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

ABSTRACTFeces from cattle production are considered important sources of bacterial contamination of food and the environment. Little is known about the combined effects of arctic temperatures and fodder tannins on rumen and hindgut bacterial populations. Individual rumen liquor and rectal fecal samples from donor steers fed either alfalfa silage or sainfoin (Onobrychis viciifoliaScop.) silage and waterad libitumwere collected weekly on the first three sampling days and fortnightly afterwards. The daily ambient temperatures were registered and averaged to weekly mean temperatures. Steers fed sainfoin silage had lower (P< 0.05) concentrations of branched-chain volatile fatty acids (VFA) than those fed alfalfa silage. All VFA concentrations were higher (P< 0.001) in rumen liquor samples than in fecal samples. The interaction of sample type and diet showed a significant effect (P< 0.05) on the proportions of the bacterial community that were from the phylaProteobacteriaandVerrucomicrobia.Ambient temperature had an indirect effect (P< 0.05) on the phylumFirmicutes, as it affected its proportional balance. The bacterial population diversity in samples appeared to decrease concurrently with the ambient temperature. The phylumFirmicutesexplained the first principal component at 64.83 and 42.58% of the total variance in rumen liquor and fecal samples, respectively. The sample type had a larger effect on bacterial communities than diet and temperature. Certain bacterial populations seemed to be better adapted than others to environmentally adverse conditions, such as less access time to nutrients due to higher motility and rate of passage of digesta caused by extreme temperatures, or antimicrobials such as tannins, possibly due to an influence of their biogeographical location within the gut.

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Microbial community dynamics during alfalfa silage with or without clostridial fermentation

Scientific Reports ◽

10.1038/s41598-020-74958-1 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Rongrong Li ◽

Di Jiang ◽

Mingli Zheng ◽

Pengjiao Tian ◽

Menghu Zheng ◽

...

Keyword(s):

Microbial Community ◽

Next Generation Sequencing ◽

Bacterial Communities ◽

Community Dynamics ◽

Ammonia Nitrogen ◽

Clostridium Tyrobutyricum ◽

Microbial Community Dynamics ◽

Vigorous Growth ◽

Alfalfa Silage ◽

Generation Sequencing

Abstract This study was conducted to examine the effects of Lactobacillus plantarum (LP) and sucrose (S) on clostridial community dynamics and correlation between clostridia and other bacteria in alfalfa silage during ensiling. Fresh alfalfa was directly ensiled without (CK) or with additives (LP, S, LP + S) for 7, 14, 28 and 56 days. Clostridial and bacterial communities were evaluated by next-generation sequencing. Severe clostridial fermentation occurred in CK, as evidenced by the high contents of butyric acid, ammonia nitrogen, and clostridia counts, whereas all additives, particularly LP + S, decreased silage pH and restrained clostridial fermentation. Clostridium perfringens and Clostridium butyricum might act as the main initiators of clostridial fermentation, with Clostridium tyrobutyricum functioning as the promoters of fermentation until the end of ensiling. Clostridium tyrobutyricum (33.5 to 98.0%) dominated the clostridial community in CK from 14 to 56 days, whereas it was below 17.7% in LP + S. Clostridium was negatively correlated with the genus Lactobacillus, but positively correlated with the genera Enterococcus, Lactococcus and Leuconostoc. Insufficient acidification promoted the vigorous growth of C. tyrobutyricum of silage in later stages, which was mainly responsible for the clostridial fermentation of alfalfa silage.

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Metagenomic analysis of the bacterial communities and their functional profiles in water and sediments of the Apies River, South Africa, as a function of land use

The Science of The Total Environment ◽

10.1016/j.scitotenv.2017.10.322 ◽

2018 ◽

Vol 616-617 ◽

pp. 326-334 ◽

Cited By ~ 31

Author(s):

Akebe Luther King Abia ◽

Arghavan Alisoltani ◽

Jitendra Keshri ◽

Eunice Ubomba-Jaswa

Keyword(s):

South Africa ◽

Land Use ◽

Bacterial Communities ◽

Metagenomic Analysis ◽

Functional Profiles

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Accounting for 16S rRNA copy number prediction uncertainty and its implications in microbial diversity analyses

10.1101/2021.08.31.458422 ◽

2021 ◽

Author(s):

Yingnan Gao ◽

Martin Wu

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Microbial Diversity ◽

Bacterial Communities ◽

Beta Diversity ◽

Copy Number ◽

Rrna Gene ◽

Prediction Uncertainty ◽

Functional Profiles ◽

Diversity Studies

Background: 16S rRNA gene has been widely used in microbial diversity studies to determine the community composition and structure. 16S rRNA gene copy number (16S GCN) varies among microbial species and this variation introduces biases to the relative cell abundance estimated using 16S rRNA read counts. To correct the biases, methods (e.g., PICRUST2) have been developed to predict 16S GCN. 16S GCN predictions come with inherent uncertainty, which is often ignored in the downstream analyses. However, a recent study suggests that the uncertainty can be so great that copy number correction is not justified in practice. Despite the significant implications in 16S rRNA based microbial diversity studies, the uncertainty associated with 16S GCN predictions has not been well characterized and its impact on microbial diversity studies needs to be investigated. Results: Here we develop RasperGade16S, a novel method and software to better model and capture the inherent uncertainty in 16S rRNA GCN prediction. RasperGade16S implements a maximum likelihood framework of pulsed evolution model and explicitly accounts for intraspecific GCN variation and heterogeneous GCN evolution rates among species. Using cross validation, we show that our method provides robust confidence estimates for the GCN predictions and outperforms PICRUST2 in both precision and recall. We have predicted GCN for 592605 OTUs in the SILVA database and tested 113842 bacterial communities that represent an exhaustive and diverse list of engineered and natural environments. We found that the prediction uncertainty is small enough for 99% of the communities that 16S GCN correction should improve their compositional and functional profiles estimated using 16S rRNA reads. On the other hand, we found that GCN variation has limited impacts on beta-diversity analyses such as PCoA, PERMANOVA and random forest test. Conclusion: We have developed a method to accurately account for uncertainty in 16S rRNA GCN predictions and the downstream analyses. For almost all 16S rRNA surveyed bacterial communities, correction of 16S GCN should improve the results when estimating their compositional and functional profiles. However, such correction is not necessary for beta-diversity analyses.

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Mechanism of Intermittent Deep Tillage and Different Depths Improving Crop Growth From the Perspective of Rhizosphere Soil Nutrients, Root System Architectures, Bacterial Communities, and Functional Profiles

Frontiers in Microbiology ◽

10.3389/fmicb.2021.759374 ◽

2022 ◽

Vol 12 ◽

Author(s):

Yabing Gu ◽

Yongjun Liu ◽

Jiaying Li ◽

Mingfeng Cao ◽

Zhenhua Wang ◽

...

Keyword(s):

Root System ◽

Soil Nutrients ◽

Crop Yield ◽

System Architecture ◽

Bacterial Communities ◽

Root System Architecture ◽

Crop Growth ◽

Deep Tillage ◽

Tillage Practices ◽

Functional Profiles

Long-term conventional shallow tillage reduced soil quality and limited the agriculture development. Intermittent deep tillage could effectively promote agricultural production, through optimizing soil structure, underground ecology system, and soil fertility. However, the microecological mechanism of intermittent deep tillage promoting agriculture production has never been reported, and the effect of tillage depth on crop growth has not been explored in detail. In this study, three levels of intermittent deep tillage (30, 40, and 50 cm) treatments were conducted in an experimental field site with over 10 years of conventional shallow tillage (20 cm). Our results indicated that intermittent deep tillage practices helped to improve plant physiological growth status, chlorophyll a, and resistance to diseases, and the crop yield and value of output were increased with the deeper tillage practices. Crop yield (18.59%) and value of output (37.03%) were highest in IDT-50. There were three mechanisms of intermittent deep tillage practices that improved crop growth: (1) Intermittent deep tillage practices increased soil nutrients and root system architecture traits, which improved the fertility and nutrient uptake of crop through root system. (2) Changing rhizosphere environments, especially for root length, root tips, pH, and available potassium contributed to dissimilarity of bacterial communities and enriched plant growth-promoting species. (3) Functions associated with stress tolerance, including signal transduction and biosynthesis of other secondary metabolites were increased significantly in intermittent deep tillage treatments. Moreover, IDT-30 only increased soil characters and root system architecture traits compared with CK, but deeper tillage could also change rhizosphere bacterial communities and functional profiles. Plant height and stem girth in IDT-40 and IDT-50 were higher compared with IDT-30, and infection rates of black shank and black root rot in IDT-50 were even lower in IDT-40. The study provided a comprehensive explanation into the effects of intermittent deep tillage in plant production and suggested an optimal depth.

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Metagenomics reveals diet-specific specialization of bacterial communities in fungus gardens of grass- and dicot-cutter ants

10.1101/250993 ◽

2018 ◽

Cited By ~ 1

Author(s):

Lily Khadempour ◽

Huan Fan ◽

Ken Keefover-Ring ◽

Camila Carlos ◽

Nilson S. Nagamoto ◽

...

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Bacterial Communities ◽

Potential Role ◽

Sequence Data ◽

Bacterial Community Composition ◽

Fungus Garden ◽

Functional Profiles ◽

Ant Fungus

AbstractLeaf-cutter ants in the genusAttaare dominant herbivores in the Neotropics. While most species ofAttacut dicots to incorporate into their fungus gardens, some species specialize on grasses. Here we examine the bacterial community associated with the fungus gardens of grass- and dicot-cutter ants to examine how changes in substrate input affect the bacterial community. We sequenced the metagenomes of 12Attafungus gardens, across four species of ants, with a total of 5.316 Gbp of sequence data. We show significant differences in the fungus garden bacterial community composition between dicot- and grass-cutter ants, with grass-cutter ants having lower diversity. Reflecting this difference in community composition, the bacterial functional profiles between the fungus gardens are significantly different. Specifically, grass-cutter ant fungus garden metagenomes are particularly enriched for genes responsible for amino acid, siderophore, and terpenoid biosynthesis while dicot-cutter ant fungus gardens metagenomes are enriched in genes involved in membrane transport. These differences in bacterial community composition and functional capacity show that different substrate inputs matter for fungus garden bacteria, and sheds light on the potential role of bacteria in mediating the ants’ transition to the use of a novel substrate.

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Metataxonomic profiling of bacterial communities and their predictive functional profiles in traditionally preserved meat products of Sikkim state in India

Food Research International ◽

10.1016/j.foodres.2020.110002 ◽

2021 ◽

Vol 140 ◽

pp. 110002

Author(s):

Meera Ongmu Bhutia ◽

Namrata Thapa ◽

H. Nakibapher Jones Shangpliang ◽

Jyoti Prakash Tamang

Keyword(s):

Bacterial Communities ◽

Meat Products ◽

Functional Profiles

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Comparative Metagenomic and Metabolomic Profiling of Rhizospheres of Panax notoginseng Grown under Forest and Field Conditions

Agronomy ◽

10.3390/agronomy11122488 ◽

2021 ◽

Vol 11 (12) ◽

pp. 2488

Author(s):

Rui Shi ◽

Haiyan Gu ◽

Shu He ◽

Binjie Xiong ◽

Youguo Huang ◽

...

Keyword(s):

Bacterial Communities ◽

Microbial Population ◽

Panax Notoginseng ◽

Field Conditions ◽

Root Weight ◽

Metagenomic Sequencing ◽

Forest Plantation ◽

Metabolomic Profiling ◽

Functional Profiles ◽

Forest Conditions

The present study investigated the potential changes in the structure of bacterial communities and their functional profiles in the rhizospheres of Panax notoginseng cultivated under field (CK) and pine forest conditions (T). The rhizospheres of two-year-old P. notoginseng plants were used to extract DNA for metagenomic sequencing and metabolites for metabolomic profiling. The results revealed a higher root weight (p < 0.05) in plants grown under the forest than CK. The rhizospheric bacterial community comprised mainly three dominant phyla including Acidobacteria, Proteobacteria, and Candidatus rokubacteria which accounted for 75% of the total microbial population. Among them, Acidobacteria was the most abundant bacterial taxa, accounting for 42.4% and 40.4% of the total populations in CK and T, respectively. Relative abundances of bacterial genera revealed that Bradyrhizobium, Candidatus koribacter and Edaphobacter, were the dominant genera in both groups. Comparatively, a higher Proteobacteria to Acidobacteria ratio was observed in forest rhizospheres than in field conditions. Candidatus Rokubacteria and Candidatus nitrostelea were identified as biomarker taxa in forest rhizospheres, while the same could be said for taxa belonging to betaproteobacteria and gammaproteobacteria, Burkholderiales and Verrucomicrobia for field rhizospheres. No differential metabolite contents were observed between the two rhizosphere groups, indicating no adverse effects of P. notoginseng cultivation on the soil quality under forest plantation.

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Dynamics of the Fermentation Products, Residual Non-structural Carbohydrates, and Bacterial Communities of Wilted and Non-wilted Alfalfa Silage With and Without Lactobacillus plantarum Inoculation

Frontiers in Microbiology ◽

10.3389/fmicb.2021.824229 ◽

2022 ◽

Vol 12 ◽

Author(s):

Fengyuan Yang ◽

Yanping Wang ◽

Shanshan Zhao ◽

Changsong Feng ◽

Xiaomiao Fan

Keyword(s):

Bacterial Community ◽

Lactobacillus Plantarum ◽

Bacterial Communities ◽

High Throughput Sequencing ◽

Bacterial Community Composition ◽

Water Soluble ◽

Soluble Carbohydrates ◽

Fermentation Products ◽

Fermentation Quality ◽

Alfalfa Silage

The aim of this study was to investigate effects of wilting and Lactobacillus plantarum inoculation on the dynamics of the fermentation products, residual non-structural carbohydrates, and bacterial communities in alfalfa silage. Fresh and wilted alfalfa were ensiled with and without L. plantarum for 10, 30, 60, and 90 days. A high-throughput sequencing method for absolute quantification of 16S rRNA was adopted to determine the bacterial community composition at different ensiling periods. For the wilted silage, the bacterial community, pH value, and ammonia nitrogen concentration remained stable in the silage at 30 days. L. plantarum inoculation accelerated lactic acid fermentation and altered the predominant genus in the wilted silage as compared with the non-inoculated group. For the non-wilted group, fast consumption of water-soluble carbohydrates (WSCs) was observed at 10 days in the non-inoculated silage along with rapid growth of undesirable Hafnia. L. plantarum inoculation inhibited growth of Hafnia at 10 days in the non-wilted silage. Clostridia fermentation occurred in the non-wilted silage at 90 days, as indicated by an increased pH, formation of butyric acid (BA), and apparent abundance of genera belonging to Clostridia. L. plantarum inoculation inhibited BA accumulation and growth of Garciella in the non-wilted silage at 90 days as compared with the non-wilted silage without inoculation, but had little effect on the growth of Clostridium sensu stricto. Overall, the high moisture content of the non-wilted alfalfa silage led to rapid consumption of WSCs and growth of harmful microorganisms at the early stage of ensiling, resulting in poor fermentation quality. Wilting and L. plantarum inoculation both improved fermentation quality and inhibited the growth of spoilage microorganisms in alfalfa silage, while L. plantarum inoculation alone failed to achieve optimum fermentation quality of non-wilted alfalfa silage.

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The Microbiota Dynamics of Alfalfa Silage During Ensiling and After Air Exposure, and the Metabolomics After Air Exposure Are Affected by Lactobacillus casei and Cellulase Addition

Frontiers in Microbiology ◽

10.3389/fmicb.2020.519121 ◽

2020 ◽

Vol 11 ◽

Author(s):

Zongfu Hu ◽

Huaxin Niu ◽

Qing Tong ◽

Jie Chang ◽

Jianhua Yu ◽

...

Keyword(s):

Mass Spectrometry ◽

Gas Chromatography ◽

Lactic Acid ◽

Bacterial Community ◽

Bacterial Communities ◽

Lactobacillus Casei ◽

Gas Chromatography Mass Spectrometry ◽

Air Exposure ◽

Fresh Matter ◽

Alfalfa Silage

Both inoculants treatment and enzyme treatment promote the reproduction of lactic acid bacteria (LAB) to produce enough lactic acid to lower pH in silage. The present study investigated the microbial community and metabolome in cellulase, Lactobacillus casei, and air treated alfalfa silage. Chopped and wilted alfalfa (first cutting, 29% dry matter) was ensiled without (CON) or with L. casei (1 × 106 cfu g–1 fresh matter) (LC) or cellulase (20,000IU, 0.5% of fresh matter) (CE) for 56 days, then exposed to air for 3 days (PO). Greater ensiling quality was observed in LC and CE, which had lower pH and higher lactic acid content than CON at 56 days of ensiling and 3 days post-oxygen exposure. Air exposure was associated with decreased lactic acid concentrations and increased yeast and mold counts in all silages. SEM showed that the structure of leaf epicuticular wax crystals were intact in fresh alfalfa, totally decomposed in CON silage, and partly preserved in CE and LC silage. Gas chromatography mass spectrometry revealed that 196 metabolites and 95 differential concentration were present in the 3 days air exposure samples. Most of these metabolites, mainly organic acids, polyols, ketones, aldehydes, are capable of antimicrobial activity. The bacterial communities were obviously different among groups and Lactobacillus developed to a dominant status in all silages. Lactobacillus became dominant in bacterial communities of LC and CE silages from days 7 to 56, and their relative abundances reached 94.17–83.93% at day 56, respectively. For CON silage, until day 56, Lactobacillus dominated the bacterial community with abundance of 75.10%. After 3 days of oxygen exposure, Lactobacillus and Enterococcus were predominant in CON, and Lactobacillus remained dominant in LC and CE silages. The results indicated that, compared to untreated silages, L. casei could be a priority inoculant for alfalfa silage to boost Lactobacillus abundance and improve fermentation quality. Our high-throughput sequencing and gas chromatography mass spectrometry results provide a deep insight into the bacterial community and metabolites in alfalfa silage.

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