Effects of different harvest frequencies on microbial community and metabolomic properties of annual ryegrass silage

Responses of microbial community dynamics, co-occurrences, functional shifts, and natural fermentation profiles of Elymus nutans silage to altitudinal gradients

IMPORTANCE

On the Qinghai-Tibet Plateau (QTP), feed shortages are common due to cold environmental conditions and the short growing season of crops. Therefore, effective preservation, such as the ensiling of local forage, is becoming increasingly important to balance the seasonal imbalance between the forage supply and the nutritional needs of domestic animals in this area. However, the structure of the microbial community of the forage, which is influenced by climatic conditions such as altitude differences, has a major impact on the fermentation quality and microbial succession of the ensiled forage. Therefore, we investigated microbial community dynamics, co-occurrence, functional shifts, and natural fermentation profiles of Elymus nutans silage as a function of altitudinal gradients. Results show that silage from Chenduo at higher elevations has better fermentation quality and higher abundance of Lacticaseibacillus and Levilactobacillus than ensiled forage from other regions. This work may contribute to guiding for silage production in QTP.

Integrated microbiology and metabolomic analysis reveal the improvement of rice straw silage quality by inoculation of Lactobacillus brevis

BACKGROUND

Ensiling technology holds promise for preserving and providing high-quality forage. However, the preservation of rice straw poses challenges due to its high lignocellulosic content and low water-soluble carbohydrate levels. Developing highly effective lactic acid bacteria (LAB) for rice straw silage remains a priority.

RESULTS

This study evaluated the impact of three LAB strains, Lactobacillus brevis R33 (Lac33), L. buchneri R17 (Lac17), and Leuconostoc pseudomesenteroides (Leu), on the fermentation quality of rice straw silage. Rice straw silage inoculated with Lac33 alone or in combination with other strains exhibited significantly lower neutral detergent fiber (NDF) (66.5% vs. 72.3%) and acid detergent fiber (ADF) (42.1% vs. 47%) contents, along with higher lactic acid (19.4 g/kg vs. not detected) and propionic acid (2.09 g/kg vs. 1.54 g/kg) contents compared to control silage. Bacterial community analysis revealed Lactobacillus dominance (> 80%) and suppression of unwanted Enterobacter and Clostridium. Metabolomic analysis highlighted increased carbohydrates and essential amino acids, indicating improved nutrient values in Lac33-inoculated rice straw silage and a potential explanation for Lac33 dominance.

CONCLUSIONS

This research identified a highly efficient LAB candidate for rice straw silage, advancing our comprehension of fermentation from integrated microbiology and metabolomic perspectives.

Microbiomics and volatile metabolomics-based investigation of changes in quality and flavor of oat (Avena sativa L.) silage at different stages

Objective

This study aimed to analyze the fermentation quality, microbial community, and volatile metabolites of oat silage harvested at two different stages, while examining the correlation between microorganisms and volatile metabolites.

Methods

Oats were harvested at two growth stages (pre-heading [PRH] and post-heading [POH] stages), followed by 90 days of natural fermentation, with 6 replicates per treatment. Pre- and post-silage samples were randomly selected for nutrient composition, fermentation parameters, microbial population, and high-throughput sequencing analysis. Volatile metabolomics analysis was also performed on samples after 90 days of fermentation to detect differences in flavor quality after silage.

Results

The effect of growth stage on the nutrient content of oats was significant, with pre-heading oats having higher crude protein and post-heading oats having higher water soluble carbohydrates content (p < 0.05). Following a 90-day fermentation period, the pH and ammonia nitrogen/total nitrogen levels in the PRH-90 (silage from pre-heading oats after 90 days of fermentation) group demonstrated a significant decrease (p < 0.05), whereas the lactic acid content was notably higher compared to the POH-90 (silage from post-heading oats after 90 days of fermentation) group (p <0.05). Lactiplantibacillus dominated in the PRH-90 group and Enterococcus dominated in the POH-90 group, with abundances of (> 86%) and (> 87%), respectively. The differential volatile metabolites of the two treatment groups were dominated by esters and terpenoids, and the differences in flavor were mainly concentrated in sweet, green, and fruity odors. The results of Kyoto encyclopedia of genes and genomes pathway enrichment analysis demonstrated three major metabolic pathways: phenylpropanoid biosynthesis, phenylalanine metabolism, and biosynthesis of secondary metabolites. Specific microorganisms were significantly correlated with flavor indicators and flavor metabolites. Lactiplantibacillus was significantly positively correlated with flavor substances indicating sweet and fruity flavors, contributing to good flavor, while Enterococcus was significantly and positively correlated with flavor substances indicating bad flavors.

Conclusion

In summary, growth stage had significant effects on nutritional components, fermentation parameters and flavor quality of oats, with the fermentation process dominated by Lactiplantibacillus leading to good flavor, while the fermentation process dominated by Enterococcus led to the development of poor flavor.

Ensiling hybrid Pennisetum with lactic acid bacteria or organic acids improved the fermentation quality and bacterial community

The aim of this study was to compare the effect of different additives on nutritional quality, fermentation variables and microbial diversity of hybrid Pennisetum silages. A control (CK - no additives) and seven treatments were tested, namely, Lactiplantibacillus plantarum (LP), Lentilactobacillus buchneri (LB), propionic acid (PA), calcium propionate (CAP), LP + LB; LP + PA and LP + CAP. In comparison with CK, all treatments increased the contents of crude protein and lactic acid, decreased the content of butyric acid, and altered the bacterial communities of the silage. Except for the CAP and LP + CAP treatments, the additives decreased pH and the ammonia nitrogen:total nitrogen (NH₃-N:TN) ratio. The results of principal component analysis revealed that the PA, LP + PA and LP + LB treatments ranked as the top three silages. The PA and LP + PA treatments exhibited higher water-soluble carbohydrate content, but lower pH, and NH₃-N:TN ratio than the other treatments. With the PA and LP + PA treatments, the relative abundances of Lactobacillus and Enterobacter decreased, and of Proteobacteria and Delftia increased, while the carbohydrate metabolism of the microorganisms improved. The LP and LB treatments reduced the Shannon and Simpson diversities. In the beta diversity, PA and LP + PA separated from the other treatments, indicating that there were differences in the composition of bacterial species. The relative abundance of Lactobacillus increased in the LP and LB treatments and of Leucanostoc and Weissella increased in the CAP and LP + CAP treatments. In summary, the addition of L. plantarum, L. buchneri, propionic acid, calcium propionate, and their combinations improved fermentation quality, inhibited harmful bacteria and conserved the nutrients of hybrid Pennisetum.

Dry matter content and inoculant alter the metabolome and bacterial community of alfalfa ensiled at high temperature

Alfalfa silage fermentation quality, metabolome, bacterial interactions, and successions as well as their predicted metabolic pathways were explored under different dry matter contents (DM) and lactic acid bacteria (LAB) inoculations. Silages were prepared from alfalfa with DM contents of 304 (LDM) and 433 (HDM) g/kg fresh weight and inoculated with Lactiplantibacillus plantarum (L. plantarum, LP), Pediococcus pentosaceus (P. pentosaceus, PP), or sterile water (control). The silages were stored at a simulated hot climate condition (35°C) and sampled at 0, 7, 14, 30, and 60 days of fermentation. The results revealed that HDM significantly improved the alfalfa silage quality and altered microbial community composition. The GC-TOF-MS analysis discovered 200 metabolites in both LDM and HDM alfalfa silage, mainly consisting of amino acids, carbohydrates, fatty acids, and alcohols. Compared with LP and control, PP-inoculated silages had increased concentrations of lactic acid (P < 0.05) and essential amino acids (threonine and tryptophan) as well as decreased pH, putrescine content, and amino acid metabolism. However, alfalfa silage inoculated with LP had higher proteolytic activities than control and PP-inoculated silage, as revealed by a higher concentration of ammonia nitrogen (NH₃-N), and also upregulated amino acid and energy metabolism. HDM content and P. pentosaceus inoculation significantly altered the composition of alfalfa silage microbiota from 7 to 60 days of ensiling. Conclusively, these results indicated that inoculation with PP exhibited great potential in enhancing the fermentation of silage with LDM and HDM via altering the microbiome and metabolome of the ensiled alfalfa, which could help in understanding and improving the ensiling practices under hot climate conditions. KEY POINTS: • HDM improved fermentation quality and declined putrescine content of alfalfa silage • P. pentosaceus inoculation enhanced the fermentation quality of alfalfa silage • P. pentosaceus is an ideal inoculant for alfalfa silage under high temperature.

Effect of different regions on fermentation profiles, microbial communities, and their metabolomic pathways and properties in Italian ryegrass silage

Introduction

Italian ryegrass is less studied in northern China due to high-quality forage grass has not been fully utilized. Full utilization of high-quality forage grass helps to alleviate the shortage of forage grass in winter and spring season and guarantee stable development of livestock production. Consequently, this study was aimed to evaluate the effects of different regions in northern China on the fermentative products, bacterial community compositions, and metabolic pathways and metabolites of Italian ryegrass silage.

Methods

The Italian ryegrass was harvested from three regions (Ordos-WK; Hohhot-AK; Ulanqab-SYK) and ensiled for 60 days. Single molecule real-time (SMRT) sequencing and ultra-high performance liquid chromatography-mass spectrometry (UHPLC-MS/MS) were used to analyze bacterial communities and metabolites, respectively.

Results

After 60 d of fermentation, the SYK group had the lowest pH (4.67), the highest lactic acid contents (95.02 g/kg DM) and largest lactic acid bacteria populations (6.66 log₁₀ cfu/g FM) among the treatment groups. In addition, the SYK group had the highest abundance of Lactiplantibacillus plantarum (63.98%). In SYK group, isoquinoline alkaloid biosynthesis was the significantly enriched (p < 0.05) and high-impact value (0.0225) metabolic pathway. In AK group, tryptophan metabolism the was the significantly enriched (p < 0.001) and high-impact value (0.1387) metabolic pathway. In WK group, citrate cycle (TCA cycle) was the significantly enriched (p < 0.001) and high-impact value (0.1174) metabolic pathway. Further, Lactiplantibacillus plantarum was positively correlated with cinnamic acid, tetranor 12-HETE, D-Mannitol, (2S)-2-amino-4-methylpentanoic acid L-Leucine, guanine, isoleucyl-aspartate and 3,4-Dihydroxyphenyl propanoate, but negatively correlated with isocitrate and D-mannose.

Discussion

In conclusion, this study can improve our understanding of the ensiling microbiology and metabolomics in different regions to further regulate the fermentation products and promote livestock production.

Effects of growth stage on the fermentation quality, microbial community, and metabolomic properties of Italian ryegrass (Lolium multiflorum Lam.) silage

Introduction

This study aimed to investigate the effects of different growth stages (booting period-SYK; initial flowering-SCK; full flowering-SSK) on the fermentation quality, microbial community, metabolic pathways and metabolomic characteristics of Italian ryegrass silage.

Methods

Single molecule real-time (SMRT) sequencing and ultra-high performance liquid chromatography-mass spectrometry (UHPLC-MS/MS) were used to analyze bacterial communities and metabolites, respectively.

Results

After 60 d of fermentation, SYK had the lowest pH and the highest lactic acid content, which were significantly different from the other groups. The bacteria with the highest abundance in SYK, SCK and SSK groups were Lactiplantibacillus plantarum (63.98%), Weissella minor (28.82%) and Levilactobacillus brevis (64.81%), respectively. In addition, among the main differential metabolites in different growth stages, the number of amino acids was the most, and the corresponding metabolic pathways were mainly amino acid metabolic pathways. The biosynthesis of phenylalanine, tyrosine and tryptophan was significantly enriched (p<0.01) at booting stage and full flowering stage. Purine metabolism and ABC transporter pathway were significantly enriched at the initial flowering (p<0.001). Lactiplantibacillus plantarum had a negative correlation with xanthine and ganoderic acid F. Weissella minor had a positive correlation with D-Mannose and ganoderic acid F. Levilactobacillus brevis had a positive correlation with xanthine, and Latilactobacillus sakei had a positive correlation with cinnamic acid, D-Mannose, 2-Hydroxycinnamic acid and uridine.

Discussion

In conclusion, this study reveals the interaction mechanisms between ryegrass raw materials at different growth stages and epiphytic microorganisms during ensiling fermentation, providing new ideas for screening functional lactic acid bacteria, and laying a theoretical foundation for the production of safe and high-quality silage.

Varieties and ensiling: Impact on chemical composition, fermentation quality and bacterial community of alfalfa

Introduction

Six species of alfalfa commonly found in northern China were collected in the present study.

Methods

The chemical composition and epiphytic microbial communities during the ensiling were analyzed; and their effects on fermentation quality and silage bacterial communities were assessed. The effects of physicochemical characteristics of alfalfa on the bacterial community were also investigated in terms of nutritional sources of microbial growth and reproduction.

Results and discussion

The results showed that the chemical composition was significantly different in various alfalfa varieties, yet, the dominant genera attached to each variety of alfalfa was similar, except for pantoea (p<0.05). After ensiling, both the fermentation quality and microbial community changed obviously (p<0.05). Specifically, ZM2 had lower pH and ammonia nitrogen (NH₃-N) content but higher LA content than other varieties of alfalfa silage. Beneficial bacteria such as Lentilactobacillus and Lactiplantibacillus were predominant in ZM2, which accounted for the higher fermentation quality. Significant correlations between the chemical composition of silage, fermentation quality and bacterial communities composition were observed. Moreover, variations in bacteria community structure during the fermentation of alfalfa were mainly influenced by water-soluble carbohydrates (36.79%) and dry matter (21.77%).

Conclusion

In conclusion, this study revealed the influence of chemical composition on microbial community and fermentation quality, laying the groundwork for future studies on high-quality silage.

Characteristics of lactic acid bacteria, microbial community and fermentation dynamics of native grass silage prepared in Inner Mongolian Plateau

Introduction

To prepare high-quality silage, we studied the chemical composition, silage fermentation, characterization, and identification of lactic acid bacteria (LAB) associated with the silage fermentation of native grass on the Inner Mongolian Plateau.

Methods

LAB were isolated from fresh native grass and their silage, and silages were prepared using a small-scale fermentation system with 2-3 cm length in plastic bags.

Results

The dominant species of native grasses used were Stipa baicalensis, Leymus chinensis, Cleistogenes squarrosa, Melissilus ruthenicus and Pulsatilla turczaninovii, which contained 47.83-59.43 % moisture, 55.12-67.74 % neutral detergent fiber (NDF), and 8.72-14.55 crude protein (CP), and these nutrients did not change greatly during ensiling. Good preservation with a relatively low pH (below 4.44) and high (p < 0.05) lactic acid content (>0.58) was obtained after ensiling. Based on the morphological and biochemical characteristics, these isolates were divided into 12 groups (A-L). All isolate strains were gram-positive and catalase-negative bacteria that produce lactic acid from glucose. Group A-K were cocci, while group L was rod-shaped. Group A-E formed D-lactic acid, but group H-K formed L-lactic acid, and other groups formed DL-lactic acid. Group A-E were heterofermentative, and Group F-L were homofermentative types of LAB. According to the 16S rRNA gene sequences analysis, strains were identified as genus Leuconostoc (A, B, and C), Weissellla (D, E), Pediococcus (F, G), Enterococcus (H, I, J and K), and Lactiplantibacillus (L). Enterococcus (E.) faecium (29.17%, percentage of total isolates) and Pediococcus (P.) acidilactici (18.75%) were the most frequently occurring dominant species.

Discussion

This study suggests that the native grasses contained abundant LAB species, and they can be used as good-quality silages in animal husbandry. In addition, the strains P. acidilactici and E. faecium were the most frequently isolated from native grass silages as dominant species which can be a potentially excellent inoculant for native grass silage.

Preservation characteristics and bacterial communities of crimped ensiled barley grains modulated by moisture content and additive application

Information about the relationships between preservation characteristics and main bacterial communities of fermented feeds can guide decision making during feed preservation and silage additive development. The objective was to evaluate fermentation quality, aerobic stability, microbial quality and bacterial profile of crimped barley grains ensiled under three moisture contents (MC): 228 (low MC), 287 (medium MC) and 345 (high MC) g/kg fresh matter; and using four additive treatments: 1. Control (CONT), 2. Formic and propionic acid-based additive (FPA), 3. Inoculation with homofermentative and heterofermentative strains of lactic acid bacteria (LAB), and 4. Salt-based additive (SALT). There was a quadratic effect (p < 0.05) of incremental MC on pH where greater decline happened from low (5.81) to medium (4.83) MC than from medium to high (4.28) MC, while lactic acid concentration and aerobic stability increased in a linear manner (p < 0.05). Ammonia-N and acetic acid concentrations increased quadratically (p < 0.05) with increasing levels of MC. The effects of additives depended on MC so that improvements in preservation characteristics in response to LAB and SALT were observed at medium and high MC, while FPA was effective at all MC levels. A minor shift was observed in bacterial ecology from raw material towards low MC samples, with Erwiniaceae sp., Enterobacterales spp. and Pseudomonas dominating the fermentation. A major change occurred in medium and high MC materials, where Fructilactobacillus dominated the fermentation in CONT, FPA and SALT silages. LAB-treated silages at medium and high MC resulted in a distinguished pattern with dominance of Lentilactobacillus followed by Lactiplantibacillus. Most abundant communities in the samples, such as Fructilactobacillus, Erwiniaceae sp., Enterobacterales spp. and Pseudomonas, were correlated with several fermentation characteristics. Our results showed that crimped barley grains could be successfully ensiled under various MC and additive treatments. Low MC feeds had higher risk to be aerobically unstable while high MC resulted in more extensive fermentation, with potentially poor fermentation quality. The suitable additive depends on the raw material characteristics as LAB and SALT require relatively high MC to be effective, while FPA showed consistent improvements over all MC levels used in the current study. Awareness of the MC of grain prior to ensiling allows to identify the risks to preservation quality and provides information for choosing an effective additive.

Fermentation quality and bacterial ecology of red clover dominated silage modulated by different management factors

Identification of bacterial communities in both the raw material and the subsequent silages provides new insights into understanding the silage fermentation process. The objective was to evaluate how different silage management factors affect silage preservation characteristics, the microbiome, and their correlations. A red clover dominated sward was used as the raw material and ensiled in pilot scale using a 3 × 4 design, with three management conditions including the level of compaction (loose and tight), and further, for the tightly compacted silages contamination with soil and faeces was conducted; and four different additive treatments with different modes of action: Control without additive (CONT), formic and propionic acid-based additive (FPA), homofermentative lactic acid bacteria inoculant (LAB) and salt-based additive (SALT). Samples of the raw material and subsequent silages were taken and routinely analysed, including DNA extraction and PCR amplification using universal primers. Tight compaction reduced slightly the extent of silage fermentation, but contamination with soil and faeces stimulated a non-desired type of fermentation with higher concentrations of ethanol, acetic acid and propionic acid and a higher pH. Use of LAB and SALT had only minimal effects on silage fermentation, but FPA clearly restricted fermentation and resulted in a better fermentation quality (lower pH, ammonia N and acetic acid concentration) of the silages compared to CONT. The FPA silages presented greater diversity of bacterial communities compared to the other silages. Proteobacteria were the most abundant in raw material, followed by Firmicutes, and major shifts happened in these communities during the silage fermentation process. Weissella was found in small amounts in the raw material but it dominated in the silages. The most abundant communities in the silages, such as Weissella, Lactobacillus and Pseudomonas, were correlated with several silage fermentation characteristics. Use of FPA improved fermentation quality of silages, but SALT and LAB differed from CONT to a smaller extent. All additives modified the bacterial profiles of grasses ensiled under different management conditions. The combination of parameters related to silage quality and bacterial communities provided a deeper understanding of the silage fermentation process and how they can be manipulated to obtain better feed quality.