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

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Reviewed Marked as Reviewed by Peace Sandy on 2024-2-18
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
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


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

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 ControlLinks
Massilia
Mortierella
Tetracladium

Revision editor(s): Spykelionel, Peace Sandy

Signature 2

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 ControlLinks
Janthinobacterium
Pseudomonas
Alternaria
Articulospora
Cladosporium
Plectosphaerella

Revision editor(s): Spykelionel, Peace Sandy