Faculty Opinions recommendation of Host preference and invasiveness of commensal bacteria in the Lotus and Arabidopsis root microbiota.

AbstractHealthy plants are colonized by microorganisms from the surrounding environment, which form stable communities and provide beneficial services to the host. Culture-independent profiling of the bacterial root microbiota shows that different plant species are colonized by distinct bacterial communities, even if they share the same habitat. It is, however, not known to what extent the host actively selects these communities and whether commensal bacteria are adapted to a specific plant species. Here, we report a sequence-indexed culture collection from roots and nodules of the model legume Lotus japonicus that contains representatives from the majority of species found in culture-independent profiles. Using taxonomically paired synthetic communities from L. japonicus and the crucifer Arabidopsis thaliana in a multi-species gnotobiotic system, we detect clear signatures of host preference among commensal bacteria in a community context, but not in mono-associations. Sequential inoculation of either host reveals strong priority effects during the assembly of the root microbiota, where established communities are resilient to invasion by late-comers. However, we found that host preference by commensal bacteria confers a competitive advantage in their native host. We reveal that host preference is prevalent in commensal bacteria from diverse taxonomic groups and that this trait is directly linked to their invasiveness into standing root-associated communities.

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Host preference and invasiveness of commensal bacteria in the Lotus and Arabidopsis root microbiota

Nature Microbiology ◽

10.1038/s41564-021-00941-9 ◽

2021 ◽

Author(s):

Kathrin Wippel ◽

Ke Tao ◽

Yulong Niu ◽

Rafal Zgadzaj ◽

Niklas Kiel ◽

...

Keyword(s):

Plant Species ◽

Host Preference ◽

Lotus Japonicus ◽

Culture Collection ◽

Community Context ◽

Commensal Bacteria ◽

Priority Effects ◽

Sequential Inoculation ◽

Taxonomic Groups ◽

Root Microbiota

AbstractRoots of different plant species are colonized by bacterial communities, that are distinct even when hosts share the same habitat. It remains unclear to what extent the host actively selects these communities and whether commensals are adapted to a specific plant species. To address this question, we assembled a sequence-indexed bacterial culture collection from roots and nodules of Lotus japonicus that contains representatives of most species previously identified using metagenomics. We analysed taxonomically paired synthetic communities from L. japonicus and Arabidopsis thaliana in a multi-species gnotobiotic system and detected signatures of host preference among commensal bacteria in a community context, but not in mono-associations. Sequential inoculation experiments revealed priority effects during root microbiota assembly, where established communities are resilient to invasion by latecomers, and that host preference of commensal bacteria confers a competitive advantage in their cognate host. Our findings show that host preference in commensal bacteria from diverse taxonomic groups is associated with their invasiveness into standing root-associated communities.

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Faculty Opinions recommendation of A specialized metabolic network selectively modulates Arabidopsis root microbiota.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.735732411.793562002 ◽

2019 ◽

Author(s):

Stanislav Kopriva

Keyword(s):

Metabolic Network ◽

Arabidopsis Root ◽

Root Microbiota

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Dicer-like proteins influence Arabidopsis root microbiota independent of RNA-directed DNA methylation

Microbiome ◽

10.1186/s40168-020-00966-y ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Richa Kaushal ◽

Li Peng ◽

Sunil K. Singh ◽

Mengrui Zhang ◽

Xinlian Zhang ◽

...

Keyword(s):

Dna Methylation ◽

Cell Wall ◽

Plant Defense ◽

Root Exudates ◽

Rrna Gene ◽

Epigenetic Factors ◽

Callose Deposition ◽

Arabidopsis Root ◽

Triple Mutation ◽

Root Microbiota

Abstract Background Plants are naturally associated with root microbiota, which are microbial communities influential to host fitness. Thus, it is important to understand how plants control root microbiota. Epigenetic factors regulate the readouts of genetic information and consequently many essential biological processes. However, it has been elusive whether RNA-directed DNA methylation (RdDM) affects root microbiota assembly. Results By applying 16S rRNA gene sequencing, we investigated root microbiota of Arabidopsis mutants defective in the canonical RdDM pathway, including dcl234 that harbors triple mutation in the Dicer-like proteins DCL3, DCL2, and DCL4, which produce small RNAs for RdDM. Alpha diversity analysis showed reductions in microbe richness from the soil to roots, reflecting the selectivity of plants on root-associated bacteria. The dcl234 triple mutation significantly decreases the levels of Aeromonadaceae and Pseudomonadaceae, while it increases the abundance of many other bacteria families in the root microbiota. However, mutants of the other examined key players in the canonical RdDM pathway showed similar microbiota as Col-0, indicating that the DCL proteins affect root microbiota in an RdDM-independent manner. Subsequently gene analysis by shotgun sequencing of root microbiome indicated a selective pressure on microbial resistance to plant defense in the dcl234 mutant. Consistent with the altered plant-microbe interactions, dcl234 displayed altered characters, including the mRNA and sRNA transcriptomes that jointly highlighted altered cell wall organization and up-regulated defense, the decreased cellulose and callose deposition in root xylem, and the restructured profile of root exudates that supported the alterations in gene expression and cell wall modifications. Conclusion Our findings demonstrate an important role of the DCL proteins in influencing root microbiota through integrated regulation of plant defense, cell wall compositions, and root exudates. Our results also demonstrate that the canonical RdDM is dispensable for Arabidopsis root microbiota. These findings not only establish a connection between root microbiota and plant epigenetic factors but also highlight the complexity of plant regulation of root microbiota.

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A specialized metabolic network selectively modulates Arabidopsis root microbiota

Science ◽

10.1126/science.aau6389 ◽

2019 ◽

Vol 364 (6440) ◽

pp. eaau6389 ◽

Cited By ~ 80

Author(s):

Ancheng C. Huang ◽

Ting Jiang ◽

Yong-Xin Liu ◽

Yue-Chen Bai ◽

James Reed ◽

...

Keyword(s):

Chain Fatty Acid ◽

Fatty Acid Esters ◽

Growth Modulation ◽

Ecological Functions ◽

Arabidopsis Root ◽

Specialized Metabolites ◽

Mustard Plant ◽

Root Microbiota ◽

Acid Esters

Plant specialized metabolites have ecological functions, yet the presence of numerous uncharacterized biosynthetic genes in plant genomes suggests that many molecules remain unknown. We discovered a triterpene biosynthetic network in the roots of the small mustard plant Arabidopsis thaliana. Collectively, we have elucidated and reconstituted three divergent pathways for the biosynthesis of root triterpenes, namely thalianin (seven steps), thalianyl medium-chain fatty acid esters (three steps), and arabidin (five steps). A. thaliana mutants disrupted in the biosynthesis of these compounds have altered root microbiota. In vitro bioassays with purified compounds reveal selective growth modulation activities of pathway metabolites toward root microbiota members and their biochemical transformation and utilization by bacteria, supporting a role for this biosynthetic network in shaping an Arabidopsis-specific root microbial community.

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