Exploring the Root Microbiome: Extracting Bacterial Community Data from the Soil, Rhizosphere, and Root Endosphere

Simmons, Tuesday; Caddell, Daniel; Deng, Siwen; Coleman‐Derr, Devin

doi:10.3791/57561-v

Cited by 7 publications

(10 citation statements)

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“…We used a detailed protocol from Simmons et al . (2018) to separate rhizosphere soil samples. Rhizosphere soils were defined as soil clinging tightly to the plant's roots.…”

Section: Methodsmentioning

confidence: 99%

Water deficit affects inter‐kingdom microbial connections in plant rhizosphere

Bazany

Wang

Delgado‐Baquerizo

et al. 2022

Environmental Microbiology

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The frequency and severity of drought are increasing due to anthropogenic climate change and are already limiting cropping system productivity in many regions around the world. Few microbial groups within plant microbiomes can potentially contribute towards the fitness and productivity of their hosts under abiotic stress events including water deficits. However, microbial communities are complex and integrative work considering the multiple co-existing groups of organisms is needed to better understand how the entire microbiome responds to environmental stresses. We hypothesize that water deficit stress will differentially shape bacterial, fungal, and protistan microbiome composition and influence interkingdom microbial interactions in the rhizospheres of corn and sugar beet. We used amplicon sequencing to profile bacterial, fungal, and protistan communities in corn and sugar beet rhizospheres grown under irrigated and water deficit conditions. The water deficit treatment had a stronger influence than host species on bacterial composition, whereas the opposite was true for protists. These results indicate that different microbial kingdoms have variable responses to environmental stress and host factors. Water deficit also influenced intra-and inter-kingdom microbial associations, wherein the protist taxa formed a separate cluster under water deficit conditions. Our findings help elucidate the influence of environmental and host drivers of bacterial, fungal, and protistan community assembly and co-occurrence in agricultural rhizosphere environments.

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“…We used a detailed protocol from Simmons et al . (2018) to separate rhizosphere soil samples. Rhizosphere soils were defined as soil clinging tightly to the plant's roots.…”

Section: Methodsmentioning

confidence: 99%

Water deficit affects inter‐kingdom microbial connections in plant rhizosphere

Bazany

Wang

Delgado‐Baquerizo

et al. 2022

Environmental Microbiology

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“…Bulk and rhizosphere soils were collected separately from each pot after the exposure experiment (10 week-old plants), using approaches similar to others. 32,33 First, the tomato plant was carefully removed from the pot using the aseptic technique. Loosely bound soil was removed from the roots by shaking and using a sterilized spatula.…”

Section: Environmental Science: Nano Papermentioning

confidence: 99%

Emerging investigator series: differential effects of carbon nanotubes and graphene on the tomato rhizosphere microbiome

You

Kerner

Shanmugam

et al. 2023

Environ. Sci.: Nano

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“…Top 5 cm from each sample were homogenized and used for total RNA extractions and measurements of nitrogen fixation and potential nitrification rates. Root samples for RNA extractions were washed in an epiphyte removal buffer, as in Simmons et al (2018). Sediment and root samples for RNA analysis were immediately flash-frozen in an ethanol dry ice bath, and stored at -80 ºC until extraction.…”

Section: Study Site Field Sampling and Sample Processingmentioning

confidence: 99%

“…performed by sonication in an epiphyte removal buffer, as detailed inSimmons et al (2018).Extracellular dissolved or sediment-adsorbed DNA was removed from bulk sediment samples according to theLever et al (2015) procedure. DNA extractions from all samples were performed using the DNeasy PowerSoil kit (Qiagen, Valencia, CA) following the manufacturer's instructions.Shotgun metagenome sequencing was performed on an Illumina NovaSeq 6000 S4 2x150 Illumina flow cell at the Georgia Tech Sequencing Core (Atlanta, GA).RNA from 4 biological replicates of both the sediment and root compartments from the tall and short phenotypes of S. alterniflora was extracted using the ZymoBIOMICS RNA Miniprep (Zymo Research Corp) kit according to the manufacturer's protocol (n: 4 replicates * 2 S. alterniflora phenotypes * 2 compartments = 16 samples).…”

mentioning

confidence: 99%

Sulfur oxidation and reduction are coupled to nitrogen fixation in the roots of a salt marsh foundation plant species

Rolando¹,

Song²,

Liu

et al. 2023

Preprint

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Symbiotic root microbiota are crucial for plant growth as they assist their hosts in nutrient acquisition. In the roots of coastal marine plants, heterotrophic activity in the rhizosphere by sulfate-reducing microorganisms has been linked to nitrogen fixation. In this study, we recovered 239 high-quality metagenome-assembled genomes (MAGs) from a salt marsh dominated by the foundation plant Spartina alterniflora, including diazotrophic sulfate-reducing and sulfur-oxidizing bacteria thriving in the root compartment. Here we show for the first time that highly-abundant sulfur-oxidizing bacteria in the roots of a coastal macrophyte encode and highly express genes for nitrogen fixation (nifHDK). Further, we leveraged a S. alterniflora biomass gradient to gain a mechanistic understanding on how root-microbe interactions respond to abiotic stress from anoxia and elevated sulfide concentration. We observed that the roots of the stressed S. alterniflora phenotype exhibited the highest rates of nitrogen fixation and expression levels of both the oxidative and reductive forms of the dissimilatory sulfite reductase gene (dsrAB). Approximately 25% and 15% of all sulfur-oxidizing dsrA and nitrogen-fixing nifK transcripts, respectively, were associated with novel MAGs of the Candidatus Thiodiazotropha genus in the roots of the stressed S. alterniflora phenotype. We conclude that the rapid cycling of sulfur in the dynamic S. alterniflora root zone is coupled to nitrogen fixation during both reductive and oxidative sulfur reactions, and that the S. alterniflora - Ca. Thiodiazotropha symbiosis is an adaptive response to anoxic and sulfidic sediment conditions, whereby the plants benefit from reduced sulfide toxicity and potential nitrogen acquisition.

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Exploring the Root Microbiome: Extracting Bacterial Community Data from the Soil, Rhizosphere, and Root Endosphere

Cited by 7 publications

References 0 publications

Water deficit affects inter‐kingdom microbial connections in plant rhizosphere

Water deficit affects inter‐kingdom microbial connections in plant rhizosphere

Emerging investigator series: differential effects of carbon nanotubes and graphene on the tomato rhizosphere microbiome

Sulfur oxidation and reduction are coupled to nitrogen fixation in the roots of a salt marsh foundation plant species

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