Diversity of a stable enrichment culture which is useful for silage inoculant and its succession in alfalfa silage

Effects of whole-plant corn and hairy vetch (Vicia villosa Roth) mixture on silage quality and microbial communities

OBJECTIVE

Hairy vetch is considered to improve the nutritional value of corn because of its high protein and mineral levels. To better understand the mechanism underlying hairy vetch regulated whole-plant corn silage fermentation, this experiment investigated the fermentation quality and bacterial community of whole-plant corn and hairy vetch mixture.

METHODS

Whole-plant corn and hairy vetch were mixed at ratios of 10:0 (Mix 10:0), 8:2 (Mix 8:2), 6:4 (Mix 6:4), 4:6 (Mix 4:6), 2:8 (Mix 2:8), and 0:10 (Mix 0:10) on a fresh weight basis. After ensiling 60 days, samples were collected to examine the fermentation dynamics, ensiling characteristics, and bacterial communities.

RESULTS

Mix 0:10, Mix 2:8, and Mix 4:6 showed poor fermentation characteristics. Mix 8:2 and Mix 6:4 silages showed high quality, based on the low pH, acetic acid, and ammonia nitrogen levels and the high lactic acid, crude protein, and crude fat contents. The bacterial diversity was affected by the mixing ratio of the two forage species. The genus Lactobacillus dominated the bacterial community in Mix 10:0 silage, whereas with the addition of hairy vetch, the relative abundance of unclassified-Enterobacter increased from 7.67% to 41.84%, and the abundance of Lactobacillus decreased from 50.66% to 13.76%.

CONCLUSION

The silage quality of whole-plant corn can be improved with inclusion levels of hairy vetch from 20% to 40%.

Phylogenetic variation in raw cow milk microbiota and the impact of forage combinations and use of silage inoculants

Introduction

The microbiota of bulk tank raw milk is known to be closely related to that of microbial niches of the on-farm environment. Preserved forage types are partof this ecosystem and previous studies have shown variations in their microbial ecology. However, little is known of the microbiota of forage ration combinations and the transfer rates of associated species to milk.

Methods

We identified raw milk bacteria that may originate from forage rations encompassing either hay (H) or grass/legume silage uninoculated (GL) as the only forage type, or a combination of GL and corn silage uninoculated (GLC), or grass/legume and corn silage both inoculated (GLICI). Forage and milk samples collected in the fall and spring from 24 dairy farms were analyzed using 16S rRNA gene high-throughput sequencing following a treatment with propidium monoazide to account for viable cells.

Results and discussion

Three community types separating H, GL, and GLICI forage were identified. While the H community was co-dominated by Enterobacteriaceae, Microbacteriaceae, Beijerinckiaceae, and Sphingomonadaceae, the GL and GLICI communities showed high proportions of Leuconostocaceae and Acetobacteraceae, respectively. Most of the GLC and GLICI rations were similar, suggesting that in the mixed forage rations involving grass/legume and corn silage, the addition of inoculant in one or both types of feed does not considerably change the microbiota. Raw milk samples were not grouped in the same way, as the GLC milk was phylogenetically different from that of GLICI across sampling periods. Raw milk communities, including the GLICI group for which cows were fed inoculated forage, were differentiated by Enterobacteriaceae and other Proteobacteria, instead of by lactic acid bacteria. Of the 113 amplicon sequence variants (ASVs) shared between forage rations and corresponding raw milk, bacterial transfer rates were estimated at 18 to 31%. Silage-based forage rations, particularly those including corn, share more ASVs with raw milk produced on corresponding farms compared to that observed in the milk from cows fed hay. These results show the relevance of cow forage rations as sources of bacteria that contaminate milk and serve to advance our knowledge of on-farm raw milk contamination.

Effects of exogenous lactic acid bacteria and maize meal on fermentation quality and microbial community of Orychophragmus violaceus silage

Orychophragmus violaceus is a local Brassicaceae in China, while most of it is directly mowed and discarded after the ornamental period. In order to develop forage resources, this study firstly evaluated the potential preservation of O. violaceus silage. O. violaceus was harvested at full-bloom stage, and ensiled without (CK) or with maize meal (Y5), lactic acid bacteria inoculant (Z) and compound additive (Y5Z) for 60 d. Results of chemical and microbiological analysis showed that a large amount of lactic acid was produced and the final pH value was below 4.1 in silages regardless of additive application. CK silage was well preserved as indicated by the low levels of dry matter loss and butyric acid content, and the predominant genus were identified as Enterococcus and Pediococcus. Y5 silage had potential health risks for humans and animals as seen by frequent occurrence of pathogenic bacteria Clostridium and Achromobacter. Z and Y5Z silages were poorly preserved, resulting in great dry matter loss and butyric acid content. Considering the abundant acetic acid production, the dominant Lactobacillus might possess a heterofermentative pathway in Z and Y5Z silages. In conclusion, O. violaceus has the potential to be long stored as silage because of its sufficient water-soluble carbohydrates, while exogenous lactic acid bacteria and maize meal generally provided little positive effect. In future research, efficient homofermentative Lactobacillus strains were suggested to be screened to further enhance the ensiling process of O. violaceus silage.

Effect of isolated lactic acid bacteria on the quality and bacterial diversity of native grass silage

Objective

The objective of this study was to isolate lactic acid bacteria (LAB) from native grasses and naturally fermented silages, determine their identity, and assess their effects on silage quality and bacterial communities of the native grasses of three steppe types fermented for 60 days.

Methods

Among the 58 isolated LAB strains, Limosilactobacillus fermentum (BL1) and Latilactobacillus graminis (BL5) were identified using 16S rRNA sequences. Both strains showed normal growth at 15- 45°C temperature, 3-6.5% NaCl concentration, and pH 4-9. Two isolated LAB strains (labeled L1 and L5) and two commercial additives (Lactiplantibacillus plantarum and Lentilactobacillus buchneri; designated as LP and LB, respectively) were added individually to native grasses of three steppe types (meadow steppe, MS; typical steppe, TS; desert steppe, DS), and measured after 60 d of fermentation. The fresh material (FM) of different steppe types was treated with LAB (1 × 10⁵ colony forming units/g fresh weight) or distilled water (control treatment [CK]).

Results

Compared with CK, the LAB treatment showed favorable effects on all three steppe types, i.e., reduced pH and increased water-soluble carbohydrate content, by modulating the microbiota. The lowest pH was found in the L5 treatment of three steppe types, at the same time, the markedly (p < 0.05) elevated acetic acid (AA) concentration was detected in the L1 and LB treatment. The composition of bacterial community in native grass silage shifted from Pantoea agglomerans and Rosenbergiella nectarea to Lentilactobacillus buchneri at the species level. The abundance of Lentilactobacillus buchneri and Lactiplantibacillus plantarum increased significantly in L1, L5, LP, and LB treatments, respectively, compared with CK (p < 0.05).

Conclusion

In summary, the addition of LAB led to the shifted of microbiota and modified the quality of silage, and L. fermentum and L. graminis improved the performance of native grass silage.

Effects of Isolated LAB on Chemical Composition, Fermentation Quality and Bacterial Community of Stipa grandis Silage

This study aimed to screen and identify lactic acid bacteria (LAB) strains from the Stipa grandis and naturally fermented silage, and assess their effects on the silage quality and bacterial community of Stipa grandis after 60 days of the fermentation process. A total of 38 LAB were isolated, and strains ZX301 and YX34 were identified as Lactiplantibacillus plantarum and Pediococcus pentosaceus using 16S rRNA sequences; they can normally grow at 10−30 °C, with a tolerance of pH and NaCl from 3.5 to 8.0 and 3 to 6.5%, respectively. Subsequently, the two isolated LAB and one commercial additive (Lactiplantibacillus plantarum) were added to Stipa grandis for ensiling for 60 days and recorded as the ZX301, YX34, and P treatments. The addition of LAB was added at 1 × 105 colony-forming unit/g of fresh weight, and the same amount of distilled water was sprayed to serve as a control treatment (CK). Compared to the CK treatment, the ZX301 and YX34 treatments exhibited a positive effect on pH reduction. The water-soluble carbohydrate content was significantly (p < 0.05) increased in ZX301, YX34, and P treatments than in CK treatment. At the genus level, the bacterial community in Stipa grandis silage involves a shift from Pantoea to Lactiplantibacillus. Compared to the CK treatment, the ZX301, YX34, and P treatments significantly (p < 0.05) increase the abundance of Pediococcus and Lactiplantibacillus, respectively. Consequently, the results indicated that the addition of LAB reconstructed microbiota and influenced silage quality. The strain ZX301 could improve the ensiling performance in Stipa grandis silage.

Effect of different organic acid additives on the fermentation quality and bacterial community of paper mulberry (Broussonetia papyrifera) silage

To investigate the effects of different organic acid additives and their concentrations on the fermentation quality and bacterial community of paper mulberry silage, paper mulberry was left untreated (control) or was treated with ethylenediaminetetraacetic acid (EDTA), propionic acid (PA) or citric acid (CA), the amount of each additive was 2 g.kg^-1 FM, 5 g.kg^-1 FM and g.kg^-1 FM. All groups were ensiled for 3, 7, 15, 30 and 60 days. Compared to the control, adding EDTA reduced protein breakdown, preserved more water-soluble carbohydrates of the silages (WSCs, 24.74 g.kg^-1 DM), and high concentrations of EDTA inhibited the activity of undesirable microorganisms. Adding PA increased the abundance of Lactiplantibacillus and decreased the abundance of Enterococcus, and it caused a rapid decrease in the pH of the silage at an early stage (from 6.50 to 5.31) while altering the microbiota, and low concentrations of PA resulted in high LA (66.22 g.kg^-1 DM) concentration and low PA (9.92 g.kg^-1 DM) concentration at 60 days of ensiling. Different concentrations of additives altered the microbial community of paper mulberry to different degrees. High concentrations of PA and CA can increase the abundance of Lactiplantibacillus. High concentrations of CA resulted in a rapid decrease in silage pH at an early stage and higher WSC concentration. These results suggest that EDTA, PA and CA can be used as additives to improve the quality of paper mulberry silage.

The reconstitution mechanism of napier grass microiota during the ensiling of alfalfa and their contributions to fermentation quality of silage

To reveal the reconstitution mechanism of exogenous microbiota and their contributions to fermentation quality during the early stage of alfalfa ensiling. The chopped alfalfa was treated with the following: distilled water (A1); napier grass microbiota (A1N); γ-ray radiation + distilled water (A0); γ-ray radiation + napier grass microbiota (A0N). Inoculating napier grass microbiota to non-irradiated alfalfa decreased the LA concentration, while enhanced the LA production of irradiated alfalfa during the 7 d of ensiling. Inoculating napier grass microbiota increased AA and ammonia-N contents and enhanced the decline of WSC for both non-irradiated and irradiated alfalfa silages. Enterococcus and Pediococcus dominated A1 silage. Leuconostocs and Lactobacillus constituted the majority of bacterial community in A0N, Lactobacillus rapidly became the predominated genera, while Lactobacillus, Leuconostocs, Enterococcus, and Pediococcus constituted the majority of bacterial community in A1N. Thus forage microbiota transplantation may be a potential practice to improve fermentation quality of less readily fermentable forages.

Dynamics of a microbial community during ensiling and upon aerobic exposure in lactic acid bacteria inoculation-treated and untreated barley silages

This study investigated the effects of lactic acid bacteria on bacterial and fungal community during the fermentation process and aerobic exposure phase of barley ensiled with preparation of lactic acid bacteria (LAB). The inoculated silages displayed higher contents of lactic acid, acetic acid, and propionic acid as well as a greater number of lactic acid bacteria during ensiling. LAB-treated silage decreased the bacterial diversity during both ensiling and aerobic exposure but increased the fungal diversity during ensiling of barley. LAB-treated silage during ensiling increased the abundance of Lactobacillus but decreased that of Weissella. After aerobic exposure, LAB-treated silage increased the abundance of Lactobacillus but decreased that of Acinetobacter. Acinetobacter, Enterococcus, Providencia, and Empedobacter were the dominant bacteria after aerobic exposure. In conclusion, LAB-treated silage enhanced the number of desirable Lactobacillus and inhibited the growth of undesirable microorganisms, such as Acinetobacter.

Effect of Lactobacillus plantarum and Lactobacillus buchneri addition on fermentation, bacterial community and aerobic stability in lucerne silage

Changes in the microbial community are closely related to the fermentation of silage. However, how host genetic variation shapes the community structure of the silage microbiota and its metabolic phenotype is poorly understood. The objective of present study was to evaluate the effects of the application of the homo-fermentative Lactobacillus plantarum and hetero-fermentative Lactobacillus buchneri strains to lucerne silage on the fermentation characteristics, aerobic stability, and microbial community and their correlations. The three silages treated with L. plantarum or L. buchneri were well preserved and had significantly lower pH values, butyric acid, propionic acid, and ammonia-N concentrations, and significantly higher residual water-soluble carbohydrate, dry matter and lactic acid contents than the controls. The treated groups had more lactic acid bacteria and lower quantities of other bacteria in their microbial communities. Inoculation of lactic acid bacteria influenced the abundances of other bacteria and controlled the silage fermentation characteristics. L. buchneri inhibited the abundance of Enterobacter_ludwigii to increase the crude protein content, L. plantarum improve the neutral detergent fibre content by affecting the abundance of Arthrobacter_sp._Ens13. In conclusion, the application of L. plantarum and L. buchneri improved the quality of lucerne silage fermentation, and L. buchneri resulted in greater improvements after aerobic exposure.

Model Microbial Consortia as Tools for Understanding Complex Microbial Communities

A major biological challenge in the postgenomic era has been untangling the composition and functions of microbes that inhabit complex communities or microbiomes. Multi-omics and modern bioinformatics have provided the tools to assay molecules across different cellular and community scales; however, mechanistic knowledge over microbial interactions often remains elusive. This is due to the immense diversity and the essentially undiminished volume of not-yet-cultured microbes. Simplified model communities hold some promise in enabling researchers to manage complexity so that they can mechanistically understand the emergent properties of microbial community interactions. In this review, we surveyed several approaches that have effectively used tractable model consortia to elucidate the complex behavior of microbial communities. We go further to provide some perspectives on the limitations and new opportunities with these approaches and highlight where these efforts are likely to lead as advances are made in molecular ecology and systems biology.

Analysis of the cocobiota and metabolites of Moniliophthora perniciosa-resistant Theobroma cacao beans during spontaneous fermentation in southern Brazil

BACKGROUND

Cocoa bean fermentation is a spontaneous process involving a succession of microbial activities, yeasts, lactic acid, and acetic acid bacteria. The spontaneous fermentation of cocoa beans by Theobroma cacao TSH565 clonal variety, a highly productive hybrid resistant to Moniliophthora perniciosa and Phytophthora spp., was investigated. The natural cocobiota involved in the spontaneous fermentation of this hybrid in southern Brazil, was investigated by using both a culture-dependent microbiological analysis and a molecular analysis. The changes in the physicochemical characteristics and the kinetics of substrate utilization and metabolite production during fermentation were also evaluated.

RESULTS

Yeasts (178) and bacteria (244) isolated during fermentation were identified by partial sequencing of the ITS and 16S rDNAs, respectively. After 144 h of fermentation, the indigenous yeast community was composed of Hanseniaspora spp., Saccharomyces spp., and Pichia spp. The bacterial population comprised Lactococcus spp., Staphylococcus spp., Acetobacter spp. and Lactobacilli strains. The kinetics of substrate transformation reflected the dynamic composition of the cocobiota. Substrates such as glucose, fructose, sucrose, and citric acid, present at the beginning of fermentation, were metabolized to produce ethanol, acetic acid, and lactic acid.

CONCLUSION

The results described here provide new insights into microbial diversity in cocoa bean-pulp mass fermentation and the kinetics of metabolites synthesis, and pave the way for the selection of starter cultures to increase efficiency and consistency to obtain homogeneous and best quality cocoa products. © 2018 Society of Chemical Industry.

Effects of inoculants Lactobacillus brevis and Lactobacillus parafarraginis on the fermentation characteristics and microbial communities of corn stover silage

To improve silage quality of crop forages, bacterial inoculants are often employed. In this study, Lactobacillus brevis SDMCC050297 and Lactobacillus parafarraginis SDMCC050300 were used as inoculants to corn stover in lab silos for ensiling. At the initial stage of ensiling, the pH value of the inoculated silages reduced more drastically, and the inoculated silages had higher lactic acid and acetic acid contents. After 20 days of ensiling, a reduction in lactic acid content coupled with an increase in acetic acid and 1,2-propanediol contents was observed in inoculated silages. Furthermore, both the amount of lactic acid bacteria and the abundance of order Lactobacillales in inoculated silages were higher than those of controls in the whole process. Meanwhile, Lb. brevis predominated before day 20 and then the dominance was shifted to Lb. parafarraginis until the late stage of ensiling. In contrast, the epiphytic Lactococcus lactic and Lb. plantarum played major roles at the beginning of naturally fermented silages and then Lb. plantarum and Lb. brevis were the most abundant at the later stage. In conclusion, these two selected strains had capability of improving the silage quality and providing the reproducible ensiling process, thus having the potential as silage inoculants.

Isolation, selection and evaluation of antagonistic yeasts and lactic acid bacteria against ochratoxigenic fungus Aspergillus westerdijkiae on coffee beans

In this study, yeasts and lactic acid bacteria (LAB) were isolated from coffee fruits and identified via biochemical and molecular approaches. The isolates represented the Pichia, Debaryomyces, Candida, Clavispora, Yarrowia, Sporobolomyces, Klyveromyces, Torulaspora and Lactobacillus genera. Four isolates, namely Pichia fermentans LPBYB13, Sporobolomyces roseus LPBY7E, Candida sp. LPBY11B and Lactobacillus brevis LPBB03, were found to have the greatest antagonist activity against an ochratoxigenic strain of Aspergillus westerdijkiae on agar tests and were selected for further characterization. Applications of P. fermentans LPBYB13 in coffee cherries artificially contaminated with A. westerdijkiae showed efficacy in reducing ochratoxin A (OTA) content up to 88%. These results highlight that P. fermentans LPBYB13 fulfils the principle requirements of an efficient biological control of aflatoxigenic fungi in coffee beans and may be seen as a reliable candidate for further validation in field conditions.

SIGNIFICANCE AND IMPACT OF THE STUDY

Studies based on microbial ecology and antagonistic interactions are important for the development of new strategies in controlling aflatoxin contamination of crops and are relevant to further biotechnological applications. This study shows that coffee fruit is a potential source for the isolation of microbial strains with antifungal ability. A new yeast strain, Pichia fermentans LPBYB13, showed efficacy in reducing growth and ochratoxin A production of Aspergillus westerdijkiae in coffee beans. Our results should encourage the use of this yeast strain on a large scale for biocontrol of aflatoxigenic fungi in coffee beans.

Pretreatment of non-sterile, rotted silage maize straw by the microbial community MC1 increases biogas production

Using microbial community MC1 to pretreat lignocellulosic materials increased the yield of biogas production, and the substrate did not need to be sterilized, lowering the cost. Rotted silage maize straw carries many microbes. To determine whether such contamination affects MC1, rotted silage maize straw was pretreated with MC1 prior to biogas production. The decreases in the weights of unsterilized and sterilized rotted silage maize straw were similar, as were their carboxymethyl cellulase activities. After 5d pretreatment, denaturing gradient gel electrophoresis and quantitative polymerase chain reaction results indicated that the proportions of five key strains in MC1 were the same in the unsterilized and sterilized groups; thus, MC1 was resistant to microbial contamination. However, its resistance to contamination decreased as the degradation time increased. Following pretreatment, volatile fatty acids, especially acetic acid, were detected, and MC1 enhanced biogas yields by 74.7% compared with the untreated group.

Phylogenetically Diverse Aerobic Anoxygenic Phototrophic Bacteria Isolated from Epilithic Biofilms in Tama River, Japan

The diversity of aerobic anoxygenic phototrophic (AAP) bacteria in freshwater environments, particularly in rivers, has not been examined in as much detail as in ocean environments. In the present study, we investigated the phylogenetic and physiological diversities of AAP bacteria in biofilms that developed on submerged stones in a freshwater river using culture methods. The biofilms collected were homogenized and inoculated on solid media and incubated aerobically in the dark. Sixty-eight red-, pink-, yellow-, orange-, or brown-colored colonies were isolated, and, of these, 28 isolates contained the photosynthetic pigment, bacteriochlorophyll (BChl) a. Phylogenetic analyses based on 16S rRNA gene sequences showed that the isolates were classified into 14 groups in 8 operational taxonomic units (OTUs) and distributed in the orders Rhodospirillales, Rhodobacterales, and Sphingomonadales of Alphaproteobacteria and in Betaproteobacteria. Physiological analyses confirmed that none of the representative isolates from any of the groups grew under anaerobic phototrophic conditions. Seven isolates in 4 OTUs showed a 16S rRNA gene sequence identity of 98.0% or less with any established species, suggesting the presence of previously undescribed species of AAP bacteria. Six isolates in 2 other OTUs had the closest relatives, which have not been reported to be AAP bacteria. Physiological comparisons among the isolates revealed differences in preferences for nutrient concentrations, BChl contents, and light-harvesting proteins. These results suggest that diverse and previously unknown AAP bacteria inhabit river biofilms.

Characterization, identification and application of lactic Acid bacteria isolated from forage paddy rice silage

There has been growing interest to develop forage rice as a new feed resource for livestock. This study was to characterize the natural population of lactic acid bacteria (LAB) and select potentially excellent strains for paddy rice silage preparation in China. One hundred and twenty-six strains were isolated and screened from paddy rice silage prepared using a small-scale fermentation system, and ninety-nine of these isolates were considered to be LAB based on their Gram-positive and catalase-negative morphology and the production of most of their metabolic products as lactic acid. These isolates were divided into eight groups (A-H) on the basis of their morphological and biochemical characteristics. The Group A to H strains were identified as Lactobacillus (L.) plantarum subsp. plantarum (species ratio: 8.1%), L. casei (5.1%), Leuconostoc (Ln.) pseudomesenteroides (11.1%), Pediococcus (P.) pentosaceus (24.2%), Enterococcus (E.) mundtii (12.1%), Lactococcus (Lc.) garvieae (15.2%), E. faecium (9.1%) and Lc. lactis subsp. lactis (15.2%) based on sequence analyses of their 16S rRNA and recA genes. P. pentosaceus was the most abundant member of the LAB population in the paddy rice silage. A selected strain, namely L. casei R 465, was found to be able to grow under low pH conditions and to improve the silage quality with low pH and a relatively high content of lactic acid. This study demonstrated that forage paddy rice silage contains abundant LAB species and its silage can be well preserved by inoculation with LAB, and that strain R 465 can be a potentially excellent inoculant for paddy rice silage.

Characterization of pMC11, a plasmid with dual origins of replication isolated from Lactobacillus casei MCJ and construction of shuttle vectors with each replicon

Many lactic acid bacteria carry different plasmids, particularly those that replicate via a theta mechanism. Here we describe Lactobacillus casei MCJ(CCTCC AB20130356), a new isolate that contains pMC11, carrying two distinct theta-type replicons. Each replicon contained an iteron in the origin of replication (oriV1 or oriV2) and a gene coding for the replicase (RepA_1 or RepB_1), both of which are essential for plasmid replication. Escherichia coli/Lactobacillus shuttle vectors were constructed with each replicon, yielding pEL5.7 and pEL5.6 that are based on oriV2 and oriV1 replicons, respectively. These plasmids showed distinct properties: pEL5.7 was capable of replicating in L. casei MCJΔ1 and Lactobacillus delbrueckii subsp. lactic LBCH-1 but failed to do so in two other tested lactobacilli strains whereas pEL5.6 replicated in three different strains, including L. casei MCJΔ1, L. casei NJ, Lactobacillus paracasei LPC-37 and L. delbrueckii subsp. lactic LBCH-1. Plasmid stability was studied: pEL5.6 and pEL5.7 were very stably maintained in L. casei, as the loss rate was lower than 1 % per generation. pEL5.7 was also stable in L. delbrueckii subsp. lactic LBCH-1 with the loss rate estimated to be 3 %. These vectors were employed to express a green fluorescent protein (GFP) using the promoter of S-layer protein SlpA from Lactobacillus acidophilus. And a growth-phase regulated expression of GFP was observed in different strains. In conclusion, these shuttle vectors provide efficient genetic tools for DNA cloning and heterologous gene expression in lactobacilli.

Enhancement of biogas production from swine manure by a lignocellulolytic microbial consortium

Anaerobic digestion of lignocellulosic wastes is limited by inefficient hydrolysis of recalcitrant substrates, leading to low biogas yield. In this study, the potential of a lignocellulolytic microbial consortium (LMC) for enhancing biogas production from fibre-rich swine manure (SM) was assessed. Biochemical methane potential assay showed that inoculation of structurally stable LMC to anaerobic digestion led to increase biogas production under mesophilic and thermophilic conditions. The greatest enhancement was observed at 37°C with a LMC/SM ratio of 1.5:1 mg VSS/g VS leading to biogas and methane yields of 355 and 180 ml/g VS(added) respectively, equivalent to 40% and 55% increases compared with the control. The LMC was shown to increase the efficiency of total solid, chemical oxygen demand removal and degradation of cellulose and hemicelluloses (1.87 and 1.65-fold, respectively). The LMC-supplemented process was stable over a 90 d biogas production period. This work demonstrates the potential of LMC for enhancing biogas from lignocellulosic wastes.

Study of the physicochemical parameters and spontaneous fermentation during the traditional production of yakupa, an indigenous beverage produced by Brazilian Amerindians

Yakupa is a traditional non-alcoholic cassava beverage produced by Brazilian Amerindians. In this work the microbial dynamics and metabolites involved in yakupa fermentation were investigated by PCR-denaturing gradient gel electrophoresis and chromatography analysis, respectively. The lactic acid bacteria (LAB) population was higher than yeast in the beginning of fermentation (5 log CFU mL(-1) and 3 log CFU mL(-1), respectively) and after 36 h both population increased reaching 7 log CFU mL(-1), remaining constant until 60 h. Culture dependent and independent methods in combination identified the bacteria Lactobacillus fermentum, L. plantarum, Weissela cibaria and W. confusa, and yeasts Saccharomyces cerevisiae and Pichia kudriavzevii. Maltose (41.2 g L(-1)), ethanol (6.5 g L(-1)) and lactic acid (7.8 g L(-1)) were the most abundant compounds identified by high performance liquid chromatography. Aldehydes, acids, alcohols and esters were identified by gas chromatography flame ionization detection. By the metabolites and PCA analysis we may assign the beverage's flavor to the microbial metabolism. Heterolactic LAB and S. cerevisiae dominated the yakupa fermentation, being responsible for the organoleptic characteristics of the final product. This is the first time that the microbial dynamics and physicochemical parameters were investigated in the yakupa beverage and it may contribute to the future selection of starter cultures to perform yakupa fermentations.

Enhancing the cellulose-degrading activity of cellulolytic bacteria CTL-6 (Clostridium thermocellum) by co-culture with non-cellulolytic bacteria W2-10 (Geobacillus sp.)

The effect of a non-cellulolytic bacterium W2-10 (Geobacillus sp.) on the cellulose-degrading activity of a cellulolytic bacterium CTL-6 (Clostridium thermocellum) was determined using cellulose materials (paper and straw) in peptone cellulose solution (PCS) medium under aerobic conditions. The results indicated that in the co-culture, addition of W2-10 resulted in a balanced medium pH, and may provide the required anaerobic environment for CTL-6. Overall, addition of W2-10 was beneficial to CTL-6 growth in the adverse environment of the PCS medium. In co-culture with W2-10, the CTL-6 cellulose degradation efficiency of filter paper and alkaline-treated wheat straw significantly increased up to 72.45 and 37.79 %, respectively. The CMCase activity and biomass of CTL-6 also increased from 0.23 U ml(-1) and 45.1 μg ml(-1) (DNA content) up to 0.47 U ml(-1) and 112.2 μg ml(-1), respectively. In addition, co-culture resulted in accumulation of acetate and propionate up to 4.26 and 2.76 mg ml(-1). This was a respective increase of 2.58 and 4.45 times, in comparison to the monoculture with CTL-6.

Screening of Lactobacillus isolated from pork sausages for potential probiotic use and evaluation of the microbiological safety of fermented products

The aim of this study was to select strains of Lactobacillus isolated from pork sausage for use as probiotics. Lactobacillus isolates were evaluated in tests based on probiotic characteristics and microbiological safety. The UFLA SAU 14, 52, and 91 isolates were differentiated by coaggregation with Listeria monocytogenes, production of lactic acid, and survival at pH 2. UFLA SAU 172 and 187 isolates had high levels of coaggregation with Salmonella Typhi and Escherichia coli, tolerance to pancreatic fluid, and adhesion to chloroform. UFLA SAU 20 and 34 isolates were characterized by exopolysaccharide production, autoaggregation, and resistance to simulated intestinal fluid. UFLA SAU 185, 238, and 258 isolates exhibited resistance to bile and adhesion to xylene. A cocktail of these 10 Lactobacillus isolates with potential probiotic properties was inoculated into pork sausage and inhibited the growth of L. monocytogenes.

Microbiological and chemical characteristics of Brazilian kefir during fermentation and storage processes

The microbial community composition and chemical characteristics of a Brazilian milk kefir sample produced during its manufacturing and refrigerated storage were investigated by culture-dependent and -independent methods and HPLC. Lactococcus lactis ssp. cremoris and ssp. lactis, Leuconostoc mesenteroides, Acetobacter lovaniensis, and Saccharomyces cerevisiae were isolated, whereas the detected bands on denaturing gel gradient electrophoresis corresponded to Lactobacillus kefiranofaciens, Lactobacillus kefiri, Lactobacillus parakefiri, and S. cerevisiae. After fermentation, lactic acid bacteria were present at levels of 10 log units, whereas acetic acid bacteria and yeast were present at levels of 7.8 and 6 log units, respectively. The lactic acid bacteria and yeast counts remained constant, whereas acetic acid bacteria counts decreased to 7.2 log units during storage. From fermentation to final storage, the pH, lactose content and citric acid of the kefir beverage decreased, followed by an increase in the concentrations of glucose, galactose, ethanol, and lactic, acetic, butyric, and propionic acids. These microbiological and chemical characteristics contribute to the unique taste and aroma of kefir. This research may serve as a basis for the future industrial production of this beverage in Brazil.

Optimization of liquid fermentation of microbial consortium WSD-5 followed by saccharification and acidification of wheat straw

The microbial consortium WSD-5 is composed of bacteria and fungi, and the cooperation and symbiosis of the contained microbes enhance the degradation ability of WSD-5. Experiment results showed that the highest cellulase and hemicellulase were obtained when ventilation volume was 4 L/min, stirring rate was 0 rpm, and substrate loading rate was 3%. After 6 days of cultivation, a 67.60% loss in wheat straw dry weight was observed. The crude enzyme secreted from WSD-5 after optimization was evaluated by experiments of saccharification and acidification. The maximum concentration of reducing sugars was 3254 mg/L after 48 h saccharification. The concentration of sCOD peaked on day 2 with a value of 4345 mg/L during acidification, and the biogas yield and methane yield were 22.3% and 32.3% higher than un-acidified samples. This study is the first attempt to explore both the saccharification and the acidification ability of crude enzymes secreted by microbial consortium.

Microbiological and physicochemical characterisation of caxiri, an alcoholic beverage produced by the indigenous Juruna people of Brazil

Caxiri is a traditional fermented alcoholic beverage produced from cassava and sweet potatoes by the indigenous Juruna or Yudjá people in Brazil. Our results showed that caxiri fermentation is invariably associated with the following: (i) an increase in the total microbial population, with yeast being the largest group detected; (ii) a decrease in reducing sugars, malic, tartaric, succinic, oxalic and propionic acid; and (iii) a final product characterised by a high content of ethanol and a high concentration of lactic acid. The microbial community dynamics were investigated by culture-based and culture-independent approaches. Fermentation was assisted by a complex microbial community that changed in structure and composition during the fermentative process. The bacterial population ranged from 3.05 to 5.33 log/mL, and the yeast population varied from 3.27 log CFU/mL to 7.34 log CFU/mL, showing that yeasts dominated the fermentation process after 48 h. A total of 343 colonies of bacteria and 205 colonies of yeasts were isolated and initially grouped by Amplified Ribosomal DNA Restriction Analysis (ARDRA) and by biochemical features. Phylogenetic analysis of the 16S rRNA gene sequences of representative isolates showed that the bacteria were mainly represented by endospore-forming low-G+C content Gram-positive bacilli (Bacillus spp.; 61.5% of the isolates), with Bacillus pumilus, Bacillus spp. (Bacillus cereus group), and Bacillus subtilis being the main species identified. The species Sphingomonas sp. and Pediococcus acidilactici were also found. The dominant yeast identified was Saccharomyces cerevisiae. Rhodotorula mucilaginosa, Pichia membranifaciens, Pichia guilliermondii and Cryptococcus luteolus were also found. According to the Polymerase Chain Reaction and Denaturing Gradient Gel Electrophoresis (PCR-DGGE) analysis, the microbial communities present during fermentation were probably from the raw materials, ambient or present on the utensils used during beverage preparation. The results indicated the necessity to combine both culture-dependent and culture-independent methods for a better description of the microbial communities in indigenous starch fermentations. Also, pH values decreased from 4.76 to 3.15 during fermentation. The ethanol concentration was 83.9 g/L and lactic acid reached 27.89 g/L by the end of the fermentation process.

A multiphasic approach for the identification of endophytic bacterial in strawberry fruit and their potential for plant growth promotion

This study used a multiphasic approach, characterized by the simultaneous use of culture-dependent and culture-independent methods, to investigate endophytic bacterial communities in strawberry (Fragaria ananassa) fruit. A total of 92 bacterial endophytes were isolated and initially grouped by their repetitive extragenic palindromic (rep)-PCR banding pattern and biochemical features. Phylogenetic analysis of the 16S rRNA gene sequences of 45 representatives showed that the isolates belonged to the species Bacillus subtilis (eight isolates), Bacillus sp. (seven isolates), Enterobacter sp. (seven isolates), Enterobacter ludwigii (six isolates), Lactobacillus plantarum (six isolates), Pseudomonas sp. (five isolates), Pantoea punctata (three isolates), and Curtobacterium citreum (three isolates). Nucleic acids were extracted from the strawberry fruit and subjected to 16S rRNA gene directed polymerase chain reaction denaturing gradient gel electrophoresis (16S rRNA PCR-DGGE). The species B. subtilis, Enterobacter sp., and Pseudomonas sp. were detected both by isolation and DGGE. The DGGE fingerprints of total bacterial DNA did not exhibit bands corresponding to several of the representative species isolated in the extinction dilution (L. plantarum, C. citreum, and P. punctata). In contrast, bands in the DGGE profile that were identified as relatives of Arthrobacter sp. and one uncultivable Erythrobacter sp. were not recovered by cultivation techniques. After isolation, the nitrogen fixation ability and the in vitro production of indole-3-acetic acid (IAA) equivalents and siderophores were evaluated. A high percentage of isolates were found to possess the ability to produce siderophores and IAA equivalents; however, only a few isolates belonging to the genera Pseudomonas and Enterobacter showed the ability to fix nitrogen. Plant growth promotion was evaluated under greenhouse conditions and revealed the ability of the Bacillus strains to enhance the number of leaves, shoot length, root dry weight, and shoot dry weight. The activity of the bacterial isolate identified as B. subtilis NA-108 exerted the greatest influence on strawberry growth and showed a 42.8% increase in number of leaves, 15.26% for high shoot, 43.5% increase in root dry weight, and a 77% increase in shoot dry weight when compared with untreated controls.

Bioreactor performance and methanogenic population dynamics in a low-temperature (5-18 °C) anaerobic fixed-bed reactor

The effect of temperature on the functionality of microbial community structure in a low temperature, anaerobic fixed-bed reactor was studied by decreasing the operating temperature from 18 °C to 5 °C. The reactor was productive within 20 days and produced stable methane content in biogas (above 77%) throughout the trial period. At 17 °C and 15 °C, chemical oxygen demand (COD) removal efficiency and biogas production of reactor were significantly reduced. These might be temperature thresholds when fixed-bed reactors are operated under low temperatures. The methanogen community composition was analyzed using 16S rRNA gene clone library screening and quantitative PCR. At low ambient temperatures, Methanomicrobiales were dominant methanogens, and they preferentially adhered to the carbon fiber carrier. The results indicated that 16S rRNA levels of Methanomicrobiales and Methanosaetaceae in adhering sludge were higher than in deposited sludge, and they all contributed to the efficient performance of the fixed-bed reactor at low operating temperatures.

Characterization of a microbial consortium capable of degrading lignocellulose

A microbial consortium, designated WCS-6, was established by successive subcultivation in the presence of rice straw under static conditions. The degradation efficiencies of WSC-6 for 0.5 g filter paper, cotton and rice straw after 3 days of cultivation were 99.0±0.7%, 76.9±1.5% and 81.3±0.8%, respectively as determined by gravimetrical methods. Nine bacterial isolates were obtained from WCS-6 plated under aerobic conditions, and sequencing of their 16S rDNA indicated that these bacteria were related to Bacillus thermoamylovorans BTa, Paenibacillus barengoltzii SAFN-016, Proteobacterium S072, Pseudoxanthomonas taiwanensis CB-226, Rhizobiaceae str. M100, Bacillus sp. E53-10, Beta proteobacterium HMD444, Petrobacter succinimandens 4BON, and Tepidiphilus margaritifer N2-214. DGGE (denaturing gradient gel electrophoresis) and sequencing of 16S rDNA sequences amplified from total consortium DNA revealed the presence of sequences related to those of Ureibacillus thermosphaericus, uncultured bacterium clone GC3, uncultured Clostridium sp. clone A1-3, Clostridium thermobutyricum, and Clostridium thermosuccinogenes in addition to the sequences identified from the cultured bacteria. The microbial community identified herein is a potential candidate consortium for the degradation of waste lignocellulosic biomass.

Identification and characterization of lactic acid bacteria isolated from mixed pasture of timothy and orchardgrass, and its badly preserved silage

In order to understand the relationship between lactic acid bacteria (LAB) species and silage fermentation, a total of 65 LAB strains isolated from mixed pasture of timothy (Phleum pratense L.) and orchardgrass (Dactylis glomerata L.), and its badly preserved silages were subjected to phenotypic and genetic analysis. According to these analyses, the isolates were divided into 13 groups, including Enterococcus gallinarum, Lactobacillus acidipiscis, L. coryniformis subsp. coryniformis, L. coryniformis subsp. torquens, L. curvatus, L. paraplantarum, L. plantarum subsp. argentoratensis, L. plantarum subsp. plantarum, L. sakei subsp. carnosus, Lactococcus garvieae, Lactococcus lactis subsp. cremoris, Leuconostoc pseudomesenteroides, Pediococcus acidilactici, Pediococcus pentosaceus, Weissella hellenica, Weissella paramesenteroides and Carnobacterium divergens. This is the first report to document that C. divergens, L. acidipiscis, L. sakei subsp. carnosus, L. garvieae, phenotypically novel L. lactis subsp. cremoris, E. gallinarum and W. hellenica are present in vegetative forage crops. L. plantarum group strains were most frequently isolated from the badly preserved silages. Some isolates showed a wide range of growth preferences for carbohydrate utilization, optimal growth pH and temperature in vitro, indicating that they have a high growth potential. These results are useful in understanding the diversity of LAB associated with decayed silage of timothy and orchardgrass.

Effects of different pretreatment strategies on corn stalk acidogenic fermentation using a microbial consortium

The effects of sulfuric acid, acetic acid, aqueous ammonia, sodium hydroxide, and steam explosion pretreatments of corn stalk on organic acid production by a microbial consortium, MC1, were determined. Steam explosion resulted in a substrate that was most favorable for microbial growth and organic acid productions. The total amounts of organic acids produced by MC1 on steam exploded, sodium hydroxide, sulfuric acid, acetic acid, and aqueous ammonia pretreated corn stalk were 2.99, 2.74, 1.96, 1.45, and 2.21g/l, respectively after 3days of fermentation at 50°C. The most prominent organic products during fermentation of steam-exploded corn stalks were formic (0.86g/l), acetic (0.59g/l), propanoic (0.27g/l), butanoic (0.62g/l), and lactic acid (0.64g/l) after 3days of fermentation; ethanol (0.18g/l), ethanediol (0.68g/l), and glycerin (3.06g/l) were also produced. These compounds would be suitable substrates for conversion to methane by anaerobic digestion.

Brazilian kefir: structure, microbial communities and chemical composition

Microbial ecology and chemical composition of Brazilian kefir beverage was performed. The microorganisms associated with Brazilian kefir were investigated using a combination of phenotypic and genotypic methods. A total of 359 microbial isolates were identified. Lactic acid bacteria (60.5%) were the major isolated group identified, followed by yeasts (30.6%) and acetic acid bacteria (8.9%). Lactobacillus paracasei (89 isolates), Lactobacillus parabuchneri (41 isolates), Lactobacillus casei (32 isolates), Lactobacillus kefiri (31 isolates), Lactococcus lactis (24 isolates), Acetobacter lovaniensis (32 isolates), Kluyveromyces lactis (31 isolates), Kazachstania aerobia (23 isolates), Saccharomyces cerevisiae (41 isolates) and Lachancea meyersii (15 isolates) were the microbial species isolated. Scanning electron microscopy showed that the microbiota was dominated by bacilli (short and curved long) cells growing in close association with lemon-shaped yeasts cells. During the 24 h of fermentation, the protein content increased, while lactose and fat content decreased. The concentration of lactic acid ranged from 1.4 to 17.4 mg/ml, and that of acetic acid increased from 2.1 to 2.73 mg/ml. The production of ethanol was limited, reaching a final mean value of 0.5 mg/ml.

Characterization of the effective cellulose degrading strain CTL-6

An efficient cellulose degrading bacteria exists in the thermophilic wheat straw-degrading community, WDC2. However, this strain cannot be isolated and cultured using conventional separation techniques under strict anaerobic conditions. We successfully isolated a strain of effective cellulose degrading bacteria CTL-6 using a wash, heat shock, and solid-liquid alternating process. Analysis of its properties revealed that, although the community containing the strain CTL-6 grew under aerobic conditions, the purified strain CTL-6 only grew under anaerobic culture conditions. The strain CTL-6 had a striking capability of degrading cellulose (80.9% weight loss after 9 days of culture). The highest efficiency value of the endocellulase (CMCase activity) was 0.404 micromol/(min mL), cellulose degradation efficiency by CTL-6 was remarkably high at 50-65 degrees C with the highest degradation efficiency observed at 60 degrees C. The 16S rRNA gene sequence analysis indicated that the closest relative to strain CTL-6 belonged to the genus Clostridium thermocellum. Strain CTL-6 was capable of utilizing cellulose, cellobiose, and glucose. Strain CTL-6 also grew with Sorbitol as the sole carbon source, whereas C. thermocellum is unable to do so.

Microbial population dynamics and changes in main nutrients during the acidification process of pig manures

This study evaluated the impact of pig manure acidification on anaerobic treatment and composition of the fecal microbial community. According to the different chemical oxygen demand (COD) in the anaerobic treatment processes, pig manure was diluted 4 times (x4), 16 times (x16), or 64 times (x64) and subjected to acidification. During the acidification process, pH, soluble chemical oxygen demand (SCOD), volatile fatty acids (VFAs), nitrogen (N), phosphorus (P) and potassium (K) were determined along with microbial population dynamics. The pH of the three dilutions first declined, and then slowly increased. The total VFAs of x4 and x16 dilutions peaked on day 15 and 20, respectively. The content of acetic acid, propanoic acid, butanoic acid and valeric acid of the x4 dilution were 23.6, 11.4, 8.8 and 0.6 g/L respectively, and that of the x16 dilution was 5.6, 2.3, 0.9 and 0.2 g/L respectively. Only acetic acid was detected in the x64 dilution, and its level peaked on day 10. The results showed that the liquid pig manure was more suitable to enter the anaerobic methanogenic bioreactors after two weeks of acidification. During the acidification process, total P concentration increased during the first ten days, then dropped sharply, and rose again to a relatively high final concentration, while total N concentration rose initially and then declined. Based on the analysis of denaturing gradient gel electrophoresis (DGGE) and 16S rRNA gene clone library, we concluded that the acidification process reduced the number of pathogenic bacteria species in pig manure.

Production of fermented cheese whey-based beverage using kefir grains as starter culture: evaluation of morphological and microbial variations

Whey valorization concerns have led to recent interest on the production of whey beverage simulating kefir. In this study, the structure and microbiota of Brazilian kefir grains and beverages obtained from milk and whole/deproteinised whey was characterized using microscopy and molecular techniques. The aim was to evaluate its stability and possible shift of probiotic bacteria to the beverages. Fluorescence staining in combination with Confocal Laser Scanning Microscopy showed distribution of yeasts in macro-clusters among the grain's matrix essentially composed of polysaccharides (kefiran) and bacteria. Denaturing gradient gel electrophoresis displayed communities included yeast affiliated to Kluyveromyces marxianus, Saccharomyces cerevisiae, Kazachatania unispora, bacteria affiliated to Lactobacillus kefiranofaciens subsp. Kefirgranum, Lactobacillus kefiranofaciens subsp. Kefiranofaciens and an uncultured bacterium also related to the genus Lactobacillus. A steady structure and dominant microbiota, including probiotic bacteria, was detected in the analyzed kefir beverages and grains. This robustness is determinant for future implementation of whey-based kefir beverages.