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 Vertical Stratification of Dissolved Organic Matter Linked to Distinct Microbial Communities in Subtropic Estuarine Sediments

2021 ◽  
Vol 12 ◽  
Author(s):  
Wenxiu Wang ◽  
Jianchang Tao ◽  
Ke Yu ◽  
Chen He ◽  
Jianjun Wang ◽  
...  
Keyword(s):  
Organic Matter ◽  
Dissolved Organic Matter ◽  
Microbial Communities ◽  
River Estuary ◽  
Niche Differentiation ◽  
Pearl River Estuary ◽  
Estuarine Sediments ◽  
Enzyme Families ◽  
The Pearl River ◽  
Dom Composition

Dissolved organic matter (DOM) provides carbon substrates and energy sources for sediment microbes driving benthic biogeochemical processes. The interactions between microbes and DOM are dynamic and complex and require the understanding based on fine-scale microbial community and physicochemical profiling. In this study, we characterized the porewater DOM composition in a 300-cm sediment core from the Pearl River estuary, China, and examined the interactions between DOM and archaeal and bacterial communities. DOM composition were highly stratified and associated with changing microbial communities. Compared to bacteria, the amplicon sequence variants of archaea showed significant Pearson correlations (r ≥ 0.65, P < 0.01) with DOM molecules of low H/C ratios, high C number and double bond equivalents, indicating that the distribution of archaea was closely correlated to recalcitrant DOM while bacteria were associated with relatively labile compounds. This was supported by the presence of auxiliary enzyme families essential for lignin degradation and bcrABCD, UbiX genes for anaerobic aromatic reduction in metagenome-assembled genomes of Bathyarchaeia. Our study demonstrates that niche differentiation between benthic bacteria and archaea may have important consequences in carbon metabolism, particularly for the transformation of recalcitrant organic carbon that may be predominant in aged marine sediments.

Carbocentric limnology: looking back, looking forward

2008 ◽  
Vol 65 (3) ◽  
pp. 543-548 ◽  
Author(s):  
Yves T Prairie
Keyword(s):  
Carbon Dioxide ◽  
Organic Matter ◽  
Microbial Community ◽  
Organic Carbon ◽  
Dissolved Organic Carbon ◽  
Carbon Budget ◽  
Metabolic Balance ◽  
Lake Ecosystems ◽  
Looking Back ◽  
Landscape Level

In this perspective article, I argue that dissolved organic carbon occupies a central role in the functioning of lake ecosystems, comparable in importance to that played by nutrients. Because lakes receive so much dissolved organic carbon from the terrestrial landscape, its accumulation in water bodies usually represents the largest pool of lacustrine organic matter within the water column. The transformation of even a small fraction of this external carbon by the microbial community can alter significantly the metabolic balance of lake ecosystems, simultaneously releasing carbon dioxide to the atmosphere and burying organic carbon in lake sediments. At the landscape level, even if they occupy a small fraction of the landscape, lakes play a surprisingly important role in the regional carbon budget, particularly when considered at the appropriate temporal scale.

scholarly journals Biochemical characteristics and bacterial community structure of the sea surface microlayer in the South Pacific Ocean

2007 ◽  
Vol 4 (4) ◽  
pp. 2809-2844 ◽  
Author(s):  
I. Obernosterer ◽  
P. Catala ◽  
R. Lami ◽  
J. Caparros ◽  
J. Ras ◽  
...  
Keyword(s):  
Organic Matter ◽  
Microbial Community ◽  
Pacific Ocean ◽  
Organic Carbon ◽  
South Pacific ◽  
Leucine Incorporation ◽  
Surface Microlayer ◽  
South Pacific Ocean ◽  
Subsurface Waters ◽  
Card Fish

Abstract. The chemical and biological characteristics of the surface microlayer were determined during a transect across the South Pacific Ocean in October-December 2004. Concentrations of particulate organic carbon (1.3 to 7.6-fold) and nitrogen (1.4 to 7), and POC:PON ratios were consistently higher in the surface microlayer as compared to subsurface waters (5 m). The large variability in particulate organic matter enrichment was negatively correlated to wind speed. No enhanced concentrations of dissolved organic carbon were detectable in the surface microlayer as compared to 5 m, but chromophoric dissolved organic matter was markedly enriched (by 2 to 4-fold) at all sites. Based on pigment analysis and cell counts, no consistent enrichment of any of the major components of the autotrophic and heterotrophic microbial community was detectable. CE-SSCP fingerprints and CARD FISH revealed that the bacterial communities present in the surface microlayer had close similarity (>76%) to those in subsurface waters. By contrast, bacterial heterotrophic production (3H-leucine incorporation) was consistently lower in the surface microlayer than in subsurface waters. By applying CARD-FISH and microautoradiography, we observed that Bacteroidetes and Gammaproteobacteria dominated leucine uptake in the surface microlayer, while in subsurface waters Bacteroidetes and Alphaproteobacteria were the major groups accounting for leucine incorporation. Our results demonstrate that the microbial community in the surface microlayer closely resembles that of the surface waters of the open ocean. However, even short time periods in the surface microlayer result in differences in bacterial groups accounting for leucine incorporation, probably as a response to the differences in the physical and chemical nature of the two layers.

scholarly journals Sources and accumulation of organic carbon in the Pearl River Estuary surface sediment as indicated by elemental, stable carbon isotopic, and carbohydrate compositions

2010 ◽  
Vol 7 (2) ◽  
pp. 2889-2926 ◽  
Author(s):  
B. He ◽  
M. Dai ◽  
W. Huang ◽  
Q. Liu ◽  
H. Chen ◽  
...  
Keyword(s):  
Organic Matter ◽  
Organic Carbon ◽  
Surface Sediments ◽  
River Estuary ◽  
Pearl River Estuary ◽  
Outer Shelf ◽  
Pearl River ◽  
Terrestrial Organic Matter ◽  
The Pearl River Estuary ◽  
The Pearl River

Abstract. Organic matter in surface sediments from the upper reach of the Pearl River Estuary and Lingdingyang Bay, as well as the adjacent northern South China Sea shelf was characterized by a variety of techniques, including elemental (C and N), stable carbon isotopic (δ 13C) composition, as well as molecular-level analyses. Total organic carbon (TOC) content was 1.61±1.20% in the upper reach down to 1.00±0.22% in Lingdingyang Bay and to 0.80±0.10% on the inner shelf and 0.58±0.06% on the outer shelf. δ13C values ranged from −25.11‰ to −21.28‰ across the studied area, with a trend of enrichment seaward. The spatial trend in C/N ratios mirrored that of δ13C, with a substantial decrease in C/N ratio from 10.9±1.3 in the Lingdingyang Bay surface sediments to 6.5±0.09 in the outer shelf surface sediments. Total carbohydrate yields ranged from 22.1 to 26.7 mg (100 mg OC)−1, and typically followed TOC concentrations in the estuarine and shelf sediments, suggesting that the relative abundance of total carbohydrate was fairly constant in TOC. Total neutral sugars as detected by the nine major monosaccharides (lyxose, rhamnose, ribose, arabinose, fucose, xylose, galactose, mannose, and glucose) yielded between 4.0 and 18.6 mg (100 mg OC)−1 in the same sediments, suggesting that a significant amount of carbohydrates were not neutral aldoses. The bulk organic matter properties, isotopic composition and C/N ratios, combined with molecular-level carbohydrate compositions were used to assess the sources and accumulation of terrestrial organic matter in the Pearl River Estuary and the adjacent northern South China Sea shelf. Results showed a mixture of terrestrial riverine organic carbon with in situ phytoplankton organic carbon in the areas studied. Using a two end-member mixing model based on δ13C values and C/N ratios, we estimated that the terrestrial organic carbon contribution to the surface sediment TOC was ca. 57±13% for Lingdingyang Bay, 19±2% for the inner shelf, which decreased further to 4.3±0.5% on the outer shelf. The molecular composition of the carbohydrate in surface sediments also suggested that the inner estuary was rich in terrestrial-derived carbohydrates but that the contribution of terrestrial-derived carbohydrates decreased offshore. Terrestrial organic carbon accumulation flux was estimated as 1.37±0.92×1011 g yr−1 in Lingdingyang Bay, which accounted for 37±25% of the terrestrial organic carbon transported to the Bay. The burial efficiency of terrestrial organic matter was markedly lower than that of suspended particulate substance (~71%) suggesting that the riverine POC undergoes significant degradation and replacement during transportation through the estuary.

A quantitative comparison of microbial community structure of estuarine sediments from microcosms and the field

1986 ◽  
Vol 32 (4) ◽  
pp. 319-325 ◽  
Author(s):  
Thomas W. Federle ◽  
Robert J. Livingston ◽  
Loretta E. Wolfe ◽  
David C. White
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Microbial Community Structure ◽  
Ecological Factors ◽  
Estuarine Sediments ◽  
Physical Factors ◽  
Multivariate Statistical ◽  
Apalachicola Bay ◽  
Sound Experiment

Estuarine soft-bottom sediments in microcosms and the field were compared with regard to microbial community structure. Community structure was determined by analyzing the fatty acids derived from the microbial lipids in the sediments. Fatty acid profiles were compared using a multivariate statistical approach. Experiments were performed using sediments from St. George Sound and Apalachicola Bay, Florida. The community structure of St. George Sound sediments was apparently controlled by epibenthic predators. In Apalachicola Bay, the dominant influences were physical factors related to the flow of the Apalachicola River. In the St. George Sound experiment, microbial communities in the microcosms differed from those in the field after only 2 weeks, and the degree of this difference increased substantially as time progressed. In the Apalachicola Bay experiment, although microbial communities in the microcosms were detectably different from those in the field, the degree of this difference was not large nor did it increase with time. This differential behavior of sediment communities from different sites may be related to the different ecological factors regulating community composition at these sites.

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

Land use change in Amazonian Dark Earth and Acrisol: Responses of organic carbon, organic matter composition and microbial carbon utilisation

2020 ◽  
Author(s):  
Klaus Jarosch ◽  
Luis Carlos Colocho Hurtarte ◽  
Konstantin Gavazov ◽  
Aleksander Westphal Muniz ◽  
Christoph Müller ◽  
...  
Keyword(s):  
Land Use ◽  
Organic Matter ◽  
Community Structure ◽  
Microbial Community ◽  
Organic Carbon ◽  
Land Use Change ◽  
Microbial Community Structure ◽  
Secondary Forest ◽  
Soil Types ◽  
Amazonian Dark Earth

<p>The conversion of tropical forest for cassava cultivation is widely known to decrease the soil organic matter (OM) and nutrient contents of highly weathered soils in the tropics. Amazonian Dark Earth (ADE) might be affected less due to their historical anthropogenic amelioration with e.g. charcoal, ceramics and bones, leading to higher soil OM and nutrient concentrations. In this study, we analysed the effect of land use change on the OM dynamics and its composition under tropical conditions, using ADE and an adjacent Acrisol (ACR) as model systems. Soil samples were obtained south of Manaus (Brazil), from a secondary forest and an adjacently located 40-year-old cassava plantation. The land use change induced a severe decrease of organic carbon (OC) concentrations in ADE (from 35 to 15 g OC kg<sup>‑1</sup>) while OC in the adjacent ACR was less affected (18 to 16 g OC kg<sup>‑1</sup>). Soils were analysed by <sup>13</sup>C NMR spectroscopy to obtain information on how the conversion of secondary forest to cassava affected the chemical composition of OM. Our results show that land use change induces differences in the OM composition: The OM in ADE changes to a more decomposed state (increase of alkyl:O/N-alkyl ratio) whereas the OM in ACR changes to a less decomposed state (decrease of alkyl:O/N-alkyl ratio). According to a molecular mixing model, land use change influenced mostly the proportion of lipids, which might be related with a change of the plant input. The incubation of the soils with <sup>13</sup>C glucose enabled resolving how soil microorganisms were affected by land use change. In both soil types ADE and ACR, land use change caused a reduction of the total <sup>13</sup>C glucose respiration by approximately one third in a 7-days incubation, implying lower microbial activity. Microorganisms in both soil types appear to be more readily active in soils under forest, since we observed a distinct lag time between <sup>13</sup>C glucose addition and respiration under cassava planation. This indicated differences in microbial community structure, which we will assess further by determining the <sup>13</sup>C label uptake by the microbial biomass and the microbial community structure using <sup>13</sup>C PLFA analysis. Preliminary results from synchrotron-based STXM demonstrate a distinct arrangement of OM at fine-sized charcoal-particle interfaces. Samples of soils receiving <sup>13</sup>C label will be further analysed by NanoSIMS with the hypothesis that charcoal interfaces foster nutrient dynamics at the microscale. Despite the high loss of OC in the ameliorated ADE through land use change, the remaining OM might improve the nutrient availability thanks to charcoal interactions compared to the ACR. Our results contribute to a better understanding of the sensitivity of OM upon land use change and how the microbial community is responding to land use change in highly weathered tropical soils.</p>

Influences of tropical monsoon climatology on the delivery and dispersal of organic carbon over the Upper Gulf of Thailand, SE Asia

2020 ◽  
Author(s):  
Bin Wu ◽  
Xiaodan Wu ◽  
Xuefa Shi ◽  
Shuqing Qiao ◽  
Shengfa Liu ◽  
...  
Keyword(s):  
Organic Matter ◽  
Organic Carbon ◽  
National Laboratory ◽  
Coastal Current ◽  
Gulf Of Thailand ◽  
Se Asia ◽  
Organic Carbon Burial ◽  
Water Stratification ◽  
Tropical Monsoon ◽  
Upper Gulf Of Thailand

<p>The seasonal reversal of monsoon climatology modulates precipitation, currents, river influx and a variety of biogeochemical processes. In the present study, we evaluated the role of tropical monsoon pertaining to fluvial discharge, sediment load, coastal current and water stratification on seasonal organic carbon dynamics during four sampling campaigns in the Upper Gulf of Thailand (UGoT), SE Asia. This study demonstrates that particulate organic carbon (POC) is closely correlated with the river influx of suspended sediment, which is generally regulated by the local rainfall. Higher POC is found near the large estuarine section (Chao Phraya River, CHAO) during southwest monsoon period and the small estuarine section (Mae Klong River, MK) during the tropical cyclones impacted November 2013. POC in the estuarine sections is influenced more by the seasonal shift than the coastal sections. Land-derived organic matter prevails in the small estuarine and coastal sections, while marine-derived organic matter dominates in the CHAO and MK impacted estuarine sections. Total organic carbon (TOC) however displays less significant seasonal monsoon variations than POC. Further, TOC tends to accumulate in the sub-silt fraction of sediments, which mainly occurs in the small estuarine and eastern coastal sections and is obviously influenced more by marine-derived factors. TOC in surface sediment of the CHAO and MK influenced sections however displays more seasonal variations with prevailing river input as evidenced by coarser sediment and higher C/N ratios. Moreover, the almost year round water stratification across the region acts as the barrier in retaining organic carbon in the estuaries and their vicinities from dispersal into the lower portion of Gulf of Thailand. High sedimentation rate (~1.1 cm·yr<sup>-1</sup>) further facilitates the organic carbon burial in the study area. The delivery, dispersal and burial of organic carbon are closely associated with the climate controlled precipitation, and thus the tropical monsoon climatology under the global warming in particular is an important factor influencing the organic carbon in the UGoT.</p><p><strong>Acknowledgements</strong></p><p>This study was supported by National Programme on Global Change and Air-Sea Interaction (GASI-02-IND-CJ05, GASI-GEOGE-03), the Natural Science Foundation of China (U1606401), the Qingdao National Laboratory for Marine Science and Technology (2016ASKJ13), the China-Thailand cooperation project “Research on Vulnerability of Coastal Zones”, and the Taishan Scholar Program of Shandong.</p>

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