Functional biodiversity and plasticity of methanogenic biomass from a full-scale mesophilic anaerobic digester treating nitrogen-rich agricultural wastes

The effect of ammonia on methanogenic biomass from a full-scale agricultural digester treating nitrogen-rich materials was characterized in batch activity assays subjected to increasing concentrations of total ammonia N. Acetotrophic and methanogenic profiles displayed prolonged lag phases and reduced specific activity rates at 6.0 gN-TAN L−1, though identical methane yields were ultimately reached. These results agreed with the expression levels of selected genes from bacteria and methanogenic archaea (qPCR of 16S rRNA and mrcA cDNA transcripts). Compound-specific isotope analysis of biogas indicated that ammonia exposure was associated to a transition in methanogenic activity from acetotrophy at 1.0 gN-TAN L−1 to intermediate and complete hydrogenotrophy at 3.5 and 6.0 gN-TAN L−1. Such pattern matched the results of 16S-Illumina sequencing of genes and transcripts in that predominant methanogens shifted, along with increasing ammonia, from the obligate acetotroph Methanosaeta to the hydrogenotrophic Methanoculleus and the poorly understood methylotrophic Methanomassiliicoccus. The underlying bacterial community structure remained rather stable but, at 6.0 gN-TAN L−1, the expression level increased considerably for a number of ribotypes that are related to potentially syntrophic genera (e.g. Clostridium, Bellilinea, Longilinea, and Bacteroides). The predominance of hydrogenotrophy at high ammonia levels clearly points to the occurrence of the syntrophic acetate oxidation (SAO), but known SAO bacteria were only found in very low numbers. The potential role of the identified bacterial and archaeal taxa with a view on SAO and on stability of the anaerobic digestion process under ammonia stress has been discussed.info:eu-repo/semantics/acceptedVersio

Solar drying in the vineyard: a sustainable technology for the recovery of nutrients from winery organic waste

The present study describes a pilot-scale experimental validation of a forced-convection greenhouse solar dryer, combined with a biofilter, for controlled atmospheric emissions. This set-up was applied to the dewatering of sewage sludge from a biological plant that treated process wastewater in a commercial Mediterranean winery. Experiments were performed after the harvest, from September onwards, during the peak generation of sludge. The average drying rate during the first 10 days of operation ranged from 1.17 to 2.24 kg m−2 d−1, depending on the measurement method, during which the water content of the sludge was reduced from 90% down to 67%. Biofiltration was quite inefficient against greenhouse gases (methane and dinitrous oxide), and direct emissions during the drying process were on average 57 g CO2-eq m−2 d−1. Ammonia and volatile organic compounds were removed with average efficiencies of 71% and 35%, but ammonia losses through volatilization represented less than 2% of the initial nitrogen content. The sludge was dried further during November, to the lowest possible water content of 14%. Both the intermediate and final sludge dried materials were characterized for their agronomical value as organic fertilizers.info:eu-repo/semantics/acceptedVersio

Volatile Organic Compounds in the Azteca/Cecropia Ant-Plant Symbiosis and the Role of Black Fungi

Black fungi of the order Chaetothyriales are grown by many tropical plant-mutualistic ants as small so-called “patches” in their nests, which are located inside hollow structures provided by the host plant (“domatia”). These fungi are introduced and fostered by the ants, indicating that they are important for the colony. As several species of Chaetothyriales tolerate, adsorb, and metabolize toxic volatiles, we investigated the composition of volatile organic compounds (VOCs) of selected domatia in the Azteca/Cecropia ant-plant mutualism. Concentrations of VOCs in ant-inhabited domatia, empty domatia, and background air were compared. In total, 211 compounds belonging to 19 chemical families were identified. Ant-inhabited domatia were dominated by ketones with 2-heptanone, a well-known ant alarm semiochemical, as the most abundant volatile. Empty domatia were characterized by relatively high concentrations of the monoterpenes d-limonene, p-cymene and β-phellandrene, as well as the heterocyclic sulphur-containing compound, benzothiazole. These compounds have biocidal properties and are primarily biosynthesized by plants as a defense mechanism. Interestingly, most of the latter compounds were present at lower concentrations in ant inhabited domatia than in non-colonized ones. We suggest that Chaetothyriales may play a role in reducing the VOCs, underlining that the mutualistic nature of these fungi as VOCs accumulation might be detrimental for the ants, especially the larvae.info:eu-repo/semantics/publishedVersio

Gut eukaryotic communities in pigs: diversity, composition and host genetics contribution

Background The pig gut microbiome harbors thousands of species of archaea, bacteria, viruses and eukaryotes such as protists and fungi. However, since the majority of published studies have been focused on prokaryotes, little is known about the diversity, host-genetic control, and contributions to host performance of the gut eukaryotic counterparts. Here we report the first study that aims at characterizing the diversity and composition of gut commensal eukaryotes in pigs, exploring their putative control by host genetics, and analyzing their association with piglets body weight. Results Fungi and protists from the faeces of 514 healthy Duroc pigs of two sexes and two different ages were characterized by 18S and ITS ribosomal RNA gene sequencing. The pig gut mycobiota was dominated by yeasts, with a high prevalence and abundance of Kazachstania spp. Regarding protists, representatives of four genera (Blastocystis, Neobalantidium, Tetratrichomonas and Trichomitus) were predominant in more than the 80% of the pigs. Heritabilities for the diversity and abundance of gut eukaryotic communities were estimated with the subset of 60d aged piglets (N = 390). The heritabilities of α-diversity and of the abundance of fungal and protists genera were low, ranging from 0.15 to 0.28. A genome wide association study reported genetic variants related to the fungal α-diversity and to the abundance of Blastocystis spp. Annotated candidate genes were mainly associated with immunity, gut homeostasis and metabolic processes. Additionally, we explored the association of gut commensal eukaryotes with piglet body weight. Our results pointed to a positive contribution of fungi from the Kazachstania genus, while protists displayed both positive (Blastocystis and Entamoeba) and negative (Trichomitus) associations with piglet body weight. Conclusions Our results point towards a minor and taxa specific genetic control over the diversity and composition of the pig gut eukaryotic communities. Moreover, we provide evidences of the associations between piglets’ body weight after weaning and members from the gut fungal and protist eukaryote community. Overall, this study highlights the relevance of considering, along with that of bacteria, the contribution of the gut eukaryote communities to better understand host-microbiome association and their role on pig performance, welfare and health.info:eu-repo/semantics/publishedVersio

Gut eukaryotic communities in pigs : diversity, composition and host genetics contribution

Background. The pig gut microbiome harbors thousands of species of archaea, bacteria, viruses and eukaryotes such as protists and fungi. However, since the majority of published studies have been focused on prokaryotes, little is known about the diversity, host-genetic control, and contributions to host performance of the gut eukaryotic counterparts. Here we report the first study that aims at characterizing the diversity and composition of gut commensal eukaryotes in pigs, exploring their putative control by host genetics, and analyzing their association with piglets body weight. Results. Fungi and protists from the faeces of 514 healthy Duroc pigs of two sexes and two different ages were characterized by 18S and ITS ribosomal RNA gene sequencing. The pig gut mycobiota was dominated by yeasts, with a high prevalence and abundance of Kazachstania spp. Regarding protists, representatives of four genera (Blastocystis, Neobalantidium, Tetratrichomonas and Trichomitus) were predominant in more than the 80% of the pigs. Heritabilities for the diversity and abundance of gut eukaryotic communities were estimated with the subset of 60d aged piglets (N = 390). The heritabilities of α-diversity and of the abundance of fungal and protists genera were low, ranging from 0.15 to 0.28. A genome wide association study reported genetic variants related to the fungal α-diversity and to the abundance of Blastocystis spp. Annotated candidate genes were mainly associated with immunity, gut homeostasis and metabolic processes. Additionally, we explored the association of gut commensal eukaryotes with piglet body weight. Our results pointed to a positive contribution of fungi from the Kazachstania genus, while protists displayed both positive (Blastocystis and Entamoeba) and negative (Trichomitus) associations with piglet body weight. Conclusions. Our results point towards a minor and taxa specific genetic control over the diversity and composition of the pig gut eukaryotic communities. Moreover, we provide evidences of the associations between piglets' body weight after weaning and members from the gut fungal and protist eukaryote community. Overall, this study highlights the relevance of considering, along with that of bacteria, the contribution of the gut eukaryote communities to better understand host-microbiome association and their role on pig performance, welfare and health

Spatially and temporally defined lysosomal leakage facilitates mitotic chromosome segregation.

Lysosomes are membrane-surrounded cytoplasmic organelles filled with a powerful cocktail of hydrolases. Besides degrading cellular constituents inside the lysosomal lumen, lysosomal hydrolases promote tissue remodeling when delivered to the extracellular space and cell death when released to the cytosol. Here, we show that spatially and temporally controlled lysosomal leakage contributes to the accurate chromosome segregation in normal mammalian cell division. One or more chromatin-proximal lysosomes leak in the majority of prometaphases, after which active cathepsin B (CTSB) localizes to the metaphase chromatin and cleaves a small subset of histone H3. Stabilization of lysosomal membranes or inhibition of CTSB activity during mitotic entry results in a significant increase in telomere-related chromosome segregation defects, whereas cells and tissues lacking CTSB and cells expressing CTSB-resistant histone H3 accumulate micronuclei and other nuclear defects. These data suggest that lysosomal leakage and chromatin-associated CTSB contribute to proper chromosome segregation and maintenance of genomic integrity

The main drivers of methane emissions differ in the growing and flooded fallow seasons in Mediterranean rice fields

Purpose To assess 1) the cumulative greenhouse gas emissions –GHG- and global warming potential (methane – CH4- and nitrous oxide) from rice fields in the growing and fallow seasons, and 2) the environmental and agronomic drivers of CH4 emissions, and their relative capacity to explain CH4 variation. Methods A two-year multisite field experiment covering the agronomic and environmental variability of a rice growing area in NE Iberian Peninsula was conducted with monthly samplings of GHG and monitoring of both environmental and agronomic factors. Information-theoretic framework analysis was used to assess the relative contribution of the environmental and agronomic variables on methane emissions. Results Two thirds of the CH4 is emitted in the fallow season. Edaphic factors exert more influence during the growing season whereas agronomic factors have a higher impact in the fallow. The implications of these findings on the design of improved mitigation options rice are discussed. Conclusions Soils with higher soil sulphate concentration, bulk density and clay content emit less CH4 in growing season. In the fallow season, the rates of both straw input and nitrogen fertilization stimulate CH4 emissions.info:eu-repo/semantics/publishedVersio

A comparison of isolation methods for black fungi degrading aromatic toxins

The prevalence of black fungi in the order Chaetothyriales has often been underestimated due to the difficulty of their isolation. In this study, three methods which are often used to isolate black fungi are compared. Enrichment on aromatic hydrocarbon appears effective in inhibiting growth of cosmopolitan microbial species and allows appearance of black fungi. We miniaturized the method for high-throughput purposes. The new procedure saves time, consumes less space and can process multiple samples simultaneously.info:eu-repo/semantics/publishedVersio

Different Storing and Processing Conditions of Human Lymphocytes do not Alter P-Glycoprotein Rhodamine 123 Efflux

P-glycoprotein (Pgp), a protein codified by Multi Drug Resistance (MDR1) gene, has a detoxifying function and might influence the toxicity and pharmacokinetics and pharmacodynamics of drugs. Sampling strategies to improve Pgp studies could be useful to optimize the sensitivity and the reproducibility of efflux assays. This study aimed to compare Pgp expression and efflux activity by measuring Rhodamine123 (Rh123) retention in lymphocytes stored under different conditions, in order to evaluate the potential utility of any of the storing conditions in Pgp functionality. Our results show no change in protein expression of Pgp by confocal studies and Western blotting, nor changes at the mRNA level (qRT-PCR). No differences in Rh123 efflux by Pgp activity assays were found between fresh and frozen lymphocytes after 24 hours of blood extraction, using either of the two Pgp specific inhibitors (VP and PSC833). Different working conditions in the 24 hours post blood extraction do not affect Rh123 efflux. These results allow standardization of Pgp activity measurement in different individuals with different timing of blood sampling and in different geographic areas. ______________

Evolution of CDC42, a putative virulence factor triggering meristematic growth in black yeasts

The cell division cycle gene (CDC42) controlling cellular polarization was studied in members of Chaetothyriales. Based on ribosomal genes, ancestral members of the order exhibit meristematic growth in view of their colonization of inert surfaces such as rock, whereas in derived members of the order the gene is a putative virulence factor involved in expression of the muriform cell, the invasive phase in human chromoblastomycosis. Specific primers were developed to amplify a portion of the gene of 32 members of the order with known position according to ribosomal phylogeny. Phylogeny of CDC42 proved to be very different. In all members of Chaetohyriales the protein sequence is highly conserved. In most species, distributed all over the phylogenetic tree, introns and 3rd codon positions are also invariant. However, a number of species had paralogues with considerable deviation in non-coding exon positions, and synchronous variation in introns, although non-synonomous variation had remained very limited. In some strains both orthologues and paralogues were present. It is concluded that CDC42 does not show any orthologous evolution, and that its paralogues haves the same function but are structurally relaxed. The variation or absence thereof could not be linked to ecological changes, from rock-inhabiting to pathogenic life style. It is concluded that eventual pathogenicity in Chaetothyriales is not expressed at the DNA level in CDC42 evolution