Complete Genome Sequence of Polycladomyces abyssicola JIR-001 T , Isolated from Hemipelagic Sediment in Deep Seawater

Here, we report the complete genome sequence of Polycladomyces abyssicola strain JIR-001, which we isolated from hemipelagic sediment in deep seawater. The genome, generated by combining long (Flongle) and short (NovaSeq) read sequencing data, is 3,197,230 bp, with a mean G+C content of 52.0%.

Subseafloor sulphide deposit formed by pumice replacement mineralisation

Seafloor massive sulphide (SMS) deposits, modern analogues of volcanogenic massive sulphide (VMS) deposits on land, represent future resources of base and precious metals. Studies of VMS deposits have proposed two emplacement mechanisms for SMS deposits: exhalative deposition on the seafloor and mineral and void space replacement beneath the seafloor. The details of the latter mechanism are poorly characterised in detail, despite its potentially significant role in global metal cycling throughout Earth’s history, because in-situ studies require costly drilling campaigns to sample SMS deposits. Here, we interpret petrographic, geochemical and geophysical data from drill holes in a modern SMS deposit and demonstrate that it formed via subseafloor replacement of pumice. Samples from the sulphide body and overlying sediment at the Hakurei Site, Izena Hole, middle Okinawa Trough indicate that sulphides initially formed as aggregates of framboidal pyrite and matured into colloform and euhedral pyrite, which were replaced by chalcopyrite, sphalerite and galena. The initial framboidal pyrite is closely associated with altered material derived from pumice, and alternating layers of pumiceous and hemipelagic sediments functioned as a factory of sulphide mineralisation. We infer that anhydrite-rich layers within the hemipelagic sediment forced hydrothermal fluids to flow laterally, controlling precipitation of a sulphide body extending hundreds of meters.

A revised chronostratigraphic framework for International Ocean Discovery Program Expedition 355 sites in Laxmi Basin, eastern Arabian Sea

International Ocean Discovery Program Expedition 355 drilled Sites U1456 and U1457 in Laxmi Basin (eastern Arabian Sea) to document the impact of the South Asian monsoon on weathering and erosion of the Himalaya. We revised the chronostratigraphic framework for these sites using a combination of biostratigraphy, magnetostratigraphy and strontium isotope stratigraphy. The sedimentary section at the two sites is similar and we divided it into six units bounded by unconformities or emplaced as a mass-transport deposit (MTD). Unit 1 underlies the MTD, and is of early–middle Miocene age at Site U1456 and early Paleocene age at Site U1457. An unconformity (U1) created by emplacement of the MTD (unit 2) during the late Miocene Epoch (at c. 9.83–9.69 Ma) separates units 1 and 2 and is identified by a marked change in lithology. Unit 3 consists of hemipelagic sediment with thin interbeds of graded sandstone of late Miocene age, separated from unit 4 by a second unconformity (U2) of 0.5–0.9 Myr duration. Unit 4 consists of upper Miocene interbedded mudstone and sandstone and hemipelagic chalk deposited between c. 8 and 6 Ma. A c. 1.4–1.6 Myr hiatus (U3) encompasses the Miocene–Pliocene boundary and separates unit 4 from unit 5. Unit 5 includes upper Pliocene – lower Pleistocene siliciclastic sediment that is separated from unit 6 by a c. 0.45 Myr hiatus (U4) in the lower Pleistocene sediments. Unit 6 includes a thick package of rapidly deposited Pleistocene sand and mud overlain by predominantly hemipelagic sediment deposited since c. 1.2 Ma.

The Granular Structure of Two Marine Carbonate Sediments

Calcareous sediments are prominent throughout the low-latitudinal offshore environment and have been known to be problematic for offshore foundation systems. These fascinating soils consist largely of the skeletal remains of single-celled marine organisms (plankton and zooplankton) and can be as geologically complex as their onshore siliceous counter parts. To enable an adequate understanding of their characteristics, in particular, their intra-granular micro-structure, it is important that geotechnical engineers do not forget about the multifaceted biological origins of these calcareous sediments and the different geological processes that created them. In this paper, the 3D models of soils grains generated from micro-computed tomography scans, scanning electeron microscope images, and optical microscope images of two calcareous sediments from two different depositional environments are presented and their geotechnical implications discussed. One is a coastal bioclastic sediment from Perth, Western Australia that is geologically similar to carbonate sediments typically used in micro-mechanics and particle crushing studies in the literature. The other is a hemipelagic sediment from a region of the North West Shelf of Australia that has historically been geotechnically problematic for engineers. The results show there is a marked difference between coastal bioclastic and hemipelagic sediments in terms of geological context and the associated particle micro-structures. This brings into question whether a coastal bioclastic calcareous sediment is a good micro-mechanical substitute for a hemipelagic one.

Planktic14C Plateaus: A Result of Short-Term Sedimentation Pulses?

The tuning of plateaus in glacial and deglacial planktic radiocarbon records to pertinent structures in the atmospheric14C record of Lake Suigetsu results in both a record of surface water reservoir ages and a centennial-scale absolute age model. However, the atmospheric origin of planktic14C plateaus may be questioned. Alternatively, plateaus may result from short pulses of increased hemipelagic sediment deposition, which challenges the technique of14C plateau tuning. To test the two rationales for the interval 23–12 cal ka, we calculated hypothetical sedimentation rates for all14C plateaus identified in five Atlantic sediment cores assuming sediment pulses that either span 10, 100, 200, or 300 yr each. These rates were compared to rates derived by14C plateau tuning that assumes an atmospheric origin of the plateaus. In each plateau suite, our hypothetical sedimentation rates result in at least one or two cases in extreme values that exceed the rates reported for short-lasting pulses of sediment deposition in contourites by a factor of 50 and therefore appear unrealistic. Moreover, they result in entire suites of plateau structures that incidentally appear closely aligned to the pattern of atmospheric14C plateau suites rather than to any pulses of climate-controlled sediment discharge.

Polycladomyces abyssicola gen. nov., sp. nov., a thermophilic filamentous bacterium isolated from hemipelagic sediment

A novel filamentous bacterium, designated strain JIR-001T, was isolated from hemipelagic sediment in deep seawater. This strain was non-motile, Gram-positive, aerobic, heterotrophic and thermophilic; colonies were of infinite form and ivory coloured with wrinkles between the centre and the edge of the colony on ISP2 medium. The isolate grew aerobically at 55–73 °C with the formation of aerial mycelia; spores were produced singly along the aerial mycelium. These morphological features show some similarities to those of the type strains of some species belonging to the family Thermoactinomycetaceae . Phylogenetic analysis based on 16S rRNA gene sequences confirmed that strain JIR-001T belongs to the family Thermoactinomycetaceae within the class Bacilli . Similarity levels between the 16S rRNA gene sequence of strain JIR-001T and those of the type strains of Thermoactinomycetaceae species were 85.5–93.5 %; highest sequence similarity was with Melghirimyces algeriensis NariEXT. In the DNA–DNA hybridization assays between strain JIR-001T and its phylogenetic neighbours the mean hybridization levels with Melghirimyces algeriensis NariEXT, Planifilum fimeticola H0165T, Planifilum fulgidum 500275T and Planifilum yunnanense LA5T were 5.3–7.5, 2.3–4.7, 2.1–4.8 and 2.5–4.9 %, respectively. The DNA G+C content of strain JIR-001T was 55.1 mol%. The major fatty acids were iso-C15 : 0, iso-C17 : 0, iso-C16 : 0 and C16 : 0. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, glucolipid, phosphatidylserine, an amino-group containing phospholipid, an unknown phospholipid and two unknown lipids. The predominant menaquinone was MK-7 and the cell-wall peptidoglycan contained meso-diaminopimelic acid, glutamic acid and alanine. On the basis of phenotypic characteristics and 16S rRNA gene sequence comparisons, strain JIR-001T is considered to represent a novel species in a new genus of the family Thermoactinomycetaceae , for which the name Polycladomyces abyssicola gen. nov., sp. nov. is proposed. The type strain of Polycladomyces abyssicola is JIR-001T ( = JCM 18147T = CECT 8074T).

Contrasting settings of serpentinite bodies in the northwestern Zagros Suture Zone, Kurdistan Region, Iraq

Protrusions and lenses of serpentinite–matrix mélanges occur at several places along the thrust faults of the Zagros Suture Zone. They separate the lower allochthonous thrust sheet, the ‘Lower Allochthon’ (i.e. Walash–Naopurdan nappe), of Paleocene–Eocene age from sediments of the Arabian platform and the upper thrust sheet of Mesozoic, ophiolite-bearing terranes termed the ‘Upper Allochthon’ (i.e. Gemo–Qandil nappe). The serpentinite–matrix mélanges occur mostly as stretched bodies (slices) on both sides of the Lower Allochthon (Hero, Halsho and Pushtashan (HHP) and Galalah, Qalander and Rayat (GQR)). Their overall chondrite-normalized rare earth element (REE) patterns form two main groups. Group One exhibits enrichment in the total REEs (> 1 × chondrite) whereas the Group Two pattern shows depletion (i.e. < 1 × chondrite). Bulk-rock MORB-normalized profiles of Group Two are almost flat in the MREE–HREE region with flattening profiles in the Gd–Lu range (> 3 times the MORB composition). In comparison with Group One, Group Two has extremely high REE content and displays variable depletions in the moderately incompatible high-field-strength elements (HFSEs) (Zr, Hf, Y) relative to their adjacent REEs. The REEs in the GQR serpentinite–matrix mélanges have a noticeably high LREE content, and a positive Eu anomaly, and their HREE content never reaches more than 1 × chondrite (i.e. < 0.01 to 1 × chondrite). The latter indicates that the hemipelagic sedimentary, melt-like components (i.e. high LREE, U/La, La/Sm and low Ba/Th) control the geochemical peculiarities of this type of serpentinite. The HHP serpentinite–matrix mélanges, however, are either equally divided between the two REE pattern groups (e.g. Hero, Halsho) or inclined towards Group One (e.g. Pushtashan). Contrary to GQR serpentinites, the variation in HHP serpentinite–matrix mélanges spans a compositional spectrum from U/La-rich to more Ba/Th-rich. Such ratio variations reflect the large variation in these two subducted sedimentary components (i.e. carbonate and hemipelagic sediment mix). The obvious differences in the trace element signatures of the GQR and HHP serpentinite–matrix mélanges might be related to plate tectonic parameters such as convergence rate, subduction age and thickness and type of subducted slab. It is more likely that the influx of subducted components to the mantle wedge relied heavily on the composition of the sedimentary inputs. These vary considerably with time from the relatively deepwater hemipelagic sediments (Qulqula Radiolarite Formation) to platform carbonate sediments (Balambo limestone). The trace element signatures of the GQR and HHP serpentinite–matrix mélanges might suggest multi-staging of the allochthonous sheet emplacement on the Arabian platform sediments.