Dynamics of the bacterial communities and predicted functional profiles in wilted alfalfa silage

Effects of lactic acid bacteria inoculants on the nutrient composition, fermentation quality, and microbial diversity of whole-plant soybean-corn mixed silage

The mixture of whole-plant soybean and whole-plant corn silage (WPSCS) is nutrient balanced and is also a promising roughage for ruminants. However, few studies have investigated the changes in bacterial community succession in WPSCS inoculated with homofermentative and heterofermentative lactic acid bacteria (LAB) and whether WPSCS inoculated with LAB can improve fermentation quality by reducing nutrient losses. This study investigated the effect of Lactobacillus plantarum (L. plantarum) or Lactobacillus buchneri (L. buchneri) on the fermentation quality, aerobic stability, and bacterial community of WPSCS. A 40:60 ratio of whole-plant soybean corn was inoculated without (CK) or with L. plantarum (LP), L. buchneri (LB), and a mixture of LP and LB (LPB), and fermented for 14, 28, and 56 days, followed by 7 days of aerobic exposure. The 56-day silage results indicated that the dry matter content of the LP and LB groups reached 37.36 and 36.67%, respectively, which was much greater than that of the CK group (36.05%). The pH values of the LP, LB, and LPB groups were significantly lower than those of the CK group (p < 0.05). The ammoniacal nitrogen content of LB was significantly lower than that of the other three groups (p < 0.05), and the ammoniacal nitrogen content of LP and LPB was significantly lower than that of CK (p < 0.05). The acetic acid content and aerobic stability of the LB group were significantly greater than those of the CK, LP, and LPB groups (p < 0.05). High-throughput sequencing revealed a dominant bacteria shift from Proteobacteria in fresh forage to Firmicutes in silage at the phylum level. Lactobacillus remained the dominant genus in all silage. Linear discriminant analysis effect size (LEFSe) analysis identified Lactobacillus as relatively abundant in LP-treated silage and Weissella in LB-treated groups. The results of KEGG pathway analysis of the 16S rRNA gene of the silage microbial flora showed that the abundance of genes related to amino acid metabolism in the LP, LB, and LPB groups was lower than that in the CK group (p < 0.05). In conclusion, LAB application can improve the fermentation quality and nutritional value of WPSCS by regulating the succession of microbial communities and metabolic pathways during ensiling. Concurrently, the LB inoculant showed the potential to improve the aerobic stability of WPSCS.

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.

Natural fermentation quality, bacteria, and functional profiles of three cuttings of alfalfa silage in a year in Inner Mongolia, China

Alfalfa is harvested two or three times a year in central and western Inner Mongolia, China. However, the variations in bacterial communities as affected by wilting and ensiling, and the ensiling characteristics of alfalfa among the different cuttings, are not fully understood. To enable a more complete evaluation, alfalfa was harvested three times a year. At each time of cutting, alfalfa was harvested at early bloom, wilted for 6 h, and then ensiled in polyethylene bags for 60 days. The bacterial communities and nutritional components of fresh alfalfa(F), wilted alfalfa(W) and ensiled alfalfa(S), and the fermentation quality and functional profile of bacterial communities of the three cuttings alfalfa silage, were then analyzed. Functional characteristics of silage bacterial communities were evaluated according to the Kyoto Encyclopedia of Genes and Genomes. The results showed that all nutritional components, fermentation quality, bacterial communities, carbohydrate, amino acid metabolism and key enzymes of bacterial communities were influenced by cutting time. The species richness of F increased from the first cutting to the third cutting; it was not changed by wilting, but was decreased by ensiling. At phylum level, Proteobacteria were more predominant than other bacteria, followed by Firmicutes (0.063–21.39%) in F and W in the first and second cuttings. Firmicutes (96.66–99.79%) were more predominant than other bacteria, followed by Proteobacteria (0.13–3.19%) in S in the first and second cuttings. Proteobacteria, however, predominated over all other bacteria in F, W, or S in the third cutting. The third-cutting silage showed the highest levels of dry matter, pH and butyric acid (p &lt; 0.05). Higher levels of pH and butyric acid were positively correlated with the most predominant genus in silage, and with Rosenbergiella and Pantoea. The third-cutting silage had the lowest fermentation quality as Proteobacteria were more predominant. This suggested that, compared with the first and second cutting, the third cutting is more likely to result in poorly preserved silage in the region studied.

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.

Isolation and identification of ligninolytic bacterium (Bacillus cereus) from buffalo (Bubalus bubalis) rumen and its effects on the fermentation quality, nutrient composition, and bacterial community of rape silage

This study aimed to isolate and identify a ligninolytic bacterium from the rumen of buffalo (Bubalus bubalis) and investigate its effects as a silage additive for whole-plant rape. Three lignin-degradation strains were isolated from the buffalo rumen, with AH7-7 being chosen for further experiments. Strain AH7-7, with acid tolerance and a 51.4% survival rate at pH 4, was identified as Bacillus cereus. It exhibited a lignin-degradation rate of 20.5% after being inoculated in a lignin-degrading medium for 8 days. We divided the rape into four groups according to the various additive compositions to examine the fermentation quality, nutritional value, and bacterial community after ensiling: Bc group (inoculated with B. cereus AH7-7 3.0 × 10⁶ CFU g FW^-1), Blac group (inoculated with B. cereus AH7-7 1.0 × 10⁶ CFU g FW^-1, L. plantarum 1.0 × 10⁶ CFU g FW^-1, and L. buchneri 1.0 × 10⁶ CFU g FW^-1), Lac group (inoculated with L. plantarum 1.5 × 10⁶ CFU g FW^-1 and L. buchneri 1.5 × 10⁶ CFU g FW^-1), and Ctrl group (no additives). After 60 days of fermentation, the application of B. cereus AH7-7 was potent in modulating the fermentation quality of silage, especially when combined with L. plantarum and L. buchneri, as indicated by lower dry matter loss and higher contents of crude protein, water-soluble carbohydrate, and lactic acid. Furthermore, treatments with the B. cereus AH7-7 additive decreased the contents of acid detergent lignin, cellulose, and hemicellulose. The B. cereus AH7-7 additive treatments reduced the bacterial diversity and optimized the bacterial community compositions of silage, with an increase in the relative abundance of beneficial Lactobacillus and a decrease in the relative abundance of undesirable Pantoea and Erwinia. Functional prediction revealed that inoculation with B. cereus AH7-7 could increase the cofactors and vitamins metabolism, amino acid metabolism, translation, replication and repair, and nucleotide metabolism, while decreasing the carbohydrate metabolism, membrane transport, and energy metabolism. In brief, B. cereus AH7-7 improved the microbial community, fermentation activity, and ultimately the quality of silage. The ensiling with B. cereus AH7-7, L. plantarum, and L. buchneri combination is an effective and practical strategy to improve the fermentation and nutrition preservation of rape silage.

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.

Evaluating the fermentation characteristics, bacterial community, and predicted functional profiles of native grass ensiled with different additives

Bioaugmentation of native grass ensiling with Lactobacillus plantarum or Lactobacillus buchneri or Pediococcus pentosaceus on the ensiling performance and bacterial community was investigated after 30 days of the fermentation process. The native grass was inoculated with distilled water, Lactobacillus plantarum, Lactobacillus plantarum, and Lactobacillus buchneri, and Lactobacillus plantarum, Lactobacillus buchneri, and Pediococcus pentosaceus as the CON treatment, T1 treatment, T2 treatment, and T3 treatment, respectively. The addition of lactic acid bacteria was added at a total of 1 × 10⁶ colony-forming unit/g of fresh weight. As expected, the markedly (p < 0.05) lower water-soluble carbohydrate content was tested in the T2 and T3 treatments compared to the CON and T1 treatments. Compared to the CON and T1 treatment, significantly (p < 0.05) higher crude protein content, and lower acid detergent fiber and neutral detergent fiber contents were found in the T2 and T3 treatments. Compared to the CON treatment, the pH significantly (p < 0.05) decreased in the lactic acid bacteria (LAB) inoculated silage, and the lowest pH was measured in the T3 treatment. Similarly, significantly higher lactic acid and acetic acid contents were also found in the T3 treatment compared to those in other treatments. After 30 days of ensiling, the Shannon and Chao1 indexes in silages decreased compared to that in the fresh materials (FMs). The principal coordinate analysis indicated that both FM and silage were distinctly separated in each treatment with no interactions on the confidence ellipse (R = 0.8933, p = 0.001). At the phylum level, the dominant phylum was shifted from Proteobacteria to Firmicutes after the fermentation process. Interestingly, Weissella dominated the fermentation in the CON treatment and Lactobacillus dominated the fermentation in all inoculated LAB silages at the genus level. Results of functional prediction analyses showed that the metabolism of amino acid, cofactors, and vitamins, and membrane transport was reduced, while the metabolism of nucleotide and majority carbohydrates was increased after ensiling. The complex LAB (Lactobacillus plantarum, Lactobacillus buchneri, and Pediococcus pentosaceus) exhibited the potential possibility to decrease pH and enhance the relative abundance of LAB in response to obtaining high-quality silage by the synergistic effects. These results suggested that the complex LAB could improve the ensiling performance of native grass silage, and lay a theoretical basis for inoculant application in native grass.

Changes to the microbiome of alfalfa during the growing season and after ensiling with Lentilactobacillus buchneri and Lentilactobacillus hilgardii inoculant

AIMS

This study evaluated changes in epiphytic microbial population of alfalfa (Medicago sativa) during the growing season. First cut forage was harvested to study the effects of an inoculant combining two obligate heterofermentative lactic acid bacteria strains on the bacterial and fungal communities and the fermentation of alfalfa silage.

METHODS AND RESULTS

The epiphytic microbiome of alfalfa was evaluated 10-times during the growing season. Alfalfa wilted to 395.0 g/kg was treated with water (Control) or with a combination of L. buchneri NCIMB 40788 and L. hilgardii CNCM-I-4785 (LBLH). Mini-silos were opened after 1, 4, 8, 16, 32, and 64 days of ensiling. The relative abundance (RA) of the epiphytic bacterial and fungal families varied during the growing season. After 1 day, Weissella was the most abundant genus and present at similar RA in the two treatments (average 80.4%). Compared with Control, LBLH had a higher RA of Lactobacillus at day 1, 16, 32, and 64, and a lower RA of Weissella from day 8 to 64. Control contained more bacteria belonging to the Enterobacteriales than LBLH up to day 16. Inoculated silage had more acetate than Control at day 32 and 64. The fungal population were similar between treatments. The enhanced development and dominance of Lactobacillus in inoculated silage led to greater accumulation of acetate and propionate, which reduced the numbers of culturable yeasts but did not markedly affect the fungal community structure.

CONCLUSIONS

The bacterial community composition of alfalfa stands in the filed changed over time and was affected by cutting. For the ensiling trial, inoculation modified the composition of the bacterial community of alfalfa, increasing the RA of Lactobacillus while reducing the RA of Weissella and of Enterobacteriaceae.

SIGNIFICANCE AND IMPACT OF STUDY

Inoculation increased the RA of Lactobacillus, hampering the dominance of Weissella in the early stages of ensiling, improving antifungal compounds production and reducing the numbers of culturable yeasts.

Innovative utilization of herbal residues: Exploring the diversity of mechanisms beneficial to regulate anaerobic fermentation of alfalfa

In order to increase the utilization of herbal residues, realize efficient utilization of resources, the bacterial community and anaerobic fermentation characteristics of alfalfa ensiling treated with 36 kinds of herbal residues were studied. All the herbal residues improved the anaerobic fermentation quality in different degrees, indicated by lower pH, NH₃-N and butyric acid concentrations. However, the contents of lactic and acetic acids varied widely in silage with different herbal residues. Pearson's correlation analysis showed that the improved fermentation quality was closely associated with the variation of lactic acid bacteria community. Consequently, the herbal residues could improve anaerobic fermentation quality by stimulating desirable Lactobacillus species and inhibiting undesirable microbes. This study provides new insights for efficient utilization of herbal residues.

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

In this study, we analyzed the fermentation quality, microbial community, and metabolome characteristics of ryegrass silage from different harvests (first harvest-AK, second harvest-BK, and third harvest-CK) and analyzed the correlation between fermentative bacteria and metabolites. The bacterial community and metabolomic characteristics were analyzed by single-molecule real-time (SMRT) sequencing and ultra-high-performance liquid chromatography-mass spectrometry (UHPLC-MS/MS), respectively. After 60 days of ensiling, the pH of BK was significantly lower than those of AK and CK, and its lactic acid content was significantly higher than those of AK and CK. Lactiplantibacillus and Enterococcus genera dominate the microbiota of silage obtained from ryegrass harvested at three different harvests. In addition, the BK group had the highest abundance of Lactiplantibacillus plantarum (58.66%), and the CK group had the highest abundance of Enterococcus faecalis (42.88%). The most annotated metabolites among the differential metabolites of different harvests were peptides, and eight amino acids were dominant in the composition of the identified peptides. In the ryegrass silage, arginine, alanine, aspartate, and glutamate biosynthesis had the highest enrichment ratio in the metabolic pathway of KEGG pathway enrichment analysis. Valyl-isoleucine and glutamylvaline were positively correlated with Lactiplantibacillus plantarum. D-Pipecolic acid and L-glutamic acid were positively correlated with Levilactobacillus brevis. L-phenylalanyl-L-proline, 3,4,5-trihydroxy-6-(2-methoxybenzoyloxy) oxane-2-carboxylic acid, and shikimic acid were negatively correlated with Levilactobacillus brevis. In conclusion, this study explains the effects of different harvest frequencies on the fermentation quality, microbial community, and metabolites of ryegrass, and improves our understanding of the ensiling mechanisms associated with different ryegrass harvesting frequencies.

Elucidating the interaction of rhizosphere bacteria and environmental factors in influencing active ingredient content of Lycium barbarum fruit in China

AIMS

This study aimed to compare the differences in the bacterial community structure of L. barbarum rhizosphere and elucidate the contribution of rhizosphere bacteria to the active ingredients of L. barbarum fruit.

METHODS AND RESULTS

This study investigated the soil and meteorological characteristics of L. barbarum rhizosphere during three growth stages across three production regions of China. High-throughput sequencing showed significant differences in the bacterial community diversity of L. barbarum rhizosphere across the three production regions, and norank_o_Gaiellales, norank_f_Anaerolineaceae, and norank_f_AKYG1722 were the highest in Ningxia. In addition, regression and path analysis revealed that pH, norank_o_Gaiellales, and norank_f_AKYG1722 significantly promoted the accumulation of total sugar and flavonoids in L. barbarum fruit directly or indirectly. Soil organic matter (SOM), norank_f_Anaerolineaceae, and humidity significantly promoted the accumulation of betaine. The average temperature during the growth stages, norank_f_AKYG1722, and norank_o_Gaiellales promoted the accumulation of polysaccharides.

CONCLUSIONS

The interaction between rhizosphere bacteria and environmental factors promoted the accumulation of active ingredients in L. barbarum fruits.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our results provided insights to improve the quality of L. barbarum fruit.