scholarly journals Rice SST Variation Shapes the Rhizosphere Bacterial Community, Conferring Tolerance to Salt Stress through Regulating Soil Metabolites

mSystems ◽  
2020 ◽  
Vol 5 (6) ◽  
Author(s):  
Tengxiang Lian ◽  
Yingyong Huang ◽  
Xianan Xie ◽  
Xing Huo ◽  
Muhammad Qasim Shahid ◽  
...  
Keyword(s):  
Salt Stress ◽  
Bacterial Community ◽  
Management Practices ◽  
High Throughput Sequencing ◽  
Crop Productivity ◽  
Soil Salinization ◽  
Rrna Gene ◽  
Content Type ◽  
Rice Mutant ◽  
Rhizosphere Bacterial Community

ABSTRACT Some plant-specific resistance genes could affect rhizosphere microorganisms by regulating the release of root exudates. In a previous study, the SST (seedling salt tolerant) gene in rice (Oryza sativa) was identified, and loss of SST function resulted in better plant adaptation to salt stress. However, whether the rice SST variation could alleviate salt stress via regulating soil metabolites and microbiota in the rhizosphere is still unknown. Here, we used transgenic plants with SST edited in the Huanghuazhan (HHZ) and Zhonghua 11 (ZH11) cultivars by the CRISPR/Cas9 system and found that loss of SST function increased the accumulation of potassium and reduced the accumulation of sodium ions in rice plants. Using 16S rRNA gene amplicon high-throughput sequencing, we found that the mutant material shifted the rhizobacterial assembly under salt-free stress. Importantly, under salt stress, the sst, HHZcas, and ZH11cas plants significantly changed the assembly of the rhizobacteria. Furthermore, the rice SST gene also affected the soil metabolites, which were closely related to the dynamics of rhizosphere microbial communities, and we further determined the relationship between the rhizosphere microbiota and soil metabolites. Overall, our results show the effects of the rice SST gene on the response to salt stress associated with the soil microbiota and metabolites in the rhizosphere. This study reveals a helpful linkage among the rice SST gene, soil metabolites, and rhizobacterial community assembly and also provides a theoretical basis for improving crop adaptation through soil microbial management practices. IMPORTANCE Soil salinization is one of the major environmental stresses limiting crop productivity. Crops in agricultural ecosystems have developed various strategies to adapt to salt stress. We used rice mutant and CRISPR-edited lines to investigate the relationships among the Squamosa promoter Binding Protein box (SBP box) family gene (SST/OsSPL10), soil metabolites, and the rhizosphere bacterial community. We found that during salt stress, there are significant differences in the rhizosphere bacterial community and soil metabolites between the plants with the SST gene and those without it. Our findings provide a useful paradigm for revealing the roles of key genes of plants in shaping rhizosphere microbiomes and their relationships with soil metabolites and offer new insights into strategies to enhance rice tolerance to high salt levels from microbial and ecological perspectives.

scholarly journals Restructuring of the Aquatic Bacterial Community by Hydric Dynamics Associated with Superstorm Sandy

2016 ◽  
Vol 82 (12) ◽  
pp. 3525-3536 ◽  
Author(s):  
Nikea Ulrich ◽  
Abigail Rosenberger ◽  
Colin Brislawn ◽  
Justin Wright ◽  
Collin Kessler ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
High Throughput ◽  
Bacterial Community Structure ◽  
High Throughput Sequencing ◽  
Storm Event ◽  
Rrna Gene ◽  
Content Type

ABSTRACTBacterial community composition and longitudinal fluctuations were monitored in a riverine system during and after Superstorm Sandy to better characterize inter- and intracommunity responses associated with the disturbance associated with a 100-year storm event. High-throughput sequencing of the 16S rRNA gene was used to assess microbial community structure within water samples from Muddy Creek Run, a second-order stream in Huntingdon, PA, at 12 different time points during the storm event (29 October to 3 November 2012) and under seasonally matched baseline conditions. High-throughput sequencing of the 16S rRNA gene was used to track changes in bacterial community structure and divergence during and after Superstorm Sandy. Bacterial community dynamics were correlated to measured physicochemical parameters and fecal indicator bacteria (FIB) concentrations. Bioinformatics analyses of 2.1 million 16S rRNA gene sequences revealed a significant increase in bacterial diversity in samples taken during peak discharge of the storm. Beta-diversity analyses revealed longitudinal shifts in the bacterial community structure. Successional changes were observed, in whichBetaproteobacteriaandGammaproteobacteriadecreased in 16S rRNA gene relative abundance, while the relative abundance of members of theFirmicutesincreased. Furthermore, 16S rRNA gene sequences matching pathogenic bacteria, including strains ofLegionella,Campylobacter,Arcobacter, andHelicobacter, as well as bacteria of fecal origin (e.g.,Bacteroides), exhibited an increase in abundance after peak discharge of the storm. This study revealed a significant restructuring of in-stream bacterial community structure associated with hydric dynamics of a storm event.IMPORTANCEIn order to better understand the microbial risks associated with freshwater environments during a storm event, a more comprehensive understanding of the variations in aquatic bacterial diversity is warranted. This study investigated the bacterial communities during and after Superstorm Sandy to provide fine time point resolution of dynamic changes in bacterial composition. This study adds to the current literature by revealing the variation in bacterial community structure during the course of a storm. This study employed high-throughput DNA sequencing, which generated a deep analysis of inter- and intracommunity responses during a significant storm event. This study has highlighted the utility of applying high-throughput sequencing for water quality monitoring purposes, as this approach enabled a more comprehensive investigation of the bacterial community structure. Altogether, these data suggest a drastic restructuring of the stream bacterial community during a storm event and highlight the potential of high-throughput sequencing approaches for assessing the microbiological quality of our environment.

scholarly journals Cadmium Exposure-Sedum alfrediiPlanting Interactions Shape the Bacterial Community in the Hyperaccumulator Plant Rhizosphere

2018 ◽  
Vol 84 (12) ◽  
pp. e02797-17 ◽  
Author(s):  
Dandi Hou ◽  
Zhi Lin ◽  
Runze Wang ◽  
Jun Ge ◽  
Shuai Wei ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Contaminated Soils ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Bacterial Community Composition ◽  
Rrna Gene ◽  
Sedum Alfredii ◽  
Cd Stress ◽  
Metal Hyperaccumulation ◽  
Content Type

ABSTRACTRhizospheric bacteria play important roles in plant tolerance and activation of heavy metals. Understanding the bacterial rhizobiome of hyperaccumulators may contribute to the development of optimized phytoextraction for metal-polluted soils. We used 16S rRNA gene amplicon sequencing to investigate the rhizospheric bacterial communities of the cadmium (Cd) hyperaccumulating ecotype (HE)Sedum alfrediiin comparison to its nonhyperaccumulating ecotype (NHE). Both planting of two ecotypes ofS. alfrediiand elevated Cd levels significantly decreased bacterial alpha-diversity and altered bacterial community structure in soils. The HE rhizosphere harbored a unique bacterial community differing from those in its bulk soil and NHE counterparts. Several key taxa fromActinobacteria,Bacteroidetes, and TM7 were especially abundant in HE rhizospheres under high Cd stress. The actinobacterial genusStreptomyceswas responsible for the majority of the divergence of bacterial community composition between the HE rhizosphere and other soil samples. In the HE rhizosphere, the abundance ofStreptomyceswas 3.31- to 16.45-fold higher than that in other samples under high Cd stress. These results suggested that both the presence of the hyperaccumulatorS. alfrediiand Cd exposure select for a specialized rhizosphere bacterial community during phytoextraction of Cd-contaminated soils and that key taxa, such as the species affiliated with the genusStreptomyces, may play an important role in metal hyperaccumulation.IMPORTANCESedum alfrediiis a well-known Cd hyperaccumulator native to China. Its potential for extracting Cd relies not only on its powerful uptake, translocation, and tolerance for Cd but also on processes underground (especially rhizosphere microbes) that facilitate root uptake and tolerance of the metal. In this study, a high-throughput sequencing approach was applied to gain insight into the soil-plant-microbe interactions that may influence Cd accumulation in the hyperaccumulatorS. alfredii. Here, we report the investigation of rhizosphere bacterial communities ofS. alfrediiin phytoremediation of different levels of Cd contamination in soils. Moreover, some key taxa in its rhizosphere identified in the study, such as the species affiliated with genusStreptomyces, may shed new light on the involvement of bacteria in phytoextraction of contaminated soils and provide new materials for phytoremediation optimization.

scholarly journals Comprehensive Effect of Salt Stress and Peanut Cultivars on the Bacterial Community Structure and Diversity of Peanut Rhizosphere Soils

2020 ◽  
Author(s):  
Yang Xu ◽  
Hong Ding ◽  
Saiqun Wen ◽  
Dunwei Ci ◽  
Guanchu Zhang ◽  
...  
Keyword(s):  
Salt Stress ◽  
Community Structure ◽  
Salt Tolerance ◽  
Bacterial Community ◽  
Stress Tolerance ◽  
Bacterial Community Structure ◽  
Rrna Gene ◽  
Rhizosphere Soils ◽  
Rhizosphere Bacterial Community ◽  
Peanut Cultivars

Abstract Background: Plant rhizosphere bacterial communities influence plant growth and stress tolerance, which differs across cultivars and external environments. Peanut (Arachis hypogaea. L) as an important oil crop cultivated worldwide. However, relatively little is known about the comprehensive effects of environmental conditions and peanut cultivars on rhizosphere bacterial community structure and diversity. Results: Here, bacterial community structure diversity from rhizosphere soils of various susceptible and resistant peanut cultivars with or without salt stress was analyzed by 16S rRNA gene deep sequencing and quantitative PCR assays. Taxonomic analysis showed that the bacterial community predominantly consisted of phyla Actinobacteria, Proteobacteria, Chloroflexi, Acidobacteria, and Cyanobacteria. Among these bacteria, numbers of beneficial bacteria Cyanobacteria and Proteobacteria increased, while that of Acidobacteria decreased after salt treatment. Metabolic function prediction showed that the percentages of reads categorized to signaling transduction and inorganic ion transport and metabolism were higher in the salt-treated soils, which may be beneficial to plant survival and salt tolerance. Conclusions: Overall, rhizosphere bacterial community structure and population metabolism are affected by salt stress, which may be conducive to peanut stress tolerance in saline-alkali soil. The study is therefore crucially important to develop the foundation for improving the salt tolerance of peanuts via modifying the soil bacterial community.

scholarly journals Differential Assembly and Shifts of the Rhizosphere Bacterial Community by a Dual Transgenic Glyphosate-Tolerant Soybean Line with and without Glyphosate Application

Horticulturae ◽  
2021 ◽  
Vol 7 (10) ◽  
pp. 374
Author(s):  
Minkai Yang ◽  
Zhongling Wen ◽  
Chenyu Hao ◽  
Aliya Fazal ◽  
Yonghui Liao ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Economic Benefits ◽  
Rrna Gene ◽  
Soybean Line ◽  
Seed Filling ◽  
Alpha And Beta Diversity ◽  
Rhizosphere Bacterial Community ◽  
Rhizosphere Bacterial Communities

Modern agriculture has gained significant economic benefits worldwide with the use of genetically modified (GM) technologies. While GM crops provide convenience to humans, their biosafety has attracted increasing concern. In this study, the Illumina MiSeq was used to perform a high-throughput sequencing of the V3-V4 hypervariable regions of 16S rRNA gene (16S rDNA) amplicons to compare the rhizosphere bacterial communities of the EPSPS/GAT dual transgenic glyphosate-tolerant soybean line Z106, its recipient variety ZH10, and Z106 with glyphosate application (Z106G) during flowering, seed filling, and maturing stages under field settings. At each of the three stages, the alpha and beta diversity of rhizosphere bacterial communities revealed no significant differences between ZH10, Z106, and Z106G. However, some bacterial taxa demonstrated a greater proportional contribution, particularly the nitrogen-fixing rhizobium Ensifer fredii, in the rhizospheric soil of Z106 at the seed filling and maturing stages, when compared to ZH10 and Z106G. The present study therefore suggests that the EPSPS/GAT dual transgenic line Z106 and exogenous glyphosate application have a minimal effect on the composition of the soybean rhizosphere bacterial community but have no impact on the structure of the rhizosphere microbial community during a single planting season.

scholarly journals Correlation of Breed, Growth Performance, and Rumen Microbiota in Two Rustic Cattle Breeds Reared Under Different Conditions

2021 ◽  
Vol 12 ◽  
Author(s):  
Matteo Daghio ◽  
Francesca Ciucci ◽  
Arianna Buccioni ◽  
Alice Cappucci ◽  
Laura Casarosa ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Growth Performance ◽  
Community Composition ◽  
Lipid Composition ◽  
High Throughput Sequencing ◽  
Bacterial Community Composition ◽  
Daily Weight Gain ◽  
Rrna Gene ◽  
Rumen Microbiota ◽  
Cattle Breeds

The use of rustic cattle is desirable to face challenges brought on by climate change. Maremmana (MA) and Aubrac (AU) are rustic cattle breeds that can be successfully used for sustainable production. In this study, correlations between two rearing systems (feedlot and grazing) and the rumen microbiota, the lipid composition of rumen liquor (RL), and the growth performance of MA and AU steers were investigated. Bacterial community composition was characterized by high-throughput sequencing of 16S rRNA gene amplicons, and the RL lipid composition was determined by measuring fatty acid (FA) and the dimethyl acetal profiles. The main factor influencing bacterial community composition was the cattle breed. Some bacterial groups were positively correlated to average daily weight gain for the two breeds (i.e., Rikenellaceae RC9 gut group, Fibrobacter and Succiniclasticum in the rumen of MA steers, and Succinivibrionaceae UCG-002 in the rumen of AU steers); despite this, animal performance appeared to be influenced by short chain FAs production pathways and by the presence of H2 sinks that divert the H2 to processes alternative to the methanogenesis.

Molecular characterization and structure of intestinal micro flora for postmortem interval estimation in SD rats

2019 ◽  
Author(s):  
Huan Li ◽  
Lu Yuan ◽  
Ruina Liu ◽  
Siruo Zhang ◽  
E Yang ◽  
...  
Keyword(s):  
Bacterial Community ◽  
High Throughput Sequencing ◽  
Interval Estimation ◽  
Pcr Amplification ◽  
Postmortem Interval ◽  
The Body ◽  
Rrna Gene ◽  
Variable Regions ◽  
Time Points ◽  
Almost All

Abstract Background The human rectum flora consists of a huge variety of bacteria and the association between individuals and their rectum bacterial community begins presently after birth and continues the whole lifetime. Once the body dies, the inherent microbes begin to break down from the inside and play a key role thereafter. Results The aim of this study was to investigate the probable shift of the rectum flora at different time intervals up to 15 days after death and to characterize the contribution for of this shift to estimate the time of death. The rectum of rats was wiped with a sterile cotton swab and the samples were proceeded for DNA extraction, PCR amplification of the 16S rRNA gene with the V3+V4 variable regions, and high throughput sequencing carried out on IonS5TMXL platform. The results were analyzed for intra-group and inter-group diversity, similarity and difference at different time points. At phylum level, Proteobacteria and Firmicutes showed major shifts, checked at 11 different intervals and emerged in the most of postmortem intervals. At the genus level, Enterococcus appeared in all groups except alive samples, Lactobacillus and Proteus appeared in most time points, and the latter showed an increasing trend after 3 days postmortem samples. At the species level, Enterococcus_faecalis and Proteus_mirabilis existed in most postmortem intervals, and the former had a downward trend after day 5 postmortem, while the latter had an upward trend. Corynebacterium_amycolatum , Entero_isolate_group_2 , Bacteroides_uniformis , Enterococcus_faecalis , Streptococcus_gallolyticus_subsp_macedonics , Clostridium_sporogenes were more abundant in 0-hour, day 1, 3, 5, 7, 13 postmortem intervals, respectively, while Proteus_mirabilis and Vagococcus_lutrae were abundant in day 15 postmortem. In addition, functional capacity analysis of Membrane_Transport, Amino_Acid_Metabolism, Nucleotide_Metabolism and Energy_Metabolism showed significant differences between alive and almost all other time points after death ( P <0.05). Conclusions All in all, bacteria at different levels (phylum, genera, species) showed different characteristic during the process of decomposition and possessed entirely different relative abundance and the structure of bacterial community in each time point shifted obviously, which suggested that the specific bacteria might imply the specific postmortem interval during decomposition.

scholarly journals Ecological Succession of Bacterial Communities during Conventionalization of Germ-Free Mice

2012 ◽  
Vol 78 (7) ◽  
pp. 2359-2366 ◽  
Author(s):  
Merritt G. Gillilland ◽  
John R. Erb-Downward ◽  
Christine M. Bassis ◽  
Michael C. Shen ◽  
Galen B. Toews ◽  
...  
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
Bacterial Communities ◽  
Structural Heterogeneity ◽  
Ecological Succession ◽  
Rrna Gene ◽  
Gi Tract ◽  
Content Type ◽  
Germ Free ◽  
Over Time

ABSTRACTLittle is known about the dynamics of early ecological succession during experimental conventionalization of the gastrointestinal (GI) tract; thus, we measured changes in bacterial communities over time, at two different mucosal sites (cecum and jejunum), with germfree C57BL/6 mice as the recipients of cecal contents (input community) from a C57BL/6 donor mouse. Bacterial communities were monitored using pyrosequencing of 16S rRNA gene amplicon libraries from the cecum and jejunum and analyzed by a variety of ecological metrics. Bacterial communities, at day 1 postconventionalization, in the cecum and jejunum had lower diversity and were distinct from the input community (dominated by eitherEscherichiaorBacteroides). However, by days 7 and 21, the recipient communities had become significantly diverse and the cecal communities resembled those of the donor and donor littermates, confirming that transfer of cecal contents results in reassembly of the community in the cecum 7 to 21 days later. However, bacterial communities in the recipient jejunum displayed significant structural heterogeneity compared to each other or the donor inoculum or the donor littermates, suggesting that the bacterial community of the jejunum is more dynamic during the first 21 days of conventionalization. This report demonstrates that (i) mature input communities do not simply reassemble at mucosal sites during conventionalization (they first transform into a “pioneering” community and over time take on the appearance, in membership and structure, of the original input community) and (ii) the specific mucosal environment plays a role in shaping the community.

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