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.

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.

Influence of DNA extraction and PCR amplification on studies of soil fungal communities based on amplicon sequencing

2011 ◽  
Vol 57 (12) ◽  
pp. 1062-1066 ◽  
Author(s):  
Lihui Xu ◽  
Sabine Ravnskov ◽  
John Larsen ◽  
Mogens Nicolaisen
Keyword(s):  
Species Richness ◽  
Microbial Communities ◽  
Dna Extraction ◽  
454 Pyrosequencing ◽  
Pcr Amplification ◽  
Amplicon Sequencing ◽  
Soil Samples ◽  
Fungal Communities ◽  
Agricultural Field ◽  
Operational Taxonomic Units

Most studies involving next-generation amplicon sequencing of microbial communities from environmental studies lack replicates. DNA extraction and PCR effects on the variation of read abundances of operational taxonomic units generated from deep amplicon 454 pyrosequencing was investigated using soil samples from an agricultural field with diseased pea. One sample was extracted four times, and one of these samples was PCR amplified four times to obtain eight replicates in total. Results showed that species richness was consistent among replicates. Variation among dominant taxa was low across replicates, whereas rare operational taxonomic units showed higher variation among replicates. The results indicate that pooling of several extractions and PCR amplicons will decrease variation among samples.

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.

scholarly journals Extremely Halophilic Biohydrogen Producing Microbial Communities from High-Salinity Soil and Salt Evaporation Pond

Fuels ◽  
2021 ◽  
Vol 2 (2) ◽  
pp. 241-252
Author(s):  
Dyah Asri Handayani Taroepratjeka ◽  
Tsuyoshi Imai ◽  
Prapaipid Chairattanamanokorn ◽  
Alissara Reungsang
Keyword(s):  
Microbial Communities ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
High Salinity ◽  
Amplicon Sequencing ◽  
Spatial Proximity ◽  
Lignocellulosic Waste ◽  
Evaporation Pond ◽  
Operational Taxonomic Units ◽  
Determining Factor

Extreme halophiles offer the advantage to save on the costs of sterilization and water for biohydrogen production from lignocellulosic waste after the pretreatment process with their ability to withstand extreme salt concentrations. This study identifies the dominant hydrogen-producing genera and species among the acclimatized, extremely halotolerant microbial communities taken from two salt-damaged soil locations in Khon Kaen and one location from the salt evaporation pond in Samut Sakhon, Thailand. The microbial communities’ V3–V4 regions of 16srRNA were analyzed using high-throughput amplicon sequencing. A total of 345 operational taxonomic units were obtained and the high-throughput sequencing confirmed that Firmicutes was the dominant phyla of the three communities. Halanaerobium fermentans and Halanaerobacter lacunarum were the dominant hydrogen-producing species of the communities. Spatial proximity was not found to be a determining factor for similarities between these extremely halophilic microbial communities. Through the study of the microbial communities, strategies can be developed to increase biohydrogen molar yield.

scholarly journals Microbial Eukaryotes: a Missing Link in Gut Microbiome Studies

mSystems ◽  
2018 ◽  
Vol 3 (2) ◽  
Author(s):  
Isabelle Laforest-Lapointe ◽  
Marie-Claire Arrieta
Keyword(s):  
Microbial Communities ◽  
Microbial Ecology ◽  
High Throughput Sequencing ◽  
Sequencing Technology ◽  
Human Gut ◽  
Microbial Eukaryotes ◽  
Host Health ◽  
High Level ◽  
Eukaryotic Organisms ◽  
New Evidence

ABSTRACTHuman-associated microbial communities include prokaryotic and eukaryotic organisms across high-level clades of the tree of life. While advances in high-throughput sequencing technology allow for the study of diverse lineages, the vast majority of studies are limited to bacteria, and very little is known on how eukaryote microbes fit in the overall microbial ecology of the human gut. As recent studies consider eukaryotes in their surveys, it is becoming increasingly clear that eukaryotes play important ecological roles in the microbiome as well as in host health. In this perspective, we discuss new evidence on eukaryotes as fundamental species of the human gut and emphasize that future microbiome studies should characterize the multitrophic interactions between microeukaryotes, other microorganisms, and the host.

scholarly journals Comparative Analysis of the Bacterial and Fungal Communities in the Gut and the Crop of Aedes albopictus Mosquitoes: A Preliminary Study

Pathogens ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 628
Author(s):  
Morgane Guégan ◽  
Edwige Martin ◽  
Claire Valiente Moro
Keyword(s):  
Aedes Albopictus ◽  
High Throughput Sequencing ◽  
Fungal Communities ◽  
Nectar Feeding ◽  
Composition And Structure ◽  
Asian Tiger ◽  
Males And Females ◽  
Preliminary Study ◽  
Bacteria And Fungi ◽  
Pathogen Vector

The Asian tiger mosquito Aedes albopictus is a major pathogen vector and one of the world’s most invasive species. In recent years, the study of mosquito-associated microbiota has received growing interest for reducing transmission of mosquito-borne pathogens. Most of studies on mosquito microbiota mainly focused on the gut bacteria. However, microorganisms can also colonize other organs and are not restricted to bacteria. In mosquitoes, the crop is the primary storage organ for sugars from the nectar feeding before it is transferred into the midgut for digestion. No study has yet investigated whether this organ can harbor microorganisms in Ae. albopictus. By using high-throughput sequencing, this study is the first to describe the microbiota including both bacteria and fungi in sugar-fed Ae. albopictus males and females. The results showed the presence of diverse and rich bacterial and fungal communities in the crop of both sexes that did not strongly differ from the community composition and structure found in the gut. Altogether, our results provide a thorough description of the crop-associated microbiota in Ae. albopictus which can open new avenues for further studies on trophic interactions between the mosquito and its microbiota.

Temporal patterns in the interaction between photosynthetic picoeukaryotes and their attached fungi in Lake Chaohu

2020 ◽  
Vol 96 (7) ◽  
Author(s):  
Changqing Liu ◽  
Xiaoli Shi ◽  
Fan Wu ◽  
Min Zhang ◽  
Guang Gao ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Fungal Communities ◽  
Lake Chaohu ◽  
Operational Taxonomic Units ◽  
Flow Cytometric ◽  
Temporal Succession ◽  
Temperature Group ◽  
Flow Cytometric Sorting ◽  
Two Temperature ◽  
Molecular Ecological Network

ABSTRACT The combination of flow cytometric sorting and high-throughput sequencing revealed the broad existence of photosynthetic picoeukaryote attached fungi (PPE-attached fungi) in Lake Chaohu. The relative sequence abundance of attached fungi was negatively correlated with that of the photosynthetic picoeukaryotes (PPEs). PPE-attached fungal communities were mainly composed of Basidiomycota, Chytridiomycota and Ascomycota. Temperature, Si and PPE community structure are the most important driving factors for the temporal succession of PPE-attached fungal communities. In particular, PPE-attached fungi can be divided into three groups from high to low temperatures. Phylogenetic molecular ecological network results indicated that the connectivity and the total number of links in the network of the high-temperature group (> 21.82°C) are higher than those in the other two temperature groups (between  9.67 and  21.82°C, and < 9.67°C, respectively). Moreover, the interaction between PPE-attached fungi and the PPEs changed from antagonistic to cooperative, with the decline in temperature. The most abundant operational taxonomic units of PPE-attached fungi were affiliated with the Cladosporium, the most common saprophytic fungus, whereas most fungal hub taxa were Chytridiomycota, the main parasite fungi of phytoplankton.

scholarly journals Microbial Communities Associated with Potato Common Scab-Suppressive Soil Determined by Pyrosequencing Analyses

Plant Disease ◽  
2012 ◽  
Vol 96 (5) ◽  
pp. 718-725 ◽  
Author(s):  
Noah Rosenzweig ◽  
James M. Tiedje ◽  
John F. Quensen ◽  
Qingxiao Meng ◽  
Jianjun J. Hao
Keyword(s):  
Microbial Communities ◽  
Common Scab ◽  
Disease Suppression ◽  
Rrna Gene ◽  
Suppressive Soil ◽  
Streptomyces Spp ◽  
Potato Common Scab ◽  
Order Of Magnitude ◽  
Disease Suppressive Soil ◽  
Conducive Soil

Potato common scab, caused by Streptomyces spp., is an annual production problem for potato growers, and not effectively controlled by current methods. A field with naturally occurring common scab suppression has been identified in Michigan, and confirmed to have a biological basis for this disease suppression. This field and an adjacent scab nursery conducive to disease were studied using pyrosequencing to compare the two microbial communities. Total DNA was extracted from both the disease-conducive and -suppressive soils. A phylogenetically taxon-informative region of the 16S rRNA gene was used to establish operational taxonomic units (OTUs) to characterize bacterial community richness and diversity. In total, 1,124 OTUs were detected and 565 OTUs (10% dissimilarity) were identified in disease-conducive soil and 859 in disease-suppressive soil, including 300 shared both between sites. Common phyla based on relative sequence abundance were Acidobacteria, Proteobacteria, and Firmicutes. Sequences of Lysobacter were found in significantly higher numbers in the disease-suppressive soil, as were sequences of group 4 and group 6 Acidobacteria. The relative abundance of sequences identified as the genus Bacillus was significantly higher by an order of magnitude in the disease-conducive soil.

scholarly journals Best practices in metabarcoding of fungi: from experimental design to results

2021 ◽  
Author(s):  
Leho Tedersoo ◽  
Mohammad Bahram ◽  
Lucie Zinger ◽  
Henrik Nilsson ◽  
Peter Kennedy ◽  
...  
Keyword(s):  
Experimental Design ◽  
Best Practices ◽  
Fungal Diversity ◽  
High Throughput Sequencing ◽  
Its Region ◽  
Fungal Communities ◽  
Sequence Variants ◽  
Transcriptomic Data ◽  
Operational Taxonomic Units ◽  
Computational Analyses

The development of high-throughput sequencing (HTS) technologies has greatly improved our capacity to identify fungi and unveil their ecological roles across a variety of ecosystems. Here we provide an overview about current best practices in metabarcoding analysis of fungal communities, from experimental design through molecular and computational analyses. By re-analysing published datasets, we find that operational taxonomic units (OTUs) outperform amplified sequence variants (ASVs) in recovering fungal diversity, which is particularly evident for long markers. Additionally, analysis of the full-length ITS region allows more accurate taxonomic placement of fungi and other eukaryotes compared with the ITS2 subregion. We conclude that metabarcoding analyses of fungi are especially promising for co-analyses with the functional metagenomic or transcriptomic data, integrating fungi in the entire microbiome, recovery of novel fungal lineages and ancient organisms as well as barcoding of old specimens including type material.

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.

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