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The aim of this study was to evaluate the effect of pen stocking density on animal performance, social behavior, and animal and pen dirtiness in fattening bulls. Two hundred sixty-three bulls (250 ± 24.7 kg BW, and 193 ± 13.2 d age) were group-housed and fed concentrate and unprocessed straw separately, both ad libitum. Animals were assigned to one of 2 different pen stocking density treatments: 1) LOW (n=112), 14 bulls/pen (5.1 m2/bull and 5 bulls/feeding space); and 2) HIGH (n=151), 19 bulls/pen (3.6 m2/bull and 7 bulls/feeding space). The study lasted 183 d. Pen concentrate intake was recorded daily. Bulls were weighed every 2 wk. Social behaviors (from d 59) and animal and pen dirtiness (from d 120) were recorded every 4 wk. Carcass quality was recorded at the slaughterhouse. Data were analyzed with a mixed effects model. Concentrate intake was not affected by treatment, but ADG (1.57 vs. 1.47 ± 0.027 kg/d) and feed efficiency (0.21 vs. 0.20 ± 0.007 kg/kg) were greater (P≤0.05) in LOW than in HIGH. Carcass quality was similar between treatments, but preslaughter weight (552 vs. 535 ± 4.6 kg) and hot carcass weight (292 vs. 284 ± 2.9 kg) was greater (P

Human-made hydrocarbon-rich environments are important reservoirs of microorganisms with specific degrading abilities and pathogenic potential. In particular, black fungi are of great interest, but their presence in the environment is frequently underestimated because they are difficult to isolate. In the frame of a biodiversity study from fuel-contaminated sites involving 30 diesel car tanks and 112 fuel pump dispensers (52 diesel and 60 gasoline, respectively), a total of 181 black fungal strains were isolated. The long cold incubation (LCI) of water-suspended samples, followed by plating on Dichloran Rose Bengal Chloramphenicol Agar (DRBC), gave isolation yields up to six times (6.6) higher than those of direct plating on DRBC, and those of enrichment with a phenolic mix. The sequencing of ITS and LSU-rDNA confirmed the dominance of potentially pathogenic fungi from the family Herpotrichiellaceae and Exophiala xenobiotica. Moreover, other opportunistic species were found, including E. opportunistica, E. oligosperma, E. phaeomuriformis, and Rhinocladiella similis. The recurrent presence of E. crusticola, Knufia epidermidis, Aureobasidium melanogenum, Cladosporium spp., and Scolecobasidium spp. was also recorded. Interestingly, 12% of total isolates, corresponding to 50% of taxa found (16/32), represent new species. All the novel taxa in this study were isolated by LCI. These findings suggest that black fungal diversity in hydrocarbon-rich niches remains largely unexplored and that LCI can be an efficient tool for further investigations.

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/publishedVersion

Made available in DSpace on 2021-06-25T10:59:32Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-05-01 Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Environmental pollution with alkylbenzene hydrocarbons such as toluene is a recurring phenomenon. Their toxicity and harmful effect on people and the environment drive the search for sustainable removal techniques such as bioremediation, which is based on the microbial metabolism of xenobiotic compounds. Melanized fungi present extremophilic characteristics, which allow their survival in inhospitable habitats such as those contaminated with hydrocarbons. Screening methodologies for testing the microbial assimilation of volatile organic compounds (VOC) are scarce despite their importance for the bioremediation of hydrocarbon associated areas. In this study, 200 strains of melanized fungi were isolated from four different hydrocarbon-related environments by using selective methods, and their biodiversity was assessed by molecular and ecological analyses. Seventeen genera and 27 species from three main orders, namely Chaetothyriales, Cladosporiales, and Pleosporales, were identified. The ecological analysis showed a particular species distribution according to their original substrate. The isolated strains were also screened for their toluene assimilation potential using a simple and inexpensive methodology based on miniaturized incubations under controlled atmospheres. The biomass produced by the 200 strains with toluene as the sole carbon source was compared against positive and negative controls, with glucose and with only mineral medium, respectively. Nineteen strains were selected as the most promising for further investigation on the biodegradation of alkylbenzenes. Center for the Study of Social Insects São Paulo State University (UNESP) GIRO Institute of Agrifood Research and Technology (IRTA), Torre Marimon Basic Pathology Department Federal University of Paraná (UFPR) Division of Microbial Resources CPQBA University of Campinas (Unicamp) Center for the Study of Social Insects São Paulo State University (UNESP) CAPES: 2013/01556-2 CNPq: 2013/01556-2 FAPESP: 2013/01556-2 CNPq: 312811/2018-7.

Intensive livestock production has a negative environmental impact by producing large amounts of animal dejections, which, if not properly managed, can contaminate nearby water bodies with nutrient excess. However, if the animal manure could be transferred efficiently to nearby crops and used as a fertilizer for the plants, pollution/contamination would be mitigated, transforming manure from a waste to a resource. This valorization of manure from waste to a resource falls within the circular economy principles, but the transportation of manure also comes at an environmental and economic cost. It is a single-objective optimization problem regarding finding the best solution for the logistics process of satisfying nutrient crops needs through livestock manure. This paper uses a centralized optimal algorithm (COA) to solve the problem, based on a realistic simulator that considers numerous real-world constraints that related work has not yet addressed. Implementation and evaluation of this method have been carried out based on extensive geolocalized data from Catalonia (Spain), one of the densest European farming regions, as a case study. The findings show that the use of treatment units in pig farms is not profitable, while applying treatment units on selected cow farms for composting manure has its merits, under an intelligent choice of cow farms. Finally, a comparison of our findings with those of two similar studies in Hangzhou, China and Minnesota, USA, are performed. info:eu-repo/semantics/publishedVersion

Blockchain is an emerging digital technology allowing ubiquitous financial transactions among distributed untrusted parties, without the need of intermediaries such as banks. This chapter examines the impact of blockchain technology in agriculture and food supply chain, presents existing ongoing projects and initiatives, and discusses overall implications, challenges and potential, with a critical view over the maturity of these projects. Our findings indicate that blockchain is a promising technology towards a transparent supply chain of food, with many ongoing initiatives in various food products and food-related issues, but many barriers and challenges still exist, which hinder its wider popularity among farmers and systems. These challenges involve technical aspects, education, policies and regulatory frameworks., This work has been partly supported by the project that has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 739578 (RISE – Call: H2020-WIDESPREAD-01-2016-2017-TeamingPhase2) and the Republic of Cyprus through the Deputy Ministry of Research, Innovation and Digital Policy.

The concurrence of structurally complex petroleum-associated contaminants at relatively high concentrations, with diverse climatic conditions and textural soil characteristics, hinders conventional bioremediation processes. Recalcitrant compounds such as high molecular weight polycyclic aromatic hydrocarbons (HMW-PAHs) and heavy alkanes commonly remain after standard soil bioremediation at concentrations above regulatory limits. The present study assessed the potential of native fungal bioaugmentation as a strategy to promote the bioremediation of an aged industrially polluted soil enriched with heavy hydrocarbon fractions. Microcosms assays were performed by means of biostimulation and bioaugmentation, by inoculating a defined consortium of six potentially hydrocarbonoclastic fungi belonging to the genera Penicillium, Ulocladium, Aspergillus, and Fusarium, which were isolated previously from the polluted soil. The biodegradation performance of fungal bioaugmentation was compared with soil biostimulation (water and nutrient addition) and with untreated soil as a control. Fungal bioaugmentation resulted in a higher biodegradation of total petroleum hydrocarbons (TPH) and of HMW-PAHs than with biostimulation. TPH (C14-C35) decreased by a 39.90 ± 1.99% in bioaugmented microcosms vs. a 24.17 ± 1.31% in biostimulated microcosms. As for the effect of fungal bioaugmentation on HMW-PAHs, the 5-ringed benzo(a)fluoranthene and benzo(a)pyrene were reduced by a 36% and 46%, respectively, while the 6-ringed benzoperylene decreased by a 28%, after 120 days of treatment. Biostimulated microcosm exhibited a significantly lower reduction of 5- and 6-ringed PAHs (8% and 5% respectively). Higher TPH and HMW-PAHs biodegradation levels in bioaugmented microcosms were also associated to a significant decrease in acute ecotoxicity (EC50) by Vibrio fischeri bioluminiscence inhibition assays. Molecular profiling and counting of viable hydrocarbon-degrading bacteria from soil microcosms revealed that fungal bioaugmentation promoted the growth of autochthonous active hydrocarbon-degrading bacteria. The implementation of such an approach to enhance hydrocarbon biodegradation should be considered as a novel bioremediation strategy for the treatment of the most recalcitrant and highly genotoxic hydrocarbons in aged industrially polluted soils.

Soil organic carbon (SOC) plays an important role on improving soil conditions and soil functions. Increasing land use changes have induced an important decline of SOC content at global scale. Increasing SOC in agricultural soils has been proposed as a strategy to mitigate climate change. Animal manure has the characteristic of enriching SOC, when applied to crop fields, while, in parallel, it could constitute a natural fertilizer for the crops. In this paper, a simulation is performed using the area of Catalonia, Spain as a case study for the characteristic low SOC in the Mediterranean, to examine whether animal manure can improve substantially the SOC of agricultural fields, when applied as organic fertilizers. Our results show that the policy goals of the 4 × 1000 strategy can be achieved only partially by using manure transported to the fields. This implies that the proposed approach needs to be combined with other strategies.

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.

Intensive livestock production might have a negative environmental impact, by producing large amounts of animal manure, which, if not properly managed, can contaminate nearby water bodies with nutrient excess. However, if animal manure is exported to nearby crop fields, to be used as organic fertilizer, pollution can be mitigated. It is a single-objective optimization problem, in regards to finding the best solution for the logistics process of satisfying nutrient needs of crops by means of livestock manure. This paper proposes three different approaches to solve the problem: a centralized optimal algorithm (COA), a decentralized nature-inspired cooperative technique, based on the foraging behaviour of ants (AIA), as well as a naive neighbour-based method (NBS), which constitutes the existing practice used today in an ad hoc, uncoordinated manner in Catalonia. Results show that the COA approach is 8.5% more efficient than the AIA. However, the AIA approach is fairer to the farmers and more balanced in terms of average transportation distances that need to be covered by each livestock farmer, while it is 1.07 times more eefficient than the NBS. Our work constitutes the first application of a decentralized AIA to this interesting real-world problem, in a domain where swarm intelligence methods are still under-exploited., Comment: Computers and Electronics in Agriculture Journal. arXiv admin note: substantial text overlap with arXiv:2006.04573

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.

The microbial disinfestation efficiency of an innovative horizontal-flow slow sand filter (HSSF) for treating nutrient solution spent from an experimental closed-loop nursery was evaluated by means of a combination of culture-dependent and independent molecular techniques. A dense inoculum of the fungal plant pathogen Fusarium oxysporum f.sp. lycopersici was applied in the fertigation system (106 cells per mL). Indigenous and introduced populations of eubacteria and fungi were assessed in the nutrient solution, the HSSF influent/effluent, and a sand bed transect by isolation on selective media, as well as by quantitative qPCR and next-generation sequencing (NGS) on target ribosomal genes. The HSSF effectively reduced viable Fusarium propagules and fungal gene content with an efficiency consistently above 99.9% (5 orders of magnitude down). On the other hand, Fusarium cells accumulated in the sand bed, indicating that physical entrapment was the main removal mechanism. The viability of retained Fusarium cells tended to decrease in time, so that treatment efficiency might be enhanced by antagonistic species from the genera Bacillus, Pseudomonas, and Trichoderma, also identified in the sand bed. Indigenous bacterial populations from the HSSF effluent were reduced by 87.2% and 99.9% in terms of colony forming units and gene counts, respectively, when compared to the influent. Furthermore, microbial populations from the HSSF effluent were different from those observed in the sand bed and the influent. In summary, the HSSF microbial disinfestation efficiency is comparable to that reported for other more intensive and costly methodologies, while allowing a significant recovery of water and nutrients.

A 26-day trial with 18 Pietrain × (Landrace × Duroc) pigs was conducted to investigate the effect of two dose levels of a specifically selected Bacillus spp. direct-fed microbial (DFM) product, on the emission of environmentally harmful gasses (methane, ammonia and hydrogen sulphide) from manure. Pigs were assigned to one of three treatments in a randomized complete block design according to their sex and initial BW. Each treatment contained three replications with two pigs per pen. The test treatments included a Bacillus spp. DFM containing 3 × 108 colony-forming unit/g, added at a low (250 mg/kg) and high (500 mg/kg) dose to an antibiotic free high fibre-based diet, and a non-supplemented control diet. Manure from pigs fed with the supplemented diets emitted lower amounts of atmospheric contaminants. The most significant reduction was observed with low DFM supplementation, in which methane and ammonia volatilization decreased ( P< 0.05) by >40% and 50%, respectively, on fresh weight basis in relation to the control. Microbiome analysis of manure by high through put sequencing techniques on eubacterial and archaeal 16S rRNA genes highlighted the complex interactions between indigenous gut microflora and inoculated Bacillus spp. The tested Bacillus DFM could be considered as a best available technique in reducing the environmental impacts of growing pigs fed with high fibre-based diets. info:eu-repo/semantics/publishedVersion

Microbial community dynamics during the anaerobic co-digestion of pig manure, pasteurized slaughterhouse waste and glycerin were studied in a lab-scale CSTR. The feed composition was optimized through progressive co-substrate additions for enhanced methane production and organic matter removal without accumulation of intermediate compounds. Microbial community structure of biomass samples was studied by means of qPCR and DGGE profiling of 16S rRNA genes (Bacteria and Archaea), and genus-specific qPCR of the methyl coenzyme M reductase gene (mcrA), which encodes for an enzyme universally involved in methanogenesis. The composition of the dominant bacterial populations remained relatively stable, when compared to those in the influent, but the highest changes were observed upon the introduction of glycerin. Biodiversity of archaea was restricted to a few representatives of the genera Methanosaeta and Methanosarcina, but Methanospirillum sp. was detected only when glycerin was introduced in the feeding. Glycerin supplementation coincided with the strongest increase in methane yield (from 0.22 to 0.64 m3CH4 m−3 d−1).

There is high interest in applying anaerobic digestion to organic wastes for the recovery of biogas as a renewable energy source. In the case of protein-rich residues, the performance of anaerobic digesters might be affected by the accumulation of ammonia and volatile fatty acids. High concentrations of these compounds impact negatively on the activity of the acetotrophic methanogenic archaea (AMA). This limitation can be overcome by promoting the enrichment within digesters of syntrophic acetate-oxidizing bacteria (SAOB) in conjunction with certain groups of hydrogenotrophic methanogenic archaea (HMA). These two microbial populations have a relatively high tolerance towards the aforementioned inhibitory compounds. Hence, when the partial pressure of hydrogen is low enough, SAOB metabolize acetate to carbon dioxide and hydrogen, which are syntrophically consumed by HMA. Once the organic matter has been biodegraded, the remaining nitrogen can be biologically removed from digester supernatants by the anaerobic ammonium oxidation (anammox). This pathway consists of the simultaneous conversion of ammonium and nitrite to (di)nitrogen gas, and, therefore, a previous partial oxidation of ammonium to nitrite under aerobic conditions is required. Interestingly, the whole process constitutes a completely autotrophic nitrogen removal strategy. This chapter compiles the current knowledge on the syntrophic oxidation of acetate and on the anaerobic oxidation of ammonium, mostly focusing on technological aspects in view of a sequential bioreactor implementation.

Deep learning constitutes a recent, modern technique for image processing and data analysis, with promising results and large potential. As deep learning has been successfully applied in various domains, it has recently entered also the domain of agriculture. In this paper, we perform a survey of 40 research efforts that employ deep learning techniques, applied to various agricultural and food production challenges. We examine the particular agricultural problems under study, the specific models and frameworks employed, the sources, nature and pre-processing of data used, and the overall performance achieved according to the metrics used at each work under study. Moreover, we study comparisons of deep learning with other existing popular techniques, in respect to differences in classification or regression performance. Our findings indicate that deep learning provides high accuracy, outperforming existing commonly used image processing techniques. info:eu-repo/semantics/acceptedVersion

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/acceptedVersion

Rhinocladiella mackenziei accounts for the majority of fungal brain infections in the Middle East, and is restricted to the arid climate zone between Saudi Arabia and Pakistan. Neurotropic dissemination caused by this fungus has been reported in immunocompromised, but also immunocompetent individuals. If untreated, the infection is fatal. Outside of humans, the environmental niche of R. mackenziei is unknown, and the fungus has been only cultured from brain biopsies. In this paper, we describe the whole-genome resequencing of two R. mackenziei strains from patients in Saudi Arabia and Qatar. We assessed intraspecies variation and genetic signatures to uncover the genomic basis of the pathogenesis, and potential niche adaptations. We found that the duplicated genes (paralogs) are more susceptible to accumulating significant mutations. Comparative genomics with other filamentous ascomycetes revealed a diverse arsenal of genes likely engaged in pathogenicity, such as the degradation of aromatic compounds and iron acquisition. In addition, intracellular accumulation of trehalose and choline suggests possible adaptations to the conditions of an arid climate region. Specifically, protein family contractions were found, including short-chain dehydrogenase/reductase SDR, the cytochrome P450 (CYP) (E-class), and the G-protein b WD-40 repeat. Gene composition and metabolic potential indicate extremotolerance and hydrocarbon assimilation, suggesting a possible environmental habitat of oil-polluted desert soil info:eu-repo/semantics/publishedVersion

Intensive farming has been linked to significant degradation of land, water and air. A common body of knowledge is needed, to allow an effective monitoring of cropping systems, fertilization and water demands, and impacts of climate change, with a focus on sustainability and protection of the physical environment. In this paper, we describe AgriBigCAT, an online software platform that uses geophysical information from various diverse sources, employing geospatial and big data analysis, together with web technologies, in order to estimate the impact of the agricultural sector on the environment, considering land, water, biodiversity and natural areas requiring protection, such as forests and wetlands. This platform can assist both the farmers’ decision-taking processes and the administration planning and policy making, with the ultimate objective of meeting the challenge of increasing food production at a lower environmental impact.

Deep learning (DL) constitutes a modern technique for image processing, with large potential. Having been successfully applied in various areas, it has recently also entered the domain of agriculture. In the current paper, a survey was conducted of research efforts that employ convolutional neural networks (CNN), which constitute a specific class of DL, applied to various agricultural and food production challenges. The paper examines agricultural problems under study, models employed, sources of data used and the overall precision achieved according to the performance metrics used by the authors. Convolutional neural networks are compared with other existing techniques, and the advantages and disadvantages of using CNN in agriculture are listed. Moreover, the future potential of this technique is discussed, together with the authors’ personal experiences after employing CNN to approximate a problem of identifying missing vegetation from a sugar cane plantation in Costa Rica. The overall findings indicate that CNN constitutes a promising technique with high performance in terms of precision and classification accuracy, outperforming existing commonly used image-processing techniques. However, the success of each CNN model is highly dependent on the quality of the data set used.

Cultures of melanized fungi representative of the black yeast orders Capnodiales (Cladosporium cladosporioides and Neohortaea acidophila) and Chaetothyriales (Cladophialophora psammophila) were confined with indoor air from the laboratory during 48 h. Volatile organic compounds (VOCs) from the headspace were analyzed by thermal desorption gas chromatography time-of-fly mass spectrometry (TD-GC-ToFMS, detection threshold 0.1 μg m−3) and compared against an abiotic control. A mixture of 71 VOCs were identified and quantified in the indoor air (total concentration 1.4 mg m−3). Most of these compounds were removed in the presence of fungal biomass, but 40 newly formed putative volatile metabolites were detected, though at comparatively low total concentrations (

Paddy rice fields are one of the most important sources of anthropogenic methane. Improving the accuracy in the CH4 budget is fundamental to identify strategies to mitigate climate change. Such improvement requires a mechanistic understanding of the complex interactions between environmental and agronomic factors determining CH4 emissions, and also the characterization of the annual temporal CH4 emissions pattern in the whole crop cycle. Hence, both the growing and fallow seasons must be included. However, most of the previous research has been based on single-factor analyses that are focused on the growing season. In order to fill this gap, a study was conducted in a Mediterranean rice agrosystem (Ebre Delta, Catalonia) following a farm-to-farm approach with the purpose of 1) evaluating the cumulative and temporal pattern of CH4 emission, and 2) conducting a multi-variate analyses to assess the associative pattern, relative contribution and temporal variation of the main explanatory variables concerning the observed CH4 emissions. Measurements of CH4 emissions and agronomic and environmental parameters in 15 commercial rice fields were monitored monthly, during a whole crop field cycle. The temporal pattern of CH4 emission followed a bi-modal distribution peaking in August and October. The cumulative annual CH4 emissions from rice fields amounted 314 kg CH4 kg ha-1, of which ca. 70% were emitted during the fallow season. The main controlling factors of the CH4 emission rate in the growing season were positive related to water level and plant cover, while soil redox was negatively related. The main controlling factors in the fallow season were water level (negatively related, conversely to the growing season), as well as straw incorporation and soil temperature (positively related). The results of this study highlight the importance of the often neglected fallow season in the accurate estimation of CH4 emissions and, thus, the necessity of measurement programs that cover the whole crop field cycle. This information is the first step for setting effective mitigation strategies based on straw and water management.

In many countries, it is difficult for government agencies to know where animal farms are located. Using satellite imaging and deep learning provides a new, effective, accurate and low-cost approach for detecting these facilities.

Four full-scale anaerobic digesters with a long history of stable operation were characterized in terms of active microbiome and metagenome. Isotopic fractionation of biogas demonstrated that acetotrophy was rather prevalent in reactors operated at 6 gTAN L−1, suggesting that syntrophic acetate oxidizing bacteria (SAOB) played a significant role in the latter. These results were generally coherent with the observed active bacterial and archaeal communities but no known SAOB were observed. Metagenome descriptions yielded 73 assembled population genomes, of which only 7 could be assigned at the species level. Gene annotation and association to relevant metabolic pathways indicated that the phyla Chloroflexi and Bacteroidales might encompass new, currently undescribed, SAOB/formate producing species that would metabolize acetate via the glycine cleavage system. The predominant hydrogenotrophic counterpart at a high ammonia content belonged to the genus Methanoculleus, which could also grow on acetate to a certain extent.

The present study assessed the diversity of black yeast-like fungi present on babassu coconut shells, a substrate rich in lipids and several volatile organic compounds (VOCs) including aromatic hydrocarbons. Using different isolation methods, one-hundred-six isolates were obtained and were identified by ITS sequencing as members of the genera Exophiala, Cladophialophora, Veronaea, and Rhinocladiella. Two novel species were discovered. Eight strains were selected for assessing their ability to grow on toluene and phenyl acetate as the sole carbon and energy source. All strains tested were able to assimilate phenyl acetate, while two out of eight were able to use toluene. VOCs profiling in babassu samples was also investigated by GC-ToF MS, revealing that a complex mixture of VOCs was emitted, which included alkylbenzenes such as toluene. Assimilation of alkylbenzenes by the black yeasts might therefore be the result of evolutionary adaptation to symbiotic interactions with higher plants. The potential relationship between lipid/aromatic hydrocarbon metabolism and pathogenicity is also discussed.

Enhanced heterotrophic denitrification by adding glucose was investigated by means of a soil column experiment which simulated the groundwater flow. The carbon-to-nitrogen ratio was the main factor determining denitrification potential under experimental conditions. The influence of stimulated denitrification on the autochthonous microbial community was investigated by quantitative PCR (qPCR), and denaturing gradient gel electrophoresis (DGGE). The qPCR detection of the nosZ genes encoding nitrous oxide reductase, and the comparison of the abundances of 16S rRNA genes revealed that the addition of glucose enhanced denitrification leading to an increase in both the total eubacteria and, in particular, in the ratio of denitrifying bacteria, which represented the 21% of the total native eubacteria on the basis of nosZ/16S rRNA gene ratio. Microbial community profiling by DGGE indicated that ribotypes closely related to the genera Acidovorax and Hydrogenophaga (Comamonadaceae family) became enriched in the soil column. The effects of biomass occurrence in the column system on soil hydrodynamics, assessed by tracer studies, revealed a reduction of porosity and a significant increase of dispersivity that could be caused by the appearance of new functional microbial biomass in the aquifer material under enhanced denitrifying conditions. The importance of investigating the microbial growth in relation to the hydrodynamic effects, during enhanced denitrification, has been revealed in the column system experiments associated with the bioremediation. Combining microbial characterisation and hydrodynamic data in a soil column system permits us to gain an insight to the limiting factors of different stimulation strategies that can be applied in the field.

The utilization of different kinds of ion exchange membrane is a common practice in bioelectrochemical systems such as two-chambered microbial fuel cells (MFCs). However, little is known about the effect of membrane materials on the anodic microbial community diversity. RESULTS The effect of two cationic and one anionic exchange membranes (Nafion N-117, Ultrex CMI-7000, and Ultrex AMI-7000) on the microbial community dynamics of Eubacteria and Archaea has been assessed in two-chambered MFCs. The experimental results indicated that the eubacterial community in the anodic chamber was not affected by the membrane materials, being predominantly populations of Bacteroidetes (Porphyromonadaceae) and β-proteobacteria (Alcaligenaceae and Comamonadaceae). On the other hand, the archaeal counterpart appears to be highly dependent on the type of membrane used, as was evidenced by the selective enrichment of Methanosarcina sp. in the MFC equipped with the membrane Nafion N-117 which was the MFC that showed the highest current production. CONCLUSIONS The results obtained in the present study suggest that membrane materials affect archaeal diversity whereas both anodofilic eubacteria and methanogenic archaea populations could play an important role in the overall MFC process performance. © 2014 Society of Chemical Industry

This study reports the biodegradation of carbon disulfide (CS2) in air biofilters packed with a pelletized mixture of composted manure and sawdust. Experiments were carried out in two lab-scale (1.2 L) biofiltration units. Biofilter B was seeded with activated sludge enriched previously on CS2-degrading biomass under batch conditions, while biofilter A was left as a negative inoculation control. This inoculum was characterized by an acidic pH and sulfate accumulation, and contained Achromobacter xylosoxidans as the main putative CS2 biodegrading bacterium. Biofilter operation start-up was unsuccessfully attempted under xerophilic conditions and significant CS2 elimination was only achieved in biofilter A upon the implementation of an intermittent irrigation regime. Sustained removal efficiencies of 90-100 % at an inlet load of up to 12 g CS2 m(-3) h(-1) were reached. The CS2 removal in this biofilter was linked to the presence of the chemolithoautotrophic bacterium Thiobacillus thioparus, known among the relatively small number of species with a reported capacity of growing on CS2 as the sole energy source. DGGE molecular profiles confirmed that this microbe had become dominant in biofilter A while it was not detected in samples from biofilter B. Conventional biofilters packed with inexpensive organic materials are suited for the treatment of low-strength CS2 polluted gases (IL

With the recent advancement of the Internet of Things (IoT), it is now possible to process a large number of sensor data streams using different large-scale IoT platforms. These IoT frameworks are used to collect, process and analyse data streams in real-time and facilitate provision of smart solutions designed to provide decision support. Existing IoT-based solutions are mainly domain-dependent, providing stream processing and analytics focusing on specific areas (smart cities, healthcare etc.). In the context of agri-food industry, a variety of external parameters belonging to different domains (e.g. weather conditions, regulations etc.) have a major influence over the food supply chain, while flexible and adaptive IoT frameworks, essential to truly realize the concept of smart farming, are currently inexistent. In this paper, we propose Agri-IoT, a semantic framework for IoT-based smart farming applications, which supports reasoning over various heterogeneous sensor data streams in real-time. Agri-IoT can integrate multiple cross-domain data streams, providing a complete semantic processing pipeline, offering a common framework for smart farming applications. Agri-IoT supports large-scale data analytics and event detection, ensuring seamless interoperability among sensors, services, processes, operations, farmers and other relevant actors, including online information sources and linked open datasets and streams available on the Web.

The removal efficiency (RE) profile of a complex mixture of volatile organic compounds (VOCs) was characterized in a full-scale biofilter treating odorous emissions from a composting plant in an urban environment. The biofilter was composed of two similar units packed with mixtures of pine bark and wood chips, and were operated in parallel. Up to 48 different VOCs were identified by gas chromatography-mass spectrometry (GC-MS) and individual RE values were calculated by comparing influent and effluent GC-MS chromatograms. Multivariate correlations on RE, the partition coefficients between octanol/water (KOW), octanol/air (KOA), and water/air (KWA), as well as biodegradability and toxicity estimates, were established by Principal Component Analysis (PCA). Biofilter RE values were positively and negatively correlated to KOA and to KWA, respectively, indicating that hydrophobic volatile compounds were more efficiently removed than the hydrophilic ones. Instead, RE was poorly correlated with estimates of the ...

BACKGROUND: This research has assessed the impact of sulfate accumulation on the performance of two biofilters treating CS2. Both biofilters were packed with a pelletized organic fertilizer and operated in downflow mode (Biofilter A) and flow reversal mode (Biofilter B). The performance of the biofilters after an excessive accumulation of sulfate has also been evaluated. RESULTS: The excessive accumulation of sulfate and the reduction in the packing material's moisture content resulted in a decrease in the initial high removal efficiency recorded during the first 50 days (approx.) of operation in both biofilters. A recovery strategy based on mixing and washing the packing material led to a sustained RE of 40 ± 9% and 62 ± 11% for Biofilters A and B, respectively. Both biofilters recovered their initial performance after irrigation. A high CO2:EC ratio suggested that secondary oxidation reactions related to heterotrophic bacteria occurred in both bioreactors. The maximum elimination capacity (ECmax) recorded in Biofilters A and B was 11.6 and 16.6 g CS2 m−3 h−1, respectively. CONCLUSIONS: This study confirmed the capacity biofilters treating CS2 have to recover after sulfate accumulation episodes and the importance of optimized irrigation strategies. The benefit of the flow reversal operating mode was highlighted. Copyright © 2012 Society of Chemical Industry

Cladophialophora is a genus of asexual black yeast-like fungi with one-celled, hydrophobic conidia which is predicted to have teleomorphs in the ascomycete genus Capronia, a member of the order Chaetothyriales. Cladophialophora species are relatively frequently involved in human disease ranging from mild cutaneous lesions to cerebral abscesses. Although the natural niche outside humans is unknown for most opportunistic Cladophialophora species, the fungi concerned are rarely isolated from environmental samples such as dead plant material, rotten wood, or soil. The objective of the present paper is to describe a novel species of Cladophialophora which was isolated from soil polluted with benzene, toluene, ethylbenzene, and xylene (BTEX). It proved to be able to grow with toluene and other related alkylbenzenes as its sole carbon and energy source. This strain is of interest for the biodegradation of toluene and other related xenobiotics under growth limiting conditions, particularly in air biofilters, dry and/or acidic soil. A preliminary genetic analysis using multilocus sequencing typing (MLST) and amplified fragments length polymorphism (AFLP) showed that this fungus was closely related to the pathogenic species Cladophialophora bantiana, sharing a C. bantiana-specific intron in SSU rDNA. However, it was unable to grow at 40 °C and proved to be non-virulent in mice. The clear phylogenetic and ecophysiological delimitation of the species is fundamental to prevent biohazard in engineered bioremediation applications. Keywords AFLP; Air biofilters; Black yeasts; Cladophialophora; In vitro antifungal activity; ITS rDNA; Neurotropism; Pathogenicity

Intensive livestock farming has been linked to excessive pollution and contamination of land, water and air. A common body of knowledge is required in order to understand and assess this impact of agriculture, and take proper countermeasures with a focus on the sustainability and the protection of the physical environment, affecting agricultural productivity as little as possible. In this paper, we examine the problem of the environmental impact of livestock agriculture, targeting animal manure, which is a serious problem in various territories of Europe and the USA. Aiming to address this problem, we have developed AgriBigCAT, an online software platform that uses geophysical information from various diverse sources, employing geospatial and big data analysis, together with web technologies, in order to estimate the impact of the livestock agricultural sector on the environment, examining possible pollution of land, water and air, considering various scenarios and potential applications to mitigate the problem. The AgriBigCAT platform can assist both the farmers' decision-making processes and the administration planning and policy making, with the ultimate objective of meeting the challenge of increasing food production at a lower environmental impact.

Submitted by Vitor Silverio Rodrigues (vitorsrodrigues@reitoria.unesp.br) on 2014-05-27T11:24:39Z No. of bitstreams: 0Bitstream added on 2014-05-27T14:30:41Z : No. of bitstreams: 1 2-s2.0-77955417388.pdf: 178136 bytes, checksum: f01b3667f8e5bd58f207a02ba8592003 (MD5) Made available in DSpace on 2014-05-27T11:24:39Z (GMT). No. of bitstreams: 0 Previous issue date: 2010-03-23 Black yeast members of the Herpotrichiellaceae present a complex ecological behavior: They are often isolated from rather extreme environments polluted with aromatic hydrocarbons, while they are also regularly involved in human opportunistic infections. A selective technique to promote the in vitro growth of herpotrichiellaceous fungi was applied to investigate their ecophysiology. Samples from natural ecological niches and man-made environments that might contain black yeasts were enriched on an inert solid support at low humidity and under a controlled atmosphere rich in volatile aromatic hydrocarbons. Benzene, toluene, and xylene were provided separately as the sole carbon and energy source via the gas phase. The assayed isolation protocol was highly specific toward mesophilic Exophiala species (70 strains of this genus out of 71 isolates). Those were obtained predominantly from creosote-treated railway ties (53 strains), but isolates were also found on wild berries (11 strains) and in guano-rich soil samples (six strains). Most of the isolates were obtained on toluene (43 strains), but enrichments on xylene and benzene also yielded herpotrichiellaceous fungi (17 and 10 isolates, respectively). Based upon morphological characterizations and DNA sequences of the full internal transcriber spacers (ITS) and the 8.5S rRNA genes, the majority of the obtained isolates were affiliated to the recently described species Exophiala xenobiotica (32 strains) and Exophiala bergeri (nine strains). Members of two other phylogenetic groups (24 and two strains, respectively) somewhat related to E. bergeri were also found, and a last group (three strains) corresponded to an undescribed Exophiala species. © 2010 The Author(s). Department of Dermatology Fujian Medical University Affiliated Union Hospital, Fuzhou Department of Dermatology and Venereology, Union Hospital, Tongji Medical College Huazhong Science and Technology University, Jiefang Dadao, Wuhan, Hubei CBS-KNAW Fungal Biodiversity Centre, Utrecht Institute of Biodiversity and Ecosystem Dynamics University of Amsterdam, Amsterdam Research Center for Medical Mycology Peking University Health Science Center, Beijing UNESP Department of Biochemistry and Microbiology Institute of Biosciences, Rio Claro, SP GIRO Technological Centre, Pompeu Fabra 1, 08100 Mollet del Vallès, Barcelona, Catalonia IRTA, Barcelona UNESP Department of Biochemistry and Microbiology Institute of Biosciences, Rio Claro, SP

The biodegradation of aromatic hydrocarbons by fungi has traditionally been considered to be of a cometabolic nature. Recently, however, an increasing number of fungi isolated from air biofilters exposed to hydrocarbon-polluted gas streams have been shown to assimilate volatile aromatic hydrocarbons as the sole source of carbon and energy. The biosystematics, ecology, and metabolism of such fungi are reviewed here, based in part on re-evaluation of a collection of published hydrocarbon-degrading isolates obtained from authors around the world. Incorrect or outdated identifications in original publications are corrected by ribosomal DNA sequence analysis. The data show that many volatile-hydrocarbon-degrading strains are closely related to, or in some cases clearly conspecific with, the very restricted number of human-pathogenic fungal species causing severe mycoses, especially neurological infections, in immunocompetent individuals. Neurochemistry features a distinctive array of phenolic and aliphatic compounds that are related to molecules involved in the metabolism of aromatic hydrocarbons. Hence, there may be physiological connections between hydrocarbon assimilation and certain patterns of mammalian infection.

Assimilation of toluene by Cladosporium sphaerospermum is initially catalyzed by toluene monooxygenase (TOMO). TOMO activity was induced by adding toluene to a glucose-pregrown culture of C. sphaerospermum. The corresponding microsomal enzyme needed NADPH and O2 to oxidize toluene and glycerol, EDTA, DTT, and PMSF for stabilization. TOMO activity was maximal at 35C and pH 7.5 and was inhibited by carbon monoxide, Metyrapone, and cytochrome c. TOMO preferred as substrates also other aromatic hydrocarbons with a short aliphatic side chain. Its reduced carbon monoxide difference spectrum showed a maximum at 451 nm. A substrate-induced Type I spectrum was observed on addition of toluene. These results indicated that TOMO is a cytochrome P450. TOMO and its corresponding reductase were eventually purified by a simultaneous purification revealing apparent molecular masses of 58 and 78 kDa, respectively. 2003 Elsevier Inc. All rights reserved.