 7 in facultative alkaliphiles. These findings suggest that a large amount of cytochrome c at high pHs (e.g., pH 10) may be advantageous for sustaining growth. To date, isolated cytochromes c of alkaliphiles have a very low midpoint redox potential (less than +100 mV) compared with those of neutralophiles (approximately +220 mV). On the other hand, the redox potential of the electron acceptor from cytochrome c, that is, cytochrome c oxidase, seems to be normal (redox potential of cytochrome a=+250 mV). This large difference in midpoint redox potential between cytochrome c and cytochrome a concomitant with the configuration (e.g., a larger negative ion capacity at the inner surface membrane than at the outer surface for the attraction of H+ to the intracellular membrane and a large amount of cyrochrome c) supporting H+-coupled electron transfer of cytochrome c may have an important meaning in the adaptation of alkaliphiles at high pHs. This respiratory system includes a more rapid and efficient H+ and e- flow across the membrane in alkaliphiles than in neutralophiles.
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Affiliation(s)
- Toshitaka Goto
- Research Institute of Genome-based Biofactory, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
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