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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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2
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Arsenic Pollution and Anaerobic Arsenic Metabolizing Bacteria in Lake Van, the World's Largest Soda Lake. LIFE (BASEL, SWITZERLAND) 2022; 12:life12111900. [PMID: 36431035 PMCID: PMC9694729 DOI: 10.3390/life12111900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/10/2022] [Accepted: 11/12/2022] [Indexed: 11/17/2022]
Abstract
Arsenic is responsible for water pollution in many places around the world and presents a serious health risk for people. Lake Van is the world's largest soda lake, and there are no studies on seasonal arsenic pollution and arsenic-resistant bacteria. We aimed to determine the amount of arsenic in the lake water and sediment, to isolate arsenic-metabolizing anaerobic bacteria and their identification, and determination of arsenic metabolism. Sampling was done from 7.5 m to represent the four seasons. Metal contents were determined by using ICP-MS. Pure cultures were obtained using the Hungate technique. Growth characteristics of the strains were determined at different conditions as well as at arsenate and arsenite concentrations. Molecular studies were also carried out for various resistance genes. Our results showed that Lake Van's total arsenic amount changes seasonally. As a result of 16S rRNA sequencing, it was determined that the isolates were members of 8 genera with arsC resistance genes. In conclusion, to sustain water resources, it is necessary to prevent chemical and microorganism-based pollution. It is thought that the arsenic-resistant bacteria obtained as a result of this study will contribute to the solution of environmental arsenic pollution problems, as they are the first data and provide the necessary basic data for the bioremediation studies of arsenic from contaminated environmental habitats. At the same time, the first data that will contribute to the creation of the seasonal arsenic map of Lake Van are obtained.
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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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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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10
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Yi C, Tan X, Bie B, Ma H, Yi H. Practical and environment-friendly indirect electrochemical reduction of indigo and dyeing. Sci Rep 2020; 10:4927. [PMID: 32188868 PMCID: PMC7080776 DOI: 10.1038/s41598-020-61795-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Accepted: 02/28/2020] [Indexed: 11/14/2022] Open
Abstract
Indigo has been widely used as a dye in the industrial dyeing due to its good color fastness in dyeing cellulose fibers. However, excess reducing agent, “insurance powder (Na2S2O4)”, was always used in the actual production of the factory, sparking serious pollution (water pollution and air pollution). Herein, we developed a practical and environment-friendly indirect electrochemical reduction of indigo, and applied this method for cloth dyeing. The electrochemical device was designed in the combination of source of electro-catalytic reduction and dyeing. The iron-triethanolamine-calcium gluconate (Fe-TEOA-Ca) complex played a role of key intermediate, and ultrasonic wave was found to speed up the indirect electro-catalytic process. The electrochemical performance of intermedia was improved by calcium ion addition. Washed with oxalic acid solution, the dyed fabric could achieve the level of color fastness in industry standard. Generally speaking, our method leads to a green route for indigo reduction using electrochemistry, which may change the crafting process of indigo dyeing in industry.
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Affiliation(s)
- Changhai Yi
- Science and Technology Institute, National Engineering Laboratory for Advanced Yarn and Fabric Formation and Clean Production, Wuhan Textile University, Wuhan, Hubei, 430200, People's Republic of China.
| | - Xiaodong Tan
- Science and Technology Institute, National Engineering Laboratory for Advanced Yarn and Fabric Formation and Clean Production, Wuhan Textile University, Wuhan, Hubei, 430200, People's Republic of China.,Department of Material Engineering, Faculty of Textile Engineering, Technical University of Liberec, Liberec, Czech Republic
| | - Bihan Bie
- Science and Technology Institute, National Engineering Laboratory for Advanced Yarn and Fabric Formation and Clean Production, Wuhan Textile University, Wuhan, Hubei, 430200, People's Republic of China
| | - Haitao Ma
- Shandong Ruyi Technology Group Company, Jining, Shandong, People's Republic of China
| | - Hong Yi
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei, 430072, People's Republic of China.
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11
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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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12
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Da X, Zhao Y, Zheng R, Wang L, Chang X, Zhang Y, Yang J, Peng F. Nakamurella antarctica sp. nov., isolated from Antarctica South Shetland Islands soil. Int J Syst Evol Microbiol 2019; 69:3710-3715. [PMID: 31665101 DOI: 10.1099/ijsem.0.003507] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A pale-yellow bacterial strain, designated S14-144T, was isolated from tundra soil sampled near the Antarctic Peninsula, South Shetland Islands (62° 22' 34″ S, 59° 42' 34″ W). The cells were strictly aerobic, Gram-stain-positive, non-motile and coccoid-shaped. Growth occurred at 4-28 °C, at pH 5.0-9.0 and in the presence of 0-5 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain S14-144T formed a lineage within the genus Nakamurella and shared the highest 16S rRNA gene sequence similarity with Nakamurella deserti 12Sc4-1T (96.5 %) and Nakamurella silvestrisS20-107T (96.4 %). The average nucleotide identity value between the genomes of strain 14-144T and the type strain of the species, N. deserti, was 72.0 % . The DNA G+C content of strain S14-144T was 61.6 mol% . The major cellular fatty acids of strain S14-144T were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and C16 : 0. The strain contained MK-8(H4) as the predominant respiratory quinone, phosphatidylethanolamine and diphosphatidylglycerol as the major polar lipids, rhamnose, ribose and glucose as the major whole-cell sugars, and meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan. On the basis of the phylogenetic, phenotypic and chemotaxonomic analysis, strain S14-144T is considered to represent a novel species of the genus Nakamurella, for which the name Nakamurella antarctica sp. nov. is proposed. The type strain is S14-144T (=CCTCC AB 2015345T=KCTC 39796T).
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Affiliation(s)
- Xuyang Da
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Yiming Zhao
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Ruichen Zheng
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Liqiu Wang
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Xulu Chang
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Yumin Zhang
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Jian Yang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China
| | - Fang Peng
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
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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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Kevbrin VV. Isolation and Cultivation of Alkaliphiles. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2019; 172:53-84. [DOI: 10.1007/10_2018_84] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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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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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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18
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Hsu TM, Welner DH, Russ ZN, Cervantes B, Prathuri RL, Adams PD, Dueber JE. Employing a biochemical protecting group for a sustainable indigo dyeing strategy. Nat Chem Biol 2018; 14:256-261. [PMID: 29309053 PMCID: PMC5866135 DOI: 10.1038/nchembio.2552] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 11/14/2017] [Indexed: 11/09/2022]
Abstract
Indigo is an ancient dye uniquely capable of producing the signature tones in blue denim; however, the dyeing process requires chemical steps that are environmentally damaging. We describe a sustainable dyeing strategy that not only circumvents the use of toxic reagents for indigo chemical synthesis but also removes the need for a reducing agent for dye solubilization. This strategy utilizes a glucose moiety as a biochemical protecting group to stabilize the reactive indigo precursor indoxyl to form indican, preventing spontaneous oxidation to crystalline indigo during microbial fermentation. Application of a β-glucosidase removes the protecting group from indican, resulting in indigo crystal formation in the cotton fibers. We identified the gene coding for the glucosyltransferase PtUGT1 from the indigo plant Polygonum tinctorium and solved the structure of PtUGT1. Heterologous expression of PtUGT1 in Escherichia coli supported high indican conversion, and biosynthesized indican was used to dye cotton swatches and a garment.
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Affiliation(s)
- Tammy M Hsu
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, USA
- UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, California, USA
| | - Ditte H Welner
- Joint BioEnergy Institute, Emeryville, California, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratories, Berkeley, California, USA
| | - Zachary N Russ
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, USA
- UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, California, USA
| | - Bernardo Cervantes
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, USA
| | - Ramya L Prathuri
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, USA
| | - Paul D Adams
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, USA
- Joint BioEnergy Institute, Emeryville, California, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratories, Berkeley, California, USA
| | - John E Dueber
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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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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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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21
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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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22
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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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23
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Zheng R, Zhao Y, Wang L, Chang X, Zhang Y, Da X, Peng F. Mucilaginibacter antarcticus sp. nov., isolated from tundra soil. Int J Syst Evol Microbiol 2016; 66:5140-5144. [DOI: 10.1099/ijsem.0.001486] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ruichen Zheng
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Yiming Zhao
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Liqiu Wang
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Xulu Chang
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Yumin Zhang
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Xuyang Da
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Fang Peng
- Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Wuhan 430072, PR China
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
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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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25
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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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26
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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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Marine extremophiles: a source of hydrolases for biotechnological applications. Mar Drugs 2015; 13:1925-65. [PMID: 25854643 PMCID: PMC4413194 DOI: 10.3390/md13041925] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 03/22/2015] [Accepted: 03/25/2015] [Indexed: 12/26/2022] Open
Abstract
The marine environment covers almost three quarters of the planet and is where evolution took its first steps. Extremophile microorganisms are found in several extreme marine environments, such as hydrothermal vents, hot springs, salty lakes and deep-sea floors. The ability of these microorganisms to support extremes of temperature, salinity and pressure demonstrates their great potential for biotechnological processes. Hydrolases including amylases, cellulases, peptidases and lipases from hyperthermophiles, psychrophiles, halophiles and piezophiles have been investigated for these reasons. Extremozymes are adapted to work in harsh physical-chemical conditions and their use in various industrial applications such as the biofuel, pharmaceutical, fine chemicals and food industries has increased. The understanding of the specific factors that confer the ability to withstand extreme habitats on such enzymes has become a priority for their biotechnological use. The most studied marine extremophiles are prokaryotes and in this review, we present the most studied archaea and bacteria extremophiles and their hydrolases, and discuss their use for industrial applications.
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28
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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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Recent advances in heterogeneous photocatalytic decolorization of synthetic dyes. ScientificWorldJournal 2014; 2014:692307. [PMID: 25054183 PMCID: PMC4099358 DOI: 10.1155/2014/692307] [Citation(s) in RCA: 199] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 04/10/2014] [Accepted: 04/14/2014] [Indexed: 11/18/2022] Open
Abstract
During the process and operation of the dyes, the wastes produced were commonly found to contain organic and inorganic impurities leading to risks in the ecosystem and biodiversity with the resultant impact on the environment. Improper effluent disposal in aqueous ecosystems leads to reduction of sunlight penetration which in turn diminishes photosynthetic activity, resulting in acute toxic effects on the aquatic flora/fauna and dissolved oxygen concentration. Recently, photodegradation of various synthetic dyes has been studied in terms of their absorbance and the reduction of oxygen content by changes in the concentration of the dye. The advantages that make photocatalytic techniques superior to traditional methods are the ability to remove contaminates in the range of ppb, no generation of polycyclic compounds, higher speed, and lower cost. Semiconductor metal oxides, typically TiO2, ZnO, SnO, NiO, Cu2O, Fe3O4, and also CdS have been utilized as photocatalyst for their nontoxic nature, high photosensitivity, wide band gap and high stability. Various process parameters like photocatalyst dose, pH and initial dye concentrations have been varied and highlighted. Research focused on surface modification of semiconductors and mixed oxide semiconductors by doping them with noble metals (Pt, Pd, Au, and Ag) and organic matter (C, N, Cl, and F) showed enhanced dye degradation compared to corresponding native semiconductors. This paper reviews recent advances in heterogeneous photocatalytic decolorization for the removal of synthetic dyes from water and wastewater. Thus, the main core highlighted in this paper is the critical selection of semiconductors for photocatalysis based on the chemical, physical, and selective nature of the poisoning dyes.
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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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Polyextremophiles and the Constraints for Terrestrial Habitability. CELLULAR ORIGIN, LIFE IN EXTREME HABITATS AND ASTROBIOLOGY 2013. [DOI: 10.1007/978-94-007-6488-0_1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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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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Reclassification of Nocardioides basaltis Kim et al. 2009 as a later synonym of Nocardioides salarius Kim et al. 2008, and emendation of the species description. Antonie van Leeuwenhoek 2012; 102:695-701. [PMID: 22772977 DOI: 10.1007/s10482-012-9768-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 06/21/2012] [Indexed: 10/28/2022]
Abstract
The taxonomic relationship between Nocardioides salarius CL-Z59(T) and Nocardioides basaltis J112(T) was established. The 16S rRNA gene sequences of the type strains showed 99.6 % similarity. The ΔT(m) for genomic DNA-DNA hybridization of N. salarius CL-Z59(T) and N. basaltis J112(T) was 0.6-1.6 °C, indicating that both strains belong to a single species. Phenotypic and chemotaxonomic characteristics showed no pronounced differences between the two species. Based on the results of the polyphasic approach, it is proposed that N. basaltis J112(T) is a later heterotypic synonym of N. salarius CL-Z59(T). An emended description of the species N. salarius is given.
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Wilson SL, Frazer C, Cumming BF, Nuin PAS, Walker VK. Cross-tolerance between osmotic and freeze-thaw stress in microbial assemblages from temperate lakes. FEMS Microbiol Ecol 2012; 82:405-15. [PMID: 22551442 DOI: 10.1111/j.1574-6941.2012.01404.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Revised: 04/21/2012] [Accepted: 04/25/2012] [Indexed: 12/01/2022] Open
Abstract
Osmotic stress can accompany increases in solute concentrations because of freezing or high-salt environments. Consequently, microorganisms from environments with a high-osmotic potential may exhibit cross-tolerance to freeze stress. To test this hypothesis, enrichments derived from the sediment and water of temperate lakes with a range of salt concentrations were subjected to multiple freeze-thaw cycles. Surviving isolates were identified and metagenomes were sampled prior to and following selection. Enrichments from alkali lakes were typically the most freeze-thaw resistant with only 100-fold losses in cell viability, and those from freshwater lakes were most susceptible, with cell numbers reduced at least 100,000-fold. Metagenomic analysis suggested that selection reduced assemblage diversity more in freshwater samples than in those from saline lakes. Survivors included known psychro-, halo- and alkali-tolerant bacteria. Characterization of freeze-thaw-resistant isolates from brine and alkali lakes showed that few isolates had ice-associating activities such as antifreeze or ice nucleation properties. However, all brine- and alkali-derived isolates had high intracellular levels of osmolytes and/or appeared more likely to form biofilms. Conversely, these phenotypes were infrequent amongst the freshwater-derived isolates. These observations are consistent with microbial cross-tolerance between osmotic and freeze-thaw stresses.
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Affiliation(s)
- Sandra L Wilson
- Department of Biology, Queen's University, Kingston, ON, Canada
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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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Alkaliphilic bacteria: applications in industrial biotechnology. J Ind Microbiol Biotechnol 2011; 38:769-90. [DOI: 10.1007/s10295-011-0968-x] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Accepted: 03/26/2011] [Indexed: 11/26/2022]
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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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Song J, Imanaka H, Imamura K, Kajitani K, Nakanishi K. Development of a highly efficient indigo dyeing method using indican with an immobilized β-glucosidase from Aspergillus niger. J Biosci Bioeng 2010; 110:281-7. [DOI: 10.1016/j.jbiosc.2010.03.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2009] [Revised: 02/16/2010] [Accepted: 03/23/2010] [Indexed: 10/19/2022]
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Fujinami S, Fujisawa M. Industrial applications of alkaliphiles and their enzymes--past, present and future. ENVIRONMENTAL TECHNOLOGY 2010; 31:845-856. [PMID: 20662376 DOI: 10.1080/09593331003762807] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Alkaliphiles are microorganisms that can grow in alkaline environments, i.e. pH >9.0. Their enzymes, especially extracellular enzymes, are able to function in their catalytic activities under high alkaline pH values because of their stability under these conditions. Proteases, protein degrading enzymes, are one of the most produced enzymes in industry. Among proteases, alkaline proteases, which are added to some detergents, are the most produced. Other alkaline enzymes, e.g. alkaline cellulases, alkaline amylases, and alkaline lipases, are also adjuncts to detergents for improving cleaning efficiency. Alkaline enzymes often show activities in a broad pH range, thermostability, and tolerance to oxidants compared to neutral enzymes. Alkaliphilic Bacillus species are the most characterized organisms among alkaliphiles. They produce so many extracellular alkaline-adapted enzymes that they are often good sources for industrial enzymes. As a patent strain, the whole genome sequence of alkaliphilic Bacillus halodurans C-125 has been sequenced for the first time. In addition, an increasing number of whole genomic sequences and structural analyses of proteins in alkaliphiles, development of genetic engineering techniques and physiological analyses will reveal the alkaline adaptation mechanisms of alkaliphilic Bacillus species and the structural basis of their enzymatic functions. This information opens up the possibility of new applications. In this paper we describe, first, the physiologies of environmental adaptations, and then the applications of enzymes and microorganisms themselves in alkaliphilic Bacillus species.
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Affiliation(s)
- Shun Fujinami
- NITE Bioresource Information Center, Department of Biotechnology, National Institute of Technology and Evaluation, 2-10-49 Nishihara, Shibuya-ku, Tokyo 151-0066, Japan
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Fabiani A, Gamalero E, Castaldini M, Cossa GP, Musso C, Pagliai M, Berta G. Microbiological polyphasic approach for soil health evaluation in an Italian polluted site. THE SCIENCE OF THE TOTAL ENVIRONMENT 2009; 407:4954-4964. [PMID: 19520418 DOI: 10.1016/j.scitotenv.2009.05.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2009] [Revised: 05/04/2009] [Accepted: 05/06/2009] [Indexed: 05/27/2023]
Abstract
The use of microorganisms as bioindicators of soil health is quite a new feature, rarely considered for the soil health evaluation in chronically-polluted industrial sites, and still suffering of the bias related to the technique applied. In this work we applied a microbiological polyphasic approach, relying on soil indigenous microorganisms as bioindicators and combining culture-dependent and -independent methods, in order to evaluate soil health of four sites (1a, 1b, 2a and 2b) inside a chemical factory with a centenary activity. Functional as well as structural aspects were comprehensively considered. Results were related to the kind of pollutants found in each site. Heavy metal pollution was recorded in sites 1b and 2b, while both organic and inorganic substances were detected in sites 1a and 2a. Based on the chemical and physical properties of the four soils, site 1b and 2b grouped together, while 1a and 2a were separated from the others. The density of the culturable bacteria was very low in site 2a, where only gram-positive were found. According to the identification of culturable bacteria, site 2a showed the lowest similarity with the other sites. Microbial activity was detected only in sites 1b and 2b. PCR-DGGE (Denaturing Gradient Gel Electrophoresis), was performed on the culturable, total and active microbial communities. Consistently with the identification of culturable bacterial strains, the molecular profile of the culturable fraction of site 2a, was clearly separated from the molecular profiles of other sites in cluster analysis. Molecular fingerprintings of the whole and active bacterial communities differed among the sites, but clustered according to the pollutants present in each site. The presence of possible key species in each site has been discussed according to the whole and active species. Since the results obtained by microbiological analysis are consistent with the chemical data, we suggest that the use of this microbiological polyphasic approach and of microorganisms as intrinsic bioindicators, can be suitable for the evaluation of soil health.
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Affiliation(s)
- A Fabiani
- Centro di ricerca per l'Agrobiologia e la Pedologia, Piazza Massimo d'Azeglio 30, Firenze, Italy
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Enzymatic reduction of complex redox dyes using NADH-dependent reductase from Bacillus subtilis coupled with cofactor regeneration. Appl Microbiol Biotechnol 2009; 85:563-71. [PMID: 19662398 DOI: 10.1007/s00253-009-2164-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2009] [Revised: 07/22/2009] [Accepted: 07/23/2009] [Indexed: 10/20/2022]
Abstract
Conventional vat dyeing involves chemical reduction of dyes into their water-soluble leuco form generating considerable amounts of toxic chemicals in effluents. In the present study, a new beta-nicotinamide adenine dinucleotide disodium salt (NADH)-dependent reductase isolated from Bacillus subtilis was used to reduce the redox dyes CI Acid Blue 74, CI Natural Orange 6, and CI Vat Blue 1 into their water-soluble leuco form. Enzymatic reduction was optimized in relation to pH and temperature conditions. The reductase was able to reduce Acid Blue 74 and Natural Orange 6 in the presence of the stoichiometrically consumed cofactor NADH; meanwhile, Vat Blue 1 required the presence of mediator 1,8-dihydroxyanthraquinone. Oxygen from air was used to reoxidize the dyes into their initial forms. The enzymatic reduction of the dyes was studied and the kinetic constants determined, and these were compared to the chemically-reduced leuco form. The enzyme responsible for the reduction showed homology to a NADH-dependent reductase from B. subtilis based on results from the MS/MS peptide mass mapping of the tryptically digested protein. Additionally, the reduction of Acid Blue 74 to its leuco form by reductase from B. subtilis was confirmed using NADH regenerated by the oxidation of formic acid with formate dehydrogenase from Candida boidinii in the same solution.
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48
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Hwang CY, Cho BC. Spongiibacter tropicus sp. nov., isolated from a Synechococcus culture. Int J Syst Evol Microbiol 2009; 59:2176-9. [DOI: 10.1099/ijs.0.005819-0] [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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49
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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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50
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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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