Natural variation in root exudation of GABA and DIMBOA impacts the maize root endosphere and rhizosphere microbiomes

Root exudates are important for shaping root-associated microbiomes. However, studies on a wider range of metabolites in exudates are required for a comprehensive understanding about their influence on microbial communities. We identified maize inbred lines that differ in exudate concentrations of DIMBOA and GABA using a semi-hydroponic system. These lines were grown in the field to determine the changes in microbial diversity and gene expression due to varying concentrations of DIMBOA and GABA in exudates using 16S rRNA amplicon sequencing and metatranscriptomics. Results showed individual and interaction effects of DIMBOA and GABA on the rhizosphere and root endosphere beta-diversity, most strongly at the V10 growth stage. The main bacterial families affected by both compounds were Ktedonobacteraceae and Xanthomonadaceae. Higher concentrations of DIMBOA in exudates affected the rhizosphere metatranscriptome, enriching for KEGG pathways associated with plant disease. This study validated the use of natural variation within plant species as a powerful approach for understanding the role of root exudates on microbiome selection. We also showed that a semi-hydroponic system can be used to identify maize genotypes that differ in GABA and DIMBOA exudate concentrations under field conditions. The impact of GABA exudation on root-associated microbiomes was shown for the first time.

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Deciphering the Influence of Multiple Anthropogenic Inputs on Taxonomic and Functional Profiles of the Microbial Communities in Yitong River, Northeast China

10.21203/rs.3.rs-729563/v1 ◽

2021 ◽

Author(s):

Ying Zhang ◽

Yang Huo ◽

Zhiruo Zhang ◽

Suiyi Zhu ◽

Wei Fan ◽

...

Keyword(s):

Microbial Communities ◽

Northeast China ◽

Environmental Changes ◽

Quantitative Polymerase Chain Reaction ◽

Amplicon Sequencing ◽

Fecal Indicator ◽

16S Rrna Amplicon Sequencing ◽

Anthropogenic Inputs ◽

Wwtp Effluent ◽

The Impact

Abstract We conducted physicochemical parameters analysis, 16S rRNA amplicon sequencing and real-time quantitative polymerase chain reaction to explore the impact of human inputs on the bacterioplankton communities within a tributary of the largest river flowing through a megacity in northeast China. Agriculture largely accounted for the alteration of diversity and functions of the microbial communities. Furthermore, nutrients were significantly declined at the reservoir outlet, and WWTP effluent discharge caused changes in the river microbial community. NH3-N and NO3--N were the main environmental factors that drive the shift of the bacteria community, and rare taxa played a more important role in the response to environmental changes compared with the abundant ones. The occurrence of the human-specific fecal indicator was mostly derived from agriculture, and its increase in relative abundance was observed in the effluent. Thus, our study provides guidance for ecological assessment and management of rivers by revealing the response pattern of river bacterioplankton to multiple types of anthropogenic stressors.

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The impact of bacterial diversity on resistance to biocides in oilfields

Scientific Reports ◽

10.1038/s41598-021-02494-7 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Gabriela Feix Pereira ◽

Harry Luiz Pilz-Junior ◽

Gertrudes Corção

Keyword(s):

Water Samples ◽

Produced Water ◽

Functional Characterization ◽

Amplicon Sequencing ◽

Oil Field ◽

Oil Fields ◽

Sulfate Reducing ◽

16S Rrna Amplicon Sequencing ◽

Dimethyl Benzyl ◽

The Impact

AbstractExtreme conditions and the availability of determinate substrates in oil fields promote the growth of a specific microbiome. Sulfate-reducing bacteria (SRB) and acid-producing bacteria (APB) are usually found in these places and can harm important processes due to increases in corrosion rates, biofouling and reservoir biosouring. Biocides such as glutaraldehyde, dibromo-nitrilopropionamide (DBNPA), tetrakis (hydroxymethyl) phosphonium sulfate (THPS) and alkyl dimethyl benzyl ammonium chloride (ADBAC) are commonly used in oil fields to mitigate uncontrolled microbial growth. The aim of this work was to evaluate the differences among microbiome compositions and their resistance to standard biocides in four different Brazilian produced water samples, two from a Southeast Brazil offshore oil field and two from different Northeast Brazil onshore oil fields. Microbiome evaluations were carried out through 16S rRNA amplicon sequencing. To evaluate the biocidal resistance, the Minimum Inhibitory Concentration (MIC) of the standard biocides were analyzed using enriched consortia of SRB and APB from the produced water samples. The data showed important differences in terms of taxonomy but similar functional characterization, indicating the high diversity of the microbiomes. The APB and SRB consortia demonstrated varying resistance levels against the biocides. These results will help to customize biocidal treatments in oil fields.

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Gut Microbiota Modulation by Dietary Barley Malt Melanoidins

Nutrients ◽

10.3390/nu12010241 ◽

2020 ◽

Vol 12 (1) ◽

pp. 241 ◽

Cited By ~ 1

Author(s):

Nesreen Aljahdali ◽

Pascale Gadonna-Widehem ◽

Pauline M. Anton ◽

Franck Carbonero

Keyword(s):

Fatty Acids ◽

Gut Microbiota ◽

Amplicon Sequencing ◽

Short Chain Fatty Acids ◽

Control Group ◽

Maillard Reaction Products ◽

Reaction Products ◽

Barley Malt ◽

16S Rrna Amplicon Sequencing ◽

The Impact

Melanoidins are the final Maillard reaction products (protein–carbohydrate complexes) produced in food by prolonged and intense heating. We assessed the impact of the consumption of melanoidins from barley malts on gut microbiota. Seventy-five mice were assigned into five groups, where the control group consumed a non-melanoidin malt diet, and other groups received melanoidin-rich malts in increments of 25% up to 100% melanoidin malts. Feces were sampled at days 0, 1, 2, 3, 7, 14, and 21 and the microbiota was determined using V4 bacterial 16S rRNA amplicon sequencing and short-chain fatty acids (SCFA) by gas chromatography. Increased melanoidins was found to result in significantly divergent gut microbiota profiles and supported sustained SCFA production. The relative abundance of Dorea, Oscillibacter, and Alisitpes were decreased, while Lactobacillus, Parasutterella, Akkermansia, Bifidobacterium, and Barnesiella increased. Bifidobacterium spp. and Akkermansia spp. were significantly increased in mice consuming the highest melanoidin amounts, suggesting remarkable prebiotic potential.

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Characterization and comparison of the bacterial communities of rhizosphere and bulk soils from cadmium-polluted wheat fields

PeerJ ◽

10.7717/peerj.10302 ◽

2020 ◽

Vol 8 ◽

pp. e10302

Author(s):

Li Song ◽

Zhenzhi Pan ◽

Yi Dai ◽

Lin Chen ◽

Li Zhang ◽

...

Keyword(s):

Bacterial Community ◽

Contaminated Soils ◽

Bacterial Communities ◽

Cadmium Concentration ◽

Normal Growth ◽

Amplicon Sequencing ◽

Negative Influence ◽

Cadmium Pollution ◽

16S Rrna Amplicon Sequencing ◽

The Impact

Cadmium pollution is becoming a serious problem due to its nondegradability and substantial negative influence on the normal growth of crops, thereby harming human health through the food chain. Rhizospheric bacteria play important roles in crop tolerance. However, there is little experimental evidence which demonstrates how various cadmium concentrations affect the bacterial community in wheat fields including rhizosphere microorganisms and nonrhizosphere (bulk) microorganisms. In this study, 16S rRNA amplicon sequencing technology was used to investigate bacterial communities in rhizosphere and bulk soils under different levels of pollution in terms of cadmium concentration. Both the richness and diversity of the rhizosphere microorganism community were higher under nonpolluted soil and very mild and mild cadmium-contaminated soils than compared with bulk soil, with a shift in community profile observed under severe cadmium pollution. Moreover, cadmium at various concentrations had greater influence on bacterial composition than for the nonpolluted site. In addition, redundancy analysis (RDA) and Spearman’s analysis elucidated the impact of exchangeable Cd and total Cd on bacterial community abundance and composition. This study suggests that cadmium imposes a distinct effect on bacterial community, both in bulk and rhizosphere soils of wheat fields. This study increases our understanding of how bacterial communities in wheat fields shaped under different concentrations of cadmium.

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Impact of Soil Microbes and Oxygen Availability on Bacterial Community Structure of Decomposing Poultry Carcasses

Animals ◽

10.3390/ani11102937 ◽

2021 ◽

Vol 11 (10) ◽

pp. 2937

Author(s):

Michelle A. Miguel ◽

Seon-Ho Kim ◽

Sang-Suk Lee ◽

Yong-Il Cho

Keyword(s):

Microbial Community ◽

Moisture Content ◽

Early Period ◽

Amplicon Sequencing ◽

Shannon Index ◽

Oxygen Availability ◽

Anaerobic Conditions ◽

Aerobic Conditions ◽

16S Rrna Amplicon Sequencing ◽

The Impact

The impact of soil with an intact microbial community and oxygen availability on moisture content, soil pH, and bacterial communities during decomposition of poultry carcasses was investigated. Poultry carcasses were decomposed in soil with or without a microbial community, under aerobic or anaerobic conditions. The samples collected in each microcosm burial set-up were analyzed by targeted 16S rRNA amplicon sequencing and Amplicon sequence variants (ASV) method. Our results showed that moisture was high in the burial set-ups under anaerobic conditions and pH was high in the burial set-ups under aerobic conditions. Meanwhile, the Chao1 and Shannon index significantly differed between the different burial set-ups and across different time points. In addition, bacterial taxa composition during the early period of decomposition differed from that of the late period. A total of 23 phyla, 901 genera, and 1992 species were identified. Firmicutes was the most dominant phyla in all burial set-ups throughout the decomposition. At day 60, Pseudogracilibacillus was dominant in the burial set-ups under aerobic conditions, while Lentibacillus dominated in the burial set-ups under anaerobic conditions. This study demonstrated that the soil microbial community and availability of oxygen significantly affected the changes in moisture content, pH, and bacterial composition during the decomposition process.

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Metagenomics and Metatranscriptomics Reveal Pathway of 3-Chloroaniline Degradation in Wastewater Reactors

10.1101/2021.05.02.442374 ◽

2021 ◽

Author(s):

Hari Seshan ◽

Ezequiel Santillan ◽

Florentin Constancias ◽

Uma Shankari Chandra Segaran ◽

Rohan B. H. Williams ◽

...

Keyword(s):

Wastewater Treatment ◽

Activated Sludge ◽

Amplicon Sequencing ◽

Wastewater Treatment Process ◽

16S Rrna Amplicon Sequencing ◽

Acclimation Period ◽

Culture Independent ◽

Mechanisms Of Adaptation ◽

Community Data ◽

The Impact

Biological wastewater treatment systems are often affected by major shifts in influent quality, including the input of various toxic chemicals. Yet the mechanisms underlying adaptation of activated sludge process performance when challenged with a sustained toxin input have not been studied in a controlled and replicated experiment. Three replicate bench-scale bioreactors were subjected to a chemical disturbance in the form of 3-chloroaniline (3-CA) input over 132 days, following an acclimation period of 58 days, while three control reactors received no 3-CA input. The nitrification process was initially affected by 3-CA input; yet all three treatment reactors evolved to biologically degrade 3-CA within three weeks of the experiment, resulting in partial nitrification recovery. 16S rRNA amplicon sequencing revealed that ammonia oxidizers were initially impacted by 3-CA, and a new ammonia oxidizing community emerged with the onset of 3-CA degradation. Combining process and microbial community data from amplicon sequencing with potential functions gleaned from assembled metagenomics and metatranscriptomics data, 3-CA degradation was shown to likely occur via a phenol monooxygenase followed by ortho-cleavage of the aromatic ring. The relative abundance of genera Gemmatimonas, Saprospiraceae OLB8 and Taibaiella correlated significantly with 3-CA degradation. This study demonstrated the impact of a sustained stress on the activated sludge community and wastewater treatment process and its subsequent recovery. Using a combination of techniques in a controlled and replicated experiment, we showed that microbial communities can evolve degradative capacity following a sustained xenobiotic input, specific functions like nitrification can fully or partially recover and targeted culture-independent approaches can be used to elucidate the mechanisms of adaptation.

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A core salivary microbiome shows the high prevalence of bacterial members yet variability across human populations

10.1101/2021.12.13.471511 ◽

2021 ◽

Author(s):

Xinwei Ruan ◽

Jiaqiang Luo ◽

Pangzhen Zhang ◽

Kate Howell

Keyword(s):

Meta Analysis ◽

Geographic Location ◽

Amplicon Sequencing ◽

Human Saliva ◽

Independent Study ◽

Human Populations ◽

Sequencing Data ◽

The Core ◽

16S Rrna Amplicon Sequencing ◽

The Impact

Human saliva contains diverse bacterial communities, reflecting human health status, dietary patterns and contributing to variability in the sensory perception of food. Many descriptions of salivary microbiome diversity compare commonalities and differences with reference to a diseased state, but the composition of healthy saliva has not been described. Here, we use a meta-analysis approach to define and explore the core membership of the human salivary microbial community by collecting and re-analysing raw 16S rRNA amplicon sequencing data from 47 studies with 2206 saliva samples. We found 68 core bacterial taxa that were consistently detected. Differences induced by various host intrinsic and behaviour factors, including gender, age, geographic location, tobacco usage, and alcohol consumption, were evident. The core of the salivary microbiome was verified by collecting and analysing saliva in an independent study, and this analysis showed that the impact of geographic variation is likely due to diet.

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Rhizobium Symbiotic Capacity Shapes Root-Associated Microbiomes in Soybean

Frontiers in Microbiology ◽

10.3389/fmicb.2021.709012 ◽

2021 ◽

Vol 12 ◽

Author(s):

Yuanhui Liu ◽

Bin Ma ◽

Wenfeng Chen ◽

Klaus Schlaeppi ◽

Matthias Erb ◽

...

Keyword(s):

Root Exudates ◽

Root Exudation ◽

Amplicon Sequencing ◽

Vital Role ◽

Plant Performance ◽

Physiochemical Properties ◽

Nod Factor ◽

Community Shift ◽

Soybean Roots ◽

Microbiome Assembly

Root-microbiome interactions are of central importance for plant performance and yield. A distinctive feature of legumes is that they engage in symbiosis with N2-fixing rhizobia. If and how the rhizobial symbiotic capacity modulates root-associated microbiomes are still not yet well understood. We determined root-associated microbiomes of soybean inoculated with wild type (WT) or a noeI mutant of Bradyrhizobium diazoefficiens USDA 110 by amplicon sequencing. UPLC-MS/MS was used to analyze root exudates. The noeI gene is responsible for fucose-methylation of Nod factor secreted by USDA 110 WT strain. Soybean roots inoculated with the noeI mutant showed a significant decrease in nodulation and root-flavonoid exudation compared to roots inoculated with WT strain. The noeI mutant-inoculated roots exhibited strong changes in microbiome assembly in the rhizosphere and rhizoplane, including reduced diversity, changed co-occurrence interactions and a substantial depletion of root microbes. Root exudates and soil physiochemical properties were significantly correlated with microbial community shift in the rhizosphere between different rhizobial treatments. These results illustrate that rhizobial symbiotic capacity dramatically alters root-associated microbiomes, in which root exudation and edaphic patterns play a vital role. This study has important implications for understanding the evolution of plant-microbiome interactions.

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Microbial Community Field Surveys Reveal Abundant Pseudomonas Population in Sorghum Rhizosphere Composed of Many Closely Related Phylotypes

Frontiers in Microbiology ◽

10.3389/fmicb.2021.598180 ◽

2021 ◽

Vol 12 ◽

Author(s):

Dawn Chiniquy ◽

Elle M. Barnes ◽

Jinglie Zhou ◽

Kyle Hartman ◽

Xiaohui Li ◽

...

Keyword(s):

Single Molecule ◽

Bacterial Species ◽

Operational Taxonomic Unit ◽

Amplicon Sequencing ◽

Sequence Variant ◽

Metagenomic Sequencing ◽

Host Genotype ◽

16S Rrna Amplicon Sequencing ◽

The Impact ◽

Surrounding Soil

While the root-associated microbiome is typically less diverse than the surrounding soil due to both plant selection and microbial competition for plant derived resources, it typically retains considerable complexity, harboring many hundreds of distinct bacterial species. Here, we report a time-dependent deviation from this trend in the rhizospheres of field grown sorghum. In this study, 16S rRNA amplicon sequencing was used to determine the impact of nitrogen fertilization on the development of the root-associated microbiomes of 10 sorghum genotypes grown in eastern Nebraska. We observed that early rhizosphere samples exhibit a significant reduction in overall diversity due to a high abundance of the bacterial genus Pseudomonas that occurred independent of host genotype in both high and low nitrogen fields and was not observed in the surrounding soil or associated root endosphere samples. When clustered at 97% identity, nearly all the Pseudomonas reads in this dataset were assigned to a single operational taxonomic unit (OTU); however, exact sequence variant (ESV)-level resolution demonstrated that this population comprised a large number of distinct Pseudomonas lineages. Furthermore, single-molecule long-read sequencing enabled high-resolution taxonomic profiling revealing further heterogeneity in the Pseudomonas lineages that was further confirmed using shotgun metagenomic sequencing. Finally, field soil enriched with specific carbon compounds recapitulated the increase in Pseudomonas, suggesting a possible connection between the enrichment of these Pseudomonas species and a plant-driven exudate profile.

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16S rRNA Amplicon Sequencing of Sediment Bacterial Communities in an Oyster Farm in Rhode Island

Microbiology Resource Announcements ◽

10.1128/mra.01074-19 ◽

2019 ◽

Vol 8 (42) ◽

Cited By ~ 1

Author(s):

Joshua T. E. Stevens ◽

Robinson W. Fulweiler ◽

Priyanka Roy Chowdhury

Keyword(s):

16S Rrna ◽

Rhode Island ◽

Bacterial Communities ◽

16S Rrna Gene Sequencing ◽

Amplicon Sequencing ◽

Rrna Gene ◽

16S Rrna Amplicon Sequencing ◽

Oyster Farm ◽

Rrna Gene Sequencing ◽

The Impact

Little is known about the impact of oyster farming on sediment microbial communities. Here, we use 16S rRNA gene sequencing to identify bacterial communities in 24 sediment samples collected from an oyster farm in Ninigret Pond, RI. A total of 13,147 unique operational taxonomic units (OTUs) were assigned, with Proteobacteria being the dominant phyla across all samples.

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