scholarly journals Diversity of Bacterium Communities in Saline-Alkali Soil in Arid Regions of Northwest China

2021 ◽  
Author(s):  
Lili Nan ◽  
Quanen Guo ◽  
shiyu cao ◽  
zongbing zhan
Keyword(s):  
Ph Value ◽  
Influencing Factor ◽  
Illumina Miseq ◽  
Northwest China ◽  
Diversity Indices ◽  
Gansu Province ◽  
Alkali Soil ◽  
Main Indicator ◽  
Chloride Sulfate ◽  
Microbial Groups

Abstract Background: The Illumina MiSeq sequencing method was practiced to investigate the bacterial diversity and composition in the 5 subtypes and 13 genera of saline-alkali soil in Gansu Province, China. Results: The results from this study show that the dominant bacterial groups were Euryarchaeota, Proteobacteria, Bacteroidetes, Actinobacteria, Firmicutes, and Gemmatimonadetes among the different salinity soil. Euryarchaeota and Proteobacteria were the main indicator species reflecting changes of the main microbial groups. Euryarchaeota was the most abundant in chloride-sulfate-type meadow solonchaks, sulfate-chloride-type meadow solonchaks, chloride-type meadow solonchaks, chloride-sulfate-type orthic solonchaks, sulfate-chloride-type orthic solonchaks, magnesium solonetz, sulfate-type dry solonchaks, chloride-sulfate-type dry solonchaks, and sulfate-chloride-type dry solonchaks, whereas Proteobacteria had the greatest abundance in sulfate-type meadow solonchaks, sulfate-type orthic solonchaks, chloride-type orthic solonchaks, and chloride-type bog solonchaks. Halobacteria was the dominant bacterial class in soil samples except sulfate-type meadow solonchaks, chloride-type orthic solonchaks, sulfate-type orthic solonchaks, and chloride-type bog solonchaks. The richness estimators of Ace and Chao 1 and the diversity indices of Shannon and Simpson revealed a less bacterial community in sulfate-chloride-type orthic solonchaks than that of other soils. Conclusions: The pH value was the most important driving force for bacterial composition (32.1%), and the second most influencing factor was sulfate anion (9.2%) and soil total salt (8.7) contents.

scholarly journals Diversity of bacterium communities in saline-alkali soil in arid regions of Northwest China

2022 ◽  
Vol 22 (1) ◽  
Author(s):  
Lili Nan ◽  
Quanen Guo ◽  
Shiyu Cao ◽  
Zongbing Zhan
Keyword(s):  
Ph Value ◽  
Influencing Factor ◽  
Illumina Miseq ◽  
Northwest China ◽  
Diversity Indices ◽  
Gansu Province ◽  
Alkali Soil ◽  
The North ◽  
Microbial Resources ◽  
Richness Estimators

Abstract Background The saline-alkali soil area accounts for over 1/4-1/5 of the land area in Gansu Province of China, which are mainly distributed in the north of Hexi corridor and Jingtai basin. The unique ecological environment contains unique and diverse microbial resources. The investigation of microbial diversity in saline environment is vital to comprehend the biological mechanisms of saline adaption, develop and utilize microbial resources. Results The Illumina MiSeq sequencing method was practiced to investigate the bacterial diversity and composition in the 5 subtypes and 13 genera of saline-alkali soil in Gansu Province, China. The results from this study show that Proteobacteria, Bacteroidetes, Actinobacteria, Firmicutes, and Gemmatimonadetes were the dominant bacterial groups in 13 saline soil. Proteobacteria had the greatest abundance in sulfate-type meadow solonchaks and orthic solonchaks, chloride-type orthic solonchaks and bog solonchaks, sulfate-chloride-type, chloride-sulfate-type, and sulfate-type dry solonchaks. Halobacteria was the dominant bacterial class in soil samples except for sulfate-type meadow solonchaks and orthic solonchaks, chloride-type orthic solonchaks and bog solonchaks. The richness estimators of Ace and Chao 1 and the diversity indices of Shannon and Simpson revealed the least diversity in bacterial community in sulfate-chloride-type orthic solonchaks. Conclusions The sulfate anion was the most important driving force for bacterial composition (17.7%), and the second most influencing factor was pH value (11.7%).

scholarly journals PSIX-6 Gastrointestinal microbiome of calves fed solid diets containing different levels and sources of NDF

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 418-419
Author(s):  
Gercino F Virgínio Júnior ◽  
Milaine Poczynek ◽  
Ana Paula Silva ◽  
Ariany Toledo ◽  
Amanda Cezar ◽  
...  
Keyword(s):  
Illumina Miseq ◽  
Diversity Indices ◽  
Dairy Calves ◽  
Rrna Gene ◽  
Gastrointestinal Microbiome ◽  
Fecal Microbiome ◽  
Miseq Platform ◽  
Holstein Calves ◽  
Ad Libitum ◽  
Different Levels

Abstract Different levels and sources of NDF can modify the gastrointestinal microbiome. This study evaluated 18 Holstein calves housed in not-bedded suspended individual cages and fed one of three treatments: 22NDF - conventional starter containing 22% NDF (n = 7); 31NDF - starter with 31% NDF, replacing part of the corn by soybean hull (n = 6); and 22NDF+H - conventional starter with 22% NDF plus coast-cross hay ad libitum (n = 5). All animals received 4 L of milk replacer daily (24% CP; 18.5% fat; diluted to 12.5% solids), divided into two meals, being weaned at 8th week of age. After weaning, animals were housed in tropical shelters, fed with the respective solid diet and coast-cross hay ad libitum for all treatments. To evaluate the microbiome, ruminal fluid samples were collected using a modified Geishauser oral probe at weeks 2, 4, 6, 8 and 10, two hours after the morning feeding, and fecal samples were collected at birth (0) and at weeks 1, 2, 4, 8 and 10. The microbial community was determined by sequencing V3 and V4 region amplicons of the 16S rRNA gene that was amplified by PCR and sequenced by the Illumina MiSeq platform. Ruminal microbiome had no differences in diversity for the effects of weeks, treatments or interaction of both factors (Table 1). In feces, the diversity indices and evenness were higher for 22NDF+H when compared to 22NDF, with no difference for 31NDF. All indices were significantly affected by calves age. At birth, calves had the greatest diversity and richness. Week 1 and 2 had less evenness and diversity. Bacteroidota, Firmicutes_A and Firmicutes_C were the most abundant phylum in rumen and feces. The supply of hay was only effective in modifying the fecal microbiome of dairy calves, suggesting a resilience in the ruminal microbiome.

scholarly journals The Fecal Bacterial Microbiota in Horses with Equine Recurrent Uveitis

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 745
Author(s):  
Michelle Martin de Bustamante ◽  
Diego Gomez ◽  
Jennifer MacNicol ◽  
Ralph Hamor ◽  
Caryn Plummer
Keyword(s):  
Beta Diversity ◽  
High Throughput Sequencing ◽  
Illumina Miseq ◽  
Diversity Indices ◽  
Rrna Gene ◽  
Linear Discriminant ◽  
Alpha And Beta Diversity ◽  
Bacterial Microbiota ◽  
Healthy Control ◽  
Equine Recurrent Uveitis

The objective of this study was to describe and compare the fecal bacterial microbiota of horses with equine recurrent uveitis (ERU) and healthy horses using next-generation sequencing techniques. Fecal samples were collected from 15 client-owned horses previously diagnosed with ERU on complete ophthalmic examination. For each fecal sample obtained from a horse with ERU, a sample was collected from an environmentally matched healthy control with no evidence of ocular disease. The Illumina MiSeq sequencer was used for high-throughput sequencing of the V4 region of the 16S rRNA gene. The relative abundance of predominant taxa, and alpha and beta diversity indices were calculated and compared between groups. The phyla Firmicutes, Bacteroidetes, Verrucomicrobia, and Proteobacteria predominated in both ERU and control horses, accounting for greater than 60% of sequences. Based on linear discriminant analysis effect size (LEfSe), no taxa were found to be enriched in either group. No significant differences were observed in alpha and beta diversity indices between groups (p > 0.05 for all tests). Equine recurrent uveitis is not associated with alteration of the gastrointestinal bacterial microbiota when compared with healthy controls.

scholarly journals Solar Brightening/Dimming over China’s Mainland: Effects of Atmospheric Aerosols, Anthropogenic Emissions, and Meteorological Conditions

2020 ◽  
Vol 13 (1) ◽  
pp. 88
Author(s):  
Hejin Fang ◽  
Wenmin Qin ◽  
Lunche Wang ◽  
Ming Zhang ◽  
Xuefang Yang
Keyword(s):  
Atmospheric Aerosols ◽  
Southern China ◽  
Influencing Factor ◽  
Precipitable Water ◽  
Northwest China ◽  
Meteorological Conditions ◽  
Anthropogenic Emissions ◽  
Main Role ◽  
Surface Solar Radiation ◽  
Climate Change Research

Surface solar radiation (SSR) is the main factor affecting the earth’s climate and environment and its variations and the reason for these variations are an important part of climate change research. In this research, we investigated the long-term variations of SSR during 1984–2016 and the quantitative influences of atmospheric aerosols, anthropogenic emissions, and meteorological conditions on SSR over China’s mainland. The results show the following: (1) The annual average SSR values had a decline trend at a rate of −0.371 Wm−2 yr−1 from 1984 to 2016 over China. (2) The aerosol optical depth (AOD) plays the main role in inducing variations in SSR over China, with r values of −0.75. Moreover, there are marked regional differences in the influence of anthropogenic emissions and meteorological conditions on SSR trends. (3) From a regional perspective, AOD is the main influencing factor on SSR in northeast China (NEC), Yunnan Plateau and surrounding regions (YPS), North China (NC), and Loess Plateau (LP), with r values of −0.65, −0.60, −0.89, and −0.50, respectively. However, the main driving factors for SSR in northwest China (NWC) are “in cloud optical thickness of all clouds” (TAUTOT) (−0.26) and black carbon (BC) anthropogenic emissions (−0.21). TAUTOT (−0.39) and total precipitable water vapor (TQV) (−0.29) are the main influencing factors of SSR in the middle-lower Yangtze Plain (MYP). The main factors that influence SSR in southern China (SC) are surface pressure (PS) (−0.66) and AOD (−0.43). This research provides insights in understanding the variations of SSR and its relationships with anthropogenic conditions and meteorological factors.

scholarly journals Prevalence of gastrointestinal parasites in free-range yaks (Bos grunniens) in Gansu Province, Northwest China

2019 ◽  
Vol 15 (1) ◽  
Author(s):  
Si-Yuan Qin ◽  
Ming-Yang Yin ◽  
Guang-Yao Song ◽  
Qi-Dong Tan ◽  
Jin-Lei Wang ◽  
...  
Keyword(s):  
Northwest China ◽  
Gansu Province ◽  
Gastrointestinal Parasites ◽  
Economic Losses ◽  
Parasitic Infections ◽  
Cattle Industry ◽  
Free Range ◽  
Bos Grunniens ◽  
High Prevalence ◽  
Different Seasons

Abstract Background Little information about the prevalence of gastrointestinal parasites in yaks (Bos grunniens) in northwest China is available. Therefore, the objective of the study was to quantify faecal egg counts of gastrointestinal parasites (helminths and coccidia) in free-range yaks from Gannan Tibetan Autonomous Prefecture, Gansu Province, Northwest China. Results Parasites were detected in 290 of 733 (39.56%) faecal samples. The results showed that Strongylidae, Trichuris spp. and Eimeria spp. were detected all year round, Strongyloides papillosus was detected in autumn and summer, and Nematodirus spp. was detected in both autumn and spring. In contrast, Fasciola spp. was only detected in spring. The prevalence rates of parasitic infections in different seasons were significantly different. Conclusions To our knowledge, this is the first investigation of gastrointestinal parasites in yaks (Bos grunniens) in Gansu, China. The results demonstrated a high prevalence of gastrointestinal parasitic infections, specifically GN infections, in yaks in GTAP and these infections can cause economic losses to the local cattle industry.

scholarly journals Assessing the Effects of Ginger Extract on Polyphenol Profiles and the Subsequent Impact on the Fecal Microbiota by Simulating Digestion and Fermentation In Vitro

Nutrients ◽  
2020 ◽  
Vol 12 (10) ◽  
pp. 3194
Author(s):  
Jing Wang ◽  
Yong Chen ◽  
Xiaosong Hu ◽  
Fengqin Feng ◽  
Luyun Cai ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Ph Value ◽  
Illumina Miseq ◽  
Short Chain Fatty Acids ◽  
Fecal Microbiota ◽  
Rrna Gene ◽  
Gut Health ◽  
Ginger Extract ◽  
Mixed Culture Fermentation

The beneficial effects of ginger polyphenols have been extensively reported. However, their metabolic characteristics and health effects on gut microbiota are poor understood. The purpose of this study was to investigate the digestion stability of ginger polyphenols and their prebiotic effects on gut microbiota by simulating digestion and fermentation in vitro. Following simulated digestion in vitro, 85% of the polyphenols were still detectable, and the main polyphenol constituents identified in ginger extract are 6-, 8-, and 10-gingerols and 6-shogaol in the digestive fluids. After batch fermentation, the changes in microbial populations were measured by 16S rRNA gene Illumina MiSeq sequencing. In mixed-culture fermentation with fecal inoculate, digested ginger extract (GE) significantly modulated the fecal microbiota structure and promoted the growth of some beneficial bacterial populations, such as Bifidobacterium and Enterococcus. Furthermore, incubation with GE could elevate the levels of short-chain fatty acids (SCFAs) accompanied by a decrease in the pH value. Additionally, the quantitative PCR results showed that 6-gingerol (6G), as the main polyphenol in GE, increased the abundance of Bifidobacterium significantly. Therefore, 6G is expected to be a potential prebiotic that improves human health by promoting gut health.

scholarly journals Alterations in the Ocular Surface Fungal Microbiome in Fungal Keratitis Patients

2019 ◽  
Vol 7 (9) ◽  
pp. 309 ◽  
Author(s):  
Prashanthi ◽  
Jayasudha ◽  
Chakravarthy ◽  
Padakandla ◽  
SaiAbhilash ◽  
...  
Keyword(s):  
Ocular Surface ◽  
Alpha Diversity ◽  
Illumina Miseq ◽  
Diversity Indices ◽  
Fungal Keratitis ◽  
Its2 Region ◽  
Healthy Individuals ◽  
Healthy Control ◽  
Fungal Microbiome ◽  
Map Analysis

Keratitis, an inflammatory disease of the eye, when neglected could lead to sight-threatening complications and ultimately blindness. Globally, over a million people are affected by keratitis annually. Keratitis has a microbial etiology and is caused by bacteria, fungi, viruses, etc. The present study compared the ocular surface fungal microbiome of healthy individuals and individuals with fungal keratitis. Fungal microbiomes from the conjunctival swabs of healthy individuals and from conjunctival swabs and corneal scrapings of individuals with fungal keratitis were generated using ITS2 region amplicons. Microbiomes were sequenced using Illumina MiSeq 2 × 250 base pair chemistry with a paired-end protocol. Based on Alpha diversity indices, phylum and genera level diversity, abundance differences, and heat map analysis, the fungal microbiomes of conjunctival swabs and corneal scrapings of individuals with fungal keratitis exhibited dysbiosis (alterations in the diversity and abundance) compared to the ocular surface microbiome of the healthy control individuals. This is the first report indicating dysbiosis in the fungal microbiome of conjunctival swabs and corneal scrapings in individuals with fungal keratitis. A total of 11 genera present in the majority of the eyes constituted the variable core ocular microbiome.

scholarly journals Seroprevalence and Risk Factors ofChlamydia abortusInfection in Tibetan Sheep in Gansu Province, Northwest China

2014 ◽  
Vol 2014 ◽  
pp. 1-6 ◽  
Author(s):  
Si-Yuan Qin ◽  
Ming-Yang Yin ◽  
Wei Cong ◽  
Dong-Hui Zhou ◽  
Xiao-Xuan Zhang ◽  
...  
Keyword(s):  
Risk Factors ◽  
Logistic Regression ◽  
Regression Analysis ◽  
Logistic Regression Analysis ◽  
Multivariate Logistic Regression Analysis ◽  
Northwest China ◽  
Gansu Province ◽  
Factors Associated ◽  
Tibetan Sheep ◽  
Different Seasons

Chlamydia abortus, an important pathogen in a variety of animals, is associated with abortion in sheep. In the present study, 1732 blood samples, collected from Tibetan sheep between June 2013 and April 2014, were examined by the indirect hemagglutination (IHA) test, aiming to evaluate the seroprevalence and risk factors ofC. abortusinfection in Tibetan sheep. 323 of 1732 (18.65%) samples were seropositive forC. abortusantibodies at the cut-off of 1 : 16. A multivariate logistic regression analysis was used to evaluate the risk factors associated with seroprevalence, which could provide foundation to prevent and controlC. abortusinfection in Tibetan sheep. Gender of Tibetan sheep was left out of the final model because it is not significant in the logistic regression analysis (P>0.05). Region, season, and age were considered as major risk factors associated withC. abortusinfection in Tibetan sheep. Our study revealed a widespread and high prevalence ofC. abortusinfection in Tibetan sheep in Gansu province, northwest China, with higher exposure risk in different seasons and ages and distinct geographical distribution.

scholarly journals Characterising the effect of crop species and fertilisation treatment on root fungal communities

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Liina Soonvald ◽  
Kaire Loit ◽  
Eve Runno-Paurson ◽  
Alar Astover ◽  
Leho Tedersoo
Keyword(s):  
Fungal Community ◽  
Farmyard Manure ◽  
Illumina Miseq ◽  
Diversity Indices ◽  
Community Diversity ◽  
Its2 Region ◽  
Minor Effect ◽  
Crop Species ◽  
A Minor ◽  
Fertilisation Treatment

Abstract Information about the root mycobiome may improve the overall quality of the plants and contribute to a valuable strategy to enhance sustainable agriculture. Therefore, we assessed differences in fungal community diversity and composition in the roots of potato, wheat and barley grown under mineral nitrogen fertilisation at five rates, with and without farmyard manure amendment. The same factorial combination of treatments has been used since 1989. Species richness and diversity, as well as community composition, of different fungal guilds were characterised using Illumina MiSeq sequencing of the ITS2 region. Crop species was the main factor determining overall fungal richness and diversity, with wheat showing the highest, and potato the lowest, richness and diversity. Pathogen diversity indices were highest in wheat plots amended with farmyard manure, whereas the lowest values were observed for potato roots. Fertilisation treatments and the interaction between crop species and fertilisation had the strongest impact on arbuscular mycorrhiza and saprotroph diversity. Crop species also determined the composition of the overall fungal community and that of fungal guilds, whereas fertilisation treatment had only a minor effect. This study highlights crop species as the main driver in shaping root fungal diversity and composition under the same environmental conditions.

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