Characterizing both bacteria and fungi improves understanding of the Arabidopsis root microbiome

Study information

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-18

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

30631088

DOI Digital object identifier for electronic documents.

http://dx.doi.org/10.1038/s41598-018-37208-z

URI

Authors

Jana Mittelstrass, Joy Bergelson, Mathew W. Horton

Journal

Scientific reports

Year

2019

Pages:

First page:

Keywords:

Arabidopsis thaliana, bacteria, fungi, microbiome, roots, leaves, field experiment

Roots provide plants mineral nutrients and stability in soil; while doing so, they come into contact with diverse soil microbes that affect plant health and productivity. Despite their ecological and agricultural relevance, the factors that shape the root microbiome remain poorly understood. We grew a worldwide panel of replicated Arabidopsis thaliana accessions outdoors and over winter to characterize their root-microbial communities. Although studies of the root microbiome tend to focus on bacteria, we found evidence that fungi have a strong influence on the structure of the root microbiome. Moreover, host effects appear to have a stronger influence on plant-fungal communities than plant-bacterial communities. Mapping the host genes that affect microbiome traits identified a priori candidate genes with roles in plant immunity; the root microbiome also appears to be strongly affected by genes that impact root and root hair development. Our results suggest that future analyses of the root microbiome should focus on multiple kingdoms, and that the root microbiome is shaped not only by genes involved in defense, but also by genes involved in plant form and physiology.

Experiment 1

Edit History Delete

Flag for review

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-18

Curated date: 2023/10/06

Curator: Spykelionel

Revision editor(s): Spykelionel, LGeistlinger, Peace Sandy, Victoria

Subjects

Location of subjects: United States of America

Host species Species from which microbiome was sampled. Contact us to have more species added.: Arabidopsis thaliana

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Accessory nerve root Accessory nerve root,Accessory portion of spinal accessory nerve,Bulbar accessory nerve,Bulbar part of accessory nerve,C11n,Cranial accessory nerve,Cranial part of accessory nerve,Cranial part of the accessory nerve,Cranial portion of eleventh cranial nerve,Internal branch of accessory nerve,Nerve XI (cranialis),Pars vagalis of nervus accessorius,Radices craniales nervi accessorii,Root of accessory nerve,accessory nerve root

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Root Root,root

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Control group (Leaves)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Test group (Roots)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: The leaf microbiome, representing the microbial communities associated with the leaves of the Arabidopsis plants.

Group 0 sample size Number of subjects in the control (unexposed) group: 4

Group 1 sample size Number of subjects in the case (exposed) group: 4

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): NIL

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V5-V7

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Roche454

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: raw counts

Statistical test: Linear Regression

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.1

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: Yes

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: Confounders controlled for: "Block Effects" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.Block Effects, Confounders controlled for: "Sequencing run" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.Sequencing run

Alpha Diversity

Richness Number of species: increased

Signature 1

Edit History Delete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-18

Curated date: 2023/10/06

Curator: Spykelionel

Revision editor(s): Spykelionel, Peace Sandy

Source: Table 1

Description: The top 10 differentially enriched genera from each kingdom and their preferred habitats. The estimates (coefficients) and P - values are from a generalized linear (Poisson) model, fit to determine the effect of the factor organ while taking into account differences in sequencing effort among samples. Note: the ‘Unassigned’ categories include diverse taxa, which themselves may be differentially enriched (or depleted) in the root relative to the leaf microbiome.

Abundance in Group 1: increased abundance in Test group (Roots)

NCBI	Quality Control	Links
Massilia
Mortierella
Tetracladium

Revision editor(s): Spykelionel, Peace Sandy

Signature 2

Edit History Delete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-18

Curated date: 2023/10/06

Curator: Spykelionel

Revision editor(s): Spykelionel, Peace Sandy

Source: Table 1

Description: The top 10 differentially enriched genera from each kingdom and their preferred habitats. The estimates (coefficients) and P - values are from a generalized linear (Poisson) model, fit to determine the effect of the factor organ while taking into account differences in sequencing effort among samples. Note: the ‘Unassigned’ categories include diverse taxa, which themselves may be differentially enriched (or depleted) in the root relative to the leaf microbiome.

Abundance in Group 1: decreased abundance in Test group (Roots)

NCBI	Quality Control	Links
Janthinobacterium
Pseudomonas
Alternaria
Articulospora
Cladosporium
Plectosphaerella

Revision editor(s): Spykelionel, Peace Sandy