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Mak A. Saito - One of the best experts on this subject based on the ideXlab platform.
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characterization of the metalloproteome of pseudoalteromonas bb2 at2 biogeochemical underpinnings for zinc manganese cobalt and nickel cycling in a ubiquitous marine Heterotroph
Metallomics, 2021Co-Authors: Michael G. Mazzotta, Matthew R. Mcilvin, Dawn M Moran, David T Wang, Kay D Bidle, Carl H Lamborg, Mak A. SaitoAbstract:Pseudoalteromonas (BB2-AT2) is a ubiquitous marine Heterotroph, often associated with labile organic carbon sources in the ocean (e.g. phytoplankton blooms and sinking particles). Heterotrophs hydrolyze exported photosynthetic material, a component of the biological carbon pump, with the use of diverse metalloenzymes containing zinc (Zn), manganese (Mn), cobalt (Co) and nickel (Ni). Studies on the metal requirements and cytosolic utilization of metals for marine Heterotrophs are scarce, despite their relevance to global carbon cycling. Here, we characterized the Zn, Mn, Co and Ni metallome of BB2-AT2. We found that the Zn metallome is complex and cytosolic Zn is associated with numerous proteins for transcription (47.2% of the metallome, obtained from singular value decomposition of the metalloproteomic data), translation (33.5%), proteolysis (12.8%) and alkaline phosphatase activity (6.4%). Numerous proteolytic enzymes also appear to be putatively associated with Mn, and to a lesser extent, Co. Putative identification of the Ni-associated proteins, phosphoglucomutase and a protein in the cupin superfamily, provides new insights for Ni utilization in marine Heterotrophs. BB2-AT2 relies on numerous transition metals for proteolytic and phosphatase activities, inferring an adaptative potential to metal limitation. Our field observations of increased alkaline phosphatase activity upon addition of Zn in field incubations suggests such metal limitation operates in sinking particulate material collected from sediment traps. Taken together, this study improves our understanding of the Zn, Mn, Co and Ni metallome of marine Heterotrophic bacteria and provides novel and mechanistic frameworks for understanding the influence of nutrient limitation on biogeochemical cycling.
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Characterization of the Fe metalloproteome of a ubiquitous marine Heterotroph, Pseudoalteromonas (BB2-AT2): multiple bacterioferritin copies enable significant Fe storage.
Metallomics, 2020Co-Authors: Michael G. Mazzotta, Matthew R. Mcilvin, Mak A. SaitoAbstract:Fe is a critical nutrient to the marine biological pump, which is the process that exports photosynthetically fixed carbon in the upper ocean to the deep ocean. Fe limitation controls photosynthetic activity in major regions of the oceans, and the subsequent degradation of exported photosynthetic material is facilitated particularly by marine Heterotrophic bacteria. Despite their importance in the carbon cycle and the scarcity of Fe in seawater, the Fe requirements, storage and cytosolic utilization of these marine Heterotrophs has been less studied. Here, we characterized the Fe metallome of Pseudoalteromonas (BB2-AT2). We found that with two copies of bacterioferritin (Bfr), Pseudoalteromonas possesses substantial capacity for luxury uptake of Fe. Fe : C in the whole cell metallome was estimated (assuming C : P stoichiometry ∼51 : 1) to be between ∼83 μmol : mol Fe : C, ∼11 fold higher than prior marine bacteria surveys. Under these replete conditions, other major cytosolic Fe-associated proteins were observed including superoxide dismutase (SodA; with other metal SOD isoforms absent under Fe replete conditions) and catalase (KatG) involved in reactive oxygen stress mitigation and aconitase (AcnB), succinate dehydrogenase (FrdB) and cytochromes (QcrA and Cyt1) involved in respiration. With the aid of singular value decomposition (SVD), we were able to computationally attribute peaks within the metallome to specific metalloprotein contributors. A putative Fe complex TonB transporter associated with the closely related Alteromonas bacterium was found to be abundant within the Pacific Ocean mesopelagic environment. Despite the extreme scarcity of Fe in seawater, the marine Heterotroph Pseudoalteromonas has expansive Fe storage capacity and utilization strategies, implying that within detritus and sinking particles environments, there is significant opportunity for Fe acquisition. Together these results imply an evolved dedication of marine Pseudoalteromonas to maintaining an Fe metalloproteome, likely due to its dependence on Fe-based respiratory metabolism.
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Characterization of the Fe Metalloproteome of a Ubiquitous Marine Heterotroph, Pseudoalteromonas (BB2-AT2): Multiple Bacterioferritin Copies Enable Significant Fe Storage
2020Co-Authors: Michael G. Mazzotta, Matthew R. Mcilvin, Mak A. SaitoAbstract:<p>Fe is a critical nutrient to the marine biological pump, which is the process that exports photosynthetically fixed carbon in<br>the upper ocean to the deep ocean. Fe limitation controls photosynthetic activity in large regions of the oceans, and the subsequent degradation of exported photosynthetic material is facilitated particularly by marine Heterotrophic bacteria. Despite their importance in the carbon cycle and the scarcity of Fe in seawater, the Fe requirements, storage and cytosolic utilization of these marine Heterotrophs has been less studied. Here, we characterized the Fe metallome of Pseudoalteromonas (BB2-AT2). We found that with two copies of bacterioferritin (Bfr), Pseudoalteromonas possesses substantial capacity for luxury uptake of Fe. Fe:C in the whole cell metallome was estimated (assuming C:P stoichiometry ~51:1) to be between ~83 μmol:mol Fe:C, ~11 fold higher than prior marine bacteria surveys, that could support growth for at least 2.6 divisions in the absence of further Fe acquisition. Under these replete conditions, other major cytosolic Fe associated proteins were observed including superoxide dismutase (SodA; with other metal SOD isoforms absent under Fe replete conditions) and catalase (KatG) involved in reactive oxygen stress mitigation and aconitase (AcnB), succinate dehydrogenase (FrdB) and cytochromes (QcrA and Cyt1) involved in respiration. With the aid of singular value decomposition (SVD), we were able to computationally attribute peaks within the metallome to specific metalloproteins contributors. An Fe complex TonB transporter associated with the closely related Alteromonas bacterium was found to be abundant within the Pacific Ocean mesopelagic environment. Despite the extreme scarcity of Fe in seawater, the marine Heterotroph, Pseudoalteromonas, has expansive Fe storage capacity and utilization strategies, implying that, within detritus and sinking particle environments, there is significant opportunity for Fe acquisition. Together these results imply an evolved dedication of marine Pseudoalteromonas to maintaining an Fe metalloproteome, likely due to its dependence on Fe-based respiratory metabolism.<br></p>
Mari K H Winkler - One of the best experts on this subject based on the ideXlab platform.
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nitrate reduction by organotrophic anammox bacteria in a nitritation anammox granular sludge and a moving bed biofilm reactor
Bioresource Technology, 2012Co-Authors: Mari K H Winkler, Elzbieta Plaza, Jozef Trela, Robbert Kleerebezem, Jingjing Yang, Bengt Hultman, Mark C M Van LoosdrechtAbstract:Abstract The effects of volatile fatty acids (VFAs) on nitrogen removal and microbial community structure in nitritation/anammox process were compared within a granular sludge reactor and a moving bed biofilm reactor. Nitrate productions in both systems were lower by 40–68% in comparison with expected nitrate production. Expected sludge production on VFAs was estimated to be 67–77% higher if Heterotrophs were the main acetate degraders suggesting that Anammox bacteria used its organotrophic capability and successfully competed with general Heterotrophs for organic carbon, which led to a reduced sludge production. FISH measurements showed a population consisting of mainly Anammox and AOB in both reactors and oxygen uptake rate (OUR) tests also confirmed that flocculent biomass consisted of a minor proportion of Heterotrophs with a large proportion of AOBs. The dominant Anammox bacterium was Candidatus “ Brocadia fulgida ” with a minor fraction of Candidatus “ Anammoxoglobus propionicus ”, both known to be capable of oxidizing VFAs.
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nitrate reduction by organotrophic anammox bacteria in a nitritation anammox granular sludge and a moving bed biofilm reactor
Bioresource Technology, 2012Co-Authors: Mari K H Winkler, Elzbieta Plaza, Jozef Trela, Robbert Kleerebezem, Jingjing Yang, Bengt Hultman, Mark C M Van LoosdrechtAbstract:The effects of volatile fatty acids (VFAs) on nitrogen removal and microbial community structure in nitritation/anammox process were compared within a granular sludge reactor and a moving bed biofilm reactor. Nitrate productions in both systems were lower by 40–68% in comparison with expected nitrate production. Expected sludge production on VFAs was estimated to be 67–77% higher if Heterotrophs were the main acetate degraders suggesting that Anammox bacteria used its organotrophic capability and successfully competed with general Heterotrophs for organic carbon, which led to a reduced sludge production. FISH measurements showed a population consisting of mainly Anammox and AOB in both reactors and oxygen uptake rate (OUR) tests also confirmed that flocculent biomass consisted of a minor proportion of Heterotrophs with a large proportion of AOBs. The dominant Anammox bacterium was Candidatus “Brocadia fulgida” with a minor fraction of Candidatus “Anammoxoglobus propionicus”, both known to be capable of oxidizing VFAs.
Michael G. Mazzotta - One of the best experts on this subject based on the ideXlab platform.
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characterization of the metalloproteome of pseudoalteromonas bb2 at2 biogeochemical underpinnings for zinc manganese cobalt and nickel cycling in a ubiquitous marine Heterotroph
Metallomics, 2021Co-Authors: Michael G. Mazzotta, Matthew R. Mcilvin, Dawn M Moran, David T Wang, Kay D Bidle, Carl H Lamborg, Mak A. SaitoAbstract:Pseudoalteromonas (BB2-AT2) is a ubiquitous marine Heterotroph, often associated with labile organic carbon sources in the ocean (e.g. phytoplankton blooms and sinking particles). Heterotrophs hydrolyze exported photosynthetic material, a component of the biological carbon pump, with the use of diverse metalloenzymes containing zinc (Zn), manganese (Mn), cobalt (Co) and nickel (Ni). Studies on the metal requirements and cytosolic utilization of metals for marine Heterotrophs are scarce, despite their relevance to global carbon cycling. Here, we characterized the Zn, Mn, Co and Ni metallome of BB2-AT2. We found that the Zn metallome is complex and cytosolic Zn is associated with numerous proteins for transcription (47.2% of the metallome, obtained from singular value decomposition of the metalloproteomic data), translation (33.5%), proteolysis (12.8%) and alkaline phosphatase activity (6.4%). Numerous proteolytic enzymes also appear to be putatively associated with Mn, and to a lesser extent, Co. Putative identification of the Ni-associated proteins, phosphoglucomutase and a protein in the cupin superfamily, provides new insights for Ni utilization in marine Heterotrophs. BB2-AT2 relies on numerous transition metals for proteolytic and phosphatase activities, inferring an adaptative potential to metal limitation. Our field observations of increased alkaline phosphatase activity upon addition of Zn in field incubations suggests such metal limitation operates in sinking particulate material collected from sediment traps. Taken together, this study improves our understanding of the Zn, Mn, Co and Ni metallome of marine Heterotrophic bacteria and provides novel and mechanistic frameworks for understanding the influence of nutrient limitation on biogeochemical cycling.
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Characterization of the Fe metalloproteome of a ubiquitous marine Heterotroph, Pseudoalteromonas (BB2-AT2): multiple bacterioferritin copies enable significant Fe storage.
Metallomics, 2020Co-Authors: Michael G. Mazzotta, Matthew R. Mcilvin, Mak A. SaitoAbstract:Fe is a critical nutrient to the marine biological pump, which is the process that exports photosynthetically fixed carbon in the upper ocean to the deep ocean. Fe limitation controls photosynthetic activity in major regions of the oceans, and the subsequent degradation of exported photosynthetic material is facilitated particularly by marine Heterotrophic bacteria. Despite their importance in the carbon cycle and the scarcity of Fe in seawater, the Fe requirements, storage and cytosolic utilization of these marine Heterotrophs has been less studied. Here, we characterized the Fe metallome of Pseudoalteromonas (BB2-AT2). We found that with two copies of bacterioferritin (Bfr), Pseudoalteromonas possesses substantial capacity for luxury uptake of Fe. Fe : C in the whole cell metallome was estimated (assuming C : P stoichiometry ∼51 : 1) to be between ∼83 μmol : mol Fe : C, ∼11 fold higher than prior marine bacteria surveys. Under these replete conditions, other major cytosolic Fe-associated proteins were observed including superoxide dismutase (SodA; with other metal SOD isoforms absent under Fe replete conditions) and catalase (KatG) involved in reactive oxygen stress mitigation and aconitase (AcnB), succinate dehydrogenase (FrdB) and cytochromes (QcrA and Cyt1) involved in respiration. With the aid of singular value decomposition (SVD), we were able to computationally attribute peaks within the metallome to specific metalloprotein contributors. A putative Fe complex TonB transporter associated with the closely related Alteromonas bacterium was found to be abundant within the Pacific Ocean mesopelagic environment. Despite the extreme scarcity of Fe in seawater, the marine Heterotroph Pseudoalteromonas has expansive Fe storage capacity and utilization strategies, implying that within detritus and sinking particles environments, there is significant opportunity for Fe acquisition. Together these results imply an evolved dedication of marine Pseudoalteromonas to maintaining an Fe metalloproteome, likely due to its dependence on Fe-based respiratory metabolism.
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Characterization of the Fe Metalloproteome of a Ubiquitous Marine Heterotroph, Pseudoalteromonas (BB2-AT2): Multiple Bacterioferritin Copies Enable Significant Fe Storage
2020Co-Authors: Michael G. Mazzotta, Matthew R. Mcilvin, Mak A. SaitoAbstract:<p>Fe is a critical nutrient to the marine biological pump, which is the process that exports photosynthetically fixed carbon in<br>the upper ocean to the deep ocean. Fe limitation controls photosynthetic activity in large regions of the oceans, and the subsequent degradation of exported photosynthetic material is facilitated particularly by marine Heterotrophic bacteria. Despite their importance in the carbon cycle and the scarcity of Fe in seawater, the Fe requirements, storage and cytosolic utilization of these marine Heterotrophs has been less studied. Here, we characterized the Fe metallome of Pseudoalteromonas (BB2-AT2). We found that with two copies of bacterioferritin (Bfr), Pseudoalteromonas possesses substantial capacity for luxury uptake of Fe. Fe:C in the whole cell metallome was estimated (assuming C:P stoichiometry ~51:1) to be between ~83 μmol:mol Fe:C, ~11 fold higher than prior marine bacteria surveys, that could support growth for at least 2.6 divisions in the absence of further Fe acquisition. Under these replete conditions, other major cytosolic Fe associated proteins were observed including superoxide dismutase (SodA; with other metal SOD isoforms absent under Fe replete conditions) and catalase (KatG) involved in reactive oxygen stress mitigation and aconitase (AcnB), succinate dehydrogenase (FrdB) and cytochromes (QcrA and Cyt1) involved in respiration. With the aid of singular value decomposition (SVD), we were able to computationally attribute peaks within the metallome to specific metalloproteins contributors. An Fe complex TonB transporter associated with the closely related Alteromonas bacterium was found to be abundant within the Pacific Ocean mesopelagic environment. Despite the extreme scarcity of Fe in seawater, the marine Heterotroph, Pseudoalteromonas, has expansive Fe storage capacity and utilization strategies, implying that, within detritus and sinking particle environments, there is significant opportunity for Fe acquisition. Together these results imply an evolved dedication of marine Pseudoalteromonas to maintaining an Fe metalloproteome, likely due to its dependence on Fe-based respiratory metabolism.<br></p>
Giuseppe C Zuccarello - One of the best experts on this subject based on the ideXlab platform.
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still acting green continued expression of photosynthetic genes in the Heterotrophic dinoflagellate pfiesteria piscicida peridiniales alveolata
PLOS ONE, 2013Co-Authors: Hae Jin Jeong, Giuseppe C ZuccarelloAbstract:The loss of photosynthetic function should lead to the cessation of expression and finally loss of photosynthetic genes in the new Heterotroph. Dinoflagellates are known to have lost their photosynthetic ability several times. Dinoflagellates have also acquired photosynthesis from other organisms, either on a long-term basis or as “kleptoplastids” multiple times. The fate of photosynthetic gene expression in Heterotrophs can be informative into evolution of gene expression patterns after functional loss, and the dinoflagellates ability to acquire new photosynthetic function through additional endosymbiosis. To explore this we analyzed a large-scale EST database consisting of 151,091 unique sequences (29,170 contigs, 120,921 singletons) obtained from 454 pyrosequencing of the Heterotrophic dinoflagellate Pfiesteria piscicida. About 597 contigs from P. piscicida showed significant homology (E-value
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Still Acting Green: Continued Expression of Photosynthetic Genes in the Heterotrophic Dinoflagellate Pfiesteria piscicida(Peridiniales, Alveolata)
2013Co-Authors: Gwang Hoon Kim, Hae Jin Jeong, Yeong Du Yoo, Sunju Kim, Ji Hee Han, Jong Won Han, Giuseppe C ZuccarelloAbstract:The loss of photosynthetic function should lead to the cessation of expression and finally loss of photosynthetic genes in the new Heterotroph. Dinoflagellates are known to have lost their photosynthetic ability several times. Dinoflagellates have also acquired photosynthesis from other organisms, either on a long-term basis or as “kleptoplastids” multiple times. The fate of photosynthetic gene expression in Heterotrophs can be informative into evolution of gene expression patterns after functional loss, and the dinoflagellates ability to acquire new photosynthetic function through additional endosymbiosis. To explore this we analyzed a large-scale EST database consisting of 151,091 unique sequences (29,170 contigs, 120,921 singletons) obtained from 454 pyrosequencing of the Heterotrophic dinoflagellate Pfiesteria piscicida. About 597 contigs from P. piscicida showed significant homology (E-value −30) with proteins associated with plastid and photosynthetic function. Most of the genes involved in the Calvin-Benson cycle were found, genes of the light-dependent reaction were also identified. Also genes of associated pathways including the chorismate pathway and genes involved in starch metabolism were discovered. BLAST searches and phylogenetic analysis suggest that these plastid-associated genes originated from several different photosynthetic ancestors. The Calvin-Benson cycle genes are mostly associated with genes derived from the secondary plastids of peridinin-containing dinoflagellates, while the light-harvesting genes are derived from diatoms, or diatoms that are tertiary plastids in other dinoflagellates. The continued expression of many genes involved in photosynthetic pathways indicates that the loss of transcriptional regulation may occur well after plastid loss and could explain the organism's ability to “capture” new plastids (i.e. different secondary endosymbiosis or tertiary symbioses) to renew photosynthetic function.
Mark C M Van Loosdrecht - One of the best experts on this subject based on the ideXlab platform.
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nitrate reduction by organotrophic anammox bacteria in a nitritation anammox granular sludge and a moving bed biofilm reactor
Bioresource Technology, 2012Co-Authors: Mari K H Winkler, Elzbieta Plaza, Jozef Trela, Robbert Kleerebezem, Jingjing Yang, Bengt Hultman, Mark C M Van LoosdrechtAbstract:The effects of volatile fatty acids (VFAs) on nitrogen removal and microbial community structure in nitritation/anammox process were compared within a granular sludge reactor and a moving bed biofilm reactor. Nitrate productions in both systems were lower by 40–68% in comparison with expected nitrate production. Expected sludge production on VFAs was estimated to be 67–77% higher if Heterotrophs were the main acetate degraders suggesting that Anammox bacteria used its organotrophic capability and successfully competed with general Heterotrophs for organic carbon, which led to a reduced sludge production. FISH measurements showed a population consisting of mainly Anammox and AOB in both reactors and oxygen uptake rate (OUR) tests also confirmed that flocculent biomass consisted of a minor proportion of Heterotrophs with a large proportion of AOBs. The dominant Anammox bacterium was Candidatus “Brocadia fulgida” with a minor fraction of Candidatus “Anammoxoglobus propionicus”, both known to be capable of oxidizing VFAs.