Purpose: The share of microbially degradable sediment organic matter (SOM) and the degradation rate depend, among others, on the intrinsic properties of SOM as well as on the type and concentration of terminal electron acceptors (TEA). Next to its role as TEA, molecular oxygen enhances SOM decay by oxygenase-mediated breakdown of complex organic molecules. This research investigated long-term SOM decay (> 250 days) under aerobic and anaerobic conditions to (1) provide a basis for sediment carbon flux estimates from the River Elbe estuary and (2) assess the potential for carbon burial in relation to redox conditions and dredging interventions. 

Methods: Long-term aerobic and anaerobic SOM decay in fluid mud, pre-consolidated and consolidated sediment layers was investigated over three years along a transect of ca. 20 km through the Port of Hamburg, starting at the first hydrodynamically determined hotspot of sedimentation after the weir in Geesthacht. Absolute differences between aerobic and anaerobic cumulative carbon mineralization were calculated, as well as their ratio. Findings were correlated to a suite of solids and pore water properties. 

Results: SOM decay followed first order multi-phase exponential decay kinetics. The ratio between C release under aerobic and anaerobic conditions ranged around 4 in the short-term, converging to a value of 2 in the long term. Strong gradients in absolute C release along the upstream–downstream transect did not reflect in a corresponding gradient of the aerobic-anaerobic ratio. C release was most strongly correlated to the water-soluble organic matter, in particular humic acids. Contact of anaerobically stabilized sediment with the oxygenated water phase induced significant release of carbon. 

Conclusion: SOM degradability in the study area exhibited strong spatial gradients in relation to the organic matter source gradient but was mainly limited by the high extent of organic matter stabilization. Under these conditions, molecular oxygen as TEA provides little thermodynamic advantage. Carbon-sensitive sediment management, considering SOM reactivity patterns in stratified depositional areas, is a powerful strategy to reduce environmental impacts of dredging measures.

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Degradability of organic matter in river sediments differs in relation to origin and age. In order to explain previously observed spatial patterns of organic matter degradability and stabilization, this study investigated sediment organic matter (SOM) properties along a tidal Elbe river transect using dissolved organic matter (DOM) fractions, density fractions, carbon stable isotopes and thermometric pyrolysis (Rock-Eval 6). These properties were linked to SOM decay rates and biological indicators such as chlorophyll a and silicic acid in the water phase, and sediment-bound extracellular polymeric substances (EPS), microbial biomass and oxygen consumption. Sediment source gradients were established using the concentration of Zn in the fraction < 20 μm as proxy. The specific Zn concentration showed that the most upstream location was nourished primarily by upstream fluviatile sediments while the other locations carried a downstream signature. The upstream location was also characterised by the highest concentrations of chlorophyll a, microbial biomass, silicic acid, EPS, humic acids and hydrophilic DOM, the most negative δ13C signature and by the highest oxygen consumption rate, with decreasing trends towards downstream locations. This trend was also evident in the decreasing SOM lability from upstream to downstream, an increasing share of total SOM found in the acid-base-extractable fractions and a
decreasing share of carbon in the light density fractions. Thermometric pyrolysis revealed the highest H-index(easily degradable SOM) for the most upstream location and the ratio of the I-index (immature SOM) to the R-
index (refractory SOM) to correlate positively with measured SOM decay rates. This study suggests that spatial patterns of SOM degradability can be explained by a source gradient, with young organic matter entering the system from upstream from predominantly biogenic sources, while down-stream sources (North Sea sediment) deliver more refractory SOM that is stabilized in organo-mineral associations to a higher extent. In the investigated sediments, dissolved organic matter represented 0.23–1.20% of the total organic carbon (TOC) from anaerobically degradable SOM, while 4.10–11.46% TOC was liberated as CO2 and CH4 after long-term incubation (250 days). Thermometric pyrolysis is shown to serve as a useful proxy for SOM degradability in river sediments, with the Hydrogen-Index (HI) correlating well with degradability and the relationship between the I-index and R-index changing consistently towards lower I-indices and higher R-indices with an increasing degree of SOM stabilization.

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Organic matter plays a major role in global ecosystems and has several functions in terrestrial and marine environments. As organic matter impacts, among others, the rheological behaviour and settling rates of mineral sediment particles, it is of great relevance to the definition and maintenance of the nautical depth in ports and waterways. The microbial decay of organic matter leads to the emission of climate forcing gases like CO2 and CH4. In this theses it will be provided fundamental insight in the behaviour of sediment organic matter in the aquatic river system. It presents analyses of field and laboratory experiments using sediment samples taken during 21 sampling campaigns between 2018 and 2020 in the Port of Hamburg, Germany. The focus lay on sampling locations with high sedimentation rates. It is investigated chemical, physical and biological parameters and their variability in space and over time. It quantifies the share of anaerobically and aerobically degradable sediment organic matter in a depth profile and along a transect of about 30 km within the tidal Elbe river. Sediment organic matter at upstream and downstream locations is mainly allochthonous as it comes from the catchment (upstream) or from North Sea (downstream). Young organic matter, entering the system from upstream, has predominantly biogenic sources. Upstream organic matter originates from the catchment, containing plankton-derived and more easily degradable components. It was shown that the most upstream location was nourished primarily by upstream fluviatile sediments. This location was characterised by the highest concentrations of chlorophyll a, microbial biomass, silicic acid, EPS, humic acids and hydrophilic organic matter, the most negative δ13C signature and by the highest oxygen consumption rate, with decreasing trends towards downstream locations. At downstream locations, organic matter is mainly of allochthonous origin, entering the harbour mainly with the tidal flood current from the direction of the North Sea. The organic matter degradability was the lowest at downstream locations and organic matter was stabilised in organo-mineral associations. It is elucidated that spatial patterns of organic matter degradability can be explained by a source gradient. It was found that sediment organic matter lability is inversely linked to its stabilisation in organo-mineral complexes. The degradability gradient could be explained by different organic matter quality in relation to its origin. A fast, medium, slowly and non-degradable pool (pool 1 to pool 4) were identified based on the measured organic matter lability. Temporal and spatial variabilities (gradient and depth) were observed as well as seasonal changes of degradable organic matter pools. An age gradient was found with easily degradable material in top layers and increasing stabilization of organic matter in organo-mineral compounds with depth. The degradability was larger in upper sediment layers. It was also larger under aerobic conditions but the differences between aerobic and anaerobic decay decreased from upstream to downstream. The investigation area mostly comprised stabilised organic matter. On average around 20 % of TOC was anaerobically degradable and around 30% of TOC was aerobically degradable. Thermometric pyrolysis was shown to serve as a useful proxy to predict organic matter degradability in river sediments, with the Hydrogen-Index (HI) correlating well with degradability. Further, it will be demonstrated that the sediment organic matter decay has a biological, chemical and physical effect on the shear strength. Degradation of organic matter significantly affects sediment strength, especially under the anaerobic conditions. The formation of gas bubbles under anaerobic conditions added an additional physical component to the effect of biological organic matter decay. The susceptibility of the sediment to yield stress changes might depend on the availability of easily XIV degradable organic matter. Pronounced spatial trends were found with higher changes in yield stress at upstream locations and lower yield stress changes at downstream locations. Finally, this thesis will demonstrate the metamorphosis of sediment properties and sediment organic matter from its state in suspension to being part of the settled and consolidated sediment as well as from upstream to downstream. Temporal and spatial gradients were found for aerobic and anaerobic carbon fluxes as well as for potentially degradable organic carbon. A first draft of a carbon flux estimate originating from the microbial decay of organic matter from the investigation area is presented which can be used for future carbon foot printing assessments, for example for port maintenance activities. @en

Anaerobic sediment organic matter decay generates methane, delays sediment consolidation, reduces sediment density, viscosity and shear strength, all impacting the sediment rheological parameters and the navigable depth. This study quantifies the share of anaerobically and aerobically degradable sediment organic matter (SOM) in a depth profile and along a transect through the tidal river Elbe in the section of the Port of Hamburg. From exponential organic matter decay functions, organic matter decay rates (mg C g_TOC⁻¹ d⁻¹) were derived and clustered with a k-Means Cluster Analysis. The reactivity of different (kinetic) organic matter pools along the river transect were characterized based on their biodegradation rates. A fast, medium, slowly and non-degradable pool (pools 1–4) were identified based on the measured organic matter lability. SOM lability decreased from upstream to downstream, evidenced by the decreasing amount of the easily degradable pool 1 material from upstream to downstream. The size of the slowly degradable pool 3, assumed to be associated with SOM bound to the mineral particles, did not show any spatial gradient and is therefore suggested to represent a baseline share of hardly accessible SOM in the investigation area (about 12%−16% of TOC). Total degradability thus appears to be governed by the amount of SOM present in addition to this basis (pool 3), which in turn follows a source gradient and an age gradient from upstream to downstream. The recalcitrant pool 4 was the largest at any part of the harbour, for any depth, and for both, anaerobic and aerobic conditions (about 75%−85% of TOC). This indicates that the sediment in the investigation area, including the uppermost fluidic and freshly settled layers, mostly comprises stabilised organic matter and contributes largely to storage of organic carbon. Differently sized anaerobic SOM pools with depth were observed as well as seasonal changes of the easily degradable SOM pool 1. The degradability was larger in upper sediment layers, it was also larger under aerobic conditions (by about 10% of TOC) but the differences between aerobic and anaerobic decay decreased from upstream to downstream.

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Purpose
Sediment organic matter (SOM) influences settling and thus the rheological behavior of suspended particles by enhancing flocculation or reducing surface charges by forming organo-mineral complexes that facilitate particle–particle interactions in consolidating sediments. It was, therefore, assumed that the microbial degradation of SOM and its spatio-temporal variability would affect sediment rheological properties and enhance port maintenance dredging and navigability of ports and waterways.

Methods
To investigate this effect, samples were taken at six locations along a transect of 30 river kilometers through the Port of Hamburg, Germany, during nine sampling campaigns within two years. The collected samples were divided into different layers based on the differences in visual consistency and strength. For analysis of SOM degradability, the samples were incubated in the laboratory for 250 days in glass bottles under aerobic and anaerobic conditions following the evolution of gas composition (CH4, CO2) and pressure in the bottle headspace over time. Yield stress was analyzed before and after the dissolved organic matter (DOM) decay using a rheometer with Couette geometry. Standard properties of solids and pore water were also analyzed.

Results
Shear strength decreased upon SOM decay under both anaerobic and aerobic conditions. Under anaerobic conditions, organic matter decay reduced static and fluidic yield stresses to an average of 74% and 79% of the fresh sample values. Consolidated layers at lower depths showed the highest absolute decrease in fluidic yield stress of up to –110 Pa due to a larger absolute amount of degradable organic matter in these layers in connection to higher bulk density. Pronounced spatial trends with higher changes in yield stress at upstream locations and lower yield stress changes at downstream locations coincided with a decreasing gradient of SOM degradability from upstream to downstream. Seasonal trends indicated that the investigation area is impacted by temporally changing factors.

Conclusion
The availability of easily degradable organic matter significantly affects sediment strength, especially under the anaerobic conditions, even when the mass loss of organic matter mass loss is small. Seasonal variability in yield stress changes upon SOM decay indicate that the site-specific responses were modulated by overarching seasonal effects impacting the entire investigation area. It was assumed that during an anaerobic decay, the formation of gas bubbles added an additional physical component to the effect of biological SOM decay.@en

The presence of clay-organic flocs in cohesive mud results in a complex rheological behavior of mud, including viscoelasticity, shear-thinning, thixotropy and two-step yielding. In this study, the effect of microbial degradation of organic matter on the rheological properties of mud samples, collected from different ports, was examined. The mud samples were collected from five different European ports (Port of Antwerp (PoA), Port of Bremerhaven (PoB), Port of Emden (PoE), Port of Hamburg (PoH) and Port of Rotterdam (PoR)), displaying varying sediment properties. The rheological analysis of fresh and degraded mud samples was performed with the help of several tests, including stress ramp-up tests, amplitude sweep tests, frequency sweep tests, time-dependent tests and structural recovery tests. The results showed: (i) a significant decrease in yield stresses and complex modulus after organic matter degradation for mud samples from PoA, PoH and PoR, (ii) a negligible change in rheological properties (yield stresses, crossover amplitude and complex modulus) for mud samples from PoB, and (iii) a significant increase in rheological properties for mud samples from PoE. For time-dependent tests, mud samples from PoB showed a substantial increase in hysteresis (~50% mean value) as compared to the changes in yield stresses and crossover amplitude. The analysis of gas production during degradation of organic matter showed a (i) significant release of carbon per g dry matter for mud samples from PoA, PoH and PoR, (ii) lower carbon release per g dry matter for mud samples from PoB, and (iii) a negligible carbon release per g dry matter for mud samples from PoE, which corresponded well with the change in rheological properties.@en

Purpose
The presence of organic matter in cohesive sediment results in the formation of clay-organic flocs, which eventually impart complex rheological behavior including shear-thinning, viscoelasticity, thixotropy and two-step yielding to mud. In this study, the influence of microbial degradation of sediment organic matter on the rheological properties of mud samples, having similar densities, was examined.

Materials and methods
Mud samples were collected from three different locations in the Port of Hamburg, Germany, displaying varying organic matter content. The rheological analysis of fresh and degraded mud samples was performed with the help of several tests including stress ramp-up tests, amplitude sweep tests, frequency sweep tests, time-dependent tests, and structural recovery tests.

Results and discussion
The results showed a significant decrease in rheological properties including yield stresses, complex modulus, etc. for degraded mud samples as compared to the fresh mud samples. The slopes of the line, correlating the change (degraded − fresh) in the above-mentioned rheological properties as a function of the same rheological property of the fresh mud, varied within the range of −0.28 to −0.49. The structural recovery tests displayed a better recovery (i.e., stronger system) in mud after the pre-shearing step for the degraded mud samples as compared to the fresh mud samples. The effect of degradation time on the rheological properties of mud samples showed two critical time periods (3 days and 150 days) after which a significant change in rheological properties of mud samples was observed.

Conclusions
This study provided a useful understanding about the influence of organic matter degradation on the rheological properties of mud, which can be used to optimize sediment management strategies in ports and waterways.@en

Purpose: The microbial turnover of sediment organic matter (OM) in ports and waterways impacts water quality, sonic depth finding and presumably also rheological properties as well as greenhouse gas emissions, especially if organic carbon is released as methane. As a consequence, sediment management practices as a whole are affected. This study aimed to discern spatial OM degradability patterns in the Port of Hamburg and investigated correlations with standard analytical properties as a basis for future predictive modelling. Materials and methods: Sediments in the Port of Hamburg were repeatedly sampled at nine locations along an east-west transect using a 1-m corer. In a stratified sampling approach, layers of suspended particulate matter (SPM), fluid mud (FM), pre-consolidated sediment (PS) and consolidated sediment (CS) were identified and individually analysed for long-term aerobic and anaerobic degradation of organic matter, DNA concentration, stable carbon isotope signature, density fractions and standard solids and pore water properties. Results and discussion: The investigation area was characterised by a distinct gradient with a 10-fold higher OM degradability in upstream areas and lower degradability in downstream areas. Concomitantly, upstream locations showed higher DNA concentrations and more negative δ¹³C values. The share of bulk sediment in the heavy density fraction as well as the proportion and absolute amount of organic carbon were significantly larger at downstream locations. A depth and hence age-related gradient was found at individual locations, showing higher degradability of the upper, younger material, concomitant with higher DNA concentration, and lower OM turnover in the deeper, older and more consolidated material. Deeper layers were also characterised by higher concentrations of pore water ammonium, indicative of anaerobic nitrogen mineralisation. Conclusions: Organic matter lability is inversely linked to its stabilisation in organo-mineral complexes. The observed degradability gradient is likely due to the different OM quality in relation to its origin. Downstream OM enters the system with the tidal flood current from the direction of the North Sea whereas upstream locations receive OM originating from the catchment, containing more autochthonous, plankton-derived and more easily degradable components. At individual sampling points, depth-related degradability gradients reflect an age gradient, with easily degradable material in top layers and increasing stabilisation of OM in organo-mineral compounds with depth.

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