Bacterial communities associated with silage of different forage crops in Malaysian climate analysed using 16S amplicon metagenomics

Utilisation of Lactiplantibacillus plantarum and propionic acid to improve silage quality of amaranth before and after wilting: fermentation quality, microbial communities, and their metabolic pathway

Objective

The aim of this study was to investigate the effects of Lactiplantibacillus plantarum (L. plantarum) and propionic acid (PA) on fermentation characteristics and microbial community of amaranth (Amaranthus hypochondriaus) silage with different moisture contents.

Methods

Amaranth was harvested at maturity stage and prepared for ensiling. There were two moisture content gradients (80%: AhG, 70%: AhS; fresh material: FM) and three treatments (control: CK, L. plantarum: LP, propionic acid: PA) set up, and silages were opened after 60 d of ensiling.

Results

The results showed that the addition of L. plantarum and PA increased lactic acid (LA) content and decreased pH of amaranth after fermentation. In particular, the addition of PA significantly increased crude protein content (p < 0.05). LA content was higher in wilted silage than in high-moisture silage, and it was higher with the addition of L. plantarum and PA (p < 0.05). The dominant species of AhGLP, AhSCK, AhSLP and AhSPA were mainly L. plantarum, Lentilactobacillus buchneri and Levilactobacillus brevis. The dominant species in AhGCK include Enterobacter cloacae, and Xanthomonas oryzae was dominated in AhGPA, which affected fermentation quality. L. plantarum and PA acted synergistically after ensiling to accelerate the succession of dominant species from gram-negative to gram-positive bacteria, forming a symbiotic microbial network centred on lactic acid bacteria. Both wilting and additive silage preparation methods increased the degree of dominance of global and overview maps and carbohydrate metabolism, and decreased the degree of dominance of amino acid metabolism categories.

Conclusion

In conclusion, the addition of L. plantarum to silage can effectively improve the fermentation characteristics of amaranth, increase the diversity of bacterial communities, and regulate the microbial community and its functional metabolic pathways to achieve the desired fermentation effect.

Method to evaluate the microbial degradation activity in silage, cow rumen with in vitro test, and in manure and slurry

Microorganisms are present everywhere and can influence a variety of processes. In agriculture and husbandry, the level of microbial activity can be crucial information, yet the methods for determining microbial activity are usually very long, complex, and costly. In this work, a novel and easy-to-use method, already in use for determining soil microbial activity, named Fertimetro was tested as a fast and cheap solution for measuring microbial activity in silages, in vitro rumen fluids, and manure and slurry. The method was adjusted for the specific conditions of the new testing environments. The results indicate that this method is adequate for measuring cellulolytic microbial activity in vitro rumen fluids, with a coefficient of repeatability (RT%) 92.2 at 24 h and 87.5 at 48 h, and also for cellulolytic microbial activity measures in manure RT% 39.0. While, due to the specific conditions in silages and slurry, this method is less adequate for measuring cellulolytic microbial activity in these environments. This work demonstrates that Fertimetro method can be used in different environments as an easy and cheaper alternative for measuring microbial activity, especially if the interest is only in quantifying the microbial activity and not in knowing the microbial species.1.Fertimetro is an easy-to-use and not costly method to evaluate microbial activity in different environments.2.This method is very adequate for measuring cellulolytic microbial activity in vitro rumen fluids and manure.

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.

Influences of Growth Stage and Ensiling Time on Fermentation Characteristics, Nitrite, and Bacterial Communities during Ensiling of Alfalfa

This study examined the impacts of growth stage and ensiling duration on the fermentation characteristics, nitrite content, and bacterial communities during the ensiling of alfalfa. Harvested alfalfa was divided into two groups: vegetative growth stage (VG) and late budding stage (LB). The fresh alfalfa underwent wilting until reaching approximately 65% moisture content, followed by natural fermentation. The experiment followed a completely randomized design, with samples collected after the wilting of alfalfa raw materials (MR) and on days 1, 3, 5, 7, 15, 30, and 60 of fermentation. The growth stage significantly influenced the chemical composition of alfalfa, with crude protein content being significantly higher in the vegetative growth stage alfalfa compared to that in the late budding stage (p < 0.05). Soluble carbohydrates, neutral detergent fiber, and acid detergent fiber content were significantly lower in the vegetative growth stage compared to the late budding stage (p < 0.05). Nitrite content, nitrate content, nitrite reductase activity, and nitrate reductase activity were all significantly higher in the vegetative growth stage compared to the late budding stage (p < 0.05). In terms of fermentation parameters, silage from the late budding stage exhibited superior characteristics compared to that from the vegetative growth stage. Compared to the alfalfa silage during the vegetative growth stage, the late budding stage group exhibited a higher lactate content and lower pH level. Notably, butyric acid was only detected in the silage from the vegetative growth stage group. Throughout the ensiling process, nitrite content, nitrate levels, nitrite reductase activity, and nitrate reductase activity decreased in both treatment groups. The dominant lactic acid bacteria differed between the two groups, with Enterococcus being predominant in vegetative growth stage alfalfa silage, and Weissella being predominant in late budding stage silage, transitioning to Lactiplantibacillus in the later stages of fermentation. On the 3rd day of silage fermentation, the vegetative growth stage group exhibited the highest abundance of Enterococcus, which subsequently decreased to its lowest level on the 15th day. Correlation analysis revealed that lactic acid bacteria, including Limosilactobacillus, Levilactobacillus, Loigolactobacillus, Pediococcus, Lactiplantibacillus, and Weissella, played a key role in nitrite and nitrate degradation in alfalfa silage. The presence of nitrite may be linked to Erwinia, unclassified_o__Enterobacterales, Pantoea, Exiguobacterium, Enterobacter, and Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium.

The Weissella and Periweissella genera: up-to-date taxonomy, ecology, safety, biotechnological, and probiotic potential

Bacteria belonging to the genera Weissella and Periweissella are lactic acid bacteria, which emerged in the last decades for their probiotic and biotechnological potential. In 2015, an article reviewing the scientific literature till that date on the taxonomy, ecology, and biotechnological potential of the Weissella genus was published. Since then, the number of studies on this genus has increased enormously, several novel species have been discovered, the taxonomy of the genus underwent changes and new insights into the safety, and biotechnological and probiotic potential of weissellas and periweissellas could be gained. Here, we provide an updated overview (from 2015 until today) of the taxonomy, ecology, safety, biotechnological, and probiotic potential of these lactic acid bacteria.

Legume-grass mixtures increase forage yield by improving soil quality in different ecological regions of the Qinghai-Tibet Plateau

Introduction

Information on the relationship between soil quality and forage yield of legume-grass mixtures in different ecological regions can guide decision-making to achieve eco-friendly and sustainable pasture production. This study's objective was to assess the effects of different cropping systems on soil physical properties, nitrogen fractions, enzyme activities, and forage yield and determine suitable legume-grass mixtures for different ecoregions.

Methods

Oats (Avena sativa L.), forage peas (Pisum sativum L.), common vetch (Vicia sativa L.), and fava beans (Vicia faba L.) were grown in monocultures and mixtures (YS: oats and forage peas; YJ: oats and common vetch; YC: oats and fava beans) in three ecological regions (HZ: Huangshui Valley; GN: Sanjiangyuan District; MY: Qilian Mountains Basin) in a split-plot design.

Results

The results showed that the forage yield decreased with increasing altitude, with an order of GN (3203 m a.s.l.; YH 8.89 t·ha-1) < HZ (2661 m; YH 9.38 t·ha-1) < MY (2513m; YH 9.78 t·ha-1). Meanwhile, the forage yield was higher for mixed crops than for single crops in all ecological regions. In the 0-10 cm soil layer, the contents of total nitrogen (TN), microbial biomass nitrogen (MBN), soil organic matter (SOM), soluble organic nitrogen (SON), urease (UE), nitrate reductase (NR), sucrase (SC), and bacterial community alpha diversity, as well as relative abundance of dominant bacteria, were higher for mixed crops than for oats unicast. In addition, soil physical properties, nitrogen fractions, and enzyme activities varied in a wider range in the 0-10 cm soil layer than in the 10-20 cm layer, with larger values in the surface layer than in the subsurface layer. MBN, SON, UE, SC and catalase (CAT) were significantly and positively correlated with forage yield (P < 0.05). Ammonium nitrogen (ANN), nitrate nitrogen (NN), SOM and cropping systems (R) were significantly and positively correlated with Shannon and bacterial community (P < 0.05). The highest yields in the three ecological regions were 13.00 t·ha-1 for YS in MY, 10.59 t·ha-1 for YC in GN, and 10.63 t·ha-1 for YS in HZ.

Discussion

We recommend planting oats and forage peas in the Qilian Mountains Basin, oats and fava beans in the Sanjiangyuan District, and oats and forage peas in Huangshui valley. Our results provide new insights into eco-friendly, sustainable, and cost-effective forage production in the Qinghai Alpine Region in China.

Using custom-built primers and nanopore sequencing to evaluate CO-utilizer bacterial and archaeal populations linked to bioH2 production

The microbial community composition of five distinct thermophilic hot springs was effectively described in this work, using broad-coverage nanopore sequencing (ONT MinION sequencer). By examining environmental samples from the same source, but from locations with different temperatures, bioinformatic analysis revealed dramatic changes in microbial diversity and archaeal abundance. More specifically, no archaeal presence was reported with universal bacterial primers, whereas a significant archaea presence and also a wider variety of bacterial species were reported. These results revealed the significance of primer preference for microbiomes in extreme environments. Bioinformatic analysis was performed by aligning the reads to 16S microbial databases for identification using three different alignment methods, Epi2Me (Fastq 16S workflow), Kraken, and an in-house BLAST tool, including comparison at the genus and species levels. As a result, this approach to data analysis had a significant impact on the genera identified, and thus, it is recommended that use of multiple analysis tools to support findings on taxonomic identification using the 16S region until more precise bioinformatics tools become available. This study presents the first compilation of the ONT-based inventory of the hydrogen producers in the designated hot springs in Türkiye.

Mixed legume-grass seeding and nitrogen fertilizer input enhance forage yield and nutritional quality by improving the soil enzyme activities in Sichuan, China

Information regarding relationships between forage yield and soil enzymes of legume-grass mixtures under nitrogen (N) fertilization can guide the decision-making during sustainable forage production. The objective was to evaluate the responses of forage yield, nutritional quality, soil nutrients, and soil enzyme activities of different cropping systems under various N inputs. Alfalfa (Medicago sativa L.), white clover (Trifolium repens L.), orchardgrass (Dactylis glomerata L.), and tall fescue (Festuca arundinacea Schreb.) were grown in monocultures and mixtures (A1: alfalfa, orchardgrass, and tall fescue; A2: alfalfa, white clover, orchardgrass, and tall fescue) under three N inputs (N1: 150 kg ha^-1; N2, 300 kg ha^-1; and N3: 450 kg ha^-1) in a split plot arrangement. The results highlight that A1 mixture under N2 input had a greater forage yield of 13.88 t ha^-1 year^-1 than the other N inputs, whereas A2 mixture under N3 input had a greater forage of 14.39 t ha^-1 year^-1 than N1 input, but it was not substantially greater than N2 input (13.80 t ha^-1 year^-1). The crude protein (CP) content of grass monocultures and mixtures significantly (P < 0.05) increased with an increase in the rate of N input, and A1 and A2 mixtures under N3 input had a greater CP content of 18.91% and 18.94% dry matter, respectively, than those of grass monocultures under various N inputs. The A1 mixture under N2 and N3 inputs had a substantially greater (P < 0.05) ammonium N content of 16.01 and 16.75 mg kg^-1, respectively, whereas A2 mixture under N3 had a greater nitrate N content of 4.20 mg kg^-1 than the other cropping systems under various N inputs. The A1 and A2 mixtures under N2 input had a substantial higher (P < 0.05) urease enzyme activity of 0.39 and 0.39 mg g^-1 24 h^-1 and hydroxylamine oxidoreductase enzyme activity of 0.45 and 0.46 mg g^-1 5 h^-1, respectively, than the other cropping systems under various N inputs. Taken together, growing legume-grass mixtures under N2 input is cost-effective, sustainable, and eco-friendly, which provide greater forage yield and improved nutritional quality by the better utilization of resources.

The microbial communities and natural fermentation quality of ensiling oat (Avena sativa L.) harvest from different elevations on the Qinghai-Tibet Plateau

Introduction

Ensiling whole-crop oat (Avena sativa L.) has attracted a growing interest in the Qinghai-Tibet Plateau. The study aimed to investigate the microbial community and chemical composition of fresh and ensiling oat harvested from six different elevations of the Qinghai-Tibet Plateau.

Method

The oat (A. sativa L. cv. Qingyin No. 1) was planted in six different sites across Qinghai-Tibet Plateau (BM, Bomi County; BY, Bayi County; DZ, Dazi County; BR, Biru County; SC, Suo County; SN, Seni County), where the elevations were in the range of 2,800-4,500 m above sea level (a. s. l.). Oat was harvested at the milk stage and ensiled for 90 days.

Results

The highest crude protein (CP) and lowest water-soluble carbohydrate (WSC) were observed in fresh oat of SN and BM, respectively, however, no distinct gradient trend in WSC and CP concentrations along the elevation gradient. The lowest LAB counts in fresh oat from the highest elevational regions of SN. After 90 days of ensiling, the pH in all oat silages was lower than 4.2, and silages from SC and SN showed a lower pH and butyric acid concentration, and higher lactic acid (LA) concentration than silages of other regions. The oat silage from BR showed the lowest LA concentration and the highest pH. The bimodal distributions of fungal and bacterial richness in fresh oat along the elevation gradient were observed, while the elevation gradients did not affect the fungal Shannon index in fresh oat. Dioszegia, Cladosporium, and Vishniacozyma were the prevalent fungal genus in fresh oat, while Wickerhamomyces, Candida, and Saccharomyces dominated the fungal communities of silages. Wickerhamomyces and Candida were the dominant genera in oat silages from BM and SC, respectively. Erwinia, Paenibacillus, Pseudomonas, Leuconostoc, and Exiguobacterium dominated the bacterial community of fresh oat, while Lactobacillus and Kosakonia were the dominant bacterial genus in oat silages. Pantoea was the most dominant bacterial genus in fresh oat from low-elevational regions (BM, BY, and DZ). Oat from SN exhibited the best fermentation quality although fresh oat of SN hosted the lowest LAB counts, indicating that high-efficient LAB might be present in fresh oat sampled from high altitudes.

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.

Exploring the differences between sole silages of gramineous forages and mixed silages with forage legumes using 16S/ITS full-length sequencing

Background/Objective

Silage characteristics of grass materials directly affect their silage qualities. To expand the source of silage raw materials and develop mixed silages underlined by exploring the positive interactions between forage grasses and legumes, three gramineous grasses, Napier grass (Pennisetum purpureum), king grass (Pennisetum sinese), and forage maize (Zea mays) were separately mixed ensiled with a combination of four forage legumes including Medicago sativa, Vicia villosa, Vicia sativa, and Trifolium repens.

Methods

The chemical composition and fermentation quality of the mixed silages were analyzed and compared with those of the sole silages of these three grasses, as well as the diversity of microbial communities, through the 16S/ITS full-length sequencing.

Results

The results showed that the inclusion of forage legumes could somewhat improve the fermentation quality, as indicated by significantly (p < 0.05) higher crude protein and lactic acid contents while lower neutral detergent fiber, acid detergent fiber contents and pH values, compared with the sole silages. Among the three types of mixed silages, the mixed king grass had the highest dry matter and crude protein content as well as lowest neutral detergent fiber and acid detergent fiber content. Meanwhile, the bacterial and fungal communities in the mixed silages were influenced by increased the relative abundance of lactic acid bacteria, which inhibited the proliferation of undesirable bacteria, such as Hafnia alvei, Enterobacter cloacae, and Serratia proteamaculanss. Co-occurrence networks identified 32 nodes with 164 positive and 18 negative correlations in bacteria and 80 nodes with two negative and 76 positive correlations in fungi during fermentation.

Conclusion

Inclusion of forage legume to grasses can improve the fermentation quality and optimize the structure of microbial community, which appears to be a feasible strategy to enhance the forage resource utilization.

Exploring the bacterial community succession and metabolic profiles of Lonicera japonica Thunb. residues during anaerobic fermentation

Discarding Lonicera japonica Thunb. (LJT) residues containing many active metabolites create tremendous waste. This study aimed to effectively use LJT residues by anaerobic fermentation. Fermentation significantly decreased the pH values and reduced the abundance of undesirable bacteria (potential pathogenic and biofilm-forming) while increasing Lactobacillus abundance. Compound additive use further improved fermentation quality (significantly increased the lactic acid (LA) content and decreased the pH values and ammonia nitrogen (a-N) content) and nutrient quality (significantly decreased the acid detergent fiber (ADF) content and increased the water-soluble carbohydrate (WSC) content) and optimized the microbial community (increased the Lactobacillus abundance). Fermentation also altered the flavonoids, alkaloids and phenols contents in the residues with minor effects on the functional metabolites amounts. The LJT residues metabolic profile was mainly attributed to its epiphytic bacteria, with a small contribution from the compound additive. Thus, compound additives may improve anaerobic LJT residue fermentation without functionally impairing the metabolites.

Current approaches on the roles of lactic acid bacteria in crop silage

Lactic acid bacteria (LAB) play pivotal roles in the preservation and fermentation of forage crops in spontaneous or inoculated silages. Highlights of silage LAB over the past decades include the discovery of the roles of LAB in silage bacterial communities and metabolism and the exploration of functional properties. The present article reviews published literature on the effects of LAB on the succession, structure, and functions of silage microbial communities involved in fermentation. Furthermore, the utility of functional LAB in silage preparation including feruloyl esterase-producing LAB, antimicrobial LAB, lactic acid bacteria with high antioxidant potential, pesticide-degrading LAB, lactic acid bacteria producing 1,2-propanediol, and low-temperature-tolerant LAB have been described. Compared with conventional LAB, functional LAB produce different effects; specifically, they positively affect animal performance, health, and product quality, among others. In addition, the metabolic profiles of ensiled forages show that plentiful probiotic metabolites with but not limited to antimicrobial, antioxidant, aromatic, and anti-inflammatory properties are observed in silage. Collectively, the current knowledge on the roles of LAB in crop silage indicates there are great opportunities to develop silage not only as a fermented feed but also as a vehicle of delivery of probiotic substances for animal health and welfare in the future.

Effects of laccase and lactic acid bacteria on the fermentation quality, nutrient composition, enzymatic hydrolysis, and bacterial community of alfalfa silage

Ensiling has long been as a mainstream technology of preserving forage for ruminant production. This study investigated the effects of bioaugmented ensiling with laccase and Pediococcus pentosaceus on the fermentation quality, nutritive value, enzymatic hydrolysis, and bacterial community of alfalfa. The application of laccase and Pediococcus pentosaceus combination was more potent in modulating the fermentation quality of silage than laccase and Pediococcus pentosaceus alone, as indicated by higher lactic acid contents and lactic acid to acetic acid ratios, and lower pH, dry matter losses, and ammonia nitrogen contents. Moreover, treatments with additive enhanced protein preservation and structural carbohydrate degradation, while increasing true protein and water-soluble carbohydrate contents. By promoting lignin degradation, treatments containing laccase further facilitated the release of sugars from cellulose compared with treatment with Pediococcus pentosaceus alone. The additive treatments reduced the bacterial diversity and optimized the bacterial community composition of silage, with an increase in the relative abundance of desirable Lactobacillus and a decrease in the relative abundance of undesirable Enterobacter and Klebsiella. PICRUSt functional prediction based on Kyoto Encyclopedia of Genes and Genomes (KEGG) databases revealed that PL and LPL treatments increased the metabolism of membrane transport, carbohydrate, and terpenoids and polyketides related to fermentation activities. It can be concluded that bioaugmented ensiling with laccase and Pediococcus pentosaceus combination can be an effective and practical strategy to improve silage fermentation and nutrient preservation of alfalfa silage.