Ontology highlight
ABSTRACT:
PROVIDER: PRJNA938606 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23630900.fastq.gz | Fastqsanger.gz | |||
| SRR23630901.fastq.gz | Fastqsanger.gz | |||
| SRR23630902.fastq.gz | Fastqsanger.gz | |||
| SRR23630903.fastq.gz | Fastqsanger.gz | |||
| SRR23630904.fastq.gz | Fastqsanger.gz |
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Project description:Bacterial community development during plant litter decomposition
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Project description:Chemical signaling in the plant microbiome can have drastic effects on microbial community structure, and on host growth and development. Previously, we demonstrated that the auxin metabolic signal interference performed by the bacterial genus Variovorax via a novel auxin degradation locus was essential for maintaining stereotypic root development in an ecologically-relevant bacterial synthetic community. Here, we dissect the Variovorax auxin degradation locus to define the genes necessary and sufficient for indole-3-acetic acid (IAA) degradation and signal interference. We determine the crystal structures and binding properties of the operon’s MarR-family repressor with IAA and other auxins. We identify auxin-degradation operons across the bacterial tree of life and define two distinct types based on gene content and metabolic products: iac-like and iad-like. We solve the structures of MarRs from representatives of each auxin degradation operon type, establishing that each have distinct IAA binding pockets. Comparison of representative IAA degrading strains from diverse bacterial genera show that while all degrade IAA, only strains containing iad-like auxin degrading operons interfere with auxin signaling in a complex synthetic community context. This suggests that iad-like operon containing strains, including Variovorax species, play a key ecological role in modulating auxins in the plant microbiome.
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Project description:Leaf metabolomes are constantly changing in response to biotic and abiotic conditions, alongside internal physiological processes. Additionally, the diversity of plant species in a surrounding community influences the leaf metabolome. However, it is rarely considered how these changes might affect the chemical composition of litter emissions, which can mediate interactions with the decomposer community. To study these effects, reproducible methods for trapping litter volatiles are essential, particularly for analyzing larger sample numbers and after longer storage periods. This study optimized and validated a solid-phase microextraction (SPME) method for analyzing small amounts of litter from Quercus petraea within a biodiversity ecosystem functioning experiment. The SPME optimization focused on the fiber material, extraction temperature, and duration of sampling. The final optimized method, using a PDMS/DVB fiber and 60-minute extraction at 70 degrees celsius, demonstrated a high reproducibility, with %RSD values ranging from 0.073 to 0.119% (intraday) and 0.115 to 0.169% (interday) for retention time, and 4.41 to 7.72% (intraday) and 7.67 to 11.0% (interday) for peak area. This makes it a reliable and reproducible approach for the collection and analysis of litter volatiles. After validation, this method was applied to test the hypothesis that oak leaf litter volatile profiles are influenced by the surrounding biodiversity. The results showed that the main compound classes in oak leaf litter were fatty acids and terpenoids. Furthermore, plot diversity level was negatively correlated with terpenoid emission rates. By detecting these changes in volatile composition, we gained further insights into how tree diversity affects litter chemistry, which may also impact the decomposer network.
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