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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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Shiny Matilda C, Madhusudan I, Gaurav Isola R, Shanthi C. Potential of proteomics to probe microbes. J Basic Microbiol 2020; 60:471-483. [PMID: 32212201 DOI: 10.1002/jobm.201900628] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 02/26/2020] [Accepted: 03/04/2020] [Indexed: 01/05/2023]
Abstract
An organism exposed to a plethora of environmental perturbations undergoes proteomic changes which enable the characterization of total proteins in it. Much of the proteomic information is obtained from genomic data. Additional information on the proteome such as posttranslational modifications, protein-protein interactions, protein localization, metabolic pathways, and so on are deduced using proteomic tools which genomics and transcriptomics fail to offer. The proteomic analysis allows identification of precise changes in proteins, which in turn solve the complexity of microbial population providing insights into the microbial metabolism, cellular pathways, and behavior of microorganisms in new environments. Furthermore, they provide clues for the exploitation of their special features for biotechnological applications. Numerous techniques for the analysis of microbial proteome such as electrophoretic, chromatographic, mass spectrometric-based methods as well as quantitative proteomics are available which facilitate protein separation, expression, identification, and quantification of proteins. An understanding of the potential of each of the proteomic tools has created a significant impact on diverse microbiological aspects and the same has been discussed in this review.
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Affiliation(s)
- Chellaiah Shiny Matilda
- Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, India
| | - Iyengar Madhusudan
- Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, India
| | - Ravi Gaurav Isola
- Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, India
| | - Chittibabu Shanthi
- Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, India
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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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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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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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Complete genome sequence of " Thiodictyon syntrophicum" sp. nov. strain Cad16 T, a photolithoautotrophic purple sulfur bacterium isolated from the alpine meromictic Lake Cadagno. Stand Genomic Sci 2018; 13:14. [PMID: 29774086 PMCID: PMC5944118 DOI: 10.1186/s40793-018-0317-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 04/24/2018] [Indexed: 11/16/2022] Open
Abstract
“Thiodictyon syntrophicum” sp. nov. strain Cad16T is a photoautotrophic purple sulfur bacterium belonging to the family of Chromatiaceae in the class of Gammaproteobacteria. The type strain Cad16T was isolated from the chemocline of the alpine meromictic Lake Cadagno in Switzerland. Strain Cad16T represents a key species within this sulfur-driven bacterial ecosystem with respect to carbon fixation. The 7.74-Mbp genome of strain Cad16T has been sequenced and annotated. It encodes 6237 predicted protein sequences and 59 RNA sequences. Phylogenetic comparison based on 16S rRNA revealed that Thiodictyon elegans strain DSM 232T the most closely related species. Genes involved in sulfur oxidation, central carbon metabolism and transmembrane transport were found. Noteworthy, clusters of genes encoding the photosynthetic machinery and pigment biosynthesis are found on the 0.48 Mb plasmid pTs485. We provide a detailed insight into the Cad16T genome and analyze it in the context of the microbial ecosystem of Lake Cadagno.
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Thiel V, Tank M, Bryant DA. Diversity of Chlorophototrophic Bacteria Revealed in the Omics Era. ANNUAL REVIEW OF PLANT BIOLOGY 2018; 69:21-49. [PMID: 29505738 DOI: 10.1146/annurev-arplant-042817-040500] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Because of recent advances in omics methodologies, knowledge of chlorophototrophy (i.e., chlorophyll-based phototrophy) in bacteria has rapidly increased. Chlorophototrophs currently are known to occur in seven bacterial phyla: Cyanobacteria, Proteobacteria, Chlorobi, Chloroflexi, Firmicutes, Acidobacteria, and Gemmatimonadetes. Other organisms that can produce chlorophylls and photochemical reaction centers may still be undiscovered. Here we summarize the current status of the taxonomy and phylogeny of chlorophototrophic bacteria as revealed by genomic methods. In specific cases, we briefly describe important ecophysiological and metabolic insights that have been gained from the application of genomic methods to these bacteria. In the 20 years since the completion of the Synechocystis sp. PCC 6803 genome in 1996, approximately 1,100 genomes have been sequenced, which represents nearly the complete diversity of known chlorophototrophic bacteria. These data are leading to new insights into many important processes, including photosynthesis, nitrogen and carbon fixation, cellular differentiation and development, symbiosis, and ecosystem functionality.
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Affiliation(s)
- Vera Thiel
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan; ,
| | - Marcus Tank
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan; ,
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA;
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, USA
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