Ontology highlight
ABSTRACT:
PROVIDER: PRJNA673381 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12955400_1.fastq.gz | Fastqsanger.gz | |||
| SRR12955400_2.fastq.gz | Fastqsanger.gz | |||
| SRR12955500_1.fastq.gz | Fastqsanger.gz | |||
| SRR12955500_2.fastq.gz | Fastqsanger.gz | |||
| SRR12955600_1.fastq.gz | Fastqsanger.gz |
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Project description:Fire is a crucial event regulating the structure and functioning of many ecosystems. Yet few studies focused on how fire affects both the taxonomic and functional diversity of soil microbial communities, along with plant diversity and soil carbon (C) and nitrogen (N) dynamics. Here, we analyze these effects for a grassland ecosystem 9-months after an experimental fire at the Jasper Ridge Global Change Experiment (JRGCE) site in California, USA. Fire altered soil microbial communities considerably, with community assembly process analysis indicating that environmental selection pressure was higher in burned sites. However, a small subset of highly connected taxa were able to withstand the disturbance. In addition, fire decreased the relative abundances of most genes associated with C degradation and N cycling, implicating a slow-down of microbial processes linked to soil C and N dynamics. In contrast, fire stimulated plant growth, likely enhancing plant-microbe competition for soil inorganic N. To synthesize our findings, we performed structural equation modeling, which showed that plants but not microbial communities were responsible for the significantly higher soil respiration rates in burned sites. In conclusion, fire is well-documented to considerable alter the taxonomic and functional composition of soil microorganisms, along with the ecosystem functioning, thus arousing feedback of ecosystem responses to affect global climate.
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Project description:Fire disturbances are becoming more common, more intense, and further-reaching across the globe, with consequences for ecosystem functioning. Importantly, fire can have strong effects on the soil microbiome, including community and functional changes after fire, but surprisingly little is known regarding the role of soil fire legacy in shaping responses to recent fire. To address this gap, we conducted a manipulative field experiment administering fire across 32 soils with varying fire legacies, including combinations of 1-7 historic fires and 1-33 years since most recent fire. We analyzed soil metatranscriptomes, determining for the first time how fire and fire legacy interactively affect metabolically-active soil taxa, the microbial regulation of important carbon (C), nitrogen (N) and phosphorus (P) cycling, expression of carbohydrate-cycling enzyme pathways, and functional gene co-expression networks. Experimental fire strongly downregulated fungal activity while upregulating many bacterial and archaeal phyla. Further, fire decreased soil capacity for microbial C and N cycling and P transport, and drastically rewired functional gene co-expression. Perhaps most importantly, we highlight a novel role of soil fire legacy in regulation of microbial C, N, and P responses to recent fire. We observed a greater number of functional genes responsive to the interactive effects of fire and fire legacy than those affected solely by recent fire, indicating that many functional genes respond to fire only under certain fire legacy contexts. Therefore, without incorporating fire legacy of soils, studies will miss important ways that fire shapes microbial roles in ecosystem functioning. Finally, we showed that fire caused significant downregulation of carbon metabolism and nutrient cycling genes in microbiomes under abnormal soil fire histories, producing a novel warning for the future: human manipulation of fire legacies, either indirectly through global change-induced fire intensification or directly through fire suppression, can negatively impact soil microbiome functional responses to new fires.
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Project description:Advances in DNA sequencing technologies has drastically changed our perception of the structure and complexity of the plant microbiome. By comparison, our ability to accurately identify the metabolically active fraction of soil microbiota and its specific functional role in augmenting plant health is relatively limited. Here, we combined our recently developed protein extraction method and an iterative bioinformatics pipeline to enable the capture and identification of extracellular proteins (metaexoproteomics) synthesised in the rhizosphere of Brassica spp. We first validated our method in the laboratory by successfully identifying proteins related to a host plant (Brassica rapa) and its bacterial inoculant, Pseudomonas putida BIRD-1. This identified numerous rhizosphere specific proteins linked to the acquisition of plant-derived nutrients in P. putida. Next, we analysed natural field-soil microbial communities associated with Brassica napus L. (oilseed rape). By combining metagenomics with metaexoproteomics, 1882 proteins were identified across bulk and rhizosphere samples. Meta-exoproteomics identified a clear shift (p<0.001) in the metabolically active fraction of the soil microbiota responding to the presence of B. napus roots that was not apparent in the composition of the total microbial community (metagenome). This metabolic shift was associated with the stimulation of rhizosphere-specialised bacteria, such as Gammaproteobacteria, Betaproteobacteria and Flavobacteriia and the upregulation of plant beneficial functions related to phosphorus and nitrogen mineralisation. Together, our metaproteomic assessment of the ‘active’ plant microbiome at the field-scale demonstrates the importance of moving past a genomic assessment of the plant microbiome in order to determine ecologically important plant-microbe interactions underpinning plant health.
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