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Bidaud CC, Monteil CL, Menguy N, Busigny V, Jézéquel D, Viollier É, Travert C, Skouri-Panet F, Benzerara K, Lefevre CT, Duprat É. Biogeochemical Niche of Magnetotactic Cocci Capable of Sequestering Large Polyphosphate Inclusions in the Anoxic Layer of the Lake Pavin Water Column. Front Microbiol 2022; 12:789134. [PMID: 35082768 PMCID: PMC8786505 DOI: 10.3389/fmicb.2021.789134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 11/19/2021] [Indexed: 11/13/2022] Open
Abstract
Magnetotactic bacteria (MTB) are microorganisms thriving mostly at oxic–anoxic boundaries of aquatic habitats. MTB are efficient in biomineralising or sequestering diverse elements intracellularly, which makes them potentially important actors in biogeochemical cycles. Lake Pavin is a unique aqueous system populated by a wide diversity of MTB with two communities harbouring the capability to sequester not only iron under the form of magnetosomes but also phosphorus and magnesium under the form of polyphosphates, or calcium carbonates, respectively. MTB thrive in the water column of Lake Pavin over a few metres along strong redox and chemical gradients representing a series of different microenvironments. In this study, we investigate the relative abundance and the vertical stratification of the diverse populations of MTB in relation to environmental parameters, by using a new method coupling a precise sampling for geochemical analyses, MTB morphotype description, and in situ measurement of the physicochemical parameters. We assess the ultrastructure of MTB as a function of depth using light and electron microscopy. We evidence the biogeochemical niche of magnetotactic cocci, capable of sequestering large PolyP inclusions below the oxic–anoxic transition zone. Our results suggest a tight link between the S and P metabolisms of these bacteria and pave the way to better understand the implication of MTB for the P cycle in stratified environmental conditions.
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Affiliation(s)
- Cécile C Bidaud
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590 - Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France.,Aix-Marseille University, CNRS, CEA, UMR 7265 Institute of Biosciences and Biotechnologies of Aix-Marseille, CEA Cadarache, Saint-Paul-lez-Durance, France.,Université de Paris, Centre de Recherches Interdisciplinaires (CRI), Paris, France
| | - Caroline L Monteil
- Aix-Marseille University, CNRS, CEA, UMR 7265 Institute of Biosciences and Biotechnologies of Aix-Marseille, CEA Cadarache, Saint-Paul-lez-Durance, France
| | - Nicolas Menguy
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590 - Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
| | - Vincent Busigny
- Université de Paris, Institut de Physique du Globe de Paris, CNRS, Paris, France
| | - Didier Jézéquel
- Université de Paris, Institut de Physique du Globe de Paris, CNRS, Paris, France.,INRAE & Université Savoie Mont Blanc, UMR CARRTEL, Thonon-les-Bains, France
| | - Éric Viollier
- LSCE, CEA/CNRS/UVSQ/IPSL, Université Paris Saclay & Université de Paris France, Gif-sur-Yvette Cedex, France
| | - Cynthia Travert
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590 - Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
| | - Fériel Skouri-Panet
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590 - Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
| | - Karim Benzerara
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590 - Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
| | - Christopher T Lefevre
- Aix-Marseille University, CNRS, CEA, UMR 7265 Institute of Biosciences and Biotechnologies of Aix-Marseille, CEA Cadarache, Saint-Paul-lez-Durance, France
| | - Élodie Duprat
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590 - Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
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van Vliet DM, von Meijenfeldt FB, Dutilh BE, Villanueva L, Sinninghe Damsté JS, Stams AJ, Sánchez‐Andrea I. The bacterial sulfur cycle in expanding dysoxic and euxinic marine waters. Environ Microbiol 2021; 23:2834-2857. [PMID: 33000514 PMCID: PMC8359478 DOI: 10.1111/1462-2920.15265] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 09/03/2020] [Accepted: 09/28/2020] [Indexed: 01/29/2023]
Abstract
Dysoxic marine waters (DMW, < 1 μM oxygen) are currently expanding in volume in the oceans, which has biogeochemical, ecological and societal consequences on a global scale. In these environments, distinct bacteria drive an active sulfur cycle, which has only recently been recognized for open-ocean DMW. This review summarizes the current knowledge on these sulfur-cycling bacteria. Critical bottlenecks and questions for future research are specifically addressed. Sulfate-reducing bacteria (SRB) are core members of DMW. However, their roles are not entirely clear, and they remain largely uncultured. We found support for their remarkable diversity and taxonomic novelty by mining metagenome-assembled genomes from the Black Sea as model ecosystem. We highlight recent insights into the metabolism of key sulfur-oxidizing SUP05 and Sulfurimonas bacteria, and discuss the probable involvement of uncultivated SAR324 and BS-GSO2 bacteria in sulfur oxidation. Uncultivated Marinimicrobia bacteria with a presumed organoheterotrophic metabolism are abundant in DMW. Like SRB, they may use specific molybdoenzymes to conserve energy from the oxidation, reduction or disproportionation of sulfur cycle intermediates such as S0 and thiosulfate, produced from the oxidation of sulfide. We expect that tailored sampling methods and a renewed focus on cultivation will yield deeper insight into sulfur-cycling bacteria in DMW.
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Affiliation(s)
- Daan M. van Vliet
- Laboratory of MicrobiologyWageningen University and Research, Stippeneng 4, 6708WEWageningenNetherlands
| | | | - Bas E. Dutilh
- Theoretical Biology and Bioinformatics, Science for LifeUtrecht University, Padualaan 8, 3584 CHUtrechtNetherlands
| | - Laura Villanueva
- Department of Marine Microbiology and BiogeochemistryRoyal Netherlands Institute for Sea Research (NIOZ), Utrecht University, Landsdiep 4, 1797 SZ, 'tHorntje (Texel)Netherlands
| | - Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and BiogeochemistryRoyal Netherlands Institute for Sea Research (NIOZ), Utrecht University, Landsdiep 4, 1797 SZ, 'tHorntje (Texel)Netherlands
- Department of Earth Sciences, Faculty of GeosciencesUtrecht University, Princetonlaan 8A, 3584 CBUtrechtNetherlands
| | - Alfons J.M. Stams
- Laboratory of MicrobiologyWageningen University and Research, Stippeneng 4, 6708WEWageningenNetherlands
- Centre of Biological EngineeringUniversity of Minho, Campus de Gualtar, 4710‐057BragaPortugal
| | - Irene Sánchez‐Andrea
- Laboratory of MicrobiologyWageningen University and Research, Stippeneng 4, 6708WEWageningenNetherlands
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Mu DS, Wang S, Liang QY, Du ZZ, Tian R, Ouyang Y, Wang XP, Zhou A, Gong Y, Chen GJ, Van Nostrand J, Yang Y, Zhou J, Du ZJ. Bradymonabacteria, a novel bacterial predator group with versatile survival strategies in saline environments. MICROBIOME 2020; 8:126. [PMID: 32867860 PMCID: PMC7460792 DOI: 10.1186/s40168-020-00902-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 07/27/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND Bacterial predation is an important selective force in microbial community structure and dynamics. However, only a limited number of predatory bacteria have been reported, and their predatory strategies and evolutionary adaptations remain elusive. We recently isolated a novel group of bacterial predators, Bradymonabacteria, representative of the novel order Bradymonadales in δ-Proteobacteria. Compared with those of other bacterial predators (e.g., Myxococcales and Bdellovibrionales), the predatory and living strategies of Bradymonadales are still largely unknown. RESULTS Based on individual coculture of Bradymonabacteria with 281 prey bacteria, Bradymonabacteria preyed on diverse bacteria but had a high preference for Bacteroidetes. Genomic analysis of 13 recently sequenced Bradymonabacteria indicated that these bacteria had conspicuous metabolic deficiencies, but they could synthesize many polymers, such as polyphosphate and polyhydroxyalkanoates. Dual transcriptome analysis of cocultures of Bradymonabacteria and prey suggested a potential contact-dependent predation mechanism. Comparative genomic analysis with 24 other bacterial predators indicated that Bradymonabacteria had different predatory and living strategies. Furthermore, we identified Bradymonadales from 1552 publicly available 16S rRNA amplicon sequencing samples, indicating that Bradymonadales was widely distributed and highly abundant in saline environments. Phylogenetic analysis showed that there may be six subgroups in this order; each subgroup occupied a different habitat. CONCLUSIONS Bradymonabacteria have unique living strategies that are transitional between the "obligate" and the so-called facultative predators. Thus, we propose a framework to categorize the current bacterial predators into 3 groups: (i) obligate predators (completely prey-dependent), (ii) facultative predators (facultatively prey-dependent), and (iii) opportunistic predators (prey-independent). Our findings provide an ecological and evolutionary framework for Bradymonadales and highlight their potential ecological roles in saline environments. Video abstract.
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Affiliation(s)
- Da-Shuai Mu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, No. 72, Jimo Binhai Road, Jimo, Qingdao, 266237, China
- Marine College, Shandong University, Weihai, 264209, China
| | - Shuo Wang
- Marine College, Shandong University, Weihai, 264209, China
| | - Qi-Yun Liang
- Marine College, Shandong University, Weihai, 264209, China
| | - Zhao-Zhong Du
- Marine College, Shandong University, Weihai, 264209, China
| | - Renmao Tian
- Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Yang Ouyang
- Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Xin-Peng Wang
- Marine College, Shandong University, Weihai, 264209, China
| | - Aifen Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Ya Gong
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, No. 72, Jimo Binhai Road, Jimo, Qingdao, 266237, China
- Marine College, Shandong University, Weihai, 264209, China
| | - Guan-Jun Chen
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, No. 72, Jimo Binhai Road, Jimo, Qingdao, 266237, China
- Marine College, Shandong University, Weihai, 264209, China
| | - Joy Van Nostrand
- Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, 73019, USA
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Zong-Jun Du
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, No. 72, Jimo Binhai Road, Jimo, Qingdao, 266237, China.
- Marine College, Shandong University, Weihai, 264209, China.
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Li J, Plouchart D, Zastepa A, Dittrich M. Picoplankton accumulate and recycle polyphosphate to support high primary productivity in coastal Lake Ontario. Sci Rep 2019; 9:19563. [PMID: 31862973 PMCID: PMC6925121 DOI: 10.1038/s41598-019-56042-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 12/03/2019] [Indexed: 11/08/2022] Open
Abstract
Phytoplankton can accumulate polyphosphate (polyP) to alleviate limitation of essential nutrient phosphorus (P). Yet polyP metabolisms in aquatic systems and their roles in P biogeochemical cycle remain elusive. Previously reported polyP enrichment in low-phosphorus oligotrophic marine waters contradicts the common view of polyP as a luxury P-storage molecule. Here, we show that in a P-rich eutrophic bay of Lake Ontario, planktonic polyP is controlled by multiple mechanisms and responds strongly to seasonal variations. Plankton accumulate polyP as P storage under high-P conditions via luxury uptake and use it under acute P stress. Low phosphorus also triggers enrichment of polyP that can be preferentially recycled to attenuate P lost. We discover that picoplankton, despite their low production rates, are responsible for the dynamic polyP metabolisms. Picoplankton store and liberate polyP to support the high primary productivity of blooming algae. PolyP mechanisms enable efficient P recycling on ecosystem and even larger scales.
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Affiliation(s)
- Jiying Li
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, ON, M1C 1A4, Canada.
| | - Diane Plouchart
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, ON, M1C 1A4, Canada
| | - Arthur Zastepa
- Canada Center for Inland Waters, Environment and Climate Change Canada, Burlington, ON, L7S 1A1, Canada
| | - Maria Dittrich
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, ON, M1C 1A4, Canada
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Effect of large magnetotactic bacteria with polyphosphate inclusions on the phosphate profile of the suboxic zone in the Black Sea. ISME JOURNAL 2019; 13:1198-1208. [PMID: 30643197 DOI: 10.1038/s41396-018-0315-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 10/11/2018] [Accepted: 11/13/2018] [Indexed: 01/17/2023]
Abstract
The Black Sea is the world's largest anoxic basin and a model system for studying processes across redox gradients. In between the oxic surface and the deeper sulfidic waters there is an unusually broad layer of 10-40 m, where neither oxygen nor sulfide are detectable. In this suboxic zone, dissolved phosphate profiles display a pronounced minimum at the upper and a maximum at the lower boundary, with a peak of particulate phosphorus in between, which was suggested to be caused by the sorption of phosphate on sinking particles of metal oxides. Here we show that bacterial polyphosphate inclusions within large magnetotactic bacteria related to the genus Magnetococcus contribute substantially to the observed phosphorus peak, as they contain 26-34% phosphorus compared to only 1-5% in metal-rich particles. Furthermore, we found increased gene expression for polyphosphate kinases by several groups of bacteria including Magnetococcaceae at the phosphate maximum, indicating active bacterial polyphosphate degradation. We propose that large magnetotactic bacteria shuttle up and down within the suboxic zone, scavenging phosphate at the upper and releasing it at the lower boundary. In contrast to a passive transport via metal oxides, this bacterial transport can quantitatively explain the observed phosphate profiles.
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Simultaneous Visualization of Enzymatic Activity in the Cytoplasm and at Polyphosphate Inclusions in Beggiatoa sp. Strain 35Flor Incubated with 18O-Labeled Water. mSphere 2018; 3:3/6/e00489-18. [PMID: 30567898 PMCID: PMC6300685 DOI: 10.1128/msphere.00489-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here we report on a new nanoscale secondary ion mass spectrometry (nanoSIMS) approach based on enzyme-mediated oxygen isotope exchange, which combines the visualization of general metabolic activity in the cytoplasm with insights into the activity of enzymes related to polyphosphate (polyP) inclusions. The polyP-accumulating strain of the large sulfur bacterium Beggiatoa was used as a model organism. Beggiatoa cultures were grown under oxic and anoxic conditions when exposed to either low- or high-sulfide conditions, which are known to influence polyP metabolism in this strain. Subsequent incubation with 18O-labeled water led to high 18O enrichments above the natural background in the cytoplasm and polyP granules derived from enzymatically mediated oxygen isotope exchange. The relative importance of polyP under the different sulfide regimes became evident by an apparent continued metabolic activity at polyP inclusions under stressfully high sulfide concentrations, in contrast to a decreased general metabolic activity in the cytoplasm. This finding confirms the role of polyP as a critical component in bacterial stress response and maintenance of a survival metabolism.IMPORTANCE Microbial organisms exert a large influence on the environment as they directly affect the turnover of essential elements. This is particularly true for polyphosphate-accumulating large sulfur bacteria, which can either accumulate phosphate as polyphosphate or degrade it and release phosphate into the environment, depending on environmental conditions. This study presents a new approach to simultaneously visualize general metabolic activity and enzymatic activity at polyphosphate granules by incubation with 18O-labeled water as the only stable isotope tracer. For this purpose, the well-studied Beggiatoa sp. strain 35Flor was used as a model organism and was exposed to different stress regimes. General metabolic activity was strongly impaired during high-stress regimes. In contrast, intense intracellular polyP cycling was not restricted to favorable or stressful conditions, highlighting the importance of polyP for general cell physiology, especially during hostile conditions. The nanoSIMS approach adds a new tool to study microorganisms involved in phosphorus cycling in the environment together with the identification of general metabolic activity.
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