1
|
Thomas F, Le Duff N, Wu TD, Cébron A, Uroz S, Riera P, Leroux C, Tanguy G, Legeay E, Guerquin-Kern JL. Isotopic tracing reveals single-cell assimilation of a macroalgal polysaccharide by a few marine Flavobacteria and Gammaproteobacteria. THE ISME JOURNAL 2021; 15:3062-3075. [PMID: 33953365 PMCID: PMC8443679 DOI: 10.1038/s41396-021-00987-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 03/25/2021] [Accepted: 04/09/2021] [Indexed: 02/03/2023]
Abstract
Algal polysaccharides constitute a diverse and abundant reservoir of organic matter for marine heterotrophic bacteria, central to the oceanic carbon cycle. We investigated the uptake of alginate, a major brown macroalgal polysaccharide, by microbial communities from kelp-dominated coastal habitats. Congruent with cell growth and rapid substrate utilization, alginate amendments induced a decrease in bacterial diversity and a marked compositional shift towards copiotrophic bacteria. We traced 13C derived from alginate into specific bacterial incorporators and quantified the uptake activity at the single-cell level, using halogen in situ hybridization coupled to nanoscale secondary ion mass spectrometry (HISH-SIMS) and DNA stable isotope probing (DNA-SIP). Cell-specific alginate uptake was observed for Gammaproteobacteria and Flavobacteriales, with carbon assimilation rates ranging from 0.14 to 27.50 fg C µm-3 h-1. DNA-SIP revealed that only a few initially rare Flavobacteriaceae and Alteromonadales taxa incorporated 13C from alginate into their biomass, accounting for most of the carbon assimilation based on bulk isotopic measurements. Functional screening of metagenomic libraries gave insights into the genes of alginolytic Alteromonadales active in situ. These results highlight the high degree of niche specialization in heterotrophic communities and help constraining the quantitative role of polysaccharide-degrading bacteria in coastal ecosystems.
Collapse
Affiliation(s)
- François Thomas
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Roscoff, France.
| | - Nolwen Le Duff
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | - Ting-Di Wu
- Institut Curie, Université Paris-Saclay, Paris, France
- Université Paris-Saclay, INSERM US43, CNRS UMS2016, Multimodal Imaging Center, Orsay, France
| | | | - Stéphane Uroz
- Université de Lorraine, INRAE, UMR1136 « Interactions Arbres-Microorganismes », Champenoux, France
| | - Pascal Riera
- Sorbonne Université, CNRS, UMR7144, Station Biologique de Roscoff (SBR), Roscoff, France
| | - Cédric Leroux
- CNRS, Sorbonne Université, FR2424, Metabomer, Station Biologique de Roscoff, Roscoff, France
| | - Gwenn Tanguy
- CNRS, Sorbonne Université, FR2424, Genomer, Station Biologique de Roscoff, Roscoff, France
| | - Erwan Legeay
- CNRS, Sorbonne Université, FR2424, Genomer, Station Biologique de Roscoff, Roscoff, France
| | - Jean-Luc Guerquin-Kern
- Institut Curie, Université Paris-Saclay, Paris, France
- Université Paris-Saclay, INSERM US43, CNRS UMS2016, Multimodal Imaging Center, Orsay, France
| |
Collapse
|
2
|
Furusawa G, Azami NA, Teh AH. Genes for degradation and utilization of uronic acid-containing polysaccharides of a marine bacterium Catenovulum sp. CCB-QB4. PeerJ 2021; 9:e10929. [PMID: 33732545 PMCID: PMC7953866 DOI: 10.7717/peerj.10929] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 01/20/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Oligosaccharides from polysaccharides containing uronic acids are known to have many useful bioactivities. Thus, polysaccharide lyases (PLs) and glycoside hydrolases (GHs) involved in producing the oligosaccharides have attracted interest in both medical and industrial settings. The numerous polysaccharide lyases and glycoside hydrolases involved in producing the oligosaccharides were isolated from soil and marine microorganisms. Our previous report demonstrated that an agar-degrading bacterium, Catenovulum sp. CCB-QB4, isolated from a coastal area of Penang, Malaysia, possessed 183 glycoside hydrolases and 43 polysaccharide lyases in the genome. We expected that the strain might degrade and use uronic acid-containing polysaccharides as a carbon source, indicating that the strain has a potential for a source of novel genes for degrading the polysaccharides. METHODS To confirm the expectation, the QB4 cells were cultured in artificial seawater media with uronic acid-containing polysaccharides, namely alginate, pectin (and saturated galacturonate), ulvan, and gellan gum, and the growth was observed. The genes involved in degradation and utilization of uronic acid-containing polysaccharides were explored in the QB4 genome using CAZy analysis and BlastP analysis. RESULTS The QB4 cells were capable of using these polysaccharides as a carbon source, and especially, the cells exhibited a robust growth in the presence of alginate. 28 PLs and 22 GHs related to the degradation of these polysaccharides were found in the QB4 genome based on the CAZy database. Eleven polysaccharide lyases and 16 glycoside hydrolases contained lipobox motif, indicating that these enzymes play an important role in degrading the polysaccharides. Fourteen of 28 polysaccharide lyases were classified into ulvan lyase, and the QB4 genome possessed the most abundant ulvan lyase genes in the CAZy database. Besides, genes involved in uronic acid metabolisms were also present in the genome. These results were consistent with the cell growth. In the pectin metabolic pathway, the strain had genes for three different pathways. However, the growth experiment using saturated galacturonate exhibited that the strain can only use the pathway related to unsaturated galacturonate.
Collapse
Affiliation(s)
- Go Furusawa
- Centre for Chemical Biology, Universiti Sains Malaysia, Bayan Lepas, Penang, Malaysia
| | - Nor Azura Azami
- Centre for Chemical Biology, Universiti Sains Malaysia, Bayan Lepas, Penang, Malaysia
| | - Aik-Hong Teh
- Centre for Chemical Biology, Universiti Sains Malaysia, Bayan Lepas, Penang, Malaysia
| |
Collapse
|
3
|
Shibata T, Fujii R, Nishioka Y, Miyake H, Mori T, Tanaka R. A Simple Analysis Method for 4-Deoxy-l- erythro-5-hexoseulose Uronic Acid by HPLC-ELSD with Column for Anion Analysis. Nat Prod Commun 2019. [DOI: 10.1177/1934578x19850990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
4-Deoxy-l- erythro-5-hexoseulose uronic acid (DEH) is a rare deoxy sugar produced from alginate by the action of an exotype alginate lyase. A simple and rapid method for analyzing DEH using high-performance liquid chromatography with evaporative light scattering detection (HPLC-ELSD) was developed in this study. For chromatography, an isocratic elution of ammonium formate buffer including formic acid and a column for anion chromatography were used. In the developed method, DEH was detected at a retention time of 3.038 minutes and limits of detection (signal-noise ratio = 3) and quantification (signal-noise ratio = 10) were 37.5 and 124.9 µg/mL as a sodium DEH, respectively. In addition, separation and detection of alginate unsaturated oligosaccharides were also tested using the method. Within an analysis time of 10 minutes, it was possible to separate and detect unsaturated disaccharide, unsaturated trisaccharide, and unsaturated tetrasaccharide prepared using poly(β-d-mannuronate) lyase and sodium alginate of high mannuronate type. The HPLC-ELSD method established in this study will be applicable for quantitative analysis of DEH and measurement of exotype alginate lyase activity.
Collapse
Affiliation(s)
- Toshiyuki Shibata
- Graduate School of Bioresources, Mie University, Tsu, Japan
- Seaweed Biorefinery Research Center, Mie University, Tsu, Japan
| | - Reona Fujii
- Graduate School of Bioresources, Mie University, Tsu, Japan
| | | | - Hideo Miyake
- Graduate School of Bioresources, Mie University, Tsu, Japan
- Seaweed Biorefinery Research Center, Mie University, Tsu, Japan
| | - Tetsushi Mori
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
| | - Reiji Tanaka
- Graduate School of Bioresources, Mie University, Tsu, Japan
- Seaweed Biorefinery Research Center, Mie University, Tsu, Japan
| |
Collapse
|
4
|
Shibata T, Fujii R, Miyake H, Tanaka R, Mori T, Takahashi M, Takagi T, Yoshikawa H, Kuroda K, Ueda M. Development of an Analysis Method for 4-Deoxy-l-erythro-5-hexoseulose Uronic Acid by LC/ESI/MS with Selected Ion Monitoring. Nat Prod Commun 2017. [DOI: 10.1177/1934578x1701200627] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
This study describes a simple and rapid analytical quantitative method for measuring 4-deoxy-L-erythro-5-hexoseulose uronic acid (DEH) using liquid chromatography-electrospray ionization-mass spectrometry (LC/ESI/MS). For a chromatographic condition, Shodex IC NI-424 column (4.6 mm i.d. x 100 mm, 5 μm) for anion analysis and an isocratic elution of 40 mM ammonium formate buffer including 0.1% formic acid (pH 3.75) at a flow rate of 0.5 mL/min was used. The column temperature was set to 40°C. In the analysis of DEH produced by exo-type alginate lyase (AlyFRB) from Falsirhodobacter sp. alg1, a peak was detected with a retention time of 3.207 min. The prepared calibration curves for DEH analysis using the selected ion monitoring (SIM) mode of a mass spectrometer revealed a good linear relationship (correlation factor: 0.9998) within the test range (0.1–100 μg/mL). The limits of detection (S/N = 3) and quantification (S/N = 10) for DEH in SIM analysis were 0.008 and 0.027 μg/mL, respectively. Using the developed condition of LC/ESI/MS analysis, separation and detection of alginate unsaturated oligosaccharides were also tested. In an analysis time of about 13 min, this method was able to separate and detect an alginate unsaturated disaccharide, a trisaccharide, and a tetrasaccaride produced by poly(β-D-mannuronate) lyase, respectively. The analysis method established in this study will contribute to the quantitative and qualitative analysis of DEH, and the activity measurement of exo-type alginate lyase.
Collapse
Affiliation(s)
- Toshiyuki Shibata
- Major of Life Sciences, Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho, Tsu, Mie 514–8507, Japan
- Japan Science and Technology Agency, CREST, 4-1-8 Hon-cho, Kawaguchi, Saitama 332–0012, Japan
| | - Reona Fujii
- Major of Life Sciences, Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho, Tsu, Mie 514–8507, Japan
- Japan Science and Technology Agency, CREST, 4-1-8 Hon-cho, Kawaguchi, Saitama 332–0012, Japan
| | - Hideo Miyake
- Major of Life Sciences, Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho, Tsu, Mie 514–8507, Japan
- Japan Science and Technology Agency, CREST, 4-1-8 Hon-cho, Kawaguchi, Saitama 332–0012, Japan
| | - Reiji Tanaka
- Major of Life Sciences, Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho, Tsu, Mie 514–8507, Japan
- Japan Science and Technology Agency, CREST, 4-1-8 Hon-cho, Kawaguchi, Saitama 332–0012, Japan
| | - Tetsushi Mori
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184–8588, Japan
- Japan Science and Technology Agency, CREST, 4-1-8 Hon-cho, Kawaguchi, Saitama 332–0012, Japan
| | - Mami Takahashi
- Faculty of Science and Engineering, Waseda University Center for Advanced Biomedical Sciences, 2–2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162–8480, Japan
- Japan Science and Technology Agency, CREST, 4-1-8 Hon-cho, Kawaguchi, Saitama 332–0012, Japan
| | - Toshiyuki Takagi
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake, Sakyo-ku, Kyoto 606–8502, Japan
- Japan Science and Technology Agency, CREST, 4-1-8 Hon-cho, Kawaguchi, Saitama 332–0012, Japan
| | - Hiroyuki Yoshikawa
- Graduate School of Engineering, Osaka University, 2–1 Yamadaoka, Suita, Osaka 565–0871, Japan
- Japan Science and Technology Agency, CREST, 4-1-8 Hon-cho, Kawaguchi, Saitama 332–0012, Japan
| | - Kouichi Kuroda
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake, Sakyo-ku, Kyoto 606–8502, Japan
- Japan Science and Technology Agency, CREST, 4-1-8 Hon-cho, Kawaguchi, Saitama 332–0012, Japan
| | - Mitsuyoshi Ueda
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake, Sakyo-ku, Kyoto 606–8502, Japan
- Japan Science and Technology Agency, CREST, 4-1-8 Hon-cho, Kawaguchi, Saitama 332–0012, Japan
| |
Collapse
|
5
|
Ryu HJ, Oh KK. Combined De-Algination Process as a Fractionation Strategy for Valorization of Brown Macroalga Saccharina japonica. Appl Biochem Biotechnol 2017; 182:238-249. [PMID: 27858350 DOI: 10.1007/s12010-016-2323-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 11/03/2016] [Indexed: 12/28/2022]
Abstract
A combined process, de-algination followed by enzymatic saccharification, was designed to produce alginate and glucose from Saccharina japonica consecutively. The process conditions of de-algination were optimized separately for each stage of acidification and alkaline extraction. Collectively, the de-algination yield was 70.1% under the following optimized conditions: 2.4 wt% of Na2CO3, 70 °C, and 100 min with the acidified S. japonica immersed in a 0.5 wt% H2SO4 solution for 2 h at room temperature. The glucan content in the de-alginated S. japonica increased to 38.0%, which was approximately fivefold higher than that of the raw S. japonica. The enzymatic hydrolysis of the de-alginated S. japonica almost completed in 9 h, affording 5.2 g (96.8% of glucan digestibility) of glucose at a de-alginated S. japonica loading of 14.2 g.
Collapse
Affiliation(s)
- Hyun Jin Ryu
- R&D Center, SugarEn Co., Ltd, Cheonan, Chungnam, 31116, South Korea
| | - Kyeong Keun Oh
- Department of Applied Chemical Engineering, Dankook University, Cheonan, Chungnam, 31116, South Korea.
| |
Collapse
|
6
|
Nishiyama R, Inoue A, Ojima T. Identification of 2-keto-3-deoxy-d-Gluconate Kinase and 2-keto-3-deoxy-d-Phosphogluconate Aldolase in an Alginate-Assimilating Bacterium, Flavobacterium sp. Strain UMI-01. Mar Drugs 2017; 15:md15020037. [PMID: 28216576 PMCID: PMC5334617 DOI: 10.3390/md15020037] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 01/26/2017] [Accepted: 02/08/2017] [Indexed: 01/21/2023] Open
Abstract
Recently, we identified an alginate-assimilating gene cluster in the genome of Flavobacterium sp. strain UMI-01, a member of Bacteroidetes. Alginate lyase genes and a 4-deoxy-l-erythro-5-hexoseulose uronic acid (DEH) reductase gene in the cluster have already been characterized; however, 2-keto-3-deoxy-d-gluconate (KDG) kinase and 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase genes, i.e., flkin and flald, still remained uncharacterized. The amino acid sequences deduced from flkin and flald showed low identities with those of corresponding enzymes of Saccharophagus degradans 2-40T, a member of Proteobacteria (Kim et al., Process Biochem., 2016). This led us to consider that the DEH-assimilating enzymes of Bacteroidetes species are somewhat deviated from those of Proteobacteria species. Thus, in the present study, we first assessed the characteristics in the primary structures of KDG kinase and KDG aldolase of the strain UMI-01, and then investigated the enzymatic properties of recombinant enzymes, recFlKin and recFlAld, expressed by an Escherichia coli expression system. Multiple-sequence alignment among KDG kinases and KDG aldolases from several Proteobacteria and Bacteroidetes species indicated that the strain UMI-01 enzymes showed considerably low sequence identities (15%-25%) with the Proteobacteria enzymes, while they showed relatively high identities (47%-68%) with the Bacteroidetes enzymes. Phylogenetic analyses for these enzymes indicated the distant relationship between the Proteobacteria enzymes and the Bacteroidetes enzymes, i.e., they formed distinct clusters in the phylogenetic tree. recFlKin and recFlAld produced with the genes flkin and flald, respectively, were confirmed to show KDG kinase and KDPG aldolase activities. Namely, recFlKin produced 1.7 mM KDPG in a reaction mixture containing 2.5 mM KDG and 2.5 mM ATP in a 90-min reaction, while recFlAld produced 1.2 mM pyruvate in the reaction mixture containing 5 mM KDPG at the equilibrium state. An in vitro alginate-metabolizing system constructed from recFlKin, recFlAld, and previously reported alginate lyases and DEH reductase of the strain UMI-01 could convert alginate to pyruvate and glyceraldehyde-3-phosphate with an efficiency of 38%.
Collapse
Affiliation(s)
- Ryuji Nishiyama
- Laboratory of Marine Biotechnology and Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, Japan.
| | - Akira Inoue
- Laboratory of Marine Biotechnology and Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, Japan.
| | - Takao Ojima
- Laboratory of Marine Biotechnology and Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, Japan.
| |
Collapse
|