scholarly journals Organic Matter Loading Modifies the Microbial Community Responsible for Nitrogen Loss in Estuarine Sediments

2015 ◽  
Vol 71 (3) ◽  
pp. 555-565 ◽  
Author(s):  
Andrew R. Babbin ◽  
Amal Jayakumar ◽  
Bess B. Ward
Keyword(s):  
Organic Matter ◽  
Microbial Community ◽  
Nitrogen Loss ◽  
Estuarine Sediments ◽  
Organic Matter Loading

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 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.

scholarly journals Benthic fluxes of dissolved organic nitrogen in the lower St. Lawrence estuary and implications for selective organic matter degradation

2013 ◽  
Vol 10 (11) ◽  
pp. 7609-7622 ◽  
Author(s):  
M. Alkhatib ◽  
P. A. del Giorgio ◽  
Y. Gelinas ◽  
M. F. Lehmann
Keyword(s):  
Organic Matter ◽  
Dissolved Organic Nitrogen ◽  
Organic Nitrogen ◽  
Bottom Water ◽  
Estuarine Sediments ◽  
Internal Source ◽  
Lawrence Estuary ◽  
Element Partitioning ◽  
Sediment Porewaters ◽  
St Lawrence Estuary

Abstract. The distribution of dissolved organic nitrogen (DON) and carbon (DOC) in sediment porewaters was determined at nine locations along the St. Lawrence estuary and in the gulf of St. Lawrence. In a previous manuscript (Alkhatib et al., 2012a), we have shown that this study area is characterized by gradients in the sedimentary particulate organic matter (POM) reactivity, bottom water oxygen concentrations, and benthic respiration rates. Based on the porewater profiles, we estimated the benthic diffusive fluxes of DON and DOC in the same area. Our results show that DON fluxed out of the sediments at significant rates (110 to 430 μmol m−2 d−1). DON fluxes were positively correlated with sedimentary POM reactivity and varied inversely with sediment oxygen exposure time (OET), suggesting direct links between POM quality, aerobic remineralization and the release of DON to the water column. DON fluxes were on the order of 30 to 64% of the total benthic inorganic fixed N loss due to denitrification, and often exceeded the diffusive nitrate fluxes into the sediments. Hence they represented a large fraction of the total benthic N exchange, a result that is particularly important in light of the fact that DON fluxes are usually not accounted for in estuarine and coastal zone nutrient budgets. In contrast to DON, DOC fluxes out of the sediments did not show any significant spatial variation along the Laurentian Channel (LC) between the estuary and the gulf (2100 ± 100 μmol m−2 d−1). The molar C / N ratio of dissolved organic matter (DOM) in porewater and the overlying bottom water varied significantly along the transect, with lowest C / N in the lower estuary (5–6) and highest C / N (> 10) in the gulf. Large differences between the C / N ratios of porewater DOM and POM are mainly attributed to a combination of selective POM hydrolysis and elemental fractionation during subsequent DOM mineralization, but selective adsorption of DOM to mineral phases could not be excluded as a potential C / N fractionating process. The extent of this C- versus N- element partitioning seems to be linked to POM reactivity and redox conditions in the sediment porewaters. Our results thus highlight the variable effects selective organic matter (OM) preservation can have on bulk sedimentary C / N ratios, decoupling the primary source C / N signatures from those in sedimentary paleoenvironmental archives. Our study further underscores that the role of estuarine sediments as efficient sinks of bioavailable nitrogen is strongly influenced by the release of DON during early diagenetic reactions, and that DON fluxes from continental margin sediments represent an important internal source of N to the ocean.

scholarly journals Microbial Community Structure Affects Marine Dissolved Organic Matter Composition

2016 ◽  
Vol 3 ◽  
Author(s):  
Elizabeth B. Kujawinski ◽  
Krista Longnecker ◽  
Katie L. Barott ◽  
Ralf J. M. Weber ◽  
Melissa C. Kido Soule
Keyword(s):  
Organic Matter ◽  
Community Structure ◽  
Microbial Community ◽  
Dissolved Organic Matter ◽  
Microbial Community Structure ◽  
Organic Matter Composition

Utilization of grass-silage nitrogen by growing sheep

1983 ◽  
Vol 100 (1) ◽  
pp. 43-62 ◽  
Author(s):  
Elisabeth Grenet
Keyword(s):  
Organic Matter ◽  
Formic Acid ◽  
Nitrogen Balance ◽  
Crude Protein ◽  
Nitrogen Loss ◽  
Nitrogen Retention ◽  
Protein Digestibility ◽  
Water Soluble ◽  
Nitrogen Intake ◽  
Green Fodder

SUMMARYThe digestibility, the voluntary intake and the nitrogen balance of 108 diets corresponding to 94 silages prepared from 20 fresh crops were measured in growing sheep. Series of silages were made from the same fresh forage. Each series included two controls: a direct-cut silage without additive and a direct-cut silage with formic acid, with a variable number of experimental silages with different additives.Rumen ammonia concentration, measured on rumen-fistulated sheep, decreased when an additive was used. It increased with nitrogen intake and was inversely related to the organic-matter digestibility and the crude-fibre digestibility. It varied with the silage composition.The crude-protein digestibility of direct-cut silages without additives was similar to or slightly higher than the crude-protein digestibility of the fresh crops. The addition of formic acid depressed the digestibility, but the addition of formaldehyde decreased it even more. The urinary nitrogen loss was higher for silages without additive than for the fresh crops and was decreased by the addition of formic acid. The addition of formaldehyde to formic acid had an additive effect.Retained nitrogen was lower in silages without additives (12% of nitrogen intake) than in parent crops (15·7%). It increased when formic acid (15·8%) was added. The addition of formaldehyde at a low rate (1·5 l/t green fodder) to the formic acid did not increase the nitrogen retention whether expressed in g/day or as percentage of nitrogen intake, but the addition of formaldehyde at a high rate (3·5 l/t green fodder) to formic acid decreased nitrogen retention. The other additives based on cereals or whey did not improve the nitrogen balance compared with formic acid. Nitrogen retention differed according to plant species.Retained nitrogen increased with digestible organic-matter intake and nitrogen intake. It increased with the silage water-soluble carbohydrate content. The higher the silage fermentation product content (ammonia, lactic acid, propionic acid), the lower the retained nitrogen. It appears that the nitrogen value of silages can be high provided that the silages are well preserved and that excessive protein breakdown is avoided.

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