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Samples collected at two different depths (ca. 3200 and ca. 4200 m) in the Setúbal and Cascais canyons off the Portuguese coast, during the HERMES RRS Charles Darwin cruise CD179, were analysed for (1) sediment biogeochemistry (TOC, TN) and (2) composition, and structural and trophic diversity of nematode communities. Multivariate PERMANOVA analysis on the nematode community data revealed differences between sediment layers that were greater than differences between canyons, water depths, and stations. This suggests that biogeochemical gradients along the vertical sediment profile are crucial in determining nematode community structure. The interaction between canyon conditions and the nematode community is illustrated by biogeochemical patterns in the sediment and the prevalence of nematode genera that are able to persist in disturbed sediments. Trophic analysis of the nematode community indicated that non-selective deposit feeders are dominant, presumably because of their non-selective feeding behaviour compared to other feeding types, which gives them a competitive advantage in exploiting lower-quality food resources. This study presents a preliminary conceptual scheme for interactions between canyon conditions and the resident fauna.

The Hakon Mosby Mud Volcano is a highly active methane seep hosting different chemosynthetic communities such as thiotrophic bacterial mats and siboglinid tubeworm assemblages. This study focuses on in situ measurements of methane fluxes to and from these different habitats, in comparison to benthic methane and oxygen consumption rates. By quantifying in situ oxygen, methane, and sulfide fluxes in different habitats, a spatial budget covering areas of 10-1000 -m diameter was established. The range of dissolved methane efflux (770-2 mmol m-2 d-1) from the center to the outer rim was associated with a decrease in temperature gradients from 46°C to < 1°C m-1, indicating that spatial variations in fluid flow control the distribution of benthic habitats and activities. Accordingly, total oxygen uptake (TOU) varied between the different habitats by one order of magnitude from 15 mmol m-2 d-1 to 161 mmol m-2 d-1. High fluid flow rates appeared to suppress benthic activities by limiting the availability of electron acceptors. Accordingly, the highest TOU was associated with the lowest fluid flow and methane efflux. This was most likely due to the aerobic oxidation of methane, which may be more relevant as a sink for methane as previously considered in submarine ecosystems.

An understanding of the balance of interspecific competition and the physical environment in structuring organismal communities is crucial because those communities structured primarily by their physical environment typically exhibit greater sensitivity to environmental change than those structured predominantly by competitive interactions. Here, using detailed phylogenetic and functional information, we investigate this question in macrofaunal assemblages from Northwest Atlantic Ocean continental slopes, a high seas region projected to experience substantial environmental change through the current century. We demonstrate assemblages to be both phylogenetically and functionally under-dispersed and thus conclude that the physical environment, not competition, may dominate in structuring deep-ocean communities. Further, we find temperature and bottom trawling intensity to be amongst the environmental factors significantly related to assemblage diversity. These results hint that deep-ocean communities are highly sensitive to their physical environment and vulnerable to environmental perturbation, including by direct disturbance through fishing, and indirectly through the changes brought about by climate change.

In an enclosure experiment, we employed two levels of inorganic NP ratios (10 and 5) for three distinct plankton communities collected along the coast of central Chile (33ºS). Each combination of community and NP level was replicated three times. The experiment lasted 12 days, and the data set include inorganic nutrients (NO3, PO4, DSi), particular organic carbon (POC), nitrogen (PON) and phosphorus (POP), Chlorophyll a, a range of fluorescence based measurements such as photochemical efficiency (Fv/Fm) and community data. The primary effect of the NP treatment was related to different concentrations of NO3, which directly influenced the biomass of phytoplankton. Additionally, low inorganic NP ratio reduced the seston NP and Chl a-C ratios, and there were some effects on the plankton community composition, e.g. benefitting Synechococcus spp in some communities.

These datasets were used to describe the diversity, ecology and role of non-scleractinian corals on scleractinian cold-water coral carbonate mounds in the Logachev Mound Province, Rockall Bank, NE Atlantic. Cold-water coral carbonate mounds, created by framework-building scleractinian corals, are also important habitats for non-scleractinian corals, whose ecology and role are understudied in deep-sea environments. In total ten non-scleractinian species were identified, which were mapped out along eight ROV video transects. Eight species were identified as black corals (three belonging to the family Schizopathidae, one each to the Leiopathidae, Cladopathidae, and Antipathidae and two to an unknown family) and two as gorgonians (Isididae and Plexauridae). The most abundant species were Leiopathes sp. and Parantipathes sp. 2. Areas with a high diversity of non-scleractinian corals are interpreted to offer sufficient food, weak inter-species competition and the presence of heterogeneous and hard settlement substrates. A difference in the density and occurrence of small vs. large colonies of Leiopathes sp. was also observed, which is likely related to a difference in the stability of the substrate they choose for settlement. Non-scleractinian corals, especially black corals, are an important habitat for crabs, crinoids, and shrimps in the Logachev Mound Province.

Acoustic estimates of herring and blue whiting abundance were obtained during the surveys using the Simrad ER60 scientific echosounder. The allocation of NASC-values to herring, blue whiting and other acoustic targets were based on the composition of the trawl catches and the appearance of echo recordings. To estimate the abundance, the allocated NASC -values were averaged for ICES-squares (0.5° latitude by 1° longitude). For each statistical square, the unit area density of fish (rA) in number per square nautical mile (N*nm-2) was calculated using standard equations (Foote et al., 1987; Toresen et al., 1998). To estimate the total abundance of fish, the unit area abundance for each statistical square was multiplied by the number of square nautical miles in each statistical square and then summed for all the statistical squares within defined subareas and over the total area. Biomass estimation was calculated by multiplying abundance in numbers by the average weight of the fish in each statistical square then summing all squares within defined subareas and over the total area. The Norwegian BEAM soft-ware (Totland and Godø 2001) was used to make estimates of total biomass.

Bacterial biofilms provide cues for the settlement of marine invertebrates such as coral larvae, and are therefore important for the resilience and recovery of coral reefs. This study aimed to better understand how ocean acidification may affect the community composition and diversity of bacterial biofilms on surfaces under naturally reduced pH conditions. Settlement tiles were deployed at coral reefs in Papua New Guinea along pH gradients created by two CO2 seeps, and upper and lower tiles surfaces were sampled 5 and 13 months after deployment. Automated Ribosomal Intergenic Spacer Analysis were used to characterize more than 200 separate bacterial communities, complemented by amplicon sequencing of the bacterial 16S rRNA gene of 16 samples. The bacterial biofilm consisted predominantly of Alpha-, Gamma- and Deltaproteobacteria, as well as Cyanobacteria, Flavobacteriia and Cytophaga, whereas putative settlement-inducing taxa only accounted for a small fraction of the community. Bacterial biofilm composition was heterogeneous with approximately 25% shared operational taxonomic units between samples. Among the observed environmental parameters, pH only had a weak effect on community composition (R² ~ 1%) and did not affect community richness and evenness. In contrast, there were strong differences between upper and lower surfaces (contrasting in light exposure and grazing intensity). There also appeared to be a strong interaction between bacterial biofilm composition and the macroscopic components of the tile community. Our results suggest that on mature settlement surfaces in situ, pH does not have a strong impact on the composition of bacterial biofilms. Other abiotic and biotic factors such as light exposure and interactions with other organisms may be more important in shaping bacterial biofilms than changes in seawater pH.

Atmospheric _p_CO~2~ is a critical component of the global carbon system and is considered to be the major control of Earth's past, present and future climate. Accurate and precise reconstructions of its concentration through geological time are, therefore, crucial to our understanding of the Earth system. Ice core records document _p_CO~2~ for the past 800 kyrs, but at no point during this interval were CO~2~ levels higher than today. Interpretation of older _p_CO~2~ has been hampered by discrepancies during some time intervals between two of the main ocean-based proxy methods used to reconstruct _p_CO~2~: the carbon isotope fractionation that occurs during photosynthesis as recorded by haptophyte biomarkers (alkenones) and the boron isotope composition (δ^11^B) of foraminifer shells. Here we present alkenone and δ^11^B-based _p_CO~2~ reconstructions generated from the same samples from the Plio-Pleistocene at ODP Site 999 across a glacial-interglacial cycle. We find a muted response to _p_CO~2~ in the alkenone record compared to contemporaneous ice core and δ^11^B records, suggesting caution in the interpretation of alkenone-based records at low _p_CO~2~ levels. This is possibly caused by the physiology of CO~2~ uptake in the haptophytes. Our new understanding resolves some of the inconsistencies between the proxies and highlights that caution may be required when interpreting alkenone-based reconstructions of _p_CO~2~.

Large organic food falls to the deep sea - such as whale carcasses and wood logs - support the development of reduced, sulfidic niches in an otherwise oxygenated, oligotrophic deep-sea environment. These transient hot spot ecosystems may serve the dispersal of highly adapted chemosynthetic organisms such as thiotrophic bivalves and siboglinid worms. Here we investigated the biogeochemical and microbiological processes leading to the development of sulfidic niches. Wood colonization experiments were carried out for the duration of one year in the vicinity of a cold seep area in the Nile deep-sea fan (Eastern Mediterranean) at depths of 1690 m. Wood logs were deployed in 2006 during the BIONIL cruise (RV Meteor M70/2 with ROV Quest, Marum, Germany) and sampled in 2007 during the Medeco-2 cruise (RV Pourquoi Pas? with ROV Victor 6000, Ifremer, France). Wood-boring bivalves played a key role in the initial degradation of the wood, the dispersal of wood chips and fecal matter around the wood log, and the provision of colonization surfaces to other organisms. Total oxygen uptake measured with a ROV-operated benthic chamber module was higher at the wood (0.5 m away) in contrast to 10 m away at a reference site (25 mmol m-2 d-1 and 1 mmol m-2 d-1, respectively), indicating an increased activity of sedimentary communities around the wood falls. Bacterial cell numbers associated with wood increased substantially from freshly submerged wood to the wood chip/fecal matter layer next to the wood experiments, as determined with Acridine Orange Direct Counts (AODC) and DAPI-stained counts. Microsensor measurements of sulfide, oxygen and pH were conducted ex situ. Sulfide fluxes were higher at the wood experiments when compared to reference measurements (19 and 32 mmol m-2 d-1 vs. 0 and 16 mmol -2 d-1, respectively). Sulfate reduction (SR) rates at the wood experiments were determined in ex situ incubations (1.3 and 2.0 mmol m-2 d-1) and fell into the lower range of SR rates previously observed from other chemosynthetic habitats at cold seeps. There was no influence of wood deposition on phosphate, silicate and nitrate concentrations, but ammonium concentrations were elevated at the wood chip-sediment boundary layer. Concentrations of dissolved organic carbon were much higher at the wood experiments (wood chip-sediment boundary layer) in comparison to measurements at the reference sites, which may indicate that cellulose degradation was highest under anoxic conditions and hence enabled by anaerobic benthic bacteria, e.g. fermenters and sulfate reducers. Our observations demonstrate that, after one year, the presence of wood at the seafloor had led to the creation of sulfidic niches, comparable to what has been observed at whale falls, albeit at lower rates.

In permafrost areas, seasonal freeze-thaw cycles result in upward and downward movements of the ground. For some permafrost areas, long-term downward movements were reported during the last decade. We measured seasonal and multi-year ground movements in a yedoma region of the Lena River Delta, Siberia, in 2013–2017, using reference rods installed deep in the permafrost. The seasonal subsidence was 1.7 ± 1.5 cm in the cold summer of 2013 and 4.8 ± 2 cm in the warm summer of 2014. Furthermore, we measured a pronounced multi-year net subsidence of 9.3 ± 5.7 cm from spring 2013 to the end of summer 2017. Importantly, we observed a high spatial variability of subsidence of up to 6 cm across a sub-meter horizontal scale. In summer 2013, we accompanied our field measurements with Differential Synthetic Aperture Radar Interferometry (DInSAR) on repeat-pass TerraSAR-X (TSX) data from the summer of 2013 to detect summer thaw subsidence over the same study area. Interferometry was strongly affected by a fast phase coherence loss, atmospheric artifacts, and possibly the choice of reference point. A cumulative ground movement map, built from a continuous interferogram stack, did not reveal a subsidence on the upland but showed a distinct subsidence of up to 2 cm in most of the thermokarst basins. There, the spatial pattern of DInSAR-measured subsidence corresponded well with relative surface wetness identified with the near infra-red band of a high-resolution optical image. Our study suggests that (i) although X-band SAR has serious limitations for ground movement monitoring in permafrost landscapes, it can provide valuable information for specific environments like thermokarst basins, and (ii) due to the high sub-pixel spatial variability of ground movements, a validation scheme needs to be developed and implemented for future DInSAR studies in permafrost environments.