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Microbiome predators in changing soils
No full textMicrobiome predators shape the soil microbiome and thereby soil functions. However, this knowledge has been obtained from small-scale observations in fundamental rather than applied settings and has focused on a few species under ambient conditions. Therefore, there are several unaddressed questions on soil microbiome predators: (1) What is the role of microbiome predators in soil functioning? (2) How does global change affect microbiome predators and their functions? (3) How can microbiome predators be applied in agriculture? We show that there is sufficient evidence for the vital role of microbiome predators in soils and stress that global changes impact their functions, something that urgently needs to be addressed to better understand soil functioning as a whole. We are convinced that there is a potential for the application of microbiome predators in agricultural settings, as they may help to sustainably increase plant growth. Therefore, we plea for more applied research on microbiome predators
CAN PREDATORS MITIGATE SOILBORNE DISEASES?
No full textSoil predators are of central importance in regulating the interaction between plants, soil, and
microbiota via a top-down control of microbes, including plant pathogens, and increased
nutrient cycling. Infections by plant pathogens trigger defence, can alter the host metabolism
and nutrient flow into the soil, leading to changes which feed-back to the soil microbiome.
However, the links between soilborne pathogens, soil predators and the soil microbiome are
only starting to be explored. We used the clubroot pathogen Plasmodiophora brassicae - a
major obstacle for the cultivation of Brassica worldwide with no effective control options - to
investigate disease induced changes of the soil microbiome and the role of soil predators in
clubroot disease development. We aim to identify potentially disease suppressive and
disease conducive predators and microbiome members, including bacteria, fungi and protist
and other top-down controller. We combined soil physicochemical analyses with longamplicon sequencing to decipher underlying drivers of taxonomic and functional changes in
the microbiome to clubroot infections in field and greenhouse experiments. Additionally,
feeding behaviour of soil predators on clubroot spores was investgated. We present insights
of the potential of soil predators to control soilborne diseases such as clubroot that might
lead to new biocontrol applications for soilborne pathogens in the future
The sensegiving role of advisors in farmer decision-making
Get PDFpeer-reviewedpeer-reviewedIn Ireland, and in several other countries around the world, a situation of economic vulnerability exists for many
farmers. Alongside this economic vulnerability, the farm management literature acknowledges that most farmers
spend little time on financial management. In this context, we argue that farm advisory services have the potential
to add value to the farming community by assisting farmers to make informed financial decisions, to combat
these economic challenges. In this study, the role of professional advisors in the strategic financial decisionmaking
process of farmers is explored to develop an understanding of how farmers avail of advice from, and
interact with, farm advisors. A qualitative research approach of 27 semi-structured interviews and a focus group
is adopted to explore the strategic financial decision-making process of farmers. The application of sensemaking
theory helps us understand how advisors provide a sensegiving role in the farmer’s decision-making process.
The evidence gathered identifies numerous professional advice sources that provide this sensegiving role in the
strategic financial decision-making process of farmers but contends that two sources, accountants and agricultural
consultants, appear most prominent. This study also reveals that the use of specific advice sources is strongly
influenced by the type of strategic decision undertaken and the farm type in operation. The results provide an
opportunity for policymakers, and those who provide advisory services to farmers, to reflect on how best to create
an environment where farmers and farm advisors can work together, to develop sustainable farm enterprises which
can contribute to rural development
Comparison of the relative impacts of acute consumption of an inulin-enriched diet, milk kefir or a commercial probiotic product on the human gut microbiome and metabolome
Get PDFpeer-reviewedIt has been established that the human gut microbiota is central to health, and, consequently, there has been a growing desire to positively modulate its composition and/or function through, for example, the use of fermented foods, prebiotics or probiotics. Here, we compare the relative impact of the daily consumption of an inulin-enriched diet (n = 10), a commercial probiotic-containing fermented milk product (FMP) (n = 10), or a traditional kefir FMP (n = 9), over a 28-day period on the gut microbiome and urine metabolome of healthy human adults. None of the treatments resulted in significant changes to clinical parameters or biomarkers tested. However, shotgun metagenomic analysis revealed that kefir consumption resulted in a significant change in taxonomy, in the form of an increased abundance of the sub-dominant FMP-associated species Lactococcus raffinolactis, which further corresponded to shifts in the urine metabolome. Overall, our results indicated that daily consumption of a single portion of kefir alone resulted in detectable changes to the gut microbiota and metabolome of consumers
Comparison of antimicrobial resistant Escherichia coli isolated from Irish commercial pig farms with and without zinc oxide and antimicrobial usage
Get PDFpeer-reviewedBackground
The prophylactic use of antimicrobials and zinc oxide (ZnO) in pig production was prohibited by the European Union in 2022 due to potential associations between antimicrobial and heavy metal usage with antimicrobial resistance (AMR) and concerns regarding environmental pollution. However, the effects of their usage on the bacterial AMR profiles on commercial pig farms are still not fully understood and previous studies examining the effect of ZnO have reported contrasting findings. The objective of this study was to examine the effects of antimicrobial and ZnO usage on AMR on commercial pig farms. Faecal and environmental samples were taken on 10 Irish commercial farms, of which 5 farms regularly used ZnO and antimicrobials (amoxicillin or sulphadiazine-trimethoprim) for the prevention of disease. The other 5 farms did not use ZnO or any other form of prophylaxis. Escherichia coli numbers were quantified from all samples using non-supplemented and supplemented Tryptone Bile X-glucuronide agar.
Results
In total 351 isolates were phenotypically analysed, and the genomes of 44 AmpC/ESBL-producing E. coli isolates from 4 farms were characterised using whole-genome sequencing. Phenotypic analysis suggested higher numbers of multi-drug resistant (MDR) E. coli isolates on farms using prophylaxis. Furthermore, farms using prophylaxis were associated with higher numbers of isolates resistant to apramycin, trimethoprim, tetracycline, streptomycin, and chloramphenicol, while resistance to ciprofloxacin was more associated with farms not using any prophylaxis. Thirty-four of the 44 AmpC/ESBL-producing E. coli strains harboured the blaCTX-M-1 resistance gene and were multi drug resistant (MDR). Moreover, network analysis of plasmids and analysis of integrons showed that antimicrobial and biocide resistance genes were frequently co-located on mobile genetic elements, indicating the possibility for co-selection during antimicrobial or biocide usage as a contributor to AMR occurrence and persistence on farms.
Conclusions
The results of this study showed evidence that antimicrobial and ZnO treatment of pigs post-weaning can favour the selection and development of AMR and MDR E. coli. Co-location of resistance genes on mobile genetic elements was observed. This study demonstrated the usefulness of phenotypic and genotypic detection of antimicrobial resistance by combining sequencing and microbiological methods
Assessing the feasibility, fidelity and acceptability of a behaviour change intervention to improve tractor safety on farms: protocol for the BeSafe tractor safety feasibility study
Get PDFpeer-reviewedBackground
In Ireland, the agriculture sector reports the highest number of fatalities even though farmers constitute only 6% of the working population. Tractor-related behaviours are implicated in 55% of all vehicle work-related fatalities and 25% of reported injuries, and many of these occur in farmyards. There is limited research on the feasibility and acceptability of behaviour change interventions to improve tractor safety. Target behaviours that promote safe operation in farmyards, determining and addressing blind spots of tractors, were identified, and an intervention was developed following the Behaviour Change Wheel Approach. The objective of the study is to examine the feasibility, fidelity and acceptability of a behaviour change intervention to enhance the safe operation of tractors in farmyards with a particular focus on tractor blind spots.
Method
A single group feasibility study will be undertaken. Approximately 16 farmers from four major farm types will be recruited for the study between August and September 2022. The intervention involves an in-person demo session, facilitated discussion and personalised safety training procedure with safety goals. The study will collect data from participants at three time points: baseline (3–10 days prior to the intervention), during the intervention and at the follow-up session (7–30 days post-intervention). Quantitative data will be collected through a pre-intervention interview and feedback surveys. A pre- and post-intervention qualitative interview will also be conducted with the participants and will be supplemented with qualitative data from recruitment logs, observational memos and logs and feedback from recruiters. Evaluation of the feasibility, acceptability and fidelity of the intervention will be guided by a pre-determined feasibility checklist, fidelity framework and theoretical framework of acceptability, respectively. Interviews will be analysed using the content analysis.
Discussion
The current study can determine the feasibility and fidelity of delivering a systematic, theoretically driven, tailored behaviour change intervention. It will also assess whether the intervention, its ingredients and delivery are acceptable to the farming population. This study will also inform the development of a future larger trial to test the effectiveness of the intervention.
Trial registration
ISRCTN Identifier: ISRCTN22219089. Date applied 29 July 202
Analysing biomarkers in oral fluid from pigs: influence of collection strategy and age of the pig
Get PDFpeer-reviewedBackground and objectives
Oral fluid (OF) is an easy-to-collect, inexpensive, fast and non-invasive sample to characterize health and welfare status of the pig. However, further standardisation of the collection methods is needed in order to use it regularly in veterinary practice. Cotton ropes are routinely used to collect OF for pathogen detection but they may not be optimal for biomarker analysis due to sample contamination. This study compared two methods (cotton ropes and sponges) to collect porcine OF for biomarker analysis. A panel of 11 biomarkers of stress, inflammation, sepsis, immunity, redox status and general homeostasis was studied.
Materials and methods
Eighteen farrow-to-finish pig farms were included in the study. In each farm, three (for sponges) or four pens of pigs (for ropes) were sampled at four age categories: the week after weaning (5 weeks), before (11–12 weeks) and after (12–13 weeks) moving to finisher facility and the week before slaughter (22–25 weeks). In total, 288 OF samples were collected with cotton ropes and 216 with sponges and analysed for the biomarkers: cortisol, alpha-amylase, oxytocin (stress), haptoglobin (inflammation), procalcitonin (sepsis), adenosine deaminase, immunoglobulin G (immune system), ferric reducing antioxidant power (redox status), and creatine kinase, lactate dehydrogenase and total protein (general homeostasis). Samples were also scored visually for dirtiness using a score from 1 (clean) to 5 (very dirty).
Results
Rope-collected OF had higher levels of dirtiness (3.7 ± 0.04) compared to sponge-collected OF (2.7 ± 0.15) and had higher values than sponges for cortisol, procalcitonin, oxytocin, haptoglobin, total protein, lactate dehydrogenase and ferric reducing antioxidant power. All biomarkers decreased in value with age. Immunoglobulin G did not perform well for any of the two collection methods.
Discussion and conclusion
The results showed a clear effect of age on the biomarkers in OF collected with both, sponges or ropes. Sponges provided a cleaner sample than cotton ropes for biomarker analysis. Both methods are easy to apply under the commercial conditions in pig farms although sponges may take more time in early weaner stages. From a practical point of view, sampling with sponges achieved the best combination of reduced sampling time and low contamination
Towards a Systems Biology View of Mitochondria in the Animal Production Industries
No full textThe mitochondria are largely responsible for converting the chemical energy derived from animal feed into the biologically usable form of intracellular ATP. The energy liberated during the subsequent hydrolysis of the ATP pool ‘foots the bioenergetic bill’ that underpins all manner of commercial traits. Because mitochondrial function is conserved across the Eukaryotes, this energy transformation is relevant to all farm species and all production systems. Particular interest has been directed towards understanding the cellular basis of the overtly bioenergetic whole animal phenotypes, especially feed efficiency. However, mitochondrial associations have also been identified for a range of other live animal, carcass, and meat quality traits.
The mitochondrion is challenging to model. It is composed of ~1500 proteins derived from two structurally independent yet co-ordinately regulated genomes. Its various biological functions, of which aerobic combustion of feed energy is just one, are a product of mitochondrial content and mitochondrial activity. Mitochondrial content is dramatically expanded in circumstances of high energetic demand. For example, the pectoralis muscle of a hummingbird boasts a tissue mitochondrial content (35%) ~10-fold higher than that of sedentary but extremely feed efficient broiler chickens (2-4%).
With a view to determining functional variation across populations of farm animals, we have developed high throughput molecular assays for estimating individual mtDNA copy number (as a proxy for tissue mitochondrial content) in broilers, sheep, and cattle. In broilers we found 1) systemic regulation across the musculature and 2) negative correlations of mitochondrial content with muscle mass. Similarly, in sheep we have found 1) systemic regulation in digestive tissue and liver and 2) that liver is the tissue whose content is most responsive to caloric intake.
Mitochondrial activity on the other hand can be approximated by measuring oxygen consumption. Unlike content, which takes months to adjust (e.g. the gradual training effect resulting from an endurance regimen), activity can alter over a few seconds (e.g. oxygen consumption at rest versus exercise). We have found that cultured peripheral blood mononuclear cells from horses seropositive for Ross River virus infection have impaired metabolic flux on a per unit mitochondrial basis but restore overall cellular performance via a compensatory increase in mitochondrial content.
A second challenge with understanding function lies in interpreting ‘omics’ data sets. For example, one study found that in rumen epithelia of steers the most feed efficient individuals had higher expression of mRNA-encoding mitochondrial proteins but lower mtDNA copy numbers. Given these challenges, we advocate measuring mitochondrial function at multiple levels of biological organisation.
As part of a strategy to better understand mitochondrial function, we have reconstructed a high-resolution co-expression network comprising 872 nodes and 12,445 edges. The network was based on publicly available data from the Cattle Gene Atlas comprising 723 RNA-seq libraries across 91 tissues from 447 individuals. Cluster analysis identified discrete modules reflecting the mtDNA genome, and those encoded proteins localising to the matrix and the inner mitochondrial membrane, respectively. This mitochondrial network can be used as a framework for interpreting molecular measurements from any tissue of any farm species
Formation mechanisms of ethyl acetate and organic acids in Kluyveromyces marxianus L1-1 in Chinese acid rice soup
Get PDFpeer-reviewedThis study aims to explore the formation mechanism of ethyl acetate and organic acids in acid rice soup (rice-acid soup) inoculated with Kluyveromyces marxianus L1-1 through the complementary analysis of transcriptome and proteome. The quantity of K. marxianus L1-1 varied significantly in the fermentation process of rice-acid soup and the first and third days were the two key turning points in the growth phase of K. marxianus L1-1. Importantly, the concentrations of ethyl acetate, ethanol, acetic acid, and L-lactic acid increased from day 1 to day 3. At least 4231 genes and 2937 proteins were identified and 610 differentially expressed proteins were annotated to 30 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways based on the analysis results of transcriptome and proteome. The key genes and proteins including up-regulated alcohol dehydrogenase family, alcohol O-acetyltransferase, acetyl-CoA C-acetyltransferase, acyl-coenzyme A thioester hydrolase, and down-regulated aldehyde dehydrogenase family were involved in glycolysis/gluconeogenesis pathways, starch and sucrose metabolism pathways, amino sugar and nucleotide sugar metabolism pathways, tricarboxylic acid (TCA) cycle, and pyruvate metabolism pathways, thus promoting the formation of ethyl acetate, organic acids, alcohols, and other esters. Our results revealed the formation mechanisms of ethyl acetate and organic acids in rice-acid soup inoculated with K. marxianus L1-1
Drought intensity alters productivity, carbon allocation and plant nitrogen uptake in fast versus slow grassland communities
No full textGrasslands face more frequent and extreme droughts; yet, their responses to increasing drought intensity are poorly understood. Increasing drought intensity likely triggers abrupt shifts (thresholds) in grassland ecosystem functioning which can implicate recovery trajectories.
Here, we determined how drought intensity affects plant productivity, and plant–soil carbon (C) and nitrogen (N) cycling. We exposed model grassland plant communities with contrasting resource acquisition strategies (a fast- vs a slow-strategy plant community), to a gradient of drought intensity. The drought gradient ranged from well-watered to severely water-limited conditions. We identified thresholds of plant community productivity (above-ground biomass) at peak drought and 2 months after re-wetting, and measured net ecosystem exchange and ecosystem respiration of C throughout the drought and recovery phases. At peak drought and 1 week after re-wetting, we traced recently acquired C from plants to the soil and into microbial biomass and fatty acids using 13C pulse labelling, and measured plant and soil N.
At peak drought, slow-strategy plant communities were more drought resistant than fast-strategy communities, as the threshold in plant productivity occurred at a higher drought intensity for the slow- than the fast-strategy community. Shortly after re-wetting, microbial uptake of recent plant-assimilated C increased with increasing past drought intensity, coinciding with an increase in soil N availability and leaf N. Threshold responses to drought intensity at peak drought translated into non-linear recovery responses, with greater compensatory growth in the fast-strategy community. At peak drought, increasing drought intensity reduced C uptake and increased relative C partitioning to leaves and microbial biomass. Upon re-wetting, plant community strategy mediated drought intensity effects on plant and soil C and N dynamics and plant recovery trajectories. The fast-strategy community recovered quickly, with higher leaf N than the slow community, while the slow community increased C allocation to microbial biomass.
Synthesis. Our findings highlight that C and N dynamics in the plant–soil system display non-linear responses to increasing drought intensity both during and after drought, which has implications for plant community recovery trajectories