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Biodegradation of synthetic polymers, in particular polyethylene terephthalate (PET), is of great importance, since environmental pollution with PET and other plastics has become a severe global problem. Here, we report on the polyester degrading ability of a novel carboxylic ester hydrolase identified in the genome of the marine hydrocarbonoclastic bacterium Pseudomonas aestusnigri VGXO14$^T$. The enzyme, designated PE-H, belongs to the type IIa family of PET hydrolytic enzymes as indicated by amino acid sequence homology. It was produced in Escherichia coli, purified and its crystal structure was solved at 1.09 Å resolution representing the first structure of a type IIa PET hydrolytic enzyme. The structure shows a typical α/β-hydrolase fold and high structural homology to known polyester hydrolases. PET hydrolysis was detected at 30°C with amorphous PET film (PETa), but not with PET film from a commercial PET bottle (PETb). A rational mutagenesis study to improve the PET degrading potential of PE-H yielded variant PE-H (Y250S) which showed improved activity, ultimately also allowing the hydrolysis of PETb. The crystal structure of this variant solved at 1.35 Å resolution allowed to rationalize the improvement of enzymatic activity. A PET oligomer binding model was proposed by molecular docking computations. Our results indicate a significant potential of the marine bacterium P. aestusnigri for PET degradation. Frontiers in microbiology 11, 114 (2020). doi:10.3389/fmicb.2020.00114 Published by Frontiers Media, Lausanne

Riverine dissolved organic carbon (DOC) contains charcoal byproducts, termed black carbon (BC). To determine the significance of BC as a sink of atmospheric CO2 and reconcile budgets, the sources and fate of this large, slow-cycling and elusive carbon pool must be constrained. The Amazon River is a significant part of global BC cycling because it exports an order of magnitude more DOC, and thus dissolved BC (DBC), than any other river. We report spatially resolved DBC quantity and radiocarbon (Δ14C) measurements, paired with molecular-level characterization of dissolved organic matter from the Amazon River and tributaries during low discharge. The proportion of BC-like polycyclic aromatic structures decreases downstream, but marked spatial variability in abundance and Δ14C values of DBC molecular markers imply dynamic sources and cycling in a manner that is incongruent with bulk DOC. We estimate a flux from the Amazon River of 1.9–2.7 Tg DBC yr−1 that is composed of predominately young DBC, suggesting that loss processes of modern DBC are important. Nature Communications, 10 ISSN:2041-1723

The oceans absorb about a quarter of the annually produced anthropogenic atmospheric carbon dioxide (CO2), resulting in a decrease in surface water pH, a process termed ocean acidification (OA). Surprisingly little is known about how OA affects the physiology of heterotrophic bacteria or the coupling of heterotrophic bacteria to phytoplankton when nutrients are limited. Previous experiments were, for the most part, undertaken during productive phases or following nutrient additions designed to stimulate algal blooms. Therefore, we performed an in situ large-volume mesocosm (similar to 55 m(3)) experiment in the Baltic Sea by simulating different fugacities of CO2 (fCO(2)) extending from present to future conditions. The study was conducted in July-August after the nominal spring bloom, in order to maintain low-nutrient conditions throughout the experiment. This resulted in phytoplankton communities dominated by small-sized functional groups (picophytoplankton). There was no consistent fCO(2)-induced effect on bacterial protein production (BPP), cell-specific BPP (csBPP) or biovolumes (BVs) of either free-living (FL) or particle-associated (PA) heterotrophic bacteria, when considered as individual components (univariate analyses). Permutational Multivariate Analysis of Variance (PERMANOVA) revealed a significant effect of the fCO(2) treatment on entire assemblages of dissolved and particulate nutrients, metabolic parameters and the bacteria-phytoplankton community. However, distance-based linear modelling only identified fCO(2) as a factor explaining the variability observed amongst the microbial community composition, but not for explaining variability within the metabolic parameters. This suggests that fCO(2) impacts on microbial metabolic parameters occurred indirectly through varying physicochemical parameters and microbial species composition. Cluster analyses examining the co-occurrence of different functional groups of bacteria and phytoplankton further revealed a separation of the four fCO(2)-treated mesocosms from both control mesocosms, indicating that complex trophic interactions might be altered in a future acidified ocean. Possible consequences for nutrient cycling and carbon export are still largely unknown, in particular in a nutrient-limited ocean. Peer reviewed

Eutrophication, global warming, and rising carbon dioxide (CO2) levels are the three most prevalent pressures impacting the biosphere. Despite their individual effects are well-known, it remains untested how oligotrophication (i.e. nutrients reduction) can alter the planktonic community responses to warming and elevated CO2 levels. Here, we performed an indoor mesocosm experiment to investigate the warming × CO2 interaction under a nutrient reduction scenario (40%) mediated by an in-lake management strategy (i.e. addition of a commercial solid-phase phosphorus sorbent -Phoslock®) on a natural freshwater plankton community. Biomass production increased under warming × CO2 relative to present-day conditions; however, a Phoslock®-mediated oligotrophication reduced such values by 30–70%. Conversely, the warming × CO2 × oligotrophication interaction stimulated the photosynthesis by 20% compared to ambient nutrient conditions, and matched with higher resource use efficiency (RUE) and nutrient demand. Surprisingly, at a group level, we found that the multi-stressors scenario increased the photosynthesis in eukaryotes by 25%, but greatly impaired in cyanobacteria (ca. −25%). This higher cyanobacterial sensitivity was coupled with a reduced light harvesting efficiency and compensation point. Since Phoslock®-induced oligotrophication unmasked a strong negative warming × CO2 effect on cyanobacteria, it becomes crucial to understand how the interplay between climate change and nutrient abatement actions may alter the, ecosystems functioning. With an integrative understanding of these processes, policy makers will design more appropriate management strategies to improve the ecological status of aquatic ecosystems without compromising their ecological attributes and functioning.

The water masses of the Arctic Ocean shelf regions are significantly influenced by river water and sea-ice processes. Since river water is highly depleted in ∂18O relative to marine waters as well as to sea-ice, the ∂18O composition and salinity of a water sample can be used to separate the different freshwater water sources. In this paper the distributions of river water, sea-ice melt water or sea-ice formation are discussed for the Kara, Laptev and Beaufort shelves based on ∂18O and salinity data. Depending on the average depth the observed fields of salinity and ∂18O values are different for each region. But comparing the overall ∂18O and salinity correlations reveals a remarkable similarity for these three Arctic shelf regions as similar local bottom-water masses are formed by sea-ice processes. Remnants of these seaice derived bottom water masses are found on all shelves during summer at a salinity of about 30. Investigations at the shelf break of the Kara Sea and Laptev Sea show that river water as well as brine waters are exported to the Arctic Ocean halocline. This export shows inter-annual variability in correlation with wind forcing during summer.

Fungi: DNA was extracted using the modified Power Soil protocol (Harkes et al., ), with 0.25 g soil per sample and Lysing matrix E beads tubes (MP Biomedicals). Fungal DNA was amplified using primers ITS4ngs and ITS3mix1‐5 (Tedersoo et al., , ) and purified using AMPure magnetic beads (Beckman Coulter). Polymerase chain reactions (PCRs) were performed with 12.5‐μL Hotstart ready mix (Fisher scientific) and approximately 50 ng of DNA per reaction. Dual tags were added to samples (Illumina dual indexing kits v1‐3) using seven cycles of PCR. PCR products were further purified using magnetic beads. The DNA was quantified using a Qubit fluorometer and equimolar pooled into libraries of 285 and 250 samples each. Mock community samples with eight fungal strains were sequenced along with the experimental samples. Sequencing was performed using Illumina MiSeq pair‐end 2x300bp. Here we give the OTU table and taxa files as well as report all OTUs unique to one site. Soil Chemistry: Chemical soil properties were determined by AgroCares BV (Wageningen, the Netherlands). Soils for chemical analysis were dried at 50°C using fruit dryers, crushed and sieved (2 mm sieve). One part of the soil sample was homogenized and pulverized (<0.2 mm) using a planetary micro mill with 10 clean metal balls for 3 min with speed 500 rpm. This sample was used to measure the total C and N by heating it to 900°C in the presence of O2, forming CO2 and N2, which were quantitatively measured with a thermal conductivity detector. Peak areas are correlated with validated calibration curves, to obtain element weight for C and N, which is recalculated to percentage by considering the sample mass. Total organic carbon (TOC) was measured using the Elementar Rapid CS cube (Elementar Analysensysteme, Germany) after removal and quantification of the total inorganic carbon (TIC) fraction as carbonates through acid (1 M HCl) treatment. Samples for soil texture were weighed and treated with 30% H2O2 for the removal of organic material, treated with dithionite solution (40 g/L Na2S2O4 in 0.3 M NaOAc, pH 3.8) for the removal of iron oxide, and treated with 1 M HCl for the removal of carbonates. After this sample treatment, the samples were measured with the Mastersizer 3,000 (Malvern Panalytical B.V., Almelo, the Netherlands) to determine the particle size distribution using laser diffraction. Soil pH (KCl) was determined using a pH electrode. The procedure for the extraction of soils using Mehlich‐3 solution as extractant was validated and executed according to Wolf and Beegle (), with one exception, the shaking time was increased from 5 to 10 min. The measurement of samples for the determination of bulk multi‐element concentrations in dry soil samples (RT: Real Totals) was carried out using the PANalytical Epsilon 3 ED‐XRF (Malvern Panalytical B.V., Almelo, the Netherlands). The procedure is in accordance with ISO18227:2014 and validated. The samples were prepared as pellets with a soil to wax ratio of 9:1. Lastly, cation exchange capacity (CEC) and the content of exchangeable cations (Al3+, Ca2+, Fe2+, K+, Mg2+, Mn2+, Na+, B+, Cu2+, Mo2+, Ni2+ and Zn2++) and anions (S2−, P3−) in soils were determined after extraction with hexamminecobalt trichloride solution. The procedure was validated and is in accordance with ISO 23470:2007. Cropping practices have a great potential to improve soil quality through changes in soil biota. Yet the effects of these soil improving cropping systems on soil fungal communities are not well known. Here, we analysed soil fungal communities using standardized measurements in 12 long‐term experiments and 20 agricultural treatments across Europe. We were interested in whether the same practices (i.e. tillage, fertilization, organic amendments and cover crops) applied across different sites have predictable and repeatable effects on soil fungal communities and guilds. The fungal communities were very variable across sites located in different soil types and climatic regions. The arbuscular mycorrhizal fungi (AMF) were the fungal guild with most unique species in individual sites while plant pathogenic fungi were most shared between the sites. The fungal communities responded to the cropping practices differently in different sites and only fertilization showed a consistent effect on AMF and plant pathogenic fungi while the response to tillage, cover crops and organic amendments were site, soil and crop species specific. We further show that the crop yield is negatively affected by cropping practices aimed at improving soil health. Yet, we show that these practices have the potential to change the fungal communities and that change in plant pathogenic fungi and in AMF is linked to the yield. We further link the soil fungal community and guilds to soil abiotic characteristics and reveal that especially Mn, K, Mg and pH affect the composition of fungi across sites. In summary, we show that fungal communities vary considerably between sites and that there are no clear directional responses in fungi or fungal guilds across sites to soil improving cropping systems but that the responses vary based on soil abiotic conditions, crop type, and climatic conditions. Details on experiments related to the data is provided in supplementary materials of the related article

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Here, the effects of a grid-spacing dependent horizontal mixing on the wave-current interactions are studied. Near the shore, wave rays diverge from channels towards bar crests because of refraction by topography and currents, in a way that depends on the rip current intensity which is itself modulated by the horizontal mixing. At low resolution with the grid-spacing dependent horizontal mixing, the wave motion is the same for both coupling modes because the wave deviation by the currents is weak. In high resolution case, however, classical results are found with the stabilizing effect of the flow by feedback of waves on currents. Lastly, wave-current interactions and the horizontal mixing strongly affect the intensity of the three-dimensional rip velocity.