Bacterial population dynamics during the ensiling of Medicago sativa (alfalfa) and subsequent exposure to air

Abstract

Aims: To describe, at high resolution, the bacterial population dynamics and chemical transformations during the ensiling of alfalfa and subsequent exposure to air. Methods and Results: Samples of alfalfa, ensiled alfalfa and silage exposed to air were collected and their bacterial population structures compared using 16S rRNA gene libraries containing approximately 1900 sequences each. Cultural and chemical analyses were also performed to complement the 16S gene sequence data. Sequence analysis revealed significant differences (P < 0Á05) in the bacterial populations at each time point. The alfalfa-derived library contained mostly sequences associated with the Gammaproteobacteria (including the genera: Enterobacter, Erwinia and Pantoea); the ensiled material contained mostly sequences associated with the lactic acid bacteria (LAB) (including the genera: Lactobacillus, Pediococcus and Lactococcus). Exposure to air resulted in even greater percentages of LAB, especially among the genus Lactobacillus, and a significant drop in bacterial diversity. Conclusions: In-depth 16S rRNA gene sequence analysis revealed significant bacterial population structure changes during ensiling and again during exposure to air. Significance and Impact of the Study: This in-depth description of the bacterial population dynamics that occurred during ensiling and simulated feed out expands our knowledge of these processes.

The dynamics of the bacterial communities developed in maize silage

“…The latter are non‐LAB, aerobic, non‐fermenting, gram‐negative bacteria, sometimes associated not just with maize silage (Li and Nishino, ), but also form a component of the lettuce epiphytic community (Weiss et al ., ). Erwinia spp., along with other gamma‐proteobacteria, colonize alfalfa (McGarvey et al ., ), lettuce (Weiss et al ., ), citrus (Yang et al ., ) biomass, but are not generally associated with the ensilage process. Here, the abundance of Enterobacteriaceae fell significantly during the early period of the ensilage, thereafter remaining low, an observation which was taken to indicate their lack of importance for silage fermentation.…”

“…Ensiling is a natural and spontaneous process that largely depends on anaerobic microbial fermentation. At the time of ensilage, the plant material harbours a range of microorganisms (the “epiphytic community”; Muck, ), but the fermentation process favours the multiplication of lactic acid bacteria (LAB; Ennahar et al ., ; Yang et al ., ; Eikmeyer et al ., ; McGarvey et al ., ) largely belonging to the genera Lactobacillus , Pediococcus , Lactococcus , Enterococcus , Streptococcus and Leuconostoc (McDonald, ; McGarvey et al ., ; Muck, ). In some cases, the representation of LAB present does not effectively establish the required anaerobic and acidic conditions, leading to spoiling through the activity of other microorganisms (Woolford, ; McDonald, ; Muck, ).…”

“…The composition of the silage microbiome has been explored using various microbiological and DNA‐based techniques (Langston and Bouma, ; Ennahar et al ., ; Parvin and Nishino, ; McEniry et al ., ; Yang et al ., ; McGarvey et al ., ). In general, these approaches are not powerful enough to identify species present in low abundance, some of which may nevertheless be critical for optimal fermentation.…”

The effect of cultivar, wilting and storage period on fermentation and the clostridial community of alfalfa silage

“…Rossi and Dellaglio (2007) reported that the occurrence of six clostridia species, and particularly Clostridium perfringens, was associated with the undesirable fermentation of maize and alfalfa silages. However, the vast majority of these investigations utilised culture-based techniques, that while informative, are notorious for underestimating the level of the clostridial diversity (McGarvey et al 2013). Recent advancements in molecular tools have enabled us to elucidate the entire structure of the complex microbial community found in nature.…”

Effects of steam explosion pretreatment and Lactobacillus buchneri inoculation on fungal community of unensiled and ensiled total mixed ration containing wheat straw during air exposure

“…7.0.1001, http://drive5.com/uparse/) (Edgar ). Representatives of each OTU were analysed using the megablast program and the NCBI nr/nt database (http://blast.ncbi.nlm.nih.gov/) (McGarvey et al ). Taxonomic classification of each OTU was determined with RDP Classifier (ver.…”