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Ramunas Stepanauskas - One of the best experts on this subject based on the ideXlab platform.
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Ubiquitous Gammaproteobacteria dominate dark Carbon Fixation in coastal sediments
The ISME Journal, 2016Co-Authors: Stefan Dyksma, Kerstin Bischof, Bernhard M Fuchs, Katy Hoffmann, Dimitri Meier, Anke Meyerdierks, Petra Pjevac, David Probandt, Michael Richter, Ramunas StepanauskasAbstract:Marine sediments are the largest Carbon sink on earth. Nearly half of dark Carbon Fixation in the oceans occurs in coastal sediments, but the microorganisms responsible are largely unknown. By integrating the 16S rRNA approach, single-cell genomics, metagenomics and transcriptomics with ^14C-Carbon assimilation experiments, we show that uncultured Gammaproteobacteria account for 70–86% of dark Carbon Fixation in coastal sediments. First, we surveyed the bacterial 16S rRNA gene diversity of 13 tidal and sublittoral sediments across Europe and Australia to identify ubiquitous core groups of Gammaproteobacteria mainly affiliating with sulfur-oxidizing bacteria. These also accounted for a substantial fraction of the microbial community in anoxic, 490-cm-deep subsurface sediments. We then quantified dark Carbon Fixation by scintillography of specific microbial populations extracted and flow-sorted from sediments that were short-term incubated with ^14C-biCarbonate. We identified three distinct gammaproteobacterial clades covering diversity ranges on family to order level (the Acidiferrobacter , JTB255 and SSr clades) that made up >50% of dark Carbon Fixation in a tidal sediment. Consistent with these activity measurements, environmental transcripts of sulfur oxidation and Carbon Fixation genes mainly affiliated with those of sulfur-oxidizing Gammaproteobacteria . The co-localization of key genes of sulfur and hydrogen oxidation pathways and their expression in genomes of uncultured Gammaproteobacteria illustrates an unknown metabolic plasticity for sulfur oxidizers in marine sediments. Given their global distribution and high abundance, we propose that a stable assemblage of metabolically flexible Gammaproteobacteria drives important parts of marine Carbon and sulfur cycles.
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Ubiquitous Gammaproteobacteria dominate dark Carbon Fixation in coastal sediments.
The ISME Journal, 2016Co-Authors: Stefan Dyksma, Kerstin Bischof, Bernhard M Fuchs, Katy Hoffmann, Anke Meyerdierks, Petra Pjevac, David Probandt, Michael Richter, Dimitri V. Meier, Ramunas StepanauskasAbstract:Marine sediments are the largest Carbon sink on earth. Nearly half of dark Carbon Fixation in the oceans occurs in coastal sediments, but the microorganisms responsible are largely unknown. By integrating the 16S rRNA approach, single-cell genomics, metagenomics and transcriptomics with (14)C-Carbon assimilation experiments, we show that uncultured Gammaproteobacteria account for 70-86% of dark Carbon Fixation in coastal sediments. First, we surveyed the bacterial 16S rRNA gene diversity of 13 tidal and sublittoral sediments across Europe and Australia to identify ubiquitous core groups of Gammaproteobacteria mainly affiliating with sulfur-oxidizing bacteria. These also accounted for a substantial fraction of the microbial community in anoxic, 490-cm-deep subsurface sediments. We then quantified dark Carbon Fixation by scintillography of specific microbial populations extracted and flow-sorted from sediments that were short-term incubated with (14)C-biCarbonate. We identified three distinct gammaproteobacterial clades covering diversity ranges on family to order level (the Acidiferrobacter, JTB255 and SSr clades) that made up >50% of dark Carbon Fixation in a tidal sediment. Consistent with these activity measurements, environmental transcripts of sulfur oxidation and Carbon Fixation genes mainly affiliated with those of sulfur-oxidizing Gammaproteobacteria. The co-localization of key genes of sulfur and hydrogen oxidation pathways and their expression in genomes of uncultured Gammaproteobacteria illustrates an unknown metabolic plasticity for sulfur oxidizers in marine sediments. Given their global distribution and high abundance, we propose that a stable assemblage of metabolically flexible Gammaproteobacteria drives important parts of marine Carbon and sulfur cycles.
Stefan Dyksma - One of the best experts on this subject based on the ideXlab platform.
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In situ abundance and Carbon Fixation activity of distinct anoxygenic phototrophs in the stratified seawater lake Rogoznica
bioRxiv, 2019Co-Authors: Petra Pjevac, Stefan Dyksma, Tobias Goldhammer, Izabela Mujakić, Michal Koblížek, Marc Mußmann, Rudolf Amann, Sandi OrlićAbstract:Abstract Sulfide-driven anoxygenic photosynthesis is an ancient microbial metabolism that contributes significantly to inorganic Carbon Fixation in stratified, sulfidic water bodies. Methods commonly applied to quantify inorganic Carbon Fixation by anoxygenic phototrophs, however, cannot resolve the contributions of distinct microbial populations to the overall process. We implemented a straightforward workflow, consisting of radioisotope labeling and flow cytometric cell sorting based on the distinct autofluorescence of bacterial photo pigments, to discriminate and quantify contributions of co-occurring anoxygenic phototrophic populations to in situ inorganic Carbon Fixation in environmental samples. This allowed us to assign 89.3 ±7.6% of daytime inorganic Carbon Fixation by anoxygenic phototrophs in Lake Rogoznica (Croatia) to an abundant chemocline-dwelling population of green sulfur bacteria (dominated by Chlorobium phaeobacteroides), whereas the co-occurring purple sulfur bacteria (Halochromatium sp.) contributed only 1.8 ±1.4%. Furthermore, we obtained two metagenome assembled genomes of green sulfur bacteria and one of a purple sulfur bacterium which provides the first genomic insights into the genus Halochromatium, confirming its high metabolic flexibility and physiological potential for mixo-and heterotrophic growth.
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Ubiquitous Gammaproteobacteria dominate dark Carbon Fixation in coastal sediments
The ISME Journal, 2016Co-Authors: Stefan Dyksma, Kerstin Bischof, Bernhard M Fuchs, Katy Hoffmann, Dimitri Meier, Anke Meyerdierks, Petra Pjevac, David Probandt, Michael Richter, Ramunas StepanauskasAbstract:Marine sediments are the largest Carbon sink on earth. Nearly half of dark Carbon Fixation in the oceans occurs in coastal sediments, but the microorganisms responsible are largely unknown. By integrating the 16S rRNA approach, single-cell genomics, metagenomics and transcriptomics with ^14C-Carbon assimilation experiments, we show that uncultured Gammaproteobacteria account for 70–86% of dark Carbon Fixation in coastal sediments. First, we surveyed the bacterial 16S rRNA gene diversity of 13 tidal and sublittoral sediments across Europe and Australia to identify ubiquitous core groups of Gammaproteobacteria mainly affiliating with sulfur-oxidizing bacteria. These also accounted for a substantial fraction of the microbial community in anoxic, 490-cm-deep subsurface sediments. We then quantified dark Carbon Fixation by scintillography of specific microbial populations extracted and flow-sorted from sediments that were short-term incubated with ^14C-biCarbonate. We identified three distinct gammaproteobacterial clades covering diversity ranges on family to order level (the Acidiferrobacter , JTB255 and SSr clades) that made up >50% of dark Carbon Fixation in a tidal sediment. Consistent with these activity measurements, environmental transcripts of sulfur oxidation and Carbon Fixation genes mainly affiliated with those of sulfur-oxidizing Gammaproteobacteria . The co-localization of key genes of sulfur and hydrogen oxidation pathways and their expression in genomes of uncultured Gammaproteobacteria illustrates an unknown metabolic plasticity for sulfur oxidizers in marine sediments. Given their global distribution and high abundance, we propose that a stable assemblage of metabolically flexible Gammaproteobacteria drives important parts of marine Carbon and sulfur cycles.
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Ubiquitous Gammaproteobacteria dominate dark Carbon Fixation in coastal sediments.
The ISME Journal, 2016Co-Authors: Stefan Dyksma, Kerstin Bischof, Bernhard M Fuchs, Katy Hoffmann, Anke Meyerdierks, Petra Pjevac, David Probandt, Michael Richter, Dimitri V. Meier, Ramunas StepanauskasAbstract:Marine sediments are the largest Carbon sink on earth. Nearly half of dark Carbon Fixation in the oceans occurs in coastal sediments, but the microorganisms responsible are largely unknown. By integrating the 16S rRNA approach, single-cell genomics, metagenomics and transcriptomics with (14)C-Carbon assimilation experiments, we show that uncultured Gammaproteobacteria account for 70-86% of dark Carbon Fixation in coastal sediments. First, we surveyed the bacterial 16S rRNA gene diversity of 13 tidal and sublittoral sediments across Europe and Australia to identify ubiquitous core groups of Gammaproteobacteria mainly affiliating with sulfur-oxidizing bacteria. These also accounted for a substantial fraction of the microbial community in anoxic, 490-cm-deep subsurface sediments. We then quantified dark Carbon Fixation by scintillography of specific microbial populations extracted and flow-sorted from sediments that were short-term incubated with (14)C-biCarbonate. We identified three distinct gammaproteobacterial clades covering diversity ranges on family to order level (the Acidiferrobacter, JTB255 and SSr clades) that made up >50% of dark Carbon Fixation in a tidal sediment. Consistent with these activity measurements, environmental transcripts of sulfur oxidation and Carbon Fixation genes mainly affiliated with those of sulfur-oxidizing Gammaproteobacteria. The co-localization of key genes of sulfur and hydrogen oxidation pathways and their expression in genomes of uncultured Gammaproteobacteria illustrates an unknown metabolic plasticity for sulfur oxidizers in marine sediments. Given their global distribution and high abundance, we propose that a stable assemblage of metabolically flexible Gammaproteobacteria drives important parts of marine Carbon and sulfur cycles.
Petra Pjevac - One of the best experts on this subject based on the ideXlab platform.
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In situ abundance and Carbon Fixation activity of distinct anoxygenic phototrophs in the stratified seawater lake Rogoznica
bioRxiv, 2019Co-Authors: Petra Pjevac, Stefan Dyksma, Tobias Goldhammer, Izabela Mujakić, Michal Koblížek, Marc Mußmann, Rudolf Amann, Sandi OrlićAbstract:Abstract Sulfide-driven anoxygenic photosynthesis is an ancient microbial metabolism that contributes significantly to inorganic Carbon Fixation in stratified, sulfidic water bodies. Methods commonly applied to quantify inorganic Carbon Fixation by anoxygenic phototrophs, however, cannot resolve the contributions of distinct microbial populations to the overall process. We implemented a straightforward workflow, consisting of radioisotope labeling and flow cytometric cell sorting based on the distinct autofluorescence of bacterial photo pigments, to discriminate and quantify contributions of co-occurring anoxygenic phototrophic populations to in situ inorganic Carbon Fixation in environmental samples. This allowed us to assign 89.3 ±7.6% of daytime inorganic Carbon Fixation by anoxygenic phototrophs in Lake Rogoznica (Croatia) to an abundant chemocline-dwelling population of green sulfur bacteria (dominated by Chlorobium phaeobacteroides), whereas the co-occurring purple sulfur bacteria (Halochromatium sp.) contributed only 1.8 ±1.4%. Furthermore, we obtained two metagenome assembled genomes of green sulfur bacteria and one of a purple sulfur bacterium which provides the first genomic insights into the genus Halochromatium, confirming its high metabolic flexibility and physiological potential for mixo-and heterotrophic growth.
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Ubiquitous Gammaproteobacteria dominate dark Carbon Fixation in coastal sediments
The ISME Journal, 2016Co-Authors: Stefan Dyksma, Kerstin Bischof, Bernhard M Fuchs, Katy Hoffmann, Dimitri Meier, Anke Meyerdierks, Petra Pjevac, David Probandt, Michael Richter, Ramunas StepanauskasAbstract:Marine sediments are the largest Carbon sink on earth. Nearly half of dark Carbon Fixation in the oceans occurs in coastal sediments, but the microorganisms responsible are largely unknown. By integrating the 16S rRNA approach, single-cell genomics, metagenomics and transcriptomics with ^14C-Carbon assimilation experiments, we show that uncultured Gammaproteobacteria account for 70–86% of dark Carbon Fixation in coastal sediments. First, we surveyed the bacterial 16S rRNA gene diversity of 13 tidal and sublittoral sediments across Europe and Australia to identify ubiquitous core groups of Gammaproteobacteria mainly affiliating with sulfur-oxidizing bacteria. These also accounted for a substantial fraction of the microbial community in anoxic, 490-cm-deep subsurface sediments. We then quantified dark Carbon Fixation by scintillography of specific microbial populations extracted and flow-sorted from sediments that were short-term incubated with ^14C-biCarbonate. We identified three distinct gammaproteobacterial clades covering diversity ranges on family to order level (the Acidiferrobacter , JTB255 and SSr clades) that made up >50% of dark Carbon Fixation in a tidal sediment. Consistent with these activity measurements, environmental transcripts of sulfur oxidation and Carbon Fixation genes mainly affiliated with those of sulfur-oxidizing Gammaproteobacteria . The co-localization of key genes of sulfur and hydrogen oxidation pathways and their expression in genomes of uncultured Gammaproteobacteria illustrates an unknown metabolic plasticity for sulfur oxidizers in marine sediments. Given their global distribution and high abundance, we propose that a stable assemblage of metabolically flexible Gammaproteobacteria drives important parts of marine Carbon and sulfur cycles.
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Ubiquitous Gammaproteobacteria dominate dark Carbon Fixation in coastal sediments.
The ISME Journal, 2016Co-Authors: Stefan Dyksma, Kerstin Bischof, Bernhard M Fuchs, Katy Hoffmann, Anke Meyerdierks, Petra Pjevac, David Probandt, Michael Richter, Dimitri V. Meier, Ramunas StepanauskasAbstract:Marine sediments are the largest Carbon sink on earth. Nearly half of dark Carbon Fixation in the oceans occurs in coastal sediments, but the microorganisms responsible are largely unknown. By integrating the 16S rRNA approach, single-cell genomics, metagenomics and transcriptomics with (14)C-Carbon assimilation experiments, we show that uncultured Gammaproteobacteria account for 70-86% of dark Carbon Fixation in coastal sediments. First, we surveyed the bacterial 16S rRNA gene diversity of 13 tidal and sublittoral sediments across Europe and Australia to identify ubiquitous core groups of Gammaproteobacteria mainly affiliating with sulfur-oxidizing bacteria. These also accounted for a substantial fraction of the microbial community in anoxic, 490-cm-deep subsurface sediments. We then quantified dark Carbon Fixation by scintillography of specific microbial populations extracted and flow-sorted from sediments that were short-term incubated with (14)C-biCarbonate. We identified three distinct gammaproteobacterial clades covering diversity ranges on family to order level (the Acidiferrobacter, JTB255 and SSr clades) that made up >50% of dark Carbon Fixation in a tidal sediment. Consistent with these activity measurements, environmental transcripts of sulfur oxidation and Carbon Fixation genes mainly affiliated with those of sulfur-oxidizing Gammaproteobacteria. The co-localization of key genes of sulfur and hydrogen oxidation pathways and their expression in genomes of uncultured Gammaproteobacteria illustrates an unknown metabolic plasticity for sulfur oxidizers in marine sediments. Given their global distribution and high abundance, we propose that a stable assemblage of metabolically flexible Gammaproteobacteria drives important parts of marine Carbon and sulfur cycles.
Solange Duhamel - One of the best experts on this subject based on the ideXlab platform.
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Heterotrophic Carbon Fixation in a Salamander-Alga Symbiosis.
Frontiers in Microbiology, 2020Co-Authors: John A. Burns, Ryan Kerney, Solange DuhamelAbstract:The unique symbiosis between a vertebrate salamander, Ambystoma maculatum, and unicellular green alga, Oophila amblystomatis, involves multiple modes of interaction. These include an ectosymbiotic interaction where the alga colonizes the egg capsule, and an intracellular interaction where the alga enters tissues and cells of the salamander. One common interaction in mutualist photosymbioses is the transfer of photosynthate from the algal symbiont to the host animal. In the A. maculatum-O. amblystomatis interaction, there is conflicting evidence regarding whether the algae in the egg capsule transfer chemical energy captured during photosynthesis to the developing salamander embryo. In experiments where we took care to separate the Carbon Fixation contributions of the salamander embryo and algal symbionts, we show that inorganic Carbon fixed by A. maculatum embryos reaches 2% of the inorganic Carbon fixed by O. amblystomatis algae within an egg capsule after 2 hours in the light. After 2 hours in the dark, inorganic Carbon fixed by A. maculatum embryos is 800% of the Carbon fixed by O. amblystomatis algae within an egg capsule. Using photosynthesis inhibitors we show that A. maculatum embryos and O. amblystomatis algae compete for available inorganic Carbon within the egg capsule environment. Our results confirm earlier studies suggesting a role of heterotrophic Carbon Fixation during vertebrate embryonic development. Our results also show that the considerable capacity of developing A. maculatum embryos for inorganic Carbon Fixation precludes our ability to distinguish any minor role of photosynthetically transferred Carbon from algal symbionts to host salamanders using biCarbonate introduced to the egg system as a marker.
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Heterotrophic Carbon Fixation in a Salamander-Alga Symbiosis
bioRxiv, 2020Co-Authors: John A. Burns, Ryan Kerney, Solange DuhamelAbstract:The unique symbiosis between a vertebrate salamander, Ambystoma maculatum, and unicellular green alga, Oophila amblystomatis, involves multiple modes of interaction. These include an ectosymbiotic interaction where the alga colonizes the egg capsule, and an intracellular interaction where the alga enters tissues and cells of the salamander. One common interaction in mutualist photosymbioses is the transfer of photosynthate from the algal symbiont to the host animal. In the A. maculatum-O. amblystomatis interaction, there is conflicting evidence regarding whether the algae in the egg capsule transfer chemical energy captured during photosynthesis to the developing salamander embryo. In experiments where we took care to separate the Carbon Fixation contributions of the salamander embryo and algal symbionts, we show that inorganic Carbon fixed by A. maculatum embryos reaches 2% of the inorganic Carbon fixed by O. amblystomatis algae within an egg capsule after 2 hours in the light. When eggs are rather incubated for 2 hours in the dark, inorganic Carbon fixed by A. maculatum embryos is 800% of the Carbon fixed by O. amblystomatis algae within an egg capsule. Using photosynthesis inhibitors we show that A. maculatum embryos and O. amblystomatis algae compete for available inorganic Carbon within the egg capsule environment. Our results confirm earlier studies suggesting a role of heterotrophic Carbon Fixation during vertebrate embryonic development. Our results also show that the considerable capacity of developing A. maculatum embryos for inorganic Carbon Fixation precludes our ability to distinguish any minor role of photosynthetically transferred Carbon from algal symbionts to host salamanders using biCarbonate introduced to the egg system as a marker.
Bernhard M Fuchs - One of the best experts on this subject based on the ideXlab platform.
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Ubiquitous Gammaproteobacteria dominate dark Carbon Fixation in coastal sediments
The ISME Journal, 2016Co-Authors: Stefan Dyksma, Kerstin Bischof, Bernhard M Fuchs, Katy Hoffmann, Dimitri Meier, Anke Meyerdierks, Petra Pjevac, David Probandt, Michael Richter, Ramunas StepanauskasAbstract:Marine sediments are the largest Carbon sink on earth. Nearly half of dark Carbon Fixation in the oceans occurs in coastal sediments, but the microorganisms responsible are largely unknown. By integrating the 16S rRNA approach, single-cell genomics, metagenomics and transcriptomics with ^14C-Carbon assimilation experiments, we show that uncultured Gammaproteobacteria account for 70–86% of dark Carbon Fixation in coastal sediments. First, we surveyed the bacterial 16S rRNA gene diversity of 13 tidal and sublittoral sediments across Europe and Australia to identify ubiquitous core groups of Gammaproteobacteria mainly affiliating with sulfur-oxidizing bacteria. These also accounted for a substantial fraction of the microbial community in anoxic, 490-cm-deep subsurface sediments. We then quantified dark Carbon Fixation by scintillography of specific microbial populations extracted and flow-sorted from sediments that were short-term incubated with ^14C-biCarbonate. We identified three distinct gammaproteobacterial clades covering diversity ranges on family to order level (the Acidiferrobacter , JTB255 and SSr clades) that made up >50% of dark Carbon Fixation in a tidal sediment. Consistent with these activity measurements, environmental transcripts of sulfur oxidation and Carbon Fixation genes mainly affiliated with those of sulfur-oxidizing Gammaproteobacteria . The co-localization of key genes of sulfur and hydrogen oxidation pathways and their expression in genomes of uncultured Gammaproteobacteria illustrates an unknown metabolic plasticity for sulfur oxidizers in marine sediments. Given their global distribution and high abundance, we propose that a stable assemblage of metabolically flexible Gammaproteobacteria drives important parts of marine Carbon and sulfur cycles.
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Ubiquitous Gammaproteobacteria dominate dark Carbon Fixation in coastal sediments.
The ISME Journal, 2016Co-Authors: Stefan Dyksma, Kerstin Bischof, Bernhard M Fuchs, Katy Hoffmann, Anke Meyerdierks, Petra Pjevac, David Probandt, Michael Richter, Dimitri V. Meier, Ramunas StepanauskasAbstract:Marine sediments are the largest Carbon sink on earth. Nearly half of dark Carbon Fixation in the oceans occurs in coastal sediments, but the microorganisms responsible are largely unknown. By integrating the 16S rRNA approach, single-cell genomics, metagenomics and transcriptomics with (14)C-Carbon assimilation experiments, we show that uncultured Gammaproteobacteria account for 70-86% of dark Carbon Fixation in coastal sediments. First, we surveyed the bacterial 16S rRNA gene diversity of 13 tidal and sublittoral sediments across Europe and Australia to identify ubiquitous core groups of Gammaproteobacteria mainly affiliating with sulfur-oxidizing bacteria. These also accounted for a substantial fraction of the microbial community in anoxic, 490-cm-deep subsurface sediments. We then quantified dark Carbon Fixation by scintillography of specific microbial populations extracted and flow-sorted from sediments that were short-term incubated with (14)C-biCarbonate. We identified three distinct gammaproteobacterial clades covering diversity ranges on family to order level (the Acidiferrobacter, JTB255 and SSr clades) that made up >50% of dark Carbon Fixation in a tidal sediment. Consistent with these activity measurements, environmental transcripts of sulfur oxidation and Carbon Fixation genes mainly affiliated with those of sulfur-oxidizing Gammaproteobacteria. The co-localization of key genes of sulfur and hydrogen oxidation pathways and their expression in genomes of uncultured Gammaproteobacteria illustrates an unknown metabolic plasticity for sulfur oxidizers in marine sediments. Given their global distribution and high abundance, we propose that a stable assemblage of metabolically flexible Gammaproteobacteria drives important parts of marine Carbon and sulfur cycles.