scholarly journals Patterns of Yeast Diversity Distribution and its Drivers in Rhizosphere Soil of Hami Melon Orchards in Different Regions of Xinjiang

2021 ◽  
Author(s):  
ShanShan Zhu ◽  
YongHui Lei ◽  
Chong Wang ◽  
YuMei Wei ◽  
ChunCheng Wang ◽  
...  
Keyword(s):  
Community Structure ◽  
High Throughput Sequencing ◽  
Yeast Species ◽  
Sequence Similarity ◽  
Climatic Conditions ◽  
Community Diversity ◽  
Sequencing Analysis ◽  
Microscopic Fungus ◽  
Yeast Diversity ◽  
Northern Xinjiang

Abstract Background: Yeast is an essential type of microscopic fungus found in the soil. It is vital to develop the resources of yeast to gain a better understanding of its role and potential in maintaining soil ecological balance and providing microbial resources. A special ecological environment is required for the evolution of yeast species. Xinjiang in China has unique climatic conditions with abundant melon and fruit resources. Here, we aimed to evaluate the diversity, community structure, and relationship between yeast species and environmental factors in Hami melon orchards in different regions of Xinjiang, China.Results: We used Illumina MiSeq high-throughput sequencing analysis to cluster 29,090 yeast sequences into 87 operational taxonomic units (OTUs) with 97% sequence similarity and 47 genera and 73 species. Most sequences (93.16%) belonged to the Basidiomycota; only a few (6.84%) belonged to Ascomycota. We detected 10 dominant genera and 11 dominant species with relative abundances > 1% in all sample sequences. We found that the yeast communities were significantly more diverse in the eastern Xinjiang region than in the southern and northern Xinjiang regions. The most dominant genera in the southern, eastern, and northern Xinjiang regions were Pseudozyma (54.77%), Solicoccozyma (28.6%), and Filobasidium (88.08%), respectively. Redundancy analysis (RDA) results indicated that the main factors influencing the structure of yeast in the study sites were CO, total phosphorus (TP), and total potassium (TK) of the soil.Conclusion: Our results suggest the presence of diversity and structural differences in yeast species among the southern, eastern, and northern Xinjiang regions. Eastern Xinjiang had the highest community diversity with a more even distribution of species. Differences in the geographical environment and the physicochemical properties of soils were probably the key factors driving yeast diversity and community structure.

scholarly journals Patterns of yeast diversity distribution and its drivers in rhizosphere soil of Hami melon orchards in different regions of Xinjiang

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
ShanShan Zhu ◽  
YongHui Lei ◽  
Chong Wang ◽  
YuMei Wei ◽  
ChunCheng Wang ◽  
...  
Keyword(s):  
Community Structure ◽  
Rhizosphere Soil ◽  
Yeast Species ◽  
Climatic Conditions ◽  
Soil Factors ◽  
Yeast Diversity ◽  
Northern Xinjiang ◽  
Yeast Community ◽  
Solar Radiation Intensity ◽  
Total Potassium

Abstract Background The unique climatic conditions of the Xinjiang region nurture rich melon and fruit resources, the melon and fruit sugar sources provide sufficient nutrients for the survival of yeast, and the diverse habitats accompanied by extreme climatic conditions promote the production of yeast diversity and strain resources. However, the relationship between yeast species and their relationship with environmental factors in the soil of Xinjiang specialty cash crop Hami melon is not clear. Here, we aimed to characterize the diversity, community structure, and relationship between yeast species and environmental factors in Hami melon orchards soils in different regions of Xinjiang, China. Results Based on Illumina MiSeq high-throughput sequencing analysis of the D1 domain of the LSU rRNA genes, the community richness of yeast in the soil of Northern Xinjiang was higher than in the Southern and Eastern Xinjiang, but the community diversity was significantly lower in the Northern Xinjiang than in the Southern and Eastern Xinjiang. A total of 86 OTUs were classified into 59 genera and 86 species. Most OTUs (90.4%) belonged to the Basidiomycota; only a few (9.6%) belonged to Ascomycota. The most dominant species in the Southern, Eastern and Northern Xinjiang were Filobasidium magnum (17.90%), Solicoccozyma aeria (35.83%) and Filobasidium magnum (75.36%), respectively. Principal coordinates analysis (PCoA) showed that the yeast community composition in the soils of the three regions were obviously different, with the Southern and Eastern Xinjiang having more similar yeast community. Redundancy analysis (RDA) showed that soil factors such as conductivity (CO), total phosphorus (TP) and Total potassium (TK) and climate factors such as average annual precipitation (PRCP), relative humidity (RH) and net solar radiation intensity (SWGNT) were significantly correlated with yeast communities (P < 0.05). Conclusion There are abundant yeast resources in the rhizosphere soil of Hami melon orchard in Xinjiang, and there are obvious differences in the diversity and community structure of yeast in the three regions of Xinjiang. Differences in climatic factors related to precipitation, humidity and solar radiation intensity and soil factors related to conductivity, total phosphorus and total potassium are key factors driving yeast diversity and community structure.

scholarly journals Illumina-based sequencing analysis of pathogenic microorganisms in dental caries patients of different Chinese ethnic groups

2019 ◽  
Vol 47 (10) ◽  
pp. 5037-5047
Author(s):  
Chen Yun ◽  
Li Zhiyan ◽  
Zhao Chong ◽  
Liu Jing ◽  
Zhang Xin ◽  
...  
Keyword(s):  
Dental Caries ◽  
Ethnic Groups ◽  
High Throughput Sequencing ◽  
Community Diversity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Control Group ◽  
Sequencing Analysis ◽  
Pathogenic Microorganisms ◽  
Effective Prevention

Objective To analyze the pathogenic community diversity of dental caries patients from Tu, Hui, Tibetan, and Han Chinese ethnic groups. Methods Forty saliva samples were collected from the following patients with dental caries: Tu from Huzhu County (n = 10), Hui from Ping’an County (n = 10), Han from Xining city (n = 10), and Tibetan from Yushu (n = 10). High-throughput sequencing of bacterial 16S rRNA genes (V3-V4) was performed using the Illumina MiSeq sequencing platform. Results Based on 97% similarity clustering, operational taxonomic units of Tu, Hui, Tibetan, and Han ethnic groups were 181, 210, 38, and 67, respectively. In Tu patients, 11 phyla, 19 classes, and 89 genera were identified, compared with 13 phyla, 21 classes, and 113 genera in Hui patients, two phyla, four classes, and 21 genera in Tibetan patients, five phyla, nine classes, and 34 genera in Han patients, and four phyla, five classes, and 12 genera from the control group. The main pathogens of dental caries included Veillonella, Aggregatibacter, Leptotrichia, Bacteroides, Granulicatella, Streptococcus, and Prevotella. Conclusion The pathogenic microorganisms of dental caries differ greatly among Tu, Hui, Tibetan, and Han ethnic groups. These findings provide a theoretical basis for the effective prevention and treatment of dental caries in different Chinese populations.

Bacterial community diversity and dynamics of Dongzhai harbor mangrove soils in China

2019 ◽  
Vol 65 (10) ◽  
pp. 703-712
Author(s):  
Peng Li ◽  
Siyu Wu ◽  
Haoneng Yin ◽  
Hongping Wu ◽  
Qin Peng ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
High Throughput Sequencing ◽  
Nature Reserve ◽  
Soil Samples ◽  
Community Diversity ◽  
Orthologous Group ◽  
Bacterial Community Diversity ◽  
National Nature Reserve ◽  
Abundant Otus

Dongzhai Harbor National Nature Reserve is the largest mangrove reserve in China, but the bacterial diversity and community structure of soils in the Dongzhai harbor mangrove (DHM) is still not well known. This study was conducted to characterize and compare the bacterial community diversity and composition of DHM soils in three typical sites (YA, entrance of wastewater and sanitary sewage; YB, located in Dongzhai Harbor National Nature Reserve; YC, near the sea) using high-throughput sequencing of the 16S rDNA. Community statistical analyses suggested that the YB and YC soils have a similar community structure, but they differ from the YA soils significantly. Proteobacteria and Chloroflexi were the ubiquitous and dominant groups that made up nearly 80% of total bacterial communities, but it was noted that Chloroflexi had a higher relative abundance in YA soil samples than YB and YC soil samples and that the operational taxonomic units (OTUs) of Anaerolineaceae, Gammaproteobacteria, and Thiogranum reached extremely significant levels. Interaction network analysis of the 50 most abundant OTUs further demonstrated that the OTUs of YA showed few interactions with YB and YC OTUs, and the Cluster of Orthologous Group (COG) involved in lipid transport and metabolism showed significant differences between the YA and YB soil samples. Our results will greatly help to understand the bacterial community variation of the DHM as human activities enhance and grow, and to identify some challenges for the restoration and management of the mangrove ecosystem.

scholarly journals Dynamics of Bacterial Community Structure in the Rhizosphere and Root Nodule of Soybean: Impacts of Growth Stages and Varieties

2021 ◽  
Author(s):  
Soo-In Sohn ◽  
Jae-Hyung Ahn ◽  
Subramani Pandian ◽  
Young-Ju Oh ◽  
Eun-Kyoung Shin ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
High Throughput Sequencing ◽  
Root Nodules ◽  
Growth Stages ◽  
Sequencing Analysis ◽  
Biolog Ecoplate ◽  
Metabolic Capability ◽  
Increasing Trend

Bacterial communities in rhizosphere and root nodules have significant contributions to the growth and productivity of the soybean (Glycine max L.). In this report, we analyzed the physiological properties and dynamics of bacterial community structure in rhizosphere and root nodules at different growth stages using BioLog EcoPlate and high-throughput sequencing technology, respectively. The BioLog assay found that the metabolic capability of rhizosphere is in increasing trend in the growth of soybeans as compared to the bulk soil. As a result of the Illumina sequencing analysis, the microbial community structure of rhizosphere and root nodules was found to be influenced by the variety and growth stage of the soybean. At the phylum level, Actinobacteria were the most abundant in rhizosphere at all growth stages, followed by Alphaproteobacteria and Acidobacteria and the phylum Bacteroidetes showed the greatest change. But, in the root nodules Alphaproteobacteria were dominant. The results of the OTU analysis exhibited the dominance of Bradyrhizobium during the entire stage of growth, but the ratio of non-rhizobial bacteria showed an increasing trend as the soybean growth progressed. These findings revealed that bacterial community in the rhizosphere and root nodules changed according to both the variety and growth stages of soybean in the field.

scholarly journals A novel foveavirus identified in wild grapevine (Vitis vinifera subsp. sylvestris)

2020 ◽  
Vol 165 (12) ◽  
pp. 2999-3002
Author(s):  
Jean-Sébastien Reynard ◽  
Justine Brodard ◽  
Eric Remoliff ◽  
Marie Lefebvre ◽  
Olivier Schumpp ◽  
...  
Keyword(s):  
Vitis Vinifera ◽  
High Throughput Sequencing ◽  
Sequence Similarity ◽  
International Committee ◽  
Species Demarcation Criterion ◽  
Replicase Gene ◽  
Sequencing Analysis ◽  
Species Demarcation ◽  
Demarcation Criterion ◽  
Wild Grapevine

Abstract We report the genome sequence of a putative new foveavirus infecting non-cultivated Vitis vinifera, tentatively named “grapevine foveavirus A” (GFVA). This virus was identified by high-throughput sequencing analysis of a European wild Vitis collected in Switzerland. Phylogenetic analysis revealed that this virus clustered with known grapevine virus T (GVT) isolates but was clearly distinct from any of them. If considering the International Committee of Taxonomy of Viruses (ICTV)-suggested foveavirus species demarcation criterion based on sequence similarity in the replicase gene/protein, this virus should be considered a member of a new species closely related to GVT. On the other hand, comparison of capsid gene/protein sequences using the same criteria indicates that GFVA is at the border of species demarcation. Whether this virus represents a highly divergent GVT isolate or a member of a distinct but closely related species is discussed.

scholarly journals Purification Effects on β-HCH Removal and Bacterial Community Differences of Vertical-Flow Constructed Wetlands with Different Vegetation Plantations

2021 ◽  
Vol 13 (23) ◽  
pp. 13244
Author(s):  
Qing Chen ◽  
Honghu Zeng ◽  
Yanpeng Liang ◽  
Litang Qin ◽  
Guangsheng Peng ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Plant Species ◽  
Constructed Wetlands ◽  
Bacterial Community Structure ◽  
High Throughput Sequencing ◽  
Community Response ◽  
Control Treatment ◽  
Acorus Calamus ◽  
Sequencing Analysis

This study aimed to investigate the removal of β-hexachlorocyclohexane (β-HCH) at realistic concentration levels (10 µg/L) in different plant species in constructed wetlands (Acorus calamus, Canna indica, Thalia dealbata, and Pontederia cordata) and the structure of the rhizosphere microbial community response of each group during summer and winter. Results showed that all groups of constructed wetlands had very good decontamination efficiency against β-HCH in water (90.86–98.17%). The species that most efficiently purified β-HCH in water was A. calamus in summer (98.17%) and C. indica in winter (96.64%). Substrate sorption was found to be the major pathway for β-HCH removal from water in the constructed wetlands. The ability of the wetland plants to absorb and purify β-HCH was limited, and C. indica had the strongest absorptive capacity among the four plant species. The mean β-HCH removal from the matrix of the planted plants increased by 5.8% compared with that of the control treatment (unplanted plants). The average β-HCH content in the plant rhizosphere substrate was 4.15 µg/kg lower than that in the non-rhizosphere substrate. High-throughput sequencing analysis revealed significant differences (P < 0.05) in the Chao1 and ACE indices of microbes in the substrate of four wetlands during summer and winter. At the genus level, the constructed wetlands with vegetation plantations showed higher microbial abundance than the constructed wetlands without vegetation plantations. In winter, the bacterial community structure of each constructed wetland was quite different, but no dominant flora in the bacterial community structure obviously changed. In summer, the bacterial community structure at the same stage was relatively small. The abundance of Actinobacteria and Sphingomonas remarkably increased over time in summer.

scholarly journals Dynamics of Bacterial Community Structure in the Rhizosphere and Root Nodule of Soybean: Impacts of Growth Stages and Varieties

2021 ◽  
Vol 22 (11) ◽  
pp. 5577
Author(s):  
Soo-In Sohn ◽  
Jae-Hyung Ahn ◽  
Subramani Pandian ◽  
Young-Ju Oh ◽  
Eun-Kyoung Shin ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
High Throughput Sequencing ◽  
Root Nodules ◽  
Growth Stages ◽  
Sequencing Analysis ◽  
Biolog Ecoplate ◽  
Metabolic Capability ◽  
Increasing Trend

Bacterial communities in rhizosphere and root nodules have significant contributions to the growth and productivity of the soybean (Glycine max (L.) Merr.). In this report, we analyzed the physiological properties and dynamics of bacterial community structure in rhizosphere and root nodules at different growth stages using BioLog EcoPlate and high-throughput sequencing technology, respectively. The BioLog assay found that the metabolic capability of rhizosphere is in increasing trend in the growth of soybeans as compared to the bulk soil. As a result of the Illumina sequencing analysis, the microbial community structure of rhizosphere and root nodules was found to be influenced by the variety and growth stage of the soybean. At the phylum level, Actinobacteria were the most abundant in rhizosphere at all growth stages, followed by Alphaproteobacteria and Acidobacteria, and the phylum Bacteroidetes showed the greatest change. But, in the root nodules Alphaproteobacteria were dominant. The results of the OTU analysis exhibited the dominance of Bradyrhizobium during the entire stage of growth, but the ratio of non-rhizobial bacteria showed an increasing trend as the soybean growth progressed. These findings revealed that bacterial community in the rhizosphere and root nodules changed according to both the variety and growth stages of soybean in the field.

scholarly journals Microbial Community Structure Drives Predatory Myxobacteria Distribution Under Different Compost Manures

2021 ◽  
Author(s):  
Wei Dai ◽  
Ning Wang ◽  
Wenhui Wang ◽  
Xianfeng Ye ◽  
Zhongli Cui ◽  
...  
Keyword(s):  
Community Structure ◽  
High Throughput Sequencing ◽  
Soil Microbial Communities ◽  
Alpha Diversity ◽  
Distribution Patterns ◽  
Diversity Indices ◽  
Community Diversity ◽  
Microbial World ◽  
Significant Difference ◽  
Compost Manure

Abstract Myxobacteria are unique predatory microorganisms with a distinct social lifestyle. The associated taxa play key roles in the microbial food webs in different ecosystems and regulate the community structures of soil microbial communities. Compared with conditions under conventional management, under organic conditions, myxobacteria abundance increases in the soil, which could be related to the presence of abundant myxobacteria in the applied compost manure. In the present study, high-throughput sequencing technologies were used to investigate the distribution patterns and drivers of predatory myxobacteria community distribution patterns in four common compost manures. According to the results, there was a significant difference in predatory myxobacteria community structure among different compost manure treatments (P < 0.05). The alpha-diversity indices of myxobacteria community under swine manure compost were the lowest (Observed OTU richness = 13.25, Chao1 = 14.83, Shannon = 0.61), and those under wormcast were the highest (Observed OTU richness = 30.25, Chao1 = 31.65, Shannon = 2.62). Bacterial community diversity and Mg2+ and Ca2+ concentrations were the major factors influencing myxobacteria distribution patterns under different compost manure treatments. In addition, pH, total nitrogen, and organic carbon influenced myxobacteria distribution in compost manure. The predator–prey relationship between prey bacteria and myxobacteria and the interaction between myxobacteria and specific bacterial taxa (Micrococcales) in compost manure could explain the influence of bacteria on myxobacteria community structure. Further investigations on the in-situ distribution patterns of predatory myxobacteria and the key bacteria influencing their distribution are would advance our understanding of the ecological distribution patterns and functions of predatory microorganisms in the microbial world.

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