1
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Kinukawa M, Ito M, Uemoto Y, Ogino A, Haruta S, Kurogi K, Watanabe T, Sasaki S, Naniwa Y, Uchiyama K, Togashi K. A potent allele marker related to low bull conception rate in Japanese Black bulls. Animal 2023; 17:100804. [PMID: 37141635 DOI: 10.1016/j.animal.2023.100804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 03/24/2023] [Accepted: 03/31/2023] [Indexed: 05/06/2023] Open
Abstract
Over the years, there has been considerable variation in the bull conception rate (BCR) of Japanese Black cattle; moreover, several Japanese Black bulls with a low BCR of ≤10% have been identified. However, the alleles responsible for the low BCR are not determined yet. Therefore, in this study, we aimed to identify single-nucleotide polymorphisms (SNPs) for predicting low BCR. To this end, the genome of Japanese Black bulls was comprehensively examined by a genome-wide association study with whole-exome sequencing (WES), and the effect of the identified marker regions on BCR was determined. The WES analysis of six sub-fertile bulls with a BCR of ≤10% and 73 normal bulls with a BCR of ≥40% identified a homozygous genotype for low BCR in Bos taurus autosome 5 in the region between 116.2 and 117.9 Mb. The g.116408653G > A SNP in this region had the most significant effect on the BCR (P-value = 1.0 × 10-23), and the GG (55.4 ± 11.2%) and AG (54.4 ± 9.4%) genotypes in the SNP had a higher phenotype than the AA (9.5 ± 6.1%) genotype for the BCR. The mixed model analysis revealed that g.116408653G > A was related to approximately 43% of the total genetic variance. In conclusion, the AA genotype of g.116408653G > A is a useful index for identifying sub-fertile Japanese Black bulls. Some positive and negative effects of SNP on the BCR were presumed to identify the causative mutations, which can help evaluate bull fertility.
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Affiliation(s)
- M Kinukawa
- Livestock Improvement Association of Japan, Inc., 316 Kanamaru, Maebashi, Gunma 371-0121, Japan.
| | - M Ito
- Department of Virology and Parasitology, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192, Japan
| | - Y Uemoto
- Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi 980-8572, Japan
| | - A Ogino
- Livestock Improvement Association of Japan, Inc., 316 Kanamaru, Maebashi, Gunma 371-0121, Japan
| | - S Haruta
- Livestock Improvement Association of Japan, Inc., 316 Kanamaru, Maebashi, Gunma 371-0121, Japan
| | - K Kurogi
- Livestock Improvement Association of Japan, Inc., 316 Kanamaru, Maebashi, Gunma 371-0121, Japan
| | - T Watanabe
- Livestock Improvement Association of Japan, Inc., 316 Kanamaru, Maebashi, Gunma 371-0121, Japan
| | - S Sasaki
- Faculty of Agriculture, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan
| | - Y Naniwa
- Livestock Improvement Association of Japan, Inc., 316 Kanamaru, Maebashi, Gunma 371-0121, Japan
| | - K Uchiyama
- Livestock Improvement Association of Japan, Inc., 316 Kanamaru, Maebashi, Gunma 371-0121, Japan
| | - K Togashi
- Livestock Improvement Association of Japan, Inc., 316 Kanamaru, Maebashi, Gunma 371-0121, Japan
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2
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Haruta S, Kakuhama H, Fukushima SI, Morohoshi S. Motility Assays of Chloroflexus. Methods Mol Biol 2023; 2646:383-390. [PMID: 36842132 DOI: 10.1007/978-1-0716-3060-0_32] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Abstract
Chloroflexus is a thermophilic, filamentous, gliding bacterium. Its multicellular filaments of several hundred micrometer length move straightforward at a speed of approximately 1-3 μm/s and occasionally reverse the moving direction. In liquid media, filaments glide on each other to form cell aggregates without tight adhesion. The molecular machinery on the cell surface that forces the gliding movement has not yet been identified. Here, we describe the cultivation methods to characterize the gliding motility of Chlroflexus and the microscopic assays to determine its gliding speed, reversal frequency, and cell-surface movements.
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Affiliation(s)
- Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan.
| | - Hinata Kakuhama
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
| | - Shun-Ichi Fukushima
- SANKEN (Institute of Scientific and Industrial Research), Osaka University, Ibaraki, Osaka, Japan
| | - Sho Morohoshi
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan.,TechnoSuruga Laboratory Co. Ltd., Shizuoka, Japan
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3
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Kawai S, Ishikawa M, Hanada S, Haruta S. Hydrogenophilus thiooxidans sp. nov., a moderately thermophilic chemotrophic bacterium unable to grow on hydrogen gas, isolated from hot spring microbial mats. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005355] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel thermophilic chemotrophic bacterium, strain SS56T, was isolated from Nakabusa Hot Spring, Japan. The isolate was a rod-shaped (1.5–2.1×0.6–0.8 µm), Gram-stain-negative bacterium. The cells of this strain grew chemoheterotrophically under aerobic and anaerobic conditions. Autotrophic growth was observed with thiosulphate and elemental sulphur under aerobic conditions but not with H2 as the electron donor. Heterotrophic growth in the presence of O2 occurred on yeast extract, tryptone, polypeptone and organic acids. Strain SS56T used nitrite as an alternative electron acceptor under anaerobic chemoheterotrophic conditions. The isolate grew between 35 and 65 °C, with the optimum at 55 °C. The pH range for growth was pH 6.0–9.0; optimal growth occurred at pH 7.0–8.0. The 16S rRNA gene sequence of strain SS56T was 98.9% identical to that of
Hydrogenophilus thermoluteolus
TH-1T. The draft genome sequence of 2401804 bp for strain SS56T gave values of 53.7% for digital DNA–DNA hybridization, 92.9% for average nucleotide identity and 93.6% for average amino acid identity compared with the genome sequence of 2223143 bp for
H. thermoluteolus
TH-1T. Based on the information described above, strain SS56T (=DSM 111892T=JCM 34254T) is proposed as the type strain of a novel species, Hydrogenophilus thiooxidans sp. nov.
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Affiliation(s)
- Shigeru Kawai
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
| | - Mikako Ishikawa
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
| | - Satoshi Hanada
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
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4
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Muramatsu S, Hirose S, Iino T, Ohkuma M, Hanada S, Haruta S. Neotabrizicola shimadae gen. nov., sp. nov., an aerobic anoxygenic phototrophic bacterium harbouring photosynthetic genes in the family Rhodobacteraceae, isolated from a terrestrial hot spring. Antonie Van Leeuwenhoek 2022; 115:731-740. [PMID: 35380297 DOI: 10.1007/s10482-022-01728-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 03/06/2022] [Indexed: 11/27/2022]
Abstract
A bacteriochlorophyll-containing bacterium, designated as strain N10T, was isolated from a terrestrial hot spring in Nagano Prefecture, Japan. Gram-stain-negative, oxidase- and catalase-positive and ovoid to rod-shaped cells showed the features of aerobic anoxygenic phototrophic bacteria, i.e., strain N10T synthesised bacteriochlorophylls under aerobic conditions and could not grow anaerobically even under illumination. Genome analysis found genes for bacteriochlorophyll and carotenoid biosynthesis, light-harvesting complexes and type-2 photosynthetic reaction centre in the chromosome. Phylogenetic analyses based on the 16S rRNA gene sequence and 92 core proteins revealed that strain N10T was located in a distinct lineage near the type species of the genera Tabrizicola and Xinfangfangia and some species in the genus Rhodobacter (e.g., Rhodobacter blasticus). Strain N10T shared < 97.1% 16S rRNA gene sequence identity with those species in the family Rhodobacteraceae. The digital DNA-DNA hybridisation, average nucleotide identity and average amino acid identity values with the relatives, Tabrizicola aquatica RCRI19T (an aerobic anoxygenic phototrophic bacterium), Xinfangfangia soli ZQBWT and R. blasticus ATCC 33485T were 19.9-20.7%, 78.2-79.1% and 69.1-70.1%, respectively. Based on the phenotypic features, major fatty acid and polar lipid compositions, genome sequence and phylogenetic position, a novel genus and species are proposed for strain N10T, to be named Neotabrizicola shimadae (= JCM 34381T = DSM 112087T). Strain N10T which is phylogenetically located among aerobic anoxygenic phototrophic bacteria (Tabrizicola), bacteriochlorophyll-deficient bacteria (Xinfangfangia) and anaerobic anoxygenic phototrophic bacteria (Rhodobacter) has great potential to promote studies on the evolution of photosynthesis in Rhodobacteraceae.
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Affiliation(s)
- So Muramatsu
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo, 192-0397, Japan
| | - Setsuko Hirose
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo, 192-0397, Japan
| | - Takao Iino
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo, 192-0397, Japan
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | - Satoshi Hanada
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo, 192-0397, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-0856, Japan
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo, 192-0397, Japan.
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Chen Y, Nishihara A, Iino T, Ohkuma M, Haruta S. Caldicellulosiruptor diazotrophicus sp. nov., a thermophilic, nitrogen-fixing fermentative bacterium isolated from a terrestrial hot spring in Japan. Int J Syst Evol Microbiol 2021; 71. [PMID: 34542397 DOI: 10.1099/ijsem.0.005014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel nitrogen-fixing fermentative bacterium, designated as YA01T, was isolated from Nakabusa hot springs in Japan. The short-rod cells of strain YA01T were Gram-positive and non-sporulating. Phylogenetic trees of the 16S rRNA gene sequence and concatenated sequences of 40 single-copy ribosomal genes revealed that strain YA01T belonged to the genus Caldicellulosiruptor and was closely related to Caldicellulosiruptor hydrothermalis 108T, Caldicellulosiruptor bescii DSM 6725T and Caldicellulosiruptor kronotskyensis 2002T. The 16S rRNA gene sequence of strain YA01T shares less than 98.1 % identity to the known Caldicellulosiruptor species. The G+C content of the genomic DNA was 34.8 mol%. Strain YA01T shares low genome-wide average nucleotide identity (90.31-91.10 %), average amino acid identity (91.45-92.10 %) and <70 % digital DNA-DNA hybridization value (41.8-44.2 %) with the three related species of the genus Caldicellulosiruptor. Strain YA01T grew at 50-78 °C (optimum, 70 °C) and at pH 5.0-9.5 (optimum, pH 6.5). Strain YA01T mainly produced acetate by consuming d(+)-glucose as a carbon source. The main cellular fatty acids were iso-C17 : 0 (35.7 %), C16 : 0 (33.3 %), DMA16 : 0 (6.6 %) and iso-C15 : 0 (5.9 %). Based on its distinct phylogenetic position, biochemical and physiological characteristics, and the major cellular fatty acids, strain YA01T is considered to represent a novel species of the genus Caldicellulosiruptor for which the name Caldicellulosiruptor diazotrophicus sp. nov. is proposed (type strain YA01T=DSM 112098T=JCM 34253T).
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Affiliation(s)
- Yuxin Chen
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
| | - Arisa Nishihara
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-0856, Japan
| | - Takao Iino
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan.,Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
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6
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Kumagai K, Yagi S, Yamaguchi T, Nagashima K, Nomura T, Watanabe M, Makuuchi R, Kawakami K, Otsuka S, Matsushima T, Kadowaki S, Haruta S, Cho H, Yamada T, Kakihara N, Imai Y, Fukunaga H, Saeki Y, Kanaji S, Boku N, Goto M. P-83 The efficacy of chemotherapy for gastric cancer with early recurrence during or after adjuvant S-1. Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.05.138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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7
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Saini MK, Sebastian A, Shirotori Y, Soulier NT, Garcia Costas AM, Drautz-Moses DI, Schuster SC, Albert I, Haruta S, Hanada S, Thiel V, Tank M, Bryant DA. Genomic and Phenotypic Characterization of Chloracidobacterium Isolates Provides Evidence for Multiple Species. Front Microbiol 2021; 12:704168. [PMID: 34220789 PMCID: PMC8245765 DOI: 10.3389/fmicb.2021.704168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 05/21/2021] [Indexed: 11/16/2022] Open
Abstract
Chloracidobacterium is the first and until now the sole genus in the phylum Acidobacteriota (formerly Acidobacteria) whose members perform chlorophyll-dependent phototrophy (i.e., chlorophototrophy). An axenic isolate of Chloracidobacterium thermophilum (strain B T ) was previously obtained by using the inferred genome sequence from an enrichment culture and diel metatranscriptomic profiling analyses in situ to direct adjustments to the growth medium and incubation conditions, and thereby a defined growth medium for Chloracidobacterium thermophilum was developed. These advances allowed eight additional strains of Chloracidobacterium spp. to be isolated from microbial mat samples collected from Mushroom Spring, Yellowstone National Park, United States, at temperatures of 41, 52, and 60°C; an axenic strain was also isolated from Rupite hot spring in Bulgaria. All isolates are obligately photoheterotrophic, microaerophilic, non-motile, thermophilic, rod-shaped bacteria. Chloracidobacterium spp. synthesize multiple types of (bacterio-)chlorophylls and have type-1 reaction centers like those of green sulfur bacteria. Light harvesting is accomplished by the bacteriochlorophyll a-binding, Fenna-Matthews-Olson protein and chlorosomes containing bacteriochlorophyll c. Their genomes are approximately 3.7 Mbp in size and comprise two circular chromosomes with sizes of approximately 2.7 Mbp and 1.0 Mbp. Comparative genomic studies and phenotypic properties indicate that the nine isolates represent three species within the genus Chloracidobacterium. In addition to C. thermophilum, the microbial mats at Mushroom Spring contain a second species, tentatively named Chloracidobacterium aggregatum, which grows as aggregates in liquid cultures. The Bulgarian isolate, tentatively named Chloracidobacterium validum, will be proposed as the type species of the genus, Chloracidobacterium. Additionally, Chloracidobacterium will be proposed as the type genus of a new family, Chloracidobacteriaceae, within the order Blastocatellales, the class Blastocatellia, and the phylum Acidobacteriota.
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Affiliation(s)
- Mohit Kumar Saini
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
| | - Aswathy Sebastian
- The Huck Institutes for the Life Sciences, The Pennsylvania State University, University Park, PA, United States
| | - Yoshiki Shirotori
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
| | - Nathan T. Soulier
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
| | - Amaya M. Garcia Costas
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
- Department of Biology, Colorado State University-Pueblo, Pueblo, CO, United States
| | - Daniela I. Drautz-Moses
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Stephan C. Schuster
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Istvan Albert
- The Huck Institutes for the Life Sciences, The Pennsylvania State University, University Park, PA, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
| | - Satoshi Hanada
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
| | - Vera Thiel
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
- DSMZ – German Culture Collection of Microorganisms and Cell Cultures, GmbH, Braunschweig, Germany
| | - Marcus Tank
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
- DSMZ – German Culture Collection of Microorganisms and Cell Cultures, GmbH, Braunschweig, Germany
| | - Donald A. Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
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8
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Kawai S, Martinez JN, Lichtenberg M, Trampe E, Kühl M, Tank M, Haruta S, Nishihara A, Hanada S, Thiel V. In-Situ Metatranscriptomic Analyses Reveal the Metabolic Flexibility of the Thermophilic Anoxygenic Photosynthetic Bacterium Chloroflexus aggregans in a Hot Spring Cyanobacteria-Dominated Microbial Mat. Microorganisms 2021; 9:microorganisms9030652. [PMID: 33801086 PMCID: PMC8004040 DOI: 10.3390/microorganisms9030652] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/17/2021] [Accepted: 03/17/2021] [Indexed: 12/13/2022] Open
Abstract
Chloroflexus aggregans is a metabolically versatile, thermophilic, anoxygenic phototrophic member of the phylum Chloroflexota (formerly Chloroflexi), which can grow photoheterotrophically, photoautotrophically, chemoheterotrophically, and chemoautotrophically. In hot spring-associated microbial mats, C. aggregans co-exists with oxygenic cyanobacteria under dynamic micro-environmental conditions. To elucidate the predominant growth modes of C. aggregans, relative transcription levels of energy metabolism- and CO2 fixation-related genes were studied in Nakabusa Hot Springs microbial mats over a diel cycle and correlated with microscale in situ measurements of O2 and light. Metatranscriptomic analyses indicated two periods with different modes of energy metabolism of C. aggregans: (1) phototrophy around midday and (2) chemotrophy in the early morning hours. During midday, C. aggregans mainly employed photoheterotrophy when the microbial mats were hyperoxic (400–800 µmol L−1 O2). In the early morning hours, relative transcription peaks of genes encoding uptake hydrogenase, key enzymes for carbon fixation, respiratory complexes as well as enzymes for TCA cycle and acetate uptake suggest an aerobic chemomixotrophic lifestyle. This is the first in situ study of the versatile energy metabolism of C. aggregans based on gene transcription patterns. The results provide novel insights into the metabolic flexibility of these filamentous anoxygenic phototrophs that thrive under dynamic environmental conditions.
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Affiliation(s)
- Shigeru Kawai
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan; (J.N.M.); (M.T.); (S.H.); (A.N.); (S.H.)
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
- Correspondence: (S.K.); (V.T.)
| | - Joval N. Martinez
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan; (J.N.M.); (M.T.); (S.H.); (A.N.); (S.H.)
- Department of Natural Sciences, College of Arts and Sciences, University of St. La Salle, Bacolod City, Negros Occidental 6100, Philippines
| | - Mads Lichtenberg
- Department of Biology, Marine Biological Section, University of Copenhagen, Strandpromenaden 5, 3000 Helsingør, Denmark; (M.L.); (E.T.); (M.K.)
| | - Erik Trampe
- Department of Biology, Marine Biological Section, University of Copenhagen, Strandpromenaden 5, 3000 Helsingør, Denmark; (M.L.); (E.T.); (M.K.)
| | - Michael Kühl
- Department of Biology, Marine Biological Section, University of Copenhagen, Strandpromenaden 5, 3000 Helsingør, Denmark; (M.L.); (E.T.); (M.K.)
| | - Marcus Tank
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan; (J.N.M.); (M.T.); (S.H.); (A.N.); (S.H.)
- DSMZ—German Culture Collection of Microorganisms and Cell Culture, GmbH Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan; (J.N.M.); (M.T.); (S.H.); (A.N.); (S.H.)
| | - Arisa Nishihara
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan; (J.N.M.); (M.T.); (S.H.); (A.N.); (S.H.)
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki 305-8566, Japan
| | - Satoshi Hanada
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan; (J.N.M.); (M.T.); (S.H.); (A.N.); (S.H.)
| | - Vera Thiel
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan; (J.N.M.); (M.T.); (S.H.); (A.N.); (S.H.)
- DSMZ—German Culture Collection of Microorganisms and Cell Culture, GmbH Inhoffenstraße 7B, 38124 Braunschweig, Germany
- Correspondence: (S.K.); (V.T.)
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9
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Chen Y, Nishihara A, Haruta S. Nitrogen-fixing Ability and Nitrogen Fixation-related Genes of Thermophilic Fermentative Bacteria in the Genus Caldicellulosiruptor. Microbes Environ 2021; 36. [PMID: 34108360 PMCID: PMC8209448 DOI: 10.1264/jsme2.me21018] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Fermentative nitrogen-fixing bacteria have not yet been examined in detail in thermal environments. In the present study, we isolated the thermophilic fermentative bacterium, strain YA01 from a hot spring. This strain grew at temperatures up to 78°C. A phylogenetic analysis based on its 16S rRNA gene sequence indicated that strain YA01 belonged to the genus Caldicellulosiruptor, which are fermentative bacteria in the phylum Firmicutes, with 97.7–98.0% sequence identity to its closest relatives. Strain YA01 clearly exhibited N2-dependent growth at 70°C. We also confirmed N2-dependent growth in the relatives of strain YA01, Caldicellulosiruptor hydrothermalis 108 and Caldicellulosiruptor kronotskyensis 2002. The nitrogenase activities of these three strains were examined using the acetylene reduction assay. Similar activities were detected for all tested strains, and were slightly suppressed by the addition of ammonium. A genome analysis revealed that strain YA01, as well as other Caldicellulosiruptor, possessed a gene set for nitrogen fixation, but lacked the nifN gene, which encodes a nitrogenase iron-molybdenum cofactor biosynthesis protein that is commonly detected in nitrogen-fixing bacteria. The amino acid sequences of nitrogenase encoded by nifH, nifD, and nifK shared 92–98% similarity in Caldicellulosiruptor. A phylogenetic tree of concatenated NifHDK sequences showed that NifHDK of Caldicellulosiruptor was in the deepest clade. To the best of our knowledge, this is the first study to demonstrate the nitrogen-fixing ability of fermentative bacteria at 70°C. Caldicellulosiruptor may have retained an ancient nitrogen-fixing enzyme system.
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Affiliation(s)
- Yuxin Chen
- Department of Biological Sciences, Tokyo Metropolitan University
| | - Arisa Nishihara
- Department of Biological Sciences, Tokyo Metropolitan University.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University
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10
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Izaki K, Haruta S. Aerobic Production of Bacteriochlorophylls in the Filamentous Anoxygenic Photosynthetic Bacterium, Chloroflexus aurantiacus in the Light. Microbes Environ 2020; 35. [PMID: 32418929 PMCID: PMC7308566 DOI: 10.1264/jsme2.me20015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Filamentous anoxygenic photosynthetic bacteria grow by photosynthesis and aerobic respiration. The present study investigated the effects of light and O2 on bacteriochlorophyll contents and the transcription levels of photosynthesis-related genes in Chloroflexus aurantiacus J-10-fl T. Under aerobic conditions, C. aurantiacus produced marked amounts of bacteriochlorophylls in the presence of light, although their production was strongly suppressed in the dark. The transcription levels of genes related to the synthesis of bacteriochlorophylls, photosystems, and chlorosomes: bchM, bchU, pufL, pufBA, and csmM, were markedly increased by illumination. These results suggest that C. aurantiacus continuously synthesizes ATP by photophosphorylation even in the presence of O2.
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Affiliation(s)
- Kazaha Izaki
- Department of Biological Sciences, Tokyo Metropolitan University
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University
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11
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Kawai S, Nishihara A, Matsuura K, Haruta S. Hydrogen-dependent autotrophic growth in phototrophic and chemolithotrophic cultures of thermophilic bacteria, Chloroflexus aggregans and Chloroflexus aurantiacus, isolated from Nakabusa hot springs. FEMS Microbiol Lett 2020; 366:5510454. [PMID: 31158281 DOI: 10.1093/femsle/fnz122] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 06/01/2019] [Indexed: 11/14/2022] Open
Abstract
The genus Chloroflexus is a deeply branching group of thermophilic filamentous anoxygenic phototrophic bacteria. The bacteria in this genus have been shown to grow well heterotrophically under anaerobic photosynthetic and aerobic respiratory conditions. We examined autotrophic growth in new isolates of Chloroflexus strains from hot springs in Nakabusa, Japan. The isolates belonging to Chloroflexus aggregans (98.7% identity of 16S rRNA gene sequence to the respective type strain) and Chloroflexus aurantiacus (99.9% identity to the respective type strain) grew photoautotrophically under a 24% H2 atmosphere. We also observed chemolithotrophic growth of these isolates under 80% H2 and 5% O2 conditions in the dark. This is the first report showing that Chloroflexus grew under both photoautotrophic and chemolithotrophic conditions in addition to photoheterotrophic and aerobic chemoheterotrophic conditions.
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Affiliation(s)
- Shigeru Kawai
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
| | - Arisa Nishihara
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
| | - Katsumi Matsuura
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
| | - Shin Haruta
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
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12
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Miyata M, Robinson RC, Uyeda TQP, Fukumori Y, Fukushima SI, Haruta S, Homma M, Inaba K, Ito M, Kaito C, Kato K, Kenri T, Kinosita Y, Kojima S, Minamino T, Mori H, Nakamura S, Nakane D, Nakayama K, Nishiyama M, Shibata S, Shimabukuro K, Tamakoshi M, Taoka A, Tashiro Y, Tulum I, Wada H, Wakabayashi KI. Tree of motility - A proposed history of motility systems in the tree of life. Genes Cells 2020; 25:6-21. [PMID: 31957229 PMCID: PMC7004002 DOI: 10.1111/gtc.12737] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/11/2019] [Accepted: 11/17/2019] [Indexed: 12/27/2022]
Abstract
Motility often plays a decisive role in the survival of species. Five systems of motility have been studied in depth: those propelled by bacterial flagella, eukaryotic actin polymerization and the eukaryotic motor proteins myosin, kinesin and dynein. However, many organisms exhibit surprisingly diverse motilities, and advances in genomics, molecular biology and imaging have showed that those motilities have inherently independent mechanisms. This makes defining the breadth of motility nontrivial, because novel motilities may be driven by unknown mechanisms. Here, we classify the known motilities based on the unique classes of movement‐producing protein architectures. Based on this criterion, the current total of independent motility systems stands at 18 types. In this perspective, we discuss these modes of motility relative to the latest phylogenetic Tree of Life and propose a history of motility. During the ~4 billion years since the emergence of life, motility arose in Bacteria with flagella and pili, and in Archaea with archaella. Newer modes of motility became possible in Eukarya with changes to the cell envelope. Presence or absence of a peptidoglycan layer, the acquisition of robust membrane dynamics, the enlargement of cells and environmental opportunities likely provided the context for the (co)evolution of novel types of motility.
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Affiliation(s)
- Makoto Miyata
- Department of Biology, Graduate School of Science, Osaka City University, Osaka, Japan.,The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Osaka, Japan
| | - Robert C Robinson
- Research Institute for Interdisciplinary Science, Okayama University, Okayama, Japan.,School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Taro Q P Uyeda
- Department of Physics, Faculty of Science and Technology, Waseda University, Tokyo, Japan
| | - Yoshihiro Fukumori
- Faculty of Natural System, Institute of Science and Engineering, Kanazawa University, Kanazawa, Japan.,WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Japan
| | - Shun-Ichi Fukushima
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan
| | - Shin Haruta
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan
| | - Michio Homma
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Kazuo Inaba
- Shimoda Marine Research Center, University of Tsukuba, Shizuoka, Japan
| | - Masahiro Ito
- Graduate School of Life Sciences, Toyo University, Gunma, Japan
| | - Chikara Kaito
- Laboratory of Microbiology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Kentaro Kato
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, Miyagi, Japan
| | - Tsuyoshi Kenri
- Laboratory of Mycoplasmas and Haemophilus, Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Seiji Kojima
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Tohru Minamino
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Hiroyuki Mori
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Shuichi Nakamura
- Department of Applied Physics, Graduate School of Engineering, Tohoku University, Miyagi, Japan
| | - Daisuke Nakane
- Department of Physics, Gakushuin University, Tokyo, Japan
| | - Koji Nakayama
- Department of Microbiology and Oral Infection, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Masayoshi Nishiyama
- Department of Physics, Faculty of Science and Engineering, Kindai University, Osaka, Japan
| | - Satoshi Shibata
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Katsuya Shimabukuro
- Department of Chemical and Biological Engineering, National Institute of Technology, Ube College, Yamaguchi, Japan
| | - Masatada Tamakoshi
- Department of Molecular Biology, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Azuma Taoka
- Faculty of Natural System, Institute of Science and Engineering, Kanazawa University, Kanazawa, Japan.,WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Japan
| | - Yosuke Tashiro
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Isil Tulum
- Department of Botany, Faculty of Science, Istanbul University, Istanbul, Turkey
| | - Hirofumi Wada
- Department of Physics, Graduate School of Science and Engineering, Ritsumeikan University, Shiga, Japan
| | - Ken-Ichi Wakabayashi
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Kanagawa, Japan
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13
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Iino T, Kawai S, Yuki M, Dekio I, Ohkuma M, Haruta S. Thermaurantimonas aggregans gen. nov., sp. nov., a moderately thermophilic heterotrophic aggregating bacterium isolated from microbial mats at a terrestrial hot spring. Int J Syst Evol Microbiol 2020; 70:1117-1121. [DOI: 10.1099/ijsem.0.003888] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Takao Iino
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Shigeru Kawai
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
| | - Masahiro Yuki
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Itaru Dekio
- Skin Microbe Laboratory, Mildix Skin Clinic, 3rd Floor, 3-98 Senju, Adachi-ku, Tokyo 120-0034, Japan
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
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14
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Lee JY, Haruta S, Kato S, Bernstein HC, Lindemann SR, Lee DY, Fredrickson JK, Song HS. Prediction of Neighbor-Dependent Microbial Interactions From Limited Population Data. Front Microbiol 2020; 10:3049. [PMID: 32038529 PMCID: PMC6985286 DOI: 10.3389/fmicb.2019.03049] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 12/18/2019] [Indexed: 11/13/2022] Open
Abstract
Modulation of interspecies interactions by the presence of neighbor species is a key ecological factor that governs dynamics and function of microbial communities, yet the development of theoretical frameworks explicit for understanding context-dependent interactions are still nascent. In a recent study, we proposed a novel rule-based inference method termed the Minimal Interspecies Interaction Adjustment (MIIA) that predicts the reorganization of interaction networks in response to the addition of new species such that the modulation in interaction coefficients caused by additional members is minimal. While the theoretical basis of MIIA was established through the previous work by assuming the full availability of species abundance data in axenic, binary, and complex communities, its extension to actual microbial ecology can be highly constrained in cases that species have not been cultured axenically (e.g., due to their inability to grow in the absence of specific partnerships) because binary interaction coefficients - basic parameters required for implementing the MIIA - are inestimable without axenic and binary population data. Thus, here we present an alternative formulation based on the following two central ideas. First, in the case where only data from axenic cultures are unavailable, we remove axenic populations from governing equations through appropriate scaling. This allows us to predict neighbor-dependent interactions in a relative sense (i.e., fractional change of interactions between with versus without neighbors). Second, in the case where both axenic and binary populations are missing, we parameterize binary interaction coefficients to determine their values through a sensitivity analysis. Through the case study of two microbial communities with distinct characteristics and complexity (i.e., a three-member community where all members can grow independently, and a four-member community that contains member species whose growth is dependent on other species), we demonstrated that despite data limitation, the proposed new formulation was able to successfully predict interspecies interactions that are consistent with experimentally derived results. Therefore, this technical advancement enhances our ability to predict context-dependent interspecies interactions in a broad range of microbial systems without being limited to specific growth conditions as a pre-requisite.
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Affiliation(s)
- Joon-Yong Lee
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
| | - Souichiro Kato
- National Institute of Advanced Industrial Science and Technology, Sapporo, Japan
| | - Hans C Bernstein
- Faculty of Biosciences, Fisheries and Economics, UiT - The Arctic University of Norway, Tromsø, Norway.,The Arctic Centre for Sustainable Energy, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Stephen R Lindemann
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, West Lafayette, IN, United States
| | - Dong-Yup Lee
- Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore, Singapore.,School of Chemical Engineering, Sungkyunkwan University, Seoul, South Korea
| | - Jim K Fredrickson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Hyun-Seob Song
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States.,Department of Biological Systems Engineering, University of Nebraska-Lincoln, Lincoln, NE, United States.,Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, United States
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15
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Hirose S, Tank M, Hara E, Tamaki H, Mori K, Takaichi S, Haruta S, Hanada S. Aquabacterium pictum sp. nov., the first aerobic bacteriochlorophyll a-containing fresh water bacterium in the genus Aquabacterium of the class Betaproteobacteria. Int J Syst Evol Microbiol 2019; 70:596-603. [PMID: 31622237 DOI: 10.1099/ijsem.0.003798] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
A strictly aerobic, bacteriochlorophyll a-containing betaproteobacterium, designated strain W35T, was isolated from a biofilm sampled at Tama River in Japan. The non-motile and rod-shaped cells formed pink-beige pigmented colonies on agar plates containing organic compounds, and showed an in vivo absorption maximum at 871 nm in the near-infrared region, typical for the presence of bacteriochlorophyll a. The new bacterial strain is Gram-negative, and oxidase- and catalase-positive. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain W35T was closely related to species in the genus Aquabacterium. The closest phylogenetic relatives of strain W35T were Aquabacterium commune B8T (97.9 % sequence similarity), Aquabacterium citratiphilum B4T (97.2 %) and Aquabacterium limnoticum ABP-4T (97.0 %). The major cellular fatty acids were C16 : 1ω7c (50.4 %), C16 : 0 (22.7 %), summed feature 8 (C18 : 1ω7c/C18 : 1ω6c; 9.7 %), C18 : 3ω6c (5.5 %), C12 : 0 (5.3 %) and C10 : 0 3OH (2.7 %). The respiratory quinone was ubiquinone-8. Predominant polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The G+C content of the genomic DNA was 70.4 mol% (genome data) and 71.4 mol% (HPLC). The genome size of strain W35T is 6.1 Mbp and average nucleotide identity analysis indicated genome similarities of strain W35T and related Aquabacterium type strains to be 78-79 %. The results of polyphasic comparisons showed that strain W35T was clearly distinguishable from other members of the genus Aquabacterium. Therefore, we propose a new species in the genus Aquabacterium, namely, Aquabacterium pictum sp. nov. The type strain is W35T (=DSM 106757T=NBRC 111963T). The description of the genus Aquabacterium is also emended.
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Affiliation(s)
- Setsuko Hirose
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1, Minami-Osawa, Hachioji, Tokyo, 192-0397, Japan
| | - Marcus Tank
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1, Minami-Osawa, Hachioji, Tokyo, 192-0397, Japan
| | - Eri Hara
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1, Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1, Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Koji Mori
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8, Kazusakamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Shinichi Takaichi
- Department of Molecular Microbiology, Tokyo University of Agriculture, 1-1-1, Sakuragaoka, Setagaya-ku, Tokyo, 156-8502, Japan
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1, Minami-Osawa, Hachioji, Tokyo, 192-0397, Japan
| | - Satoshi Hanada
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1, Minami-Osawa, Hachioji, Tokyo, 192-0397, Japan
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16
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Abstract
Chloroflexus aggregans is a thermophilic filamentous anoxygenic phototrophic bacterium frequently found in microbial mats in natural hot springs. C. aggregans often thrives with cyanobacteria that engage in photosynthesis to provide it with an organic substrate; however, it sometimes appears as the dominant phototroph in microbial mats without cyanobacteria. This suggests that C. aggregans has the ability to grow photoautotrophically. However, photoautotrophic growth has not been observed in any cultured strains of C. aggregans. We herein attempted to isolate a photoautotrophic strain from C. aggregansdominated microbial mats in Nakabusa hot spring in Japan. Using an inorganic medium, we succeeded in isolating a new strain that we designated "ACA-12". A phylogenetic analysis based on 16S rRNA gene and 16S-23S rRNA gene internal transcribed spacer (ITS) region sequences revealed that strain ACA-12 was closely related to known C. aggregans strains. Strain ACA-12 showed sulfide consumption along with autotrophic growth under anaerobic light conditions. The deposited elemental sulfur particles observed by microscopy indicated that sulfide oxidation occurred, similar to that in photoautotrophic strains in the related species, C. aurantiacus. Moreover, we found that other strains of C. aggregans, including the type strain, also exhibited a slight photoautotrophic growing ability, whereas strain ACA-12 showed the fastest growth rate. This is the first demonstration of photoautotrophic growth with sulfide in C. aggregans. The present results strongly indicate that C. aggregans is associated with inorganic carbon incorporation using sulfide as an electron donor in hot spring microbial mats.
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Affiliation(s)
- Nanako Kanno
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University
| | - Shin Haruta
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University
| | - Satoshi Hanada
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University
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17
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Song HS, Lee JY, Haruta S, Nelson WC, Lee DY, Lindemann SR, Fredrickson JK, Bernstein HC. Minimal Interspecies Interaction Adjustment (MIIA): Inference of Neighbor-Dependent Interactions in Microbial Communities. Front Microbiol 2019; 10:1264. [PMID: 31263456 PMCID: PMC6584816 DOI: 10.3389/fmicb.2019.01264] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 05/21/2019] [Indexed: 02/01/2023] Open
Abstract
An intriguing aspect in microbial communities is that pairwise interactions can be influenced by neighboring species. This creates context dependencies for microbial interactions that are based on the functional composition of the community. Context dependent interactions are ecologically important and clearly present in nature, yet firmly established theoretical methods are lacking from many modern computational investigations. Here, we propose a novel network inference method that enables predictions for interspecies interactions affected by shifts in community composition and species populations. Our approach first identifies interspecies interactions in binary communities, which is subsequently used as a basis to infer modulation in more complex multi-species communities based on the assumption that microbes minimize adjustments of pairwise interactions in response to neighbor species. We termed this rule-based inference minimal interspecies interaction adjustment (MIIA). Our critical assessment of MIIA has produced reliable predictions of shifting interspecies interactions that are dependent on the functional role of neighbor organisms. We also show how MIIA has been applied to a microbial community composed of competing soil bacteria to elucidate a new finding that – in many cases – adding fewer competitors could impose more significant impact on binary interactions. The ability to predict membership-dependent community behavior is expected to help deepen our understanding of how microbiomes are organized in nature and how they may be designed and/or controlled in the future.
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Affiliation(s)
- Hyun-Seob Song
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Joon-Yong Lee
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
| | - William C Nelson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Dong-Yup Lee
- Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore, Singapore.,School of Chemical Engineering, Sungkyunkwan University, Suwon, South Korea
| | - Stephen R Lindemann
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, West Lafayette, IN, United States.,Department of Nutrition Science, Purdue University, West Lafayette, IN, United States
| | - Jim K Fredrickson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Hans C Bernstein
- Faculty of Biosciences, Fisheries and Economics, UiT - The Arctic University of Norway, Tromsø, Norway.,The Arctic Centre for Sustainable Energy, UiT - The Arctic University of Norway, Tromsø, Norway
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18
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Kawai S, Kamiya N, Matsuura K, Haruta S. Symbiotic Growth of a Thermophilic Sulfide-Oxidizing Photoautotroph and an Elemental Sulfur-Disproportionating Chemolithoautotroph and Cooperative Dissimilatory Oxidation of Sulfide to Sulfate. Front Microbiol 2019; 10:1150. [PMID: 31178849 PMCID: PMC6543001 DOI: 10.3389/fmicb.2019.01150] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 05/06/2019] [Indexed: 11/13/2022] Open
Abstract
A thermophilic filamentous anoxygenic photosynthetic bacterium, Chloroflexus aggregans, is widely distributed in neutral to slightly alkaline hot springs. Sulfide has been suggested as an electron donor for autotrophic growth in microbial mats dominated with C. aggregans, but remarkable photoautotrophic growth of isolated C. aggregans has not been observed with sulfide as the sole electron source. From the idea that sulfide is oxidized to elemental sulfur by C. aggregans and the accumulation of elemental sulfur may have an inhibitory effect for the growth, the effects of an elemental sulfur-disproportionating bacterium that consumes elemental sulfur was examined on the autotrophic growth of C. aggregans, strain NA9-6, isolated from Nakabusa hot spring. A sulfur-disproportionating bacterium, Caldimicrobium thiodismutans strain TF1, also isolated from Nakabusa hot spring was co-cultured with C. aggregans. C. aggregans and C. thiodismutans were successfully co-cultured in a medium containing thiosulfate as the sole electron source and bicarbonate as the sole carbon source. Quantitative conversion of thiosulfate to sulfate and a small transient accumulation of sulfide was observed in the co-culture. Then the electron source of the established co-culture was changed from thiosulfate to sulfide, and the growth of C. aggregans and C. thiodismutans was successfully observed with sulfide as the sole electron donor for the autotrophic growth of the co-culture. During the cultivation in the light, simultaneous consumption and accumulation of sulfide and sulfate, respectively, were observed, accompanied with the increase of cellular DNAs of both species. C. thiodismutans likely works as an elemental sulfur scavenger for C. aggregans, and C. aggregans seems to work as a sulfide scavenger for C. thiodismutans. These results suggest that C. aggregans grows autotrophically with sulfide as the electron donor in the co-culture with C. thiodismutans, and the consumption of elemental sulfur by C. thiodismutans enabled the continuous growth of the C. aggregans in the symbiotic system. This study shows a novel symbiotic relationship between a sulfide-oxidizing photoautotroph and an elemental sulfur-disproportionating chemolithoautotroph via cooperative dissimilatory sulfide oxidation to sulfate.
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Affiliation(s)
- Shigeru Kawai
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
| | - Naoki Kamiya
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
| | - Katsumi Matsuura
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
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19
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Haruta S, Yamamoto K. Model Microbial Consortia as Tools for Understanding Complex Microbial Communities. Curr Genomics 2018; 19:723-733. [PMID: 30532651 PMCID: PMC6225455 DOI: 10.2174/1389202919666180911131206] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 07/19/2018] [Accepted: 09/03/2018] [Indexed: 02/08/2023] Open
Abstract
A major biological challenge in the postgenomic era has been untangling the composition and functions of microbes that inhabit complex communities or microbiomes. Multi-omics and modern bioinformatics have provided the tools to assay molecules across different cellular and community scales; however, mechanistic knowledge over microbial interactions often remains elusive. This is due to the immense diversity and the essentially undiminished volume of not-yet-cultured microbes. Simplified model communities hold some promise in enabling researchers to manage complexity so that they can mechanistically understand the emergent properties of microbial community interactions. In this review, we surveyed several approaches that have effectively used tractable model consortia to elucidate the complex behavior of microbial communities. We go further to provide some perspectives on the limitations and new opportunities with these approaches and highlight where these efforts are likely to lead as advances are made in molecular ecology and systems biology.
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Affiliation(s)
- Shin Haruta
- Address correspondence to this author at the Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan; Tel: +81-42-677-2580; Fax: +81-42-677-2559; E-mail:
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20
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Nishihara A, Matsuura K, Tank M, McGlynn SE, Thiel V, Haruta S. Nitrogenase Activity in Thermophilic Chemolithoautotrophic Bacteria in the Phylum Aquificae Isolated under Nitrogen-Fixing Conditions from Nakabusa Hot Springs. Microbes Environ 2018; 33:394-401. [PMID: 30473565 PMCID: PMC6307999 DOI: 10.1264/jsme2.me18041] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The phylum Aquificae comprises chemolithoautotrophic thermophilic to hyperthermophilic bacteria, in which the nitrogenase reductase gene (nifH) has been reported. However, nitrogen-fixing activity has not yet been demonstrated in members of this deeply branching bacterial phylum. We isolated two thermophilic diazotrophic strains from chemosynthetic microbial communities in slightly alkaline hot springs (≥70°C) in Nakabusa, Nagano Prefecture, Japan. A phylogenetic analysis based on 16S rRNA genes identified these strains as members of the genus Hydrogenobacter within Aquificae. Their NifH sequences showed 96.5 and 97.4% amino acid sequence identities to that from Hydrogenobacter thermophilus TK-6. Nitrogenase activity, measured by acetylene reduction, was confirmed in both strains at 70°C. These novel strains grew under semi-aerobic conditions by using CO2 as the sole carbon source and N2 as the sole nitrogen source in media containing hydrogen and/or thiosulfate. To the best of our knowledge, this is the first demonstration of active nitrogen fixation in thermophilic bacteria at 70°C and in the phylum Aquificae.
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Affiliation(s)
- Arisa Nishihara
- Department of Biological Sciences, Tokyo Metropolitan University
| | - Katsumi Matsuura
- Department of Biological Sciences, Tokyo Metropolitan University
| | - Marcus Tank
- Department of Biological Sciences, Tokyo Metropolitan University
| | - Shawn E McGlynn
- Department of Biological Sciences, Tokyo Metropolitan University.,Earth-Life Science Institute, Tokyo Institute of Technology.,Biofunctional Catalyst Research Team, RIKEN Center for Sustainable Resource Science.,Blue Marble Space Institute of Science
| | - Vera Thiel
- Department of Biological Sciences, Tokyo Metropolitan University
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University
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21
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Nishihara A, Thiel V, Matsuura K, McGlynn SE, Haruta S. Phylogenetic Diversity of Nitrogenase Reductase Genes and Possible Nitrogen-Fixing Bacteria in Thermophilic Chemosynthetic Microbial Communities in Nakabusa Hot Springs. Microbes Environ 2018; 33:357-365. [PMID: 30404970 PMCID: PMC6307998 DOI: 10.1264/jsme2.me18030] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Chemosynthetic microbial communities develop and form dense cell aggregates in slightly alkaline sulfidic hot springs in the temperature range of 70–86°C at Nakabusa, Japan. Nitrogenase activity has recently been detected in the microbial communities collected. To identify possible members capable of nitrogen fixation, we examined the diversities of 16S rRNA and nitrogenase reductase (NifH) gene sequences in four types of chemosynthetic communities with visually different colors and thicknesses. The results of a 16S rRNA gene analysis indicated that all four microbial communities had similar bacterial constituents; the phylum Aquificae was the dominant member, followed in abundance by Thermodesulfobacteria, Firmicutes, and Thermotogae. Most of the NifH sequences were related to sequences reported in hydrothermal vents and terrestrial hot springs. The results of a phylogenetic analysis of NifH sequences revealed diversity in this gene among the communities collected, distributed within 7 phylogenetic groups. NifH sequences affiliated with Aquificae (Hydrogenobacter/Thermocrinis) and Firmicutes (Caldicellulosiruptor) were abundant. At least two different energy metabolic pathways appeared to be related to nitrogen fixation in the communities analyzed; aerobic sulfur/hydrogen-oxidizing bacteria in Aquificae and fermentative bacteria in Firmicutes. The metabolic characteristics of these two dominant phyla differed from those previously inferred from nitrogenase activity assays on chemosynthetic communities, which were associated with hydrogen-dependent autotrophic sulfate reduction. These assays may correspond to the observed NifH sequences that are distantly related to the known species of Thermodesulfovibrio sp. (Nitrospirae) detected in the present study. The activities of nitrogen-fixing organisms in communities may depend on redox states as well as the availability of electron donors, acceptors, and carbon sources.
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Affiliation(s)
- Arisa Nishihara
- Department of Biological Sciences, Tokyo Metropolitan University
| | - Vera Thiel
- Department of Biological Sciences, Tokyo Metropolitan University
| | - Katsumi Matsuura
- Department of Biological Sciences, Tokyo Metropolitan University
| | - Shawn E McGlynn
- Department of Biological Sciences, Tokyo Metropolitan University.,Earth-Life Science Institute, Tokyo Institute of Technology.,Biofunctional Catalyst Research Team, RIKEN Center for Sustainable Resource Science.,Blue Marble Space Institute of Science
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University
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22
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Sato Y, Mizusawa J, Nakamura K, Fukagawa T, Katai H, Haruta S, Yamada M, Takagi M, Tamura S, Yoshimura T, Inada T, Hirabayashi N, Wada I, Kodera Y, Tokunaga M, Yoshikawa T, Boku N, Sano T, Sasako M, Terashima M. Diagnosis of invasion depth in resectable advanced gastric cancer for neoadjuvant chemotherapy: An exploratory analysis of JCOG1302A. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy282.040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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23
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Nishihara A, Haruta S, McGlynn SE, Thiel V, Matsuura K. Nitrogen Fixation in Thermophilic Chemosynthetic Microbial Communities Depending on Hydrogen, Sulfate, and Carbon Dioxide. Microbes Environ 2018; 33:10-18. [PMID: 29367473 PMCID: PMC5877335 DOI: 10.1264/jsme2.me17134] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 10/28/2017] [Indexed: 12/20/2022] Open
Abstract
The activity of nitrogen fixation measured by acetylene reduction was examined in chemosynthetic microbial mats at 72-75°C in slightly-alkaline sulfidic hot springs in Nakabusa, Japan. Nitrogenase activity markedly varied from sampling to sampling. Nitrogenase activity did not correlate with methane production, but was detected in samples showing methane production levels less than the maximum amount, indicating a possible redox dependency of nitrogenase activity. Nitrogenase activity was not affected by 2-bromo-ethane sulfonate, an inhibitor of methanogenesis. However, it was inhibited by the addition of molybdate, an inhibitor of sulfate reduction and sulfur disproportionation, suggesting the involvement of sulfate-reducing or sulfur-disproportionating organisms. Nitrogenase activity was affected by different O2 concentrations in the gas phase, again supporting the hypothesis of a redox potential dependency, and was decreased by the dispersion of mats with a homogenizer. The loss of activity that occurred from dispersion was partially recovered by the addition of H2, sulfate, and carbon dioxide. These results suggested that the observed activity of nitrogen fixation was related to chemoautotrophic sulfate reducers, and fixation may be active in a limited range of ambient redox potential. Since thermophilic chemosynthetic communities may resemble ancient microbial communities before the appearance of photosynthesis, the present results may be useful when considering the ancient nitrogen cycle on earth.
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Affiliation(s)
- Arisa Nishihara
- Department of Biological Sciences, Tokyo Metropolitan UniversityMinami-Osawa, Hachioji, Tokyo 192–0397Japan
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan UniversityMinami-Osawa, Hachioji, Tokyo 192–0397Japan
| | - Shawn E. McGlynn
- Department of Biological Sciences, Tokyo Metropolitan UniversityMinami-Osawa, Hachioji, Tokyo 192–0397Japan
- Earth-Life Science Institute, Tokyo Institute of TechnologyOokayama, Meguro-ku, Tokyo 152–8551Japan
- Biofunctional Catalyst Research Team, RIKEN Center for Sustainable Resource ScienceWako-shi 351–0198Japan
- Blue Marble Space Institute of ScienceSeattle, WA 98145–1561USA
| | - Vera Thiel
- Department of Biological Sciences, Tokyo Metropolitan UniversityMinami-Osawa, Hachioji, Tokyo 192–0397Japan
| | - Katsumi Matsuura
- Department of Biological Sciences, Tokyo Metropolitan UniversityMinami-Osawa, Hachioji, Tokyo 192–0397Japan
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24
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Kanno N, Matsuura K, Haruta S. Different Metabolomic Responses to Carbon Starvation between Light and Dark Conditions in the Purple Photosynthetic Bacterium, Rhodopseudomonas palustris. Microbes Environ 2018. [PMID: 29540639 PMCID: PMC5877347 DOI: 10.1264/jsme2.me17143] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Purple photosynthetic bacteria utilize light energy for growth. We previously demonstrated that light energy contributed to prolonging the survival of multiple purple bacteria under carbon-starved conditions. In order to clarify the effects of illumination on metabolic states under carbon-starved, non-growing conditions, we herein compared the metabolic profiles of starved cells in the light and dark using the purple bacterium, Rhodopseudomonas palustris. The metabolic profiles of starved cells in the light were markedly different from those in the dark. After starvation for 5 d in the light, cells showed increases in the amount of ATP and the NAD+/NADH ratio. Decreases in the amounts of most metabolites related to glycolysis and the TCA cycle in energy-rich starved cells suggest the active utilization of these metabolites for the modification of cellular components. Starvation in the dark induced the consumption of cellular compounds such as amino acids, indicating that the degradation of these cellular components produced ATP in order to maintain viability under energy-poor conditions. The present results suggest that intracellular energy levels alter survival strategies under carbon-starved conditions through metabolism.
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Affiliation(s)
- Nanako Kanno
- Department of Biological Sciences, Tokyo Metropolitan University
| | - Katsumi Matsuura
- Department of Biological Sciences, Tokyo Metropolitan University
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University
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25
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Wasai S, Kanno N, Matsuura K, Haruta S. Increase of Salt Tolerance in Carbon-Starved Cells of Rhodopseudomonas palustris Depending on Photosynthesis or Respiration. Microorganisms 2018; 6:microorganisms6010004. [PMID: 29316629 PMCID: PMC5874618 DOI: 10.3390/microorganisms6010004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 12/22/2017] [Accepted: 01/03/2018] [Indexed: 12/26/2022] Open
Abstract
Bacteria in natural environments are frequently exposed to nutrient starvation and survive against environmental stresses under non-growing conditions. In order to determine the energetic influence on survivability during starvation, changes in salt tolerance were investigated using the purple photosynthetic bacterium Rhodopseudomonas palustris after carbon starvation under photosynthetic conditions in comparison with anaerobic and aerobic dark conditions. Tolerance to a treatment with high concentration of salt (2.5 M NaCl for 1 h) was largely increased after starvation under anaerobically light and aerobically dark conditions. The starved cells under the conditions of photosynthesis or aerobic respiration contained high levels of cellular ATP, but starvation under the anaerobic dark conditions resulted in a decrease of cellular ATP contents. To observe the large increase of the salt tolerance, incubation of starved cells for more than 18 h under illumination was needed. These results suggest that the ATP-dependent rearrangement of cells induced salt tolerance.
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Affiliation(s)
- Sawa Wasai
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan.
| | - Nanako Kanno
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan.
| | - Katsumi Matsuura
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan.
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan.
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26
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Shimizu T, Horiguchi K, Hatanaka Y, Masuda S, Shimada K, Matsuura K, Haruta S. Nitrite-reducing ability is related to growth inhibition by nitrite in Rhodobacter sphaeroides f. sp. denitrificans. Biosci Biotechnol Biochem 2018; 82:148-151. [DOI: 10.1080/09168451.2017.1412247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Abstract
Growth inhibition of Rhodobacter sphaeroides f. sp. denitrificans IL106 by nitrite under anaerobic-light conditions became less pronounced when the gene encoding nitrite reductase was deleted. Growth of another deletion mutant of the genes encoding nitric oxide reductase was severely suppressed by nitrite. Our results suggest that nitrite reductase increases the sensitivity to nitrite through the production of nitric oxide.
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Affiliation(s)
- Takayuki Shimizu
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
| | - Kouhei Horiguchi
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
| | - Yui Hatanaka
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
| | - Shinji Masuda
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, Yokohama, Japan
| | - Keizo Shimada
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
| | - Katsumi Matsuura
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
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27
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Haruta S, Iino T, Ohkuma M, Suzuki KI, Igarashi Y. Ca 2+ in Hybridization Solutions for Fluorescence in situ Hybridization Facilitates the Detection of Enterobacteriaceae. Microbes Environ 2017; 32:142-146. [PMID: 28515389 PMCID: PMC5478537 DOI: 10.1264/jsme2.me16186] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Fluorescence in situ hybridization (FISH) has been employed to identify microorganisms at the single cell level under a microscope. Extensive efforts have been made to improve and extend the FISH technique; however, the development of a widely applicable protocol is a continuing challenge. The present study evaluated the effects of divalent cations in the hybridization solution on the FISH-based detection of various species of bacteria and archaea with rRNA-targeted probes. A flow cytometric analysis after FISH with a standard hybridization buffer detected positive signals from less than 30% of Escherichia coli IAM 1264 cells. However, the number of cells with positive signals increased to more than 90% after the addition of calcium chloride to the hybridization buffer. Mn2+ also had positive effects, whereas Mg2+ did not. The positive effects of Ca2+ were similarly observed for bacteria belonging to Enterobacteriaceae, including Enterobacter sakazakii IAM 12660T, E. aerogenes IAM 12348, Klebsiella planticola IAM 14202, and Salmonella enterica subsp. enterica serovar Typhimurium strain LT2. These results indicate that the supplementation of Ca2+ to the hybridization buffer for FISH contributes to the efficient detection of Enterobacteriaceae cells.
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Affiliation(s)
- Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University.,Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Takao Iino
- Japan Collection of Microorganisms, RIKEN BioResource Center.,NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE)
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Center
| | - Ken-Ichiro Suzuki
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE)
| | - Yasuo Igarashi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo.,Research Center of Bioenergy and Bioremediation, Southwest University
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28
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Kanno N, Matsuura K, Haruta S. Differences in Survivability under Starvation Conditions Among Four Species of Purple Nonsulfur Phototrophic Bacteria. Microbes Environ 2017; 32:93. [PMID: 28367919 PMCID: PMC5371083 DOI: 10.1264/jsme2.me14013e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Affiliation(s)
- Nanako Kanno
- Graduate School of Science and Engineering, Tokyo Metropolitan University
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29
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Haruta S, Saito Y, Futamata H. Editorial: Development of Microbial Ecological Theory: Stability, Plasticity, and Evolution of Microbial Ecosystems. Front Microbiol 2017; 7:2069. [PMID: 28066386 PMCID: PMC5174121 DOI: 10.3389/fmicb.2016.02069] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 12/07/2016] [Indexed: 12/02/2022] Open
Affiliation(s)
- Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University Hachioji, Japan
| | - Yasuhisa Saito
- Department of Mathematics, Shimane University Matsue, Japan
| | - Hiroyuki Futamata
- Research Institute of Green Science and Technology, Shizuoka UniversityShizuoka, Japan; Department of Applied Chemistry and Biochemical Engineering, Shizuoka UniversityHamamatsu, Japan
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30
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Hirose S, Matsuura K, Haruta S. Phylogenetically Diverse Aerobic Anoxygenic Phototrophic Bacteria Isolated from Epilithic Biofilms in Tama River, Japan. Microbes Environ 2016; 31:299-306. [PMID: 27453124 PMCID: PMC5017807 DOI: 10.1264/jsme2.me15209] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The diversity of aerobic anoxygenic phototrophic (AAP) bacteria in freshwater environments, particularly in rivers, has not been examined in as much detail as in ocean environments. In the present study, we investigated the phylogenetic and physiological diversities of AAP bacteria in biofilms that developed on submerged stones in a freshwater river using culture methods. The biofilms collected were homogenized and inoculated on solid media and incubated aerobically in the dark. Sixty-eight red-, pink-, yellow-, orange-, or brown-colored colonies were isolated, and, of these, 28 isolates contained the photosynthetic pigment, bacteriochlorophyll (BChl) a. Phylogenetic analyses based on 16S rRNA gene sequences showed that the isolates were classified into 14 groups in 8 operational taxonomic units (OTUs) and distributed in the orders Rhodospirillales, Rhodobacterales, and Sphingomonadales of Alphaproteobacteria and in Betaproteobacteria. Physiological analyses confirmed that none of the representative isolates from any of the groups grew under anaerobic phototrophic conditions. Seven isolates in 4 OTUs showed a 16S rRNA gene sequence identity of 98.0% or less with any established species, suggesting the presence of previously undescribed species of AAP bacteria. Six isolates in 2 other OTUs had the closest relatives, which have not been reported to be AAP bacteria. Physiological comparisons among the isolates revealed differences in preferences for nutrient concentrations, BChl contents, and light-harvesting proteins. These results suggest that diverse and previously unknown AAP bacteria inhabit river biofilms.
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Affiliation(s)
- Setsuko Hirose
- Department of Biological Sciences, Tokyo Metropolitan University
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31
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Affiliation(s)
- Shin Haruta
- Graduate School of Science and Engineering, Tokyo Metropolitan University
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32
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Fukushima SI, Morohoshi S, Hanada S, Matsuura K, Haruta S. Gliding motility driven by individual cell-surface movements in a multicellular filamentous bacterium Chloroflexus aggregans. FEMS Microbiol Lett 2016; 363:fnw056. [PMID: 26946537 DOI: 10.1093/femsle/fnw056] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2016] [Indexed: 11/14/2022] Open
Abstract
Chloroflexus aggregans is an unbranched multicellular filamentous bacterium having the ability of gliding motility. The filament moves straightforward at a constant rate, ∼3 μm sec(-1) on solid surface and occasionally reverses the moving direction. In this study, we successfully detected movements of glass beads on the cell-surface along long axis of the filament indicating that the cell-surface movement was the direct force for gliding. Microscopic analyses found that the cell-surface movements were confined to a cell of the filament, and each cell independently moved and reversed the direction. To understand how the cellular movements determine the moving direction of the filament, we proposed a discrete-time stochastic model; sum of the directions of the cellular movements determines the moving direction of the filament only when the filament pauses, and after moving, the filament keeps the same directional movement until all the cells pause and/or move in the opposite direction. Monte Carlo simulation of this model showed that reversal frequency of longer filaments was relatively fixed to be low, but the frequency of shorter filaments varied widely. This simulation result appropriately explained the experimental observations. This study proposed the relevant mechanism adequately describing the motility of the multicellular filament in C. aggregans.
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Affiliation(s)
- Shun-Ichi Fukushima
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
| | - Sho Morohoshi
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
| | - Satoshi Hanada
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
| | - Katsumi Matsuura
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
| | - Shin Haruta
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
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33
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Vanini R, Kabbara S, Elia E, Piancastelli A, Guglielminetti D, Tuveri M, Tuveri A, Nicolo E, Tomizawa K, Kuroyanagi H, Matoba S, Moriyama J, Toda S, Hanaoka Y, Fukui Y, Haruta S, Clara ES, Tang S, Tan WB, Wijerathne S, Hu J, Shabbir A, Lomanto D, Son G, Park S, Pietrantoni S, Pietrantoni C, Nishihara M, Takehara H, Nakagawa H, Kuniyoshi N, Aka H, Takushi Y, Miyahira T, Hanashiro N, Okushima N, Mayer F, Lechner M, Öfner D, Bittner R, Köhler G, Fortelny R, Köckerling F, Lim R, Berney C, Kato J, Iuamoto L, Meyer A, Floridi A, Bombelli E, Giuliani D, Galli I, Monti M, Longo A, Pisano G, Li J, Tian D. Topic: Inguinal Hernia - Tailored surgery. Hernia 2015; 19 Suppl 1:S287-92. [PMID: 26518825 DOI: 10.1007/bf03355373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- R Vanini
- Casa di Cura Privata Malatesta Novello, Cesena, Italy
| | - S Kabbara
- Casa di Cura Privata Malatesta Novello, Cesena, Italy
| | - E Elia
- Casa di Cura Privata Malatesta Novello, Cesena, Italy
| | | | | | - M Tuveri
- U.O. Chirurgia Generale, Ospedale N.S. di Bonaria, San Gavino Monreale, Italy
| | - A Tuveri
- U. O. Chirurgia Generale, CDC Sant'Elena, Quartu Sant Elena, Italy
| | - E Nicolo
- Dept. of General Surgery, Jefferson Hospital, Pittsburgh, USA
| | - K Tomizawa
- Toranomon Hospital Surgery, Tokyo, Japan
| | | | | | | | | | | | | | | | - E Sta Clara
- Minimally Invasive Surgery Centre, Department of Surgery, National University Health System (NUHS), Singapore, Singapore.,Minimally Invasive Surgical Centre, Department of Surgery, Yong Loo Lin School of Medicine, National University Singapore, Singapore, Singapore
| | - S Tang
- Minimally Invasive Surgery Centre, Department of Surgery, National University Health System (NUHS), Singapore, Singapore.,Minimally Invasive Surgical Centre, Department of Surgery, Yong Loo Lin School of Medicine, National University Singapore, Singapore, Singapore
| | - W B Tan
- Minimally Invasive Surgery Centre, Department of Surgery, National University Health System (NUHS), Singapore, Singapore.,Minimally Invasive Surgical Centre, Department of Surgery, Yong Loo Lin School of Medicine, National University Singapore, Singapore, Singapore
| | - S Wijerathne
- Minimally Invasive Surgery Centre, Department of Surgery, National University Health System (NUHS), Singapore, Singapore
| | - J Hu
- Minimally Invasive Surgery Centre, Department of Surgery, National University Health System (NUHS), Singapore, Singapore.,Minimally Invasive Surgical Centre, Department of Surgery, Yong Loo Lin School of Medicine, National University Singapore, Singapore, Singapore
| | - A Shabbir
- Minimally Invasive Surgery Centre, Department of Surgery, National University Health System (NUHS), Singapore, Singapore.,Minimally Invasive Surgical Centre, Department of Surgery, Yong Loo Lin School of Medicine, National University Singapore, Singapore, Singapore
| | - D Lomanto
- Minimally Invasive Surgery Centre, Department of Surgery, National University Health System (NUHS), Singapore, Singapore.,Minimally Invasive Surgical Centre, Department of Surgery, Yong Loo Lin School of Medicine, National University Singapore, Singapore, Singapore
| | - G Son
- Yangsan Busan National Univ. Hospital, Yangsan-si, Gyeongsangnam-do, South Korea
| | - S Park
- Yangsan Busan National Univ. Hospital, Yangsan-si, Gyeongsangnam-do, South Korea
| | - S Pietrantoni
- General Surgery Department (Director: C. Pietrantoni), S.S. Filippo e Nicola Hospital, Avezzano, AQ, Italy
| | | | | | - H Takehara
- Heart-life Hospital, Nakagami-gun, Japan
| | - H Nakagawa
- Heart-life Hospital, Nakagami-gun, Japan
| | | | - H Aka
- Heart-life Hospital, Nakagami-gun, Japan
| | - Y Takushi
- Heart-life Hospital, Nakagami-gun, Japan
| | - T Miyahira
- Heart-life Hospital, Nakagami-gun, Japan
| | | | - N Okushima
- Heart-life Hospital, Nakagami-gun, Japan
| | - F Mayer
- Department of Surgery, Paracelsus Medical University, Salzburg, Austria
| | - M Lechner
- Department of Surgery, Paracelsus Medical University, Salzburg, Austria
| | - D Öfner
- Department of Surgery, Paracelsus Medical University, Salzburg, Austria
| | - R Bittner
- Winghofer Medicum Hernia Center, Rottenburg, Germany
| | - G Köhler
- Department Surgery, Sisters of Charity Hospital, Linz, Austria
| | - R Fortelny
- Department of General Surgery, Wilhelminenspital, Vienna, Austria
| | - F Köckerling
- Department of Surgery and Center of Minimally Invasive Surgery, Vivantes Hospital, Berlin, Germany
| | - R Lim
- Department of Surgery, University of N.S.W., Bankstown-Lidcombe Hospital, Bankstown, Australia
| | - C Berney
- Department of Surgery, University of N.S.W., Bankstown-Lidcombe Hospital, Bankstown, Australia
| | - J Kato
- University of Sao Paulo Medical School, Sao Paulo, Brazil
| | - L Iuamoto
- University of Sao Paulo Medical School, Sao Paulo, Brazil
| | - A Meyer
- Director of Abdominal Wall Repair Center, Samaritano Hospital, Sao Paulo, Brazil
| | - A Floridi
- U.O. Chirugia Genarele, A.O. Ospedale Maggiore di Crema, Crema, Italy
| | - E Bombelli
- U.O. Chirugia Genarele, A.O. Ospedale Maggiore di Crema, Crema, Italy
| | - D Giuliani
- U.O. Chirugia Genarele, A.O. Ospedale Maggiore di Crema, Crema, Italy
| | - I Galli
- U.O. Chirugia Genarele, A.O. Ospedale Maggiore di Crema, Crema, Italy
| | - M Monti
- U.O. Chirugia Genarele, A.O. Ospedale Maggiore di Crema, Crema, Italy
| | - A Longo
- U.O. Chirugia Genarele, A.O. Ospedale Maggiore di Crema, Crema, Italy
| | - G Pisano
- U.O. Chirugia Genarele, A.O. Ospedale Maggiore di Crema, Crema, Italy
| | - J Li
- The 2nd Affiliated Hospital of Jilin University, Changchun, China
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34
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Hori T, Haruta S, Sasaki D, Hanajima D, Ueno Y, Ogata A, Ishii M, Igarashi Y. Reorganization of the bacterial and archaeal populations associated with organic loading conditions in a thermophilic anaerobic digester. J Biosci Bioeng 2015; 119:337-44. [DOI: 10.1016/j.jbiosc.2014.09.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2014] [Revised: 07/28/2014] [Accepted: 09/02/2014] [Indexed: 10/24/2022]
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35
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Morohoshi S, Matsuura K, Haruta S. Secreted protease mediates interspecies interaction and promotes cell aggregation of the photosynthetic bacterium Chloroflexus aggregans. FEMS Microbiol Lett 2014; 362:1-5. [PMID: 25673656 DOI: 10.1093/femsle/fnu046] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Interspecies interactions were studied in hot spring microbial mats where diverse species of bacterial cells are densely packed. The anoxygenic photosynthetic bacterium, Chloroflexus aggregans, has been widely found in the microbial mats as a major component in terrestrial hot springs in Japan at the temperature from 50 to 70°C. C. aggregans shows cellular motility to form a microbial mat-like dense cell aggregate. The aggregating ability of C. aggregans was affected by another bacterial species, strain BL55a (related to Bacillus licheniformis) isolated from the microbial mats containing C. aggregans. Cell aggregation rate of C. aggregans was promoted by the addition of culture supernatants of strain BL55a. Similar effects were also detected from other bacterial isolates, specifically Geobacillus sp. and Aeribacillus sp. Protease activity was detected from the culture supernatants from all of these isolates. The promoting effect of strain BL55a was suppressed by a serine protease inhibitor, phenylmethylsulfonyl fluoride. A purified serine protease, subtilisin obtained from B. licheniformis, showed a promoting effect on the cell aggregation. These results suggest that an extracellular protease, secreted from co-existing bacterial species promoted the aggregating motility of C. aggregans. This is the first report that exogenous protease affects bacterial cellular motility.
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Affiliation(s)
- Sho Morohoshi
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
| | - Katsumi Matsuura
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
| | - Shin Haruta
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
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Hori T, Akuzawa M, Haruta S, Ueno Y, Ogata A, Ishii M, Igarashi Y. Involvement of a novel fermentative bacterium in acidification in a thermophilic anaerobic digester. FEMS Microbiol Lett 2014; 361:62-67. [PMID: 25273502 DOI: 10.1111/1574-6968.12611] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 09/26/2014] [Accepted: 09/26/2014] [Indexed: 11/28/2022] Open
Abstract
Acidification results from the excessive accumulation of volatile fatty acids and the breakthrough of buffering capacity in anaerobic digesters. However, little is known about the identity of the acidogenic bacteria involved. Here, we identified an active fermentative bacterium during acidification in a thermophilic anaerobic digester by sequencing and phylogenetic analysis of isotopically labeled rRNA. The digestion sludge retrieved from the beginning of pH drop in the laboratory-scale anaerobic digester was incubated anaerobically at 55 °C for 4 h during which 13C-labeled glucose was supplemented repeatedly. 13CH4 and 13CO2 were produced after substrate addition. RNA extracts from the incubated sludge was density-separated by ultracentrifugation, and then bacterial communities in the density fractions were screened by terminal restriction fragment length polymorphism and clone library analyses based on 16S rRNA transcripts. Remarkably, a novel lineage within the genus Thermoanaerobacterium became abundant with increasing the buoyant density and predominated in the heaviest fraction of RNA. The results in this study indicate that a thermoacidophilic bacterium exclusively fermented the simple carbohydrate glucose, thereby playing key roles in acidification in the thermophilic anaerobic digester.
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Affiliation(s)
- Tomoyuki Hori
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan .,Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Masateru Akuzawa
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Shin Haruta
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.,Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, Hachioji-shi, Tokyo, Japan
| | - Yoshiyuki Ueno
- Kajima Technical Research Institute, Chofu-shi, Tokyo, Japan
| | - Atsushi Ogata
- Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Masaharu Ishii
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Yasuo Igarashi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.,Research Center of Bioenergy and Bioremediation, Southwest University, BeiBei District, Chongqing, China
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Kanno N, Matsuura K, Haruta S. Differences in survivability under starvation conditions among four species of purple nonsulfur phototrophic bacteria. Microbes Environ 2014; 29:326-8. [PMID: 24941957 PMCID: PMC4159045 DOI: 10.1264/jsme2.me14013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Survivability under carbon-starvation conditions was investigated in four species of purple phototrophic bacteria: Rhodopseudomonas palustris, Rhodobacter sphaeroides, Rhodospirillum rubrum, and Rubrivivax gelatinosus. All these test organisms survived longer in the light than in the dark. ATP levels in the cultures were maintained in the light, which indicated that survivability was supported by photosynthesis. Survivability and tolerance against hypertonic stress in the dark was higher in Rhodopseudomonas palustris, which is widely distributed in natural environments including soils, than in the three other species.
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Affiliation(s)
- Nanako Kanno
- Graduate School of Science and Engineering, Tokyo Metropolitan University
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Affiliation(s)
- Shin Haruta
- Graduate School of Science and Engineering, Tokyo Metropolitan University
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Haruta S, Yoshida T, Aoi Y, Kaneko K, Futamata H. Challenges for complex microbial ecosystems: combination of experimental approaches with mathematical modeling. Microbes Environ 2013; 28:285-94. [PMID: 23995424 PMCID: PMC4070964 DOI: 10.1264/jsme2.me13034] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
In the past couple of decades, molecular ecological techniques have been developed to elucidate microbial diversity and distribution in microbial ecosystems. Currently, modern techniques, represented by meta-omics and single cell observations, are revealing the incredible complexity of microbial ecosystems and the large degree of phenotypic variation. These studies propound that microbiological techniques are insufficient to untangle the complex microbial network. This minireview introduces the application of advanced mathematical approaches in combination with microbiological experiments to microbial ecological studies. These combinational approaches have successfully elucidated novel microbial behaviors that had not been recognized previously. Furthermore, the theoretical perspective also provides an understanding of the plasticity, robustness and stability of complex microbial ecosystems in nature.
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Affiliation(s)
- Shin Haruta
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University
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Iino T, Tamaki H, Tamazawa S, Ueno Y, Ohkuma M, Suzuki KI, Igarashi Y, Haruta S. Candidatus Methanogranum caenicola: a novel methanogen from the anaerobic digested sludge, and proposal of Methanomassiliicoccaceae fam. nov. and Methanomassiliicoccales ord. nov., for a methanogenic lineage of the class Thermoplasmata. Microbes Environ 2013; 28:244-50. [PMID: 23524372 PMCID: PMC4070666 DOI: 10.1264/jsme2.me12189] [Citation(s) in RCA: 193] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The class Thermoplasmata harbors huge uncultured archaeal lineages at the order level, so-called Groups E2 and E3. A novel archaeon Kjm51a affiliated with Group E2 was enriched from anaerobic sludge in the present study. Clone library analysis of the archaeal 16S rRNA and mcrA genes confirmed a unique archaeal population in the enrichment culture. The 16S rRNA gene-based phylogeny revealed that the enriched archaeon Kjm51a formed a distinct cluster within Group E2 in the class Thermoplasmata together with Methanomassiliicoccus luminyensis B10T and environmental clone sequences derived from anaerobic digesters, bovine rumen, and landfill leachate. Archaeon Kjm51a showed 87.7% 16S rRNA gene sequence identity to the closest cultured species, M. luminyensis B10T, indicating that archaeon Kjm51a might be phylogenetically novel at least at the genus level. In fluorescence in situ hybridization analysis, archaeon Kjm51a was observed as coccoid cells completely corresponding to the archaeal cells detected, although bacterial rod cells still coexisted. The growth of archaeon Kjm51a was dependent on the presence of methanol and yeast extract, and hydrogen and methane were produced in the enrichment culture. The addition of 2-bromo ethanesulfonate to the enrichment culture completely inhibited methane production and increased hydrogen concentration, which suggested that archaeon Kjm51a is a methanol-reducing hydrogenotrophic methanogen. Taken together, we propose the provisional taxonomic assignment, named Candidatus Methanogranum caenicola, for the enriched archaeon Kjm51a belonging to Group E2. We also propose to place the methanogenic lineage of the class Thermoplasmata in a novel order, Methanomassiliicoccales ord. nov.
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Affiliation(s)
- Takao Iino
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3–1–1 Koyadai, Tsukuba, Ibaraki 305–0074, Japan.
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Everroad RC, Otaki H, Matsuura K, Haruta S. Diversification of bacterial community composition along a temperature gradient at a thermal spring. Microbes Environ 2012; 27:374-81. [PMID: 22673306 PMCID: PMC4103544 DOI: 10.1264/jsme2.me11350] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
To better understand the biogeography and relationship between temperature and community structure within microbial mats, the bacterial diversity of mats at a slightly alkaline, sulfide-containing hot spring was explored. Microbial mats that developed at temperatures between 75-52°C were collected from an area of approximately 1 m(2) in Nakabusa, Nagano, Japan. Bacterial 16S rRNA genes from these samples were examined by terminal restriction fragment length polymorphism (T-RFLP) and clone library analysis. T-RFLP profiles revealed 66 unique fragments (T-RFs). Based on total T-RFs observed in environmental profiles and clone libraries, a temperature effect on diversity was determined, with complexity in the community increasing as temperature decreased. The T-RF pattern indicated four distinct community assemblages related to temperature. Members of the Aquificales and particularly the sulfur-oxidizing bacterium Sulfurihydrogenibium were present at all temperatures and were the dominant component of mats taken at 75-67°C. Sulfide oxidation, which persisted throughout the temperature gradient, was the presumed dominant pathway of primary production above 67°C. As temperature decreased, successive additions of anoxygenic and oxygenic phototrophs increased primary productivity, allowing for diversification of the community.
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Affiliation(s)
- R Craig Everroad
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1–1 Minami-Osawa, Hachioji-shi, Tokyo 192–0397, Japan
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Kawaguchi R, Tanase Y, Haruta S, Nagai A, Yoshida S, Furukawa N, Ooi H, Kobayashi K. Paclitaxel plus Carboplatin Chemotherapy for Primary Peritoneal Carcinoma: A Study of 22 Cases and Comparison with Stage III-IV Ovarian Serous Carcinoma. Case Rep Oncol 2012; 5:173-80. [PMID: 22666209 PMCID: PMC3364097 DOI: 10.1159/000338402] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The aim of this study was to assess the clinical characteristics and outcome of patients with either primary peritoneal carcinoma (PPC) or ovarian serous carcinoma (OSC) treated with paclitaxel plus carboplatin chemotherapy. We retrospectively identified 22 PPC patients and 55 stage III–IV OSC patients treated between 2002 and 2007. After exploratory laparotomy, all patients received paclitaxel and carboplatin every 3 weeks, with the goal of optimal cytoreduction. There were no statistically significant differences between the PPC and OSC groups with regard to tumor stage, residual tumor after debulking surgery (initial or interval), serum cancer antigen (CA) 125 levels at diagnosis, and completion of first-line chemotherapy. The progression-free survival (PFS) durations were 12.7 months (95% CI, 6.3–18.5) in the patients with PPC and 15.9 months (95% CI, 13.3–18.5) in those with OSC (p = 0.016). However, the median survival durations were 26.5 months (95% CI, 14.6–38.3) in the patients with PPC and 38 months (95% CI, 23.8–53.8) in those with OSC (p = 0.188). Survival was longer for all patients whose CA125 levels normalized to 26 U/ml during and after treatment. Overall survival (OS) of the patients with PPC was similar to that of the patients with OSC, suggesting that management for advanced-stage OSC would be similar to that for PPC. The combination of optimal debulking with paclitaxel plus carboplatin chemotherapy may offer patients the most effective treatment. The CA125 nadir after cytoreductive surgery can be considered a prognostic factor for OS and PFS in patients with PPC.
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Affiliation(s)
- R Kawaguchi
- Department of Obstetrics and Gynecology, Nara Medical University, Kashihara, Japan
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Okubo T, Tsukui T, Maita H, Okamoto S, Oshima K, Fujisawa T, Saito A, Futamata H, Hattori R, Shimomura Y, Haruta S, Morimoto S, Wang Y, Sakai Y, Hattori M, Aizawa SI, Nagashima KVP, Masuda S, Hattori T, Yamashita A, Bao Z, Hayatsu M, Kajiya-Kanegae H, Yoshinaga I, Sakamoto K, Toyota K, Nakao M, Kohara M, Anda M, Niwa R, Jung-Hwan P, Sameshima-Saito R, Tokuda SI, Yamamoto S, Yamamoto S, Yokoyama T, Akutsu T, Nakamura Y, Nakahira-Yanaka Y, Hoshino YT, Hirakawa H, Mitsui H, Terasawa K, Itakura M, Sato S, Ikeda-Ohtsubo W, Sakakura N, Kaminuma E, Minamisawa K. Complete genome sequence of Bradyrhizobium sp. S23321: insights into symbiosis evolution in soil oligotrophs. Microbes Environ 2012; 27:306-15. [PMID: 22452844 PMCID: PMC4036050 DOI: 10.1264/jsme2.me11321] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Accepted: 02/28/2012] [Indexed: 11/12/2022] Open
Abstract
Bradyrhizobium sp. S23321 is an oligotrophic bacterium isolated from paddy field soil. Although S23321 is phylogenetically close to Bradyrhizobium japonicum USDA110, a legume symbiont, it is unable to induce root nodules in siratro, a legume often used for testing Nod factor-dependent nodulation. The genome of S23321 is a single circular chromosome, 7,231,841 bp in length, with an average GC content of 64.3%. The genome contains 6,898 potential protein-encoding genes, one set of rRNA genes, and 45 tRNA genes. Comparison of the genome structure between S23321 and USDA110 showed strong colinearity; however, the symbiosis islands present in USDA110 were absent in S23321, whose genome lacked a chaperonin gene cluster (groELS3) for symbiosis regulation found in USDA110. A comparison of sequences around the tRNA-Val gene strongly suggested that S23321 contains an ancestral-type genome that precedes the acquisition of a symbiosis island by horizontal gene transfer. Although S23321 contains a nif (nitrogen fixation) gene cluster, the organization, homology, and phylogeny of the genes in this cluster were more similar to those of photosynthetic bradyrhizobia ORS278 and BTAi1 than to those on the symbiosis island of USDA110. In addition, we found genes encoding a complete photosynthetic system, many ABC transporters for amino acids and oligopeptides, two types (polar and lateral) of flagella, multiple respiratory chains, and a system for lignin monomer catabolism in the S23321 genome. These features suggest that S23321 is able to adapt to a wide range of environments, probably including low-nutrient conditions, with multiple survival strategies in soil and rhizosphere.
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Affiliation(s)
- Takashi Okubo
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Takahiro Tsukui
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Hiroko Maita
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
- Laboratory for Plant Genome Informatics, Kazusa DNA Research Institute, 2–6–7 Kazusakamatari, Kisarazu, Chiba 292–0818, Japan
| | - Shinobu Okamoto
- Database Center for Life Science (DBCLS), Research Organization of Information and Systems (ROIS), 2–11–16 Yayoi, Bunkyo-ku, Tokyo 113–0032, Japan
| | - Kenshiro Oshima
- Graduate School of Frontier Sciences, University of Tokyo, 5–1–5, Kashiwa-no-ha, Kashiwa, Chiba 277–8561, Japan
| | - Takatomo Fujisawa
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization for Information and Systems, Yata, Mishima, Shizuoka 411–85, Japan
| | - Akihiro Saito
- Department of Material and Life Science, Faculty of Science and Technology, Shizuoka Institute of Science and Technology 2200–2 Toyosawa, Fukuroi, Shizuoka 437–8555, Japan
| | - Hiroyuki Futamata
- Department of Material Science and Chemical Engineering, Shizuoka University, 3–5–1 Jyohoku, Naka-ku, Hamamatsu, Shizuoka, 432–8561, Japan
| | - Reiko Hattori
- Attic Lab, 1–6–2–401 Komegafukuro, Aobaku, Sendai, Miyagi 980–0813, Japan
| | - Yumi Shimomura
- National Institute for Agro-Environmental Sciences, 3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604, Japan
| | - Shin Haruta
- Graduate School of Science and Engineering, Tokyo Metropolitan University, 1–1 Minami-Osawa, Hachioji-shi, Tokyo 192–0397, Japan
| | - Sho Morimoto
- National Institute for Agro-Environmental Sciences, 3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604, Japan
| | - Yong Wang
- National Institute for Agro-Environmental Sciences, 3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604, Japan
| | - Yoriko Sakai
- National Institute for Agro-Environmental Sciences, 3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604, Japan
| | - Masahira Hattori
- Graduate School of Frontier Sciences, University of Tokyo, 5–1–5, Kashiwa-no-ha, Kashiwa, Chiba 277–8561, Japan
| | - Shin-ichi Aizawa
- Department of Life Sciences, Prefectural University of Hiroshima, 562 Nanatsuka, Shobara, Hiroshima 727–0023, Japan
| | - Kenji V. P. Nagashima
- Graduate School of Science and Engineering, Tokyo Metropolitan University, 1–1 Minami-Osawa, Hachioji-shi, Tokyo 192–0397, Japan
| | - Sachiko Masuda
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Tsutomu Hattori
- Attic Lab, 1–6–2–401 Komegafukuro, Aobaku, Sendai, Miyagi 980–0813, Japan
| | - Akifumi Yamashita
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Zhihua Bao
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Masahito Hayatsu
- National Institute for Agro-Environmental Sciences, 3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604, Japan
| | - Hiromi Kajiya-Kanegae
- Database Center for Life Science (DBCLS), Research Organization of Information and Systems (ROIS), 2–11–16 Yayoi, Bunkyo-ku, Tokyo 113–0032, Japan
| | - Ikuo Yoshinaga
- Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606–8502, Japan
| | - Kazunori Sakamoto
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba 271–8510, Japan
| | - Koki Toyota
- Tokyo University of Agriculture and Technology, 2–24–16, Naka, Koganei, Tokyo 184–8588, Japan
| | - Mitsuteru Nakao
- Database Center for Life Science (DBCLS), Research Organization of Information and Systems (ROIS), 2–11–16 Yayoi, Bunkyo-ku, Tokyo 113–0032, Japan
| | - Mitsuyo Kohara
- Laboratory for Plant Genome Informatics, Kazusa DNA Research Institute, 2–6–7 Kazusakamatari, Kisarazu, Chiba 292–0818, Japan
| | - Mizue Anda
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Rieko Niwa
- National Institute for Agro-Environmental Sciences, 3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604, Japan
| | - Park Jung-Hwan
- Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606–8502, Japan
| | - Reiko Sameshima-Saito
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422–8529, Japan
| | - Shin-ichi Tokuda
- National Institute of Vegetable and Tea Sciences, National Agriculture and Food Research Organization, 3–1–1 Kannondai, Tsukuba, Ibaraki 305–8666, Japan
| | - Sumiko Yamamoto
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization for Information and Systems, Yata, Mishima, Shizuoka 411–85, Japan
| | - Syuji Yamamoto
- Department of Material Science and Chemical Engineering, Shizuoka University, 3–5–1 Jyohoku, Naka-ku, Hamamatsu, Shizuoka, 432–8561, Japan
| | - Tadashi Yokoyama
- Institute of Agriculture, Tokyo university of Agriculture and Technology, 3–5–8 Saiwaicho, Fuchu, Tokyo 183–8509, Japan
| | - Tomoko Akutsu
- Laboratory for Plant Genome Informatics, Kazusa DNA Research Institute, 2–6–7 Kazusakamatari, Kisarazu, Chiba 292–0818, Japan
| | - Yasukazu Nakamura
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization for Information and Systems, Yata, Mishima, Shizuoka 411–85, Japan
| | - Yuka Nakahira-Yanaka
- Graduate School of Life and Environment Sciences, University of Tsukuba, 1–1–1 Ten-noudai, Tsukuba, Ibaraki 305–8572, Japan
| | - Yuko Takada Hoshino
- National Institute for Agro-Environmental Sciences, 3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604, Japan
| | - Hideki Hirakawa
- Laboratory for Plant Genome Informatics, Kazusa DNA Research Institute, 2–6–7 Kazusakamatari, Kisarazu, Chiba 292–0818, Japan
| | - Hisayuki Mitsui
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Kimihiro Terasawa
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Manabu Itakura
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Shusei Sato
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
- Laboratory for Plant Genome Informatics, Kazusa DNA Research Institute, 2–6–7 Kazusakamatari, Kisarazu, Chiba 292–0818, Japan
| | - Wakako Ikeda-Ohtsubo
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Natsuko Sakakura
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization for Information and Systems, Yata, Mishima, Shizuoka 411–85, Japan
| | - Eli Kaminuma
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization for Information and Systems, Yata, Mishima, Shizuoka 411–85, Japan
| | - Kiwamu Minamisawa
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
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Otaki H, Everroad RC, Matsuura K, Haruta S. Production and consumption of hydrogen in hot spring microbial mats dominated by a filamentous anoxygenic photosynthetic bacterium. Microbes Environ 2012; 27:293-9. [PMID: 22446313 PMCID: PMC4036054 DOI: 10.1264/jsme2.me11348] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2011] [Accepted: 02/14/2012] [Indexed: 11/12/2022] Open
Abstract
Microbial mats containing the filamentous anoxygenic photosynthetic bacterium Chloroflexus aggregans develop at Nakabusa hot spring in Japan. Under anaerobic conditions in these mats, interspecies interaction between sulfate-reducing bacteria as sulfide producers and C. aggregans as a sulfide consumer has been proposed to constitute a sulfur cycle; however, the electron donor utilized for microbial sulfide production at Nakabusa remains to be identified. In order to determine this electron donor and its source, ex situ experimental incubation of mats was explored. In the presence of molybdate, which inhibits biological sulfate reduction, hydrogen gas was released from mat samples, indicating that this hydrogen is normally consumed as an electron donor by sulfate-reducing bacteria. Hydrogen production decreased under illumination, indicating that C. aggregans also functions as a hydrogen consumer. Small amounts of hydrogen may have also been consumed for sulfur reduction. Clone library analysis of 16S rRNA genes amplified from the mats indicated the existence of several species of hydrogen-producing fermentative bacteria. Among them, the most dominant fermenter, Fervidobacterium sp., was successfully isolated. This isolate produced hydrogen through the fermentation of organic carbon. Dispersion of microbial cells in the mats resulted in hydrogen production without the addition of molybdate, suggesting that simultaneous production and consumption of hydrogen in the mats requires dense packing of cells. We propose a cyclic electron flow within the microbial mats, i.e., electron flow occurs through three elements: S (elemental sulfur, sulfide, sulfate), C (carbon dioxide, organic carbon) and H (di-hydrogen, protons).
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Affiliation(s)
- Hiroyo Otaki
- Department of Biological Sciences, Tokyo Metropolitan University, Minami-Osawa 1–1, Hachioji-shi, Tokyo 192–0397, Japan
| | - R. Craig Everroad
- Department of Biological Sciences, Tokyo Metropolitan University, Minami-Osawa 1–1, Hachioji-shi, Tokyo 192–0397, Japan
| | - Katsumi Matsuura
- Department of Biological Sciences, Tokyo Metropolitan University, Minami-Osawa 1–1, Hachioji-shi, Tokyo 192–0397, Japan
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University, Minami-Osawa 1–1, Hachioji-shi, Tokyo 192–0397, Japan
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Hirose S, Nagashima KVP, Matsuura K, Haruta S. Diversity of purple phototrophic bacteria, inferred from pufM gene, within epilithic biofilm in Tama River, Japan. Microbes Environ 2012; 27:327-9. [PMID: 22446305 PMCID: PMC4036046 DOI: 10.1264/jsme2.me11306] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The diversity of purple phototrophic bacteria in algae-dominated biofilm of a streambed in Tama River, Japan was investigated. Clone library analysis of the pufM gene encoding a subunit of the photochemical reaction center of purple bacteria detected 18 operational taxonomic units (OTUs) in several classes of Proteobacteria. Most of the OTUs showed less than 85% identity to the PufM amino acid sequences of known phototrophic bacteria. These results suggest that phylogenetically divergent and unknown purple phototrophic bacteria are present in the epilithic biofilm of the river.
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Affiliation(s)
- Setsuko Hirose
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo 192-0397, Japan
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Hori T, Sasaki D, Haruta S, Shigematsu T, Ueno Y, Ishii M, Igarashi Y. Detection of active, potentially acetate-oxidizing syntrophs in an anaerobic digester by flux measurement and formyltetrahydrofolate synthetase (FTHFS) expression profiling. Microbiology (Reading) 2011; 157:1980-1989. [PMID: 21474532 DOI: 10.1099/mic.0.049189-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Syntrophic oxidation of acetate, so-called reversed reductive acetogenesis, is one of the most important degradation steps in anaerobic digesters. However, little is known about the genetic diversity of the micro-organisms involved. Here we investigated the activity and composition of potentially acetate-oxidizing syntrophs using a combinatorial approach of flux measurement and transcriptional profiling of the formyltetrahydrofolate synthetase (FTHFS) gene, an ecological biomarker for reductive acetogenesis. During the operation of a thermophilic anaerobic digester, volatile fatty acids were mostly depleted, suggesting a high turnover rate for dissolved H(2), and hydrogenotrophic methanogens were the dominant archaeal members. Batch cultivation of the digester microbiota with (13)C-labelled acetate indicated that syntrophic oxidation accounted for 13.1-21.3 % of methane production from acetate. FTHFS genes were transcribed in the absence of carbon monoxide, methoxylated compounds and inorganic electron acceptors other than CO(2), which is implicated in the activity of reversed reductive acetogenesis; however, expression itself does not distinguish whether biosynthesis or biodegradation is functioning. The mRNA- and DNA-based terminal RFLP and clone library analyses indicated that, out of nine FTHFS phylotypes detected, the FTHFS genes from the novel phylotypes I-IV in addition to the known syntroph Thermacetogenium phaeum (i.e. phylotype V) were specifically expressed. These transcripts arose from phylogenetically presumed homoacetogens. The results of this study demonstrate that hitherto unidentified phylotypes of homoacetogens are responsible for syntrophic acetate oxidation in an anaerobic digester.
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Affiliation(s)
- Tomoyuki Hori
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukisamu-Higashi 2-17-2-1, Toyohira-ku, Sapporo 062-8517, Japan.,Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Daisuke Sasaki
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Shin Haruta
- Graduate School of Science and Engineering, Tokyo Metropolitan University, Minami-Osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan.,Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Toru Shigematsu
- Department of Food Science, Faculty of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata 956-8603, Japan
| | - Yoshiyuki Ueno
- Kajima Technical Research Institute, Tobitakyu 2-19-1, Chofu-shi, Tokyo 182-0036, Japan
| | - Masaharu Ishii
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yasuo Igarashi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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Akuzawa M, Hori T, Haruta S, Ueno Y, Ishii M, Igarashi Y. Distinctive responses of metabolically active microbiota to acidification in a thermophilic anaerobic digester. Microb Ecol 2011; 61:595-605. [PMID: 21240482 DOI: 10.1007/s00248-010-9788-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2010] [Accepted: 11/29/2010] [Indexed: 05/30/2023]
Abstract
Acidification is one of the most common and serious problems inducing process failure in anaerobic digesters. The production of volatile fatty acids (VFAs) mainly triggers acidic shock. However, little is known about the bacteria involved in the processes of acidogenic metabolism, such as fermentation and reductive acetogenesis. Here, the metabolic responses of a methanogenic community to the acidification and resulting process deterioration were investigated using transcriptional profiling of both the 16S rRNA and formyltetrahydrofolate synthetase (FTHFS) genes. The 16S rRNA-based analyses demonstrated that the dynamic shift of bacterial populations was closely correlated with reactor performance, especially with VFA accumulation levels. The pH drop accompanied by an increase in VFAs stimulated the metabolic activation of an uncultured Chloroflexi subphylum I bacterium. The subphylum has been characterized as a fermentative carbohydrate degrader using culture- and molecular-based ecophysiological assays. At the beginning of VFA accumulation, FTHFS genes were expressed; the transcripts were derived from phylogenetically predicted homoacetogens, suggesting that reductive acetogenesis was operated by hitherto unidentified bacteria. When acetate concentrations were high, the FTHFS expression ceased and Thermoanaerobacterium aciditolerans proliferated selectively. This thermoacidophilic bacterium would play a decisive role in acetate production via fermentative metabolism. The results of this study reveal for the first time that an uncultured Chloroflexi, T. aciditolerans, and novel homoacetogens were metabolically associated with acidic shock and subsequent VFA accumulation in an anaerobic digester.
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Affiliation(s)
- Masateru Akuzawa
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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Sasaki D, Hori T, Haruta S, Ueno Y, Ishii M, Igarashi Y. Methanogenic pathway and community structure in a thermophilic anaerobic digestion process of organic solid waste. J Biosci Bioeng 2011; 111:41-6. [DOI: 10.1016/j.jbiosc.2010.08.011] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Revised: 08/05/2010] [Accepted: 08/20/2010] [Indexed: 10/19/2022]
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Yamamoto K, Haruta S, Kato S, Ishii M, Igarashi Y. Determinative Factors of Competitive Advantage between Aerobic Bacteria for Niches at the Air-Liquid Interface. Microbes Environ 2010; 25:317-20. [DOI: 10.1264/jsme2.me10147] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Kyosuke Yamamoto
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Shin Haruta
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University
| | - Souichiro Kato
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Masaharu Ishii
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Yasuo Igarashi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo
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Abstract
In nature, microorganisms live by interacting with each other. Microbiological studies that only consider pure cultures are not sufficient to adequately describe the natural behaviour of microbes. Several microbial interactions have been recognized to affect the growth or metabolism of others; e.g. syntrophic cometabolism, competition, production of inhibitors or activators, and predation. It is believed that third-party organisms easily affect the two-species relationships and these relationships form the basis of interspecies networks within microbial communities. A microbial network contributes to 'functional redundancy' or 'structural diversity' and the microbial communities effectively act as a multicellular organism. It is necessary to understand not only the physiological activity of members within microbial communities but also their roles to regulate the activity or population of others. To access the microbial network, we require (i) comprehensive determination of all possible interspecies relationships among microbes, (ii) knock-out experiments by which certain members can be removed or suppressed, and (iii) supplemental addition of microbes or activation of certain members. Microbial network studies have started using defined microbial communities, i.e. a mixed culture that is composed of three or four species. In order to expand these studies to microflora in nature, microbial ecology requires the help of mathematical biology.
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Affiliation(s)
- Shin Haruta
- Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan.
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