Evolution of fungal populations in corn silage conserved under polyethylene or biodegradable films

The bacterial and yeast microbiota in livestock forages in Hungary

BACKGROUND

Along bacteria, yeasts are common in forages and forage fermentations as spoilage microbes or as additives, yet few studies exist with species-level data on these fungi's occurrence in feedstuff. Active dry yeast and other yeast-based products are also common feed additives in animal husbandry. Here, we aimed to characterize both fermented and non-fermented milking cow feedstuff samples from Hungary to assess their microbial diversity in the first such study from Central Europe.

RESULTS

We applied long-read bacterial metabarcoding to 10 fermented and 25 non-fermented types of samples to assess bacterial communities and their characteristics, surveyed culturable mold and yeast abundance, and identified culturable yeast species. Fermented forages showed the abundance of Aerococcaceae, Bacillaceae, Brucellaceae, Lactobacillaceae, Staphylococcaceae, and Thermoactinomycetaceae, non-fermented ones had Cyanothecaceae, Enterobacteriaceae, Erwiniaceae, Gomontiellaceae, Oxalobacteraceae, Rhodobiaceae, Rickettsiaceae, and Staphylococcaceae. Abundances of bacterial families showed mostly weak correlation with yeast CFU numbers, only Microcoleaceae (positive) and Enterococcaceae and Alcaligenaceae (negative correlation) showed moderate correlation. We identified 14 yeast species, most commonly Diutina rugosa, Pichia fermentans, P. kudriavzevii, and Wickerhahomyces anomalus. We recorded S. cerevisiae isolates only from animal feed mixes with added active dry yeast, while the species was completely absent from fermented forages. The S. cerevisiae isolates showed high genetic uniformity.

CONCLUSION

Our results show that both fermented and non-fermented forages harbor diverse bacterial microbiota, with higher alpha diversity in the latter. The bacterial microbiome had an overall weak correlation with yeast abundance, but yeasts were present in the majority of the samples, including four new records for forages as a habitat for yeasts. Yeasts in forages mostly represented common species including opportunistic pathogens, along with a single strain of Saccharomyces used as a feed mix additive.

Ensiling process and pomegranate peel extract as a natural additive in potential prevention of fungal and mycotoxin contamination in silage

A study was conducted on six animal feed centers in Israel where fungal and mycotoxin presence was examined in maize and wheat silages. Fumonisin mycotoxins FB₁ and FB₂ were present in every maize silage sample analyzed. Interestingly, no correlation was found between the occurrence of specific mycotoxins and the presence of the fungal species that might produce them in maize and wheat silages. We further investigated the effect of pomegranate peel extract (PPE) on Fusarium infection and fumonisin biosynthesis in laboratory-prepared maize silage. PPE had an inhibitory effect on FB₁ and FB₂ biosynthesis by Fusarium proliferatum, which resulted in up to 90 % reduction of fumonisin production in silage samples compared to untreated controls. This finding was supported by qRT-PCR analysis, showing downregulation of key genes involved in the fumonisin-biosynthesis pathway under PPE treatment. Our results present promising new options for the use of natural compounds that may help reduce fungal and mycotoxin contamination in agricultural foodstuff, and potentially replace traditionally used synthetic chemicals.

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The mycotoxins fumonisin B₁ and B₂ were detected in all analyzed maize silage samples.

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No correlation was found between mycotoxins and their fungal sources in silages.

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Treatment with PPE demonstrated strong anti-mycotoxigenic activity in silages samples.

Multi-Mycotoxin Contamination of Maize Silages in Flanders, Belgium: Monitoring Mycotoxin Levels from Seed to Feed

Maize silage, which in Europe is the main feed for dairy cattle in winter, can be contaminated by mycotoxins. Mycotoxigenic Fusarium spp. originating from field infections may survive in badly sealed silages or re-infect at the cutting edge during feed-out. In this way, mycotoxins produced in the field may persist during the silage process. In addition, typical silage fungi such as Penicillium spp. and Aspergillus spp. survive in silage conditions and produce mycotoxins. In this research, 56 maize silages in Flanders were sampled over the course of three years (2016-2018). The concentration of 22 different mycotoxins was investigated using a multi-mycotoxin liquid chromatography-tandem mass spectrometry (LC-MS/MS) method, and the presence of DNA of three Fusarium spp. (F. graminearum, F. culmorum and F. verticillioides) was analyzed in a selection of these samples using quantitative polymerase chain reaction (qPCR). Every maize silage contained at least two different mycotoxins. Nivalenol (NIV) and deoxynivalenol (DON) were the most prevalent (both in 97.7% of maize silages), followed by ENN B (88.7%). Concentrations often exceeded the EU recommendations for DON and zearalenone (ZEN), especially in 2017 (21.3% and 27.7% of the maize silages, respectively). No correlations were found between fungal DNA and mycotoxin concentrations. Furthermore, by ensiling maize with a known mycotoxin load in a net bag, the mycotoxin contamination could be monitored from seed to feed. Analysis of these net bag samples revealed that the average concentration of all detected mycotoxins decreased after fermentation. We hypothesize that mycotoxins are eluted, degraded, or adsorbed during fermentation, but certain badly preserved silages are prone to additional mycotoxin production during the stable phase due to oxygen ingression, leading to extremely high toxin levels.

Effect on the ensilage performance and microbial community of adding Neolamarckia cadamba leaves to corn stalks

To comprehensively evaluate the fermentation performance and microbial community of corn stalks (CS) silage mixed with Neolamarckia cadamba leaves (NCL), CS were ensiled with four levels (0%, 10%, 30% and 50% of fresh weight) of NCL for 1, 7, 14, 30, 60 days in two trials. The results showed that all silages were well preserved with low pH (3.60-3.88) and ammonia nitrogen content (0.08-0.19% DM). The silage samples with NCL displayed lower (P < 0.05) acetic acid, propionic acid and ammonia nitrogen contents and lactic acid bacteria population during ensiling than control silages (100% CS). The addition of NCL also influenced the distribution of bacterial and fungal communities. Fungal diversity (Shannon's indices were 5.15-5.48 and 2.85-4.27 in trial 1 and trial 2 respectively) increased while the relative abundances of Lactobacillus, Leuconostocs, Acetobacter and two moulds (Aspergillus and Fusarium) decreased after added NCL. In summary, mixing NCL is a promising effective approach to preserve protein of CS silage and inhibit the growth of undesirable bacteria and mould, thus to improve the forage quality to some extent.

Feasibility of Utilizing Biodegradable Plastic Film to Cover Corn Silage under Farm Conditions

The degree of anaerobiosis and its maintenance over the conservation period are key factors in obtaining high quality silage. There is currently a demand to replace petroleum-based plastic films with biodegradable materials with suitable mechanical properties. This work has evaluated, under outdoor conditions, the shelf life of a Mater-Bi® biodegradable plastic (MB) film and its effects on the fermentative characteristics, microbial counts and aerobic stability of corn silage, and compared it with commercially available polyethylene (PE) and high oxygen barrier (OB) films. Corn (409 g DM/kg) was ensiled in 30 drive-over piles covered with MB, PE or OB films. The piles were opened after 21, 85, 133, 195 and 230 d of conservation. The effect of the film was assessed in silage sample close to (CF) and far (FF) from the film. The OB film allowed high quality corn silages to be obtained with similar pH, lactic acid, yeast and mold counts for CF and FF during the entire 230 d of conservation. The PE film showed similar values for the FF and CF areas for the first conservation period (until 133 d). The MB film showed a similar silage quality to OB until day 85, after which it underwent biodegradation and lost its ability to preserve silage in a good state.

Aspergillus fumigatus population dynamics and sensitivity to demethylation inhibitor fungicides in whole-crop corn, high moisture corn and wet grain corn silages

BACKGROUND

Aspergillus fumigatus, the causal agent of aspergillosis in humans, is commonly present as a saprophyte in various organic substrates, such as spoiled silages. Aspergillosis is generally combated with demethylation inhibitor (DMI) fungicides, but the recent appearance of resistant medical and environmental strains made current treatment strategies less reliable. The goal of this study was to determine the evolution of A. fumigatus populations during the ensiling process of whole-crop corn, high moisture corn and wet grain corn, and to monitor the sensitivity of isolates from treated and untreated fields to one medical and one agricultural DMI fungicide.

RESULTS

A. fumigatus was isolated from fresh forage at harvest at rather low concentrations (10²  cfu g^-1 ). The low frequency lingered during the silage process (at 60 and 160 days), whereas it significantly increased during air exposure (at 7 and 14 days of air exposure). Field treatment of corn with a mixture of prothioconazole and tebuconazole did not affect the sensitivity of A. fumigatus isolates. One of 29 isolates from the untreated plot was resistant to voriconazole. A unique amino acid substitution (E427K) was detected in the cyp51A gene of 10 of 12 sequenced isolates, but was not associated with DMI resistance.

CONCLUSION

A. fumigatus significantly increased during aerobic deterioration of ensilaged corn after silo opening, compared with the low presence in fresh corn and during ensiling. Field treatment of corn with DMI fungicides did not affect the sensitivity of A. fumigatus isolates collected from fresh and ensiled corn. © 2019 Society of Chemical Industry.

Impact of Saccharomyces cerevisiae and Lactobacillus buchneri on microbial communities during ensiling and aerobic spoilage of corn silage1

The objective of this study was to assess the impact of Saccharomyces cerevisiae in combination with Lactobacillus buchneri on the fermentation characteristics, aerobic stability, nutritive value, and microbial communities of corn silage. Whole crop corn (39% DM) was either uninoculated (Control) or inoculated with S. cerevisiae and L. buchneri at the following concentrations: S. cerevisiae 104 cfu/g fresh forage (S4), S. cerevisiae 105 cfu/g (S5), S. cerevisiae 104 cfu/g + L. buchneri 105 cfu/g (S4L5), and S. cerevisiae 105 cfu/g + L. buchneri 104 cfu/g (S5L4), and ensiled in mini silos for 118 d, followed by 7 d of aerobic exposure. Changes in fermentation characteristics and nutritive value were assessed in terminal silages. Saccharomyces cerevisiae, L. buchneri, and total yeast, fungal, and bacterial communities in silage were estimated using quantitative PCR. Composition of bacterial and fungal communities during ensiling and aerobic exposure was measured using 16S rDNA and ITS sequencing, respectively. In the first 7 d of ensiling, the concentration of lactic acid rapidly increased (P < 0.01) in all silages, with the pH declining to 4.0 (P < 0.001) and thereafter remaining stable (P = 0.23). Although S4L5 contained a higher (P = 0.03) concentration of acetic acid than Control, other fermentation characteristics were did not differ among terminal silages. Inoculation with S. cerevisiae had no detrimental effect on the aerobic stability of silage, whereas L. buchneri did not prevent spoilage as the pH across all silages averaged 8.0 after 7 d of aerobic exposure. Total yeast (P = 0.42), bacterial (P = 0.13), and fungal (P = 0.89) communities were not altered by the inoculants after ensiling or aerobic exposure. Sequencing identified temporal shifts of bacterial and fungal communities during ensiling and aerobic exposure. Concentrations of S. cerevisiae and L. buchneri in all inoculated silages remained greater (P < 0.01) than Control after ensiling, with numbers of S. cerevisiae increasing after 7 d of aerobic exposure. Bacterial communities in silages inoculated with S. cerevisiae and L. buchneri clustered separately from other silages, an observation that was not apparent for fungal communities. Our findings suggest that aerobic exposure could potentially increase the abundance of S. cerevisiae with probiotic properties in corn silage just prior to feeding.

Characterization of Tifton 85 bermudagrass haylage with different layers of polyethylene film and storage time

OBJECTIVE

The objective was to characterize the fermentative and microbiological profile of Tifton 85 bermudagrass haylage with different layers of polyethylene film and storage time.

METHODS

The experimental design consisted of a randomized block design with four and six wrapping layers (100 and 150 microns in total. respectively) allocated in the main plots, through repeated measures analysis (30, 60, and 90 days of storage) with four replicates.

RESULTS

The storage time and number of wrapping layers did not show changes in the population of Clostridium and lactic acid bacteria. A decrease was observed in the enterobacteria population with an increase in the storage period in the two wrapping layers studied. Upon opening of the haylage at 30 days, the population of Bacillus was lower in haylages made with six layers of wrapping (3.63 log colony forming units/g). No growth of Listeria sp. or Salmonella sp. was observed during the experimental period. The fungal genera with a greater occurrence were Penicillium sp. and Fusarium sp. The following mycotoxins were not detected: ochratoxin A, fumonisins, and zearalenone. Relative to the organic butyric, propionic, and acetic acids, the haylages presented a low concentration of lactic acid; this may have prevented a drop in the pH, which was high when the silos were opened (5.4). The levels of ammoniacal nitrogen and soluble carbohydrates presented no variation among the number of wrapping layers, with an overall average of 35.55 and 38.04 g/kg.

CONCLUSION

Tifton 85 bermudagrass haylage wrapped with four and six layers presented adequate fermentation and microbiological characteristics in the evaluated periods.

Molecular characterization and sensitivity to demethylation inhibitor fungicides of Aspergillus fumigatus from orange-based compost

Aspergillus fumigatus, the causal agent of human aspergilloses, is known to be non-pathogenic in plants. It is present as saprophyte in different types of organic matter and develops rapidly during the high-temperature phase of the composting process. Aspergilloses are treated with demethylation inhibitor (DMI) fungicides and resistant isolates have been recently reported. The present study aims to estimate the abundance, genetic diversity and DMI sensitivity of A. fumigatus during the composting process of orange fruits. Composting of orange fruits resulted in a 100-fold increase in A. fumigatus frequency already after 1 week, demonstrating that the degradation of orange fruits favoured the growth of A. fumigatus in compost. Most of A. fumigatus isolates belonged to mating type 2, including those initially isolated from the orange peel, whereas mating type 1 evolved towards the end of the composting process. None of the A. fumigatus isolates expressed simultaneously both mating types. The 52 investigated isolates exhibited moderate SSR polymorphisms by formation of one major (47 isolates) and one minor cluster (5 isolates). The latter included mating type 1 isolates from the last sampling and the DMI-resistant reference strains. Only few isolates showed cyp51A polymorphisms but were sensitive to DMIs as all the other isolates. None of the A. fumigatus isolates owned any of the mutations associated with DMI resistance. This study documents a high reproduction rate of A. fumigatus during the composting process of orange fruits, requesting specific safety precautions in compost handling. Furthermore, azole residue concentrations in orange-based compost were not sufficient to select A. fumigatus resistant genotypes.

Abundance, genetic diversity and sensitivity to demethylation inhibitor fungicides of Aspergillus fumigatus isolates from organic substrates with special emphasis on compost

BACKGROUND

Aspergillus fumigatus is a widespread fungus that colonizes dead organic substrates but it can also cause fatal human diseases. Aspergilloses are treated with demethylation inhibitor (DMI) fungicides; however, resistant isolates appeared recently in the medical and also environmental area. The present study aims at molecular characterizing and quantifying A. fumigatus in major environmental habitats and determining its sensitivity to medical and agricultural DMI fungicides.

RESULTS

A. fumigatus was isolated only rarely from soil and meadow/forest organic matter but high concentrations (10³ to 10⁷  cfu/g) were detected in substrates subjected to elevated temperatures, such as compost and silage. High genetic diversity of A. fumigatus from compost was found based on SSR markers, distinguishing among fungal isolates even when coming from the same substrate sample, while subclustering was observed based on mutations in cyp51A gene. Several cyp51A amino acid substitutions were found in 15 isolates, although all isolates were fully sensitive to the tested DMI fungicides, with exception of one isolate in combination with one fungicide.

CONCLUSION

This study suggests that the tested A. fumigatus isolates collected in Italy, Spain and Hungary from the fungus' major living habitats (compost) and commercial growing substrates are not potential carriers for DMI resistance in the environment. © 2017 Society of Chemical Industry.

Redefining Agricultural Residues as Bioenergy Feedstocks

The use of plant biomass is a sustainable alternative to the reduction of CO₂ emissions. Agricultural residues are interesting bioenergy feedstocks because they do not compete with food and add extra value to the crop, which might help to manage these residues in many regions. Breeding crops for dual production of food and bioenergy has been reported previously, but the ideal plant features are different when lignocellulosic residues are burnt for heat or electricity, or fermented for biofuel production. Stover moisture is one of the most important traits in the management of agricultural waste for bioenergy production which can be modified by genetic improvement. A delayed leaf senescence or the stay-green characteristic contributes to higher grain and biomass yield in standard, low nutrient, and drought-prone environments. In addition, the stay-green trait could be favorable for the development of dual purpose varieties because this trait could be associated with a reduction in biomass losses and lodging. On the other hand, the stay-green trait could be detrimental for the management of agricultural waste if it is associated with higher stover moisture at harvest, although this hypothesis has been insufficiently tested. In this paper, a review of traits relevant to the development of dual purpose varieties is presented with particular emphasis on stover moisture and stay-green, because less attention has been paid to these important traits in the literature. The possibility of developing new varieties for combined production is discussed from a breeding perspective.