High-throughput sequencing reveals bacterial community composition in the rhizosphere of the invasive plant Flaveria bidentis

Weed Research ◽  
2017 ◽  
Vol 57 (3) ◽  
pp. 204-211 ◽  
Author(s):  
Z Song ◽  
R H Zhang ◽  
W D Fu ◽  
T Zhang ◽  
J Yan ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Invasive Plant ◽  
Bacterial Community Composition ◽  
Flaveria Bidentis

Impacts of invasive plant species on soil biodiversity: a case study of dog-strangling vine (Vincetoxicum rossicum) in a Canadian National Park

2018 ◽  
Vol 98 (4) ◽  
pp. 716-723 ◽  
Author(s):  
Laura N. Bugiel ◽  
Stuart W. Livingstone ◽  
Marney E. Isaac ◽  
Roberta R. Fulthorpe ◽  
Adam R. Martin
Keyword(s):  
Bacterial Community ◽  
Microbial Diversity ◽  
Community Composition ◽  
Invasive Plant ◽  
Bacterial Community Composition ◽  
Anthropogenic Disturbances ◽  
Soil Parameters ◽  
Invasive Plant Species ◽  
Vincetoxicum Rossicum ◽  
Soil Bacterial

Soil microbial diversity is expected to be altered by the establishment of invasive plant species, such as dog-strangling vine (DSV) [Vincetoxicum rossicum (Apocynaceae)]. However, in urban ecosystems where DSV invasion is high, there is little research evaluating the impacts of DSV and other anthropogenic disturbances on microbial diversity. Our study was based in Rouge National Urban Park, Canada, where we used terminal restriction fragment length polymorphism data to evaluate (i) if DSV has a detectable impact on soil bacterial community composition and (ii) if these impacts occur independently of other anthropogenic change or soil characteristics. Variation in soil bacterial communities was greatly reduced in DSV-invaded sites vs. less-invaded sites. The degree of DSV invasion independently explained 23.8% of variation in bacterial community composition: a value similar to the explanatory power of proximity to roadways (which explained 22.6% of the variation in community composition), and considerably greater than soil parameters (pH, moisture, carbon, and nitrogen concentrations) which explained only between 6.0% and 10.0% of variation in bacterial community composition. Our findings indicate that DSV influences soil bacterial community composition independent of other anthropogenic disturbances and soil parameters, with potential impacts on multiple facets of plant–soil interactions and plant invasion dynamics.

scholarly journals Correlation of Breed, Growth Performance, and Rumen Microbiota in Two Rustic Cattle Breeds Reared Under Different Conditions

2021 ◽  
Vol 12 ◽  
Author(s):  
Matteo Daghio ◽  
Francesca Ciucci ◽  
Arianna Buccioni ◽  
Alice Cappucci ◽  
Laura Casarosa ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Growth Performance ◽  
Community Composition ◽  
Lipid Composition ◽  
High Throughput Sequencing ◽  
Bacterial Community Composition ◽  
Daily Weight Gain ◽  
Rrna Gene ◽  
Rumen Microbiota ◽  
Cattle Breeds

The use of rustic cattle is desirable to face challenges brought on by climate change. Maremmana (MA) and Aubrac (AU) are rustic cattle breeds that can be successfully used for sustainable production. In this study, correlations between two rearing systems (feedlot and grazing) and the rumen microbiota, the lipid composition of rumen liquor (RL), and the growth performance of MA and AU steers were investigated. Bacterial community composition was characterized by high-throughput sequencing of 16S rRNA gene amplicons, and the RL lipid composition was determined by measuring fatty acid (FA) and the dimethyl acetal profiles. The main factor influencing bacterial community composition was the cattle breed. Some bacterial groups were positively correlated to average daily weight gain for the two breeds (i.e., Rikenellaceae RC9 gut group, Fibrobacter and Succiniclasticum in the rumen of MA steers, and Succinivibrionaceae UCG-002 in the rumen of AU steers); despite this, animal performance appeared to be influenced by short chain FAs production pathways and by the presence of H2 sinks that divert the H2 to processes alternative to the methanogenesis.

scholarly journals Local domestication of microbes via cassava beer fermentation

2014 ◽  
Author(s):  
Alese Colehour ◽  
James F Meadow ◽  
Tara J Cepon-Robins ◽  
Theresa E Gildner ◽  
Melissa A Liebert ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Bacterial Communities ◽  
Manihot Esculenta ◽  
Nutritional Quality ◽  
High Throughput Sequencing ◽  
Bacterial Community Composition ◽  
Ribosomal Gene ◽  
Ecuadorian Amazon ◽  
Traditional Fermentation

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.

scholarly journals Local domestication of microbes via cassava beer fermentation

2014 ◽  
Author(s):  
Alese Colehour ◽  
James F Meadow ◽  
Tara J Cepon-Robins ◽  
Theresa E Gildner ◽  
Melissa A Liebert ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Bacterial Communities ◽  
Manihot Esculenta ◽  
Nutritional Quality ◽  
High Throughput Sequencing ◽  
Bacterial Community Composition ◽  
Ribosomal Gene ◽  
Ecuadorian Amazon ◽  
Traditional Fermentation

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.

Characterization of bacterial diversity in drinking water by pyrosequencing

2013 ◽  
Vol 13 (2) ◽  
pp. 358-367 ◽  
Author(s):  
Yan Zhang ◽  
Qiang He
Keyword(s):  
Drinking Water ◽  
Bacterial Community ◽  
Bacterial Diversity ◽  
Clone Library ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Bacterial Community Composition ◽  
Environmental Distribution ◽  
Clone Library Analysis

Controlling microbial contamination of drinking water is critical to public health. However, understanding of the microbial ecology of drinking water remains incomplete. Representing the first application of high-throughput sequencing in drinking water microbiology, the objective of this study is to evaluate pyrosequencing as a high-throughput technique for the characterization of bacterial diversity in drinking water in comparison with conventional clone library analysis. Pyrosequencing and clone library analysis were performed in parallel to study the bacterial community composition in drinking water samples following the concentration of microbial biomass in drinking water with ultrafiltration. Validated by clone library analysis, pyrosequencing was confirmed as a highly efficient deep-sequencing technique to characterize the bacterial diversity in drinking water. Sequences of Alphaproteobacteria and Betaproteobacteria dominated the bacterial community in drinking water with Oxalobacteraceae and Methylobacteriaceae as the most abundant bacterial families, which is consistent with the prominent abundance of these populations frequently detected in various freshwater environments where source waters originate. Bacterial populations represented by the most abundant sequences in drinking water were closely related to cultures of metabolically versatile bacterial taxa widely distributed in the environment, suggesting a potential link between environmental distribution, metabolic characteristics, and abundance in drinking water.

scholarly journals Comparison of the fecal microbiota of two free-ranging Chinese subspecies of the leopard (Panthera pardus) using high-throughput sequencing

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6684 ◽  
Author(s):  
Siyu Han ◽  
Yu Guan ◽  
Hailong Dou ◽  
Haitao Yang ◽  
Meng Yao ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Gut Microbiota ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Bacterial Community Composition ◽  
Rrna Gene ◽  
Panthera Pardus ◽  
Invasive Approach ◽  
Fecal Samples ◽  
Significant Difference

The analysis of gut microbiota using fecal samples provides a non-invasive approach to understand the complex interactions between host species and their intestinal bacterial community. However, information on gut microbiota for wild endangered carnivores is scarce. The goal of this study was to describe the gut microbiota of two leopard subspecies, the Amur leopard (Panthera pardus orientalis) and North Chinese leopard (Panthera pardus japonensis). Fecal samples from the Amur leopard (n = 8) and North Chinese leopard (n = 13) were collected in Northeast Tiger and Leopard National Park and Shanxi Tieqiaoshan Provincial Nature Reserve in China, respectively. The gut microbiota of leopards was analyzed via high-throughput sequencing of the V3–V4 region of bacterial 16S rRNA gene using the Life Ion S5™ XL platform. A total of 1,413,825 clean reads representing 4,203 operational taxonomic units (OTUs) were detected. For Amur leopard samples, Firmicutes (78.4%) was the dominant phylum, followed by Proteobacteria (9.6%) and Actinobacteria (7.6%). And for the North Chinese leopard, Firmicutes (68.6%), Actinobacteria (11.6%) and Fusobacteria (6.4%) were the most predominant phyla. Clostridiales was the most diverse bacterial order with 37.9% for Amur leopard and 45.7% for North Chinese leopard. Based on the beta-diversity analysis, no significant difference was found in the bacterial community composition between the Amur leopard and North Chinese leopard samples. The current study provides the initial data about the composition and structure of the gut microbiota for wild Amur leopards and North Chinese leopards, and has laid the foundation for further investigations of the health, dietary preferences and physiological regulation of leopards.

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