scholarly journals Microbial Communities and Organic Matter Composition in Surface and Subsurface Sediments of the Helgoland Mud Area, North Sea

2015 ◽  
Vol 6 ◽  
Author(s):  
Oluwatobi E. Oni ◽  
Frauke Schmidt ◽  
Tetsuro Miyatake ◽  
Sabine Kasten ◽  
Matthias Witt ◽  
...  
Keyword(s):  
Organic Matter ◽  
Microbial Communities ◽  
North Sea ◽  
Organic Matter Composition ◽  
Subsurface Sediments ◽  
Area North ◽  
Mud Area

scholarly journals Comparing soil biogeochemical processes in novel and natural boreal forest ecosystems

2013 ◽  
Vol 10 (4) ◽  
pp. 7521-7548 ◽  
Author(s):  
S. A. Quideau ◽  
M. J. B. Swallow ◽  
C. E. Prescott ◽  
S. J. Grayston ◽  
S.-W. Oh
Keyword(s):  
Organic Matter ◽  
Boreal Forest ◽  
Microbial Communities ◽  
Nutrient Availability ◽  
Forest Ecosystems ◽  
Biogeochemical Processes ◽  
Natural Ecosystems ◽  
Natural Landscape ◽  
Organic Matter Composition ◽  
Anthropogenic Ecosystems

Abstract. Emulating the variability that exists in the natural landscape prior to disturbance should be a goal of soil reconstruction and land reclamation efforts following resource extraction. Long-term ecosystem sustainability within reclaimed landscapes can only be achieved with the re-establishment of biogeochemical processes between reconstructed soils and plants. In this study, we assessed key soil biogeochemical attributes (nutrient availability, organic matter composition, and microbial communities) in reconstructed, novel, anthropogenic ecosystems covering different reclamation treatments following open-cast mining for oil extraction. We compared the attributes to those present in a range of natural soils representative of mature boreal forest ecosystems in the same area of northern Alberta. Soil nutrient availability was determined in situ with resin probes, organic matter composition was described with 13C nuclear magnetic resonance spectroscopy and soil microbial community structure was characterized using phospholipid fatty acid analysis. Significant differences among natural ecosystems were apparent in nutrient availability and seemed more related to the dominant tree cover than to soil type. When analyzed together, all natural forests differed significantly from the novel ecosystems, in particular with respect to soil organic matter composition. However, there was some overlap between the reconstructed soils and some of the natural ecosystems in nutrient availability and microbial communities, but not in organic matter characteristics. Hence, our results illustrate the importance of considering the range of natural landscape variability, and including several soil biogeochemical attributes when comparing novel, anthropogenic ecosystems to the mature ecosystems that constitute ecological targets.

scholarly journals Distinct microbial populations are tightly linked to the profile of dissolved iron in the methanic sediments of the Helgoland mud area, North Sea

2015 ◽  
Vol 06 ◽  
Author(s):  
Oluwatobi Oni ◽  
Tetsuro Miyatake ◽  
Sabine Kasten ◽  
Tim Richter-Heitmann ◽  
David Fischer ◽  
...  
Keyword(s):  
North Sea ◽  
Microbial Populations ◽  
Dissolved Iron ◽  
Area North ◽  
Mud Area

scholarly journals Kinetics and identities of extracellular peptidases in subsurface sediments of the White Oak River Estuary, NC

2016 ◽  
Author(s):  
Andrew D. Steen ◽  
Richard T. Kevorkian ◽  
Jordan T. Bird ◽  
Nina Dombrowski ◽  
Brett J. Baker ◽  
...  
Keyword(s):  
Organic Matter ◽  
Microbial Community ◽  
Organic Carbon ◽  
Microbial Communities ◽  
River Estuary ◽  
Estuarine Sediments ◽  
White Oak ◽  
Organic Carbon Burial ◽  
Subsurface Sediments ◽  
Extracellular Peptidases

AbstractAnoxic subsurface sediments contain communities of heterotrophic microorganisms that metabolize organic carbon at extraordinarily slow rates. In order to assess the mechanisms by which subsurface microorganisms access detrital sedimentary organic matter, we measured kinetics of a range of extracellular peptidases in anoxic sediments of the White Oak River estuary, NC. Nine distinct peptidase substrates were enzymatically hydrolyzed at all depths. Potential peptidase activities (Vmax) decreased with increasing sediment depth, although Vmax expressed on a per cell basis was approximately the same at all depths. Half-saturation constants (Km) decreased with depth, indicating peptidases that functioned more efficiently at low substrate concentrations. Potential activities of extracellular peptidases acting on molecules that are enriched in degraded organic matter (D-phenylalanine and L-ornithine) increased relative to enzymes that act on L-phenylalanine, further suggesting microbial community adaptation to access degraded organic matter. Nineteen classes of predicted, exported peptidases were identified in genomic data from the same site, of which genes for class C25 (gingipain-like) peptidases represented more than 40% at each depth. Methionine aminopeptidases, zinc carboxypeptidases, and class S24-like peptidases, which are involved in single-stranded DNA repair, were also abundant. These results suggest a subsurface heterotrophic microbial community that primarily accesses low-quality detrital organic matter via a diverse suite of well-adapted extracellular enzymes.ImportanceBurial of organic carbon in marine and estuarine sediments represents a long-term sink for atmospheric carbon dioxide. Globally, ∼40% of organic carbon burial occurs in anoxic estuaries and deltaic systems. However, the ultimate controls on the amount of organic matter that is buried in sediments, versus oxidized into CO2, are poorly constrained. Here we used a combination of enzyme assays and metagenomic analysis to identify how subsurface microbial communities catalyze the first step of proteinaceous organic carbon degradation. Our results show that microbial communities in deeper sediments are adapted to access molecules characteristic of degraded organic matter, suggesting that those heterotrophs are adapted to life in the subsurface.

scholarly journals Comparing soil biogeochemical processes in novel and natural boreal forest ecosystems

2013 ◽  
Vol 10 (8) ◽  
pp. 5651-5661 ◽  
Author(s):  
S. A. Quideau ◽  
M. J. B. Swallow ◽  
C. E. Prescott ◽  
S. J. Grayston ◽  
S.-W. Oh
Keyword(s):  
Organic Matter ◽  
Boreal Forest ◽  
Microbial Communities ◽  
Nutrient Availability ◽  
Forest Ecosystems ◽  
Biogeochemical Processes ◽  
Natural Ecosystems ◽  
Natural Landscape ◽  
Organic Matter Composition ◽  
Anthropogenic Ecosystems

Abstract. Emulating the variability that exists in the natural landscape prior to disturbance should be a goal of soil reconstruction and land reclamation efforts following resource extraction. Long-term ecosystem sustainability within reclaimed landscapes can only be achieved with the re-establishment of biogeochemical processes between reconstructed soils and plants. In this study, we assessed key soil biogeochemical attributes (nutrient availability, organic matter composition, and microbial communities) in reconstructed, novel, anthropogenic ecosystems, covering different reclamation treatments following open-cast mining for oil extraction. We compared the attributes to those present in a range of natural soils representative of mature boreal forest ecosystems in the same area of Northern Alberta. Soil nutrient availability was determined in situ with resin probes, organic matter composition was described with 13C nuclear magnetic resonance spectroscopy and soil microbial community structure was characterized using phospholipid fatty acid analysis. Significant differences among natural ecosystems were apparent in nutrient availability and seemed more related to the dominant tree cover than to soil type. When analyzed together, all natural forests differed significantly from the novel ecosystems, in particular with respect to soil organic matter composition. However, there was some overlap between the reconstructed soils and some of the natural ecosystems in nutrient availability and microbial communities, but not in organic matter characteristics. Hence, our results illustrate the importance of considering the range of natural landscape variability and including several soil biogeochemical attributes when comparing novel, anthropogenic ecosystems to the mature ecosystems that constitute ecological targets.

scholarly journals Kinetics and Identities of Extracellular Peptidases in Subsurface Sediments of the White Oak River Estuary, North Carolina

2019 ◽  
Vol 85 (19) ◽  
Author(s):  
Andrew D. Steen ◽  
Richard T. Kevorkian ◽  
Jordan T. Bird ◽  
Nina Dombrowski ◽  
Brett J. Baker ◽  
...  
Keyword(s):  
Organic Matter ◽  
Microbial Community ◽  
Organic Carbon ◽  
Microbial Communities ◽  
River Estuary ◽  
Estuarine Sediments ◽  
White Oak ◽  
Organic Carbon Burial ◽  
Subsurface Sediments ◽  
Extracellular Peptidases

ABSTRACT Anoxic subsurface sediments contain communities of heterotrophic microorganisms that metabolize organic carbon at extraordinarily low rates. In order to assess the mechanisms by which subsurface microorganisms access detrital sedimentary organic matter, we measured kinetics of a range of extracellular peptidases in anoxic sediments of the White Oak River Estuary, NC. Nine distinct peptidase substrates were enzymatically hydrolyzed at all depths. Potential peptidase activities (Vmax) decreased with increasing sediment depth, although Vmax expressed on a per-cell basis was approximately the same at all depths. Half-saturation constants (Km) decreased with depth, indicating peptidases that functioned more efficiently at low substrate concentrations. Potential activities of extracellular peptidases acting on molecules that are enriched in degraded organic matter (d-phenylalanine and l-ornithine) increased relative to enzymes that act on l-phenylalanine, further suggesting microbial community adaptation to access degraded organic matter. Nineteen classes of predicted, exported peptidases were identified in genomic data from the same site, of which genes for class C25 (gingipain-like) peptidases represented more than 40% at each depth. Methionine aminopeptidases, zinc carboxypeptidases, and class S24-like peptidases, which are involved in single-stranded-DNA repair, were also abundant. These results suggest a subsurface heterotrophic microbial community that primarily accesses low-quality detrital organic matter via a diverse suite of well-adapted extracellular enzymes. IMPORTANCE Burial of organic carbon in marine and estuarine sediments represents a long-term sink for atmospheric carbon dioxide. Globally, ∼40% of organic carbon burial occurs in anoxic estuaries and deltaic systems. However, the ultimate controls on the amount of organic matter that is buried in sediments, versus oxidized into CO2, are poorly constrained. In this study, we used a combination of enzyme assays and metagenomic analysis to identify how subsurface microbial communities catalyze the first step of proteinaceous organic carbon degradation. Our results show that microbial communities in deeper sediments are adapted to access molecules characteristic of degraded organic matter, suggesting that those heterotrophs are adapted to life in the subsurface.

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