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.

scholarly journals Diversity and pathogenicity of microbial communities causing grape sour rot in eastern coastal areas of China

2019 ◽  
Author(s):  
Huanhuan Gao ◽  
Xiangtian Yin ◽  
Xilong Jiang ◽  
Hongmei Shi ◽  
Yang Yang ◽  
...  
Keyword(s):  
Microbial Communities ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Bacterial Species ◽  
Traditional Culture ◽  
Coastal Areas ◽  
Culture Methods ◽  
Sour Rot ◽  
Table Grapes ◽  
Bacteria And Fungi

Background As a polymicrobial disease, grape sour rot can lead to the decrease in the yield of grape berries and wine quality. The diversity of microbial communities in sour rot-infected grapes depends on the planting location of grapes and the identified methods. The east coast of China is one of the most important grape and wine regions in China and even in the world. Methods To identify the pathogenic microorganism s causing sour rot in table grapes of eastern coastal areas of China, the diversity and abundance of the bacteria and fungi were assessed based on two methods, including traditional culture-methods, and 16S rRNA and ITS gene high-throughput sequencing . Then the pathogenicity of cultivable microorganisms was determined in laboratory. Results Based on traditional culture-methods, we identified 15 cultivable bacterial species and 10 fungal species from sour rot-infected grapes. The p athogenicity assay confirmed five cultivated fungi species (three Aspergillus species, Alternaria tenuissima, and Fusarium proliferatum), and four bacteria species (two Cronobacter species, Serratia marcescens and Lysinibacillus fusiformis) as mainly pathogenic on grape. A. tenuissima, and F. proliferatum were the firstly discovered as pathogens on harvesting grape. Moreover, high-throughput sequencing revealed the OTUs numbers of bacteria and fungi were 1343.33 and 1038.67 respectively. Proteobacteria (72.15%) and Firmicutes (26.83%) were dominant phylums among the 19 bacterial phyla identified, while Ascomycota (93.86%) was the dominant fungal phylum. Then, bacteria such as Acetobacter sp., Gluconobacter sp., Bacillus sp., and Lactococcus sp. and fungi such as Incertae sedis sp., Issatchenkia terricola, Colletotrichum viniferum, Hanseniaspora vineae, Saprochaete gigas, and Candida diversa took the vast majority ofmicrobial species in sour rot-infected grapes. Therefore, more accurate and abundant microbial communities in sour rot-infected grapes could be identified using the traditional culture-methods and high-throughput sequencing.

scholarly journals Diversity and pathogenicity of microbial communities causing grape sour rot in eastern coastal areas of China

2019 ◽  
Author(s):  
Huanhuan Gao ◽  
Xiangtian Yin ◽  
Xilong Jiang ◽  
Hongmei Shi ◽  
Yang Yang ◽  
...  
Keyword(s):  
Microbial Communities ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Bacterial Species ◽  
Traditional Culture ◽  
Coastal Areas ◽  
Culture Methods ◽  
Sour Rot ◽  
Table Grapes ◽  
Bacteria And Fungi

Background As a polymicrobial disease, grape sour rot can lead to the decrease in the yield of grape berries and wine quality. The diversity of microbial communities in sour rot-infected grapes depends on the planting location of grapes and the identified methods. The east coast of China is one of the most important grape and wine regions in China and even in the world. Methods To identify the pathogenic microorganism s causing sour rot in table grapes of eastern coastal areas of China, the diversity and abundance of the bacteria and fungi were assessed based on two methods, including traditional culture-methods, and 16S rRNA and ITS gene high-throughput sequencing . Then the pathogenicity of cultivable microorganisms was determined in laboratory. Results Based on traditional culture-methods, we identified 15 cultivable bacterial species and 10 fungal species from sour rot-infected grapes. The p athogenicity assay confirmed five cultivated fungi species (three Aspergillus species, Alternaria tenuissima, and Fusarium proliferatum), and four bacteria species (two Cronobacter species, Serratia marcescens and Lysinibacillus fusiformis) as mainly pathogenic on grape. A. tenuissima, and F. proliferatum were the firstly discovered as pathogens on harvesting grape. Moreover, high-throughput sequencing revealed the OTUs numbers of bacteria and fungi were 1343.33 and 1038.67 respectively. Proteobacteria (72.15%) and Firmicutes (26.83%) were dominant phylums among the 19 bacterial phyla identified, while Ascomycota (93.86%) was the dominant fungal phylum. Then, bacteria such as Acetobacter sp., Gluconobacter sp., Bacillus sp., and Lactococcus sp. and fungi such as Incertae sedis sp., Issatchenkia terricola, Colletotrichum viniferum, Hanseniaspora vineae, Saprochaete gigas, and Candida diversa took the vast majority ofmicrobial species in sour rot-infected grapes. Therefore, more accurate and abundant microbial communities in sour rot-infected grapes could be identified using the traditional culture-methods and high-throughput sequencing.

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 Wine Yeast Terroir: Separating the Wheat from the Chaff—for an Open Debate

2020 ◽  
Vol 8 (5) ◽  
pp. 787 ◽  
Author(s):  
Hervé Alexandre
Keyword(s):  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Abiotic Factors ◽  
Soil Microbial Communities ◽  
Consumer Preference ◽  
Wine Yeast ◽  
Wine Quality ◽  
Critical Feature ◽  
Wine Production ◽  
Sequencing Technologies

Wine terroir is characterized by a specific taste and style influenced by the cultivar of the fermented grapes, geographical factors such as the vineyard, mesoclimate, topoclimate, and microclimate, soil geology and pedology, and the agronomic approach used. These characteristics together define the concept of “terroir”. Thus, regional distinctive flavors in wine have been the subject of many studies aimed at better understanding the link between the wine and the vineyard. Indeed, the identification of key environmental elements involved in the regional variation of grape and wine quality characteristics is a critical feature for improving wine production in terms of consumer preference and economic appreciation. Many studies have demonstrated the role of abiotic factors in grape composition and consequently in wine style. Biotic factors are also involved such as grape microbial communities. However, the occurrence and effects of region-specific microbiota in defining wine characteristics are more controversial issues. Indeed, several studies using high throughput sequencing technologies have made it possible to describe microbial communities and revealed a link between grape must and soil microbial communities, and the geography of the territory. Based on these observations, the concept of “microbial terroir” emerged. However, this concept has been subject to contradictory studies. The aim of this opinion article is to take a step back and examine in perspective the concept of microbial terroir, by comparing numerous data from different studies and providing arguments in favor of or against this concept to stimulate discussion and point out that experimental research is still needed to study the contribution of this assembly of microorganisms to the final product and to support or refute the concept.

Analysis of the structure of bacterial and fungal communities in disease suppressive and disease conducive tobacco-planting soils in China

Soil Research ◽  
2020 ◽  
Vol 58 (1) ◽  
pp. 35
Author(s):  
Lin Gao ◽  
Rui Wang ◽  
Jiaming Gao ◽  
Fangming Li ◽  
Guanghua Huang ◽  
...  
Keyword(s):  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Soil Samples ◽  
Fungal Communities ◽  
Sequencing Technology ◽  
Operational Taxonomic Units ◽  
Tobacco Cultivation ◽  
Bacteria And Fungi ◽  
Disease Suppressive Soil ◽  
Conducive Soil

To clarify the differences between microbial communities resident in disease suppressive soil (DSS) and disease conducive soil (DCS) in tobacco cultivation, representative soil samples were collected from tobacco plantations in Shengjiaba, China, and the structure and diversity of the resident bacterial and fungal communities were analysed using high-throughput sequencing technology. Our results showed a greater number of operational taxonomic units associated with bacteria and fungi in DSS than in DCS. At the phylum level, abundances of Chloroflexi, Saccharibacteria, Firmicutes, and Planctomycetes in DSS were lower than in DCS, but abundance of Gemmatimonadetes was significantly higher. Abundances of Zygomycota and Chytridiomycota were higher in DSS than DCS, but abundance of Rozellomycota was significantly lower. At the genus level, abundances of 18 bacterial and nine fungal genera varied significantly between DSS and DCS. Relative abundances of Acidothermus, Microbacterium, Curtobacterium, and Colletotrichum were higher in DCS than DSS. The Shannon and Chao1 indices of DSS microbial communities were higher than those of DCS communities. High microbial diversity reduces the incidence of soil-borne diseases in tobacco plantations and promotes the formation of DSSs.

The distribution of active β-glucosidase-producing microbial communities in composting

2017 ◽  
Vol 63 (12) ◽  
pp. 998-1008 ◽  
Author(s):  
Xiangyun Zang ◽  
Meiting Liu ◽  
Han Wang ◽  
Yihong Fan ◽  
Haichang Zhang ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Cellulose Degradation ◽  
Cellulose Hydrolysis ◽  
Bacterial Phyla ◽  
Metabolic Activities ◽  
Bacteria And Fungi ◽  
A Minor ◽  
Dominant Bacteria ◽  
Global Carbon

The composting ecosystem is a suitable source for the discovery of novel microorganisms and secondary metabolites. Cellulose degradation is an important part of the global carbon cycle, and β-glucosidases complete the final step of cellulose hydrolysis by converting cellobiose to glucose. This work analyzes the succession of β-glucosidase-producing microbial communities that persist throughout cattle manure – rice straw composting, and evaluates their metabolic activities and community advantage during the various phases of composting. Fungal and bacterial β-glucosidase genes belonging to glycoside hydrolase families 1 and 3 (GH1 and GH3) amplified from DNA were classified and gene abundance levels were analyzed. The major reservoirs of β-glucosidase genes were the fungal phylum Ascomycota and the bacterial phyla Firmicutes, Actinobacteria, Proteobacteria, and Deinococcus–Thermus. This indicates that a diverse microbial community utilizes cellobiose. The succession of dominant bacteria was also detected during composting. Firmicutes was the dominant bacteria in the thermophilic phase of composting; there was a shift to Actinomycetes in the maturing stage. Proteobacteria accounted for the highest proportions during the heating and thermophilic phases of composting. By contrast, the fungal phylum Ascomycota was a minor microbial community constituent in thermophilic phase of composting. Combined with the analysis of the temperature, cellulose degradation rate and the carboxymethyl cellulase and β-glucosidase activities showed that the bacterial GH1 family β-glucosidase genes make greater contribution in cellulose degradation at the later thermophilic stage of composting. In summary, even GH1 bacteria families β-glucosidase genes showing low abundance in DNA may be functionally important in the later thermophilic phase of composting. The results indicate that a complex community of bacteria and fungi expresses β-glucosidases in compost. Several β-glucosidase-producing bacteria and fungi identified in this study may represent potential indicators of composting in cellulose degradation.

scholarly journals Long-Term Thinning Does not Significantly Affect Soil Water-Stable Aggregates and Diversity of Bacteria and Fungi in Chinese Fir (Cunninghamia lanceolata) Plantations in Eastern China

Forests ◽  
2018 ◽  
Vol 9 (11) ◽  
pp. 687 ◽  
Author(s):  
Xiangrong Cheng ◽  
Wenli Xing ◽  
Haijing Yuan ◽  
Mukui Yu
Keyword(s):  
Microbial Communities ◽  
Nitrogen Concentration ◽  
Eastern China ◽  
Soil Microbial Communities ◽  
Chinese Fir ◽  
Long Term Effects ◽  
Water Stable Aggregates ◽  
Bacteria And Fungi ◽  
Chinese Fir Plantation

Soil structure and microbial communities are sensitive to forest disturbance. However, little is known about the long-term effects of forest thinning on water-stable aggregates (WSA), and the community composition and diversity of soil microorganisms. In this study, we investigated soil chemical properties, WSA, and communities of bacteria and fungi in conventionally managed Chinese fir plantation stands and repeatedly thinned plantation stands with medium and high tree densities 18 years after the thinning treatments. The distribution patterns of WSA fractions were similar in the three thinning treatments. The mass proportion was the highest in the macro-aggregates fraction, followed by the clay + silt fraction, and it was the lowest in the micro-aggregates fraction. The soil organic carbon (SOC) concentrations in different WSA fractions decreased with decreasing aggregate size. The WSA fractions, stability, and aggregate-associated carbon were not significantly different among the three treatments 18 years after the thinning treatments. The total nitrogen concentration of the macro-aggregates fraction was significantly higher in the stands thinned intensively than in the conventionally managed stands. The abundance of minor bacteria and fungi species was different, although no significant differences were observed in the overall bacterial and fungal composition and diversity between the three treatments. Our results indicate that, compared with the conventionally managed stands, soil WSA stability and soil microbial communities in repeatedly thinned Chinese fir stands may recover over one rotation of Chinese fir plantation and that this is accompanied by the recovery of stand growth and soil nutrition.

scholarly journals The Composition of Root-Associated Bacteria and Fungi of Astragalus mongholicus and Their Relationship With the Bioactive Ingredients

2021 ◽  
Vol 12 ◽  
Author(s):  
Yanmei Li ◽  
Yang Liu ◽  
Hui Zhang ◽  
Yan Yang ◽  
Gehong Wei ◽  
...  
Keyword(s):  
Soil Properties ◽  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Fungal Community Composition ◽  
Associated Bacteria ◽  
Operational Taxonomic Units ◽  
Multivariate Correlation ◽  
Decay Pattern ◽  
Bioactive Ingredients ◽  
Bacteria And Fungi

Astragalus membranaceus (Fisch.) Bge. var. mongholicus, which is used in traditional Chinese medicine, contains several bioactive ingredients. The root-associated microbial communities play a crucial role in the production of secondary metabolites in plants. However, the correlation of root-associated bacteria and fungi with the bioactive ingredients production in A. mongholicus has not been elucidated. This study aimed to examine the changes in soil properties, root bioactive ingredients, and microbial communities in different cultivation years. The root-associated bacterial and fungal composition was analyzed using high-throughput sequencing. The correlation between root-associated bacteria and fungi, soil properties, and six major bioactive ingredients were examined using multivariate correlation analysis. Results showed that soil properties and bioactive ingredients were distinct across different cultivation years. The composition of the rhizosphere microbiome was different from that of the root endosphere microbiome. The bacterial community structure was affected by the cultivation year and exhibited a time-decay pattern. Soil properties affected the fungal community composition. It was found that 18 root-associated bacterial operational taxonomic units (OTUs) and four fungal OTUs were positively and negatively correlated with bioactive ingredient content, respectively. The abundance of Stenotrophomonas in the rhizosphere was positively correlated with astragaloside content. Phyllobacterium and Inquilinus in the endosphere were positively correlated with the calycosin content. In summary, this study provided a new opportunity and theoretical reference for improving the production and quality of in A. mongholicus, which thus increase the pharmacological value of A. mongholicus.

Variety features differentiate microbiota in the grape leaves

2020 ◽  
Vol 66 (11) ◽  
pp. 653-663 ◽  
Author(s):  
Shiwei Zhang ◽  
Yuan Wang ◽  
Xi Chen ◽  
Bingjian Cui ◽  
Zhihui Bai ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Habitat Preferences ◽  
Pinot Noir ◽  
Rrna Gene ◽  
Wine Grape ◽  
Linear Discriminant ◽  
Unweighted Unifrac ◽  
Bacteria And Fungi

The dependence of plant health and crop quality on the epiphytic microbial community has been extensively addressed, but little is known about plant-associated microbial communities under natural conditions. In this study, the bacterial and fungal communities on grape leaves were analyzed by 16S rRNA gene and internal transcribed spacer high-throughput sequencing, respectively. The results showed differences in the composition of the microbial communities on leaf samples of nine wine grape varieties. The most abundant bacterial genus was Pseudomonas, and the top three varieties with Pseudomonas were Zinfandel (22.6%), Syrah (21.6%), and Merlot (13.5%). The most abundant fungal genus was Alternaria, and the cultivar with the lowest abundance of Alternaria was Zinfandel (33.6%), indicating that these communities had different habitat preferences. The linear discriminant analysis effect size of all species showed that the bacteria Enterococcus, Massilia, and Kocuria were significantly enriched on the leaves of Merlot, Syrah, Cabernet Sauvignon, respectively; Pseudomonadales and Pantoea on Zinfandel; and Bacillus, Turicibacter, and Romboutsia on Pinot Noir. Similarly, the fungi Cladosporium, Phoma, and Sporormiella were significantly enriched on Zinfandel, Lon, and Gem, respectively. Both Bray–Curtis and unweighted UniFrac revealed that bacteria and fungi have a significant impact (P < 0.01), and the results further proved that variety is the most important factor affecting the microbial community. The findings indicate that some beneficial or harmful microorganisms existing on the wine grape leaves might affect the health of the grape plants and the wine-making process.

scholarly journals Changes in soil microbial communities at Jinsha earthen site are associated with earthen site deterioration

2020 ◽  
Author(s):  
Jing Li ◽  
Xiaoyue Zhang ◽  
Lin Xiao ◽  
Ke Liu ◽  
Yue Li ◽  
...  
Keyword(s):  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Soil Microbial Communities ◽  
Fungal Communities ◽  
Yeast Genus ◽  
Soil Microbial ◽  
Physicochemical Factors ◽  
Permanent Loss ◽  
Relative Abundances ◽  
Bacteria And Fungi

Abstract Background: Earthen sites are immobile cultural relics and an important part of cultural heritage with historical, artistic and scientific values. The deterioration of features in earthen sites result in permanent loss of cultural information, causing immeasurable damage to the study of history and culture. Most research on the deterioration of earthen sites has concentrated on the physicochemical factors, and information on microbial communities in earthen sites and their relationship with the earthen site deterioration is scarce. We used high-throughput sequencing to analyze bacterial and fungal communities in soils from earthen walls with different degree of deterioration at Jinsha earthen site to characterize the communities and their correlation with environmental factors, and compare community structures and the relative abundances of individual taxa associated with different degree of deterioration for identifying possible marker taxa.Results: The relative abundances of Proteobacteria and Firmicutes were higher and that of Actinobacteria lower with higher degree of deterioration. At the genus level, the relative abundances of Rubrobacter were highest in all sample groups except in the most deteriorated samples where that of Bacteroides was highest. The relative abundance of the yeast genus Candida was highest in the severely deteriorated sample group. The bacterial phylum Bacteroidetes and genus Bacteroides, and fungal class Saccharomycetes that includes Candida sp. were specific for the most deteriorated samples. For both bacteria and fungi, the differences in community composition were associated with differences in EC, moisture, pH, and the concentrations of NH4+, K+, Mg2+, Ca2+ and SO42-. Conclusion: The microbial communities in soil with different degree of deterioration were distinctly different, and deterioration was accompanied with bigger changes in the bacterial than in the fungal community. In addition, the deteriorated soil contained higher concentrations of soluble salts. Potentially, the accumulation of Bacteroides and Candida plays an important role in the deterioration of earthen features. Further work is needed to conclude whether controlling the growth of the bacteria and fungi with high relative abundances in the deteriorated samples can be applied to alleviate deterioration.

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