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Narihara S, Chida S, Matsunaga N, Akimoto R, Akimoto M, Hagio A, Mori T, Nittami T, Sato M, Mun S, Kang H, Back JH, Takeda M. Taxonomic characterization of Sphaerotilus microaerophilus sp. nov., a sheath-forming microaerophilic bacterium of activated sludge origin. Arch Microbiol 2024; 206:252. [PMID: 38727820 PMCID: PMC11087309 DOI: 10.1007/s00203-024-03991-9] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 04/30/2024] [Accepted: 05/01/2024] [Indexed: 05/13/2024]
Abstract
A microaerophilic Gram-stain-negative bacilliform bacterial strain, FB-5 T, was isolated from activated sludge in Yokohama, Japan, that exhibited filamentous growth and formed a microtube (sheath). Cells were motile using a single polar flagellum. The optimum growth temperature and pH were 30 °C and 7.5, respectively. Strain FB-5 T was catalase-negative. Peptides and amino acids were utilized as energy and carbon sources. Sugars and organic acids were not utilized. Vitamin B12 enhanced the growth of strain FB-5 T. Sulfur-dependent lithotrophic growth was possible. Major respiratory quinone was UQ-8. Major fatty acids were C16:1ω7 and C16:0. The genomic DNA G + C content was 69.16%. Phylogenetic analysis of the 16S rRNA gene suggested that strain FB-5 T belongs to the genus Sphaerotilus. The close relatives were S. natans subsup. sulfidivorans and S. natans subsup. natans with 98.0% and 97.8% similarity based on the 16S rRNA gene analysis, respectively. The genome size (6.06 Mbp) was larger than that (4.39-5.07 Mbp) of the Sphaerotilus strains. The AAI values against the related strains ranged from 71.0 to 72.5%. The range of ANI values was 81.7 - 82.5%. In addition to these distinguishable features of the genome, the core genome and dDDH analyses suggested that this strain is a novel member of the genus Sphaerotilus. Based on its physiological properties and genomic features, strain FB-5 T is considered as a novel species of the genus Sphaerotilus, for which the name S. microaerophilus sp. nov. is proposed. The type strain is FB-5 T (= JCM 35424 T = KACC 23146 T).
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Affiliation(s)
- Shiori Narihara
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5, Hodogaya, Yokohama, 240-8501, Japan
| | - Shun Chida
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5, Hodogaya, Yokohama, 240-8501, Japan
| | - Naoki Matsunaga
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5, Hodogaya, Yokohama, 240-8501, Japan
| | - Ryosuke Akimoto
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5, Hodogaya, Yokohama, 240-8501, Japan
| | - Mizuki Akimoto
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5, Hodogaya, Yokohama, 240-8501, Japan
| | - Aoi Hagio
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5, Hodogaya, Yokohama, 240-8501, Japan
| | - Tomomi Mori
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5, Hodogaya, Yokohama, 240-8501, Japan
| | - Tadashi Nittami
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5, Hodogaya, Yokohama, 240-8501, Japan
| | - Michio Sato
- School of Agriculture, Meiji University, 1-1-1 Higashimita, Tama, Kawasaki, 214-8571, Japan
| | - Sehui Mun
- Department of Food Science and Nutrition, Gwangju University, 277, Hyodeok-Ro, Nam-Gu, Gwangju, 61743, Korea
| | - Hyeonjin Kang
- Department of Food Science and Nutrition, Gwangju University, 277, Hyodeok-Ro, Nam-Gu, Gwangju, 61743, Korea
| | - Ji Hwan Back
- Department of Food Science and Nutrition, Gwangju University, 277, Hyodeok-Ro, Nam-Gu, Gwangju, 61743, Korea
| | - Minoru Takeda
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5, Hodogaya, Yokohama, 240-8501, Japan.
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Kunoh T, Yamamoto T, Ono E, Sugimoto S, Takabe K, Takeda M, Utada AS, Nomura N. Identification of lthB, a Gene Encoding a Putative Glycosyltransferase Family 8 Protein Required for Leptothrix Sheath Formation. Appl Environ Microbiol 2023; 89:e0191922. [PMID: 36951572 PMCID: PMC10132092 DOI: 10.1128/aem.01919-22] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 02/20/2023] [Indexed: 03/24/2023] Open
Abstract
The bacterium Leptothrix cholodnii generates cell chains encased in sheaths that are composed of woven nanofibrils. The nanofibrils are mainly composed of glycoconjugate repeats, and several glycosyltransferases (GTs) are required for its biosynthesis. However, only one GT (LthA) has been identified to date. In this study, we screened spontaneous variants of L. cholodnii SP6 to find those that form smooth colonies, which is one of the characteristics of sheathless variants. Genomic DNA sequencing of an isolated variant revealed an insertion in the locus Lcho_0972, which encodes a putative GT family 8 protein. We thus designated this protein LthB and characterized it using deletion mutants and antibodies. LthB localized adjacent to the cell envelope. ΔlthB cell chains were nanofibril free and thus sheathless, indicating that LthB is involved in nanofibril biosynthesis. Unlike the ΔlthA mutant and the wild-type strain, which often generate planktonic cells, most ΔlthB organisms presented as long cell chains under static conditions, resulting in deficient pellicle formation, which requires motile planktonic cells. These results imply that sheaths are not required for elongation of cell chains. Finally, calcium depletion, which induces cell chain breakage due to sheath loss, abrogated the expression of LthA, but not LthB, suggesting that these GTs cooperatively participate in glycoconjugate biosynthesis under different signaling controls. IMPORTANCE In recent years, the regulation of cell chain elongation of filamentous bacteria via extracellular signals has attracted attention as a potential strategy to prevent clogging of water distribution systems and filamentous bulking of activated sludge in industrial settings. However, a fundamental understanding of the ecology of filamentous bacteria remains elusive. Since sheath formation is associated with cell chain elongation in most of these bacteria, the molecular mechanisms underlying nanofibril sheath formation, including the intracellular signaling cascade in response to extracellular stimuli, must be elucidated. Here, we isolated a sheathless variant of L. cholodnii SP6 and thus identified a novel glycosyltransferase, LthB. Although mutants with deletions of lthA, encoding another GT, and lthB were both defective for nanofibril formation, they exhibited different phenotypes of cell chain elongation and pellicle formation. Moreover, LthA expression, but not LthB expression, was influenced by extracellular calcium, which is known to affect nanofibril formation, indicating the functional diversities of LthA and LthB. Such molecular insights are critical for a better understanding of ecology of filamentous bacteria, which, in turn, can be used to improve strategies to control filamentous bacteria in industrial facilities.
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Affiliation(s)
- Tatsuki Kunoh
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Tatsuya Yamamoto
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Erika Ono
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Shinya Sugimoto
- Department of Bacteriology, The Jikei University School of Medicine, Tokyo, Japan
- Jikei Center for Biofilm Science and Technology, The Jikei University School of Medicine, Tokyo, Japan
| | - Kyosuke Takabe
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Minoru Takeda
- Division of Materials Science and Chemical Engineering, Faculty of Engineering, Yokohama National University, Yokohama, Kanagawa, Japan
| | - Andrew S. Utada
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
- Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Nobuhiko Nomura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
- Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Ibaraki, Japan
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Kunoh T, Yamamoto T, Prasad M, Ono E, Li X, Sugimoto S, Iida E, Obana N, Takeda M, Nomura N, Utada AS. Porous Pellicle Formation of a Filamentous Bacterium, Leptothrix. Appl Environ Microbiol 2022; 88:e0134122. [PMID: 36416549 DOI: 10.1128/aem.01341-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The bacterium Leptothrix cholodnii generates filaments encased in a sheath comprised of woven nanofibrils. In static liquid culture, L. cholodnii moves toward the air-liquid interface, where it forms porous pellicles. Observations of aggregation at the interface reveal that clusters consisting of only a few bacteria primarily grow by netting free cells. These growing clusters hierarchically enlarge through the random docking of other small clusters. We find that the bacteria swim using their polar flagellum toward the interface, where their sheath assists them in intertwining with others and thereby promotes the formation of small clusters. In contrast, sheathless hydrophobic mutant cells get stuck to the interface. We find that the nanofibril sheath is vital for robust pellicle formation as it lowers cell surface hydrophobicity by 60%, thereby reducing their adsorption and enabling cells to move toward and stick together at the air-liquid interface. IMPORTANCE Efficient and sustainable management of water resources is becoming a fundamental issue for supporting growing populations and for developing economic activity. Fundamental to this management is the treatment of wastewater. Microorganisms are the active component of activated sludge that is employed in the biodegradation process of many wastewater treatment facilities. However, uncontrolled growth of filamentous bacteria such as Sphaerotilus often results in filamentous bulking, lowering the efficiency of water treatment systems. To prevent this undesirable condition, strategies based on a fundamental understanding of the ecology of filamentous bacteria are required. Although the filamentous bacterium Leptothrix cholodnii, which is closely related to Sphaerotilus, is a minor inhabitant of activated sludge, its complete genome sequence is known, making gene manipulation relatively easy. Moreover, L. cholodnii generates porous pellicles under static conditions, which may be a characteristic of filamentous bulking. We show that both swimming motility and nanofibril-mediated air-liquid interface attachment are required for porous pellicle formation. These insights are critical for a better understanding of the characteristics of filamentous bulking and might improve strategies to control activated sludge.
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Ingino P, Tiew KH, Obst M. Suitability of lectin binding studies for the characterization of redox-active microbial environmental biofilms. AMB Express 2022; 12:140. [DOI: 10.1186/s13568-022-01479-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 10/23/2022] [Indexed: 11/08/2022] Open
Abstract
AbstractAquatic environmental microbial biofilms grow in a broad range of redox environments from oxic to methanogenic, and they often also establish internal redox gradients. In technical applications, biofilms are also subjected to controlled redox conditions. Studies on biofilms often make use of fluorescence microscopic imaging techniques together with lectin binding analysis to gain insights into structure, composition, and functions of the biofilms. Here we studied the direct influence of redox potentials on fluorescence lectin binding analyses (FLBA) for two commonly used lectin-fluorophore conjugates. An effect of the electrical potential on signal intensity was observed and found to be statistically significant. The signal intensity changes however, remained within the range of a few percent total. A significant drop in intensity was only observed for extremely oxidizing potentials, typically not found under environmental conditions. Our results showed that the fluorophore itself and not the lectin binding to the respective glycoconjugate causes fluorescence changes. The two tested lectin-fluorophores are shown to be suitable for studying the distribution and composition of EPS in environmental biofilms or technical applications and under varying redox conditions.
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Kunoh T, Yamamoto T, Sugimoto S, Ono E, Nomura N, Utada AS. Leptothrix cholodnii Response to Nutrient Limitation. Front Microbiol 2021; 12:691563. [PMID: 34248917 PMCID: PMC8264430 DOI: 10.3389/fmicb.2021.691563] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 05/27/2021] [Indexed: 11/13/2022] Open
Abstract
Microorganisms are widely utilized for the treatment of wastewater in activated sludge systems. However, the uncontrolled growth of filamentous bacteria leads to bulking and adversely affects wastewater treatment efficiency. To clarify the nutrient requirements for filament formation, we track the growth of a filamentous bacterium, Leptothrix cholodnii SP-6 in different nutrient-limited conditions using a high aspect-ratio microfluidic chamber to follow cell-chain elongation and sheath formation. We find that limitations in Na+, K+, and Fe2+ yield no observable changes in the elongation of cell chains and sheath formation, whereas limitations of C, N, P, or vitamins lead to more pronounced changes in filament morphology; here we observe the appearance of partially empty filaments with wide intercellular gaps. We observe more dramatic differences when SP-6 cells are transferred to media lacking Mg2+ and Ca2+. Loss of Mg2+ results in cell autolysis, while removal of Ca2+ results in the catastrophic disintegration of the filaments. By simultaneously limiting both carbon and Ca2+ sources, we are able to stimulate planktonic cell generation. These findings paint a detailed picture of the ecophysiology of Leptothrix, which may lead to improved control over the unchecked growth of deleterious filamentous bacteria in water purification systems.
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Affiliation(s)
- Tatsuki Kunoh
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Tatsuya Yamamoto
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Shinya Sugimoto
- Department of Bacteriology, Jikei Center for Biofilm Research and Technology, The Jikei University School of Medicine, Minato-ku, Japan
| | - Erika Ono
- School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Nobuhiko Nomura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan.,Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Japan
| | - Andrew S Utada
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan.,Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Japan
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Tamura K, Kunoh T, Nakanishi M, Kusano Y, Takada J. Preparation and Characterization of Additional Metallic Element-Containing Tubular Iron Oxides of Bacterial Origin. ACS Omega 2020; 5:27287-27294. [PMID: 33134691 PMCID: PMC7594126 DOI: 10.1021/acsomega.0c03574] [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] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/02/2020] [Indexed: 06/11/2023]
Abstract
Biogenic microtubular iron oxides (BIOXs) derived from Leptothrix spp. are known as promising multifunctional materials for industrial applications such as ceramic pigments and catalyst carriers. Here, we report unprecedented BIOX products with additive depositions of various metallic elements prepared by a newly devised "two-step" method using an artificial culture system of Leptothrix cholodnii strain OUMS1; the method comprises a biotic formation of immature organic sheaths and subsequent abiotic deposition of Fe and intended elements on the sheaths. Chemical composition ratios of the additional elements Al, Zr, and Ti in the respective BIOXs were arbitrarily controllable depending on initial concentrations of metallic salts added to reaction solutions. Raman spectroscopy exemplified an existence of Fe-O-Al linkage in the Al-containing BIOX matrices. Time-course analyses revealed the underlying physiological mechanism for the BIOX formation. These results indicate that our advanced method can contribute greatly to creations of innovative bioderived materials with improved functionalities.
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Affiliation(s)
- Katsunori Tamura
- Graduate
School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
- Bengala
Techno-Lab, 1-19-5-1006
Miyamae, Kawasaki-shi, Kanagawa 216-0007, Japan
| | - Tatsuki Kunoh
- Graduate
School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Makoto Nakanishi
- Graduate
School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Yoshihiro Kusano
- Department
of Applied Chemistry and Biotechnology, Okayama University of Science, 1-1 Ridai-cho, Kita-ku, Okayama 700-0005, Japan
| | - Jun Takada
- Graduate
School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
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Kunoh T, Morinaga K, Sugimoto S, Miyazaki S, Toyofuku M, Iwasaki K, Nomura N, Utada AS. Polyfunctional Nanofibril Appendages Mediate Attachment, Filamentation, and Filament Adaptability in Leptothrix cholodnii. ACS Nano 2020; 14:5288-5297. [PMID: 31804801 DOI: 10.1021/acsnano.9b04663] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Leptothrix is a species of Fe/Mn-oxidizing bacteria known to form long filaments composed of chains of cells that eventually produce a rigid tube surrounding the filament. Prior to the formation of this brittle microtube, Leptothrix cells secrete hair-like structures from the cell surface, called nanofibrils, which develop into a soft sheath that surrounds the filament. To clarify the role of nanofibrils in filament formation in L. cholodnii SP-6, we analyze the behavior of individual cells and multicellular filaments in high-aspect ratio microfluidic chambers using time-lapse and intermittent in situ fluorescent staining of nanofibrils, complemented with atmospheric scanning electron microscopy. We show that in SP-6 nanofibrils are important for attachment and their distribution on young filaments post-attachment is correlated to the directionality of filament elongation. Elongating filaments demonstrate a surprising ability to adapt to their physical environment by changing direction when they encounter obstacles: they bend or reverse direction depending on the angle of the collision. We show that the forces involved in the collision can be used to predict the behavior of filament. Finally, we show that as filaments grow in length, the older region becomes confined by the sheath, while the newly secreted nanofibrils at the leading edge of the filament form a loose, divergent, structure from which cells periodically escape.
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Affiliation(s)
| | | | - Shinya Sugimoto
- Department of Bacteriology and Jikei Center for Biofilm Research and Technology, The Jikei University School of Medicine, 3-25-8, Nishi-Shimbashi, Minato-ku, Tokyo 105-8461, Japan
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Jubb AM, Eskelsen JR, Yin X, Zheng J, Philben MJ, Pierce EM, Graham DE, Wullschleger SD, Gu B. Characterization of iron oxide nanoparticle films at the air-water interface in Arctic tundra waters. Sci Total Environ 2018; 633:1460-1468. [PMID: 29758898 DOI: 10.1016/j.scitotenv.2018.03.332] [Citation(s) in RCA: 1] [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] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 03/26/2018] [Accepted: 03/27/2018] [Indexed: 06/08/2023]
Abstract
Massive amounts of organic carbon have accumulated in Arctic permafrost and soils due to anoxic and low temperature conditions that limit aerobic microbial respiration. Alternative electron acceptors are thus required for microbes to degrade organic carbon in these soils. Iron or iron oxides have been recognized to play an important role in carbon cycle processes in Arctic soils, although the exact form and role as an electron acceptor or donor remain poorly understood. Here, Arctic biofilms collected during the summers of 2016 and 2017 from tundra surface waters on the Seward Peninsula of western Alaska were characterized with a suite of microscopic and spectroscopic methods. We hypothesized that these films contain redox-active minerals bound to biological polymers. The major components of the films were found to be iron oxide nanoparticle aggregates associated with extracellular polymeric substances. The observed mineral phases varied between films collected in different years with magnetite (Fe2+Fe23+O4) nanoparticles (<5nm) predominantly identified in the 2016 films, while for films collected in 2017 ferrihydrite-like amorphous iron oxyhydroxides were found. While the exact formation mechanism of these Artic iron oxide films remains to be explored, the presence of magnetite and other iron oxide/oxyhydroxide nanoparticles at the air-water interface may represent a previously unknown source of electron acceptors for continual anaerobic microbial respiration of organic carbon within poorly drained Arctic tundra.
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Affiliation(s)
- Aaron M Jubb
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
| | - Jeremy R Eskelsen
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Xiangping Yin
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jianqiu Zheng
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Michael J Philben
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Eric M Pierce
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - David E Graham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Stan D Wullschleger
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Baohua Gu
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN, USA.
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Makita H. Iron-oxidizing bacteria in marine environments: recent progresses and future directions. World J Microbiol Biotechnol 2018; 34:110. [PMID: 29974320 DOI: 10.1007/s11274-018-2491-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 06/26/2018] [Indexed: 10/28/2022]
Abstract
Iron-oxidizing bacteria (FeOB) refers to a group of bacteria with the ability to exchange and accumulate divalent iron dissolved in water as trivalent iron inside and outside the bacterial cell. Most FeOB belong the largest bacterial phylum, Proteobacteria. Within this phylum, FeOB with varying physiology with regards to their response to oxygen (obligate aerobes, facultative and obligate anaerobes) and pH optimum for proliferation (neutrophiles, moderate and extreme acidophiles) can be found. Although FeOB have been reported from a wide variety of environments, most of them have not been isolated and their biochemical characteristics remain largely unknown. This is especially true for those living in the marine realm, where the properties of FeOB was not known until the isolation of the Zetaproteobacteria Mariprofundus ferrooxydans, first reported in 2007. Since the proposal of Zetaproteobacteria by Emerson et al., the detection and isolation of those microorganisms from the marine environment has greatly escalated. Furthermore, FeOB have also recently been reported from works on ocean drilling and metal corrosion. This review aims to summarize the current state of phylogenetic and physiological diversity in marine FeOB, the significance of their roles in their environments (on both global and local scales), as well as their growing importance and applications in the industry.
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Kunoh T, Nakanishi M, Kusano Y, Itadani A, Ando K, Matsumoto S, Tamura K, Kunoh H, Takada J. Biosorption of metal elements by exopolymer nanofibrils excreted from Leptothrix cells. Water Res 2017; 122:139-147. [PMID: 28599159 DOI: 10.1016/j.watres.2017.05.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [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: 01/24/2017] [Revised: 05/02/2017] [Accepted: 05/03/2017] [Indexed: 06/07/2023]
Abstract
Leptothrix species, aquatic Fe-oxidizing bacteria, excrete nano-scaled exopolymer fibrils. Once excreted, the fibrils weave together and coalesce to form extracellular, microtubular, immature sheaths encasing catenulate cells of Leptothrix. The immature sheaths, composed of aggregated nanofibrils with a homogeneous-looking matrix, attract and bind aqueous-phase inorganics, especially Fe, P, and Si, to form seemingly solid, mature sheaths of a hybrid organic-inorganic nature. To verify our assumption that the organic skeleton of the sheaths might sorb a broad range of other metallic and nonmetallic elements, we examined the sorption potential of chemically and enzymatically prepared protein-free organic sheath remnants for 47 available elements. The sheath remnants were found by XRF to sorb each of the 47 elements, although their sorption degree varied among the elements: >35% atomic percentages for Ti, Y, Zr, Ru, Rh, Ag, and Au. Electron microscopy, energy dispersive x-ray spectroscopy, electron and x-ray diffractions, and Fourier transform infrared spectroscopy analyses of sheath remnants that had sorbed Ag, Cu, and Pt revealed that (i) the sheath remnants comprised a 5-10 nm thick aggregation of fibrils, (ii) the test elements were distributed almost homogeneously throughout the fibrillar aggregate, (iii) the nanofibril matrix sorbing the elements was nearly amorphous, and (iv) these elements plausibly were bound to the matrix by ionic binding, especially via OH. The present results show that the constitutive protein-free exopolymer nanofibrils of the sheaths can contribute to creating novel filtering materials for recovering and recycling useful and/or hazardous elements from the environment.
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Affiliation(s)
- Tatsuki Kunoh
- Core Research for Evolutionary Science and Technology (CREST), Japan Science and Technology Agency (JST), Okayama 700-8530, Japan; Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Makoto Nakanishi
- Core Research for Evolutionary Science and Technology (CREST), Japan Science and Technology Agency (JST), Okayama 700-8530, Japan; Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Yoshihiro Kusano
- Department of Applied Chemistry and Biotechnology, Okayama University of Science, Okayama, 700-0005, Japan
| | - Atsushi Itadani
- Department of Human Sciences, Obihiro University of Agriculture and Veterinary Medicine, Hokkaido, 080-8555, Japan; Graduate School of Science and Technology, Niigata University, Niigata, 950-2181, Japan
| | - Kota Ando
- Graduate School of Science and Technology, Niigata University, Niigata, 950-2181, Japan
| | - Syuji Matsumoto
- Core Research for Evolutionary Science and Technology (CREST), Japan Science and Technology Agency (JST), Okayama 700-8530, Japan; Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Katsunori Tamura
- Core Research for Evolutionary Science and Technology (CREST), Japan Science and Technology Agency (JST), Okayama 700-8530, Japan; Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Hitoshi Kunoh
- Core Research for Evolutionary Science and Technology (CREST), Japan Science and Technology Agency (JST), Okayama 700-8530, Japan; Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Jun Takada
- Core Research for Evolutionary Science and Technology (CREST), Japan Science and Technology Agency (JST), Okayama 700-8530, Japan; Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan.
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Kunoh T, Matsumoto S, Nagaoka N, Kanashima S, Hino K, Uchida T, Tamura K, Kunoh H, Takada J. Amino group in Leptothrix sheath skeleton is responsible for direct deposition of Fe(III) minerals onto the sheaths. Sci Rep 2017; 7:6498. [PMID: 28747653 PMCID: PMC5529543 DOI: 10.1038/s41598-017-06644-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [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] [Received: 01/13/2017] [Accepted: 06/15/2017] [Indexed: 11/09/2022] Open
Abstract
Leptothrix species produce microtubular organic-inorganic materials that encase the bacterial cells. The skeleton of an immature sheath, consisting of organic exopolymer fibrils of bacterial origin, is formed first, then the sheath becomes encrusted with inorganic material. Functional carboxyl groups of polysaccharides in these fibrils are considered to attract and bind metal cations, including Fe(III) and Fe(III)-mineral phases onto the fibrils, but the detailed mechanism remains elusive. Here we show that NH2 of the amino-sugar-enriched exopolymer fibrils is involved in interactions with abiotically generated Fe(III) minerals. NH2-specific staining of L. cholodnii OUMS1 detected a terminal NH2 on its sheath skeleton. Masking NH2 with specific reagents abrogated deposition of Fe(III) minerals onto fibrils. Fe(III) minerals were adsorbed on chitosan and NH2-coated polystyrene beads but not on cellulose and beads coated with an acetamide group. X-ray photoelectron spectroscopy at the N1s edge revealed that the terminal NH2 of OUMS1 sheaths, chitosan and NH2-coated beads binds to Fe(III)-mineral phases, indicating interaction between the Fe(III) minerals and terminal NH2. Thus, the terminal NH2 in the exopolymer fibrils seems critical for Fe encrustation of Leptothrix sheaths. These insights should inform artificial synthesis of highly reactive NH2-rich polymers for use as absorbents, catalysts and so on.
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Affiliation(s)
- Tatsuki Kunoh
- Core Research for Evolutionary Science and Technology (CREST), Japan Science and Technology Agency (JST), Okayama University, Okayama, 700-8530, Japan.,Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Syuji Matsumoto
- Core Research for Evolutionary Science and Technology (CREST), Japan Science and Technology Agency (JST), Okayama University, Okayama, 700-8530, Japan.,Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Noriyuki Nagaoka
- Advanced Research Center for Oral and Craniofacial Sciences, Okayama University Dental School, Okayama, 700-8558, Japan
| | | | | | - Tetsuya Uchida
- Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Katsunori Tamura
- Core Research for Evolutionary Science and Technology (CREST), Japan Science and Technology Agency (JST), Okayama University, Okayama, 700-8530, Japan.,Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Hitoshi Kunoh
- Core Research for Evolutionary Science and Technology (CREST), Japan Science and Technology Agency (JST), Okayama University, Okayama, 700-8530, Japan.,Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Jun Takada
- Core Research for Evolutionary Science and Technology (CREST), Japan Science and Technology Agency (JST), Okayama University, Okayama, 700-8530, Japan. .,Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan.
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12
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Nedkov I, Slavov L, Angelova R, Blagoev B, Kovacheva D, Abrashev MV, Iliev M, Groudeva V. Biogenic nanosized iron oxides obtained from cultivation of iron bacteria from the genus Leptothrix. J Biol Phys 2016; 42:587-600. [PMID: 27572254 DOI: 10.1007/s10867-016-9426-3] [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] [Received: 10/21/2015] [Accepted: 07/19/2016] [Indexed: 10/21/2022] Open
Abstract
A detailed investigation of nanostructured iron oxides/(oxy)hydroxides gathered after cultivation of bacteria from the genus Leptothrix as iron (II) oxidizers is presented. A specific type of medium is selected for the cultivation of the bacteria. Results for sediment powder and bio-film on glass substrate samples from the same media are discussed. XRD, Raman spectroscopy, SEM, and TEM images and PPMS measurements are used to prove the exact composition of the biogenic products and to interpret the oxidation process. Analysis of the data collected shows that around 80 % of the iron (II) from the growth medium has been transformed into iron (III) in the form of different (oxy)hydroxides, with the rest found to be in a mixed 2,5 valence in magnetite. Our investigation shows that the bio-film sample has a phase content different from that of the powdered biomass and that lepidocrocite (γ-FeOOH) is the predominant and the initial biogenic phase in both samples. Magnetite nanoparticles are a secondary product in the bio-film, part of which possesses a defective quasi-maghemite surface layer. In the powdered biomass, the oxidation steps are not fully completed. The initial products are non-stoichiometric and due to the mixed ferric and ferrous ions present, they develop into: (i) lepidocrocite (γ-FeOOH) as a basic sediment, (ii) magnetite (Fe3O4) and (iii) goethite (α-FeOOH) in small quantities. The average size of all iron-bearing particles is found to be below 30 nm. The magnetic measurements performed show a superparamagnetic behavior of the material at room temperature.
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Affiliation(s)
- I Nedkov
- Institute of Electronics, Bulgarian Academy of Sciences, 72, Tsarigradsko Chaussee Blvd, 1784, Sofia, Bulgaria
| | - L Slavov
- Institute of Electronics, Bulgarian Academy of Sciences, 72, Tsarigradsko Chaussee Blvd, 1784, Sofia, Bulgaria
| | - R Angelova
- Institute of Electronics, Bulgarian Academy of Sciences, 72, Tsarigradsko Chaussee Blvd, 1784, Sofia, Bulgaria. .,Faculty of Biology, St. Kliment Ohrdiski University of Sofia, 8, Dragan Tsankov Blvd, 1164, Sofia, Bulgaria.
| | - B Blagoev
- Institute of Electronics, Bulgarian Academy of Sciences, 72, Tsarigradsko Chaussee Blvd, 1784, Sofia, Bulgaria
| | - D Kovacheva
- Institute of General and Inorganic Chemistry, Bulgarian Academy of Sciences, bl. 11 Acad. Georgi Bonchev Str., 1113, Sofia, Bulgaria
| | - M V Abrashev
- Faculty of Physics, Sofia University, 5 James Bourchier Blvd, 1164, Sofia, Bulgaria
| | - M Iliev
- Faculty of Biology, St. Kliment Ohrdiski University of Sofia, 8, Dragan Tsankov Blvd, 1164, Sofia, Bulgaria
| | - V Groudeva
- Faculty of Biology, St. Kliment Ohrdiski University of Sofia, 8, Dragan Tsankov Blvd, 1164, Sofia, Bulgaria
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13
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Kunoh T, Nagaoka N, McFarlane IR, Tamura K, El-Naggar MY, Kunoh H, Takada J. Dissociation and Re-Aggregation of Multicell-Ensheathed Fragments Responsible for Rapid Production of Massive Clumps of Leptothrix Sheaths. Biology (Basel) 2016; 5:biology5030032. [PMID: 27490579 PMCID: PMC5037351 DOI: 10.3390/biology5030032] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 07/21/2016] [Accepted: 07/22/2016] [Indexed: 01/30/2023]
Abstract
Species of the Fe/Mn-oxidizing bacteria Leptothrix produce tremendous amounts of microtubular, Fe/Mn-encrusted sheaths within a few days in outwells of groundwater that can rapidly clog water systems. To understand this mode of rapid sheath production and define the timescales involved, behaviors of sheath-forming Leptothrix sp. strain OUMS1 were examined using time-lapse video at the initial stage of sheath formation. OUMS1 formed clumps of tangled sheaths. Electron microscopy confirmed the presence of a thin layer of bacterial exopolymer fibrils around catenulate cells (corresponding to the immature sheath). In time-lapse videos, numerous sheath filaments that extended from the periphery of sheath clumps repeatedly fragmented at the apex of the same fragment, the fragments then aggregated and again elongated, eventually forming a large sheath clump comprising tangled sheaths within two days. In this study, we found that fast microscopic fragmentation, dissociation, re-aggregation and re-elongation events are the basis of the rapid, massive production of Leptothrix sheaths typically observed at macroscopic scales.
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Affiliation(s)
- Tatsuki Kunoh
- Core Research for Evolutionary Science and Technology (CREST), Japan Science and Technology Agency (JST), Okayama 700-0082, Japan.
- Graduate School of Natural Science and Technology, Okayama University, Okayama 700-0082, Japan.
| | - Noriyuki Nagaoka
- Advanced Research Center for Oral and Craniofacial Sciences, Okayama University Dental School, Okayama 700-8558, Japan.
| | - Ian R McFarlane
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089, USA.
| | - Katsunori Tamura
- Core Research for Evolutionary Science and Technology (CREST), Japan Science and Technology Agency (JST), Okayama 700-0082, Japan.
- Graduate School of Natural Science and Technology, Okayama University, Okayama 700-0082, Japan.
| | - Mohamed Y El-Naggar
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089, USA.
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA.
| | - Hitoshi Kunoh
- Core Research for Evolutionary Science and Technology (CREST), Japan Science and Technology Agency (JST), Okayama 700-0082, Japan.
- Graduate School of Natural Science and Technology, Okayama University, Okayama 700-0082, Japan.
| | - Jun Takada
- Core Research for Evolutionary Science and Technology (CREST), Japan Science and Technology Agency (JST), Okayama 700-0082, Japan.
- Graduate School of Natural Science and Technology, Okayama University, Okayama 700-0082, Japan.
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14
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Kunoh T, Hashimoto H, Suzuki T, Hayashi N, Tamura K, Takano M, Kunoh H, Takada J. Direct Adherence of Fe(III) Particles onto Sheaths of Leptothrix sp. Strain OUMS1 in Culture. Minerals 2016; 6:4. [DOI: 10.3390/min6010004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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15
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Ishihara H, Hashimoto H, Taketa E, Suzuki T, Mandai K, Kunoh H, Takada J. Silicon-Rich, Iron Oxide Microtubular Sheath Produced by an Iron-Oxidizing Bacterium, Leptothrix sp. Strain OUMS1, in Culture. Minerals 2014; 4:565-77. [DOI: 10.3390/min4030565] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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16
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Takeda M, Miyanoiri Y, Nogami T, Oda K, Saito T, Kato K, Koizumi J, Katahira M. Structural Analysis of the Fundamental Polymer of the Sheath Constructed by Sphaerotilus natans. Biosci Biotechnol Biochem 2014; 71:2992-8. [DOI: 10.1271/bbb.70395] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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17
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Makita H, Nakahara Y, Fukui H, Miyanoiri Y, Katahira M, Seki H, Takeda M, Koizumi JI. Identification of 2-(Cysteinyl)amido-2-deoxy-D-galacturonic Acid Residue from the Sheath ofLeptothrix cholodnii. Biosci Biotechnol Biochem 2014; 70:1265-8. [PMID: 16717434 DOI: 10.1271/bbb.70.1265] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The sheath of Leptothrix cholodnii is a glycoconjugate composed of a polysaccharide and a peptide rich in cysteine. In this study, structural determination of the hydrazinolyzate of the sheath was carried out. Since the hydrazinolyzate is a polysaccharide incorporated with cysteine, it was S-derivatized with a thiol-specific fluorogenic reagent, 4-(aminosulfonyl)-7-fluoro-2,1,3-benzoxadiazole (ABD-F). Fluorescent fragments were purified by HPLC, and their structures were analyzed by mass spectrometry and NMR spectroscopy. The sheath was found to contain 2-(cysteinyl)amido-2-deoxy-D-galacturonic acid residue.
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Affiliation(s)
- Hiroko Makita
- Division of Materials Science and Chemical Engineering, Faculty of Engineering, Yokonama National University, Japan.
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18
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Jin H, Li B, Peng X, Chen L. Metagenomic analyses reveal phylogenetic diversity of carboxypeptidase gene sequences in activated sludge of a wastewater treatment plant in Shanghai, China. ANN MICROBIOL 2013; 64:689-697. [PMID: 24860282 PMCID: PMC4028537 DOI: 10.1007/s13213-013-0704-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [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: 01/04/2013] [Accepted: 08/01/2013] [Indexed: 12/03/2022] Open
Abstract
Activated sludge of wastewater treatment plants carries a diverse microflora. However, up to 80–90 % of microorganisms in activated sludge cannot be cultured by current laboratory techniques, leaving an enzyme reservoir largely unexplored. In this study, we investigated carboxypeptidase diversity in activated sludge of a wastewater treatment plant in Shanghai, China, by a culture-independent metagenomic approach. Three sets of consensus degenerate hybrid oligonucleotide primers (CODEHOPs) targeting conserved domains of public carboxypeptidases have been designed to amplify carboxypeptidase gene sequences in the metagenomic DNA of activated sludge by PCR. The desired amplicons were evaluated by carboxypeptidase sequence clone libraries and phylogenetic analyses. We uncovered a significant diversity of carboxypeptidases present in the activated sludge. Deduced carboxypeptidase amino acid sequences (127–208 amino acids) were classified into three distinct clusters, α, β, and γ. Sequences belonging to clusters α and β shared 58–97 % identity to known carboxypeptidase sequences from diverse species, whereas sequences in the cluster γ were remarkably less related to public carboxypeptidase homologous in the GenBank database, strongly suggesting that novel carboxypeptidase families or microbial niches exist in the activated sludge. We also observed numerous carboxypeptidase sequences that were much closer to those from representative strains present in industrial and sewage treatment and bioremediation. Thermostable and halotolerant carboxypeptidase sequences were also detected in clusters α and β. Coexistence of various carboxypeptidases is evidence of a diverse microflora in the activated sludge, a feature suggesting a valuable gene resource to be further explored for biotechnology application.
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Affiliation(s)
- Hao Jin
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, Engineering Centre for Quality Control and Risk Assessment of Aquatic Products, College of Food Science and Technology, Shanghai Ocean University, 999 Hu Cheng Huan Road, Shanghai, 201306 People’s Republic of China
| | - Bailin Li
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, Engineering Centre for Quality Control and Risk Assessment of Aquatic Products, College of Food Science and Technology, Shanghai Ocean University, 999 Hu Cheng Huan Road, Shanghai, 201306 People’s Republic of China
| | - Xu Peng
- Department of Biology, Copenhagen University, Ole Maaløes Vej 5, 2200 N Copenhagen, Denmark
| | - Lanming Chen
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, Engineering Centre for Quality Control and Risk Assessment of Aquatic Products, College of Food Science and Technology, Shanghai Ocean University, 999 Hu Cheng Huan Road, Shanghai, 201306 People’s Republic of China
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19
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Suzuki T, Ishihara H, Toyoda K, Shiraishi T, Kunoh H, Takada J. Autolysis of Bacterial Cells Leads to Formation of Empty Sheaths by Leptothrix spp. Minerals 2013; 3:247-57. [DOI: 10.3390/min3020247] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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20
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Ishihara H, Suzuki T, Hashimoto H, Kunoh H, Takada J. Initial Parallel Arrangement of Extracellular Fibrils Holds a Key for Sheath Frame Construction by Leptothrix sp. Strain OUMS1. Minerals 2013; 3:73-81. [DOI: 10.3390/min3010073] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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21
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Suzuki T, Ishihara H, Furutani M, Shiraishi T, Kunoh H, Takada J. A Novel Method for Culturing of Leptothrix sp. Strain OUMS1 in Natural Conditions. Minerals 2012; 2:118-28. [DOI: 10.3390/min2020118] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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22
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Takeda M, Kawasaki Y, Umezu T, Shimura S, Hasegawa M, Koizumi J. Patterns of sheath elongation, cell proliferation, and manganese(II) oxidation in Leptothrix cholodnii. Arch Microbiol 2012; 194:667-73. [DOI: 10.1007/s00203-012-0801-6] [Citation(s) in RCA: 15] [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: 11/08/2011] [Revised: 02/08/2012] [Accepted: 02/13/2012] [Indexed: 10/28/2022]
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23
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Furutani M, Suzuki T, Ishihara H, Hashimoto H, Kunoh H, Takada J. Initial Assemblage of Bacterial Saccharic Fibrils and Element Deposition to Form an Immature Sheath in Cultured Leptothrix sp. Strain OUMS1. Minerals 2011; 1:157-66. [DOI: 10.3390/min1010157] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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24
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Kondo K, Takeda M, Ejima W, Kawasaki Y, Umezu T, Yamada M, Koizumi JI, Mashima T, Katahira M. Study of a novel glycoconjugate, thiopeptidoglycan, and a novel polysaccharide lyase, thiopeptidoglycan lyase. Int J Biol Macromol 2011; 48:256-62. [DOI: 10.1016/j.ijbiomac.2010.11.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2010] [Revised: 11/15/2010] [Accepted: 11/16/2010] [Indexed: 10/18/2022]
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25
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: an update for the period 2005-2006. Mass Spectrom Rev 2011; 30:1-100. [PMID: 20222147 DOI: 10.1002/mas.20265] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
This review is the fourth update of the original review, published in 1999, on the application of MALDI mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2006. The review covers fundamental studies, fragmentation of carbohydrate ions, method developments, and applications of the technique to the analysis of different types of carbohydrate. Specific compound classes that are covered include carbohydrate polymers from plants, N- and O-linked glycans from glycoproteins, glycated proteins, glycolipids from bacteria, glycosides, and various other natural products. There is a short section on the use of MALDI-TOF mass spectrometry for the study of enzymes involved in glycan processing, a section on industrial processes, particularly the development of biopharmaceuticals and a section on the use of MALDI-MS to monitor products of chemical synthesis of carbohydrates. Large carbohydrate-protein complexes and glycodendrimers are highlighted in this final section.
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Affiliation(s)
- David J Harvey
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, Oxford OX1 3QU, UK.
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26
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Abstract
In the 1830s, iron bacteria were among the first groups of microbes to be recognized for carrying out a fundamental geological process, namely the oxidation of iron. Due to lingering questions about their metabolism, coupled with difficulties in culturing important community members, studies of Fe-oxidizing bacteria (FeOB) have lagged behind those of other important microbial lithotrophic metabolisms. Recently, research on lithotrophic, oxygen-dependent FeOB that grow at circumneutral pH has accelerated. This work is driven by several factors including the recognition by both microbiologists and geoscientists of the role FeOB play in the biogeochemistry of iron and other elements. The isolation of new strains of obligate FeOB allowed a better understanding of their physiology and phylogeny and the realization that FeOB are abundant at certain deep-sea hydrothermal vents. These ancient microorganisms offer new opportunities to learn about fundamental biological processes that can be of practical importance.
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Affiliation(s)
- David Emerson
- Bigelow Laboratory for Ocean Sciences, West Boothbay Harbor, Maine 04575, USA.
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27
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Takeda M, Kondo K, Yamada M, Koizumi JI, Mashima T, Matsugami A, Katahira M. Solubilization and structural determination of a glycoconjugate which is assembled into the sheath of Leptothrix cholodnii. Int J Biol Macromol 2010; 46:206-11. [DOI: 10.1016/j.ijbiomac.2009.12.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2009] [Revised: 12/03/2009] [Accepted: 12/09/2009] [Indexed: 10/20/2022]
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28
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Martín-gonzález A, Wierzchos J, Gutiérrez JC, Alonso J, Ascaso C. Microbial Cretaceous park: biodiversity of microbial fossils entrapped in amber. Naturwissenschaften 2009; 96:551-64. [DOI: 10.1007/s00114-009-0508-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2008] [Revised: 01/12/2009] [Accepted: 01/22/2009] [Indexed: 11/25/2022]
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29
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Takeda M, Yoneya A, Miyazaki Y, Kondo K, Makita H, Kondoh M, Suzuki I, Koizumi JI. Prosthecobacter fluviatilis sp. nov., which lacks the bacterial tubulin btubA and btubB genes. Int J Syst Evol Microbiol 2008; 58:1561-5. [PMID: 18599695 DOI: 10.1099/ijs.0.65787-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [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
Leptothrix cholodnii is a sheathed bacterium often found in metal-rich and oligotrophic aquatic environments. A bacterial strain that is able to degrade the NaOH-treated sheath of L. cholodnii was isolated. The isolate was a Gram-negative, aerobic and prosthecate bacterium. The optimum growth temperature and pH were 30 degrees C and pH 7.0, respectively. The DNA G+C content was 62.9 mol%. The major respiratory quinone was MK-6. A phylogenetic analysis based on the 16S rRNA gene indicated that the isolate is a member of the genus Prosthecobacter. The nearest relative was the type strain of Prosthecobacter vanneervenii, with a similarity of 97.1 %. However, the isolate does not possess the bacterial tubulin genes, btubA and btubB, unique to known species of the genus Prosthecobacter. It is proposed that the isolate represents a novel species, Prosthecobacter fluviatilis sp. nov. The type strain is HAQ-1(T) (=JCM 14805(T) =KACC 12649(T) =KCTC 22182(T)).
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Affiliation(s)
- Minoru Takeda
- Division of Materials Science and Chemical Engineering, Faculty of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya, Yokohama 240-8501, Japan.
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