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Methodological aspects of investigating the resistome in pig farm environments
Get PDFA typical One Health issue, antimicrobial resistance (AMR) development and its spread among people, animals, and the environment attracts significant research attention. The animal sector is one of the major contributors to the development and dissemination of AMR and accounts for more than 50 % of global antibiotics usage. The use of antibiotics exerts a selective pressure for resistant bacteria in the exposed microbiome, but many questions about the epidemiology of AMR in farm environments remain unanswered. This is connected to several methodological challenges and limitations, such as inconsistent sampling methods, complexity of farm environment samples and the lack of standardized protocols for sample collection, processing and bioinformatical analysis. In this project, we combined metagenomics and bioinformatics to optimise the methodology for reproducible research on the resistome in complex samples from the indoor farm environment. The work included optimizing sample collection, transportation, and storage, as well as DNA extraction, sequencing, and bioinformatic analysis, such as metagenome assembly and antibiotic resistance gene (ARG) detection. Our studies suggest that the current most optimal and cost-effective pipeline for ARG search should be based on Illumina sequencing of sock sample material at high depth (at least 25 M 250 bp PE for AMR gene families and 43 M for gene variants). We present a computational analysis utilizing MEGAHIT assembly to balance the identification of bacteria carrying ARGs with the potential loss of diversity and abundance of resistance genes. Our findings indicate that searching against multiple ARG databases is essential for detecting the highest diversity of ARGs
Root Circumnutation Reduces Mechanical Resistance to Soil Penetration
Get PDFRoot circumnutation, the helical movement of growing root tips, is a widely observed behaviour of plants. However, our mechanistic understanding of the impacts of root circumnutation on root growth and soil exploration is limited. Here, we deployed a unique combination of penetrometer measurements, X-ray computed tomography and time-lapse imaging, and cavity expansion modelling to unveil the effects of root circumnutation on the mechanical resistance to soil penetration. To simulate differences in circumnutation amplitude and frequency occurring among plant species, genotypes and environmental conditions, we inserted cone penetrometers with varying bending stiffness into soil samples that were subjected to orbital movement at different velocities. We show that greater circumnutation intensity, determined by a greater circumnutation frequency in conjunction with a larger circumnutation amplitude, decreased the mechanical resistance to soil penetration. Cavity expansion theory and X-ray computed tomography provided evidence that increased circumnutation intensity reduces friction at the cone-soil interface, indicating a link between root circumnutation and the ability of plants to overcome mechanical constraints to root growth. We conclude that circumnutation is a key component of root foraging behaviour and propose that genotypic differences in circumnutation intensity can be leveraged to adapt crops to soils with greater mechanical resistance
Highly efficient boron/sulfur-modified activated biochar for removal of reactive dyes from water: Kinetics, isotherms, thermodynamics, and regeneration studies
Get PDFWater pollutants such as synthetic dyes can cause significant problems for human health and ecosystems due to their chemical properties and environmental interactions. Contamination of surface and underground water caused by the discharge of synthetic dyes is a widespread problem that arises primarily from industrial activities such as textile manufacturing, leather processing, paper production, and plastics industries. Since adsorption is one of the most efficient and reliable methods to remove pollutants from water, in this work, pine tree logging residues (LR) were used to produce boron/sulfur chemically modified biochars with superior adsorption performance and recyclability. The biochars were produced using a two-step pyrolysis procedure with potassium hydroxide as a chemical activator. The specific surface areas (B.E.T.) of the biochars were 2645 m2 g-1 for the boron-treated biochar (LR-Boron), 2524 m2 g- 1 for the sulfur-treated (LR-Sulfur), and 3141 m2 g- 1 for the control biochar (LR-Control, without boron or sulfur), respectively. The LR-Boron biochar showed an exceptional degree of graphitization of (ID/IG=0.45), while the LR-Sulfur biochar displayed an ID/IG= 1.02; for comparison, the LR-Control exhibited an ID/IG= 0.81, showing that the sample subjected to boron treatment created carbon- rich in graphitic structures. The three biochars were evaluated as adsorbents for removing reactive black-5 azo dye (RB-5) from water and mixtures of several dyes in synthetic aqueous effluents. The adsorption data showed that all carbons exhibited outstanding RB-5 removal performance. Kinetic measurements were well fitted by the Avrami fractional order model, and the LR-sulfur carbon displayed the fastest adsorption kinetics. Isotherm measurements were well fitted by the Liu model, with a theoretical Qmax of around 1419 mg g- 1 (LR-Control), 1586 mg g-1 (LR-Boron), and 1766 mg g-1 (LR-Sulfur) at 316 K. The presence of sulfur-functional groups on the LR-Sulfur biochar surface was probably the reason for the superior adsorption performance of this biochar. Both sulfur and boron-treated biochars exhibited higher regeneration potentials, maintaining around 60-67 % removal capacity after 7 cycles compared to 35 % for the LR-Control biochar. Thermodynamic adsorption studies showed that the adsorption process was endothermic, favorable, and compatible with physical adsorption. All produced biochars were highly efficient for removal of pollutants from concentrated synthetic effluents
‘Relational Values’ is Neither a Necessary nor Justified Ethical Concept
Get PDF‘Relational value’ (RV) has intuitive credibility due to the shortcomings of existing axiological categories regarding recognizing the ethical relevance of people’s relations to nature. But RV is justified by arguments and analogies that do not hold up to closer scrutiny, which strengthens the assumption that RV is redundant. While RV may provide reasons for ethically considering some relations, much work remains to show that RV is a concept that does something existing axiological concepts cannot, beyond empirically describing relations people have to environmental areas and places
Asparagopsis taxiformis supplementation to mitigate enteric methane emissions in dairy cows – effects on performance and metabolism
Get PDFMethane emissions from ruminant digestion contribute significantly to global anthropogenic greenhouse gas emissions. Members of the phylum Rhodophyta (red algae), particularly Asparagopsis sp., have shown promising results in reducing methane emissions in ruminants, due to their high content of halogenated methane analog compounds. However, knowledge is lacking regarding the effects of red algae on animal performance and metabolism. This study investigated the effects of dairy cow diet supplementation with Asparagopsis taxiformis on enteric methane performance, metabolism of bromine and iodine, and health status of the cows. Thirty lactating Nordic Red dairy cows fed a total mixed ration, were blocked according to parity and days in milk, and randomly assigned to one of 3 diets: a control diet with no Asparagopsis taxiformis (CON), a diet with 0.15% Asparagopsis taxiformis on an organic matter (OM) basis (L-AT), and a diet with 0.3% Asparagopsis taxiformis on an OM basis (H-AT). The cows were fed the experimental diets continuously for 13 weeks, beginning with a baseline week (wk 0), which served as covariate by week where all cows received the basal diet. Individual feed intake and milk yield were recorded automatically throughout the experiment. Milk composition was determined by collecting milk samples during each milking session on 2 consecutive days every experimental week. While enteric methane and hydrogen levels were measured continuously by the GreenFeed system. Feces grab samples were collected as spot samples from a subset of 6 cows per treatment after milking during sampling wk 0, 2, 4, 8, and 12. Urine spot samples were collected from the same subset of cows during the same weeks as fecal samples. One urine sample was taken per day on 2 consecutive days, and the samples were analyzed for wk 12. Rumen fluid was collected after morning milking using a stomach tube in wk 0, 2, 4, and 12. We observed a 30% reduction in methane production in the H-AT group, with a concomitant increase in hydrogen production by 383%. However, the interaction between treatment and week showed that the AT effect on methane reduction began to diminish by wk 9 of the experiment. In the L-AT group, methane was reduced by 7.6% and hydrogen production was increased by 70%. However, dry matter intake (DMI) was 7% lower and energy-corrected milk (ECM) yield was 2% lower in the H-AT group compared with the other 2 groups. Total concentration of volatile fatty acids in rumen fluid was lower in the H-AT group compared with CON, with a reduction in acetate concentration and an increase in propionate, butyrate and valerate in the H-AT group. Bromine concentration was 5-fold higher and iodine concentration was 9-fold higher in milk from the H-AT group compared with CON. Bromine concentration in feces and urine samples from H-AT cows was approximately 4-fold and 9-fold higher, respectively, than in samples from CON cows. Metabolic profiling revealed a reduction in cholesterol levels and a decrease in the ferric-reducing ability of plasma in the H-AT treatment group compared with the CON group, as well as an increase in plasma magnesium concentration in the H-AT group. In conclusion, using 0.3% Asparagopsis taxiformis as an additive in dairy cow feed rations can mitigate enteric methane emissions, but this reduction was observed only during the first 8 weeks of the experiment, with no effect on methane emissions from wk 9 to 12. Additionally, it may have negative effects on DMI and ECM yield. Further long-term studies on red algae as methane inhibitor is needed to examine its sustained inhibitory effects over time and its impact on various metabolic processes. The effects appear to decline after wk 8 and influence several metabolic mechanisms
Earth observation reveals reduced winter wheat growth and the importance of plant available water during drought
Get PDFDrought poses increasing challenges to global food production. Knowledge about the influence of drought on crop development and the role of soil properties for crop drought severity is important in drought risk analysis and for mitigating drought impacts at the landscape level. Here, we tested if satellite images from Sentinel-2 could be used to assess the impacts of drought on crop development and the influence of soil properties on crop drought responses at the landscape scale and what the responses were. As a case study, we assessed winter wheat growth on 13 fields belonging to commercial farmers in southern Sweden in a dry year (2018) and in a year with normal weather conditions (2021). To track crop growth, the green leaf area index (GLAI) was estimated from satellite imagery using a radiative transfer model. Proxies for winter wheat growth rate, peak GLAI, and the timing of peak GLAI were derived from the GLAI development at the single-field level. We then compared the crop growth proxies between the 2 years and related the year-to-year differences between fields to measured soil properties. We found lower estimated growth rates, lower peak GLAI, and earlier peak GLAI in the dry year compared to the year with normal weather conditions. A higher peak GLAI in the dry year was related to a higher growth rate, and this was not shown in the year with normal precipitation. Differences in crop development between years were large for some fields but small for other fields, suggesting that soil properties play a role in crop response to drought. We found that fields with a higher plant available water capacity had a higher growth rate in the dry year and smaller relative differences in growth rate between the 2 years. This shows the importance of soils in mitigating drought conditions, which will likely become more relevant in an increasingly drier climate. Our case study demonstrates that satellite-derived crop growth proxies can identify crop responses to drought events and that satellite imagery can be used to discover impacts of soil properties on crop development at scales relevant to commercial farming
Social fish have larger brains and greater relative telencephalon sizes: support for the social brain hypothesis from wild, intraspecific comparisons
No full textThe social brain hypothesis (SBH) posits that complex social environments drive the evolution of larger brains and enlargement of specific brain regions. Among species comparisons often report contrasting relationships between social complexity and brain size, potentially due to confounding effects of phylogeny, morphology and ecology. Here, we explore this relationship in a single fish species, combining behavioural observations and brain measurements of two wild populations of the cichlid Neolamprologus brevis, which occupies similar ecological niches across its range but inhabits contrasting social environments depending on local shelter abundance. We quantified social behaviour and brain size to assess whether increased social interactions are associated with greater relative brain size or region-specific neuroanatomical adaptations. We found that individuals from the more socially complex population, which exhibited more frequent social interactions, had significantly larger total brain volumes compared to the less social population. We also found that the more social population exhibited relatively larger telencephalon and smaller hypothalamus volumes, suggesting mosaic adaptation to social demands. Feeding behaviour did not differ between populations, suggesting that differences in energy intake are unlikely to account for brain size variation. By integrating behavioural and neuroanatomical data, our study provides empirical support for the SBH in a natural, within-species comparison
Metatranscriptome analysis to unveil the molecular signatures of transcriptionally active pathogens associated with bovine mastitis
No full textBovine mastitis, a multi-etiological disease, is driven by complex microbial consortia; however, the transcriptional activity of pathogens and their underlying molecular mechanisms remains insufficiently explored. To the best of our knowledge, no metatranscriptome study on bovine mastitis is available in the public domain that identifies transcriptionally active pathogens and their associated molecular signatures. In this study, an in silico metatranscriptomics approach is employed on publicly available bovine mastitis RNA sequencing (RNA-Seq) datasets to identify transcriptionally active pathogens and their gene expression signatures. The analysis of unmapped reads (those not mapped to the bovine genome) identified 25 transcriptionally active pathogenic genera, accounting for 8,995 sequences, approximately from 500 bacterial strains of different species. Major findings of the study includes: (I) list of emerging pathogens "Pseudomonas, Stenotrophomonas, Comamonas, and Sphingomonas" actively contributing to disease development alongside well-known pathogens; (II) expression profiling of 4,121 virulence proteins, 484 peptidases, 432 secretory proteins, and 74 antimicrobial resistance genes; (III) identification of numerous hypothetical proteins in Staphylococcus (112), Mycoplasma (69), and Escherichia (32), representing potential source for diagnostics and multi-epitope vaccine candidates; and (IV) negative correlations between beneficial bacteria (Blautia, Bacillus, Lactobacillus) and pathogenic species in microbial co-occurrence interaction networks, suggesting opportunities for microbiome-based therapeutic strategies to treat subclinical mastitis. This study demonstrated the advantages of the metatranscriptomics approach and publicly available dual RNA-Seq datasets in unraveling the complexity of polymicrobial infectious diseases
Effects of a fishery closure on the European eel stock on the Swedish west coast
No full textFishing bans are implemented as management measures aimed at rebuilding depleted stocks, albeit with varying levels of success. In 2012, the commercial fishery for the European eel stock on the Swedish west coast was closed to increase the spawning migration from this local stock. However, despite being regarded as one of the most important management measures implemented in Swedish eel management, an assessment of the effects of this fishing closure on the eel stock has not previously been conducted. Here, in an integrated analysis, we use historical catch data in conjunction with standardized fisheries independent fyke-net data from three sites along the Swedish west coast to build a novel stock assessment model to quantify the effects of the fishery closure. The model is length-based, and escapement rates-that is, the rate at which eels escape from the system to migrate to and spawn in the Sargasso Sea-are estimated as an integral part of the analysis. Our results suggest that total escapement has increased fourfold compared to historical levels (compared to 1988-2011) and that the stock has reached its potential maximum escapement under current low recruitment conditions. Hence, the fishing closure seems to have had its intended effect of rebuilding a depleted stock, though it should be acknowledged that post fishing closure estimates of eel escapement are based on survey data from only three local sites. Nevertheless, our study constitutes a rare example of where the effects of management actions targeting European eel have been quantified
Greenhouse gas emissions from ditches in oil palm plantations on tropical peatlands in Malaysia
No full textTropical peatlands, which store 20% of global peat carbon, are increasingly threatened by conversion to alternative land-uses such as oil palm plantations, pulp wood plantations, crop growth or other economic activities. This transformation involves peatland drainage, which lowers water tables, exposes peat to oxygen, and alters greenhouse gas (GHG) emissions: increasing carbon dioxide (CO2) and nitrous oxide (N2O) fluxes while reducing methane (CH4) emissions from soils. However, drainage ditches created in the process may become significant sources of CH4 due to anoxic conditions. This study quantified GHG fluxes from drainage ditches in Sarawak, Malaysia, through spatial sampling conducted during the daytime in the transitional period between the drier and wetter seasons using portable trace gas analyzers. Median fluxes were 0.19 g CH4 m-2 d-1, 17.1 g CO2 m-2 d-1, and - 0.12 mg N2O m-2 d-1. Physical water parameters such as pH, oxygen concentration, temperature, and oxidation-reduction potential were found to be significant drivers of GHG fluxes. The median emissions from ditches in one hectare of land were 5.84 kg CO2 ha-1 d-1, 2.78 kg CH4 as CO2 eq ha-1 d-1, and - 0.001 kg N2O as CO2 eq ha-1 d-1. These findings underscore the role of drainage ditches as CH4 sources in tropical peatland agriculture, highlighting the need for further research into GHG management in these modified landscapes