Modelling seabed sediment physical properties and organic matter content in the Firth of Clyde

High-quality quantitative maps of seabed sedimentary physical and geochemical properties have numerous research and conservation applications, including habitat and ecosystem modelling, marine spatial planning, and ecosystem service mapping. However, such maps are lacking for many ecologically and economically important marine areas. Using legacy data supplemented by measurements from recent benthic surveys, modelled hydrodynamic variables, and high-resolution bathymetry, quantitative maps for the top 10 cm of seabed sediment were generated via a combination of statistical and machine-learning techniques for the Firth of Clyde, a semi-enclosed coastal sea on the west coast of Scotland. The maps include sediment fractions of mud, sand, and gravel; whole-sediment median grain size; sediment permeability and porosity; rates of natural seabed abrasion; and sediment particulate organic carbon and nitrogen content. Properties were mapped over an unstructured grid so that very high resolutions were achieved close to the coastlines, where sediments may be expected to be spatially heterogeneous. Overall, the maps reveal extensive areas of very low sediment permeability coupled with low rates of natural seabed disturbance. Moreover, muddy sediments in the inner Firth of Clyde, Inchmarnock Water, and the sea lochs are enriched in organic carbon and nitrogen relative to the sediments of the outer Firth of Clyde. As a demonstration of the value of these maps, the standing stock of organic carbon and nitrogen in the surficial sediments of the Clyde was calculated. The Clyde stores 3.42 and 0.33 million t of organic carbon and nitrogen in the top 10 cm of seabed sediment, respectively, substantially contributing to Scotland's coastal and shelf blue carbon stocks. Data products are available from https://doi.org/10.15129/2003faa2-ee93-4c11-bb16-48485f5f136d (Heath and Pace, 2021).

Morphology and Late Pleistocene-Holocene Sedimentation of the Strait of İstanbul (Bosphorus): A review

The Bosphorus (Istanbul Strait) is natural strait that connects the Black Sea with the Aegean Sea via the Sea of Marmara and Dardanelles Strait. It is a 31 km long and 3.5 km wide winding channel, with an irregular bottom morphology. It has depressions up to -110 m deep, and two sills with depths of -35 and -58 m in the south and north, respectively.Presently, a two-layer water exchange exists through the strait, with the Mediterranean and Black Sea waters forming the lower and upper layers, respectively. The Bosphorus channel extends as shelf valleys on the Black Sea and Sea of Marmara shelves. However, it operated as a river valley or an estuary during the stadial low-stand periods.The infill sedimentary succession of the Bosphorus channel is up to ∼100 m thick above the Palaeozoic-Cretaceous basement with an irregular topography. The oldest sediments are sandy to muddy fluvial-lacustrine facies of late Pleistocene age, which are preserved only in up to -160 m-deep scoured depressions of the basement. They are overlain by mid-late Holocene estuarine-marine shelly sandy to muddy sediments with patches of bioherms and shelly lag deposits.The Bosphorus outlet areas of the Black Sea and Sea of Marmara are characterized by a submarine fan and a shelf valley, respectively. The fan system in the Black Sea started depositing ∼900 yr after the initial vigorous marine water incursion at ∼8.4 14C kyr BP. On the Marmara shelf, extension of the Bosphorus channel is a sinuous shelf valley with a channel-leveé complex, which was deposited by the Black Sea outflow during the 11-10 14C kyr BP. Catastrophic floodings of the Sea of Marmara by torrential Black Sea outflows during the Greenland Interstadial melt water pulses, as well as the strong Mediterranean current towards the Black Sea during the interglacial periods, were responsible for carving the Bosphorus channel and the shelf valleys, as well as removing the sediments belonging to the earlier periods.

TAPHONOMY AND DEPOSITIONAL SETTING OF THE SHRINGASAURUS INDICUS (ARCHOSAUROMORPHA: ALLOKOTOSAURIA) BONEBED FROM THE MIDDLE TRIASSIC DENWA FORMATION, SATPURA GONDWANA BASIN, INDIA

ABSTRACT A bonebed of multiple skeletons of the Triassic horned reptile Shringasaurus indicus was discovered in the upper Denwa Formation, Satpura Gondwana Basin, India. The monotaxic bonebed contains multiple individuals of different ontogenic stages indicating herding behavior by Shringasaurus indicus. The herd was a mixed-sex herd. The adult and sub-adult bones in the bonebed exceed the number of juvenile bones. The distribution of the bones was slightly patchy, bones of different individuals were admixed, and several bones were piled up implying mass mortality. The bonebed occurs in a fine-grained mudrock that is hydraulically incompatible with long-distance transport and concentration by currents. Sedimentary facies analysis indicates that the bonebed accumulated and was buried in a crevasse splay deposit between two ENE-WSW trending channel-fill complexes. The northern channel-fill complex was formed by unidirectional flow with lateral channel migration towards the south and with minor contemporaneous tectonic subsidence. Repeated breaching of the levee by this channel flow led to the incremental development of the crevasse splay deposit. The herd of Shringasaurus indicus, which lived near to the perennial channel, was drowned en masse and the carcasses were trapped within the muddy sediments of the crevasse splay deposit. Apart from a partially articulated skeleton, the rest of the bones were disarticulated but remained associated. The bones show little evidence of post-mortem modifications. With a continuous supply of the sediments through the spillover channels, the bones were buried before complete disarticulation and dispersal had taken place.

Biological Abundance and Diversity in Organic-Rich Sediments From a Florida Barrier Island Lagoon

Organic-rich sediments in estuaries and the coastal ocean are often a product of land clearing, runoff of excess nutrients and other human activities. They can harbor pollutants, oxygen-consuming microbes and toxic hydrogen sulfide (H2S), thereby creating a hostile environment for infauna. In one barrier island lagoon, the Indian River Lagoon (IRL), Florida, layers of organic-rich sediments have increased substantially in thickness and areal extent over the past 60 years. Geochemical properties of these muddy sediments have been described; however, less is known about their habitability. We analyzed infauna and geochemical properties of 102 samples taken during wet and dry seasons at 17 locations spanning 60 km of the lagoon. We quantified infaunal abundance and diversity (Shannon-Wiener, H′) and determined Pearson’s correlation coefficients for effective number of species (ENS = eH′) vs. sediment porosity (ϕ = 0.69–0.95), organic carbon (1–8%), nitrogen (0.1–0.7%), silt + clay (16–99%), porewater H2S (5–3,600 μM), and other environmental variables. Small bivalves accounted for 70% of the organisms collected, followed by gastropods, polychaetes and other biota. The bivalves were predominantly Macoma spp., Mulinia lateralis and Parastarte triquetra with average abundances of 3,896, 2,049, and 926 individuals per m2, respectively. High abundance of some species, such as Macoma, showed that these opportunists had adapted to poor quality sediments. More than two-thirds of the 35 species collected were present at <100 individuals per m2 of sediment. Cluster analysis identified four groups of stations with significantly different geochemical properties. Permutation analyses of variance indicated that the four groups also represented statistically different infaunal communities. Diversity decreased with increasing sediment concentrations of organic carbon, nitrogen and silt + clay; however, community richness at our most prolific station along the perimeter of muddy deposits was ∼7 times lower than found previously in sandy sediments from the IRL. The results identified areas where infaunal communities have experienced the greatest stress due to accumulation of organic-rich sediments. Results from this study help support management plans for remediation of organic-rich mud and improvement of sediment and water quality, especially in areas identified with low ENS.

On the investigation of vertical uncertainty of depth sounding in a shallow environment with muddy seabed: Preliminary results from a launch operation of a dual-frequency echosounder

Hydrographic echosounder has been the standard instrument that provides a measure of water depths. In a muddy environment, this detection is not as straightforward as it seems; low gradient of acoustic impedance presence within the water-sediment interface resulting in vertical separation of liquid-solid boundary detected by different frequencies of depth sounding system. In this study, we investigate the depths measured by a dual-frequency hydrographic echosounder in a muddy environment, coupled with a simultaneous probing of the water-seabed interface by means of a free-falling cone penetrometer. We intend to understand the extent of the uncertainty of a depth-sounding system to precisely locate the liquid-solid boundary within the water-seabed interface, specifically at Patimban coasts, situated in the north coast part of Java Island, where muddy sediments dominate the seabed. From our investigation, we found that standard high-frequency sounding (200 kHz) underestimates the physical depth by 0.26 ± 0.17 m, while standard low-frequency sounding (24 kHz) overestimates the physical depth by 0.23 ± 0.19 m and tends to give inconsistent measures. Our study suggests the importance of considering these measures of discrepancy when depth sounding is being carried out in a muddy environment.

Nitrogen cycling in muddy sediments of Great Peconic Bay, USA: Seasonal N reaction balances and multi-year flux patterns

To better understand the capacity of sediments to serve as both source and sink of nitrogen (N) and to identify any evidence of evolving changes in sedimentary N cycling, N2 production, N remineralization, and N2 fixation were studied over a multi-year period (2010–2015) in bioturbated mud of Great Peconic Bay, a temperate northeastern U. S. estuary. Benthic fluxes and rates of organic matter remineralization were measured using in situ and ex situ incubations. Net annual NH+ 4, NO–3/NO–2, and N2–N fluxes (μ = 1.1, 0.03, and 1.2 mmol m –2d –1) were close to averages for comparable sedi- mentary environments from surveys of published field studies. Net N2 fluxes (by membrane inlet mass spectrometry) were influenced in different periods by temperature, oxygenation of sediment, pulsed Corg, and the activity of benthic macrofauna and benthic microalgae, although no single physical or biogeochemical variable showed a strong, direct relationship with net N2 fluxes over all sampling periods. In situ measurements sometimes showed more dynamic and higher amplitude diurnal N flux cycles than did ex situ incubations, suggesting ex situ incubations did not fully capture impacts of bioirrigation or benthic photosynthesis.15 N tracer experiments indicated anammox was < 7% of total N2 production. Acetylene reduction assays demonstrated C2 H4 production to depths ≥ 15 cm and suggested N2 fixation may have approached 25% of gross N2 production(3:1 C2 H4 : N2). Mass balances incorporating independently measured N remineralization estimates were consistent with measured levels of N2 fixation. Overall, complex balances of competing processes governed sedimentary N cycling seasonally, and N2 production dominated N2 fixation. Measured N2 fixation was consistent with constraints from N remineralization rates and net N fluxes except in episodic conditions (e. g., algal blooms). There was no indication of progressive changes in N cycling magnitudes or relative N reaction balances over the study period.

Chromosome-level genome assembly of Scapharca kagoshimensis reveals the expanded molecular basis of heme biosynthesis in ark shell

Ark shells are commercially important clam species that inhabit in muddy sediments of shallow coasts in East Asia. For a long time, the lack of genome resources has hindered scientific research of ark shells. Here, we reported a high-quality chromosome-level genome assembly of Scapharca kagoshimensis, with an aim to unravel the molecular basis of heme biosynthesis, and develop genomic resources for genetic breeding and population genetics in ark shells. Nineteen scaffolds corresponding to 19 chromosomes were constructed from 938 contigs (contig N50=2.01 Mb) to produce a final high-quality assembly with a total length of 1.11 Gb and scaffold N50 around 60.64 Mb. The genome assembly represents 93.4% completeness via matching 303 eukaryota core conserved genes. A total of 24,908 protein-coding genes were predicted and 24,551 genes (98.56%) of which were functionally annotated. The enrichment analyses suggested that genes in heme biosynthesis pathways were expanded and positive selection of the hemoglobin genes was also found in the genome of S. kagoshimensis, which gives important insights into the molecular mechanisms and evolution of the heme biosynthesis in mollusca. The valuable genome assembly of S. kagoshimensis would provide a solid foundation for investigating the molecular mechanisms that underlie the diverse biological functions and evolutionary adaptations of S. kagoshimensis.

Modelling seabed sediment physical properties and organic matter content in the Firth of Clyde

High quality quantitative maps of seabed sedimentary physical and geochemical properties have numerous research and conservation applications, including habitat and ecosystem modelling, marine spatial planning and ecosystem service mapping. However, such maps are lacking for many ecologically and economically important marine areas. Using legacy data supplemented by measurements from recent benthic surveys, modelled hydrodynamic variables and high resolution bathymetry, quantitative maps for the top 10 cm of seabed sediment were generated via a combination of statistical and machine-learning techniques for the Firth of Clyde, a semi-enclosed coastal sea on the west coast of Scotland. The maps include sediment fractions of mud, sand and gravel, whole-sediment median grain size, sediment permeability and porosity, rates of natural seabed abrasion, and sediment particulate organic carbon and nitrogen content. Properties were mapped over an unstructured grid, so that very high resolutions were achieved close to the coastlines, where sediments may be expected to be spatially heterogeneous. Overall, the maps reveal extensive areas of very low sediment permeability coupled with low rates of natural seabed disturbance. Moreover, muddy sediments in the inner Firth of Clyde, Inchmarnock Water and the sea lochs are enriched in organic carbon and nitrogen relative to the sediments of the outer Firth of Clyde. As a demonstration of the value of these maps, the standing stock of organic carbon and nitrogen in the surficial sediments of the Clyde was calculated. The Clyde stores 3.42 and 0.33 million tonnes of organic carbon and nitrogen in the top 10 cm of seabed sediment, respectively, substantially contributing to Scotland’s coastal and shelf blue carbon stocks. Data products are available from: https://doi.org/10.15129/2003faa2-ee93-4c11-bb16-48485f5f136d.

The 2011 Tohoku-oki tsunami-induced sediment remobilization on the Sendai shelf, Japan, from a comparison of pre- and post-tsunami surface sediments

Tsunamis are generally considered to disturb the seafloor, rework surface sediments, and change seafloor environments. However, the response of the seafloor to such extreme wave events has not been fully elucidated. Herein, we compare the surface sediments before and after the 2011 Tohoku-oki tsunami on the Sendai shelf and demonstrate that both sandy and muddy sediments were significantly reworked on the shelf. Muddy sediments (> 10 cm thick) were redeposited as graded mud with no or little bioturbation, characterizing the offshore muddy tsunami deposit, while well-sorted sand was found as the sandy tsunami deposit. This redeposited layer could also be retained in the shelf mud sequence. The results imply that the high friction velocity of the tsunami wave and its long-term effect on Sendai Bay might contribute to the large sediment reworking. Part of the resuspended mud moved offshore to the slope area as turbidity currents. Thus, the tsunami is an important mechanism not only for shelf sedimentation but also for deep-sea sedimentation along active plate margins. The detection of 134Cs derived from the Fukushima Daiichi Nuclear Power Plant accident in the redeposited mud indicates that the suspended shelf water state was maintained for some days after the tsunami.