scholarly journals Seed-Transmitted Bacteria and Fungi Dominate Juvenile Plant Microbiomes

2021 ◽  
Vol 12 ◽  
Author(s):  
David Johnston-Monje ◽  
Janneth P. Gutiérrez ◽  
Luis Augusto Becerra Lopez-Lavalle
Keyword(s):  
High Throughput Sequencing ◽  
Brachypodium Distachyon ◽  
Brachiaria Decumbens ◽  
Operational Taxonomic Units ◽  
Bacterial Microbiome ◽  
Fungal Populations ◽  
To Come ◽  
Bacteria And Fungi ◽  
Plant Life Cycle

Plant microbiomes play an important role in agricultural productivity, but there is still much to learn about their provenance, diversity, and organization. In order to study the role of vertical transmission in establishing the bacterial and fungal populations of juvenile plants, we used high-throughput sequencing to survey the microbiomes of seeds, spermospheres, rhizospheres, roots, and shoots of the monocot crops maize (B73), rice (Nipponbare), switchgrass (Alamo), Brachiaria decumbens, wheat, sugarcane, barley, and sorghum; the dicot crops tomato (Heinz 1706), coffee (Geisha), common bean (G19833), cassava, soybean, pea, and sunflower; and the model plants Arabidopsis thaliana (Columbia-0) and Brachypodium distachyon (Bd21). Unsterilized seeds were planted in either sterile sand or farm soil inside hermetically sealed jars, and after as much as 60 days of growth, DNA was extracted to allow for amplicon sequence-based profiling of the bacterial and fungal populations that developed. Seeds of most plants were dominated by Proteobacteria and Ascomycetes, with all containing operational taxonomic units (OTUs) belonging to Pantoea and Enterobacter. All spermospheres also contained DNA belonging to Pseudomonas, Bacillus, and Fusarium. Despite having only seeds as a source of inoculum, all plants grown on sterile sand in sealed jars nevertheless developed rhizospheres, endospheres, and phyllospheres dominated by shared Proteobacteria and diverse fungi. Compared to sterile sand-grown seedlings, growth on soil added new microbial diversity to the plant, especially to rhizospheres; however, all 63 seed-transmitted bacterial OTUs were still present, and the most abundant bacteria (Pantoea, Enterobacter, Pseudomonas, Klebsiella, and Massilia) were the same dominant seed-transmitted microbes observed in sterile sand-grown plants. While most plant mycobiome diversity was observed to come from soil, judging by read abundance, the dominant fungi (Fusarium and Alternaria) were also vertically transmitted. Seed-transmitted fungi and bacteria appear to make up the majority of juvenile crop plant microbial populations by abundance, and based on occupancy, there seems to be a pan-angiosperm seed-transmitted core bacterial microbiome. Further study of these seed-transmitted microbes will be important to understand their role in plant growth and health, as well as their fate during the plant life cycle and may lead to innovations for agricultural inoculant development.

scholarly journals Characterization of the gut DNA and RNA viromes in a cohort of Chinese residents and visiting Pakistanis

2020 ◽  
Author(s):  
Qiulong Yan ◽  
Yu Wang ◽  
Xiuli Chen ◽  
Hao Jin ◽  
Guangyang Wang ◽  
...  
Keyword(s):  
Ethnic Origin ◽  
Chinese Adults ◽  
Bacterial Composition ◽  
Operational Taxonomic Units ◽  
Dna And Rna ◽  
Bacterial Microbiome ◽  
Chinese Cohort ◽  
Host Genetic

AbstractBackgroundTrillions of viruses inhabit the gastrointestinal tract. Some of them have been well-studied on their roles in infection and human health, but the majority remain unsurveyed. It has been established that the composition of the gut virome is highly variable based on the changes of diet, physical state, and environmental factors. However, the effect of host genetic factors, e.g. ethnic origin, on the gut virome is rarely investigated.Methods and ResultsHere, we characterized and compared the gut virome in a cohort of local Chinese residents and visiting Pakistani individuals, each group containing 24 healthy adults and 6 children. Using metagenomic shotgun sequencing and assembly of fecal samples, a huge number of viral operational taxonomic units (vOTUs) were identified for profiling the DNA and RNA viromes. National background contributed a primary variation to individuals’ gut virome. Compared with the Chinese adults, the Pakistan adults showed higher macrodiversity and different compositional and functional structures in their DNA virome and lower diversity and altered composition in their RNA virome. The virome variations of Pakistan children were inherited from the that of the adults but also tended to share similar characteristics with the Chinese cohort. We also analyzed and compared the bacterial microbiome between two cohorts and further revealed numerous connections between virus and bacterial host. Statistically, the gut DNA and RNA viromes were covariant to some extent (p<0.001), and they both influenced the holistic bacterial composition and vice versa.ConclusionsThis study provides an overview of gut viral community in Chinese and visiting Pakistanis and proposes a considerable role of ethnic origin in shaping the virome.

scholarly journals Exploring Microbial Resource of Different Rhizocompartments of Dominant Plants Along the Salinity Gradient Around the Hypersaline Lake Ejinur

2021 ◽  
Vol 12 ◽  
Author(s):  
Junqing Luo ◽  
Zhechao Zhang ◽  
Yazhou Hou ◽  
Fengwei Diao ◽  
Baihui Hao ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Salt Lake ◽  
Salinity Gradient ◽  
Salt Lakes ◽  
Hypersaline Environment ◽  
Hypersaline Lake ◽  
Littoral Zones ◽  
Microbial Resources ◽  
Bacteria And Fungi

Lake littoral zones can also be regarded as another extremely hypersaline environment due to hypersaline properties of salt lakes. In this study, high-throughput sequencing technique was used to analyze bacteria and fungi from different rhizocompartments (rhizosphere and endosphere) of four dominant plants along the salinity gradient in the littoral zones of Ejinur Salt Lake. The study found that microbial α-diversity did not increase with the decrease of salinity, indicating that salinity was not the main factor on the effect of microbial diversity. Distance-based redundancy analysis and regression analysis were used to further reveal the relationship between microorganisms from different rhizocompartments and plant species and soil physicochemical properties. Bacteria and fungi in the rhizosphere and endosphere were the most significantly affected by SO42–, SOC, HCO3–, and SOC, respectively. Correlation network analysis revealed the potential role of microorganisms in different root compartments on the regulation of salt stress through synergistic and antagonistic interactions. LEfSe analysis further indicated that dominant microbial taxa in different rhizocompartments had a positive response to plants, such as Marinobacter, Palleronia, Arthrobacter, and Penicillium. This study was of great significance and practical value for understanding salt environments around salt lakes to excavate the potential microbial resources.

scholarly journals Characterization of the bacterial microbiome of Rhipicephalus (Boophilus) microplus collected from Pecari tajacu “Sajino” Madre de Dios, Peru

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jesús Rojas-Jaimes ◽  
David Lindo-Seminario ◽  
Germán Correa-Núñez ◽  
Benoit Diringer
Keyword(s):  
Animal Health ◽  
Boophilus Microplus ◽  
Adult Males ◽  
Pathogenic Potential ◽  
Core Microbiome ◽  
Operational Taxonomic Units ◽  
Madre De Dios ◽  
Bacterial Microbiome ◽  
Pecari Tajacu

AbstractTicks are arthropods that can host and transmit pathogens to wild animals, domestic animals, and even humans. The bacterial microbiome of adult (males and females) and nymph Rhipicephalus microplus ticks collected from a collared peccary, Pecari tajacu, captured in the rural area of Botijón Village in the Amazon region of Madre de Dios, Peru, was evaluated using metagenomics. The Chao1 and Shannon–Weaver analyses indicated greater bacterial richness and diversity in female ticks (GARH; 375–4.15) and nymph ticks (GARN; 332–4.75) compared to that in male ticks (GARM; 215–3.20). Taxonomic analyses identified 185 operational taxonomic units representing 147 bacterial genera. Of the 25 most prevalent genera, Salmonella (17.5%) and Vibrio (15.0%) showed the highest relative abundance followed by several other potentially pathogenic genera, such as Paracoccus (7.8%), Staphylococcus (6.8%), Pseudomonas (6.6%), Corynebacterium (5.0%), Cloacibacterium (3.6%), and Acinetobacter (2.5%). In total, 19.7% of the detected genera are shared by GARH, GARM, and GARN, and they can be considered as the core microbiome of R. microplus. To the best of our knowledge, this study is the first to characterize the microbiome of ticks collected from P. tajacu and to report the presence of Salmonella and Vibrio in R. microplus. The pathogenic potential and the role of these bacteria in the physiology of R. microplus should be further investigated due to the possible implications for public health and animal health in populations neighboring the habitat of P. tajacu.

scholarly journals Endosymbiotic bacteria are prevalent and diverse in agricultural spiders

2019 ◽  
Author(s):  
Jennifer A. White ◽  
Alexander Styer ◽  
Laura C. Rosenwald ◽  
Meghan M. Curry ◽  
Kelton D. Welch ◽  
...  
Keyword(s):  
Population Dynamics ◽  
High Throughput Sequencing ◽  
Diagnostic Pcr ◽  
Spider Species ◽  
Web Studies ◽  
Operational Taxonomic Units ◽  
Endosymbiotic Bacteria ◽  
Bacterial Microbiome ◽  
Bacterial Endosymbionts ◽  
Symbiotic Microbiota

AbstractMaternally inherited bacterial endosymbionts are common in arthropods, but their distribution and prevalence is poorly characterized in many host taxa. For example, spiders (Araneae) have received little attention, but initial surveys suggest that vertically transmitted symbionts may be common. Here, we characterized endosymbiont infection in a community of agricultural spiders. Using a combination of diagnostic PCR and high-throughput sequencing of the bacterial microbiome, we evaluated symbiont infection in 267 individual spiders representing 14 species in 3 families. We found 27 Operational Taxonomic Units (OTUs) that are likely endosymbiotic, including several strains of Wolbachia, Rickettsia and Cardinium, all of which are vertically transmitted and frequently associated with reproductive manipulation of arthropod hosts. Seventy percent of spider species had individuals that tested positive for one or more endosymbiotic OTUs, and specimens frequently contained multiple symbiotic strain types. The most symbiont-rich species, Idionella rugosa, had eight endosymbiotic OTUs, with as many as five present in the same specimen. Individual specimens within infected spider species had a variety of symbiotypes, differing from one another in the presence or absence of symbiotic strains. Our sample included both starved and unstarved specimens, and dominant bacterial OTUs were consistent per host species, regardless of feeding status. We conclude that spiders contain a remarkably diverse symbiotic microbiota. Spiders would be an informative group for investigating endosymbiont population dynamics in time and space, and unstarved specimens collected for other purposes (e.g., food web studies) could be used, with caution, for such investigations.

Role of Yeasts in the Cranberry Fruit Rot Disease Complex

Plant Disease ◽  
2020 ◽  
Author(s):  
Zachary David Zalewski ◽  
Rae Page ◽  
Richard Lankau ◽  
Patricia McManus
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
The Other ◽  
Fruit Rot ◽  
Internal Transcribed Spacer Region ◽  
Operational Taxonomic Units ◽  
Inhibition Of Growth ◽  
Hanseniaspora Uvarum ◽  
Rot Disease

Cranberry fruit rot (CFR) is an economically important disease caused by at least 10 species of filamentous fungi. Despite the application of fungicides, incidence of CFR is sometimes high, raising the possibility of a role for microbes other than fungi in the CFR complex. Isolation of microbes from rotten berries on media that favor either bacteria or yeasts resulted in mucoid colonies from fewer than 15% of dry-harvested rotten berries but up to 60% of wet-harvested berries. The mucoid colonies were identified as yeasts, primarily in the family Saccharomycetaceae. Inoculation of sound berries with three yeasts, Hanseniaspora uvarum, Pichia fermentans, and Pichia terricola, resulted in significantly higher incidence and severity of rot symptoms compared to mock-inoculated controls; these yeasts were recovered from inoculated berries, providing evidence of their pathogenicity. The minimum concentrations of azoxystrobin, chlorothalonil, and prothioconazole that resulted in 80% inhibition of growth compared to untreated controls (MIC80) were determined for a subset of yeasts. In general, MIC80s were higher for azoxystrobin and prothioconazole (usually >64 µg/ml) than for chlorothalonil (usually ≤1 µg/ml). To complement culture-dependent studies, DNA was isolated from wet- and dry-harvested rotten berries, and fungi were identified to the level of family by high-throughput sequencing of the fungal internal transcribed spacer region (ITS2). There were no fungal families consistently detected among samples by one method (culturing or high-throughput sequencing) and missed by the other that have not previously been reported in cranberry; however, some fungal families were found to be more abundant by one method versus the other. Harvest method (wet or dry) had a significant effect on the composition of fungal communities of rotten berries (P < 0.001), and operational taxonomic units representing the Saccharomycetaceae were more abundant in wet- than dry-harvested berries. Taken together, the results suggest that some yeasts are pathogenic to cranberry and may be especially relevant in wet-harvested berries.

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.

Microbial community structure and function prediction of two typical biocrusts in the Mu Us Sandland, Northwest China

2021 ◽  
Author(s):  
Chang Tian ◽  
Jiao Xi ◽  
Mengchen Ju ◽  
Yahong Li ◽  
Qi Guo ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Organic Carbon ◽  
Fungal Community ◽  
High Throughput Sequencing ◽  
Shannon Index ◽  
Operational Taxonomic Units ◽  
Relative Abundances ◽  
Bacteria And Fungi ◽  
Moss Crust

&lt;p&gt;Biocrusts (Biological soil crusts) are a living ground cover widely distributed in arid and semi-arid regions worldwide and provide important ecological functions in ecosystems. As an important part of biocrusts, the microorganisms in the formation and succession of biocrusts should not be underestimated. However, the microbial processes among different types of biocrusts are poorly understood. We used high-throughput sequencing to identify soil bacteria and fungal community in two types of biocrusts, lichen crust and moss crust, in the Mu Us Sandland. The aims were to explore the composition, diversity, and ecological function of the microbial community in two types of biocrusts. Our study found that (1) The diversity of bacterial and fungal communities was significantly different between the two types of biocrusts. The Shannon index (6.18) of fungi in moss crust was higher than that (5.75) in lichen crust, and the operational taxonomic units of bacteria and fungi in moss crust were also higher than those in lichen crust by 3.22% and 30.61%, respectively. The bacteria and fungi community structure in two types of biocrusts were significantly different, while the differences were not significant. (2) In the microbiomes of lichen and moss biocrusts, Actinomycetes, Cyanobacteria, and Proteobacteria, the sum of which accounted for 68.01% in lichen crust and 59.88% in moss crust at operational taxonomic units level, were dominant phylum of bacteria, while the dominant phylum of fungi was mainly Ascomycota. Microcoleus (11.10%) and Exophiala (7.37%) were dominant genera in lichen crust, while the dominant genus in moss crust was RB41 (5.16%). (3) The pH, soil dissolved organic carbon, and soil organic carbon were the top three factors that correlated with both bacterial and fungal community structures. (4) The metabolic function of the bacterial community in two types of biocrusts was quite different. The relative abundances of metabolic pathways in moss crust, such as chemoheterotrophy, ureolysis, aromatic compound degradation, and nitrate reduction, were significantly higher than those in lichen crust, however, the relative abundances of cyanobacteria, oxygenic photoautotrophy, photoautotrophy, and phototrophy were significantly lower (ANOVA, P&lt;0.05). Altogether, our study suggests that the biocrust types have significant effects on the pH, taxonomic, and metabolic diversity, providing a theoretical basis for improving the physicochemical properties of the surface soil in the desertification land ecosystem.&lt;/p&gt;

scholarly journals Comprehensive Analysis of Bacterial Community Structure and Diversity in Sichuan Dark Tea (Camellia sinensis)

2021 ◽  
Vol 12 ◽  
Author(s):  
Kuan Yan ◽  
Linfeng Yan ◽  
Lina Meng ◽  
Hongbing Cai ◽  
Ailing Duan ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
High Throughput Sequencing ◽  
Well Being ◽  
Good Health ◽  
Operational Taxonomic Units ◽  
Cluster Data ◽  
Specific Stage ◽  
Development Goals ◽  
Probiotic Food ◽  
Bacteria And Fungi

Bacteria and fungi present during pile-fermentation of Sichuan dark tea play a key role in the development of its aesthetic properties, such as color, taste, and fragrance. In our previous study, high-throughput sequencing of dark tea during fermentation revealed Aspergillus was abundant, but scarce knowledge is available about bacterial communities during pile-fermentation. In this study, we rigorously explored bacterial diversity in Sichuan dark tea at each specific stage of piling. Analysis of cluster data revealed 2,948 operational taxonomic units, which were divided into 42 phyla, 98 classes, 247 orders, 461 families, 1,052 genera, and 1,888 species. Certain members of the family Enterobacteriaceae were dominant at early stages of fermentation YC, W1, and W2; Pseudomonas at middle stage W3; and the highest bacterial diversity was observed at the final quality-determining stage W4. Noticeably, probiotics, such as Bacillus, Lactobacillus, Bifidobacterium, and Saccharopolyspora were also significantly higher at the quality-determining stage W4. Our findings might help in precise bacterial inoculation for probiotic food production by increasing the health benefits of Sichuan dark tea. This research also falls under the umbrella of the “Establish Good Health and Well-Being” Sustainable Development Goals of the United Nations Organization.

scholarly journals Characterization of the Bacterial Microbiome of Rhipicephalus (Boophilus) Microplus Collected From Pecari Tajacu “sajino” Madre De Dios, Peru

2020 ◽  
Author(s):  
JESUS ROJAS-JAIMES ◽  
David Lindo Seminario ◽  
German Correa Núñez ◽  
Benoit Diringer
Keyword(s):  
Animal Health ◽  
Boophilus Microplus ◽  
Adult Males ◽  
Pathogenic Potential ◽  
Core Microbiome ◽  
Operational Taxonomic Units ◽  
Madre De Dios ◽  
Bacterial Microbiome ◽  
Pecari Tajacu

Abstract Background: Ticks are arthropods that can host and transmit pathogens to wild animals, domestic animals, and even humans. Methods: The bacterial microbiome of adult (males and females) and nymph Rhipicephalus microplus ticks collected from a collared peccary, Pecari tajacu, captured in the rural area of ​​Botijón Village in the Amazon region of Madre de Dios, Peru, was evaluated using metagenomics. Results: The Chao1 and Shannon–Weaver analyses indicated greater bacterial richness and diversity in female ticks (GARH; 375–4.15) and nymph ticks (GARN; 332–4.75) compared to that in male ticks (GARM; 215–3.20). Taxonomic analyses identified 185 operational taxonomic units representing 147 bacterial genera. Of the 25 most prevalent genera, Salmonella (17.5%) and Vibrio (15.0%) showed the highest relative abundance followed by several other potentially pathogenic genera, such as Paracoccus (7.8%), Staphylococcus (6.8%), Pseudomonas (6.6%), Corynebacterium (5.0%), Cloacibacterium (3.6%), and Acinetobacter (2.5%). In total, 19.7% of the detected genera are shared by GARH, GARM, and GARN, and they can be considered as the core microbiome of R. microplus.Conclusions: To the best of our knowledge, this study is the first to characterize the microbiome of ticks collected from P. tajacu and to report the presence of Salmonella and Vibrio in R. microplus. The pathogenic potential and the role of these bacteria in the physiology of R. microplus should be further investigated due to the possible implications on public health and animal health in populations neighboring the habitat of P. tajacu.

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