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Daan R. Speth - One of the best experts on this subject based on the ideXlab platform.
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the metagenome of the marine anammox bacterium candidatus scalindua profunda illustrates the versatility of this globally important Nitrogen Cycle bacterium
Environmental Microbiology, 2013Co-Authors: Jack Van De Vossenberg, Boran Kartal, Hans J. C. T. Wessels, Jia Yan, Bas E. Dutilh, Wouter J. Maalcke, Dagmar Woebken, Eva M Janssenmegens, Guus Roeselers, Daan R. SpethAbstract:Anaerobic ammonium-oxidizing (anammox) bacteria are responsible for a significant portion of the loss of fixed Nitrogen from the oceans, making them important players in the global Nitrogen Cycle. To date, marine anammox bacteria found in marine water columns and sediments worldwide belong almost exclusively to the ‘Candidatus Scalindua’ species, but the molecular basis of their metabolism and competitive fitness is presently unknown. We applied community sequencing of a marine anammox enrichment culture dominated by ‘Candidatus Scalindua profunda’ to construct a genome assembly, which was subsequently used to analyse the most abundant gene transcripts and proteins. In the S. profunda assembly, 4756 genes were annotated, and only about half of them showed the highest identity to the only other anammox bacterium of which a metagenome assembly had been constructed so far, the freshwater ‘Candidatus Kuenenia stuttgartiensis’. In total, 2016 genes of S. profunda could not be matched to the K. stuttgartiensis metagenome assembly at all, and a similar number of genes in K. stuttgartiensis could not be found in S. profunda. Most of these genes did not have a known function but 98 expressed genes could be attributed to oligopeptide transport, amino acid metabolism, use of organic acids and electron transport. On the basis of the S. profunda metagenome, and environmental metagenome data, we observed pronounced differences in the gene organization and expression of important anammox enzymes, such as hydrazine synthase (HzsAB), nitrite reductase (NirS) and inorganic Nitrogen transport proteins. Adaptations of Scalindua to the substrate limitation of the ocean may include highly expressed ammonium, nitrite and oligopeptide transport systems and pathways for the transport, oxidation, and assimilation of small organic compounds that may allow a more versatile lifestyle contributing to the competitive fitness of Scalindua in the marine realm.
Jack Van De Vossenberg - One of the best experts on this subject based on the ideXlab platform.
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the metagenome of the marine anammox bacterium candidatus scalindua profunda illustrates the versatility of this globally important Nitrogen Cycle bacterium
Environmental Microbiology, 2013Co-Authors: Jack Van De Vossenberg, Boran Kartal, Hans J. C. T. Wessels, Jia Yan, Bas E. Dutilh, Wouter J. Maalcke, Dagmar Woebken, Eva M Janssenmegens, Guus Roeselers, Daan R. SpethAbstract:Anaerobic ammonium-oxidizing (anammox) bacteria are responsible for a significant portion of the loss of fixed Nitrogen from the oceans, making them important players in the global Nitrogen Cycle. To date, marine anammox bacteria found in marine water columns and sediments worldwide belong almost exclusively to the ‘Candidatus Scalindua’ species, but the molecular basis of their metabolism and competitive fitness is presently unknown. We applied community sequencing of a marine anammox enrichment culture dominated by ‘Candidatus Scalindua profunda’ to construct a genome assembly, which was subsequently used to analyse the most abundant gene transcripts and proteins. In the S. profunda assembly, 4756 genes were annotated, and only about half of them showed the highest identity to the only other anammox bacterium of which a metagenome assembly had been constructed so far, the freshwater ‘Candidatus Kuenenia stuttgartiensis’. In total, 2016 genes of S. profunda could not be matched to the K. stuttgartiensis metagenome assembly at all, and a similar number of genes in K. stuttgartiensis could not be found in S. profunda. Most of these genes did not have a known function but 98 expressed genes could be attributed to oligopeptide transport, amino acid metabolism, use of organic acids and electron transport. On the basis of the S. profunda metagenome, and environmental metagenome data, we observed pronounced differences in the gene organization and expression of important anammox enzymes, such as hydrazine synthase (HzsAB), nitrite reductase (NirS) and inorganic Nitrogen transport proteins. Adaptations of Scalindua to the substrate limitation of the ocean may include highly expressed ammonium, nitrite and oligopeptide transport systems and pathways for the transport, oxidation, and assimilation of small organic compounds that may allow a more versatile lifestyle contributing to the competitive fitness of Scalindua in the marine realm.
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revising the Nitrogen Cycle in the peruvian oxygen minimum zone
Proceedings of the National Academy of Sciences of the United States of America, 2009Co-Authors: Phyllis Lam, Jack Van De Vossenberg, Dagmar Woebken, Gaute Lavik, Marlene Mark Jensen, Markus Schmid, Dimitri Gutierrez, Rudolf Amann, Mike S M Jetten, Marcel M. M. KuypersAbstract:The oxygen minimum zone (OMZ) of the Eastern Tropical South Pacific (ETSP) is 1 of the 3 major regions in the world where oceanic Nitrogen is lost in the pelagic realm. The recent identification of anammox, instead of denitrification, as the likely prevalent pathway for Nitrogen loss in this OMZ raises strong questions about our understanding of Nitrogen cycling and organic matter remineralization in these waters. Without detectable denitrification, it is unclear how NH4+ is remineralized from organic matter and sustains anammox or how secondary NO2− maxima arise within the OMZ. Here we show that in the ETSP-OMZ, anammox obtains 67% or more of NO2− from nitrate reduction, and 33% or less from aerobic ammonia oxidation, based on stable-isotope pairing experiments corroborated by functional gene expression analyses. Dissimilatory nitrate reduction to ammonium was detected in an open-ocean setting. It occurred throughout the OMZ and could satisfy a substantial part of the NH4+ requirement for anammox. The remaining NH4+ came from remineralization via nitrate reduction and probably from microaerobic respiration. Altogether, deep-sea NO3− accounted for only ≈50% of the Nitrogen loss in the ETSP, rather than 100% as commonly assumed. Because oceanic OMZs seem to be expanding because of global climate change, it is increasingly imperative to incorporate the correct Nitrogen-loss pathways in global biogeochemical models to predict more accurately how the Nitrogen Cycle in our future ocean may respond.
Dagmar Woebken - One of the best experts on this subject based on the ideXlab platform.
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the metagenome of the marine anammox bacterium candidatus scalindua profunda illustrates the versatility of this globally important Nitrogen Cycle bacterium
Environmental Microbiology, 2013Co-Authors: Jack Van De Vossenberg, Boran Kartal, Hans J. C. T. Wessels, Jia Yan, Bas E. Dutilh, Wouter J. Maalcke, Dagmar Woebken, Eva M Janssenmegens, Guus Roeselers, Daan R. SpethAbstract:Anaerobic ammonium-oxidizing (anammox) bacteria are responsible for a significant portion of the loss of fixed Nitrogen from the oceans, making them important players in the global Nitrogen Cycle. To date, marine anammox bacteria found in marine water columns and sediments worldwide belong almost exclusively to the ‘Candidatus Scalindua’ species, but the molecular basis of their metabolism and competitive fitness is presently unknown. We applied community sequencing of a marine anammox enrichment culture dominated by ‘Candidatus Scalindua profunda’ to construct a genome assembly, which was subsequently used to analyse the most abundant gene transcripts and proteins. In the S. profunda assembly, 4756 genes were annotated, and only about half of them showed the highest identity to the only other anammox bacterium of which a metagenome assembly had been constructed so far, the freshwater ‘Candidatus Kuenenia stuttgartiensis’. In total, 2016 genes of S. profunda could not be matched to the K. stuttgartiensis metagenome assembly at all, and a similar number of genes in K. stuttgartiensis could not be found in S. profunda. Most of these genes did not have a known function but 98 expressed genes could be attributed to oligopeptide transport, amino acid metabolism, use of organic acids and electron transport. On the basis of the S. profunda metagenome, and environmental metagenome data, we observed pronounced differences in the gene organization and expression of important anammox enzymes, such as hydrazine synthase (HzsAB), nitrite reductase (NirS) and inorganic Nitrogen transport proteins. Adaptations of Scalindua to the substrate limitation of the ocean may include highly expressed ammonium, nitrite and oligopeptide transport systems and pathways for the transport, oxidation, and assimilation of small organic compounds that may allow a more versatile lifestyle contributing to the competitive fitness of Scalindua in the marine realm.
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revising the Nitrogen Cycle in the peruvian oxygen minimum zone
Proceedings of the National Academy of Sciences of the United States of America, 2009Co-Authors: Phyllis Lam, Jack Van De Vossenberg, Dagmar Woebken, Gaute Lavik, Marlene Mark Jensen, Markus Schmid, Dimitri Gutierrez, Rudolf Amann, Mike S M Jetten, Marcel M. M. KuypersAbstract:The oxygen minimum zone (OMZ) of the Eastern Tropical South Pacific (ETSP) is 1 of the 3 major regions in the world where oceanic Nitrogen is lost in the pelagic realm. The recent identification of anammox, instead of denitrification, as the likely prevalent pathway for Nitrogen loss in this OMZ raises strong questions about our understanding of Nitrogen cycling and organic matter remineralization in these waters. Without detectable denitrification, it is unclear how NH4+ is remineralized from organic matter and sustains anammox or how secondary NO2− maxima arise within the OMZ. Here we show that in the ETSP-OMZ, anammox obtains 67% or more of NO2− from nitrate reduction, and 33% or less from aerobic ammonia oxidation, based on stable-isotope pairing experiments corroborated by functional gene expression analyses. Dissimilatory nitrate reduction to ammonium was detected in an open-ocean setting. It occurred throughout the OMZ and could satisfy a substantial part of the NH4+ requirement for anammox. The remaining NH4+ came from remineralization via nitrate reduction and probably from microaerobic respiration. Altogether, deep-sea NO3− accounted for only ≈50% of the Nitrogen loss in the ETSP, rather than 100% as commonly assumed. Because oceanic OMZs seem to be expanding because of global climate change, it is increasingly imperative to incorporate the correct Nitrogen-loss pathways in global biogeochemical models to predict more accurately how the Nitrogen Cycle in our future ocean may respond.
Boran Kartal - One of the best experts on this subject based on the ideXlab platform.
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the metagenome of the marine anammox bacterium candidatus scalindua profunda illustrates the versatility of this globally important Nitrogen Cycle bacterium
Environmental Microbiology, 2013Co-Authors: Jack Van De Vossenberg, Boran Kartal, Hans J. C. T. Wessels, Jia Yan, Bas E. Dutilh, Wouter J. Maalcke, Dagmar Woebken, Eva M Janssenmegens, Guus Roeselers, Daan R. SpethAbstract:Anaerobic ammonium-oxidizing (anammox) bacteria are responsible for a significant portion of the loss of fixed Nitrogen from the oceans, making them important players in the global Nitrogen Cycle. To date, marine anammox bacteria found in marine water columns and sediments worldwide belong almost exclusively to the ‘Candidatus Scalindua’ species, but the molecular basis of their metabolism and competitive fitness is presently unknown. We applied community sequencing of a marine anammox enrichment culture dominated by ‘Candidatus Scalindua profunda’ to construct a genome assembly, which was subsequently used to analyse the most abundant gene transcripts and proteins. In the S. profunda assembly, 4756 genes were annotated, and only about half of them showed the highest identity to the only other anammox bacterium of which a metagenome assembly had been constructed so far, the freshwater ‘Candidatus Kuenenia stuttgartiensis’. In total, 2016 genes of S. profunda could not be matched to the K. stuttgartiensis metagenome assembly at all, and a similar number of genes in K. stuttgartiensis could not be found in S. profunda. Most of these genes did not have a known function but 98 expressed genes could be attributed to oligopeptide transport, amino acid metabolism, use of organic acids and electron transport. On the basis of the S. profunda metagenome, and environmental metagenome data, we observed pronounced differences in the gene organization and expression of important anammox enzymes, such as hydrazine synthase (HzsAB), nitrite reductase (NirS) and inorganic Nitrogen transport proteins. Adaptations of Scalindua to the substrate limitation of the ocean may include highly expressed ammonium, nitrite and oligopeptide transport systems and pathways for the transport, oxidation, and assimilation of small organic compounds that may allow a more versatile lifestyle contributing to the competitive fitness of Scalindua in the marine realm.
Wouter J. Maalcke - One of the best experts on this subject based on the ideXlab platform.
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the metagenome of the marine anammox bacterium candidatus scalindua profunda illustrates the versatility of this globally important Nitrogen Cycle bacterium
Environmental Microbiology, 2013Co-Authors: Jack Van De Vossenberg, Boran Kartal, Hans J. C. T. Wessels, Jia Yan, Bas E. Dutilh, Wouter J. Maalcke, Dagmar Woebken, Eva M Janssenmegens, Guus Roeselers, Daan R. SpethAbstract:Anaerobic ammonium-oxidizing (anammox) bacteria are responsible for a significant portion of the loss of fixed Nitrogen from the oceans, making them important players in the global Nitrogen Cycle. To date, marine anammox bacteria found in marine water columns and sediments worldwide belong almost exclusively to the ‘Candidatus Scalindua’ species, but the molecular basis of their metabolism and competitive fitness is presently unknown. We applied community sequencing of a marine anammox enrichment culture dominated by ‘Candidatus Scalindua profunda’ to construct a genome assembly, which was subsequently used to analyse the most abundant gene transcripts and proteins. In the S. profunda assembly, 4756 genes were annotated, and only about half of them showed the highest identity to the only other anammox bacterium of which a metagenome assembly had been constructed so far, the freshwater ‘Candidatus Kuenenia stuttgartiensis’. In total, 2016 genes of S. profunda could not be matched to the K. stuttgartiensis metagenome assembly at all, and a similar number of genes in K. stuttgartiensis could not be found in S. profunda. Most of these genes did not have a known function but 98 expressed genes could be attributed to oligopeptide transport, amino acid metabolism, use of organic acids and electron transport. On the basis of the S. profunda metagenome, and environmental metagenome data, we observed pronounced differences in the gene organization and expression of important anammox enzymes, such as hydrazine synthase (HzsAB), nitrite reductase (NirS) and inorganic Nitrogen transport proteins. Adaptations of Scalindua to the substrate limitation of the ocean may include highly expressed ammonium, nitrite and oligopeptide transport systems and pathways for the transport, oxidation, and assimilation of small organic compounds that may allow a more versatile lifestyle contributing to the competitive fitness of Scalindua in the marine realm.