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Di Nezio F, Roman S, Buetti-Dinh A, Sepúlveda Steiner O, Bouffard D, Sengupta A, Storelli N. Motile bacteria leverage bioconvection for eco-physiological benefits in a natural aquatic environment. Front Microbiol 2023; 14:1253009. [PMID: 38163082 PMCID: PMC10756677 DOI: 10.3389/fmicb.2023.1253009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 11/23/2023] [Indexed: 01/03/2024] Open
Abstract
Introduction Bioconvection, a phenomenon characterized by the collective upward swimming of motile microorganisms, has mainly been investigated within controlled laboratory settings, leaving a knowledge gap regarding its ecological implications in natural aquatic environments. This study aims to address this question by investigating the influence of bioconvection on the eco-physiology of the anoxygenic phototrophic sulfur bacteria community of meromictic Lake Cadagno. Methods Here we comprehensively explore its effects by comparing the physicochemical profiles of the water column and the physiological traits of the main populations of the bacterial layer (BL). The search for eco-physiological effects of bioconvection involved a comparative analysis between two time points during the warm season, one featuring bioconvection (July) and the other without it (September). Results A prominent distinction in the physicochemical profiles of the water column centers on light availability, which is significantly higher in July. This minimum threshold of light intensity is essential for sustaining the physiological CO2 fixation activity of Chromatium okenii, the microorganism responsible for bioconvection. Furthermore, the turbulence generated by bioconvection redistributes sulfides to the upper region of the BL and displaces other microorganisms from their optimal ecological niches. Conclusion The findings underscore the influence of bioconvection on the physiology of C. okenii and demonstrate its functional role in improving its metabolic advantage over coexisting phototrophic sulfur bacteria. However, additional research is necessary to confirm these results and to unravel the multiscale processes activated by C. okenii's motility mechanisms.
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Affiliation(s)
- Francesco Di Nezio
- Department of Environment, Constructions, and Design, Institute of Microbiology, University of Applied Sciences and Arts of Southern Switzerland (SUPSI), Mendrisio, Switzerland
- Department of Plant Sciences, University of Geneva, Geneva, Switzerland
| | - Samuele Roman
- Department of Environment, Constructions, and Design, Institute of Microbiology, University of Applied Sciences and Arts of Southern Switzerland (SUPSI), Mendrisio, Switzerland
- Alpine Biology Center Foundation, Bellinzona, Switzerland
| | - Antoine Buetti-Dinh
- Department of Environment, Constructions, and Design, Institute of Microbiology, University of Applied Sciences and Arts of Southern Switzerland (SUPSI), Mendrisio, Switzerland
| | - Oscar Sepúlveda Steiner
- Department of Surface Waters – Research and Management, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Kastanienbaum, Switzerland
- Civil and Environmental Engineering, University of California, Davis, Davis, CA, United States
| | - Damien Bouffard
- Department of Surface Waters – Research and Management, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Kastanienbaum, Switzerland
- Faculty of Geosciences and Environment, Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
| | - Anupam Sengupta
- Department of Physics and Materials Science, Physics of Living Matter Group, Luxembourg City, Luxembourg
| | - Nicola Storelli
- Department of Environment, Constructions, and Design, Institute of Microbiology, University of Applied Sciences and Arts of Southern Switzerland (SUPSI), Mendrisio, Switzerland
- Department of Plant Sciences, University of Geneva, Geneva, Switzerland
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2
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Bacterial, Phytoplankton, and Viral Distributions and Their Biogeochemical Contexts in Meromictic Lake Cadagno Offer Insights into the Proterozoic Ocean Microbial Loop. mBio 2022; 13:e0005222. [PMID: 35726916 PMCID: PMC9426590 DOI: 10.1128/mbio.00052-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lake Cadagno, a permanently stratified high-alpine lake with a persistent microbial bloom in its chemocline, has long been considered a model for the low-oxygen, high-sulfide Proterozoic ocean. Although the lake has been studied for over 25 years, the absence of concerted study of the bacteria, phytoplankton, and viruses, together with primary and secondary production, has hindered a comprehensive understanding of its microbial food web. Here, the identities, abundances, and productivity of microbes were evaluated in the context of Lake Cadagno biogeochemistry. Photosynthetic pigments together with 16S rRNA gene phylogenies suggest the prominence of eukaryotic phytoplankton chloroplasts, primarily chlorophytes. Chloroplasts closely related to those of high-alpine-adapted Ankyra judayi persisted with oxygen in the mixolimnion, where photosynthetic efficiency was high, while chloroplasts of Closteriopsis-related chlorophytes peaked in the chemocline and monimolimnion. The anoxygenic phototrophic sulfur bacterium Chromatium dominated the chemocline along with Lentimicrobium, a genus of known fermenters. Secondary production peaked in the chemocline, which suggested that anoxygenic primary producers depended on heterotrophic nutrient remineralization. The virus-to-microbe ratio peaked with phytoplankton abundances in the mixolimnion and were at a minimum where Chromatium abundance was highest, trends that suggest that viruses may play a role in the modulation of primary production. Through the combined analysis of bacterial, eukaryotic, viral, and biogeochemical spatial dynamics, we provide a comprehensive synthesis of the Lake Cadagno microbial loop. This study offers a new ecological perspective on how biological and geochemical connections may have occurred in the chemocline of the Proterozoic ocean, where eukaryotic microbial life is thought to have evolved.
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3
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Philippi M, Kitzinger K, Berg JS, Tschitschko B, Kidane AT, Littmann S, Marchant HK, Storelli N, Winkel LHE, Schubert CJ, Mohr W, Kuypers MMM. Purple sulfur bacteria fix N 2 via molybdenum-nitrogenase in a low molybdenum Proterozoic ocean analogue. Nat Commun 2021; 12:4774. [PMID: 34362886 PMCID: PMC8346585 DOI: 10.1038/s41467-021-25000-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 07/15/2021] [Indexed: 01/04/2023] Open
Abstract
Biological N2 fixation was key to the expansion of life on early Earth. The N2-fixing microorganisms and the nitrogenase type used in the Proterozoic are unknown, although it has been proposed that the canonical molybdenum-nitrogenase was not used due to low molybdenum availability. We investigate N2 fixation in Lake Cadagno, an analogue system to the sulfidic Proterozoic continental margins, using a combination of biogeochemical, molecular and single cell techniques. In Lake Cadagno, purple sulfur bacteria (PSB) are responsible for high N2 fixation rates, to our knowledge providing the first direct evidence for PSB in situ N2 fixation. Surprisingly, no alternative nitrogenases are detectable, and N2 fixation is exclusively catalyzed by molybdenum-nitrogenase. Our results show that molybdenum-nitrogenase is functional at low molybdenum conditions in situ and that in contrast to previous beliefs, PSB may have driven N2 fixation in the Proterozoic ocean.
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Affiliation(s)
- Miriam Philippi
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Katharina Kitzinger
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany.
| | - Jasmine S Berg
- Department of Environmental Systems Science, ETH-Zurich, Zurich, Switzerland
| | - Bernhard Tschitschko
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Abiel T Kidane
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Sten Littmann
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Hannah K Marchant
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Nicola Storelli
- Laboratory of Applied Microbiology, Department of Environment, Constructions and Design, University of Applied Sciences of Southern Switzerland (SUPSI), Bellinzona, Switzerland
| | - Lenny H E Winkel
- Department of Environmental Systems Science, ETH-Zurich, Zurich, Switzerland.,Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Carsten J Schubert
- Department of Environmental Systems Science, ETH-Zurich, Zurich, Switzerland.,Eawag, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Wiebke Mohr
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Marcel M M Kuypers
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
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4
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Block KR, O'Brien JM, Edwards WJ, Marnocha CL. Vertical structure of the bacterial diversity in meromictic Fayetteville Green Lake. Microbiologyopen 2021; 10:e1228. [PMID: 34459548 PMCID: PMC8330806 DOI: 10.1002/mbo3.1228] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 07/16/2021] [Accepted: 07/19/2021] [Indexed: 11/08/2022] Open
Abstract
The permanently stratified water columns in euxinic meromictic lakes produce niche environments for phototrophic sulfur oxidizers and diverse sulfur metabolisms. While Green Lake (Fayetteville, New York, NY) is known to host a diverse community of ecologically important sulfur bacteria, analyses of its microbial communities, to date, have been largely based on pigment analysis and smaller datasets from Sanger sequencing techniques. Here, we present the results of next-generation sequencing of the eubacterial community in the context of the water column geochemistry. We observed abundant purple and green sulfur bacteria, as well as anoxygenic photosynthesis-capable cyanobacteria within the upper monimolimnion. Amidst the phototrophs, we found other sulfur-cycling bacteria including sulfur disproportionators and chemotrophic sulfur oxidizers, further detailing our understanding of the sulfur cycle and microbial ecology of euxinic, meromictic lakes.
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Affiliation(s)
| | - Joy M. O'Brien
- Department of BiologyNiagara UniversityLewistonNew YorkUSA
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5
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Rojas CA, De Santiago Torio A, Park S, Bosak T, Klepac-Ceraj V. Organic Electron Donors and Terminal Electron Acceptors Structure Anaerobic Microbial Communities and Interactions in a Permanently Stratified Sulfidic Lake. Front Microbiol 2021; 12:620424. [PMID: 33967973 PMCID: PMC8103211 DOI: 10.3389/fmicb.2021.620424] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 03/23/2021] [Indexed: 01/04/2023] Open
Abstract
The extent to which nutrients structure microbial communities in permanently stratified lakes is not well understood. This study characterized microbial communities from the anoxic layers of the meromictic and sulfidic Fayetteville Green Lake (FGL), NY, United States, and investigated the roles of organic electron donors and terminal electron acceptors in shaping microbial community structure and interactions. Bacterial communities from the permanently stratified layer below the chemocline (monimolimnion) and from enrichment cultures inoculated by lake sediments were analyzed using 16S rRNA gene sequencing. Results showed that anoxygenic phototrophs dominated microbial communities in the upper monimolimnion (21 m), which harbored little diversity, whereas the most diverse communities resided at the bottom of the lake (∼52 m). Organic electron donors explained 54% of the variation in the microbial community structure in aphotic cultures enriched on an array of organic electron donors and different inorganic electron acceptors. Electron acceptors only explained 10% of the variation, but were stronger drivers of community assembly in enrichment cultures supplemented with acetate or butyrate compared to the cultures amended by chitin, lignin or cellulose. We identified a range of habitat generalists and habitat specialists in both the water column and enrichment samples using Levin's index. Network analyses of interactions among microbial groups revealed Chlorobi and sulfate reducers as central to microbial interactions in the upper monimolimnion, while Syntrophaceae and other fermenting organisms were more important in the lower monimolimnion. The presence of photosynthetic microbes and communities that degrade chitin and cellulose far below the chemocline supported the downward transport of microbes, organic matter and oxidants from the surface and the chemocline. Collectively, our data suggest niche partitioning of bacterial communities via interactions that depend on the availability of different organic electron donors and terminal electron acceptors. Thus, light, as well as the diversity and availability of chemical resources drive community structure and function in FGL, and likely in other stratified, meromictic lakes.
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Affiliation(s)
- Connie A. Rojas
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States
- Ecology, Evolution, and Behavior, Michigan State University, East Lansing, MI, United States
| | - Ana De Santiago Torio
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Serry Park
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States
| | - Tanja Bosak
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Vanja Klepac-Ceraj
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States
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6
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Di Nezio F, Beney C, Roman S, Danza F, Buetti-Dinh A, Tonolla M, Storelli N. Anoxygenic photo- and chemo-synthesis of phototrophic sulfur bacteria from an alpine meromictic lake. FEMS Microbiol Ecol 2021; 97:6123714. [PMID: 33512460 PMCID: PMC7947596 DOI: 10.1093/femsec/fiab010] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/27/2021] [Indexed: 12/11/2022] Open
Abstract
Meromictic lakes are interesting ecosystems to study anaerobic microorganisms due their permanent stratification allowing the formation of a stable anoxic environment. The crenogenic meromictic Lake Cadagno harbors an important community of anoxygenic phototrophic sulfur bacteria responsible for almost half of its total productivity. Besides their ability to fix CO2 through photosynthesis, these microorganisms also showed high rates of dark carbon fixation via chemosyntesis. Here, we grew in pure cultures three populations of anoxygenic phototrophic sulfur bacteria previously isolated from the lake, accounting for 72.8% of the total microbial community and exibiting different phenotypes: (1) the motile, large-celled purple sulfur bacterium (PSB) Chromatium okenii, (2) the small-celled PSB Thiodictyon syntrophicum and (3) the green sulfur bacterium (GSB) Chlorobium phaeobacteroides. We measured their ability to fix CO2 through photo- and chemo-synthesis, both in situ in the lake and in laboratory under different incubation conditions. We also evaluated the efficiency and velocity of H2S photo-oxidation, an important reaction in the anoxygenic photosynthesis process. Our results confirm that phototrophic sulfur bacteria strongly fix CO2 in the presence of light and that oxygen increases chemosynthesis at night, in laboratory conditions. Moreover, substancial differences were displayed between the three selected populations in terms of activity and abundance.
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Affiliation(s)
- Francesco Di Nezio
- Laboratory of Applied Microbiology (LMA), Department of Environmental Constructions and Design (DACD), University of Applied Sciences and Arts of Southern Switzerland (SUPSI), via Mirasole 22a, 6500 Bellinzona, Switzerland.,Microbiology Unit, Department of Botany and Plant Biology (BIVEG), University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, 1211 Geneva, Switzerland
| | - Clarisse Beney
- Laboratory of Applied Microbiology (LMA), Department of Environmental Constructions and Design (DACD), University of Applied Sciences and Arts of Southern Switzerland (SUPSI), via Mirasole 22a, 6500 Bellinzona, Switzerland.,Microbiology Unit, Department of Botany and Plant Biology (BIVEG), University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, 1211 Geneva, Switzerland
| | - Samuele Roman
- Laboratory of Applied Microbiology (LMA), Department of Environmental Constructions and Design (DACD), University of Applied Sciences and Arts of Southern Switzerland (SUPSI), via Mirasole 22a, 6500 Bellinzona, Switzerland.,Alpine Biology Center Foundation, via Mirasole 22a, 6500 Bellinzona, Switzerland
| | - Francesco Danza
- Laboratory of Applied Microbiology (LMA), Department of Environmental Constructions and Design (DACD), University of Applied Sciences and Arts of Southern Switzerland (SUPSI), via Mirasole 22a, 6500 Bellinzona, Switzerland
| | - Antoine Buetti-Dinh
- Laboratory of Applied Microbiology (LMA), Department of Environmental Constructions and Design (DACD), University of Applied Sciences and Arts of Southern Switzerland (SUPSI), via Mirasole 22a, 6500 Bellinzona, Switzerland
| | - Mauro Tonolla
- Laboratory of Applied Microbiology (LMA), Department of Environmental Constructions and Design (DACD), University of Applied Sciences and Arts of Southern Switzerland (SUPSI), via Mirasole 22a, 6500 Bellinzona, Switzerland.,Microbiology Unit, Department of Botany and Plant Biology (BIVEG), University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, 1211 Geneva, Switzerland.,Alpine Biology Center Foundation, via Mirasole 22a, 6500 Bellinzona, Switzerland
| | - Nicola Storelli
- Laboratory of Applied Microbiology (LMA), Department of Environmental Constructions and Design (DACD), University of Applied Sciences and Arts of Southern Switzerland (SUPSI), via Mirasole 22a, 6500 Bellinzona, Switzerland
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7
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Mansor M, Xu J. Benefits at the nanoscale: a review of nanoparticle-enabled processes favouring microbial growth and functionality. Environ Microbiol 2020; 22:3633-3649. [PMID: 32705763 DOI: 10.1111/1462-2920.15174] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/17/2020] [Accepted: 07/21/2020] [Indexed: 11/29/2022]
Abstract
Nanoparticles are ubiquitous and co-occur with microbial life in every environment on Earth. Interactions between microbes and nanoparticles impact the biogeochemical cycles via accelerating various reaction rates and enabling biological processes at the smallest scales. Distinct from microbe-mineral interactions at large, microbe-nanoparticle interactions may involve higher levels of active recognition and utilization of the reactive, changeable, and thereby 'moldable' nano-sized inorganic phases by microbes, which has been given minimal attention in previous reviews. Here we have compiled the various cases of microbe-nanoparticle interactions with clear and potential benefits to the microbial cells and communities. Specifically, we discussed (i) the high bioavailabilities of nanoparticles due to increased specific surface areas and size-dependent solubility, with a focus on environmentally-relevant iron(III) (oxyhydr)oxides and pyrite, (ii) microbial utilization of nanoparticles as 'nano-tools' for electron transfer, chemotaxis, and storage units, and (iii) speculated benefits of precipitating 'moldable' nanoparticles in extracellular biomineralization. We further discussed emergent questions concerning cellular level responses to nanoparticle-associated cues, and the factors that affect nanoparticles' bioavailabilities beyond size-dependent effects. We end the review by proposing a framework towards more quantitative approaches and by highlighting promising techniques to guide future research in this exciting field.
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Affiliation(s)
- Muammar Mansor
- Geomicrobiology, Center for Applied Geoscience, University of Tuebingen, Tuebingen, 72076, Germany
| | - Jie Xu
- Department of Geological Sciences, the University of Texas at El Paso, El Paso, Texas, 79968, USA
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8
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Luedin SM, Storelli N, Danza F, Roman S, Wittwer M, Pothier JF, Tonolla M. Mixotrophic Growth Under Micro-Oxic Conditions in the Purple Sulfur Bacterium " Thiodictyon syntrophicum". Front Microbiol 2019; 10:384. [PMID: 30891015 PMCID: PMC6413534 DOI: 10.3389/fmicb.2019.00384] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 02/13/2019] [Indexed: 12/23/2022] Open
Abstract
The microbial ecosystem of the meromictic Lake Cadagno (Ticino, Swiss Alps) has been studied intensively in order to understand structure and functioning of the anoxygenic phototrophic sulfur bacteria community living in the chemocline. It has been found that the purple sulfur bacterium "Thiodictyon syntrophicum" strain Cad16T, belonging to the Chromatiaceae, fixes around 26% of all bulk inorganic carbon in the chemocline, both during day and night. With this study, we elucidated for the first time the mode of carbon fixation of str. Cad16T under micro-oxic conditions with a combination of long-term monitoring of key physicochemical parameters with CTD, 14C-incorporation experiments and quantitative proteomics using in-situ dialysis bag incubations of str. Cad16T cultures. Regular vertical CTD profiling during the study period in summer 2017 revealed that the chemocline sank from 12 to 14 m which was accompanied by a bloom of cyanobacteria and the subsequent oxygenation of the deeper water column. Sampling was performed both day and night. CO2 assimilation rates were higher during the light period compared to those in the dark, both in the chemocline population and in the incubated cultures. The relative change in the proteome between day and night (663 quantified proteins) comprised only 1% of all proteins encoded in str. Cad16T. Oxidative respiration pathways were upregulated at light, whereas stress-related mechanisms prevailed during the night. These results indicate that low light availability and the co-occurring oxygenation of the chemocline induced mixotrophic growth in str. Cad16T. Our study thereby helps to further understand the consequences micro-oxic conditions for phototrophic sulfur oxidizing bacteria. The complete proteome data have been deposited to the ProteomeXchange database with identifier PXD010641.
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Affiliation(s)
- Samuel M. Luedin
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
- Laboratory of Applied Microbiology, Department of Environment, Constructions and Design, University of Applied Sciences of Southern Switzerland (SUPSI), Bellinzona, Switzerland
- Spiez Laboratory, Biology Division, Federal Office for Civil Protection, Spiez, Switzerland
| | - Nicola Storelli
- Laboratory of Applied Microbiology, Department of Environment, Constructions and Design, University of Applied Sciences of Southern Switzerland (SUPSI), Bellinzona, Switzerland
| | - Francesco Danza
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
- Laboratory of Applied Microbiology, Department of Environment, Constructions and Design, University of Applied Sciences of Southern Switzerland (SUPSI), Bellinzona, Switzerland
| | - Samuele Roman
- Laboratory of Applied Microbiology, Department of Environment, Constructions and Design, University of Applied Sciences of Southern Switzerland (SUPSI), Bellinzona, Switzerland
- Alpine Biology Center Foundation, Bellinzona, Switzerland
| | - Matthias Wittwer
- Spiez Laboratory, Biology Division, Federal Office for Civil Protection, Spiez, Switzerland
| | - Joël F. Pothier
- Environmental Genomics and System Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Mauro Tonolla
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
- Laboratory of Applied Microbiology, Department of Environment, Constructions and Design, University of Applied Sciences of Southern Switzerland (SUPSI), Bellinzona, Switzerland
- Alpine Biology Center Foundation, Bellinzona, Switzerland
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9
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Luedin SM, Liechti N, Cox RP, Danza F, Frigaard NU, Posth NR, Pothier JF, Roman S, Storelli N, Wittwer M, Tonolla M. Draft Genome Sequence of Chromatium okenii Isolated from the Stratified Alpine Lake Cadagno. Sci Rep 2019; 9:1936. [PMID: 30760771 PMCID: PMC6374484 DOI: 10.1038/s41598-018-38202-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 12/21/2018] [Indexed: 01/07/2023] Open
Abstract
Blooms of purple sulfur bacteria (PSB) are important drivers of the global sulfur cycling oxidizing reduced sulfur in intertidal flats and stagnant water bodies. Since the discovery of PSB Chromatium okenii in 1838, it has been found that this species is characteristic of for stratified, sulfidic environments worldwide and its autotrophic metabolism has been studied in depth since. We describe here the first high-quality draft genome of a large-celled, phototrophic, γ-proteobacteria of the genus Chromatium isolated from the stratified alpine Lake Cadagno, C. okenii strain LaCa. Long read technology was used to assemble the 3.78 Mb genome that encodes 3,016 protein-coding genes and 67 RNA genes. Our findings are discussed from an ecological perspective related to Lake Cadagno. Moreover, findings of previous studies on the phototrophic and the proposed chemoautotrophic metabolism of C. okenii were confirmed on a genomic level. We additionally compared the C. okenii genome with other genomes of sequenced, phototrophic sulfur bacteria from the same environment. We found that biological functions involved in chemotaxis, movement and S-layer-proteins were enriched in strain LaCa. We describe these features as possible adaptions of strain LaCa to rapidly changing environmental conditions within the chemocline and the protection against phage infection during blooms. The high quality draft genome of C. okenii strain LaCa thereby provides a basis for future functional research on bioconvection and phage infection dynamics of blooming PSB.
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Affiliation(s)
- Samuel M Luedin
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland.
- Laboratory of Applied Microbiology, Department of Environment, Constructions and Design, University of Applied Sciences of Southern Switzerland (SUPSI), Bellinzona, Switzerland.
- Biology Division, Spiez Laboratory, Federal Office for Civil Protection, Spiez, Switzerland.
| | - Nicole Liechti
- Biology Division, Spiez Laboratory, Federal Office for Civil Protection, Spiez, Switzerland
- Interfaculty Bioinformatics Unit, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Raymond P Cox
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Francesco Danza
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
- Laboratory of Applied Microbiology, Department of Environment, Constructions and Design, University of Applied Sciences of Southern Switzerland (SUPSI), Bellinzona, Switzerland
| | | | - Nicole R Posth
- Department of Biology, University of Southern Denmark, Odense, Denmark
- Department of Geosciences and Natural Resource Management (IGN), University of Copenhagen, Copenhagen, Denmark
| | - Joël F Pothier
- Environmental Genomics and System Biology Research Group, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Samuele Roman
- Laboratory of Applied Microbiology, Department of Environment, Constructions and Design, University of Applied Sciences of Southern Switzerland (SUPSI), Bellinzona, Switzerland
- Alpine Biology Center Foundation, Bellinzona, Switzerland
| | - Nicola Storelli
- Laboratory of Applied Microbiology, Department of Environment, Constructions and Design, University of Applied Sciences of Southern Switzerland (SUPSI), Bellinzona, Switzerland
| | - Matthias Wittwer
- Biology Division, Spiez Laboratory, Federal Office for Civil Protection, Spiez, Switzerland
| | - Mauro Tonolla
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland.
- Laboratory of Applied Microbiology, Department of Environment, Constructions and Design, University of Applied Sciences of Southern Switzerland (SUPSI), Bellinzona, Switzerland.
- Alpine Biology Center Foundation, Bellinzona, Switzerland.
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10
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Bacterial diversity in the water column of meromictic Lake Cadagno and evidence for seasonal dynamics. PLoS One 2018; 13:e0209743. [PMID: 30586464 PMCID: PMC6306205 DOI: 10.1371/journal.pone.0209743] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 12/11/2018] [Indexed: 11/19/2022] Open
Abstract
The meromictic Lake Cadagno is characterized by a compact chemocline with high concentrations of anoxygenic phototrophic purple and green sulfur bacteria. However, a complete picture of the bacterial diversity, and in particular of effects of seasonality and compartmentalization is missing. To characterize bacterial communities and elucidate relationships between them and their surrounding environment high-throughput 16S rRNA gene pyrosequencing was conducted. Proteobacteria, Chlorobi, Verrucomicrobia, and Actinobacteria were the dominant groups in Lake Cadagno water column. Moreover, bacterial interaction within the chemocline and between oxic and anoxic lake compartments were investigated through fluorescence in situ hybridization (FISH) and flow cytometry (FCM). The different populations of purple sulfur bacteria (PSB) and green sulfur bacteria (GSB) in the chemocline indicate seasonal dynamics of phototrophic sulfur bacteria composition. Interestingly, an exceptional bloom of a cyanobacteria population in the oxic-anoxic transition zone affected the common spatial distribution of phototrophic sulfur bacteria with consequence on chemocline location and water column stability. Our study suggests that both bacterial interactions between different lake compartments and within the chemocline can be a dynamic process influencing the stratification structure of Lake Cadagno water column.
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