scholarly journals Bacterial Communities and Prediction of Microbial Metabolic Pathway in Rice Wine Koji From Different Regions in China

2022 ◽  
Vol 12 ◽  
Author(s):  
Xinxin Zhao ◽  
Fanshu Xiang ◽  
Fengxian Tang ◽  
Wenchao Cai ◽  
Zhuang Guo ◽  
...  

Rice wine koji, a traditional homemade starter culture in China, is nutritious and delicious. The final quality of rice wine koji is closely related to the structure of its microbial community. However, the diversity of natural microorganisms in rice wine koji from different regions has not been evaluated. In this study, the microbial population of 92 naturally fermented rice koji samples collected from Hubei, Guangxi, and Sichuan was systematically analyzed by high-throughput sequencing. From all the rice wine koji samples, 22 phyla and 479 bacterial genera were identified. Weissella, Pediococcus, Lactobacillus, Enterobacter, Lactococcus, Pantoea, Bacillus, Staphylococcus, and Leuconostoc were the dominant genera in rice wine koji. The bacterial community structure of rice wine koji samples from different regions was significantly different (p < 0.05). The bacterial community composition of the samples from Hubei and Guangxi was similar, but significantly different from that of SC samples (p < 0.05). These differences may be caused by variations in geography, environment, or manufacturing. In addition, the results of microbial phenotype prediction by BugBase and bacterial functional potential prediction by PICRUSt showed that eight of the nine predicted phenotypic functions of rice wine koji samples from different regions were significantly different (p < 0.05) and that vigorous bacterial metabolism occurred in rice wine koji samples.

2014 ◽  
Author(s):  
Alese Colehour ◽  
James F Meadow ◽  
Tara J Cepon-Robins ◽  
Theresa E Gildner ◽  
Melissa A Liebert ◽  
...  

Cassava beer, or chicha, is typically consumed daily by the indigenous Shuar people of the Ecuadorian Amazon. This traditional beverage made from cassava tuber (Manihot esculenta) improves nutritional quality and flavor while extending shelf life in a tropical climate. Bacteria responsible for chicha fermentation could be a source of microbes beneficial to human health, but little is known regarding the microbiology of chicha. We investigated bacterial community composition of chicha batches using Illumina high-throughput sequencing. Fermented chicha samples were collected from seven Shuar households in two neighboring villages in the Morona-Santiago region of Ecuador, and the composition of the bacterial communities within each chicha sample was determined by sequencing a region of the 16S ribosomal gene. Members of the genus Lactobacillus dominated all samples, demonstrating that chicha is a source of organisms related to known probiotics. Significantly greater taxonomic similarity was observed between communities in chicha samples taken within a village than those from different villages. Community composition varied among chicha samples, even those separated by short geographic distances, suggesting that ecological and/or evolutionary processes, including human preference, may be responsible for creating locally adapted and regionally resilient ferments. Our results suggest that traditional fermentation may be a form of domestication that provides endemic beneficial inocula for consumers.


2014 ◽  
Author(s):  
Alese Colehour ◽  
James F Meadow ◽  
Tara J Cepon-Robins ◽  
Theresa E Gildner ◽  
Melissa A Liebert ◽  
...  

Cassava beer, or chicha, is typically consumed daily by the indigenous Shuar people of the Ecuadorian Amazon. This traditional beverage made from cassava tuber (Manihot esculenta) improves nutritional quality and flavor while extending shelf life in a tropical climate. Bacteria responsible for chicha fermentation could be a source of microbes beneficial to human health, but little is known regarding the microbiology of chicha. We investigated bacterial community composition of chicha batches using Illumina high-throughput sequencing. Fermented chicha samples were collected from seven Shuar households in two neighboring villages in the Morona-Santiago region of Ecuador, and the composition of the bacterial communities within each chicha sample was determined by sequencing a region of the 16S ribosomal gene. Members of the genus Lactobacillus dominated all samples, demonstrating that chicha is a source of organisms related to known probiotics. Significantly greater taxonomic similarity was observed between communities in chicha samples taken within a village than those from different villages. Community composition varied among chicha samples, even those separated by short geographic distances, suggesting that ecological and/or evolutionary processes, including human preference, may be responsible for creating locally adapted and regionally resilient ferments. Our results suggest that traditional fermentation may be a form of domestication that provides endemic beneficial inocula for consumers.


2022 ◽  
Vol 12 ◽  
Author(s):  
Fengyuan Yang ◽  
Yanping Wang ◽  
Shanshan Zhao ◽  
Changsong Feng ◽  
Xiaomiao Fan

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.


2021 ◽  
Author(s):  
Lidong Lin ◽  
Nengfei Wang ◽  
Wenbing Han ◽  
Botao Zhang ◽  
Jiaye Zang ◽  
...  

Abstract The present study assessed the diversity and composition of bacterial communities in glacial runoff and glacial soils in the Midre Lovénbreen glacier region of Svalbard. A total of 6,593 operational taxonomic units were identified by high-throughput sequencing. The results showed differences in bacterial community composition between the upper and lower reaches of glacial runoff. The abundance of Actinobacteria, Firmicutes, Betaproteobacteria and Gammaproteobacteria in the upper reaches of glacial runoff was higher than that in the lower reaches. In contrast, the the abundance of Cyanobacteria and Alphaproteobacteria in the downstream of glacial runoff was higher than that in the upstream. In addition, we compared bacterial diversity and composition between glacial runoff areas and soils. The chart analysis showed that bacterial diversity in glacial soil was higher than that in the glacial runoff. Some typical bacteria in the soil, such as Actinobacteria, entered glacial runoff through contact between them. The abundance of Acidobacteria, Sphingobacterium and Flavobacterium was higher in glacial soil. Weighted correlation network analysis showed that the core bacteria in glacial runoff and glacial soil were typical bacteria in different habitats. Distance-based redundancy analysis revealed that NO 2 - -N was the most significant factor affecting the distribution of soil bacterial community, while NO 3 - -N was the most significant factor affecting the distribution of glacial runoff bacterial community.


2018 ◽  
Vol 84 (12) ◽  
pp. e02797-17 ◽  
Author(s):  
Dandi Hou ◽  
Zhi Lin ◽  
Runze Wang ◽  
Jun Ge ◽  
Shuai Wei ◽  
...  

ABSTRACTRhizospheric bacteria play important roles in plant tolerance and activation of heavy metals. Understanding the bacterial rhizobiome of hyperaccumulators may contribute to the development of optimized phytoextraction for metal-polluted soils. We used 16S rRNA gene amplicon sequencing to investigate the rhizospheric bacterial communities of the cadmium (Cd) hyperaccumulating ecotype (HE)Sedum alfrediiin comparison to its nonhyperaccumulating ecotype (NHE). Both planting of two ecotypes ofS. alfrediiand elevated Cd levels significantly decreased bacterial alpha-diversity and altered bacterial community structure in soils. The HE rhizosphere harbored a unique bacterial community differing from those in its bulk soil and NHE counterparts. Several key taxa fromActinobacteria,Bacteroidetes, and TM7 were especially abundant in HE rhizospheres under high Cd stress. The actinobacterial genusStreptomyceswas responsible for the majority of the divergence of bacterial community composition between the HE rhizosphere and other soil samples. In the HE rhizosphere, the abundance ofStreptomyceswas 3.31- to 16.45-fold higher than that in other samples under high Cd stress. These results suggested that both the presence of the hyperaccumulatorS. alfrediiand Cd exposure select for a specialized rhizosphere bacterial community during phytoextraction of Cd-contaminated soils and that key taxa, such as the species affiliated with the genusStreptomyces, may play an important role in metal hyperaccumulation.IMPORTANCESedum alfrediiis a well-known Cd hyperaccumulator native to China. Its potential for extracting Cd relies not only on its powerful uptake, translocation, and tolerance for Cd but also on processes underground (especially rhizosphere microbes) that facilitate root uptake and tolerance of the metal. In this study, a high-throughput sequencing approach was applied to gain insight into the soil-plant-microbe interactions that may influence Cd accumulation in the hyperaccumulatorS. alfredii. Here, we report the investigation of rhizosphere bacterial communities ofS. alfrediiin phytoremediation of different levels of Cd contamination in soils. Moreover, some key taxa in its rhizosphere identified in the study, such as the species affiliated with genusStreptomyces, may shed new light on the involvement of bacteria in phytoextraction of contaminated soils and provide new materials for phytoremediation optimization.


2019 ◽  
Author(s):  
Juanjuan Fu ◽  
Yilan Luo ◽  
Pengyue Sun ◽  
Jinzhu Gao ◽  
Donghao Zhao ◽  
...  

Abstract Background: Perturbations in the abiotic stress directly or indirectly affect plants and root-associated microbial communities. Shade stress presents one of the major abiotic limitations for turfgrass growth, as light availability is severely reduced under a leaf canopy. Studies have shown that shade stress influences plant growth and alters plant metabolism, yet little is known about how it affects the structure of rhizosphere soil bacterial communities. In this study, a glasshouse experiment was conducted to examine the impact of shade stress on the physiology of two contrasting shade-tolerant turfgrasses and their rhizosphere soil microbes. Shade-tolerant dwarf lilyturf (Ophiopogon japonicus, OJ) and shade-intolerant perennial turf-type ryegrasss (Lolium perenne, LP) were used. Bacterial community composition was assayed using high-throughput sequencing. Results: Our physiochemical data showed that under shade stress, OJ maintained higher photosynthetic capacity and root growth, thus OJ was found to be more shade-tolerant than LP. Illumina sequencing data revealed that shade stress had little impact on the diversity of the OJ and LP’s bacterial communities, but instead impacted the composition of bacterial communities. The bacterial communities were mostly composed of Proteobacteria and Acidobacteria in OJ soil. Further pairwise fitting analysis showed that a positive correlation of shade-tolerance in two turfgrasses and their bacterial community compositions. Several soil properties (NO3--N, NH4+-N, AK) showed a tight coupling with several major bacterial communities under shade stress, indicating that they are important drivers determining bacterial community structures. Moreover, OJ shared core bacterial taxa known to promote plant growth and confer tolerance to shade stress, which suggests common principles underpinning OJ-microbe interactions. Conclusion: OJ was more shade-tolerant than LP. Shifts in rhizosphere soil bacterial community structure play a vital role in shade-tolerance of OJ plants.


2020 ◽  
Vol 96 (4) ◽  
Author(s):  
Syrie M Hermans ◽  
Matthew Taylor ◽  
Gwen Grelet ◽  
Fiona Curran-Cournane ◽  
Hannah L Buckley ◽  
...  

ABSTRACT Bacterial communities are crucial to soil ecosystems and are known to be sensitive to environmental changes. However, our understanding of how present-day soil bacterial communities remain impacted by historic land uses is limited; implications for their functional potential are especially understudied. Through 16S rRNA gene amplicon and shotgun metagenomic sequencing, we characterized the structure and functional potential of soil bacterial communities after land use conversion. Sites converted from pine plantations to dairy pasture were sampled five- and eight-years post conversion. The bacterial community composition and functional potential at these sites were compared to long-term dairy pastures and pine forest reference sites. Bacterial community composition and functional potential at the converted sites differed significantly from those at reference sites (P = 0.001). On average, they were more similar to those in the long-term dairy sites and showed gradual convergence (P = 0.001). Differences in composition and functional potential were most strongly related to nutrients such as nitrogen, Olsen P and the carbon to nitrogen ratio. Genes related to the cycling of nitrogen, especially denitrification, were underrepresented in converted sites compared to long-term pasture soils. Together, our study highlights the long-lasting impacts land use conversion can have on microbial communities, and the implications for future soil health and functioning.


2020 ◽  
Vol 8 (5) ◽  
pp. 642 ◽  
Author(s):  
María Gómez-Brandón ◽  
Manuel Aira ◽  
Natielo Santana ◽  
Marcos Pérez-Losada ◽  
Jorge Domínguez

Vermicomposting has been found as a profitable approach to dispose of and treat large quantities of raw grape marc. However, less information is available with regard to its efficiency for treating distillery winery byproducts, even though distillation has been widely used as a way to economically valorize grape marc. As such, we sought to characterize the compositional and functional changes in bacterial communities during vermicomposting of distilled grape marc by using 16S rRNA high-throughput sequencing. Samples were collected at the initiation of vermicomposting and at days 14, 21, 28, 35 and 42. There were significant changes (p < 0.0001) in the bacterial community composition of distilled grape marc after 14 days of vermicomposting that were accompanied by twofold increases in bacterial richness and diversity from a taxonomic and phylogenetic perspective. This was followed by significant increases in functional diversity of the bacterial community, including metabolic capacity, lignin and cellulose metabolism, and salicylic acid synthesis. These findings indicate that the most striking compositional and functional bacterial community changes took place during the active phase of the process. They also pinpoint functional attributes that may be related to the potential beneficial effects of distilled grape marc vermicompost when applied on soil and plants.


2021 ◽  
Vol 9 (11) ◽  
pp. 2260
Author(s):  
Qianqian Zhang ◽  
Zhenbing Wu ◽  
Juan Zhao ◽  
Guojie Wang ◽  
Jingwen Hao ◽  
...  

Bacterial community plays a key role in environmental and ecological processes of river ecosystems. Given the special climatic and geographical conditions, studying the compositional characteristics of microorganisms in highland rivers and the relationship between such microorganisms and water physicochemical factors is important for an in-depth understanding of microbial ecological mechanisms. In the present study, high-throughput sequencing was used to investigate and study the bacterioplankton community of the Huangshui River in the ecotone zone of the Qinghai Plateau and Loess Plateau. The results showed that the Huangshui River had significantly lower alpha diversity than the plain rivers. Despite the similarity in their environmental conditions, the main taxonomic compositions of the bacterial communities were distinct between the Huangshui River and polar regions (the Arctic and Antarctica). Proteobacteria accounted for the largest proportion (30.79–99.98%) of all the sequences, followed by Firmicutes (0–49.38%). Acidiphilium was the most numerous genera, which accounted for 0.03–86.16% of the assigned 16S reads, followed by Acidocella (0–95.9%), both belonging to Alphaproteobacteria. The diverse taxa of potential pathogens, such as Acinetobacter, Pseudomonas, and Aeromonas, were also identified. A principal coordinates analysis, coupled with a canonical correspondence analysis, showed spatial variations in the bacterial community composition. The water physical properties (e.g., Cr6+, total phosphorus, and CODMn); altitude; and land use (e.g., urban land cover and aquaculture) determined the distribution of the bacterioplankton composition. PICRUSt2 revealed that the overall functional profiles of the bacterial communities in different samples were similar, and our results suggested the potential health risks of water sources in this area. This work provided valuable insight into the composition of the plankton bacterial community and its relationship with the environmental factors in the Huangshui River in the ecotone zone of the Qinghai Plateau and Loess Plateau and a theoretical foundation for ecological health management.


PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10866
Author(s):  
Heqing Huang ◽  
Jianhui Liu ◽  
Fanghui Zhang ◽  
Kangwen Zhu ◽  
Chunhua Yang ◽  
...  

Urban rivers represent a unique ecosystem in which pollution occurs regularly, altering the biogeochemical characteristics of waterbodies and sediments. However, little is presently known about the spatiotemporal patterns of planktonic and sediment bacterial community diversities and compositions in urban rivers. Herein, Illumina MiSeq high-throughput sequencing was performed to reveal the spatiotemporal dynamics of bacterial populations in Liangtan River, a heavily polluted urban river in Chongqing City (China). The results showed the richness and diversity of sediment bacteria were significantly higher than those of planktonic bacteria, whereas a strong overlap (46.7%) in OTUs was identified between water and sediment samples. Bacterial community composition remarkably differed in waters and sediments. Planktonic bacterial communities were dominated by Proteobacteria, Bacteroidetes, Cyanobacteria and Actinobacteria, while sediment bacterial communities mainly included Proteobacteria, Actinobacteria, Chloroflexi and Bacteroidetes. Additionally, several taxonomic groups of potential bacterial pathogens showed an increasing trend in water and sediment samples from residential and industrial areas (RI). Variation partition analysis (VPA) indicated that temperature and nutrient were identified as the main drivers determining the planktonic and sediment bacterial assemblages. These results highlight that bacterial communities in the polluted urban river exhibit spatiotemporal variation due to the combined influence of environmental factors associated with sewage discharge and hydropower dams.


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