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Li X, Gao X, Cheng M, Lu X, Zhao Z. Augmentation of saline wastewater treatment via functional enrichment of bacteria and optimized distribution in constructed wetlands combined with slag-sponges at different temperatures. CHEMOSPHERE 2024; 358:142194. [PMID: 38692369 DOI: 10.1016/j.chemosphere.2024.142194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/24/2024] [Accepted: 04/27/2024] [Indexed: 05/03/2024]
Abstract
China's aquatic environment continues to face several difficulties. Ecological constructed wetland systems (CWs) can be used to treat polluted saline water to alleviate water shortages regionally and globally. However, the performance is limited by low temperatures. To expand the use of CWs, we introduced a slag-sponge, a flaky material derived from alkaline waste slag, to create a newly constructed wetland system that can operate at both low and high temperatures. We evaluated its effectiveness by placing it at different heights in our devices. The results showed that the treatment was effective for saline wastewater with multiple contaminants. The efficiency was 20% higher than that of traditional CWs. Slag-sponges were found to carry pore structures and exhibit thermal insulation, which led to the enrichment of functional microbial communities (Chryseobacterium and Exiguerium) at low temperatures according to the microbial species analysis. The enhanced CWs offer another option for the treatment of polluted saline water in the environment and provide promising strategies for the utilization of waste slag.
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Affiliation(s)
- Xiao Li
- College of Oceanography and Ecological Science, Shanghai Ocean University, Engineering Research Center for Water Environment Ecology in Shanghai, China; Shanghai Textile Architecture Design and Research Institute Co., Ltd., Shanghai, China
| | - Xueqing Gao
- College of Oceanography and Ecological Science, Shanghai Ocean University, Engineering Research Center for Water Environment Ecology in Shanghai, China
| | - Mengqi Cheng
- College of Oceanography and Ecological Science, Shanghai Ocean University, Engineering Research Center for Water Environment Ecology in Shanghai, China; Department of Chemical, Biological and Environmental Engineering, Autonomous University of Barcelona, Spain
| | - Xian Lu
- College of Oceanography and Ecological Science, Shanghai Ocean University, Engineering Research Center for Water Environment Ecology in Shanghai, China
| | - Zhimiao Zhao
- College of Oceanography and Ecological Science, Shanghai Ocean University, Engineering Research Center for Water Environment Ecology in Shanghai, China; Hebei Key Laboratory of Wetland Ecology and Conservation, Hengshui, Hebei, China.
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2
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Sumida T, Hiraoka S, Usui K, Ishiwata A, Sengoku T, Stubbs KA, Tanaka K, Deguchi S, Fushinobu S, Nunoura T. Genetic and functional diversity of β-N-acetylgalactosamine-targeting glycosidases expanded by deep-sea metagenome analysis. Nat Commun 2024; 15:3543. [PMID: 38730244 PMCID: PMC11087588 DOI: 10.1038/s41467-024-47653-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 04/08/2024] [Indexed: 05/12/2024] Open
Abstract
β-N-Acetylgalactosamine-containing glycans play essential roles in several biological processes, including cell adhesion, signal transduction, and immune responses. β-N-Acetylgalactosaminidases hydrolyze β-N-acetylgalactosamine linkages of various glycoconjugates. However, their biological significance remains ambiguous, primarily because only one type of enzyme, exo-β-N-acetylgalactosaminidases that specifically act on β-N-acetylgalactosamine residues, has been documented to date. In this study, we identify four groups distributed among all three domains of life and characterize eight β-N-acetylgalactosaminidases and β-N-acetylhexosaminidase through sequence-based screening of deep-sea metagenomes and subsequent searching of public protein databases. Despite low sequence similarity, the crystal structures of these enzymes demonstrate that all enzymes share a prototype structure and have diversified their substrate specificities (oligosaccharide-releasing, oligosaccharide/monosaccharide-releasing, and monosaccharide-releasing) through the accumulation of mutations and insertional amino acid sequences. The diverse β-N-acetylgalactosaminidases reported in this study could facilitate the comprehension of their structures and functions and present evolutionary pathways for expanding their substrate specificity.
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Affiliation(s)
- Tomomi Sumida
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan.
| | - Satoshi Hiraoka
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Keiko Usui
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | | | - Toru Sengoku
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Kanazawa-ku, Yokohama, Japan
| | - Keith A Stubbs
- School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Katsunori Tanaka
- RIKEN, Cluster for Pioneering Research, Wako, Saitama, Japan
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan
| | - Shigeru Deguchi
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Shinya Fushinobu
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
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3
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Dang YR, Cha QQ, Liu SS, Wang SY, Li PY, Li CY, Wang P, Chen XL, Tian JW, Xin Y, Chen Y, Zhang YZ, Qin QL. Phytoplankton-derived polysaccharides and microbial peptidoglycans are key nutrients for deep-sea microbes in the Mariana Trench. MICROBIOME 2024; 12:77. [PMID: 38664737 PMCID: PMC11044484 DOI: 10.1186/s40168-024-01789-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 03/04/2024] [Indexed: 04/28/2024]
Abstract
BACKGROUND The deep sea represents the largest marine ecosystem, driving global-scale biogeochemical cycles. Microorganisms are the most abundant biological entities and play a vital role in the cycling of organic matter in such ecosystems. The primary food source for abyssal biota is the sedimentation of particulate organic polymers. However, our knowledge of the specific biopolymers available to deep-sea microbes remains largely incomplete. One crucial rate-limiting step in organic matter cycling is the depolymerization of particulate organic polymers facilitated by extracellular enzymes (EEs). Therefore, the investigation of active EEs and the microbes responsible for their production is a top priority to better understand the key nutrient sources for deep-sea microbes. RESULTS In this study, we conducted analyses of extracellular enzymatic activities (EEAs), metagenomics, and metatranscriptomics from seawater samples of 50-9305 m from the Mariana Trench. While a diverse array of microbial groups was identified throughout the water column, only a few exhibited high levels of transcriptional activities. Notably, microbial populations actively transcribing EE genes involved in biopolymer processing in the abyssopelagic (4700 m) and hadopelagic zones (9305 m) were primarily associated with the class Actinobacteria. These microbes actively transcribed genes coding for enzymes such as cutinase, laccase, and xyloglucanase which are capable of degrading phytoplankton polysaccharides as well as GH23 peptidoglycan lyases and M23 peptidases which have the capacity to break down peptidoglycan. Consequently, corresponding enzyme activities including glycosidases, esterase, and peptidases can be detected in the deep ocean. Furthermore, cell-specific EEAs increased at 9305 m compared to 4700 m, indicating extracellular enzymes play a more significant role in nutrient cycling in the deeper regions of the Mariana Trench. CONCLUSIONS Transcriptomic analyses have shed light on the predominant microbial population actively participating in organic matter cycling in the deep-sea environment of the Mariana Trench. The categories of active EEs suggest that the complex phytoplankton polysaccharides (e.g., cutin, lignin, and hemicellulose) and microbial peptidoglycans serve as the primary nutrient sources available to deep-sea microbes. The high cell-specific EEA observed in the hadal zone underscores the robust polymer-degrading capacities of hadal microbes even in the face of the challenging conditions they encounter in this extreme environment. These findings provide valuable new insights into the sources of nutrition, the key microbes, and the EEs crucial for biopolymer degradation in the deep seawater of the Mariana Trench. Video Abstract.
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Affiliation(s)
- Yan-Ru Dang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Qian-Qian Cha
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Sha-Sha Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Shu-Yan Wang
- College of Marine Life Sciences & Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Ping-Yi Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, National Laboratory for Marine Science and Technology, Qingdao, China
| | - Chun-Yang Li
- College of Marine Life Sciences & Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, National Laboratory for Marine Science and Technology, Qingdao, China
| | - Peng Wang
- College of Marine Life Sciences & Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, National Laboratory for Marine Science and Technology, Qingdao, China
| | - Ji-Wei Tian
- College of Marine Life Sciences & Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Yu Xin
- College of Marine Life Sciences & Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Yin Chen
- College of Marine Life Sciences & Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
| | - Yu-Zhong Zhang
- College of Marine Life Sciences & Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, National Laboratory for Marine Science and Technology, Qingdao, China.
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.
| | - Qi-Long Qin
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, National Laboratory for Marine Science and Technology, Qingdao, China.
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4
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Balmonte JP, Giebel HA, Arnosti C, Simon M, Wietz M. Distinct bacterial succession and functional response to alginate in the South, Equatorial, and North Pacific Ocean. Environ Microbiol 2024; 26:e16594. [PMID: 38418376 DOI: 10.1111/1462-2920.16594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 01/26/2024] [Indexed: 03/01/2024]
Abstract
The availability of alginate, an abundant macroalgal polysaccharide, induces compositional and functional responses among marine microbes, but these dynamics have not been characterized across the Pacific Ocean. We investigated alginate-induced compositional and functional shifts (e.g., heterotrophic production, glucose turnover, hydrolytic enzyme activities) of microbial communities in the South Subtropical, Equatorial, and Polar Frontal North Pacific in mesocosms. We observed that shifts in response to alginate were site-specific. In the South Subtropical Pacific, prokaryotic cell counts, glucose turnover, and peptidase activities changed the most with alginate addition, along with the enrichment of the widest range of particle-associated taxa (161 amplicon sequence variants; ASVs) belonging to Alteromonadaceae, Rhodobacteraceae, Phormidiaceae, and Pseudoalteromonadaceae. Some of these taxa were detected at other sites but only enriched in the South Pacific. In the Equatorial Pacific, glucose turnover and heterotrophic prokaryotic production increased most rapidly; a single Alteromonas taxon dominated (60% of the community) but remained low (<2%) elsewhere. In the North Pacific, the particle-associated community response to alginate was gradual, with a more limited range of alginate-enriched taxa (82 ASVs). Thus, alginate-related ecological and biogeochemical shifts depend on a combination of factors that include the ability to utilize alginate, environmental conditions, and microbial interactions.
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Affiliation(s)
- John Paul Balmonte
- Department of Earth, Marine and Environmental Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Earth and Environmental Sciences, Lehigh University, Bethlehem, PA, USA
| | - Helge-Ansgar Giebel
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Carol Arnosti
- Department of Earth, Marine and Environmental Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Matthias Wietz
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
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5
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Yang J, Zhang L, Lin S, Li W, Liu C, Yan J, Li S, Long L. Structural insights of a SusD-like protein in marine Bacteroidetes bacteria reveal the molecular basis for chitin recognition and acquisition. FEBS J 2024; 291:584-595. [PMID: 37845429 DOI: 10.1111/febs.16974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/02/2023] [Accepted: 10/12/2023] [Indexed: 10/18/2023]
Abstract
Efficient recognition and transportation of chitin oligosaccharides are crucial steps for the utilization of chitin by heterotrophic bacteria. In this study, we employed structural biological and biochemical approaches to investigate the substrate recognition and acquisition mechanism of a novel chitin-binding SusD-like protein, AqSusD, which is derived from the chitin utilization gene cluster of a marine Bacteroides strain (Aquimarina sp. SCSIO 21287). We resolved the crystal structures of the AqSusD apo-protein and its complex with chitin oligosaccharides. Our results revealed that some crucial residues (Gln67, Phe87, and Asp276) underwent significant conformational changes to form tighter substrate binding sites for ligand binding. Moreover, we identified the functions of key amino acid residues and discovered that π-π stacking and hydrogen bonding between AqSusD and the ligand played significant roles in recognition of the protein for chitin oligosaccharide binding. Based on our findings and previous investigations, we put forward a model for the mechanism of chitin oligosaccharide recognition, capture, and transport by AqSusD, in collaboration with the membrane protein AqSusC. Our study deepens the understanding of the molecular-level "selfish" use of polysaccharides such as chitin by Bacteroides.
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Affiliation(s)
- Jian Yang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Liping Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Shanshan Lin
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Wei Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Chen Liu
- Guangzhou Quality Supervision and Testing Institute, China
| | - Jingheng Yan
- Guangzhou Quality Supervision and Testing Institute, China
| | - Shubo Li
- College of Light Industry and Food Engineering, Guangxi University, Nanning, China
| | - Lijuan Long
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
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6
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Brown S, Lloyd CC, Giljan G, Ghobrial S, Amann R, Arnosti C. Pulsed inputs of high molecular weight organic matter shift the mechanisms of substrate utilisation in marine bacterial communities. Environ Microbiol 2024; 26:e16580. [PMID: 38254313 DOI: 10.1111/1462-2920.16580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024]
Abstract
Heterotrophic bacteria hydrolyze high molecular weight (HMW) organic matter extracellularly prior to uptake, resulting in diffusive loss of hydrolysis products. An alternative 'selfish' uptake mechanism that minimises this loss has recently been found to be common in the ocean. We investigated how HMW organic matter addition affects these two processing mechanisms in surface and bottom waters at three stations in the North Atlantic Ocean. A pulse of HMW organic matter increased cell numbers, as well as the rate and spectrum of extracellular enzymatic activities at both depths. The effects on selfish uptake were more differentiated: in Gulf Stream surface waters and productive surface waters south of Newfoundland, selfish uptake of structurally simple polysaccharides increased upon HMW organic matter addition. The number of selfish bacteria taking up structurally complex polysaccharides, however, was largely unchanged. In contrast, in the oligotrophic North Atlantic gyre, despite high external hydrolysis rates, the number of selfish bacteria was unchanged, irrespective of polysaccharide structure. In deep bottom waters (> 4000 m), structurally complex substrates were processed only by selfish bacteria. Mechanisms of substrate processing-and the extent to which hydrolysis products are released to the external environment-depend on substrate structural complexity and the resident bacterial community.
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Affiliation(s)
- Sarah Brown
- Environment, Ecology, and Energy Program, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina, USA
| | - C Chad Lloyd
- Department of Earth, Marine and Environmental Sciences, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Greta Giljan
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Sherif Ghobrial
- Department of Earth, Marine and Environmental Sciences, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Carol Arnosti
- Department of Earth, Marine and Environmental Sciences, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
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7
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Sannino DR, Arroyo FA, Pepe-Ranney C, Chen W, Volland JM, Elisabeth NH, Angert ER. The exceptional form and function of the giant bacterium Ca. Epulopiscium viviparus revolves around its sodium motive force. Proc Natl Acad Sci U S A 2023; 120:e2306160120. [PMID: 38109545 PMCID: PMC10756260 DOI: 10.1073/pnas.2306160120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 11/09/2023] [Indexed: 12/20/2023] Open
Abstract
Epulopiscium spp. are the largest known heterotrophic bacteria; a large cigar-shaped individual is a million times the volume of Escherichia coli. To better understand the metabolic potential and relationship of Epulopiscium sp. type B with its host Naso tonganus, we generated a high-quality draft genome from a population of cells taken from a single fish. We propose the name Candidatus Epulopiscium viviparus to describe populations of this best-characterized Epulopiscium species. Metabolic reconstruction reveals more than 5% of the genome codes for carbohydrate active enzymes, which likely degrade recalcitrant host-diet algal polysaccharides into substrates that may be fermented to acetate, the most abundant short-chain fatty acid in the intestinal tract. Moreover, transcriptome analyses and the concentration of sodium ions in the host intestinal tract suggest that the use of a sodium motive force (SMF) to drive ATP synthesis and flagellar rotation is integral to symbiont metabolism and cellular biology. In natural populations, genes encoding both F-type and V-type ATPases and SMF generation via oxaloacetate decarboxylation are among the most highly expressed, suggesting that ATPases synthesize ATP and balance ion concentrations across the cell membrane. High expression of these and other integral membrane proteins may allow for the growth of its extensive intracellular membrane system. Further, complementary metabolism between microbe and host is implied with the potential provision of nitrogen and B vitamins to reinforce this nutritional symbiosis. The few features shared by all bacterial behemoths include extreme polyploidy, polyphosphate synthesis, and thus far, they have all resisted cultivation in the lab.
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Affiliation(s)
| | | | - Charles Pepe-Ranney
- Soil & Crop Sciences Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY14853
| | - Wenbo Chen
- Department of Microbiology, Cornell University, Ithaca, NY14853
| | - Jean-Marie Volland
- Laboratory for Research in Complex Systems, Menlo Park, CA94025
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Nathalie H. Elisabeth
- Department of Energy Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA94720
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8
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Priest T, Vidal-Melgosa S, Hehemann JH, Amann R, Fuchs BM. Carbohydrates and carbohydrate degradation gene abundance and transcription in Atlantic waters of the Arctic. ISME COMMUNICATIONS 2023; 3:130. [PMID: 38071398 PMCID: PMC10710508 DOI: 10.1038/s43705-023-00324-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/17/2023] [Accepted: 10/25/2023] [Indexed: 02/13/2024]
Abstract
Carbohydrates are chemically and structurally diverse, represent a substantial fraction of marine organic matter and are key substrates for heterotrophic microbes. Studies on carbohydrate utilisation by marine microbes have been centred on phytoplankton blooms in temperate regions, while far less is known from high-latitude waters and during later seasonal stages. Here, we combine glycan microarrays and analytical chromatography with metagenomics and metatranscriptomics to show the spatial heterogeneity in glycan distribution and potential carbohydrate utilisation by microbes in Atlantic waters of the Arctic. The composition and abundance of monomers and glycan structures in POM varied with location and depth. Complex fucose-containing sulfated polysaccharides, known to accumulate in the ocean, were consistently detected, while the more labile β-1,3-glucan exhibited a patchy distribution. Through 'omics analysis, we identify variations in the abundance and transcription of carbohydrate degradation-related genes across samples at the community and population level. The populations contributing the most to transcription were taxonomically related to those known as primary responders and key carbohydrate degraders in temperate ecosystems, such as NS4 Marine Group and Formosa. The unique transcription profiles for these populations suggest distinct substrate utilisation potentials, with predicted glycan targets corresponding to those structurally identified in POM from the same sampling sites. By combining cutting-edge technologies and protocols, we provide insights into the carbohydrate component of the carbon cycle in the Arctic during late summer and present a high-quality dataset that will be of great value for future comparative analyses.
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Affiliation(s)
- Taylor Priest
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland.
| | - Silvia Vidal-Melgosa
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- University of Bremen, MARUM, Bremen, Germany
| | - Jan-Hendrik Hehemann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- University of Bremen, MARUM, Bremen, Germany
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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9
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Clerc EE, Raina JB, Keegstra JM, Landry Z, Pontrelli S, Alcolombri U, Lambert BS, Anelli V, Vincent F, Masdeu-Navarro M, Sichert A, De Schaetzen F, Sauer U, Simó R, Hehemann JH, Vardi A, Seymour JR, Stocker R. Strong chemotaxis by marine bacteria towards polysaccharides is enhanced by the abundant organosulfur compound DMSP. Nat Commun 2023; 14:8080. [PMID: 38057294 DOI: 10.1038/s41467-023-43143-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 11/01/2023] [Indexed: 12/08/2023] Open
Abstract
The ability of marine bacteria to direct their movement in response to chemical gradients influences inter-species interactions, nutrient turnover, and ecosystem productivity. While many bacteria are chemotactic towards small metabolites, marine organic matter is predominantly composed of large molecules and polymers. Yet, the signalling role of these large molecules is largely unknown. Using in situ and laboratory-based chemotaxis assays, we show that marine bacteria are strongly attracted to the abundant algal polysaccharides laminarin and alginate. Unexpectedly, these polysaccharides elicited stronger chemoattraction than their oligo- and monosaccharide constituents. Furthermore, chemotaxis towards laminarin was strongly enhanced by dimethylsulfoniopropionate (DMSP), another ubiquitous algal-derived metabolite. Our results indicate that DMSP acts as a methyl donor for marine bacteria, increasing their gradient detection capacity and facilitating their access to polysaccharide patches. We demonstrate that marine bacteria are capable of strong chemotaxis towards large soluble polysaccharides and uncover a new ecological role for DMSP in enhancing this attraction. These navigation behaviours may contribute to the rapid turnover of polymers in the ocean, with important consequences for marine carbon cycling.
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Affiliation(s)
- Estelle E Clerc
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | | | - Johannes M Keegstra
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Zachary Landry
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Sammy Pontrelli
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Uria Alcolombri
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
- Institute for Life Sciences, Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Bennett S Lambert
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Valerio Anelli
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Flora Vincent
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
- Developmental Biology Unit, European Molecular Biological Laboratory, Heidelberg, 69117, Germany
| | | | - Andreas Sichert
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Frédéric De Schaetzen
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Rafel Simó
- Institut de Ciències del Mar, CSIC, Barcelona, Catalonia, Spain
| | | | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Justin R Seymour
- Climate Change Cluster, University of Technology Sydney, Ultimo, Australia
| | - Roman Stocker
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland.
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10
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Tran DQ, Milke F, Niggemann J, Simon M. The diatom Thalassiosira rotula induces distinct growth responses and colonization patterns of Roseobacteraceae, Flavobacteria and Gammaproteobacteria. Environ Microbiol 2023; 25:3536-3555. [PMID: 37705313 DOI: 10.1111/1462-2920.16506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 09/03/2023] [Indexed: 09/15/2023]
Abstract
Diatoms as important phytoplankton components interact with and are colonized by heterotrophic bacteria. This colonization has been studied extensively in the past but a distinction between the bacterial colonization directly on diatom cells or on the aggregated organic material, exopolymeric substances (EPS), was little addressed. Here we show that the diatom Thalassiosira rotula and EPS were differently colonized by strains of Roseobacteraceae and Flavobacteriaceae in two and tree partner treatments and an enriched natural bacterial community as inoculum. In two partner treatments, the algae and EPS were generally less colonized than in the three partner treatments. Two strains benefitted greatly from the presence of another partner as the proportions of their subpopulations colonizing the diatom cell and the EPS were much enhanced relative to their two partner treatments. Highest proportions of bacteria colonizing the diatom and EPS occurred in the treatment inoculated with the enriched natural bacterial community. Dissolved organic carbon, amino acids and carbohydrates produced by T. rotula were differently used by the bacteria in the two and three partner treatments and most efficiently by the enriched natural bacterial community. Our approach is a valid model system to study physico-chemical bacteria-diatom interactions with increasing complexity.
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Affiliation(s)
- Den Quoc Tran
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Felix Milke
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Jutta Niggemann
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
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11
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Wang YW, Wang XH, Zhang J, Du ZJ, Mu DS. Cerina litoralis gen. nov., sp. nov., a novel potential polysaccharide degrading bacterium of the family Flavobacteriaceae, isolated from marine sediment. Antonie Van Leeuwenhoek 2023; 116:1447-1455. [PMID: 37899393 DOI: 10.1007/s10482-023-01888-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 09/14/2023] [Indexed: 10/31/2023]
Abstract
The Gram-strain-negative, facultative anaerobic, chemoheterotrophic, short-rod-shaped, non-motile, forming yellow colonies strain, designated F89T, was isolated from marine sediment of Xiaoshi Island, Weihai. Strain F89T grew at 15-37 °C (optimally at 28 °C), at pH 6.0-8.5 (optimally at pH 7.0) and in the presence of 1-5% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain F89T was related to the family Flavobacteriaceae. F89T had highest 16S rRNA gene sequence similarity to Maribacter cobaltidurans MCCC 1K03318T (93.3%). The predominant cellular fatty acids of F89T were iso-C15:0, iso-C15:0 G and Summed Feature 3. The main respiratory quinone of F89T was menaquinone 6 (MK-6), consistent with that observed for all related strains. The polar lipid profile of strain F89T contained phosphatidylethanolamine, two aminolipids and three unidentified polar lipids. The genomic DNA G + C content of strain F89T was 42.7%. Strain F89T encoded 121 glycoside hydrolases and was a potential polysaccharide degrading bacterium. Differential phenotypic and genotypic characteristics of the strain showed that F89T should be classified as a novel genus in Flavobacteriaceae, for which the name Cerina litoralis is proposed. The type strain is F89T (= MCCC 1H00510T = KCTC 92203T).
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Affiliation(s)
- Ya-Wei Wang
- Marine College, Shandong University, Weihai, 264209, Shandong, China
| | - Xin-Hui Wang
- ANU Joint Science College, Shandong University, Weihai, 264209, Shandong, China
| | - Jing Zhang
- Marine College, Shandong University, Weihai, 264209, Shandong, China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, 264209, Shandong, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, Shandong, China
- Weihai Research Institute of Industrial Technology of Shandong University, Weihai, China
| | - Da-Shuai Mu
- Marine College, Shandong University, Weihai, 264209, Shandong, China.
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, Shandong, China.
- Weihai Research Institute of Industrial Technology of Shandong University, Weihai, China.
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12
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Nappi J, Goncalves P, Khan T, Majzoub ME, Grobler AS, Marzinelli EM, Thomas T, Egan S. Differential priority effects impact taxonomy and functionality of host-associated microbiomes. Mol Ecol 2023; 32:6278-6293. [PMID: 34995388 DOI: 10.1111/mec.16336] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/01/2021] [Accepted: 12/16/2021] [Indexed: 01/24/2023]
Abstract
Most multicellular eukaryotes host complex communities of microorganisms, but the factors that govern their assembly are poorly understood. The settlement of specific microorganisms may have a lasting impact on community composition, a phenomenon known as the priority effect. Priority effects of individual bacterial strains on a host's microbiome are, however, rarely studied and their impact on microbiome functionality remains unknown. We experimentally tested the effect of two bacterial strains (Pseudoalteromonas tunicata D2 and Pseudovibrio sp. D323) on the assembly and succession of the microbial communities associated with the green macroalga Ulva australis. Using 16S rRNA gene sequencing and qPCR, we found that both strains exert a priority effect, with strain D2 causing initially strong but temporary taxonomic changes and strain D323 causing weaker but consistent changes. Consistent changes were predominately facilitatory and included taxa that may benefit the algal host. Metagenome analyses revealed that the strains elicited both shared (e.g., depletion of type III secretion system genes) and unique (e.g., enrichment of antibiotic resistance genes) effects on the predicted microbiome functionality. These findings indicate strong idiosyncratic effects of colonizing bacteria on the structure and function of host-associated microbial communities. Understanding the idiosyncrasies in priority effects is key for the development of novel probiotics to improve host condition.
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Affiliation(s)
- Jadranka Nappi
- Centre of Marine Science and Innovation, School of Biological and Environmental Science, University of New South Wales, Sydney, NSW, Australia
| | - Priscila Goncalves
- Centre of Marine Science and Innovation, School of Biological and Environmental Science, University of New South Wales, Sydney, NSW, Australia
| | - Tahsin Khan
- Centre of Marine Science and Innovation, School of Biological and Environmental Science, University of New South Wales, Sydney, NSW, Australia
| | - Marwan E Majzoub
- Centre of Marine Science and Innovation, School of Biological and Environmental Science, University of New South Wales, Sydney, NSW, Australia
| | - Anna Sophia Grobler
- Centre of Marine Science and Innovation, School of Biological and Environmental Science, University of New South Wales, Sydney, NSW, Australia
| | - Ezequiel M Marzinelli
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Sydney Institute of Marine Science, Mosman, NSW, Australia
| | - Torsten Thomas
- Centre of Marine Science and Innovation, School of Biological and Environmental Science, University of New South Wales, Sydney, NSW, Australia
| | - Suhelen Egan
- Centre of Marine Science and Innovation, School of Biological and Environmental Science, University of New South Wales, Sydney, NSW, Australia
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13
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Berdan EL, Roger F, Wellenreuther M, Kinnby A, Cervin G, Pereyra R, Töpel M, Johannesson K, Butlin RK, André C. A metabarcoding analysis of the wrackbed microbiome indicates a phylogeographic break along the North Sea-Baltic Sea transition zone. Environ Microbiol 2023; 25:1659-1673. [PMID: 37032322 DOI: 10.1111/1462-2920.16379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 03/18/2023] [Indexed: 04/11/2023]
Abstract
Sandy beaches are biogeochemical hotspots that bridge marine and terrestrial ecosystems via the transfer of organic matter, such as seaweed (termed wrack). A keystone of this unique ecosystem is the microbial community, which helps to degrade wrack and re-mineralize nutrients. However, little is known about this community. Here, we characterize the wrackbed microbiome as well as the microbiome of a primary consumer, the seaweed fly Coelopa frigida, and examine how they change along one of the most studied ecological gradients in the world, the transition from the marine North Sea to the brackish Baltic Sea. We found that polysaccharide degraders dominated both microbiomes, but there were still consistent differences between wrackbed and fly samples. Furthermore, we observed a shift in both microbial communities and functionality between the North and Baltic Sea driven by changes in the frequency of different groups of known polysaccharide degraders. We hypothesize that microbes were selected for their abilities to degrade different polysaccharides corresponding to a shift in polysaccharide content in the different seaweed communities. Our results reveal the complexities of both the wrackbed microbial community, with different groups specialized to different roles, and the cascading trophic consequences of shifts in the near shore algal community.
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Affiliation(s)
- Emma L Berdan
- Department of Marine Sciences, The University of Gothenburg, Tjärnö Marine Laboratory, 452 96, Strömstad, Sweden
| | - Fabian Roger
- Lund University, Centre for Environmental and Climate Science, Sölvegatan 37, 223 62, Lund, Sweden
| | - Maren Wellenreuther
- The New Zealand Institute for Plant & Food Research Ltd, Nelson, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Alexandra Kinnby
- Department of Marine Sciences, The University of Gothenburg, Tjärnö Marine Laboratory, 452 96, Strömstad, Sweden
| | - Gunnar Cervin
- Department of Marine Sciences, The University of Gothenburg, Tjärnö Marine Laboratory, 452 96, Strömstad, Sweden
| | - Ricardo Pereyra
- Department of Marine Sciences, The University of Gothenburg, Tjärnö Marine Laboratory, 452 96, Strömstad, Sweden
| | - Mats Töpel
- Department of Marine Sciences, The University of Gothenburg, Tjärnö Marine Laboratory, 452 96, Strömstad, Sweden
| | - Kerstin Johannesson
- Department of Marine Sciences, The University of Gothenburg, Tjärnö Marine Laboratory, 452 96, Strömstad, Sweden
| | - Roger K Butlin
- Department of Marine Sciences, The University of Gothenburg, Tjärnö Marine Laboratory, 452 96, Strömstad, Sweden
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Carl André
- Department of Marine Sciences, The University of Gothenburg, Tjärnö Marine Laboratory, 452 96, Strömstad, Sweden
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14
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Dutschei T, Beidler I, Bartosik D, Seeßelberg JM, Teune M, Bäumgen M, Ferreira SQ, Heldmann J, Nagel F, Krull J, Berndt L, Methling K, Hein M, Becher D, Langer P, Delcea M, Lalk M, Lammers M, Höhne M, Hehemann JH, Schweder T, Bornscheuer UT. Marine Bacteroidetes enzymatically digest xylans from terrestrial plants. Environ Microbiol 2023; 25:1713-1727. [PMID: 37121608 DOI: 10.1111/1462-2920.16390] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 04/18/2023] [Indexed: 05/02/2023]
Abstract
Marine Bacteroidetes that degrade polysaccharides contribute to carbon cycling in the ocean. Organic matter, including glycans from terrestrial plants, might enter the oceans through rivers. Whether marine bacteria degrade structurally related glycans from diverse sources including terrestrial plants and marine algae was previously unknown. We show that the marine bacterium Flavimarina sp. Hel_I_48 encodes two polysaccharide utilization loci (PULs) which degrade xylans from terrestrial plants and marine algae. Biochemical experiments revealed activity and specificity of the encoded xylanases and associated enzymes of these PULs. Proteomics indicated that these genomic regions respond to glucuronoxylans and arabinoxylans. Substrate specificities of key enzymes suggest dedicated metabolic pathways for xylan utilization. Some of the xylanases were active on different xylans with the conserved β-1,4-linked xylose main chain. Enzyme activity was consistent with growth curves showing Flavimarina sp. Hel_I_48 uses structurally different xylans. The observed abundance of related xylan-degrading enzyme repertoires in genomes of other marine Bacteroidetes indicates similar activities are common in the ocean. The here presented data show that certain marine bacteria are genetically and biochemically variable enough to access parts of structurally diverse xylans from terrestrial plants as well as from marine algal sources.
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Affiliation(s)
- Theresa Dutschei
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany
| | - Irena Beidler
- Department of Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Daniel Bartosik
- Department of Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology e.V., Greifswald, Germany
| | - Julia-Maria Seeßelberg
- Department of Protein Biochemistry, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Michelle Teune
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany
| | - Marcus Bäumgen
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany
| | - Soraia Querido Ferreira
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany
| | - Julia Heldmann
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany
| | - Felix Nagel
- Department of Biophysical Chemistry, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Joris Krull
- Institute of Marine Biotechnology e.V., Greifswald, Germany
- Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Leona Berndt
- Department of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Karen Methling
- Department of Cellular Biochemistry and Metabolomics, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Martin Hein
- Department of Organic Chemistry, Institute of Chemistry, University of Rostock, Rostock, Germany
| | - Dörte Becher
- Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Peter Langer
- Department of Organic Chemistry, Institute of Chemistry, University of Rostock, Rostock, Germany
| | - Mihaela Delcea
- Department of Biophysical Chemistry, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Michael Lalk
- Department of Cellular Biochemistry and Metabolomics, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Michael Lammers
- Department of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Matthias Höhne
- Department of Protein Biochemistry, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Jan-Hendrik Hehemann
- Institute of Marine Biotechnology e.V., Greifswald, Germany
- Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Thomas Schweder
- Department of Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology e.V., Greifswald, Germany
| | - Uwe T Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany
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15
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Dedysh SN. Describing difficult-to-culture bacteria: Taking a shortcut or investing time to discover something new? Syst Appl Microbiol 2023; 46:126439. [PMID: 37413783 DOI: 10.1016/j.syapm.2023.126439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/17/2023] [Accepted: 06/29/2023] [Indexed: 07/08/2023]
Abstract
Despite the growing interest in isolating representatives of poorly studied and as-yet-uncultivated bacterial phylogenetic groups, these microorganisms remain difficult objects for taxonomic studies. The time required for describing one of these fastidious bacteria is commonly measured in several years. What is even more problematic, many routine laboratory tests, which were originally developed for fast-growing and fast-responding microorganisms, are not fully suitable for many environmentally relevant, slow-growing bacteria. Standard techniques used in chemotaxonomic analyses do not identify unique lipids produced by these bacteria. A common practice of preparing taxonomic descriptions that report a minimal set of features to name a newly isolated organism deepens a gap between microbial ecologists and taxonomists. By contrast, investing time in detailed analysis of cell biology and experimental verification of genome-encoded capabilities of newly isolated microorganisms opens a window for novel, unexpected findings, which may shape our ideas about the functional role of these microbes in the environment.
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Affiliation(s)
- Svetlana N Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia.
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16
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Giljan G, Brown S, Lloyd CC, Ghobrial S, Amann R, Arnosti C. Selfish bacteria are active throughout the water column of the ocean. ISME COMMUNICATIONS 2023; 3:11. [PMID: 36739317 PMCID: PMC9899235 DOI: 10.1038/s43705-023-00219-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/22/2023] [Accepted: 01/26/2023] [Indexed: 02/06/2023]
Abstract
Heterotrophic bacteria in the ocean invest carbon, nitrogen, and energy in extracellular enzymes to hydrolyze large substrates to smaller sizes suitable for uptake. Since hydrolysis products produced outside of a cell may be lost to diffusion, the return on this investment is uncertain. Selfish bacteria change the odds in their favor by binding, partially hydrolyzing, and transporting polysaccharides into the periplasmic space without loss of hydrolysis products. We expected selfish bacteria to be most common in the upper ocean, where phytoplankton produce abundant fresh organic matter, including complex polysaccharides. We, therefore, sampled water in the western North Atlantic Ocean at four depths from three stations differing in physiochemical conditions; these stations and depths also differed considerably in microbial community composition. To our surprise, we found that selfish bacteria are common throughout the water column of the ocean, including at depths greater than 5500 m. Selfish uptake as a strategy thus appears to be geographically-and phylogenetically-widespread. Since processing and uptake of polysaccharides require enzymes that are highly sensitive to substrate structure, the activities of these bacteria might not be reflected by measurements relying on uptake only of low molecular weight substrates. Moreover, even at the bottom of the ocean, the supply of structurally-intact polysaccharides, and therefore the return on enzymatic investment, must be sufficient to maintain these organisms.
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Affiliation(s)
- Greta Giljan
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Sarah Brown
- Environment, Ecology, and Energy Program, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
| | - C Chad Lloyd
- Department of Earth, Marine, and Environmental Sciences, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
| | - Sherif Ghobrial
- Department of Earth, Marine, and Environmental Sciences, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Carol Arnosti
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany.
- Department of Earth, Marine, and Environmental Sciences, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA.
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17
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Reintjes G, Klassen L, Abbott DW. Visualization of Carbohydrate Uptake Using Fluorescent Polysaccharides. Methods Mol Biol 2023; 2657:241-249. [PMID: 37149536 DOI: 10.1007/978-1-0716-3151-5_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Fluorescently labeled polysaccharides enable the visualization of carbohydrate-bacterial interactions and the quantification of carbohydrate hydrolysis rates in cultures and complex communities. Here, we present the method of generating polysaccharides conjugated to the fluorescent molecule, fluoresceinamine. Further, we describe the protocol of incubating these probes in bacterial cultures and complex environmental microbial communities, visualizing bacterial-probe interactions using fluorescence microscopy, and quantifying these interactions using flow cytometry. Finally, we present a novel approach for the in situ metabolic phenotyping of bacterial cells using fluorescently activated cell sorting coupled with omics-based analysis.
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Affiliation(s)
- Greta Reintjes
- Max Planck Institute for Marine Microbiology, Department of Molecular Ecology, Bremen, Germany.
| | - Leeann Klassen
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB, Canada
| | - D Wade Abbott
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB, Canada
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18
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Smułek W, Kaczorek E. Factors Influencing the Bioavailability of Organic Molecules to Bacterial Cells-A Mini-Review. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27196579. [PMID: 36235114 PMCID: PMC9570905 DOI: 10.3390/molecules27196579] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/29/2022] [Accepted: 10/01/2022] [Indexed: 11/26/2022]
Abstract
The bioavailability of organic compounds to bacterial cells is crucial for their vital activities. This includes both compounds that are desirable to the cells (e.g., sources of energy, carbon, nitrogen, and other nutrients) and undesirable compounds that are toxic to the cells. For this reason, bioavailability is an issue of great importance in many areas of human activity that are related to bacteria, e.g., biotechnological production, bioremediation of organic pollutants, and the use of antibiotics. This article proposes a classification of factors determining bioavailability, dividing them into factors at the physicochemical level (i.e., those related to the solubility of a chemical compound and its transport in aqueous solution) and factors at the microbiological level (i.e., those related to adsorption on the cell surface and those related to transport into the cell). Awareness of the importance of and the mechanisms governing each of the factors described allows their use to change bioavailability in the desired direction.
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19
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Urvoy M, Gourmelon M, Serghine J, Rabiller E, L'Helguen S, Labry C. Free-living and particle-attached bacterial community composition, assembly processes and determinants across spatiotemporal scales in a macrotidal temperate estuary. Sci Rep 2022; 12:13897. [PMID: 35974094 PMCID: PMC9381549 DOI: 10.1038/s41598-022-18274-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 08/08/2022] [Indexed: 11/14/2022] Open
Abstract
Bacteria play an important role in biogeochemical cycles as they transform and remineralize organic matter. Particles are notable hotspots of activity, hosting particle-attached (PA) communities that can differ largely from their free-living (FL) counterparts. However, long-standing questions remain concerning bacterial community assembly processes and driving factors. This study investigated the FL and PA community compositions and determinants within the Aulne estuary and the Bay of Brest coastal waters (France). Our results revealed that the FL and PA community compositions greatly varied with salinity and season, explaining a larger part of the variance than the sampling fraction. Both the FL and PA communities were driven by deterministic assembly processes and impacted by similar factors. The FL-PA dissimilarity varied across space and time. It decreased in the estuarine stations compared to the freshwater and marine ends, and in summer. Interestingly, a significant proportion of the FL and PA communities' β-diversity and dissimilarity was explained by cohesion, measuring the degree of taxa co-occurrence. This suggested the importance of co-occurrence patterns in shaping the FL and PA community compositions. Our results shed light on the factors influencing estuarine bacterial communities and provide a first step toward understanding their biogeochemical impacts.
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Affiliation(s)
- Marion Urvoy
- Ifremer, DYNECO, 29280, Plouzané, France. .,CNRS, IRD, Ifremer, UMR 6539, Laboratoire des Sciences de l'Environnement Marin (LEMAR), Université de Bretagne Occidentale, 29280, Plouzané, France.
| | | | | | | | - Stéphane L'Helguen
- CNRS, IRD, Ifremer, UMR 6539, Laboratoire des Sciences de l'Environnement Marin (LEMAR), Université de Bretagne Occidentale, 29280, Plouzané, France
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20
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Manna V, Zoccarato L, Banchi E, Arnosti C, Grossart H, Celussi M. Linking lifestyle and foraging strategies of marine bacteria: selfish behaviour of particle-attached bacteria in the northern Adriatic Sea. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:549-558. [PMID: 35362215 PMCID: PMC9546125 DOI: 10.1111/1758-2229.13059] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 03/13/2022] [Accepted: 03/13/2022] [Indexed: 06/14/2023]
Abstract
Microbe-mediated enzymatic hydrolysis of organic matter entails the production of hydrolysate, the recovery of which may be more or less efficient. The selfish uptake mechanism, recently discovered, allows microbes to hydrolyze polysaccharides and take up large oligomers, which are then degraded in the periplasmic space. By minimizing the hydrolysate loss, selfish behaviour may be profitable for free-living cells dwelling in a patchy substrate landscape. However, selfish uptake seems to be tailored to algal-derived polysaccharides, abundant in organic particles, suggesting that particle-attached microbes may use this strategy. We tracked selfish polysaccharides uptake in surface microbial communities of the northeastern Mediterranean Sea, linking the occurrence of this processing mode with microbial lifestyle. Additionally, we set up fluorescently labelled polysaccharides incubations supplying phytodetritus to investigate a 'pioneer' scenario for particle-attached microbes. Under both conditions, selfish behaviour was almost exclusively carried out by particle-attached microbes, suggesting that this mechanism may represent an advantage in the race for particle exploitation. Our findings shed light on the selfish potential of particle-attached microbes, suggesting multifaceted foraging strategies exerted by particle colonizers.
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Affiliation(s)
- Vincenzo Manna
- National Institute of Oceanography and Applied Geophysics – OGSDepartment of OceanographyTriesteItaly
| | - Luca Zoccarato
- Leibniz Institute for Freshwater Ecology and Inland Fisheries (IGB)Department of Experimental LimnologyZur alten Fischerhuette 2, D‐16775 StechlinGermany
| | - Elisa Banchi
- National Institute of Oceanography and Applied Geophysics – OGSDepartment of OceanographyTriesteItaly
| | - Carol Arnosti
- University of North Carolina – Chapel HillDepartment of Earth, Marine, and Environmental SciencesChapel HillNC27599USA
| | - Hans‐Peter Grossart
- Leibniz Institute for Freshwater Ecology and Inland Fisheries (IGB)Department of Experimental LimnologyZur alten Fischerhuette 2, D‐16775 StechlinGermany
- Potsdam UniversityInstitute for Biochemistry and BiologyMaulbeeralle 2, D‐14469 PotsdamGermany
| | - Mauro Celussi
- National Institute of Oceanography and Applied Geophysics – OGSDepartment of OceanographyTriesteItaly
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21
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Consuming fresh macroalgae induces specific catabolic pathways, stress reactions and Type IX secretion in marine flavobacterial pioneer degraders. THE ISME JOURNAL 2022; 16:2027-2039. [PMID: 35589967 PMCID: PMC9296495 DOI: 10.1038/s41396-022-01251-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 04/28/2022] [Accepted: 05/09/2022] [Indexed: 12/20/2022]
Abstract
Macroalgae represent huge amounts of biomass worldwide, largely recycled by marine heterotrophic bacteria. We investigated the strategies of bacteria within the flavobacterial genus Zobellia to initiate the degradation of whole algal tissues, which has received little attention compared to the degradation of isolated polysaccharides. Zobellia galactanivorans DsijT has the capacity to use fresh brown macroalgae as a sole carbon source and extensively degrades algal tissues via the secretion of extracellular enzymes, even in the absence of physical contact with the algae. Co-cultures experiments with the non-degrading strain Tenacibaculum aestuarii SMK-4T showed that Z. galactanivorans can act as a pioneer that initiates algal breakdown and shares public goods with other bacteria. A comparison of eight Zobellia strains, and strong transcriptomic shifts in Z. galactanivorans cells using fresh macroalgae vs. isolated polysaccharides, revealed potential overlooked traits of pioneer bacteria. Besides brown algal polysaccharide degradation, they notably include oxidative stress resistance proteins, type IX secretion system proteins and novel uncharacterized polysaccharide utilization loci. Overall, this work highlights the relevance of studying fresh macroalga degradation to fully understand the metabolic and ecological strategies of pioneer microbial degraders, key players in macroalgal biomass remineralization.
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22
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Baudrexl M, Fida T, Berk B, Schwarz WH, Zverlov VV, Groll M, Liebl W. Biochemical and Structural Characterization of Thermostable GH159 Glycoside Hydrolases Exhibiting α-L-Arabinofuranosidase Activity. Front Mol Biosci 2022; 9:907439. [PMID: 35847984 PMCID: PMC9278983 DOI: 10.3389/fmolb.2022.907439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Functional, biochemical, and preliminary structural properties are reported for three glycoside hydrolases of the recently described glycoside hydrolase (GH) family 159. The genes were cloned from the genomic sequences of different Caldicellulosiruptor strains. This study extends the spectrum of functions of GH159 enzymes. The only activity previously reported for GH159 was hydrolytic activity on β-galactofuranosides. Activity screening using a set of para-nitrophenyl (pNP) glycosides suggested additional arabinosidase activity on substrates with arabinosyl residues, which has not been previously reported for members of GH159. Even though the thermophilic enzymes investigated—Cs_Gaf159A, Ch_Gaf159A, and Ck_Gaf159A—cleaved pNP-α-l-arabinofuranoside, they were only weakly active on arabinogalactan, and they did not cleave arabinose from arabinan, arabinoxylan, or gum arabic. However, the enzymes were able to hydrolyze the α-1,3-linkage in different arabinoxylan-derived oligosaccharides (AXOS) with arabinosylated xylose at the non-reducing end (A3X, A2,3XX), suggesting their role in the intracellular hydrolysis of oligosaccharides. Crystallization and structural analysis of the apo form of one of the Caldicellulosiruptor enzymes, Ch_Gaf159A, enabled the elucidation of the first 3D structure of a GH159 member. This work revealed a five-bladed β-propeller structure for GH159 enzymes. The 3D structure and its substrate-binding pocket also provides an explanation at the molecular level for the observed exo-activity of the enzyme. Furthermore, the structural data enabled the prediction of the catalytic amino acids. This was supported by the complete inactivation by mutation of residues D19, D142, and E190 of Ch_Gaf159A.
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Affiliation(s)
- Melanie Baudrexl
- Chair of Microbiology, Technical University of Munich, Freising, Germany
| | - Tarik Fida
- Chair of Microbiology, Technical University of Munich, Freising, Germany
| | - Berkay Berk
- Chair of Microbiology, Technical University of Munich, Freising, Germany
| | | | - Vladimir V. Zverlov
- Chair of Microbiology, Technical University of Munich, Freising, Germany
- Institute of Molecular Genetics, Russian Academy of Science, Moscow, Russia
| | - Michael Groll
- Chair of Biochemistry, Center for Protein Assemblies, Technical University of Munich, Garching, Germany
| | - Wolfgang Liebl
- Chair of Microbiology, Technical University of Munich, Freising, Germany
- *Correspondence: Wolfgang Liebl,
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23
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Technical pipeline for screening microbial communities as a function of substrate specificity through fluorescent labelling. Commun Biol 2022; 5:444. [PMID: 35545700 PMCID: PMC9095699 DOI: 10.1038/s42003-022-03383-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 04/20/2022] [Indexed: 12/16/2022] Open
Abstract
The study of specific glycan uptake and metabolism is an effective tool in aiding with the continued unravelling of the complexities in the human gut microbiome. To this aim fluorescent labelling of glycans may provide a powerful route towards this target. Here, we successfully used the fluorescent label 2-aminobenzamide (2-AB) to monitor and study microbial degradation of labelled glycans. Both single strain and co-cultured fermentations of microbes from the common human-gut derived Bacteroides genus, are able to grow when supplemented with 2-AB labelled glycans of different monosaccharide composition, degrees of acetylation and polymerization. Utilizing a multifaceted approach that combines chromatography, mass spectrometry, microscopy and flow cytometry techniques, it is possible to better understand the metabolism of labelled glycans in both supernatants and at a single cell level. We envisage this combination of complementary techniques will help further the understanding of substrate specificity and the role it plays within microbial communities. A reductive amination-based fluorophore labelling of complex wood-derived glycans provides a proof-of-principle multi-modal platform for monitoring glycan uptake by bacteria.
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24
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Hettle AG, Vickers CJ, Boraston AB. Sulfatases: Critical Enzymes for Algal Polysaccharide Processing. FRONTIERS IN PLANT SCIENCE 2022; 13:837636. [PMID: 35574087 PMCID: PMC9096561 DOI: 10.3389/fpls.2022.837636] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 04/04/2022] [Indexed: 06/15/2023]
Abstract
Microbial sulfatases are important biocatalysts in the marine environment where they play a key role in the catabolic biotransformation of abundant sulphated algal polysaccharides. The sulphate esters decorating algal polysaccharides, such as carrageenan, fucoidan and ulvan, can constitute up to 40% of the biopolymer dry weight. The use of this plentiful carbon and energy source by heterotrophic microbes is enabled in part by the sulfatases encoded in their genomes. Sulfatase catalysed hydrolytic removal of sulphate esters is a key reaction at various stages of the enzymatic cascade that depolymerises sulphated polysaccharides into monosaccharides that can enter energy yielding metabolic pathways. As the critical roles of sulfatases in the metabolism of sulphated polysaccharides from marine algae is increasingly revealed, the structural and functional analysis of these enzymes becomes an important component of understanding these metabolic pathways. The S1 family of formylglycine-dependent sulfatases is the largest and most functionally diverse sulfatase family that is frequently active on polysaccharides. Here, we review this important sulfatase family with emphasis on recent developments in studying the structural and functional relationship between sulfatases and their sulphated algal polysaccharide substrates. This analysis utilises the recently proposed active site nomenclature for sulfatases. We will highlight the key role of sulfatases, not only in marine carbon cycling, but also as potential biocatalysts for the production of a variety of novel tailor made sulphated oligomers, which are useful products in, for example, pharmaceutical or cosmetic applications.
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Affiliation(s)
- Andrew G. Hettle
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Chelsea J. Vickers
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Alisdair B. Boraston
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
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25
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Abstract
Here we review the application of molecular biological approaches to mineral precipitation in modern marine microbialites. The review focuses on the nearly two decades of nucleotide sequencing studies of the microbialites of Shark Bay, Australia; and The Bahamas. Molecular methods have successfully characterized the overall community composition of mats, pinpointed microbes involved in key metabolisms, and revealed patterns in the distributions of microbial groups and functional genes. Molecular tools have become widely accessible, and we can now aim to establish firmer links between microbes and mineralization. Two promising future directions include “zooming in” to assess the roles of specific organisms, microbial groups, and surfaces in carbonate biomineralization and “zooming out” to consider broader spans of space and time. A middle ground between the two can include model systems that contain representatives of important microbial groups, processes, and metabolisms in mats and simplify hypothesis testing. These directions will benefit from expanding reference datasets of marine microbes and enzymes and enrichments of representative microbes from mats. Such applications of molecular tools should improve our ability to interpret ancient and modern microbialites and increase the utility of these rocks as long-term recorders of microbial processes and environmental chemistry.
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26
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Giljan G, Arnosti C, Kirstein IV, Amann R, Fuchs BM. Strong seasonal differences of bacterial polysaccharide utilization in the North Seas over an annual cycle. Environ Microbiol 2022; 24:2333-2347. [PMID: 35384240 DOI: 10.1111/1462-2920.15997] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 03/26/2022] [Accepted: 04/02/2022] [Indexed: 11/29/2022]
Abstract
Marine heterotrophic bacteria contribute considerably to global carbon cycling, in part by utilizing phytoplankton-derived polysaccharides. The patterns and rates of two different polysaccharide utilization modes - extracellular hydrolysis and selfish uptake - have previously been found to change during spring phytoplankton bloom events. Here we investigated seasonal changes in bacterial utilization of three polysaccharides, laminarin, xylan, and chondroitin sulfate. Strong seasonal differences were apparent in mode and speed of polysaccharide utilization, as well as in bacterial community compositions. Compared to the winter month of February, during the spring bloom in May, polysaccharide utilization was detected earlier in the incubations and a higher portion of all bacteria took up laminarin selfishly. Highest polysaccharide utilization was measured in June and September, mediated by bacterial communities that were significantly different from spring assemblages. Extensive selfish laminarin uptake, for example, was detectible within a few hours in June, while extracellular hydrolysis of chondroitin was dominant in September. In addition to the well-known Bacteroidota and Gammaproteobacteria clades, the numerically minor verrucomicrobial clade Pedosphaeraceae could be identified as a rapid laminarin utilizer. In summary, polysaccharide utilization proved highly variable over the seasons, both in mode and speed, and also by the bacterial clades involved. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Greta Giljan
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Carol Arnosti
- Department of Marine Sciences, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
| | - Inga V Kirstein
- Alfred-Wegner-Institute Helmholtz-Center for Polar and Marine Research, Biological Station Helgoland, Helgoland, Germany
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Bernhard M Fuchs
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
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27
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Liu S, Longnecker K, Kujawinski EB, Vergin K, Bolaños LM, Giovannoni SJ, Parsons R, Opalk K, Halewood E, Hansell DA, Johnson R, Curry R, Carlson CA. Linkages Among Dissolved Organic Matter Export, Dissolved Metabolites, and Associated Microbial Community Structure Response in the Northwestern Sargasso Sea on a Seasonal Scale. Front Microbiol 2022; 13:833252. [PMID: 35350629 PMCID: PMC8957919 DOI: 10.3389/fmicb.2022.833252] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/31/2022] [Indexed: 01/04/2023] Open
Abstract
Deep convective mixing of dissolved and suspended organic matter from the surface to depth can represent an important export pathway of the biological carbon pump. The seasonally oligotrophic Sargasso Sea experiences annual winter convective mixing to as deep as 300 m, providing a unique model system to examine dissolved organic matter (DOM) export and its subsequent compositional transformation by microbial oxidation. We analyzed biogeochemical and microbial parameters collected from the northwestern Sargasso Sea, including bulk dissolved organic carbon (DOC), total dissolved amino acids (TDAA), dissolved metabolites, bacterial abundance and production, and bacterial community structure, to assess the fate and compositional transformation of DOM by microbes on a seasonal time-scale in 2016–2017. DOM dynamics at the Bermuda Atlantic Time-series Study site followed a general annual trend of DOC accumulation in the surface during stratified periods followed by downward flux during winter convective mixing. Changes in the amino acid concentrations and compositions provide useful indices of diagenetic alteration of DOM. TDAA concentrations and degradation indices increased in the mesopelagic zone during mixing, indicating the export of a relatively less diagenetically altered (i.e., more labile) DOM. During periods of deep mixing, a unique subset of dissolved metabolites, such as amino acids, vitamins, and benzoic acids, was produced or lost. DOM export and compositional change were accompanied by mesopelagic bacterial growth and response of specific bacterial lineages in the SAR11, SAR202, and SAR86 clades, Acidimicrobiales, and Flavobacteria, during and shortly following deep mixing. Complementary DOM biogeochemistry and microbial measurements revealed seasonal changes in DOM composition and diagenetic state, highlighting microbial alteration of the quantity and quality of DOM in the ocean.
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Affiliation(s)
- Shuting Liu
- Department of Ecology, Evolution and Marine Biology, Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Krista Longnecker
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Elizabeth B Kujawinski
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Kevin Vergin
- Microbial DNA Analytics, Phoenix, OR, United States
| | - Luis M Bolaños
- School of Biosciences, University of Exeter, Exeter, United Kingdom.,Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Stephen J Giovannoni
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Rachel Parsons
- Bermuda Institute of Ocean Sciences, Saint George's, Bermuda
| | - Keri Opalk
- Department of Ecology, Evolution and Marine Biology, Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Elisa Halewood
- Department of Ecology, Evolution and Marine Biology, Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Dennis A Hansell
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States
| | - Rod Johnson
- Bermuda Institute of Ocean Sciences, Saint George's, Bermuda
| | - Ruth Curry
- Bermuda Institute of Ocean Sciences, Saint George's, Bermuda
| | - Craig A Carlson
- Department of Ecology, Evolution and Marine Biology, Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
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28
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Li G, Guo R, Wu S, Cheng S, Li J, Liu Z, Xie W, Sun X, Zhang Q, Li Z, Xu J, Wu J, Wei Z, Hu F. Characterization of Agarolytic Pathway in a Terrestrial Bacterium Cohnella sp. LGH. Front Microbiol 2022; 13:828687. [PMID: 35432256 PMCID: PMC9008576 DOI: 10.3389/fmicb.2022.828687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 02/17/2022] [Indexed: 11/13/2022] Open
Abstract
Previously, we have reported that an endo-type β-agarase AgaW was responsible for the hydrolysis of agarose into the major product neoagarotetraose in a terrestrial agar-degrading bacterium Cohnella sp. LGH. Here, we identify and characterize the following depolymerization pathway in strain LGH through the genomic and enzymatic analysis. In the pathway, neoagarotetraose was depolymerized by a novel α-neoagarooligosaccharide (NAOS) hydrolase CL5012 into 3,6-anhydro-α-L-galactose (L-AHG) and agarotriose; Agarotriose was further depolymerized by a novel agarolytic β-galactosidase CL4994 into D-galactose and neoagarobiose; Neoagarobiose was finally depolymerized by CL5012 into L-AHG and D-galactose. Although α-agarase has not been identified in strain LGH, the combined action of CL5012 and CL4994 unexpectedly plays a critical role in the depolymerization of agarotetraose, one theoretical product of α-agarase hydrolysis of agarose. In this pathway, agarotetraose was depolymerized by CL4994 into D-galactose and neoagarotriose; Neoagarotriose was then depolymerized by CL5012 into L-AHG and agarobiose. Furthermore, another novel endo-type β-agarase CL5055 was identified as an isozyme of AgaW with different pH preference in the hydrolysis of agarose into α-NAOSs. Strain LGH seemed to lack a common exo-type β-agarase responsible for the direct depolymerization of agarose or neoagarooligosaccharide into neoagarobiose. These results highlight the diversity of agarolytic manner in bacteria and provide a novel insight on the diversity of agarolytic pathways.
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Affiliation(s)
- Gen Li
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Plant Immunity, Nanjing, China
| | - Rui Guo
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Shuqi Wu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Si Cheng
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Jiaqi Li
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Zhenzhen Liu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Wangliang Xie
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Xiaolin Sun
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Qiuyi Zhang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Zihan Li
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - JiaZheng Xu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Jun Wu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Jun Wu,
| | - Zhong Wei
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Plant Immunity, Nanjing, China
| | - Feng Hu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
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29
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Li Z, Huang X, Guo Y, Zhang C, Yang L, Du X, Ni H, Wang X, Zhu Y. Toward Understanding the Alginate Catabolism in Microbulbifer sp. ALW1 by Proteomics Profiling. Front Bioeng Biotechnol 2022; 10:829428. [PMID: 35372316 PMCID: PMC8967155 DOI: 10.3389/fbioe.2022.829428] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 01/31/2022] [Indexed: 11/18/2022] Open
Abstract
The bacterial strain of Microbulbifer sp. ALW1 has demonstrated visible ability of degrading the cell wall of Laminaria japonica, and biochemical characterization has been performed on some individual enzymes to elucidate its genetic basis. However, it still remains elusive how strain ALW1 successfully breaks down the major cell wall component alginate polysaccharide and colonizes on its marine host. In this study, a mass spectrometry-based quantitative analysis of the extracellular and intracellular proteomes was introduced to elucidate the alginate degradation pathway in ALW1 strain. Mass spectrometry and biochemical assays indicated that strain ALW1 could effectively degrade alginate polysaccharide into disaccharides and trisaccharides within 12 h. Proteome analysis identified 156 and 1,047 proteins exclusively localized in extracellular and intracellular compartments, respectively, with 1,086 protein identities of dual localization. Functional annotation of the identified proteins suggested the involvement of diverse catalytic enzymes and non-catalytic molecules for the cleavage and metabolism of alginate polysaccharide. A simplified pathway was constructed to demonstrate the extracellular digestion, active transport, and intracellular conversion of alginate polysaccharide and its fragmented oligosaccharides, casting a picture of genetic loci controlling alginate catabolism by ALW1 strain. This study aims to provide a guide for utilization and genetic manipulation of the bacterial strain ALW1 for efficient alginate oligosaccharides production by fermentation.
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Affiliation(s)
- Zhipeng Li
- College of Ocean Food and Biology Engineering, Jimei University, Xiame, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering Technology, Xiamen, China
- Research Center of Food Biotechnology of Xiamen City, Xiamen, China
| | - Xiaoyi Huang
- College of Ocean Food and Biology Engineering, Jimei University, Xiame, China
| | - Yuxi Guo
- College of Ocean Food and Biology Engineering, Jimei University, Xiame, China
| | - Chenghao Zhang
- College of Ocean Food and Biology Engineering, Jimei University, Xiame, China
| | - Liang Yang
- College of Ocean Food and Biology Engineering, Jimei University, Xiame, China
| | - Xiping Du
- College of Ocean Food and Biology Engineering, Jimei University, Xiame, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering Technology, Xiamen, China
- Research Center of Food Biotechnology of Xiamen City, Xiamen, China
| | - Hui Ni
- College of Ocean Food and Biology Engineering, Jimei University, Xiame, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering Technology, Xiamen, China
- Research Center of Food Biotechnology of Xiamen City, Xiamen, China
| | - Xuchu Wang
- Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Ministry of Education, Hainan Normal University, Haikou, China
- *Correspondence: Xuchu Wang, ; Yanbing Zhu,
| | - Yanbing Zhu
- College of Ocean Food and Biology Engineering, Jimei University, Xiame, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering Technology, Xiamen, China
- Research Center of Food Biotechnology of Xiamen City, Xiamen, China
- *Correspondence: Xuchu Wang, ; Yanbing Zhu,
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30
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Metabolism of a hybrid algal galactan by members of the human gut microbiome. Nat Chem Biol 2022; 18:501-510. [PMID: 35289327 DOI: 10.1038/s41589-022-00983-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 01/27/2022] [Indexed: 12/12/2022]
Abstract
Native porphyran is a hybrid of porphryan and agarose. As a common element of edible seaweed, this algal galactan is a frequent component of the human diet. Bacterial members of the human gut microbiota have acquired polysaccharide utilization loci (PULs) that enable the metabolism of porphyran or agarose. However, the molecular mechanisms that underlie the deconstruction and use of native porphyran remains incompletely defined. Here, we have studied two human gut bacteria, porphyranolytic Bacteroides plebeius and agarolytic Bacteroides uniformis, that target native porphyran. This reveals an exo-based cycle of porphyran depolymerization that incorporates a keystone sulfatase. In both PULs this cycle also works together with a PUL-encoded agarose depolymerizing machinery to synergistically reduce native porphyran to monosaccharides. This provides a framework for understanding the deconstruction of a hybrid algal galactan, and insight into the competitive and/or syntrophic relationship of gut microbiota members that target rare nutrients.
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31
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Leng H, Zhao W, Xiao X. Cultivation and metabolic insights of an uncultured clade, Bacteroidetes VC2.1 Bac22 (Candidatus Sulfidibacteriales ord. nov.), from deep-sea hydrothermal vents. Environ Microbiol 2022; 24:2484-2501. [PMID: 35165999 DOI: 10.1111/1462-2920.15931] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 01/05/2022] [Accepted: 01/31/2022] [Indexed: 01/28/2023]
Abstract
Bacteroidetes VC2.1 Bac22 (referred to as VC2.1) is an uncultured clade that is widely distributed in marine ecosystems, including hydrothermal vents, oxygen-minimum zones and other anoxic, sulfide-rich environments. However, the lack of cultured representatives and sequenced genomes of VC2.1 limit our understanding of its physiology, metabolism and ecological functions. Here, we obtained a stable co-culture of VC2.1 with autotrophic microbes by establishing an autotrophy-based enrichment from a hydrothermal vent chimney sample. We recovered a high-quality metagenome-assembled genome (MAG) that belonged to VC2.1. Phylogenetic analyses of both 16S rRNA genes and conserved protein markers suggested that VC2.1 belongs to a novel order in the Bacteroidetes phylum, which we named Candidatus Sulfidibacteriales. The metabolic reconstruction of this MAG indicated that VC2.1 could utilize polysaccharides, protein polymers and fatty acids as well as flexibly obtain energy via NO/N2 O reduction and polysulfide reduction. Our results reveal the ecological potential of this novel Bacteroidetes for complex organic carbons mineralization and N2 O sinks in deep-sea hydrothermal vents. Furthermore, guided by the genome information, we designed a new culture medium in which starch, ammonium and polysulfide were used as the carbon source, nitrogen source and electron acceptor respectively, to isolate VC2.1 successfully.
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Affiliation(s)
- Hao Leng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,International Center for Deep Life Investigation (IC-DLI), Shanghai Jiao Tong University, Shanghai, China
| | - Weishu Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,International Center for Deep Life Investigation (IC-DLI), Shanghai Jiao Tong University, Shanghai, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,International Center for Deep Life Investigation (IC-DLI), Shanghai Jiao Tong University, Shanghai, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, China
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32
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Bartlau N, Wichels A, Krohne G, Adriaenssens EM, Heins A, Fuchs BM, Amann R, Moraru C. Highly diverse flavobacterial phages isolated from North Sea spring blooms. THE ISME JOURNAL 2022; 16:555-568. [PMID: 34475519 PMCID: PMC8776804 DOI: 10.1038/s41396-021-01097-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 08/17/2021] [Indexed: 11/24/2022]
Abstract
It is generally recognized that phages are a mortality factor for their bacterial hosts. This could be particularly true in spring phytoplankton blooms, which are known to be closely followed by a highly specialized bacterial community. We hypothesized that phages modulate these dense heterotrophic bacteria successions following phytoplankton blooms. In this study, we focused on Flavobacteriia, because they are main responders during these blooms and have an important role in the degradation of polysaccharides. A cultivation-based approach was used, obtaining 44 lytic flavobacterial phages (flavophages), representing twelve new species from two viral realms. Taxonomic analysis allowed us to delineate ten new phage genera and ten new families, from which nine and four, respectively, had no previously cultivated representatives. Genomic analysis predicted various life styles and genomic replication strategies. A likely eukaryote-associated host habitat was reflected in the gene content of some of the flavophages. Detection in cellular metagenomes and by direct-plating showed that part of these phages were actively replicating in the environment during the 2018 spring bloom. Furthermore, CRISPR/Cas spacers and re-isolation during two consecutive years suggested that, at least part of the new flavophages are stable components of the microbial community in the North Sea. Together, our results indicate that these diverse flavophages have the potential to modulate their respective host populations.
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Affiliation(s)
- Nina Bartlau
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Antje Wichels
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Biologische Anstalt Helgoland, Heligoland, Germany
| | - Georg Krohne
- Imaging Core Facility, Biocenter, University of Würzburg, Würzburg, Germany
| | | | - Anneke Heins
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
| | - Cristina Moraru
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany.
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Kieft B, Li Z, Bryson S, Hettich RL, Pan C, Mayali X, Mueller RS. Phytoplankton exudates and lysates support distinct microbial consortia with specialized metabolic and ecophysiological traits. Proc Natl Acad Sci U S A 2021; 118:e2101178118. [PMID: 34620710 PMCID: PMC8521717 DOI: 10.1073/pnas.2101178118] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2021] [Indexed: 11/18/2022] Open
Abstract
Blooms of marine phytoplankton fix complex pools of dissolved organic matter (DOM) that are thought to be partitioned among hundreds of heterotrophic microbes at the base of the food web. While the relationship between microbial consumers and phytoplankton DOM is a key component of marine carbon cycling, microbial loop metabolism is largely understood from model organisms and substrates. Here, we took an untargeted approach to measure and analyze partitioning of four distinct phytoplankton-derived DOM pools among heterotrophic populations in a natural microbial community using a combination of ecogenomics, stable isotope probing (SIP), and proteomics. Each 13C-labeled exudate or lysate from a diatom or a picocyanobacterium was preferentially assimilated by different heterotrophic taxa with specialized metabolic and physiological adaptations. Bacteroidetes populations, with their unique high-molecular-weight transporters, were superior competitors for DOM derived from diatom cell lysis, rapidly increasing growth rates and ribosomal protein expression to produce new relatively high C:N biomass. Proteobacteria responses varied, with relatively low levels of assimilation by Gammaproteobacteria populations, while copiotrophic Alphaproteobacteria such as the Roseobacter clade, with their diverse array of ABC- and TRAP-type transporters to scavenge monomers and nitrogen-rich metabolites, accounted for nearly all cyanobacteria exudate assimilation and produced new relatively low C:N biomass. Carbon assimilation rates calculated from SIP data show that exudate and lysate from two common marine phytoplankton are being used by taxonomically distinct sets of heterotrophic populations with unique metabolic adaptations, providing a deeper mechanistic understanding of consumer succession and carbon use during marine bloom events.
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Affiliation(s)
- Brandon Kieft
- Department of Microbiology, Oregon State University, Corvallis, OR 97331;
| | - Zhou Li
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN 37996
| | - Samuel Bryson
- Department of Microbiology, Oregon State University, Corvallis, OR 97331
- Department of Civil & Environmental Engineering, The University of Washington, Seattle, WA 98195
| | - Robert L Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830
| | - Chongle Pan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN 37996
- Department of Microbiology and Plant Microbiology, University of Oklahoma, Norman, OK 73019
| | - Xavier Mayali
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
| | - Ryan S Mueller
- Department of Microbiology, Oregon State University, Corvallis, OR 97331;
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Sichert A, Cordero OX. Polysaccharide-Bacteria Interactions From the Lens of Evolutionary Ecology. Front Microbiol 2021; 12:705082. [PMID: 34690949 PMCID: PMC8531407 DOI: 10.3389/fmicb.2021.705082] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 09/09/2021] [Indexed: 11/29/2022] Open
Abstract
Microbes have the unique ability to break down the complex polysaccharides that make up the bulk of organic matter, initiating a cascade of events that leads to their recycling. Traditionally, the rate of organic matter degradation is perceived to be limited by the chemical and physical structure of polymers. Recent advances in microbial ecology, however, suggest that polysaccharide persistence can result from non-linear growth dynamics created by the coexistence of alternate degradation strategies, metabolic roles as well as by ecological interactions between microbes. This complex "landscape" of degradation strategies and interspecific interactions present in natural microbial communities appears to be far from evolutionarily stable, as frequent gene gain and loss reshape enzymatic repertoires and metabolic roles. In this perspective, we discuss six challenges at the heart of this problem, ranging from the evolution of genetic repertoires, phenotypic heterogeneity in clonal populations, the development of a trait-based ecology, and the impact of metabolic interactions and microbial cooperation on degradation rates. We aim to reframe some of the key questions in the study of polysaccharide-bacteria interactions in the context of eco-evolutionary dynamics, highlighting possible research directions that, if pursued, would advance our understanding of polysaccharide degraders at the interface between biochemistry, ecology and evolution.
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Schmidt JM, Royalty TM, Lloyd KG, Steen AD. Potential Activities and Long Lifetimes of Organic Carbon-Degrading Extracellular Enzymes in Deep Subsurface Sediments of the Baltic Sea. Front Microbiol 2021; 12:702015. [PMID: 34603228 PMCID: PMC8485070 DOI: 10.3389/fmicb.2021.702015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 08/12/2021] [Indexed: 11/17/2022] Open
Abstract
Heterotrophic microorganisms in marine sediments produce extracellular enzymes to hydrolyze organic macromolecules, so their products can be transported inside the cell and used for energy and growth. Therefore, extracellular enzymes may mediate the fate of organic carbon in sediments. The Baltic Sea Basin is a primarily depositional environment with high potential for organic matter preservation. The potential activities of multiple organic carbon-degrading enzymes were measured in samples obtained by the International Ocean Discovery Program Expedition 347 from the Little Belt Strait, Denmark, core M0059C. Potential maximum hydrolysis rates (Vmax) were measured at depths down to 77.9mbsf for the following enzymes: alkaline phosphatase, β-d-xylosidase, β-d-cellobiohydrolase, N-acetyl-β-d-glucosaminidase, β-glucosidase, α-glucosidase, leucyl aminopeptidase, arginyl aminopeptidase, prolyl aminopeptidase, gingipain, and clostripain. Extracellular peptidase activities were detectable at depths shallower than 54.95mbsf, and alkaline phosphatase activity was detectable throughout the core, albeit against a relatively high activity in autoclaved sediments. β-glucosidase activities were detected above 30mbsf; however, activities of other glycosyl hydrolases (β-xylosidase, β-cellobiohydrolase, N-acetyl-β-glucosaminidase, and α-glucosidase) were generally indistinguishable from zero at all depths. These extracellular enzymes appear to be extremely stable: Among all enzymes, a median of 51.3% of enzyme activity was retained after autoclaving for an hour. We show that enzyme turnover times scale with the inverse of community metabolic rates, such that enzyme lifetimes in subsurface sediments, in which metabolic rates are very slow, are likely to be extraordinarily long. A back-of-the-envelope calculation suggests enzyme lifetimes are, at minimum, on the order of 230days, and may be substantially longer. These results lend empirical support to the hypothesis that a population of subsurface microbes persist by using extracellular enzymes to slowly metabolize old, highly degraded organic carbon.
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Affiliation(s)
- Jenna M Schmidt
- Department of Earth and Planetary Sciences, College of Arts and Sciences, The University of Tennessee, Knoxville, TN, United States
| | - Taylor M Royalty
- Department of Microbiology, University of Tennessee - Knoxville, Knoxville, TN, United States
| | - Karen G Lloyd
- Department of Microbiology, University of Tennessee - Knoxville, Knoxville, TN, United States
| | - Andrew D Steen
- Department of Microbiology, University of Tennessee - Knoxville, Knoxville, TN, United States.,Department of Earth and Planetary Sciences, College of Arts and Sciences, The University of Tennessee, Knoxville, TN, United States
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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.
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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
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McKee LS, La Rosa SL, Westereng B, Eijsink VG, Pope PB, Larsbrink J. Polysaccharide degradation by the Bacteroidetes: mechanisms and nomenclature. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:559-581. [PMID: 34036727 DOI: 10.1111/1758-2229.12980] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 05/22/2021] [Accepted: 05/23/2021] [Indexed: 06/12/2023]
Abstract
The Bacteroidetes phylum is renowned for its ability to degrade a wide range of complex carbohydrates, a trait that has enabled its dominance in many diverse environments. The best studied species inhabit the human gut microbiome and use polysaccharide utilization loci (PULs), discrete genetic structures that encode proteins involved in the sensing, binding, deconstruction, and import of target glycans. In many environmental species, polysaccharide degradation is tightly coupled to the phylum-exclusive type IX secretion system (T9SS), which is used for the secretion of certain enzymes and is linked to gliding motility. In addition, within specific species these two adaptive systems (PULs and T9SS) are intertwined, with PUL-encoded enzymes being secreted by the T9SS. Here, we discuss the most noteworthy PUL and non-PUL mechanisms that confer specific and rapid polysaccharide degradation capabilities to the Bacteroidetes in a range of environments. We also acknowledge that the literature showcasing examples of PULs is rapidly expanding and developing a set of assumptions that can be hard to track back to original findings. Therefore, we present a simple universal description of conserved PUL functions and how they are determined, while proposing a common nomenclature describing PULs and their components, to simplify discussion and understanding of PUL systems.
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Affiliation(s)
- Lauren S McKee
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, 106 91, Sweden
- Wallenberg Wood Science Center, Stockholm, 100 44, Sweden
| | | | - Bjørge Westereng
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Vincent G Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Phillip B Pope
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Johan Larsbrink
- Wallenberg Wood Science Center, Stockholm, 100 44, Sweden
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, 412 96, Sweden
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Alejandre-Colomo C, Francis B, Viver T, Harder J, Fuchs BM, Rossello-Mora R, Amann R. Cultivable Winogradskyella species are genomically distinct from the sympatric abundant candidate species. ISME COMMUNICATIONS 2021; 1:51. [PMID: 36747039 PMCID: PMC9723794 DOI: 10.1038/s43705-021-00052-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/16/2021] [Accepted: 08/17/2021] [Indexed: 02/08/2023]
Abstract
Winogradskyella is a genus within the phylum Bacteroidetes with a clear marine origin. Most members of this genus have been found associated with marine animals and algae, but also with inorganic surfaces such as sand. In this study, we analyzed genomes of eleven species recently isolated from surface seawater samples from the North Sea during a single spring algae bloom. Corresponding metagenomes yielded a single Candidatus species for this genus. All species in culture, with the exception of W. ursingii, affiliated with a Winogradskyella lineage characterized by large genomes (~4.3 ± 0.4 Mb), with high complexity in their carbohydrate and protein degradation genes. Specifically, the polysaccharide utilization loci (PULs) were diverse within each individual strain, indicating large substrate versatility. Although present in the North Sea, the abundances of these strains were at, or below, the detection limit of the metagenomes. In contrast, the single species, classified as Candidatus W. atlantica, to which all North Sea MAGs belonged, affiliated with a lineage in which the cultivated representatives showed small genomes of ~3.0-3.5 Mb, with the MAGs having ~2.3 Mb. In Ca. W. atlantica, genome streamlining has apparently resulted in the loss of biosynthesis pathways for several amino acids including arginine, methionine, leucine and valine, and the PUL loci were reduced to a single one for utilizing laminarin. This as-yet uncultivated species seems to capitalize on sporadically abundant substrates that are released by algae blooms, mainly laminarin. We also suggest that this streamlined genome might be responsible for the lack of growth on plates for this Candidatus species, in contrast to growth of the less abundant but coexisting members of the genus.
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Affiliation(s)
- Carlota Alejandre-Colomo
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Miquel Marques 21, 07190, Esporles, Spain
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany
| | - Ben Francis
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany
| | - Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Miquel Marques 21, 07190, Esporles, Spain
| | - Jens Harder
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany
| | - Bernhard M Fuchs
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Miquel Marques 21, 07190, Esporles, Spain.
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany.
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Francis B, Urich T, Mikolasch A, Teeling H, Amann R. North Sea spring bloom-associated Gammaproteobacteria fill diverse heterotrophic niches. ENVIRONMENTAL MICROBIOME 2021; 16:15. [PMID: 34404489 PMCID: PMC8371827 DOI: 10.1186/s40793-021-00385-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 08/10/2021] [Indexed: 05/22/2023]
Abstract
BACKGROUND The planktonic bacterial community associated with spring phytoplankton blooms in the North Sea is responsible for a large amount of carbon turnover in an environment characterised by high primary productivity. Individual clades belonging to the Gammaproteobacteria have shown similar population dynamics to Bacteroidetes species, and are thus assumed to fill competing ecological niches. Previous studies have generated large numbers of metagenome assembled genomes and metaproteomes from these environments, which can be readily mined to identify populations performing potentially important ecosystem functions. In this study we attempt to catalogue these spring bloom-associated Gammaproteobacteria, which have thus far attracted less attention than sympatric Alphaproteobacteria and Bacteroidetes. METHODS We annotated 120 non-redundant species-representative gammaproteobacterial metagenome assembled genomes from spring bloom sampling campaigns covering the four years 2010-2012 and 2016 using a combination of Prokka and PfamScan, with further confirmation via BLAST against NCBI-NR. We also matched these gene annotations to 20 previously published metaproteomes covering those sampling periods plus the spring of 2009. RESULTS Metagenome assembled genomes with clear capacity for polysaccharide degradation via dedicated clusters of carbohydrate active enzymes were among the most abundant during blooms. Many genomes lacked gene clusters with clearly identifiable predicted polysaccharide substrates, although abundantly expressed loci for the uptake of large molecules were identified in metaproteomes. While the larger biopolymers, which are the most abundant sources of reduced carbon following algal blooms, are likely the main energy source, some gammaproteobacterial clades were clearly specialised for smaller organic compounds. Their substrates range from amino acids, monosaccharides, and DMSP, to the less expected, such as terpenoids, and aromatics and biphenyls, as well as many 'unknowns'. In particular we uncover a much greater breadth of apparent methylotrophic capability than heretofore identified, present in several order level clades without cultivated representatives. CONCLUSIONS Large numbers of metagenome assembled genomes are today publicly available, containing a wealth of readily accessible information. Here we identified a variety of predicted metabolisms of interest, which include diverse potential heterotrophic niches of spring bloom-associated Gammaproteobacteria. Features such as those identified here could well be fertile ground for future experimental studies.
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Affiliation(s)
- Ben Francis
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Tim Urich
- Institute for Microbiology, University of Greifswald, Greifswald, Germany
| | - Annett Mikolasch
- Institute for Microbiology, University of Greifswald, Greifswald, Germany
| | - Hanno Teeling
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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Khomyakova MA, Merkel AY, Slobodkin AI. Perlabentimonas gracilis gen. nov., sp. nov., a gliding aerotolerant anaerobe of the order Bacteroidales, isolated from a terrestrial mud volcano. Syst Appl Microbiol 2021; 44:126245. [PMID: 34392063 DOI: 10.1016/j.syapm.2021.126245] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/22/2021] [Accepted: 07/29/2021] [Indexed: 11/15/2022]
Abstract
A novel anaerobic bacterium (strain M08_MBT) was isolated from a terrestrial mud volcano (Taman Peninsula, Russia). Gram-stain-negative cells were straight and slender rods with gliding motility, occasionally forming long filaments. The isolate was mesophilic, slightly halo- and alkaliphilic chemoorganoheterotroph, growing on carbohydrates (starch, dextrin, pectin, glucose, fructose, mannose, maltose, trehalose, lactose, sucrose) and proteinaceous compounds (peptone, tryptone, gelatin, casein and albumin). Strain M08_MBT tolerated 3% oxygen in the gas phase while catalase negative. The dominant cellular fatty acids of strain M08_MBT were C15:0, C15:1 and C13:0 acids. 16S rRNA gene sequence analysis revealed that strain M08_MBT belongs to the order Bacteroidales and only distantly related to other cultivated members of this order (85.12-90.01% 16S rRNA gene similarity). The genome of strain M08_MBT had a size of 4.37 Mb with a DNA G + C content of 43.5 mol% (WGS). The genes involved in gliding motility, proteolysis, central carbon metabolism, and oxygen tolerance were listed in genome annotation. Based on the phenotypic and genotypic characteristics, strain M08_MBT represents a novel species of a novel genus within family Tenuifilaceae, with proposed name Perlabentimonas gracilis gen. nov., sp. nov. The type strain is M08_ MBT (=DSM 110720 T = VKM B-3471 T). This is the first representative of Bacteroidales isolated in pure culture from a mud volcano.
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Affiliation(s)
- M A Khomyakova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave., 33, bld. 2, 119071 Moscow, Russia.
| | - A Y Merkel
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave., 33, bld. 2, 119071 Moscow, Russia
| | - A I Slobodkin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave., 33, bld. 2, 119071 Moscow, Russia
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Mechanisms involved in the active secretion of CTX-M-15 β-lactamase by pathogenic E. coli ST131. Antimicrob Agents Chemother 2021; 65:e0066321. [PMID: 34310213 DOI: 10.1128/aac.00663-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Infections caused by antimicrobial resistant bacterial pathogens are fast becoming an important global health issue. Strains of Escherichia coli are common causal agents of urinary tract infection and can carry multiple resistance genes. This includes the gene blaCTX-M-15 that encodes for an extended spectrum beta-lactamase (ESBL). While studying antimicrobial resistance (AMR) in the environment we isolated several strains of E. coli ST131 downstream of a waste water treatment plan (WWTP) in a local river. These isolates were surviving in the river sediment and characterisation proved that a multi-resistant phenotype was evident. Here, we show that E. coli strain 48 (river isolate ST131), provided a protective effect against a third-generation cephalosporin (cefotaxime) for a susceptible E. coli strain 33 (river isolate ST3576) through secretion of a functional ESBL into the growth medium. Furthermore, extracellular ESBL activity was stable for at least 24 h after secretion. Proteomic and molecular genetic analyses identified CTX-M-15 as the major secreted ESBL responsible for the observed protective effect. In contrast to previous studies, outer-membrane vesicles (OMVs) were not the route for CTX-M-15 secretion. Indeed, mutation of the Type I secretion system led to a significant reduction in the growth of the ESBL-producing strain as well as a significantly reduced ability to confer protective effect. We speculate that CTX-M-15 secretion, mediated through active secretion using molecular machinery provides a public goods service by facilitating the survival of otherwise susceptible bacteria in the presence of cefotaxime.
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Zhang L, Li X, Zhang X, Li Y, Wang L. Bacterial alginate metabolism: an important pathway for bioconversion of brown algae. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:158. [PMID: 34275475 PMCID: PMC8286568 DOI: 10.1186/s13068-021-02007-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/04/2021] [Indexed: 06/13/2023]
Abstract
Brown macroalgae have attracted great attention as an alternative feedstock for biorefining. Although direct conversion of ethanol from alginates (major components of brown macroalgae cell walls) is not amenable for industrial production, significant progress has been made not only on enzymes involved in alginate degradation, but also on metabolic pathways for biorefining at the laboratory level. In this article, we summarise recent advances on four aspects: alginate, alginate lyases, different alginate-degrading systems, and application of alginate lyases and associated pathways. This knowledge will likely inspire sustainable solutions for further application of both alginate lyases and their associated pathways.
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Affiliation(s)
- Lanzeng Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Xue Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Xiyue Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Yingjie Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
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Bäumgen M, Dutschei T, Bornscheuer UT. Marine Polysaccharides: Occurrence, Enzymatic Degradation and Utilization. Chembiochem 2021; 22:2247-2256. [PMID: 33890358 PMCID: PMC8360166 DOI: 10.1002/cbic.202100078] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/21/2021] [Indexed: 12/13/2022]
Abstract
Macroalgae species are fast growing and their polysaccharides are already used as food ingredient due to their properties as hydrocolloids or they have potential high value bioactivity. The degradation of these valuable polysaccharides to access the sugar components has remained mostly unexplored so far. One reason is the high structural complexity of algal polysaccharides, but also the need for suitable enzyme cocktails to obtain oligo- and monosaccharides. Among them, there are several rare sugars with high value. Recently, considerable progress was made in the discovery of highly specific carbohydrate-active enzymes able to decompose complex marine carbohydrates such as carrageenan, laminarin, agar, porphyran and ulvan. This minireview summarizes these achievements and highlights potential applications of the now accessible abundant renewable resource of marine polysaccharides.
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Affiliation(s)
- Marcus Bäumgen
- Department of Biotechnology & Enzyme CatalysisInstitute of Biochemistry, University of Greifswald17487GreifswaldGermany
| | - Theresa Dutschei
- Department of Biotechnology & Enzyme CatalysisInstitute of Biochemistry, University of Greifswald17487GreifswaldGermany
| | - Uwe T. Bornscheuer
- Department of Biotechnology & Enzyme CatalysisInstitute of Biochemistry, University of Greifswald17487GreifswaldGermany
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Pollak S, Gralka M, Sato Y, Schwartzman J, Lu L, Cordero OX. Public good exploitation in natural bacterioplankton communities. SCIENCE ADVANCES 2021; 7:7/31/eabi4717. [PMID: 34321201 PMCID: PMC8318375 DOI: 10.1126/sciadv.abi4717] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 06/10/2021] [Indexed: 05/19/2023]
Abstract
Bacteria often interact with their environment through extracellular molecules that increase access to limiting resources. These secretions can act as public goods, creating incentives for exploiters to invade and "steal" public goods away from producers. This phenomenon has been studied extensively in vitro, but little is known about the occurrence and impact of public good exploiters in the environment. Here, we develop a genomic approach to systematically identify bacteria that can exploit public goods produced during the degradation of polysaccharides. Focusing on chitin, a highly abundant marine biopolymer, we show that public good exploiters are active in natural chitin degrading microbial communities, invading early during colonization, and potentially hindering degradation. In contrast to in vitro studies, we find that exploiters and degraders belong to distant lineages, facilitating their coexistence. Our approach opens novel avenues to use the wealth of genomic data available to infer ecological roles and interactions among microbes.
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Affiliation(s)
- Shaul Pollak
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Matti Gralka
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yuya Sato
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan
| | - Julia Schwartzman
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Lu Lu
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Otto X Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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Miksch S, Meiners M, Meyerdierks A, Probandt D, Wegener G, Titschack J, Jensen MA, Ellrott A, Amann R, Knittel K. Bacterial communities in temperate and polar coastal sands are seasonally stable. ISME COMMUNICATIONS 2021; 1:29. [PMID: 36739458 PMCID: PMC9723697 DOI: 10.1038/s43705-021-00028-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 05/13/2021] [Accepted: 05/24/2021] [Indexed: 04/18/2023]
Abstract
Coastal sands are biocatalytic filters for dissolved and particulate organic matter of marine and terrestrial origin, thus, acting as centers of organic matter transformation. At high temporal resolution, we accessed the variability of benthic bacterial communities over two annual cycles at Helgoland (North Sea), and compared it with seasonality of communities in Isfjorden (Svalbard, 78°N) sediments, where primary production does not occur during winter. Benthic community structure remained stable in both, temperate and polar sediments on the level of cell counts and 16S rRNA-based taxonomy. Actinobacteriota of uncultured Actinomarinales and Microtrichales were a major group, with 8 ± 1% of total reads (Helgoland) and 31 ± 6% (Svalbard). Their high activity (frequency of dividing cells 28%) and in situ cell numbers of >10% of total microbes in Svalbard sediments, suggest Actinomarinales and Microtrichales as key heterotrophs for carbon mineralization. Even though Helgoland and Svalbard sampling sites showed no phytodetritus-driven changes of the benthic bacterial community structure, they harbored significantly different communities (p < 0.0001, r = 0.963). The temporal stability of benthic bacterial communities is in stark contrast to the dynamic succession typical of coastal waters, suggesting that pelagic and benthic bacterial communities respond to phytoplankton productivity very differently.
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Affiliation(s)
| | - Mirja Meiners
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - David Probandt
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Gunter Wegener
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Jürgen Titschack
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Senckenberg am Meer, Wilhelmshaven, Germany
| | - Maria A Jensen
- UNIS, The University Centre in Svalbard, Longyearbyen, Norway
| | - Andreas Ellrott
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Katrin Knittel
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
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Dürwald A, Zühlke MK, Schlüter R, Gebbe R, Bartosik D, Unfried F, Becher D, Schweder T. Reaching out in anticipation: bacterial membrane extensions represent a permanent investment in polysaccharide sensing and utilization. Environ Microbiol 2021; 23:3149-3163. [PMID: 33876569 DOI: 10.1111/1462-2920.15537] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 04/12/2021] [Accepted: 04/15/2021] [Indexed: 01/03/2023]
Abstract
Outer membrane extensions are common in many marine bacteria. However, the function of these surface enlargements or extracellular compartments is poorly understood. Using a combined approach of microscopy and subproteome analyses, we therefore examined Pseudoalteromonas distincta ANT/505, an Antarctic polysaccharide degrading gamma-proteobacterium. P. distincta produced outer membrane vesicles (MV) and vesicle chains (VC) on polysaccharide and non-polysaccharide carbon sources during the exponential and stationary growth phase. Surface structures of carbohydrate-grown cells were equipped with increased levels of highly substrate-specific proteins. At the same time, proteins encoded in all other polysaccharide degradation-related genomic regions were also detected in MV and VC samples under all growth conditions, indicating a basal expression. In addition, two alkaline phosphatases were highly abundant under non-limiting phosphate conditions. Surface structures may thus allow rapid sensing and fast responses in nutritionally deprived environments. It may also facilitate efficient carbohydrate processing and reduce loss of substrates and enzymes by diffusion as important adaptions to the aquatic ecosystem.
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Affiliation(s)
- Alexandra Dürwald
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, 17487, Germany
| | - Marie-Katherin Zühlke
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, 17487, Germany.,Institute of Marine Biotechnology, Greifswald, 17489, Germany
| | - Rabea Schlüter
- Imaging Center of the Department of Biology, University of Greifswald, Greifswald, 17489, Germany
| | - Rebecca Gebbe
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, 17487, Germany
| | - Daniel Bartosik
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, 17487, Germany
| | - Frank Unfried
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, 17487, Germany.,Institute of Marine Biotechnology, Greifswald, 17489, Germany
| | - Dörte Becher
- Institute of Marine Biotechnology, Greifswald, 17489, Germany.,Microbial Proteomics, Institute of Microbiology, University Greifswald, Greifswald, 17487, Germany
| | - Thomas Schweder
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, 17487, Germany.,Institute of Marine Biotechnology, Greifswald, 17489, Germany
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47
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Xenophontos C, Taubert M, Harpole WS, Küsel K. Phylogenetic and metabolic diversity have contrasting effects on the ecological functioning of bacterial communities. FEMS Microbiol Ecol 2021; 97:6136281. [PMID: 33587113 DOI: 10.1093/femsec/fiab017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 02/12/2021] [Indexed: 12/14/2022] Open
Abstract
Quantifying the relative contributions of microbial species to ecosystem functioning is challenging, because of the distinct mechanisms associated with microbial phylogenetic and metabolic diversity. We constructed bacterial communities with different diversity traits and employed exoenzyme activities (EEAs) and carbon acquisition potential (CAP) from substrates as proxies of bacterial functioning to test the independent effects of these two aspects of biodiversity. We expected that metabolic diversity, but not phylogenetic diversity would be associated with greater ecological function. Phylogenetically relatedness should intensify species interactions and coexistence, therefore amplifying the influence of metabolic diversity. We examined the effects of each diversity treatment using linear models, while controlling for the other, and found that phylogenetic diversity strongly influenced community functioning, positively and negatively. Metabolic diversity, however, exhibited negative or non-significant relationships with community functioning. When controlling for different substrates, EEAs increased along with phylogenetic diversity but decreased with metabolic diversity. The strength of diversity effects was related to substrate chemistry and the molecular mechanisms associated with each substrate's degradation. EEAs of phylogenetically similar groups were strongly affected by within-genus interactions. These results highlight the unique flexibility of microbial metabolic functions that must be considered in further ecological theory development.
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Affiliation(s)
- Constantinos Xenophontos
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, 07743 Jena, Germany, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
| | - Martin Taubert
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, 07743 Jena, Germany, Germany
| | - W Stanley Harpole
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany.,Department of Physiological Diversity, Helmholtz-Center for Environmental Research (UFZ), Permoserstraße 15, 04318 Leipzig, Germany.,Institute of Biology, Martin Luther University of Halle-Wittenberg, Weinbergweg 10, 06120 Halle (Saale), Germany
| | - Kirsten Küsel
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, 07743 Jena, Germany, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
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Chernysheva N, Bystritskaya E, Likhatskaya G, Nedashkovskaya O, Isaeva M. Genome-Wide Analysis of PL7 Alginate Lyases in the Genus Zobellia. Molecules 2021; 26:2387. [PMID: 33924031 PMCID: PMC8073546 DOI: 10.3390/molecules26082387] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 04/15/2021] [Indexed: 12/04/2022] Open
Abstract
We carried out a detailed investigation of PL7 alginate lyases across the Zobellia genus. The main findings were obtained using the methods of comparative genomics and spatial structure modeling, as well as a phylogenomic approach. Initially, in order to elucidate the alginolytic potential of Zobellia, we calculated the content of polysaccharide lyase (PL) genes in each genome. The genus-specific PLs were PL1, PL6, PL7 (the most abundant), PL14, PL17, and PL40. We revealed that PL7 belongs to subfamilies 3, 5, and 6. They may be involved in local and horizontal gene transfer and gene duplication processes. Most likely, an individual evolution of PL7 genes promotes the genetic variability of the Alginate Utilization System across Zobellia. Apparently, the PL7 alginate lyases may acquire a sub-functionalization due to diversification between in-paralogs.
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Affiliation(s)
| | | | | | | | - Marina Isaeva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159, Pr. 100 let Vladivostoku, 690022 Vladivostok, Russia; (N.C.); (E.B.); (G.L.); (O.N.)
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49
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Wolter LA, Mitulla M, Kalem J, Daniel R, Simon M, Wietz M. CAZymes in Maribacter dokdonensis 62-1 From the Patagonian Shelf: Genomics and Physiology Compared to Related Flavobacteria and a Co-occurring Alteromonas Strain. Front Microbiol 2021; 12:628055. [PMID: 33912144 PMCID: PMC8072126 DOI: 10.3389/fmicb.2021.628055] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 03/10/2021] [Indexed: 02/05/2023] Open
Abstract
Carbohydrate-active enzymes (CAZymes) are an important feature of bacteria in productive marine systems such as continental shelves, where phytoplankton and macroalgae produce diverse polysaccharides. We herein describe Maribacter dokdonensis 62–1, a novel strain of this flavobacterial species, isolated from alginate-supplemented seawater collected at the Patagonian continental shelf. M. dokdonensis 62–1 harbors a diverse array of CAZymes in multiple polysaccharide utilization loci (PUL). Two PUL encoding polysaccharide lyases from families 6, 7, 12, and 17 allow substantial growth with alginate as sole carbon source, with simultaneous utilization of mannuronate and guluronate as demonstrated by HPLC. Furthermore, strain 62-1 harbors a mixed-feature PUL encoding both ulvan- and fucoidan-targeting CAZymes. Core-genome phylogeny and pangenome analysis revealed variable occurrence of these PUL in related Maribacter and Zobellia strains, indicating specialization to certain “polysaccharide niches.” Furthermore, lineage- and strain-specific genomic signatures for exopolysaccharide synthesis possibly mediate distinct strategies for surface attachment and host interaction. The wide detection of CAZyme homologs in algae-derived metagenomes suggests global occurrence in algal holobionts, supported by sharing multiple adaptive features with the hydrolytic model flavobacterium Zobellia galactanivorans. Comparison with Alteromonas sp. 76-1 isolated from the same seawater sample revealed that these co-occurring strains target similar polysaccharides but with different genomic repertoires, coincident with differing growth behavior on alginate that might mediate ecological specialization. Altogether, our study contributes to the perception of Maribacter as versatile flavobacterial polysaccharide degrader, with implications for biogeochemical cycles, niche specialization and bacteria-algae interactions in the oceans.
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Affiliation(s)
- Laura A Wolter
- Institute for Chemistry and Biology of the Marine Environment, Oldenburg, Germany.,JST ERATO Nomura Project, Faculty of Life and Environmental Sciences, Tsukuba, Japan
| | - Maximilian Mitulla
- Institute for Chemistry and Biology of the Marine Environment, Oldenburg, Germany
| | - Jovan Kalem
- Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, Oldenburg, Germany
| | - Matthias Wietz
- Institute for Chemistry and Biology of the Marine Environment, Oldenburg, Germany.,Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
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50
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Niche-adaptation in plant-associated Bacteroidetes favours specialisation in organic phosphorus mineralisation. THE ISME JOURNAL 2021; 15:1040-1055. [PMID: 33257812 PMCID: PMC8115612 DOI: 10.1038/s41396-020-00829-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 10/30/2020] [Indexed: 02/07/2023]
Abstract
Bacteroidetes are abundant pathogen-suppressing members of the plant microbiome that contribute prominently to rhizosphere phosphorus mobilisation, a frequent growth-limiting nutrient in this niche. However, the genetic traits underpinning their success in this niche remain largely unknown, particularly regarding their phosphorus acquisition strategies. By combining cultivation, multi-layered omics and biochemical analyses we first discovered that all plant-associated Bacteroidetes express constitutive phosphatase activity, linked to the ubiquitous possession of a unique phosphatase, PafA. For the first time, we also reveal a subset of Bacteroidetes outer membrane SusCD-like complexes, typically associated with carbon acquisition, and several TonB-dependent transporters, are induced during Pi-depletion. Furthermore, in response to phosphate depletion, the plant-associated Flavobacterium used in this study expressed many previously characterised and novel proteins targeting organic phosphorus. Collectively, these enzymes exhibited superior phosphatase activity compared to plant-associated Pseudomonas spp. Importantly, several of the novel low-Pi-inducible phosphatases and transporters, belong to the Bacteroidetes auxiliary genome and are an adaptive genomic signature of plant-associated strains. In conclusion, niche adaptation to the plant microbiome thus appears to have resulted in the acquisition of unique phosphorus scavenging loci in Bacteroidetes, enhancing their phosphorus acquisition capabilities. These traits may enable their success in the rhizosphere and also present exciting avenues to develop sustainable agriculture.
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