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Titanium dioxide, frequently used in commonplace products, is now regularly detected in aquatic environments. Understanding its toxic effects on native biota is essential. However, combined toxicity with commonly occurring pollutants, such as the pharmaceutical diclofenac, may provide more insight into environmental situations. Therefore, the present study aimed to evaluate the effects of titanium dioxide and diclofenac, individually and combined, on the macrophyte Egeria densa. Diclofenac uptake and removal by the macrophyte were assessed. Diclofenac and titanium dioxide were mixed prior to exposure to allow binding, which was assessed. Toxicity of the individual compounds and the combination was evaluated by assaying enzymes as bioindicators of biotransformation and the antioxidative system. Cytosolic glutathione S-transferase and glutathione reductase activities were increased by diclofenac, titanium dioxide, and the combination. Both enzymes’ activities were more significantly elevated by diclofenac and the combination than nanoparticles alone. Microsomal glutathione S-transferase was unaffected by diclofenac exposure but inhibited with titanium dioxide and the mixture. Diclofenac elicited the most significant response. Based on the data, the cytosolic enzymes effectively prevented damage.

openaire: EC/H2020/648925/EU//BHIVE Funding Information: We thank Kuisma Littunen and Kim Kataja who assisted with substrate preparation and Nelly Monties who assisted with enzyme production. We also thank Professor A. McGuigan (University of Toronto) for helpful discussions. Funding Information: We thank the following granting agencies for their financial support: the European Research Council (ERC) (Consolidator Grant no. BHIVE – 648925) (MM, EJ, VL and ERM); Jenny and Antti Wihuri Foundation (Centre for Young Synbio Scientists) (TK); Academy of Finland Postdoctoral Researcher Grant No. 331853 (TP); The French national research agency (anr) Grant No. ANR-18-CES43-DECO (TE and CD). Publisher Copyright: © 2022, The Author(s). Background : Substrate accessibility remains a key limitation to the efficient enzymatic deconstruction of lignocellulosic biomass. Limited substrate accessibility is often addressed by increasing enzyme loading, which increases process and product costs. Alternatively, considerable efforts are underway world-wide to identify amorphogenesis-inducing proteins and protein domains that increase the accessibility of carbohydrate-active enzymes to targeted lignocellulose components. Results : We established a three-dimensional assay, PACER (plant cell wall model for the analysis of non-catalytic and enzymatic responses), that enables analysis of enzyme migration through defined lignocellulose composites. A cellulose/azo-xylan composite was made to demonstrate the PACER concept and then used to test the migration and activity of multiple xylanolytic enzymes. In addition to non-catalytic domains of xylanases, the potential of loosenin-like proteins to boost xylanase migration through cellulose/azo-xylan composites was observed. Conclusions : The PACER assay is inexpensive and parallelizable, suitable for screening proteins for ability to increase enzyme accessibility to lignocellulose substrates. Using the PACER assay, we visualized the impact of xylan-binding modules and loosenin-like proteins on xylanase mobility and access to targeted substrates. Given the flexibility to use different composite materials, the PACER assay presents a versatile platform to study impacts of lignocellulose components on enzyme access to targeted substrates.

Continuous low-cost bulk biolixiviant production remains as one of the main challenges of heterotrophic bioleaching towards large scale application. This study aimed at developing non-aseptic Gluconobacter oxydans-amended fluidized-bed reactor (FBR) process for continuous production of gluconic acid for efficient leaching of rare earth elements (REEs) and base metals from spent nickel-metal-hydride (NiMH) batteries. In preliminary experiments, the FBR became contaminated and massively overgrown by air-borne fungus, Leptobacillium leptobactrum. In a series of batch bioassays, operational conditions were investigated to discourage the fungal activity i.e., an ecologically engineered niche for gluconic acid production. High gluconate concentration (≥100 g/l) and/or low pH (≤2.5) gave a selective preference for G. oxydans growth over L. leptobactrum and controlled the activity of possible contaminants during FBR continuous operation. The highest gluconic acid production rate of 390 g/l∙d with corresponding glucose-to-gluconic acid conversion yield of 94% was obtained at hydraulic retention time (HRT) of 6.3 h and 380 g/l∙d glucose loading rate. Using the FBR effluents as leaching agents, respectively, total base metals and REEs leaching yields of up to 82% and 55% were achieved within 7 days at 1% (w/v) spent battery pulp density. The obtained glucose-to-gluconic acid conversion rates and yields were one of the highest reported for any glucose biotransformation process. The REE leaching yields were higher than those reported for similar high metal-grade REE secondary sources. The high-rate glucose-to-gluconic acid bioconversion in the non-aseptic system utilizing microbial ecology based FBR operation strategy rather than aseptic chemostats indicates industrial feasibility of gluconic acid production and thus, the applicability of heterotrophic bioleaching. publishedVersion

Background Vegetated building envelopes (VBEs), such as vegetated roofs and facades, are becoming more frequent in urban planning nowadays. However, harsh growing conditions restrain the application of VBEs. Plant growth-promoting microbes (PGPMs) might help ease the stresses, but first, it is necessary to investigate how to ensure their survival and growth under VBE conditions. Methods We conducted three experiments to test the impact of various factors on the microbial populations of inoculated PGPMs in VBEs, a mycorrhizal fungus Rhizophagus irregularis and a bacterium Bacillus amyloliquefaciens. The first experiment was conducted by inoculating the two PGPMs separately in Sedum roof plots, and the microbial populations associated with Poa alpina was monitored for two consecutive years under local weather conditions. The second experiment was conducted in a laboratory testing the effect of substrate pH (substrates collected from balcony gardens) on R. irregularis population associated with Trifolium repens and Viola tricolor. The third experiment was conducted on a meadow roof testing the effect of biochar amendment on R. irregularis population associated with Thymus serpyllum and Fragaria vesca. Results In the first experiment, Bacillus was found to associate with P. alpina, but Rhizophagus wasn't. Yet, the fungus induced high Bacillus population density in the Rhizophagus treated plots in the first year. In the second experiment, Rhizophagus abundance in T. repens was higher in the neutral substrate (6–6.5), while V. tricolor was more colonized in acidic substrate (5–5.5), suggesting an important interactive effect of substrate pH and plant species on Rhizophagus abundance. The third experiment suggested a negligible impact of biochar amendment on Rhizophagus abundance for both host plants. Conclusion Three experiments demonstrate that PGPM inoculation on VBEs is feasible, and various factors and interactions affect the PGPM populations. This paper provides reference and inspiration for other VBE research involving substrate microbial manipulation.

Neurodegenerative diseases are characterized by the abnormal accumulation of aggregated proteins in the brain. Using in vivo pulse isotope labeling, we screened the proteome for changes in protein turnover and abundance in multiple mouse models of neurodegeneration. These data suggest that the disease state of pathologically affected tissue is characterized by a proteome-wide increase in protein turnover and repair. In contrast, in healthy wild-type mice, aging in the mammalian brain is associated with a global slowdown in protein turnover.

The use of alternative, natural fibers instead of synthetic reinforcements in polymeric matrix composites, subjected to certain out-of-plane loads, requires a study on the susceptibility to damage. The aim of this work is to study the impact behavior and the stiffness reduction in flax and carbon fibre reinforced plastic laminates subjected to a 15 J drop-tower test. The detection of selected damage mechanisms was done by high-speed optical and infrared cameras monitoring the full-field deformation and temperatures on the composite surface. The elastic response of the laminates was modelled by a finite element method and ply failure was analyzed by the Hashin’s and Puck’s failure criteria. The results of thermal and strain measurements indicated the primary cracks due to the bending effect for the flax laminate. For the carbon laminate, the final fibre breaking was indicated. Numerical results showed the accuracy of the Puck’s criterion about the prediction of first stages of the impact failure. publishedVersion Non

This study investigated for the first time if ammonia tolerant methanogenic consortia can be stored in gel (biogel) and used in a later time on-demand as bioaugmentation inocula, to efficiently relieve ammonia inhibition in continuous biomethanation systems. Moreover, wood biochar was assessed as a potential enhancer of the novel biogel bioaugmentation process. Three thermophilic (55 °C), continuous stirred-tank reactors (RBgel, RChar and RMix), operated at 4.5 g NH4+-N L-1 were exposed to biogel, biochar and mixture of biogel and biochar, respectively, while a fourth reactor (RCtrl) was used as control. The results showed that the methane production yields of RMix, RChar and RBgel increased by 28.6%, 20.2% and 10.7%, respectively compared to RCtrl. The highest methane yield was achieved by the synergistic interaction between biogel and biochar. Additionally, biogel stimulated a rapid recovery of Methanoculleus thermophilus sp. and syntrophic acetate oxidising bacteria populations.

Hydrogen-producing mixed cultures were subjected to a 48-h downward or upward temperature fluctuation from 55 to 35 or 75 °C. Hydrogen production was monitored during the fluctuations and for three consecutive batch cultivations at 55 °C to evaluate the impact of temperature fluctuations and bioaugmentation with synthetic mixed culture of known H2 producers either during or after the fluctuation. Without augmentation, H2 production was significantly reduced during the downward temperature fluctuation and no H2 was produced during the upward fluctuation. H2 production improved significantly during temperature fluctuation when bioaugmentation was applied to cultures exposed to downward or upward temperatures. However, when bioaugmentation was applied after the fluctuation, i.e., when the cultures were returned to 55 °C, the H2 yields obtained were between 1.6 and 5% higher than when bioaugmentation was applied during the fluctuation. Thus, the results indicate the usefulness of bioaugmentation in process recovery, especially if bioaugmentation time is optimised.

Plastic debris degrades in the water environments due to various factors such as mechanical stress. Small-sized degradation products, including plastic monomers, are currently monitored using equipment which might be unsuitable for screening. Here, we developed a recombinant whole-cell bacterial biosensor, which could be used for this type of monitoring. The Escherichia coli pBAV1K-ACU-lucFF cells contain a luciferase-based reporter system under the control of acrylic acid specific promoter. The biosensor cells were used to detect acrylic acid monomers from both sterile water and spiked lake water samples, indicating usability with environmental samples. Furthermore, poly(acrylic acid) was incubated in salt water, and the biosensor cells could identify acrylic acid monomers originating from it. Thus, the cells could be used to observe similar processes in the environment. The results show that the bacterial biosensors could complement the current research methods of plastic monomer monitoring in water environments with a potential for higher throughputs. publishedVersion

Distinct microbial assemblages evolve in anaerobic digestion (AD) reactors to drive sequential conversions of organics to methane. The spatio-temporal development of three such assemblages (granules, biofilms, planktonic) derived from the same inoculum was studied in replicated bioreactors treating long-chain fatty acids (LCFA)-rich wastewater at 20 °C at hydraulic retention times (HRTs) of 12–72 h. We found granular, biofilm and planktonic assemblages differentiated by diversity, structure, and assembly mechanisms; demonstrating a spatial compartmentalisation of the microbiomes from the initial community reservoir. Our analysis linked abundant Methanosaeta and Syntrophaceae-affiliated taxa (Syntrophus and uncultured) to their putative, active roles in syntrophic LCFA bioconversion. LCFA loading rates (stearate, palmitate), and HRT, were significant drivers shaping microbial community dynamics and assembly. This study of the archaea and syntrophic bacteria actively valorising LCFAs at short HRTs and 20 °C will help uncover the microbiology underpinning anaerobic bioconversions of fats, oil and grease. publishedVersion

In this study, strategies for recovery of ammonia-stressed AD reactors were attempted, by addition of preserved bioaugmentation consortium in gel (BioG), fresh consortium in liquid medium (BioL), woodchip biochar (BW), and straw biochar (BS). In comparison to control group with ammonia, effective treatments, i.e., BioG, BioL, BW and BS raised the maximum methane production rate by 77%, 23%, 35%, and 24%, respectively. BW possibly acted as interspecies electrical conduits for Direct Electron Transfer based on conductivity and SEM analysis. BioG facilitated slow release of bioaugmentation inocula from gel into the AD system, which protected them from a direct environmental shock. According to microbial analysis, both BioG, BioL and BW resulted in increased relative abundance of Methanothermobacter thermautotrophicus; and BS induced selective raise of Methanosarcina thermophila. The increase of methanogens via these strategies led to the faster recovery of the AD process. publishedVersion

Methane (CH4) is a sustainable carbon feedstock for value-added chemical production in aerobic CH4-oxidizing bacteria (methanotrophs). Under substrate-limited (e.g., oxygen and nitrogen) conditions, CH4 oxidation results in the production of various short-chain organic acids and platform chemicals. These CH4-derived products could be broadened by utilizing them as feedstocks for heterotrophic bacteria. As a proof of concept, a two-stage system for CH4 abatement and 1-alkene production was developed in this study. Type I and Type II methanotrophs, Methylobacter tundripaludum SV96 and Methylocystis rosea SV97, respectively, were investigated in batch tests under different CH4 and air supplementation schemes. CH4 oxidation under either microaerobic or aerobic conditions induced the production of formate, acetate, succinate, and malate in M. tundripaludum SV96, accounting for 4.8–7.0% of consumed carbon from CH4 (C-CH4), while M. rosea SV97 produced the same compounds except for malate, and with lower efficiency than M. tundripaludum SV96, accounting for 0.7–1.8% of consumed C-CH4. For the first time, this study demonstrated the use of organic acid-rich spent media of methanotrophs cultivating engineered Acinetobacter baylyi ADP1 ‘tesA-undA cells for 1-alkene production. The highest yield of 1-undecene was obtained from the spent medium of M. tundripaludum SV96 at 68.9 ± 11.6 μmol mol Csubstrate–1. However, further large-scale studies on fermenters and their optimization are required to increase the production yields of organic acids in methanotrophs.

Studies that quantify plant methane (CH4) emission rely on the accurate measurement of small changes in the mixing ratio of CH4 that coincide with much larger changes in the mixing ratio of volatile organic compounds (VOCs). Here, we assessed whether 11 commonly occurring VOCs (e.g. methanol, α- and β-pinene, Δ3-carene) interfered with the quantitation of CH4 by five laser-absorption spectroscopy and Fourier-transformed infrared spectroscopy (FTIR) based CH4 analysers, and quantified the interference of seven compounds on three instruments. Our results showed minimal interference with laser-based analysers and underlined the importance of identifying and compensating for interferences with FTIR instruments. When VOCs were not included in the spectral library, they exerted a strong bias on FTIR-based instruments (64–1800 ppbv apparent CH4 ppmv−1 VOC). Minor (0.7–126 ppbv ppmv−1) interference with FTIR-based measurements were also detected when the spectrum of the interfering VOC was included in the library. In contrast, we detected only minor ( ppbv ppmv−1) and transient (< 1 min) VOC interferences on laser-absorption spectroscopy-based analysers. Overall, our results demonstrate that VOC interferences have only minor effects on CH4 flux measurements in soil chambers, but may severely impact stem and shoot flux measurements. Laser-absorption-based instruments are better suited for quantifying CH4 fluxes from plant leaves and stems than FTIR-based instruments; however, significant interferences in shoot chamber measurements could not be excluded for any of the tested instruments. Our results furthermore showed that FTIR can precisely quantify VOC mixing ratios and could therefore provide a method complementary to proton-transfer-reaction mass spectrometry (PTR-MS).

Microbial electrochemical technologies (MET), also known as bioelectrochemical systems (BES), use microorganisms as biocatalysts to recover valuable resources like bioelectricity, hydrogen, nutrients, metals, and industrial chemicals from wastes and wastewaters. MET are therefore expected to play a key role in waste management and reduction of the carbon footprint in the near future. However, considerable fundamental and technological challenges still need to be addressed before using MET in practice. Rapid start-up, as well as an efficient and stable performance, are the pre-requisites to achieve commercialization of MET. Although considerable advancements have been made in this field in the past two decades, no general conclusion has been drawn about how to start-up BES in the most efficient manner. This review aims to survey and critically analyze start-up strategies proposed in the literature to favor a fast and efficient establishment of electrochemically active microorganisms onto bioanodes or biocathodes and promote their activity over a long period of operation. Various aspects of BES start-up, including inoculum selection, elimination of competitive microorganisms, and selection of operational parameters for enrichment of electroactive biofilms are covered. In summary, inoculation with already enriched culture, imposing of an anode potential or using polarity reversal at the cathode are the potential methods for ensuring fast and efficient BES start-up. Electrode configuration and hydrodynamic conditions are also major aspects to be considered for biofilm formation and development. acceptedVersion

Microbial sulfate reduction possesses a potential risk for the long-term safety of spent nuclear fuel repositories because under expected repository conditions sulfide is the main corroding agent for copper and copper-coated steel canisters foreseen in the Scandinavian disposal concepts. It is thus essential to understand and quantify the processes and factors impacting microbial sulfide production within and around compacted bentonite, which is planned to be used as a buffer material in many repository concepts. In the present study reactive transport modelling was applied to increase the understanding of diffusion cell experiments, which brought sand layers with or without inoculated microorganisms in contact with compacted and saturated bentonites of different mineralogy. Model results obtained for a sodium bentonite from Wyoming and a calcium bentonite from Bulgaria gave strong evidence for the activation of bentonite indigenous microorganisms, at least in zones of a reduced density close to the bentonite/sand interface. For all experiments, the calculations indicated that after an initial phase of favourable conditions, microbial activity was limited by the (bio-)availability of organic carbon. In the Bulgarian bentonite, characterized by a very low gypsum content, the model furthermore suggested some intermediate control of microbial sulfate reduction by sulfate availability. The present study thus demonstrated the rapid evolution of a transport limited system in settings where zones of microbial activity are in contact with highly compacted microbially-inactive bentonite. Gypsum dissolution calculated and determined experimentally for the Wyoming bentonite indicated significant gypsum dissolution in the first 2 cm from the interface during 450 days. The reactive transport model applied successfully in this study for the description of an experimental system followed the conceptual models for microbial sulfate reduction in repository settings. The results obtained offer insights regarding the mechanism and magnitude of biogeochemical reactions that might occur in the vicinity of the bentonite buffer surrounding the waste canister and in so doing, may be relevant for the near field of HLW repositories. publishedVersion

Whole-cell bacterial biosensors can be applied for the screening of antibacterial properties of extracts. We constructed a biosensor panel consisting of four different bacterial biosensor strains: Escherichia, Staphylococcus, Acinetobacter and Pseudomonas for expanded screening potential. The functionality of the panel was first evaluated with known antibacterial compounds: ethanol, naphthoquinones (juglone, lawsone, plumbagin) and a flavonoid (quercetin). Natural extracts comprise a vast source of potential new antibacterials for diverse functional purposes. To demonstrate the utilization of the panel for screening of a demanding sample material, round-leaved sundew (Drosera rotundifolia) extracts were used as an example. Differences between field- and laboratory originating sundew extracts could be detected. This demonstrates the efficiency of the developed biosensor panel in the rapid screening of the antibacterial properties of plant extracts. acceptedVersion

Replacement of synthetic pesticides with biochemical alternatives and other biological and mechanical control methods represents a future need in plant protection. We investigated if slow pyrolysis liquids (PL) originating from hardwoods, which contain a wide range of organic compounds, can be used to control giant hogweed (Heracleum mantegazzianum) either by (i) spraying directly on the seeds (Carum carvi seeds used as substitute) and seedlings or by (ii) covering seedlings with PL-containing mulching material (PLM). The effectiveness of the methods was evaluated in laboratory and greenhouse experiments using seedlings of various ages, PLs produced from aspen (Populus sp.), birch (Betula sp.) and willow (Salix sp.) and various PL/PLM application doses. In addition, the biodegradation of birch-derived PL was investigated. All tested liquids inhibited C. carvi seed germination effectively when used at > 20% concentrations and only slight differences existed among PLs produced from different biomasses. Direct spraying of PL on H. mantegazzianum seedlings was ineffective. PLM (containing 7.5%-40% of PL) inhibited seedling development effectively. Birch PL was readily biodegradable. Further product development is needed because the chemical composition of the PLs in PLM and their modes of action are poorly understood. The weed-inhibiting effect of PLM likely results from the PL and the mechanical barrier constituted by PL-bound peat fibers. (C) 2020 The Author(s). Published by Elsevier B.V.

Sulfide formed by sulfate-reducing microorganisms (SRM) is a potential safety risk in the geological disposal of spent nuclear fuel (SNF) enclosed in copper canisters because it can corrode copper. The canisters will be isolated from the environment by surrounding them with compacted bentonite. This study shows experimentally that the organic matter naturally present in compacted bentonites can become dissolved and sustain biological sulfate reduction. The experiment was conducted in cell systems consisting of an interface of compacted bentonite (at dry density of 1314–1368 kg m−3) and a low-porosity sand layer representing an excavation-damaged zone of the host rock. Some cells were inoculated with SRM and groundwater microorganisms and some were not. Varying concentrations of organic matter and sulfate in the sand layer solution resulted from partial dissolution of the studied bentonites (Wyoming, Indian, and Bulgarian). The dissolved organic matter promoted biological sulfate reduction, as demonstrated by the decrease in sulfate concentration in the sand layer solution and the formation of sulfide iron precipitates in the inoculated cells relative to the uninoculated cells. Other anaerobic microorganisms (e.g., methanogens) also became active in the cells and they along with the SRM were found to grow within the sand and/or bentonite layers of the cells. The findings of this study show that bentonites can sustain biological sulfate reduction in areas with lower density and immobilize possibly formed sulfides. However, the extent of these capabilities seems to be affected by the mineralogy of bentonites in the studied density range. acceptedVersion

To mitigate global warming, humankind has been forced to develop new efficient energy solutions based on renewable energy sources. Hydrothermal liquefaction (HTL) is a promising technology that can efficiently produce bio-oil from several biomass sources. The HTL process uses sub- or supercritical water for producing bio-oil, water-soluble organics, gaseous products and char. Black liquor mainly contains cooking chemicals (mainly alkali salts) lignin and the hemicellulose parts of the wood chips used for cellulose digestion. This review explores the effects of different process parameters, solvents and catalysts for the HTL of black liquor or black liquor-derived lignin. Using short residence times under near- or supercritical water conditions may improve both the quality and the quantity of the bio-oil yield. The quality and yield of bio-oil can be further improved by using solvents (e.g., phenol) and catalysts (e.g., alkali salts, zirconia). However, the solubility of alkali salts present in black liquor can lead to clogging problem in the HTL reactor and process tubes when approaching supercritical water conditions. publishedVersion

PART ONE A Review on the Joint International Conference of Nordic Forum of Sino-Western Studies and 20th International Symposium on Bicosmology LIU Jing (Macau University of Science and Technology) From 6th to 7th August 2019, the "2019 International Conference of Nordic Forum of Sino-Western Studies", sponsored by the Nordic Forum of Sino-Western Studies and 20th International Symposium on Biocosmology, was held at the University of Helsinki, Finland. PART TWO A Report on the International Research Project Regarding the Topic of the Impact of Religious Values on Chinese Social Life by JIANG Miao (China Academy of Social Sciences) During the period 20 to 21 August, 2019, a two day workshop titled “The Impact of Religious Values on Chinese Social Life” was held at the Culture Center Sofia, Helsinki, Finland. The workshop was most successful from its commencement, throughout all presentations and session proceedings, and in achievement of its overall goals and objectives. Non

Corregium: 10.1016/j.forpol.2021.102455 In line with the Sustainable Development Goals of the UN 2030 Agenda, the circular bioeconomy concept is gaining greater political momentum and research interest. A circular bioeconomy implies a more efficient resource management of bio-based renewable resources by integrating circular economy principles into the bioeconomy. These ideas have been well received at industry level since they are deemed to foster cost reductions, innovation and competitiveness. While recent scientific literature has dwelt on sustainability-related circular business models, empirical research on company-level implementation is only just emerging. Our study contributes to addressing this research lacuna by seeking answers to two questions: 1. How do small and medium-sized enterprises (SMEs) propose, create and deliver, and capture value through circular bioeconomy business models?; and 2. What are the business challenges and opportunities related to the operationalization of such business models? To this end, we employed content analysis on interview data gathered from managers in Finnish SME companies from the field of packaging, textiles, composite materials, cosmetics and pharmaceutical products. We outlined the main business model archetypes, and identified the key characteristics that enable value capture and delivery for various stakeholders. The contribution of this study is duly two-fold. From the perspective of a theoretical contribution, we expand and refine the conceptualization of sustainable circular bioeconomy and related business models. In addition, based on our findings, we provide insights and recommendations for researchers and policy-makers to advance the sustainability transition to a circular bioeconomy in the context of the forest-based industry, and for the management of SMEs to reflect on company viability and growth.

(1) In Finland, in recent years, the combustion of dry reed canary grass (RCG, Phalaris arundinacea) grown intensively on cutover peatlands, has decreased markedly. We therefore made experiments in two areas to assess the alternative of using freshly harvested RCG grown for biogas production on cutover peatland. We measured both biogas production and combustion energy release. (2) The experiments show that the RCG biomass yields in total solids (TS) in both areas, with two cuts a year, were surprisingly small (yields of 2.7 and 4.2 Mg ha-1 [1 Mg ha-1 = 100 g m-2 ]); having biogas and combustion potentials, on the two areas, of 277–348 dm3 kg-1 VS (volatile solids) and 14.8–16.3 MJ kg-1 TS, and 11.8–21.9 MWh ha-1 in combustion. (3) Fresh RCG may produce larger biomass yields if cut several times a year, together with lower lignin proportion, and better suitability for biogas production compared with spring harvested dry RCG. (4) For cutover peatlands there are several after-use possibilities, however, with different benefits and challenges. For example, peat soil emissions may be affected during the after-use period, and this should be considered when planning the use of cutover peatlands. publishedVersion

Anaerobic treatment of sedimented fibers collected from bottom of a bay that had been receiving pulp and paper mill wastewater for about 70 years were studied for the first time in semi-continuously fed continuously stirred tank reactors (CSTR). Anaerobic treatment of the fiber sediment was shown to be feasible, without dilution and with nitrogen and buffer supplement, at organic loading rates (OLR) up to 2.5 kg VS/m3d and hydraulic retention times (HRT) of 60 d resulting in methane yields of 201 ± 18 L CH4/kg VS. Co-digestion of sedimented fiber with sewage sludge at an OLR of 1.5 kg VS/m3d and HRT of 20 d resulted in a methane production of 246 ± 10 L CH4/kg VS. The techno-economic feasibility of mono and co-digestion process together with several case dependent factors such as maximum operable OLR, digestate utilization needs to be evaluated before making further conclusions for larger scale remediation applications. acceptedVersion

Previously identified twelve plant cell wall degradation-associated genes of the white rot fungus Phlebia radiata were studied by RT-qPCR in semi-aerobic solid-state cultures on lignocellulose waste material, and on glucose-containing reference medium. Wood-decay-involved enzyme activities and ethanol production were followed to elucidate both the degradative and fermentative processes. On the waste lignocellulose substrate, P. radiata carbohydrate-active enzyme (CAZy) genes encoding cellulolytic and hemicellulolytic activities were significantly upregulated whereas genes involved in lignin modification displayed a more complex response. Two lignin peroxidase genes were differentially expressed on waste lignocellulose compared to glucose medium, whereas three manganese peroxidase-encoding genes were less affected. On the contrary, highly significant difference was noticed for three cellulolytic genes (cbhI_1, eg1, bgl1) with higher expression levels on the lignocellulose substrate than on glucose. This indicates expression of the wood-attacking degradative enzyme system by the fungus also on the recycled, waste core board material. During the second week of cultivation, ethanol production increased on the core board to 0.24 g/L, and extracellular activities against cellulose, xylan, and lignin were detected. Sugar release from the solid lignocellulose resulted with concomitant accumulation of ethanol as fermentation product. Our findings confirm that the fungus activates its white rot decay system also on industrially processed lignocellulose adopted as growth substrate, and under semi-aerobic cultivation conditions. Thus, P. radiata is a good candidate for lignocellulose-based renewable biotechnology to make biofuels and biocompounds from materials with less value for recycling or manufacturing.

Constructed wetlands provide cost-efficient nutrient removal, with minimal input of human labor and energy, and their number is globally increasing. However, in northern latitudes, wetlands are rarely utilized, because their nutrient removal efficiency has been questioned due to the cold climate. Here, we studied nutrient retention and nitrogen removal in a boreal constructed wetland (4-ha) receiving treated nitrogen-rich wastewater. On a yearly basis, most of the inorganic nutrients were retained by the wetland. The highest retention efficiency was found during the ice-free period, being 79% for ammonium-nitrogen (NH4+-N), 71% for nitrate-nitrogen (NO3--N), and 88% for phosphate-phosphorus (PO43--P). Wetland also acted as a buffer zone during the disturbed nitrification process of the wastewater treatment plant. Denitrification varied between 106 and 252 mg N m-2 d-1 during the ice-free period. During the ice-cover period, total gaseous nitrogen removal was 147 mg N m-2 d-1, from which 66% was removed as N2, 28.5% as N2O through denitrification, and 5.5% as N2 through anammox. Nearly 2600 kg N y-1 was estimated to be removed through microbial gaseous N-production which equaled 72% of NO3--N and 60% of TN yearly retention in the wetland. The wetland retained nutrients even in winter, when good oxygen conditions prevailed under ice. The results suggest that constructed wetlands are an efficient option for wastewater nitrogen removal and nutrient retention also in cold climates. acceptedVersion

Concentrated sulphurous and saline streams, produced for example by pulp and paper and petrochemical industries, pose challenges for both environmental and processes management. In this study, the potential of biological recovery of S0 from haloalkaline thiosulphate solution in a Thioalkalivibrio versutus amended continuous-flow fluidized bed bioreactor (FBBR) was investigated using different (12−5 h) hydraulic retention times (HRT) as well as physico-chemical means to separate the S0 produced. S2O32− was biotransformed to SO42− and S0 with the highest biotransformation efficiency of 99.9 %. At 7 h HRT, the capacity of the FBBR was reached, seen as incomplete thiosulphate conversion. S0 production rate increased up to 6.3 ± 0.6 g S/l/d at HRT 7 h, whilst the average S0 yield was 27 ± 2 %. The presence of biologically produced S0 was visual and identified by scanning electron microscopy. Separation of S0 from the effluent by centrifugation at 3417 relative centrifugal force (rcf) resulted in 93 % separation, while among the four tested coagulants, FeCl2 at 0.5 g/l resulted in 40 % separation. Also, FeCl2 enhanced thiosulphate biotransformation rates. In summary, continuous biological S0 production followed by separation by centrifugation indicates potential for sulphur recovery from alkaline and saline industrial streams. publishedVersion

Background. Manganese peroxidases (MnP) and lignin peroxidases (LiP) are haem-including fungal secreted class-II peroxidases, which are interesting oxidoreductases in protein engineering aimed at design of biocatalysts for lignin and lignocellulose conversion, dye compound degradation, activation of aromatic compounds, and biofuel production. Objective. Recombinant short-type MnP (Pr-MnP3) of the white rot fungus Phlebia radiata, and its manganese-binding site (E40, E44, D186) directed variants were produced and characterized. To allow catalytic applications, enzymatic bleaching of Reactive Blue 5 and conversion of lignin-like compounds by engineered class-II peroxidases were explored. Method. Pr-MnP3 and its variants were expressed in Escherichia coli. The resultant body proteins were lysed, purified and refolded into haem-including enzymes in 6-7% protein recovery, and examined spectroscopically and kinetically. Results. Successful production of active enzymes was attained, with spectral characteristics of high-spin class-II peroxidases. Recombinant Pr-MnP3 demonstrated high affinity to Mn2+, which was noticeably affected by single (D186H/N) and double (E40H+E44H) mutations. Without addition of Mn2+, Pr-MnP3 was able to oxidize ABTS and decolorize Reactive Blue 5. Pc-LiPH8, its Trp-radical site variants, and engineered CiP-LiP demonstrated conversion of veratryl alcohol and dimeric non-phenolic lignin-model compounds (arylglycerol-β-aryl ethers) with production of veratraldehyde, which is evidence for cation radical formation with subsequent Cα-Cβ cleavage. Pc-LiPH8 and CiP variants were able to effectively oxidize and convert the phenolic dimer (guaiacylglycerol-β–guaiacyl ether). Conclusion. Our results demonstrate suitability of engineered MnP and LiP peroxidases for dye-decolorizing, and efficiency of LiP and its variants for activation and degradation of phenolic and non-phenolic lignin-like aryl ether-linked compounds.

The azoles (represented by penconazole, cyproconazole, and tebuconazole in this study) are frequently used agrochemicals to protect various crops against mildew and fungi. They are considered as endocrine disruptors, because they block the biosynthesis (on the level of enzymes inhibition) of biochemicals with steroid structure. Besides targeted impacts, they can partly get into the soil with the rainfall or litter fall and influence/block the biosynthesis of sterols of non-target organisms. In this sense, the risk of disruption of rhizosphere plant-microbial symbiosis and dynamic processes in the soil solution by azoles is of high importance to be evaluated. We have developed an analytical methodology for determination of penconazole, cyproconazole, and tebuconazole in soil solution using capillary electrophoresis with a photodiode array detector at UV-214 nm and acidic electrolyte solution (pH 1.48). The results were also compared with mass spectrometric measurements using mu-TOF mass spectrometry. There approx. 90% of present azoles were bound in the soil solution matrix. The detection limit for these azoles is about 10(-7) mol dm(-3). Because of very low pK(a) of azoles, we have to consider deprotonation of azoles and consequently the high affinity to create complexes with cations. The majority of present azoles in soil solution might form neutral adducts with mono-cations, making them invisible in electrospray mass spectra. [GRAPHICS] .

Background and aims In forestry-drained peatlands, drying leads to changes in C cycling which could affect peat δ13C. Furthermore, the δ13C profile of the entire peat column may reveal effects of earlier climatic periods. Methods We measured peat δ13C and C inventories in adjacent peat profiles, two collected from undrained and two from the drained side of a bog that was partially ditch-drained 37 years earlier. The cores were sliced into 10-cm subsamples for analyses; matching of the profiles based on surface levelling, peat stratigraphic correlation and a horizontal ash layer found in both profiles. Results Surface subsidence of 30 cm was observed in the dried site and the uppermost 160 cm in the undrained site contained an excess of 5.9 kg m−2 of C compared with the corresponding strata of the ditch-drained site. The δ13C values increased but markedly only in the thin surface layer of the drained site, indicating low δ13C of the missing C (ca. –30‰). In the deeper strata, dating to Mid-Holocene, high dry bulk density, C%, N%, humification index and low C/N ratio were connected to low δ13C of peat. Conclusions Drainage of 37 years increased δ13C values in the upper peat profile of the drained bog and led to the selective loss of 13C depleted C. Results indicate that C balance studies can be aided by C isotope analyses. Low δ13C values in the peat profile indicate the existence of a wet fen stage during the moist and warm period during Mid-Holocene.

Freshwater ecosystems represent a significant natural source of methane (CH4). CH4 produced through anaerobic decomposition of organic matter (OM) in lake sediment and water column can be either oxidized to carbon dioxide (CO2) by methanotrophic microbes or emitted to the atmosphere. While the role of CH4 oxidation as a CH4 sink is widely accepted, neither the magnitude nor the drivers behind CH4 oxidation are well constrained. In this study, we aimed to gain more specific insight into CH4 oxidation in the water column of a seasonally stratified, typical boreal lake, particularly under hypoxic conditions. We used 13CH4 incubations to determine the active CH4 oxidation sites and the potential CH4 oxidation rates in the water column, and we measured environmental variables that could explain CH4 oxidation in the water column. During hypolimnetic hypoxia, 91% of available CH4 was oxidized in the active CH4 oxidation zone, where the potential CH4 oxidation rates gradually increased from the oxycline to the hypolimnion. Our results showed that in warm springs, which become more frequent, early thermal stratification with cold well-oxygenated hypolimnion delays the period of hypolimnetic hypoxia and limits CH4 production. Thus, the delayed development of hypolimnetic hypoxia may partially counteract the expected increase in the lacustrine CH4 emissions caused by the increasing organic carbon load from forested catchments.

Start-up of bioelectrochemical systems (BESs) fed with brewery wastewater was compared at different adjusted anode potentials (−200 and 0 mV vs. Ag/AgCl) and external resistances (50 and 1000 Ω). Current generation stabilized faster with the external resistances (9 ± 3 and 1.70 ± 0.04 A/m3 with 50 and 1000 Ω, respectively), whilst significantly higher current densities of 76 ± 39 and 44 ± 9 A/m3 were obtained with the adjusted anode potentials of −200 and 0 mV vs. Ag/AgCl, respectively. After start-up, when operated using 47 Ω external resistance, the current densities and Coulombic efficiencies of all BESs stabilized to 9.5 ± 2.9 A/m3 and 12 ± 2%, respectively, demonstrating that the start-up protocols were not critical for long-term BES operation in microbial fuel cell mode. With adjusted anode potentials, two times more biofilm biomass (measured as protein) was formed by the end of the experiment as compared to start-up with the fixed external resistances. After start-up, the organics in the brewery wastewater, mainly sugars and alcohols, were transformed to acetate (1360 ± 250 mg/L) and propionate (610 ± 190 mg/L). Optimized start-up is required for prompt BES recovery, for example, after process disturbances. Based on the results of this study, adjustment of anode potential to −200 mV vs. Ag/AgCl is recommended for fast BES start-up. acceptedVersion

We studied natural and forestry-drained peatlands to examine the effect of over 34 years lowered water table on the δ13C values of vegetation, bulk peat and subsoil. In the seven studied sites, δ13C in the basal peat layer was 1.1 and 1.2 ‰ lower than that of the middle-layer and surface layer, respectively. Furthermore, there was a positive correlation between the δ13C values of the basal and surface peat layers, possibly due to carbon (C) recycling within the peat column. In the same mire complex, natural fen peat δ13C values were lower than those of the nearby bog, possibly due to the dominance of vascular plants on fen and the generally larger share of recycled C in the fens than in the bogs. Furthermore, natural and 51 years previously drained fen and bog, on the opposite sides of a ditch on the same mire complex, showed no significant differences in δ13C values. Plant δ13C values were lower, while δ13C values of subsoil were higher in the drained than in the natural site of the fen. acceptedVersion

Modifiable hydrogels have revealed tremendous insight into how physical characteristics of cells’ 3D environment drive stem cell lineage specification. However, in native tissues, cells do not passively receive signals from their niche. Instead they actively probe and modify their pericellular space to suit their needs, yet the dynamics of cells’ reciprocal interactions with their pericellular environment when encapsulated within hydrogels remains relatively unexplored. Here, we show that human bone marrow stromal cells (hMSC) encapsulated within hyaluronic acid-based hydrogels modify their surroundings by synthesizing, secreting and arranging proteins pericellularly or by degrading the hydrogel. hMSC’s interactions with this local environment have a role in regulating hMSC fate, with a secreted proteinaceous pericellular matrix associated with adipogenesis, and degradation with osteogenesis. Our observations suggest that hMSC participate in a bi-directional interplay between the properties of their 3D milieu and their own secreted pericellular matrix, and that this combination of interactions drives fate., 3D hydrogels have provided information on the physical requirements of stem cell fate, but the contribution of interactions with the pericellular environment are under-explored. Here the authors show that pericellular matrix secreted by human bone marrow stromal cells (hMSC) embedded in a HA-based hydrogel contribute to hMSC fate.

Addition of biochar into a soil changes its water retention properties by modifying soil textural and structural properties. In addition, internal micrometer-scale porosity that is able to directly store readily plant available water affects soil water retention properties. This study shows how precise knowledge of the internal micrometer-scale pore size distribution of biochar can deepen the understanding of the biochar-water interactions in soils. The micrometer-scale porosity of willow biochar was quantitatively and qualitatively characterized using X-ray tomography, 3D image analysis and Helium ion microscopy. The effect of biochar application on clay soil water retention was studied by conventional water retention curve approach. The results indicate that the internal pores of biochar, with sizes of at 50 and 10 μm (equivalent pore diameter), increased soil porosity and the amount of readily plant available water. After biochar addition, changes in soil porosity were detected at pore size regimes 5–10 and 25 μm, i.e. biochar pore sizes multiplied by factor 0.5. The detected pore size distribution of biochar does not predict directly (1:1 compatibility) the changes observed in the soil moisture characteristics. It is likely that biochar chemistry and pore morphology affect biochar-water interactions via e.g. surface roughness and contact angle. In addition, biochar induced changes in soil structure and texture affected soil moisture characteristics. However, the approach presented is an attractive pathway to more generalized understanding on how and why biochar internal porosity affects soil moisture characteristics. publishedVersion

Climate change along with anthropogenic activities changes biogeochemical conditions in lake ecosystems, modifying the sediment microbial communities. Wastewater effluents introduce nutrients and organic material but also novel microbes to lake ecosystems, simulating forthcoming increases in catchment loadings. In this work, we first used 16s rRNA gene sequencing to study how the overall sediment microbial community responds to wastewater in six boreal lakes. To examine forthcoming changes in the lake biogeochemistry, we focused on the ammonia-oxidizing archaea (AOA) and bacteria (AOB), and examined their functional and compositional community response to wastewater. Although we found the least diverse and least resistant prokaryotic communities from the most wastewater-influenced sediments, the community changed fast toward the natural composition with the diminishing influence of wastewater. Each lake hosted a unique resistant AOA community, while AOB communities were adapting, responding to environmental conditions as well as receiving new members from WWTPs. In general, AOB dominated in numbers in wastewater-influenced sediments, while the ratio between AOA and AOB increased when moving toward pristine conditions. Our results suggest that although future climate-change-driven increases in nutrient loading and microbial migration might significantly disrupt lake sediment microbiomes, they can promote nitrification through adapting and abundant AOB communities. publishedVersion

A furan-based synthetic biopolymer composed of a bifuran monomer and ethylene glycol was synthesized through melt polycondensation, and the resulting polyester was found to have promising thermal and mechanical properties. The bifuran monomer, dimethyl 2,2′-bifuran-5,5′-dicarboxylate, was prepared using a palladium-catalyzed, phosphine ligand-free direct coupling protocol. A titanium-catalyzed polycondensation procedure was found effective at polymerizing the bifuran monomer with ethylene glycol. The prepared bifuran polyester exhibited several intriguing properties including high tensile modulus. In addition, the bifuran monomer furnished the polyester with a relatively high glass transition temperature. Films prepared from the new polyester also had excellent oxygen and water barrier properties, which were found to be superior to those of poly(ethylene terephthalate). Moreover, the novel polyester also has good ultraviolet radiation blocking properties. acceptedVersion

Efficient synthetic methods for carbazole-based small molecule electron donors with donor–acceptor (D–A) and A–D–A type structures were developed. In order to study the relation between chemical structures and material properties, the prepared compounds were characterized in detail using absorption spectroscopy, differential pulse voltammetry, and computational methods. In addition, symmetrical A–D–A type compounds were tested as an active layer component in bulk heterojunction based organic solar cell (OSC) devices with conventional structure. The results show that the two compound types have many similar properties. However, the extended molecular structure of A–D–A type compounds offer better film forming properties and higher molar absorption coefficients compared with the D–A type materials. Furthermore, the attachment of fluoro substituents in the A units has a positive effect on all solar cell device parameters. Moreover, the computational studies revealed that the molecular structures are twisted between the central carbazole D unit and π-bridge which may result in inefficient intramolecular charge transfer and, also, relatively limited short-circuit currents in OSC devices. acceptedVersion

Growth and fatty acid production of microalga Selenastrum sp. with associated bacteria was studied in lab-scale experiments in three composting leachate liquids. Nutrient reduction in cultures was measured at different initial substrate strengths. A small, pilot-scale photobioreactor (PBR) was used to verify labscale results. Similar growth conditions supported growth of both Selenastrum and bacteria. CO2 feed enhanced the production of biomass and lipids in PBR (2.4 g L-1 and 17% DW) compared to lab-scale (0.1-1.6 g L-1 and 4.0-6.5% DW) experiments. Also prolonged cultivation time increased lipid content in PBR. At both scales, NH4-N with an initial concentration of ca. 40 mg L-1 was completely removed from the biowaste leachate. In lab-scale, maximal COD reduction was over 2000 mg L-1, indicating mixotrophic growth of Selenastrum. Co-cultures are efficient in composting leachate liquid treatment, and conversion of waste to biomass is a promising approach to improve the bioeconomy of composting plants. (C) 2017 The Authors. Published by Elsevier Ltd.

Reconstructing stock herding strategies and land use is key to comprehending past human social organization and economy. We present laser-ablation strontium and carbon isotope data from 25 cattle (Bos taurus) to reconstruct mobility and infer herding management at the Swiss lakeside settlement of Arbon Bleiche 3, occupied for only 15 years (3384-3370 BC). Our results reveal three distinct isotopic patterns that likely reflect different herding strategies: 1) localized cattle herding, 2) seasonal movement, and 3) herding away from the site year-round. Different strategies of herding are not uniformly represented in various areas of the settlement, which indicates specialist modes of cattle management. The pressure on local fodder capacities and the need for alternative herding regimes must have involved diverse access to grazing resources. Consequently, the increasing importance of cattle in the local landscape was likely to have contributed to the progress of socio-economic differentiation in early agricultural societies in Europe.

Despite high performance, municipal wastewater treatment plants (WWTPs) still discharge significant amounts of organic material and nitrogen and even microbes into the receiving water bodies, altering physico-chemical conditions and microbial functions. In this study, we examined how nitrified wastewater affects the microbiology of boreal lake sediments. Microbial community compositions were assessed with next generation sequencing of the 16S rRNA gene, and a more detailed view on nitrogen transformation processes was gained with qPCR targeting on functional genes (nirS, nirK, nosZI, nosZII, amoAarchaea, and amoAbacteria). In both of the two studied lake sites, the microbial community composition differed significantly between control point and wastewater discharge point, and a gradual shift toward natural community composition was seen downstream following the wastewater gradient. SourceTracker analysis predicted that ∼2% of sediment microbes were of WWTP-origin on the study site where wastewater was freely mixed with the lake water, while when wastewater was specially discharged to the sediment surface, ∼6% of microbes originated from WWTP, but the wastewater-influenced area was more limited. In nitrogen transformation processes, the ratio between nitrifying archaea (AOA) and bacteria (AOB) was affected by wastewater effluent, as the AOA abundance decreased from the control point (AOA:AOB 28:1 in Keuruu, 11:1 in Petäjävesi) to the wastewater-influenced sampling points, where AOB dominated (AOA:AOB 1:2–1:15 in Keuruu, 1:3–1:19 in Petäjävesi). The study showed that wastewater can affect sediment microbial community through importing nutrients and organic material and altering habitat characteristics, but also through bringing wastewater-originated microbes to the sediment, and may thus have significant impact on the freshwater biogeochemistry, especially in the nutrient-poor boreal ecosystems. publishedVersion

Ethanol production from non-pretreated lignocellulose was carried out in a consolidated bioprocess with wood-decay fungi of phlebioid Polyporales. Ethanol production was attempted on glucose, spruce wood sawdust and waste core board. Substantial quantities of ethanol were achieved, and isolate Phlebia radiata 0043 produced 5.9 g/L of ethanol reaching the yield of 10.4% ethanol from core board lignocellulose substrate. Acidic initial culture conditions (pH 3) induced ethanol fermentation compared to the more neutral environment. Together with bioethanol, the fungi were able to produce organic acids such as oxalate and fumarate, thus broadening their capacity and applicability as efficient organisms to be utilized for bioconversion of various lignocelluloses. In conclusion, fungi of Phlebia grow on, convert and saccharify solid lignocellulose waste materials without pre-treatments resulting in accumulation of ethanol and organic acids. These findings will aid in applying fungal biotechnology for production of biofuels and biocompounds.

Increasing interest for the landfill mining and the amount of fine fraction (FF) in landfills (40–70% (w/w) of landfill content) mean that sustainable treatment and utilization methods for FF are needed. For this study FF (

International audience; The highly ordered protein backbone of virus particles makes them attractive candidates for use as enzyme nano-carriers (ENCs). We have previously developed a non-covalent and versatile approach for adhesion of enzymes to virus particles. This approach makes use of z33, a peptide derived from the B-domain of Staphylococcus aureus protein A, which binds to the Fc domain of many immunoglobulins. We have demonstrated that with specific antibodies addressed against the viral capsid proteins (CPs) an 87% coverage of z33-tagged proteins can be achieved on potyvirus particles. 4-coumarate coenzyme A ligase (4CL2) and stilbene synthase (STS) catalyze consecutive steps in the resveratrol synthetic pathway. In this study, these enzymes were modified to carry an N-terminal z33 peptide and a C-terminal 6xHis tag to obtain (z)4CL2(His) and (z)STS(His), respectively. A protein chimera, (z)4CL2::STS(His), with the same modifications was also generated from the genetic fusion of both mono-enzyme encoding genes. All z33 enzymes were biologically active after expression in Escherichia coli as revealed by LC-MS analysis to identify resveratrol and assembled readily into macromolecular complexes with Potato virus A particles and α-PVA CP antibodies. To test simultaneous immobilization-purification, we applied the double antibody sandwich - ELISA protocol to capture active z33-containg mono-enzymes and protein chimera directly from clarified soluble cell lysates onto the virus particle surface. These immobilized enzymes were able to synthesize resveratrol. We present here a bottom up approach to immobilize active enzymes onto virus-based ENCs and discuss the potential to utilize this method in the purification and configuration of nano-devices.

A fine fraction (FF) was mined from two Finnish municipal solid waste (MSW) landfills in Kuopio (1- to 10-year-old, referred as new landfill) and Lohja (24- to 40-year-old, referred as old landfill) in order to characterize FF. In Kuopio the FF (

Time-resolved x-ray solution scattering reveals the conformational signaling mechanism of a bacterial phytochrome., Phytochromes are light sensor proteins found in plants, bacteria, and fungi. They function by converting a photon absorption event into a conformational signal that propagates from the chromophore through the entire protein. However, the structure of the photoactivated state and the conformational changes that lead to it are not known. We report time-resolved x-ray scattering of the full-length phytochrome from Deinococcus radiodurans on micro- and millisecond time scales. We identify a twist of the histidine kinase output domains with respect to the chromophore-binding domains as the dominant change between the photoactivated and resting states. The time-resolved data further show that the structural changes up to the microsecond time scales are small and localized in the chromophore-binding domains. The global structural change occurs within a few milliseconds, coinciding with the formation of the spectroscopic meta-Rc state. Our findings establish key elements of the signaling mechanism of full-length bacterial phytochromes.

Reactive oxygen species (ROS) have important functions in plant stress responses and development. In plants, ozone and pathogen infection induce an extracellular oxidative burst that is involved in the regulation of cell death. However, very little is known about how plants can perceive ROS and regulate the initiation and the containment of cell death. We have identified an Arabidopsis thaliana protein, GRIM REAPER (GRI), that is involved in the regulation of cell death induced by extracellular ROS. Plants with an insertion in GRI display an ozone-sensitive phenotype. GRI is an Arabidopsis ortholog of the tobacco flower-specific Stig1 gene. The GRI protein appears to be processed in leaves with a release of an N-terminal fragment of the protein. Infiltration of the N-terminal fragment of the GRI protein into leaves caused cell death in a superoxide-and salicylic acid-dependent manner. Analysis of the extracellular GRI protein yields information on how plants can initiate ROS-induced cell death during stress response and development. Reactive oxygen species (ROS) have important functions in plant stress responses and development. In plants, ozone and pathogen infection induce an extracellular oxidative burst that is involved in the regulation of cell death. However, very little is known about how plants can perceive ROS and regulate the initiation and the containment of cell death. We have identified an Arabidopsis thaliana protein, GRIM REAPER (GRI), that is involved in the regulation of cell death induced by extracellular ROS. Plants with an insertion in GRI display an ozone-sensitive phenotype. GRI is an Arabidopsis ortholog of the tobacco flower-specific Stig1 gene. The GRI protein appears to be processed in leaves with a release of an N-terminal fragment of the protein. Infiltration of the N-terminal fragment of the GRI protein into leaves caused cell death in a superoxide-and salicylic acid-dependent manner. Analysis of the extracellular GRI protein yields information on how plants can initiate ROS-induced cell death during stress response and development. Reactive oxygen species (ROS) have important functions in plant stress responses and development. In plants, ozone and pathogen infection induce an extracellular oxidative burst that is involved in the regulation of cell death. However, very little is known about how plants can perceive ROS and regulate the initiation and the containment of cell death. We have identified an Arabidopsis thaliana protein, GRIM REAPER (GRI), that is involved in the regulation of cell death induced by extracellular ROS. Plants with an insertion in GRI display an ozone-sensitive phenotype. GRI is an Arabidopsis ortholog of the tobacco flower-specific Stig1 gene. The GRI protein appears to be processed in leaves with a release of an N-terminal fragment of the protein. Infiltration of the N-terminal fragment of the GRI protein into leaves caused cell death in a superoxide-and salicylic acid-dependent manner. Analysis of the extracellular GRI protein yields information on how plants can initiate ROS-induced cell death during stress response and development.

Background The symbiotic phenotype of Neorhizobium galegae, with strains specifically fixing nitrogen with either Galega orientalis or G. officinalis, has made it a target in research on determinants of host specificity in nitrogen fixation. The genomic differences between representative strains of the two symbiovars are, however, relatively small. This introduced a need for a dataset representing a larger bacterial population in order to make better conclusions on characteristics typical for a subset of the species. In this study, we produced draft genomes of eight strains of N. galegae having different symbiotic phenotypes, both with regard to host specificity and nitrogen fixation efficiency. These genomes were analysed together with the previously published complete genomes of N. galegae strains HAMBI 540T and HAMBI 1141. Results The results showed that the presence of an additional rpoN sigma factor gene in the symbiosis gene region is a characteristic specific to symbiovar orientalis, required for nitrogen fixation. Also the nifQ gene was shown to be crucial for functional symbiosis in both symbiovars. Genome-wide analyses identified additional genes characteristic of strains of the same symbiovar and of strains having similar plant growth promoting properties on Galega orientalis. Many of these genes are involved in transcriptional regulation or in metabolic functions. Conclusions The results of this study confirm that the only symbiosis-related gene that is present in one symbiovar of N. galegae but not in the other is an rpoN gene. The specific function of this gene remains to be determined, however. New genes that were identified as specific for strains of one symbiovar may be involved in determining host specificity, while others are defined as potential determinant genes for differences in efficiency of nitrogen fixation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1576-3) contains supplementary material, which is available to authorized users.

Background: Recent progress in environmental microbiology has revealed vast populations of microbes in any given habitat that cannot be detected by conventional culturing strategies. The use of sensitive genetic detection methods such as CARD-FISH and in situ PCR have been limited by the cell wall permeabilization requirement that cannot be performed similarly on all cell types without lysing some and leaving some unpermeabilized. Furthermore, the detection of low copy targets such as genes present in single copies in the microbial genomes, has remained problematic. Methodology/Principal Findings: We describe an emulsion-based procedure to trap individual microbial cells into picoliter-volume polyacrylamide droplets that provide a support for genetic material and therefore allow degradation of cellular material to expose the individual genomes. The polyacrylamide droplets are subsequently converted into picoliter-scale reactors for genome amplification. The amplified genomes are labelled based on the presence of a target gene and differentiated from those that do not contain the gene by flow cytometry. Using the Escherichia coli strains XL1 and MC1061, which differ with respect to the presence (XL1) or absence (MC1061) of a single copy of a tetracycline resistance gene per genome, we demonstrate that XL1 genomes present at 0.01% of MC1061 genomes can be differentiated using this method. Using a spiked sediment microbial sample, we demonstrate that the method is applicable to complex environmental microbial communities as a target gene-based screen for individual microbes. Conclusions/Significance: The genomic support for complete cell degradation allows an exposure of individual genomes of environmental bacteria. The genome exposure followed by genome amplification and labelling combines the benefits of in situ-PCR and FISH methods and permits the detection cells with single copy chromosomal targets in complex mixtures of microbial cells. The method could be optimized for fluorescence-activated cell sorting to enrich genetic material of interest from complex environmental samples.

Fine fraction (FF, 4/kgVS), while water addition and leachate recirculation depressed methane production slightly, to 16.1 and 16.4LCH4/kgVS, respectively. Organic matter was also removed via the leachate and was measured as chemical oxygen demand (COD). Calculated removal of organic matter in gas and leachate was highest in LBR with water addition (59gCOD/kgVS), compared with LBR without water addition or with leachate recirculation (51gCOD/kgVS). Concentrations of COD, ammonium nitrogen and anions in leachate decreased during the experiment, indicating washout mechanism caused by water additions. Aeration increased sulfate and nitrate concentrations in leachate due to oxidized sulfide and ammonium. Molecular weight distributions of leachates showed that all the size categories decreased, especially low molecular weight compounds, which were reduced the most. Aerobic stabilization resulted in the lowest final VS/TS (13.1%), lowest respiration activity (0.9-1.2mgO2/gTS), and lowest methane production after treatment (0.0-0.8LCH4/kgVS), with 29% of VS being removed from FF. Anaerobic stabilization methods also reduced organic matter by 9-20% compared with the initial amount. Stabilization reduced the quantity of soluble nitrogen in FF and did not alter concentration of soluble and insoluble phosphorus, and insoluble nitrogen. All four stabilization methods decreased organic matter and thus are possible stabilization methods for FF, but aerobic treatment was the most efficient in this study. acceptedVersion

White rot fungus Dichomitus squalens is an efficient lignocellulose degrading basidiomycete and a promising source for new plant cell wall polysaccharides depolymerizing enzymes. In this work, we focused on cellobiohydrolases (CBHs) of D. squalens. The native CBHI fraction of the fungus, consisting three isoenzymes, was purified and it maintained the activity for 60 min at 50°C, and was stable in acidic pH. Due to the lack of enzyme activity assay for detecting only CBHII activity, CBHII of D. squalens was produced recombinantly in an industrially important ascomycete host, Trichoderma reesei. CBH enzymes of D. squalens showed potential in hydrolysis of complex lignocellulose substrates sugar beet pulp and wheat bran, and microcrystalline cellulose, Avicel. Recombinant CBHII (rCel6A) of D. squalens hydrolysed all the studied plant biomasses. Compared to individual activities, synergistic effect between rCel6A and native CBHI fraction of D. squalens was significant in the hydrolysis of Avicel. Furthermore, the addition of laccase to the mixture of CBHI fraction and rCel6A significantly enhanced the amount of released reducing sugars from sugar beet pulp. Especially, synergy between individual enzymes is a crucial factor in the tailor-made enzyme mixtures needed for hydrolysis of different plant biomass feedstocks. Our data supports the importance of oxidoreductases in improved enzyme cocktails for lignocellulose saccharification.