Abstract
We characterized the effects of crop residue derived biochar on tomato growth, soil microbial diversity, and rhizosphere-level gene expression responses in an organic production system. Shoot fresh biomass and fruit yield were assessed at the end of the growing cycle. The corresponding transcriptomic response of the roots, the soil microbial community profiles, and the active transcripts within the communities were quantified using a metatranscriptomic approach at four different developmental stages of the plant. Biochar treatment did not impact shoot biomass or fruit production; however, metatranscriptome analysis revealed that the gene expression activity of the tomato rhizosphere changes over time in response to the biochar treatment, with a number of bacteria with known benefits to soil health and plant growth displaying increased gene expression (e.g., Rhizobiaceae, Pseudomonadaceae, Micromonosporaceae, Sphingomonadaceae). Streptomycetaceae were expressed at the highest levels in the rhizosphere. Biochar seemed to attenuate the expression of this bacteria by the end of the time course, possibly due to the rise in competition for resources driven by the increased activity of other beneficial microbes. Notably, pathogenic fungi in the soil displayed generally reduced expression in the biochar-amended rhizosphere in comparison with the control. In addition to the assessment of the rhizosphere microbiome, transcriptome analysis and gene ontology analysis of tomato roots revealed functional enrichment of genes associated with nitrogen metabolic processes, regulation of metabolic processes, and production of organic compounds in the biochar treated rhizosphere. Together, these results suggest that biochar amendment enhances gene expression of beneficial soil microbes, and also impacts gene expression in the plant roots, which may in turn lead to improvements in soil and plant health. The results of this study provide foundations and a methodology for using metatranscriptomic approaches to investigate the impacts of biochar or other soil amendments in different crops, varying soil types, and with greater experimental complexity. The findings of such investigations will inform the development of biochar-based soil amendment strategies to enhance soil fertility and crop health in a wide range of production systems.
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Claims 8
Claim · model-written summary
Biochar did not affect tomato shoot biomass.
- Taxon
- tomato
Solanum lycopersicumt0 - Treatment
- Biochar treatmente0
- Outcome
- shoot biomasse0
- Direction
- did not impacte0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Biochar treatment did not impact shoot biomass or fruit production”
t0“Metatranscriptomic analysis of tomato rhizospheres reveals insight into plant-microbiome molecular response to biochar-amended organic soil”
Claim · model-written summary
Biochar did not affect tomato fruit production.
- Taxon
- tomatoSolanum lycopersicumt0
- Treatment
- Biochar treatmente0
- Outcome
- fruit productione0
- Direction
- did not impacte0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Biochar treatment did not impact shoot biomass or fruit production”
t0“Metatranscriptomic analysis of tomato rhizospheres reveals insight into plant-microbiome molecular response to biochar-amended organic soil”
Claim · model-written summary
Tomato rhizosphere gene expression changed over time with biochar treatment.
- Taxon
- tomatoSolanum lycopersicume0
- Treatment
- biochar treatmente0
- Outcome
- gene expression activity of the tomato rhizospheree0
- Direction
- changes over timee0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“the gene expression activity of the tomato rhizosphere changes over time in response to the biochar treatment”
Claim · model-written summary
Several beneficial rhizosphere bacterial families showed increased gene expression with biochar.
- Taxon
- tomatoSolanum lycopersicumt0
- Treatment
- biochart0
- Interactor
- Rhizobiaceae, Pseudomonadaceae, Micromonosporaceae, SphingomonadaceaeMicromonosporaceaeSphingomonadaceaeRhizobiaceaePseudomonadaceaee0symbiont
- Outcome
- gene expressione0
- Direction
- increasede0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“a number of bacteria with known benefits to soil health and plant growth displaying increased gene expression (e.g., Rhizobiaceae, Pseudomonadaceae, Micromonosporaceae, Sphingomonadaceae)”
t0“Metatranscriptomic analysis of tomato rhizospheres reveals insight into plant-microbiome molecular response to biochar-amended organic soil”
Claim · model-written summary
Streptomycetaceae had the highest expression in the tomato rhizosphere.
- Taxon
- tomatoSolanum lycopersicumt0
- Interactor
- StreptomycetaceaeStreptomycetaceaee0symbiont
- Outcome
- Streptomycetaceae were expressede0
- Direction
- highest levelse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Streptomycetaceae were expressed at the highest levels in the rhizosphere.”
t0“Metatranscriptomic analysis of tomato rhizospheres reveals insight into plant-microbiome molecular response to biochar-amended organic soil”
Claim · model-written summary
Biochar appeared to attenuate Streptomycetaceae expression by the end of the study.
- Taxon
- tomatoSolanum lycopersicumt0
- Treatment
- Biochare0
- Interactor
- StreptomycetaceaeStreptomycetaceaee1symbionte0
- Outcome
- expression of this bacteriae0
- Direction
- attenuatee0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Biochar seemed to attenuate the expression of this bacteria by the end of the time course”
t0“Metatranscriptomic analysis of tomato rhizospheres reveals insight into plant-microbiome molecular response to biochar-amended organic soil”
e1“Streptomycetaceae were expressed at the highest levels in the rhizosphere.”
Claim · model-written summary
Pathogenic fungi showed generally lower expression in biochar-amended rhizospheres than controls.
- Taxon
- tomatoSolanum lycopersicumt0
- Treatment
- biochar-amended rhizospheree0
- Interactor
- pathogenic fungie0pathogen
- Outcome
- pathogenic fungi in the soil displayed generally reduced expressione0
- Direction
- reducede0
- Comparator
- the controle0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“pathogenic fungi in the soil displayed generally reduced expression in the biochar-amended rhizosphere in comparison with the control”
t0“Metatranscriptomic analysis of tomato rhizospheres reveals insight into plant-microbiome molecular response to biochar-amended organic soil”
Claim · model-written summary
Tomato roots under biochar treatment were enriched for nitrogen metabolism, metabolic regulation and organic-compound production genes.
- Taxon
- tomatoSolanum lycopersicume0
- Treatment
- biochar treated rhizospheree0
- Outcome
- functional enrichment of genes associated with nitrogen metabolic processes, regulation of metabolic processes, and production of organic compoundse0
- Direction
- enrichmente0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“tomato roots revealed functional enrichment of genes associated with nitrogen metabolic processes, regulation of metabolic processes, and production of organic compounds in the biochar treated rhizosphere”
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