Seed longevity is controlled by metacaspases.

To survive extreme desiccation, seeds enter a period of quiescence that can last millennia. Seed quiescence involves the accumulation of protective storage proteins and lipids through unknown adjustments in protein homeostasis (proteostasis). Here, we show that mutation of all six type-II metacaspase (MCA-II) proteases in Arabidopsis thaliana disturbs proteostasis in seeds. MCA-II mutant seeds fail to restrict the AAA ATPase CELL DIVISION CYCLE 48 (CDC48) at the endoplasmic reticulum to discard misfolded proteins, compromising seed storability. Endoplasmic reticulum (ER) localization of CDC48 relies on the MCA-IIs-dependent cleavage of PUX10 (ubiquitination regulatory X domain-containing 10), the adaptor protein responsible for titrating CDC48 to lipid droplets. PUX10 cleavage enables the shuttling of CDC48 between lipid droplets and the ER, providing an important regulatory mechanism sustaining spatiotemporal proteolysis, lipid droplet dynamics, and protein homeostasis. In turn, the removal of the PUX10 adaptor in MCA-II mutant seeds partially restores proteostasis, CDC48 localization, and lipid droplet dynamics prolonging seed lifespan. Taken together, we uncover a proteolytic module conferring seed longevity.

Occurrence, sources and water column distribution trends of suspended particle-associated aliphatic and polycyclic aromatic hydrocarbons in the open northeastern Mediterranean Sea.

Herein, we study the occurrence and water column distribution trends of suspended particle-associated aliphatic (AHCs) and polycyclic aromatic hydrocarbons (PAHs) collected from 36 offshore/deep sea locations across the open northeastern Mediterranean Sea. Total concentrations of the determined compounds fall within the range previously reported for non-polluted coastal and open sea locations worldwide. Mixed natural and anthropogenic sources were evident for the studied compounds, based on their molecular profile and several diagnostic indices. In all cases, an enhanced fossil signal typifying chronic oil pollution was evident along the water column. AHCs and PAHs mixtures characteristics varied significantly within the studied sub-regions, highlighting the importance of inputs from various point sources and dispersion pathways. The circulation characteristics of water masses along with biogeochemical features impact on the water column distribution trends and overall fate of the determined compounds in the study area.

A proxitome-RNA-capture approach reveals that processing bodies repress coregulated hub genes.

Cellular condensates are usually ribonucleoprotein assemblies with liquid- or solid-like properties. Because these subcellular structures lack a delineating membrane, determining their compositions is difficult. Here we describe a proximity-biotinylation approach for capturing the RNAs of the condensates known as processing bodies (PBs) in Arabidopsis (Arabidopsis thaliana). By combining this approach with RNA detection, in silico, and high-resolution imaging approaches, we studied PBs under normal conditions and heat stress. PBs showed a much more dynamic RNA composition than the total transcriptome. RNAs involved in cell wall development and regeneration, plant hormonal signaling, secondary metabolism/defense, and RNA metabolism were enriched in PBs. RNA-binding proteins and the liquidity of PBs modulated RNA recruitment, while RNAs were frequently recruited together with their encoded proteins. In PBs, RNAs follow distinct fates: in small liquid-like PBs, RNAs get degraded while in more solid-like larger ones, they are stored. PB properties can be regulated by the actin-polymerizing SCAR (suppressor of the cyclic AMP)-WAVE (WASP family verprolin homologous) complex. SCAR/WAVE modulates the shuttling of RNAs between PBs and the translational machinery, thereby adjusting ethylene signaling. In summary, we provide an approach to identify RNAs in condensates that allowed us to reveal a mechanism for regulating RNA fate.

Thirty years of a bottom oxygen depletion-renewal cycle in the coastal yet deep environment of the West Saronikos Gulf (Greece): Its drivers and the impact on the benthic communities.

In the period 1987-2017, a series of physical and chemical measurements related to oxygen variability at a trough area with a maximum depth of ~420 m in the West Saronikos Gulf, reveal the following: In the early 90s, deep winter mixing occurred resulting in an oxygenation down to ~420 m followed by an oxygen decline. This decline reached near-bottom hypoxic conditions (O2 < ~62 µM (µmol/L)) after 1998, while a denitrification phase occurred after 2000 and a complete bottom anoxia in 2005. In June 2012, an oxygenation down to ~350 m was detected that most likely occurred in winter 2012. The 2012 oxygenation raised the until-then anoxic bottom concentrations to hypoxic ones in the years towards 2017 via vertical diffusive oxygen transfer. Observations of the benthic communities during the hypoxia, severe hypoxia (O2 < ~15 µM) and oxygen recovery phases showed a peak of opportunists in the hypoxia and a long faunal depletion in the severe hypoxia phases. A reversal in the benthic community structure appeared after the oxygenation of 2012 with the (re)appearance of opportunists while, in 2017, the community showed signs of retreat to earlier stages. The main anthropogenic pressure that could tentatively affect the oxygen concentration in the study area is posed by the Athens treated-sewage outfall at ~40 km away from the trough, which inputs organic matter into the Saronikos Gulf through effluent water of reduced salinity that, in addition, may alter the stratification opposing the vertical mixing. We show that the treated sewage output had no influence on a) the stratification, b) the particulate and dissolved organic carbon and c) the sewage-derived organic matter. Instead, the long-term dissolved oxygen variability with the deep renewal events was mostly driven by the large-scale atmosphere-ocean conditions (heat exchange and evaporation-minus-precipitation budget) that determine the hydrographic characteristics and the winter mixing.

Plant condensates: no longer membrane-less?

Cellular condensation is a reinvigorated area of study in biology, with scientific discussions focusing mainly on the forces that drive condensate formation, properties, and functions. Usually, condensates are called 'membrane-less' to highlight the absence of a surrounding membrane and the lack of associated contacts. In this opinion article we take a different direction, focusing on condensates that may be interfacing with membranes and their possible functions. We also highlight changes in condensate material properties brought about by condensate-membrane interactions, proposing how condensates-membrane interfaces could potentially affect interorganellar communication, development, and growth, but also adaptation in an evolutionary context. We would thus like to stimulate research in this area, which is much less understood in plants compared with the animal field.

Dataset on the imprint of the Agia Zoni II tanker oil spill on the marine ecosystem of Saronikos Gulf.

These data relate to the research article entitled "Imprint and short-term fate of the Agia Zoni II tanker oil spill on the marine ecosystem of Saronikos Gulf" by Parinos et al., 2019 [1]. The dataset includes the concentrations of 32 individual compounds/groups of polycyclic aromatic hydrocarbons (PAHs) determined in 235 seawater samples and 55 sediment samples analyzed during the monitoring survey conducted by the Hellenic Centre for Marine Research (H.C.M.R.) following the September 2017 Agia Zoni II heavy fuel oil (HFO) spill incident in Saronikos Gulf, Greece. The survey effort included 69 seawater sampling sites, of which 55 coastal and 14 open sea areas, and 22 sediment sampling sites across the inner Saronikos Gulf, aiming to assess the spatial and temporal imprint of the spilled oil during the first six months from the incident. The data were acquired by means of gas chromatography - mass spectrometry, following proper pre-treatment of the collected samples. This dataset is, to the best of our knowledge, the very first PAHs record related to the Agia Zoni II oil spill incident, that should be of interest for future scientific research on this and HFO spills in general.

Occurrence and spatial distribution of 158 pharmaceuticals, drugs of abuse and related metabolites in offshore seawater.

The occurrence and spatial distribution of 158 pharmaceuticals and drugs of abuse were studied in seawater of the Eastern Mediterranean Sea (Saronikos Gulf and Elefsis Bay in central Aegean Sea). This area is affected by various anthropogenic pressures as it receives the treated wastewater of the greatest Athens area and off-shore input fluxes. This study constitutes the largest one in terms of number of analytes in this environmental compartment. It provides the first evidence on the occurrence of several pharmaceuticals in marine environment including amoxicillin, lidocaine, citalopram or tramadol, among others. 22 samples were collected at three different depths in 9 sampling stations in order to assess the presence and the spatial distribution of the target compounds. A multi-residue method based on solid phase extraction and liquid chromatography coupled to tandem mass spectrometry was developed for the determination of the 158 target substances and validated for seawater sample analysis. 38 out of the 158 target compounds were detected, 15 of them with frequencies of detection equal to or higher than 50%. The highest detected values corresponded to amoxicillin, caffeine and salicylic acid, with concentrations in the range of < 5.0-127.8 ng L(-1); 5.2-78.2 ng L(-1) and < 0.4-53.3 ng L(-1), respectively. Inputs from the wastewater treatment plant (WWTP) of Athens revealed to be the main source of pollution in the Inner Saronikos Gulf, whereas, other anthropogenic pressures such as contamination from shipping activity, industrial effluents, dredging and/or inputs from land proved to be also relevant. Τhe concentrations of some compounds varied significantly with depth suggesting that currents play an important role in the dilution of the target compounds.

Biochemical biomarker responses to pollution in selected sentinel organisms across the Eastern Mediterranean and the Black Sea.

Pollution effects were assessed by means of biochemical biomarkers (catalase, glutathione S-transferase and acetylcholinesterase activities, and metallothioneins content) in five species at selected coastal sites across the Eastern Mediterranean and the Black Sea. The mussel Mytilus galloprovincialis, a well-established sentinel species, was investigated in the Adriatic Sea, Aegean Sea, and Black Sea. The mussel Brachidontes pharaonis and the striped red mullet Mullus surmuletus were used in the Levantine Sea where M. galloprovincialis is not present. The white seabream Diplodus sargus sargus and the gastropod Rapana venosa were additionally sampled in the Adriatic and the Black Sea, respectively. Mussels showed catalase, glutathione S-transferase, and acetylcholinesterase responses to pollution in most geographical areas while the response of metallothioneins was restricted to a few sites. R. venosa showed marked responses of catalase and metallothioneins whereas both fish species did not generally exhibit variations in biomarker values among sites. The approach based on the reference deviation concept using the "Integrated Biological Responses version 2" index was useful for the interpretation of overall biomarker responses.

Chemical inputs from a karstic submarine groundwater discharge (SGD) into an oligotrophic Mediterranean coastal area.

The impacts of nutrient and other chemical inputs released by a submarine groundwater discharge (SGD) on the marine environment of an oligotrophic Mediterranean coastal area (Messiniakos Gulf, SE Ionian Sea) are investigated through a multidisciplinary approach. Nutrients and organic pollutants associated with the SGD are presented to study the chemical characteristics of the SGD and to investigate its effect on the marine ecosystem in comparison to freshwater discharges of the water bodies of Messinia Prefecture. Nutrient and organic pollutant fluxes were calculated from (214)Bi-based SGD estimates. An average of 22×10(3) mol of silicate per month and 8×10(3) mol of nitrate per month were released via the SGD. Nutrient concentrations at the mouth of the SGD were three times higher than in Messiniakos Gulf, and NO3(-) was the primary Dissolved Inorganic Nitrogen form discharged by SGD. Organic pollutant concentrations associated with agricultural activities were low at the SGD. The implementation of a Eutrophication Index (E.I.) showed that the water column at the SGD site corresponds to Moderate/Bad ecological quality, whereas the status switches rapidly to Good at a small distance from the SGD. Coastal areas influenced by river or sewage discharge correspond to a Moderate/Good ecological status. The BENTIX index used for the classification of the ecological quality status of the benthic macroinvertebrate communities showed that the SGD has a minor influence compared to the other freshwater discharges in Messiniakos Gulf. Though the SGD has a considerable outflow, morphology and hydrodynamics of the area favor the rapid dispersion of the upwelling water and degrades the SGD's effect even on a regional scale.

Impact of dredged urban river sediment on a Saronikos Gulf dumping site (Eastern Mediterranean): sediment toxicity, contaminant levels, and biomarkers in caged mussels.

Impacts of chemical contaminants associated with dumping of dredged urban river sediments at a coastal disposal area in Saronikos Gulf (Eastern Mediterranean) were investigated through a combined approach of sediment toxicity testing and active biomonitoring with caged mussels. Chemical analyses of aliphatic hydrocarbons (AHs), polycyclic aromatic hydrocarbons (PAHs), Cu, and Zn in combination with the solid phase Microtox® test were performed on sediments. Concentrations of PAHs, AHs, Cu, and Zn as well as multiple biomarkers of contaminant exposure and/or effects were measured in caged mussels. Sediments in the disposal and neighboring area showed elevated PAHs and AHs concentrations and were characterized as toxic by the solid-phase Microtox® test during and after dumping operations. Biomarker results in the caged mussels indicated sublethal effects mainly during dumping operations, concomitantly with high concentrations of PAHs and AHs in the caged mussel tissues. Cu and Zn concentrations in sediments and caged mussels were generally not elevated except for sediments at the site in the disposal area that received the major amount of dredges. High PAHs and AHs levels as well as sublethal effects in the caged mussels were not persistent after termination of operations. The combined bioassay-biomarker approach proved useful for detecting toxicological impacts of dredged river sediment disposal in sediments and the water column. Nevertheless, further research is needed to evaluate whether sediment toxicity will have long-term effects on benthic communities of the disposal area.

Influence of pollution history on the response of coastal bacterial and nanoeukaryote communities to crude oil and biostimulation assays.

Pollution history has often been proposed to explain site-dependent bioremediation efficiencies, but this hypothesis has been poorly explored. Here, bacteria and their heterotrophic nanoflagellates (HNF) predators originating from pristine and chronically oil-polluted coastal sites were subjected to crude oil ± nutrients or emulsifier amendments. The addition of crude oil had a more visible effect on bacteria originating from the pristine site with a higher increase in the activity of given OTU and inactivation of other petroleum-sensitive bacteria, as revealed by DNA and RNA-based comparison. Such changes resulted in a delay in microbial growth and in a lower bacterial degradation of the more complex hydrocarbons. Biostimulation provoked a selection of different bacterial community assemblages and stirred metabolically active bacteria. This resulted in a clear increase of the peak of bacteria and their HNF predators and higher oil degradation, irrespective of the pollution history of the site.

Active biomonitoring in Greek coastal waters: application of the integrated biomarker response index in relation to contaminant levels in caged mussels.

An integrated approach using biomarkers and contaminant levels in mussels Mytilus galloprovincialis L. was employed to assess chemical contamination in Greek coastal waters within the framework of the MYTIMED program. Biomarkers (metallothioneins, glutathione S-transferase, catalase, acetylcholinesterase and RNA:DNA ratio) have been previously described in mussels caged at 14 sites in coastal areas influenced by different types of anthropogenic activities. This study applied a biomarker index, the Integrated Biomarker Response (IBR) to summarize biomarker responses and relate stress levels to concentrations of organochlorine compounds (PCBs, DDTs), polycyclic aromatic hydrocarbons (PAHs), and metals (Cu, Ni, Fe, Zn) measured in the mussel tissues. The IBR index indicated environmental stress at sites near cities and industries and was overall related to organic contaminants, but also elevated metal concentrations at certain sites. Slightly increased IBR values at few sites away from known pollution sources were not accompanied with increased contaminant levels suggesting stress possibly caused by natural factors. Results confirmed the usefulness of integration of biological effects measurements and chemical analysis for the assessment of chemical contamination in coastal waters.

A multi-criteria approach for the dumping of dredged material in the Thermaikos Gulf, Northern Greece.

A multi-criteria approach was applied for the disposal into the sea of ∼1,100,000 m(3) of sediment, dredged from a coastal area in the northeastern part of the Thermaikos Gulf. This sediment (classified as muddy) is distributed vertically into two distinct Layers (A and B) with the thickness of the surficial sedimentary unit ranging from 7 to 54 cm. Its geochemistry reveals increased Cr and Ni concentrations, which may be attributed to natural enrichment through the erosion of the adjacent igneous and metamorphic rocks. In addition, a low to moderate contamination from urban-originated heavy metals, like Cu, Pb and Zn as well as from aliphatic and polycyclic hydrocarbons was identified for the upper Layer A. However, the limited proportion (5.5%) of the polluted Layer A in the total volume of the dredged material could not affect the good quality (assessed by the Sediment Quality Guidelines) of the bulk sediment. The identification of the optimum marine dumping site was based on (a) the physicochemical similarity (detected by the application of a cluster analysis) of the dredged material with the surficial deposits of potential dumping sites in the Outer Thermaikos Gulf, and (b) the consideration, based on previous studies, of various criteria related to the disposal area such as deep-water circulation, influence on living resources, impact on economical (aquaculture, fishing, navigation), recreational (fishing) and military activities.