Integrated metagenomics and metatranscriptomics analyses of root-associated soil from transgenic switchgrass.
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ABSTRACT:
SUBMITTER: Chauhan A
PROVIDER: S-EPMC4132618 | biostudies-literature | 2014 Aug
REPOSITORIES: biostudies-literature
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Project description:BackgroundSamples collected from CF patient airways often contain large amounts of host-derived nucleic acids that interfere with recovery and purification of microbial and viral nucleic acids. This study describes metagenomic and metatranscriptomic methods that address these issues.MethodsMicrobial and viral metagenomes, and microbial metatranscriptomes, were successfully prepared from sputum samples from five adult CF patients.ResultsContaminating host DNA was dramatically reduced in the metagenomes. Each CF patient presented a unique microbiome; in some Pseudomonas aeruginosa was replaced by other opportunistic bacteria. Even though the taxonomic composition of the microbiomes is very different, the metabolic potentials encoded by the community are very similar. The viral communities were dominated by phages that infect major CF pathogens. The metatranscriptomes reveal differential expression of encoded metabolic potential with changing health status.ConclusionsMicrobial and viral metagenomics combined with microbial transcriptomics characterize the dynamic polymicrobial communities found in CF airways, revealing both the taxa present and their current metabolic activities. These approaches can facilitate the development of individualized treatment plans and novel therapeutic approaches.
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Project description:Genetic engineering has been used to decrease the lignin content and to change the lignin composition of switchgrass (Panicum virgatum L.) to decrease cell wall recalcitrance to enable more efficient cellulosic biofuel production. Previous greenhouse and field studies showed that downregulation of the gene encoding switchgrass caffeic acid O-methyltransferase (COMT) and overexpression of the switchgrass PvMYB4 (MYB4) gene effectively improved ethanol yield. To understand potential environmental impacts of cultivating these transgenic bioenergy crops in the field, we quantified the effects of field cultivation of transgenic switchgrass on soil organic carbon (SOC) dynamics. Total and active SOC as well as soil respiration were measured in soils grown with two COMT-downregulated transgenic lines (COMT2 and COMT3), three MYB4-overexpressed transgenic lines (L1, L6, and L8), and their corresponding non-transgenic controls. No differences in total SOC, dissolved organic carbon (DOC), and permanganate oxidizable carbon (POXC) were detected between transgenic and non-transgenic treatments for both COMT (10.4-11.1 g kg-1 for SOC, 60.0-64.8 mg kg-1 for DOC, and 299-384 mg kg-1 for POXC) and MYB4 lines (6.89-8.21 g kg-1 for SOC, 56.0-61.1 mg kg-1 for DOC, and 177-199 mg kg-1 for POXC). Soil CO2-carbon (CO2-C) production from the COMT2 transgenic line was not significantly different from its non-transgenic control. In contrast, the COMT3 transgenic line had greater soil CO2-C production than its non-transgenic control (210 vs. 165 µg g-1) after 72 days of laboratory incubation. Combining the improvement in ethanol yield and biomass production reported in previous studies with negligible change in SOC and soil respiration, COMT2 could be a better biofuel feedstock than COMT3 for environmental conservation and cost-effective biofuel production. On the other hand, MYB4 transgenic line L8 produced more biomass and total ethanol per hectare while it released more CO2-C than the control (253 vs. 207 µg g-1). Long-term in situ monitoring of transgenic switchgrass systems using a suite of soil and environmental variables is needed to determine the sustainability of growing genetically modified bioenergy crops.
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Project description:BackgroundOne method for rejuvenating land polluted with anthropogenic contaminants is through phytoremediation, the reclamation of land through the cultivation of specific crops. The capacity for phytoremediation crops, such as Salix spp., to tolerate and even flourish in contaminated soils relies on a highly complex and predominantly cryptic interacting community of microbial life.MethodsHere, Illumina HiSeq 2500 sequencing and de novo transcriptome assembly were used to observe gene expression in washed Salix purpurea cv. 'Fish Creek' roots from trees pot grown in petroleum hydrocarbon-contaminated or non-contaminated soil. All 189,849 assembled contigs were annotated without a priori assumption as to sequence origin and differential expression was assessed.ResultsThe 839 contigs differentially expressed (DE) and annotated from S. purpurea revealed substantial increases in transcripts encoding abiotic stress response equipment, such as glutathione S-transferases, in roots of contaminated trees as well as the hallmarks of fungal interaction, such as SWEET2 (Sugars Will Eventually Be Exported Transporter). A total of 8252 DE transcripts were fungal in origin, with contamination conditions resulting in a community shift from Ascomycota to Basidiomycota genera. In response to contamination, 1745 Basidiomycota transcripts increased in abundance (the majority uniquely expressed in contaminated soil) including major monosaccharide transporter MST1, primary cell wall and lamella CAZy enzymes, and an ectomycorrhiza-upregulated exo-β-1,3-glucanase (GH5). Additionally, 639 DE polycistronic transcripts from an uncharacterised Enterobacteriaceae species were uniformly in higher abundance in contamination conditions and comprised a wide spectrum of genes cryptic under laboratory conditions but considered putatively involved in eukaryotic interaction, biofilm formation and dioxygenase hydrocarbon degradation.ConclusionsFungal gene expression, representing the majority of contigs assembled, suggests out-competition of white rot Ascomycota genera (dominated by Pyronema), a sometimes ectomycorrhizal (ECM) Ascomycota (Tuber) and ECM Basidiomycota (Hebeloma) by a poorly characterised putative ECM Basidiomycota due to contamination. Root and fungal expression involved transcripts encoding carbohydrate/amino acid (C/N) dialogue whereas bacterial gene expression included the apparatus necessary for biofilm interaction and direct reduction of contamination stress, a potential bacterial currency for a role in tripartite mutualism. Unmistakable within the metatranscriptome is the degree to which the landscape of rhizospheric biology, particularly the important but predominantly uncharacterised fungal genetics, is yet to be discovered.
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