scholarly journals Seasonal Variation Characteristics of Bacteria and Fungi in PM2.5 in Typical Basin Cities of Xi’an and Linfen, China

Atmosphere ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 809
Author(s):  
Sen Wang ◽  
Wanyu Liu ◽  
Jun Li ◽  
Haotian Sun ◽  
Yali Qian ◽  
...  
Keyword(s):  
Seasonal Variation ◽  
Relative Abundance ◽  
Pathogenic Bacteria ◽  
High Throughput Sequencing ◽  
Fine Particulate Matter ◽  
Ecological Functions ◽  
Factors Affecting ◽  
Bacterial Phyla ◽  
Variation Characteristics ◽  
Bacteria And Fungi

Microorganisms existing in airborne fine particulate matter (PM2.5) have key implications in biogeochemical cycling and human health. In this study, PM2.5 samples, collected in the typical basin cities of Xi’an and Linfen, China, were analyzed through high-throughput sequencing to understand microbial seasonal variation characteristics and ecological functions. For bacteria, the highest richness and diversity were identified in autumn. The bacterial phyla were dominated by Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes. Metabolism was the most abundant pathway, with the highest relative abundance found in autumn. Pathogenic bacteria (Pseudomonas, Acinetobacter, Serratia, and Delftia) were positively correlated with most disease-related pathways. Besides, C cycling dominated in spring and summer, while N cycling dominated in autumn and winter. The relative abundance of S cycling was highest during winter in Linfen. For fungi, the highest richness was found in summer. Basidiomycota and Ascomycota mainly constituted the fungal phyla. Moreover, temperature (T) and sulfur dioxide (SO2) in Xi’an, and T, SO2, and nitrogen dioxide (NO2) in Linfen were the key factors affecting microbial community structures, which were associated with different pollution characteristics in Xi’an and Linfen. Overall, these results provide an important reference for the research into airborne microbial seasonal variations, along with their ecological functions and health impacts.

scholarly journals Seasonal Variation in the Rhizosphere and Non-Rhizosphere Microbial Community Structures and Functions of Camellia yuhsienensis Hu

2020 ◽  
Vol 8 (9) ◽  
pp. 1385
Author(s):  
Jun Li ◽  
Ziqiong Luo ◽  
Chenhui Zhang ◽  
Xinjing Qu ◽  
Ming Chen ◽  
...  
Keyword(s):  
Seasonal Variation ◽  
Microbial Community ◽  
High Throughput Sequencing ◽  
Sulfur Metabolism ◽  
Pathogen Resistance ◽  
High Yield ◽  
Glutathione Metabolism ◽  
Oilseed Crop ◽  
Soil Microbial ◽  
Bacteria And Fungi

Camellia yuhsienensis Hu, endemic to China, is a predominant oilseed crop, due to its high yield and pathogen resistance. Past studies have focused on the aboveground parts of C. yuhsienensis, whereas the microbial community of the rhizosphere has not been reported yet. This study is the first time to explore the influence of seasonal variation on the microbial community in the rhizosphere of C. yuhsienensis using high-throughput sequencing. The results showed that the dominant bacteria in the rhizosphere of C. yuhsienensis were Chloroflexi, Proteobacteria, Acidobacteria, Actinobacteria, and Planctomycetes, and the dominant fungi were Ascomycota, Basidiomycota, and Mucoromycota. Seasonal variation has significant effects on the abundance of the bacterial and fungal groups in the rhizosphere. A significant increase in bacterial abundance and diversity in the rhizosphere reflected the root activity of C. yuhsienensis in winter. Over the entire year, there were weak correlations between microorganisms and soil physiochemical properties in the rhizosphere. In this study, we found that the bacterial biomarkers in the rhizosphere were chemoorganotrophic Gram-negative bacteria that grow under aerobic conditions, and fungal biomarkers, such as Trichoderma, Mortierella, and Lecanicillium, exhibited protection against pathogens in the rhizosphere. In the rhizosphere of C. yuhsienensis, the dominant functions of the bacteria included nitrogen metabolism, oxidative phosphorylation, glycine, serine and threonine metabolism, glutathione metabolism, and sulfur metabolism. The dominant fungal functional groups were endophytes and ectomycorrhizal fungi of a symbiotroph trophic type. In conclusion, seasonal variation had a remarkable influence on the microbial communities and functions, which were also significantly different in the rhizosphere and non-rhizosphere of C. yuhsienensis. The rhizosphere of C. yuhsienensis provides suitable conditions with good air permeability that allows beneficial bacteria and fungi to dominate the soil microbial community, which can improve the growth and pathogen resistance of C. yuhsienensis.

scholarly journals Effects of particle size of ground alfalfa hay on caecal bacteria and archaea populations of rabbits

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7910
Author(s):  
Mei Yuan ◽  
Siqiang Liu ◽  
Zhisheng Wang ◽  
Lizhi Wang ◽  
Bai Xue ◽  
...  
Keyword(s):  
Particle Size ◽  
Relative Abundance ◽  
High Throughput Sequencing ◽  
Methanogenic Archaea ◽  
Particle Sizes ◽  
Sequencing Technology ◽  
Bacterial Phyla ◽  
Treatment Groups ◽  
Alfalfa Hay ◽  
Alfalfa Meal

This work was aimed to investigate the effects of the different particle size of ground alfalfa hay on caecal microbial and archeal communities of rabbits. One hundred-twenty New Zealand rabbits (950.3 ± 8.82 g) were allocated into four treatments, with five replicates in each treatment and six rabbits in each replicate. The particle sizes of the alfalfa meal in the four treatment diets were 2,500, 1,000, 100 and 10 µm respectively, while the other ingredients were ground through a 2.5 mm sieve. High-throughput sequencing technology was applied to examine the differences in bacteria and methanogenic archaea diversity in the caecum of the four treatment groups of rabbits. A total of 745,946 bacterial sequences (a mean of 31,081 ± 13,901 sequences per sample) and 539,227 archaeal sequences (a mean of 22,468 ± 2,443 sequences per sample) were recovered from twenty-four caecal samples, and were clustered into 9,953 and 2,246 OTUs respectively. A total of 26 bacterial phyla with 465 genera and three archaeal phyla with 10 genera were identified after taxonomic summarization. Bioinformatic analyses illustrated that Firmicutes (58.69% ∼ 68.50%) and Bacteroidetes (23.96% ∼ 36.05%) were the two most predominant bacterial phyla and Euryarchaeota (over 99.9%) was the most predominant archaeal phyla in the caecum of all rabbits. At genus level, as the particle size of alfalfa decreased from 2,500 to 10 µm, the relative abundances of Ruminococcaceae UCG-014 (P < 0.001) and Lactobacillus (P = 0.043) were increased and Ruminococcaceae UCG-005 (P = 0.012) was increased first and then decreased when the alfalfa particle size decreased, while Lachnospiraceae NK4A136 group (P = 0.016), Ruminococcaceae NK4A214 (P = 0.044), Christensenellaceae R-7 group (P = 0.019), Lachnospiraceae other (Family) (P = 0.011) and Ruminococcaceae UCG-013 (P = 0.021) were decreased. The relative abundance of Methanobrevibacter was increased from 62.48% to 90.40% (P < 0.001), whereas the relative abundance of Methanosphaera was reduced from 35.47% to 8.62% (P < 0.001). In conclusion, as the particle size of alfalfa meal decreased, both the bacterial and archaeal population in the caecum of rabbit experienced alterations, however archaea response earlier than bacteria to the decrease of alfalfa meal particle size.

scholarly journals Diversity and spoilage potential of microbial communities associated with grape sour rot in eastern coastal areas of China

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9376
Author(s):  
Huanhuan Gao ◽  
Xiangtian Yin ◽  
Xilong Jiang ◽  
Hongmei Shi ◽  
Yang Yang ◽  
...  
Keyword(s):  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Eastern China ◽  
Grape Berry ◽  
Wine Quality ◽  
Bacterial Phyla ◽  
Sour Rot ◽  
Bacteria And Fungi ◽  
Polymicrobial Disease

As a polymicrobial disease, sour rot decreases grape berry yield and wine quality. The diversity of microbial communities in sour rot-affected grapes depends on the cultivation site, but the microbes responsible for this disease in eastern coastal China, has not been reported. To identify the microbes that cause sour grape rot in this important grape-producing region, the diversity and abundance of bacteria and fungi were assessed by metagenomic analysis and cultivation-dependent techniques. A total of 15 bacteria and 10 fungi were isolated from sour rot-affected grapes. High-throughput sequencing of PCR-amplicons generated from diseased grapes revealed 1343 OTUs of bacteria and 1038 OTUs of fungi. Proteobacteria and Firmicutes were dominant phyla among the 19 bacterial phyla identified. Ascomycota was the dominant fungal phylum and the fungi Issatchenkia terricola, Colletotrichum viniferum, Hanseniaspora vineae, Saprochaete gigas, and Candida diversa represented the vast majority ofmicrobial species associated with sour rot-affected grapes. An in vitro spoilage assay confirmed that four of the isolated bacteria strains (two Cronobacter species, Serratia marcescens and Lysinibacillus fusiformis) and five of the isolated fungi strains (three Aspergillus species, Alternaria tenuissima, and Fusarium proliferatum) spoiled grapes. These microorganisms, which appear responsible for spoiling grapes in eastern China, appear closely related to microbes that cause this plant disease around the world.

Analysis of microbial changes in the rhizosphere of unplanted and planted Atractylodes lancea via high-throughput sequencing

2020 ◽  
Author(s):  
Yan Xu ◽  
Junfeng Niu ◽  
Lijun Chen ◽  
Xiaoqiang Wu ◽  
Zhongmin Dong ◽  
...  
Keyword(s):  
Microbial Community ◽  
High Throughput ◽  
Relative Abundance ◽  
High Throughput Sequencing ◽  
Community Diversity ◽  
Continuous Cropping ◽  
Pests And Diseases ◽  
Atractylodes Lancea ◽  
Bacteria And Fungi ◽  
The Relationship

Abstract Background Atractylodes lancea is a traditional Chinese medicine, which typically requires more than 3–4 years of continuous cropping to obtain the underground medicinal components. With continuous cropping years, the quality and yields of A. lancea medicinal materials decrease, while pests and diseases increase. These aspects are intimately correlated with rhizospheric microorganisms. Methods This research paper employed high-throughput sequencing for its detection in soil that was cultivated for three years and never cultivated to clarify the relationship between the microbial diversity of the rhizosphere and continuous A. lancea cropping. Results The rhizosphere microbial community was altered following the continuous cropping of A. lancea. The bacterial diversity and richness were observed to decrease, while the fungal community diversity increased, and richness decreased. The total OUTs of the soil bacteria and fungi of unplanted and planted A. lancea were 59.58% and 37.65%, respectively. At the phylum level, the relative abundance of Proteobacteria, Gemmatimonadetes, Acidobacteria and Chloroflexi decreased, whereas the relative abundance of Mortierellomycota increased. At the genus level, Bradyrhizobium, Striaticonidium, Dactylonectria, Sphingomonas, Burkholderiaceae, Rhodanobacter, Arthrobacter, Scleroderma, Mortierella and Penicillium were significantly different between the two sample groups. Conclusions Our results revealed that following the cultivation of A. lancea, the rhizospheric microbial community was altered. This study preliminarily determined the

scholarly journals Phyllospheric Microbial Composition and Diversity of the Tobacco Leaves Infected by Didymella segeticola

2021 ◽  
Vol 12 ◽  
Author(s):  
Yu Huang ◽  
Han-Cheng Wang ◽  
Liu-Ti Cai ◽  
Wenhong Li ◽  
Daiwei Pan ◽  
...  
Keyword(s):  
Disease Severity ◽  
Relative Abundance ◽  
High Throughput Sequencing ◽  
Abiotic Factors ◽  
Alpha Diversity ◽  
Disease Index ◽  
Microbial Composition ◽  
Tobacco Leaves ◽  
Tobacco Leaf ◽  
Bacterial Phyla

A Myriad of biotic and abiotic factors inevitably affects the growth and production of tobacco (Nicotiana tabacum L.), which is a model crop and sought-after worldwide for its foliage. Among the various impacts the level of disease severity poses on plants, the influence on the dynamics of phyllospheric microbial diversity is of utmost importance. In China, recurring reports of a phyto-pathogen, Didymella segeticola, a causal agent of tobacco leaf spot, accentuate the need for its in-depth investigation. Here, a high-throughput sequencing technique, IonS5TMXL was employed to analyze tobacco leaves infected by D. segeticola at different disease severity levels, ranging from T1G (least disease index) to T4G (highest disease index), in an attempt to explore the composition and diversity of phyllospheric microbiota. In all healthy and diseased tobacco leaves, the most dominant fungal phylum was Ascomycota with a high prevalence of genus Didymella, followed by Boeremia, Meyerozyma and Alternaria, whereas in the case of bacterial phyla, Proteobacteria was prominent with Pseudomonas being a predominant genus, followed by Pantoea. The relative abundance of fungi, i.e., Didymella and Boeremia (Ascomycota) and bacteria, i.e., Pseudomonas and Pantoea (Proteobacteria) were higher in diseased groups compared to healthy groups. Healthy tissues exhibited relatively rich and diverse fungal communities in contrast with diseased groups. The infection of D. segeticola had a complex and significant effect on fungal as well as bacterial alpha diversity. FUNGuild analysis indicated that the relative abundance of pathotrophs and saprotrophs in diseased tissues proportionally increased with disease severity. PICRUSt analysis of diseased tissues indicated that the relative abundance of bacterial cell motility and membrane transport-related gene sequences elevated with an increase in disease severity from T1G to T3G and then tended to decrease at T4G. Conclusively, the current study shows the typical characteristics of the tobacco leaf microbiome and provides insights into the distinct microbiome shifts on tobacco leaves infected by D. segeticola.

scholarly journals Bacterial diversity in the gastrointestinal tracts of Rhinolophus luctus and Murina leucogaster in Henan Province, China

2019 ◽  
Vol 69 (13) ◽  
pp. 1407-1414 ◽  
Author(s):  
Yan Sun ◽  
Zhimin Yuan ◽  
Yuming Guo ◽  
Yuanzhao Qin ◽  
Yongtian Ban ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
High Throughput ◽  
Disease Transmission ◽  
Pathogenic Bacteria ◽  
High Throughput Sequencing ◽  
Rrna Gene ◽  
Human Pathogens ◽  
Sequencing Platform ◽  
Bacterial Phyla ◽  
Gastrointestinal Bacteria

Abstract Purpose Previous studies have assessed the diversity of gastrointestinal bacteria in bats and reported that some of the strains are pathogenic to humans; therefore, bats are considered to be potential reservoirs of zoonotic pathogens. However, the bacterial diversity and types of pathogenic bacteria in the gastrointestinal tracts of Rhinolophus luctus and Murina leucogaster have not yet been determined. Humans frequently come into contact with these species; therefore, assessments of their gut microbiota, especially potential pathogens, are essential for public health. In the present study, MiSeq high-throughput sequencing was used to address this research gap, and the results were compared with those reported previously. Methods The V3–V4 regions of the 16S rRNA gene were sequenced using the MiSeq high-throughput sequencing platform to determine the bacterial community of the stomach and the intestines of R. luctus and M. leucogaster. Results The bacteria in the gastrointestinal tracts of R. luctus and M. leucogaster were classified into three and four main bacterial phyla, respectively. In both R. luctus and M. leucogaster, the dominant phylum was Proteobacteria (stomach 86.07% and 95.79%, intestines 91.87% and 88.78%, respectively), followed by Firmicutes (stomach 13.84% and 4.19%, intestines 8.11% and 11.20%, respectively). In total, 18 and 20 bacterial genera occurred in a relative abundance of 0.01% or more in the gastrointestinal tracts of R. luctus and M. leucogaster, respectively. In R. luctus, the dominant genera were Lactococcus (10.11%) and Paeniclostridium (3.41%) in the stomach, and Undibacterium (28.56%) and Paeniclostridium (4.69%) in the intestines. In M. leucogaster, the dominant genera were Undibacterium (54.41%) and Burkholderia (5.28%) in the stomach, and Undibacterium (29.67%) and Enterococcus (7.19%) in the intestines. Among the detected gastrointestinal tract flora of R. luctus and M. leucogaster, 12 bacterial genera were pathogenic or opportunistic pathogens. Conclusion A high number of human pathogens were detected in the gastrointestinal tracts of R. luctus and M. leucogaster, which demonstrates the urgency for increased efforts in the prevention and management of bat-to-human disease transmission from these species.

scholarly journals Gut Microbiome in a Russian Cohort of Pre- and Post-Cholecystectomy Female Patients

2021 ◽  
Vol 11 (4) ◽  
pp. 294
Author(s):  
Irina Grigor’eva ◽  
Tatiana Romanova ◽  
Natalia Naumova ◽  
Tatiana Alikina ◽  
Alexey Kuznetsov ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Relative Abundance ◽  
Gut Microbiome ◽  
Gallstone Disease ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Bacterial Phyla ◽  
Female Patients ◽  
Composition And Structure ◽  
Before And After

The last decade saw extensive studies of the human gut microbiome and its relationship to specific diseases, including gallstone disease (GSD). The information about the gut microbiome in GSD-afflicted Russian patients is scarce, despite the increasing GSD incidence worldwide. Although the gut microbiota was described in some GSD cohorts, little is known regarding the gut microbiome before and after cholecystectomy (CCE). By using Illumina MiSeq sequencing of 16S rRNA gene amplicons, we inventoried the fecal bacteriobiome composition and structure in GSD-afflicted females, seeking to reveal associations with age, BMI and some blood biochemistry. Overall, 11 bacterial phyla were identified, containing 916 operational taxonomic units (OTUs). The fecal bacteriobiome was dominated by Firmicutes (66% relative abundance), followed by Bacteroidetes (19%), Actinobacteria (8%) and Proteobacteria (4%) phyla. Most (97%) of the OTUs were minor or rare species with ≤1% relative abundance. Prevotella and Enterocossus were linked to blood bilirubin. Some taxa had differential pre- and post-CCE abundance, despite the very short time (1–3 days) elapsed after CCE. The detailed description of the bacteriobiome in pre-CCE female patients suggests bacterial foci for further research to elucidate the gut microbiota and GSD relationship and has potentially important biological and medical implications regarding gut bacteria involvement in the increased GSD incidence rate in females.

scholarly journals Taxonomic and Functional Characteristics of the Gill and Gastrointestinal Microbiota and Its Correlation with Intestinal Metabolites in NEW GIFT Strain of Farmed Adult Nile Tilapia (Oreochromis niloticus)

2021 ◽  
Vol 9 (3) ◽  
pp. 617
Author(s):  
Zhenbing Wu ◽  
Qianqian Zhang ◽  
Yaoyao Lin ◽  
Jingwen Hao ◽  
Shuyi Wang ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Oreochromis Niloticus ◽  
Nile Tilapia ◽  
High Throughput Sequencing ◽  
Gas Chromatography Mass Spectrometry ◽  
Gastrointestinal Mucosa ◽  
Gastrointestinal Microbiota ◽  
Linear Discriminant ◽  
Intestinal Microbes ◽  
Nile Tilapia Oreochromis Niloticus

The gill and gastrointestinal tract are primary entry routes for pathogens. The symbiotic microbiota are essential to the health, nutrition and disease of fish. Though the intestinal microbiota of Nile tilapia (Oreochromis niloticus) has been extensively studied, information on the mucosa-associated microbiota of this species, especially the gill and gastrointestinal mucosa-associated microbiota, is lacking. This study aimed to characterize the gill and gastrointestinal mucosa- and digesta-associated microbiota, as well as the intestinal metabolite profiles in the New Genetically Improved Farmed Tilapia (NEW GIFT) strain of farmed adult Nile tilapia by high-throughput sequencing and gas chromatography/mass spectrometry metabolomics. The diversity, structure, composition, and predicted function of gastrointestinal microbiota were significantly different across gastrointestinal regions and sample types (Welch t-test; p < 0.05). By comparing the mucosa- and digesta-associated microbiota, linear discriminant analysis (LDA) effect size (LEfSe) analysis revealed that Pelomonas, Ralstoniapickettii, Comamonadaceae, and Staphylococcus were significantly enriched in the mucosa-associated microbiota, whereas many bacterial taxa were significantly enriched in the digesta-associated microbiota, including Chitinophagaceae, Cetobacterium, CandidatusCompetibacter, Methyloparacoccus, and chloroplast (LDA score > 3.5). Furthermore, Undibacterium, Escherichia–Shigella, Paeniclostridium, and Cetobacterium were dominant in the intestinal contents and mucosae, whereas Sphingomonasaquatilis and Roseomonasgilardii were commonly found in the gill and stomach mucosae. The Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) analysis revealed that the predictive function of digesta-associated microbiota significantly differed from that of mucosa-associated microbiota (R = 0.8152, p = 0.0001). In addition, our results showed a significant interdependence between specific intestinal microbes and metabolites. Notably, the relative abundance values of several potentially beneficial microbes, including Undibacterium, Crenothrix, and Cetobacterium, were positively correlated with most intestinal metabolites, whereas the relative abundance values of some potential opportunistic pathogens, including Acinetobacter, Mycobacterium, Escherichia–Shigella, Paeniclostridium, Aeromonas, and Clostridiumsensustricto 1, were negatively correlated with most intestinal metabolites. This study revealed the characteristics of gill and gastrointestinal mucosa-associated and digesta-associated microbiota of farmed Nile tilapia and identified a close correlation between intestinal microbes and metabolites. The results serve as a basis for the effective application of targeted probiotics or prebiotics in the diet to regulate the nutrition and health of farmed tilapia.

scholarly journals Urbanization pressures alter tree rhizosphere microbiomes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Carl L. Rosier ◽  
Shawn W. Polson ◽  
Vincent D’Amico ◽  
Jinjun Kan ◽  
Tara L. E. Trammell
Keyword(s):  
Organic Matter ◽  
Relative Abundance ◽  
Tree Species ◽  
High Throughput Sequencing ◽  
Regional Climate ◽  
Keystone Species ◽  
Fagus Grandifolia ◽  
Yellow Poplar ◽  
Individual Tree ◽  
Structural Formation

AbstractThe soil microbial community (SMC) provides critical ecosystem services including organic matter decomposition, soil structural formation, and nutrient cycling. Studies suggest plants, specifically trees, act as soil keystone species controlling SMC structure via multiple mechanisms (e.g., litter chemistry, root exudates, and canopy alteration of precipitation). Tree influence on SMC is shaped by local/regional climate effects on forested environments and the connection of forests to surrounding landscapes (e.g., urbanization). Urban soils offer an ideal analog to assess the influence of environmental conditions versus plant species-specific controls on SMC. We used next generation high throughput sequencing to characterize the SMC of specific tree species (Fagus grandifolia [beech] vs Liriodendron tulipifera [yellow poplar]) across an urban–rural gradient. Results indicate SMC dissimilarity within rural forests suggests the SMC is unique to individual tree species. However, greater urbanization pressure increased SMC similarity between tree species. Relative abundance, species richness, and evenness suggest that increases in similarity within urban forests is not the result of biodiversity loss, but rather due to greater overlap of shared taxa. Evaluation of soil chemistry across the rural–urban gradient indicate pH, Ca+, and organic matter are largely responsible for driving relative abundance of specific SMC members.

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