scholarly journals Endophytic bacterial communities of oilseed rape associate with genotype-specific resistance against Verticillium longisporum

2019 ◽  
Vol 96 (1) ◽  
Author(s):  
Stefanie P Glaeser ◽  
Iulian Gabur ◽  
Hossein Haghighi ◽  
Jens-Ole Bartz ◽  
Peter Kämpfer ◽  
...  
Keyword(s):  
Oilseed Rape ◽  
Relative Abundance ◽  
Bacterial Communities ◽  
Quantitative Resistance ◽  
Bacterial Community Composition ◽  
Phylogenetic Group ◽  
Rrna Gene ◽  
Host Genotype ◽  
Brassica Napus L ◽  
Verticillium Longisporum

ABSTRACT Associations of endophytic bacterial community composition of oilseed rape (Brassica napus L.) with quantitative resistance against the soil-borne fungal pathogen Verticillium longisporum was assessed by 16S rRNA gene amplicon sequencing in roots and hypocotyls of four plant lines with contrasting genetic composition in regard to quantitative resistance reactions. The plant compartment was found to be the dominating driving factor for the specificity of bacterial communities in healthy plants. Furthermore, V. longisporum infection triggered a stabilization of phylogenetic group abundance in replicated samples suggesting a host genotype-specific selection. Genotype-specific associations with bacterial phylogenetic group abundance were identified by comparison of plant genotype groups (resistant versus susceptible) and treatment groups (healthy versus V. longisporum-infected) allowing dissection into constitutive and induced directional association patterns. Relative abundance of Flavobacteria, Pseudomonas, Rhizobium and Cellvibrio was associated with resistance/susceptibility. Relative abundance of Flavobacteria and Cellvibrio was increased in resistant genotypes according to their known ecological functions. In contrast, a higher relative abundance of Pseudomonas and Rhizobium, which are known to harbor many species with antagonistic properties to fungal pathogens, was found to be associated with susceptibility, indicating that these groups do not play a major role in genetically controlled resistance of oilseed rape against V. longisporum.

scholarly journals A Grain-Based SARA Challenge Affects the Composition of Epimural and Mucosa-Associated Bacterial Communities throughout the Digestive Tract of Dairy Cows

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1658
Author(s):  
Jan C. Plaizier ◽  
Anne-Mette Danscher ◽  
Paula A. Azevedo ◽  
Hooman Derakhshani ◽  
Pia H. Andersen ◽  
...  
Keyword(s):  
Digestive Tract ◽  
Relative Abundance ◽  
Bacterial Communities ◽  
Dry Matter ◽  
Control Diet ◽  
Rrna Gene ◽  
Ruminal Acidosis ◽  
Clustering Patterns ◽  
The 16S Rrna Gene ◽  
Distal Jejunum

The effects of a subacute ruminal acidosis (SARA) challenge on the composition of epimural and mucosa-associated bacterial communities throughout the digestive tract were determined in eight non-lactating Holstein cows. Treatments included feeding a control diet containing 19.6% dry matter (DM) starch and a SARA-challenge diet containing 33.3% DM starch for two days after a 4-day grain step-up. Subsequently, epithelial samples from the rumen and mucosa samples from the duodenum, proximal, middle and distal jejunum, ileum, cecum and colon were collected. Extracted DNA from these samples were analyzed using MiSeq Illumina sequencing of the V4 region of the 16S rRNA gene. Distinct clustering patterns for each diet existed for all sites. The SARA challenge decreased microbial diversity at all sites, with the exception of the middle jejunum. The SARA challenge also affected the relative abundances of several major phyla and genera at all sites but the magnitude of these effects differed among sites. In the rumen and colon, the largest effects were an increase in the relative abundance of Firmicutes and a reduction of Bacteroidetes. In the small intestine, the largest effect was an increase in the relative abundance of Actinobacteria. The grain-based SARA challenge conducted in this study did not only affect the composition and cause dysbiosis of epimural microbiota in the rumen, it also affected the mucosa-associated microbiota in the intestines. To assess the extent of this dysbiosis, its effects on the functionality of these microbiota must be determined in future.

scholarly journals Impact of Maize–Mushroom Intercropping on the Soil Bacterial Community Composition in Northeast China

Agronomy ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 1526
Author(s):  
Xiaoqin Yang ◽  
Yang Wang ◽  
Luying Sun ◽  
Xiaoning Qi ◽  
Fengbin Song ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Northeast China ◽  
Management Practice ◽  
Bacterial Community Composition ◽  
Soil Microbial Communities ◽  
Chemical Properties ◽  
Crop Productivity ◽  
Rrna Gene ◽  
Soil Bacterial Communities ◽  
Soil Bacterial

Conservative agricultural practices have been adopted to improve soil quality and maintain crop productivity. An efficient intercropping of maize with mushroom has been developed in Northeast China. The objective of this study was to evaluate and compare the effects of planting patterns on the diversity and structure of the soil bacterial communities at a 0–20 cm depth in the black soil zone of Northeast China. The experiment consisted of monoculture of maize and mushroom, and intercropping in a split-plot arrangement. The characteristics of soil microbial communities were performed by 16S rRNA gene amplicom sequencing. The results showed that intercropping increased soil bacterial richness and diversity compared with maize monoculture. The relative abundances of Acidobacteria, Chloroflexi, Saccharibacteria and Planctomycetes were significantly higher, whereas Proteobacteria and Firmicutes were lower in intercropping than maize monoculture. Redundancy analysis suggested that pH, NO3−-N and NH4+-N contents had a notable effect on the structure of the bacterial communities. Moreover, intercropping significantly increased the relative abundance of carbohydrate metabolism pathway functional groups. Overall, these findings demonstrated that intercropping of maize with mushroom strongly impacts the physical and chemical properties of soil as well as the diversity and structure of the soil bacterial communities, suggesting this is a sustainable agricultural management practice in Northeast China.

scholarly journals Changes of Bacterial Communities in Response to Prolonged Hydrodynamic Disturbances in the Eutrophic Water-Sediment Systems

2019 ◽  
Vol 16 (20) ◽  
pp. 3868
Author(s):  
Haomiao Cheng ◽  
Ling Cheng ◽  
Liang Wang ◽  
Tengyi Zhu ◽  
Wei Cai ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Bacterial Communities ◽  
16S Rrna Gene Sequencing ◽  
Aquatic Environments ◽  
Rrna Gene ◽  
Evolutionary Trend ◽  
Ecological Evaluation ◽  
Eutrophic Water ◽  
Rrna Gene Sequencing ◽  
Opposite Tendency

The effects of hydrodynamic disturbances on the bacterial communities in eutrophic aquatic environments remain poorly understood, despite their importance to ecological evaluation and remediation. This study investigated the evolution of bacterial communities in the water–sediment systems under the influence of three typical velocity conditions with the timescale of 5 weeks. The results demonstrated that higher bacterial diversity and notable differences were detected in sediment compared to water using the 16S rRNA gene sequencing. The phyla Firmicutes and γ-Proteobacteria survived better in both water and sediment under stronger water disturbances. Their relative abundance peaked at 36.0%, 33.2% in water and 38.0%, 43.6% in sediment, respectively, while the phylum Actinobacteria in water had the opposite tendency. Its relative abundance grew rapidly in static control (SC) and peaked at 44.8%, and it almost disappeared in disturbance conditions. These phenomena were caused by the proliferation of genus Exiguobacterium (belonging to Firmicutes), Citrobacter, Acinetobacter, Pseudomonas (belonging to γ-Proteobacteria), and hgcI_clade (belonging to Actinobacteria). The nonmetric multidimensional scaling (NMDS) and Venn analysis also revealed significantly different evolutionary trend in the three water-sediment systems. It was most likely caused by the changes of geochemical characteristics (dissolved oxygen (DO) and nutrients). This kind of study can provide helpful information for ecological assessment and remediation strategy in eutrophic aquatic environments.

scholarly journals Impact of Biochar Application to Soil on the Root-Associated Bacterial Community Structure of Fully Developed Greenhouse Pepper Plants

2011 ◽  
Vol 77 (14) ◽  
pp. 4924-4930 ◽  
Author(s):  
Max Kolton ◽  
Yael Meller Harel ◽  
Zohar Pasternak ◽  
Ellen R. Graber ◽  
Yigal Elad ◽  
...  
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
Relative Abundance ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Bacterial Community Composition ◽  
Systemic Resistance ◽  
Rrna Gene ◽  
Molecular Fingerprinting ◽  
Content Type ◽  
Biochar Amendment

ABSTRACTAdding biochar to soil has environmental and agricultural potential due to its long-term carbon sequestration capacity and its ability to improve crop productivity. Recent studies have demonstrated that soil-applied biochar promotes the systemic resistance of plants to several prominent foliar pathogens. One potential mechanism for this phenomenon is root-associated microbial elicitors whose presence is somehow augmented in the biochar-amended soils. The objective of this study was to assess the effect of biochar amendment on the root-associated bacterial community composition of mature sweet pepper (Capsicum annuumL.) plants. Molecular fingerprinting (denaturing gradient gel electrophoresis and terminal restriction fragment length polymorphism) of 16S rRNA gene fragments showed a clear differentiation between the root-associated bacterial community structures of biochar-amended and control plants. The pyrosequencing of 16S rRNA amplicons from the rhizoplane of both treatments generated a total of 20,142 sequences, 92 to 95% of which were affiliated with theProteobacteria,Bacteroidetes,Actinobacteria, andFirmicutesphyla. The relative abundance of members of theBacteroidetesphylum increased from 12 to 30% as a result of biochar amendment, while that of theProteobacteriadecreased from 71 to 47%. TheBacteroidetes-affiliatedFlavobacteriumwas the strongest biochar-induced genus. The relative abundance of this group increased from 4.2% of total root-associated operational taxonomic units (OTUs) in control samples to 19.6% in biochar-amended samples. Additional biochar-induced genera included chitin and cellulose degraders (ChitinophagaandCellvibrio, respectively) and aromatic compound degraders (HydrogenophagaandDechloromonas). We hypothesize that these biochar-augmented genera may be at least partially responsible for the beneficial effect of biochar amendment on plant growth and viability.

scholarly journals Structure and Function of Bacterial Communities Emerging from Different Sources under Identical Conditions

2006 ◽  
Vol 72 (1) ◽  
pp. 212-220 ◽  
Author(s):  
Silke Langenheder ◽  
Eva S. Lindström ◽  
Lars J. Tranvik
Keyword(s):  
Environmental Conditions ◽  
Bacterial Communities ◽  
Fragment Length Polymorphism ◽  
Bacterial Community Composition ◽  
Rrna Gene ◽  
Polymorphism Analysis ◽  
Scale Functions ◽  
And Function ◽  
Different Sources ◽  
The 16S Rrna Gene

ABSTRACT The aim of this study was to compare two major hypotheses concerning the formation of bacterial community composition (BCC) at the local scale, i.e., whether BCC is determined by the prevailing local environmental conditions or by “metacommunity processes.” A batch culture experiment where bacteria from eight distinctly different aquatic habitats were regrown under identical conditions was performed to test to what extent similar communities develop under similar selective pressure. Differently composed communities emerged from different inoculum communities, as determined by terminal restriction fragment length polymorphism analysis of the 16S rRNA gene. There was no indication that similarity increased between communities upon growth under identical conditions compared to that for growth at the ambient sampling sites. This suggests that the history and distribution of taxa within the source communities were stronger regulating factors of BCC than the environmental conditions. Moreover, differently composed communities were different with regard to specific functions, such as enzyme activities, but maintained similar broad-scale functions, such as biomass production and respiration.

scholarly journals Diversity analysis and function prediction of rhizo- and endophytic bacterial communities of Senecio vulgaris L. (Asteraceae) in an invasive range

2018 ◽  
Author(s):  
Dandan Cheng ◽  
Zhongsai Tian ◽  
Liang Feng ◽  
Lin Xu ◽  
Hongmei Wang
Keyword(s):  
Bacterial Communities ◽  
Plant Pathogens ◽  
Bacterial Community Composition ◽  
Plant Invasions ◽  
Function Prediction ◽  
Alien Plants ◽  
Central China ◽  
Rrna Gene ◽  
Mountainous Area ◽  
Senecio Vulgaris

Because increasing evidence has confirmed the importance of plant-associated bacteria for plant growth and productivity, it is believed that interactions between bacteria and alien plants play an important role in plant invasions. However, the diversity of bacterial communities associated with invasive plants is poorly understood. Therefore, we investigated the diversity of rhizo- and endophytic bacteria associated with the invasive annual plant Senecio vulgaris L (Asteraceae) based on bacterial 16S rRNA gene data obtained from 57 samples of four S. vulgaris populations in a subtropical mountainous area in central China. Significant differences in diversity were observed between plant compartments. Rhizosphere harbored much more bacterial OTUs and showed higher alpha diversity than the leaf and root endosphere. Bacterial community composition differed substantially between compartments and locations in relative abundance profiles, especially at phyla and family level. However, the top five phyla (Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria and Acidobacteria) comprised more than 90% of abundance in all the bacterial communities. And similar endophytic communities with a shared core set of bacteria were observed from different S. vulgaris populations. According to the function prediction based on the identification and abundance information of the OTU, bacteria characterized as plant pathogens, as well as those involved in ureolysis and nitrate reduction, were rich in endophytic communities. This study reveals the microbiomes and their putative function in the invasive S. vulgaris plants and is also the first step for future studies on the role of interactions between bacteria and alien plants in plant invasions.

scholarly journals The Presence of Denitrifiers In Bacterial Communities of Urban Stormwater Best Management Practices (BMPs)

2021 ◽  
Author(s):  
Natalie C. Hall ◽  
Masoumeh Sikaroodi ◽  
Dianna Hogan ◽  
R. Christian Jones ◽  
Patrick M. Gillevet
Keyword(s):  
Best Management Practices ◽  
Bacterial Communities ◽  
Management Practices ◽  
Agricultural Land ◽  
Bacterial Community Composition ◽  
Rrna Gene ◽  
Sand Filters ◽  
Best Management ◽  
Nitrogen Inputs ◽  
Surface Sand

AbstractStormwater best management practices (BMPs) are engineered structures that attempt to mitigate the impacts of stormwater, which can include nitrogen inputs from the surrounding drainage area. The goal of this study was to assess bacterial community composition in different types of stormwater BMP soils to establish whether a particular BMP type harbors more denitrification potential. Soil sampling took place over the summer of 2015 following precipitation events. Soils were sampled from four bioretention facilities, four dry ponds, four surface sand filters, and one dry swale. 16S rRNA gene analysis of extracted DNA and RNA amplicons indicated high bacterial diversity in the soils of all BMP types sampled. An abundance of denitrifiers was also indicated in the extracted DNA using presence/absence of nirS, nirK, and nosZ denitrification genes. BMP soil bacterial communities were impacted by the surrounding soil physiochemistry. Based on the identification of a metabolically-active community of denitrifiers, this study has indicated that denitrification could potentially occur under appropriate conditions in all types of BMP sampled, including surface sand filters that are often viewed as providing low potential for denitrification. The carbon content of incoming stormwater could be providing bacterial communities with denitrification conditions. The findings of this study are especially relevant for land managers in watersheds with legacy nitrogen from former agricultural land use.

scholarly journals The leaf bacterial microbiota of female and male kiwifruit plants in distinct seasons: assessing the impact of Pseudomonas syringae pv. actinidiae

2021 ◽  
Author(s):  
Aitana Ares ◽  
Joana Pereira ◽  
Eva Garcia ◽  
Joana Costa ◽  
Igor Tiago
Keyword(s):  
Bacterial Community ◽  
Pseudomonas Syringae ◽  
Relative Abundance ◽  
Bacterial Communities ◽  
Defense Mechanisms ◽  
Abiotic Factors ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Sequencing Platform ◽  
The Impact

The pandemic Pseudomonas syringae pv. actinidiae (Psa) has been compromising the production of the kiwifruit industry in major producing countries. Abiotic factors and plant gender are known to influence the disease outcome. To better understand their impact, we have determined the diversity of the leafs bacterial communities using the V5-V6 region of the 16S rRNA gene amplicon on the Illumina MiSeq sequencing platform. Healthy and diseased female and male kiwifruit plants were analyzed in two consecutive seasons: spring and autumn. This work describes whether the season, plant gender and the presence of Psa can affect the leaves bacterial community. Fifty bacterial operational taxonomic units (OTUs) were identified and assigned to five phyla distributed by 14 different families and 23 genera. The leaves of healthy female and male kiwi plants share most of the identified bacterial populations, that undergoes major seasonal changes. In both cases a substantial increase of the relative abundance of genus Methylobacterium is observed in autumn. The presence of Psa induced profound changes on leaves bacterial communities structure translated into a reduction in the relative abundance of previously dominant genera that had been found in healthy plants, namely Hymenobacter, Sphingomonas and Massilia. The impact of Psa was less pronounced in the bacterial community structure of male plants in both seasons. Some of the naturally occurring genera have the potential to act as an antagonist or as enhancers of the defense mechanisms paving the way for environmentally friendly and sustainable disease control.

244 Fertility Outcomes Associated with Reproductive Tract Cytokines and Microbiota in Postpartum Beef Cows

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 128-129
Author(s):  
Rebecca K Poole ◽  
Taylor B Ault-Seay ◽  
Rebecca R Payton ◽  
Phillip R Myer ◽  
Andrea S Lear ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Transforming Growth Factor Beta ◽  
Bacterial Communities ◽  
Reproductive Tract ◽  
Transforming Growth Factor ◽  
Pearson Correlation ◽  
Transrectal Ultrasound ◽  
Beef Cows ◽  
Rrna Gene ◽  
Concentration Data

Abstract Local immune activity in the reproductive tract is crucial in the response to uterine diseases, normal reproductive functions, and establishing pregnancy. Few studies have evaluated the influence of the local immune environment of the reproductive tract on fertility outcomes. The objectives were to 1) evaluate reproductive cytokine concentrations in postpartum cows undergoing estrus synchronization followed by timed artificial insemination (TAI) and 2) correlate reproductive bacterial communities with cytokine concentrations. Angus cows (n = 20) were subjected to a 7-Day Co-Synch protocol with pre-synchronization beginning 21 days prior (d -21) to TAI (d 0). Uterine and vaginal flushes were collected on d -21 and -2. Pregnancy was determined by transrectal ultrasound on d 30. Bacterial community profiling and analyses were conducted targeting the V1 to V3 hypervariable regions of the 16S rRNA gene. Cytokine concentrations for interleukin (IL)-1b, IL-6, IL-10, and transforming growth factor beta (TGF-β) were determined by commercial ELISA kits. Concentration data were analyzed using PROC MIXED and correlations using Pearson correlation in SAS. No differences were detected in vaginal samples (P >0.05). No differences in IL-10 or IL-1b concentrations were detected in uterine samples (P >0.05). Uterine TGF-β concentrations were greater in resulting pregnant than non-pregnant cows (44.0 ± 13.4 pg/mL vs 14.7 ± 4.9 pg/mL; P = 0.05). Uterine TGF-β was negatively correlated with the relative abundance of genera Treponema (r = -0.668; P = 0.05) in resulting non-pregnant cows on d -21. Uterine IL-6 concentrations were greater in resulting non-pregnant than pregnant cows (198.7 ± 21.8 pg/mL vs 144.3 ± 16.1 pg/mL; P = 0.05). Uterine IL-6 and the relative abundance of genera Butyrivibrio were positively correlated (r = 0.742; P = 0.02) in resulting non-pregnant cows on d -21. These results suggest possible relationships between uterine bacterial communities and cytokines prior to TAI that may ultimately affect fertility outcomes in beef cattle.

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