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 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 Diversity analysis of the rhizospheric and endophytic bacterial communities of Senecio vulgaris L. (Asteraceae) in an invasive range

PeerJ ◽  
2019 ◽  
Vol 6 ◽  
pp. e6162 ◽  
Author(s):  
Dandan Cheng ◽  
Zhongsai Tian ◽  
Liang Feng ◽  
Lin Xu ◽  
Hongmei Wang
Keyword(s):  
Bacterial Communities ◽  
Rhizobium Leguminosarum ◽  
Bacterial Community Composition ◽  
Alpha Diversity ◽  
Central China ◽  
Resistant Bacteria ◽  
Rrna Gene ◽  
Mountainous Area ◽  
Phosphate Solubilizing Bacteria ◽  
Senecio Vulgaris

Increasing evidence has confirmed the importance of plant-associated bacteria for plant growth and productivity, and thus it is hypothesized that interactions between bacteria and alien plants might play an important role in plant invasions. However, the diversity of the bacterial communities associated with invasive plants is poorly understood. We therefore investigated the diversity of rhizospheric and endophytic bacteria associated with the invasive annual plant Senecio vulgaris L. (Asteraceae) based on 16S rRNA gene data obtained from 57 samples of four Senecio vulgaris populations in a subtropical mountainous area in central China. Significant differences in diversity were observed between plant compartments. Specifically, the rhizosphere harbored many more bacterial operational taxonomic units and showed higher alpha diversity than the leaf and root endospheres. The relative abundance profiles of the bacterial community composition differed substantially between the compartments and populations, especially at the phylum and family levels. However, the top five phyla (Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, and Acidobacteria) accounted for more than 90% of all the bacterial communities. Moreover, similar endophytic communities with a shared core set of bacteria were observed from different Senecio vulgaris populations. Heavy-metal-resistant, phosphate-solubilizing bacteria (Brevundimonas diminuta), nitrogen-fixing bacteria (Rhizobium leguminosarum), and cold-resistant bacteria (Exiguobacterium sibiricum) were present in the endosphere at relatively high abundance. This study, which reveals the structure of bacterial communities and their putative function in invasive Senecio vulgaris plants, is the first step in investigating the role of plant–bacteria interactions in the invasion of this species in China.

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 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 Bacterial Chitinolytic Communities Respond to Chitin and pH Alteration in Soil

2012 ◽  
Vol 79 (1) ◽  
pp. 263-272 ◽  
Author(s):  
Anna M. Kielak ◽  
Mariana Silvia Cretoiu ◽  
Alexander V. Semenov ◽  
Søren J. Sørensen ◽  
Jan Dirk van Elsas
Keyword(s):  
16S Rrna ◽  
Bacterial Communities ◽  
Plant Pathogens ◽  
Structural Changes ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Acid Soil ◽  
Rrna Gene ◽  
Content Type ◽  
Soil Suppressiveness ◽  
Gradient Gel Electrophoresis

ABSTRACTChitin amendment is a promising soil management strategy that may enhance the suppressiveness of soil toward plant pathogens. However, we understand very little of the effects of added chitin, including the putative successions that take place in the degradative process. We performed an experiment in moderately acid soil in which the level of chitin, next to the pH, was altered. Examination of chitinase activities revealed fast responses to the added crude chitin, with peaks of enzymatic activity occurring on day 7. PCR-denaturing gradient gel electrophoresis (DGGE)-based analyses of 16S rRNA andchiAgenes showed structural changes of the phylogenetically and functionally based bacterial communities following chitin addition and pH alteration. Pyrosequencing analysis indicated (i) that the diversity ofchiAgene types in soil is enormous and (i) that differentchiAgene types are selected by the addition of chitin at different prevailing soil pH values. Interestingly, a major role of Gram-negative bacteria versus a minor one ofActinobacteriain the immediate response to the added chitin (based on 16S rRNA gene abundance andchiAgene types) was indicated. The results of this study enhance our understanding of the response of the soil bacterial communities to chitin and are of use for both the understanding of soil suppressiveness and the possible mining of soil for novel enzymes.

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 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 Native and invading yellow starthistle (Centaurea solstitialis) microbiomes differ in composition and diversity of bacteria

2017 ◽  
Author(s):  
Patricia Lu-Irving ◽  
Julia Harenčár ◽  
Hailey Sounart ◽  
Shana R Welles ◽  
Sarah M Swope ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Plant Pathogens ◽  
Bacterial Community Composition ◽  
Microbial Interactions ◽  
Invasion Success ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
List Type ◽  
Plant Genotype ◽  
Yellow Starthistle

SUMMARYInvasive species could benefit from introduction to locations with favorable species interactions. Microbiomes are an important source of interactions that vary across regions. We examine whether bacterial communities could explain more favorable microbial interactions in highly invasive populations of yellow starthistle.We sequenced amplicons of prokaryotic 16S rRNA genes to characterize bacterial community composition in the phyllosphere, ectorhizosphere, and endorhizosphere of plants from seven invading populations in California, USA and eight native populations in Europe. We tested for differentiation of microbiomes by geography, plant compartment, and plant genotype.Bacterial communities differed significantly between native and invaded ranges within plant compartments, with consistently lower diversity in plants from the invaded range. Genera containing known plant pathogens also showed lower diversity in invaded range plants. The diversity of bacteria in roots was positively correlated with plant genotype diversity within both ranges, but this relationship did not explain microbial differences between ranges.Our findings reveal changes in the composition and diversity of bacterial interactions in invading plants, consistent with observations of altered soil interactions in this invasion. These results call for further study of the sources of variation in microbiomes and the potential for bacteria to facilitate invasion success.

scholarly journals 196 Direct comparison of human microbiota-associated (HMA) gnotobiotic piglet and mouse models

2019 ◽  
Vol 97 (Supplement_2) ◽  
pp. 114-115
Author(s):  
Nirosh D Aluthge ◽  
Wesley A Tom ◽  
Alison C Bartenslager ◽  
Thomas E Burkey ◽  
Kelly D Heath ◽  
...  
Keyword(s):  
Animal Models ◽  
Gut Microbiota ◽  
Bacterial Communities ◽  
Statistical Significance ◽  
Bacterial Community Composition ◽  
Rrna Gene ◽  
Human Donor ◽  
Fecal Samples ◽  
Human Microbiota ◽  
Nutritional Studies

Abstract The objective of this study was to compare the establishment of human fecal bacterial communities in porcine and murine animal models. Many gut microbiota studies use human microbiota-associated (HMA) rodents as translational animal models; however, it has been questioned as to how successfully a human microbiota can be established in rodents considering the many differences that exist between rodents and humans. The domestic pig (Sus scrofa domesticus) has many anatomical, physiological, and immunological similarities to humans and has been widely used as a model for humans in biomedical and nutritional studies. Thus, the porcine model may be an alternative to rodent models in gut microbiota research. The current study was designed to evaluate the establishment of the same human donor microbiota in the rodent and pig models. Both germ-free piglets and mice (C3H/HeN) were transplanted with fecal microbiota from four human donors: Infant (0–5 m), child (1–12 yrs), adult (18–64 yrs), and elderly (65+ yrs). To monitor the establishment of the transplanted microbiota, weekly fecal samples were collected for 5 wks. All fecal samples were subjected to 16S rRNA gene-based amplicon sequencing using the Illumina MiSeqTM platform to characterize bacterial community composition. Unweighted unifrac distances were compared between the bacterial communities of the human donor and the corresponding HMA porcine and murine fecal samples. Statistical significance was tested using the Mann-Whitney U test (P = 0.05). This analysis suggested that more taxa are colonized in the mice compared to the piglets receiving the same infant donor microbiota, while for the child, adult, and elderly donors, the piglet model established the human donor microbiota better than the mice receiving the same donor samples. This suggests that in the latter stages of human development, more species of the human fecal inoculum colonizes the pig gut compared to the mouse gut.

scholarly journals Urbanization-induced environmental changes strongly affect wetland soil bacterial community composition and diversity

2021 ◽  
Author(s):  
Xinyu Yi ◽  
Chen Ning ◽  
Shuailong Feng ◽  
Haiqiang Gao ◽  
Jianlun Zhao ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Environmental Changes ◽  
Bacterial Community Composition ◽  
Soil Microbial Communities ◽  
Environmental Drivers ◽  
Wetland Soil ◽  
Rrna Gene ◽  
Soil Microbial ◽  
Soil Bacterial

Abstract Soil microbial communities potentially serve as indicators for their responses to changes in various ecosystems at scales from a region to the globe. However, changes in wetland soil bacterial communities and how they are related to urbanization intensities remains poorly understood. Here, we collected sixty soil samples along urbanization intensity gradients from twenty wetlands. We measured a range of environmental factors and characterized bacterial communities structure using 16S rRNA gene amplicon sequencing that targeted the V4-V5 region. Our results revealed the dominant soil microbial phyla included Proteobacteria (39.3%), Acidobacteria (21.4%) and Chloroflexi (12.3%) in the wetlands, and showed a significant divergence of composition in intensive urbanization area (UI_4) than other places. A critical "threshold" exists in the soil bacterial diversity, demonstrating different patterns: a gradual increase in the areas of low-to-intermediate disturbances but a significant decrease in highly urbanized areas where metabolic functions were significantly strong. Additionally, soil pH, total phosphorus (TP), available phosphorus (AP ) and ammonia nitrogen (NH4+-N) made a significant contribution to variations in bacterial communities, explaining 49.6%, 35.1%, 26.2% and 30.7% of the total variance, respectively. pH and NH4+-N were identified as the main environmental drivers to determine bacterial community structure and diversity in the urban wetlands. Our results highlight collective changes in multiple environmental variables induced by urbanization rather than by the proportion of impervious surface area (ISA), which were potentially attributed to the spatial heterogeneity along different urbanization gradients.

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