BioQuery-ASP: querying biomedical databases and ontologies using answer set programming

Erdem, Esra; Öztok, Umut

doi:10.14806/ej.18.b.551

Cited by 5 publications

(3 citation statements)

References 81 publications

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“…The CCS reads were processed with DADA2 software packages (16S rRNA gene and ITS specific workflow) (version 1.8) [ 58 ], and analyzed with phyloseq for alpha and beta diversity (version 1.25.2) [ 59 ]. For 16s rRNA gene CCS data, the DADA2 workflow follows primer trimming, quality filtering, and de-replication.…”

Section: Methodsmentioning

confidence: 99%

Influence of Tall Fescue Epichloë Endophytes on Rhizosphere Soil Microbiome

et al. 2021

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Tall fescue (Lolium arundinaceum (Schreb.) S.J. Darbyshire) often forms a symbiotic relationship with fungal endophytes (Epichloë coenophiala), which provides increased plant performance and greater tolerance to environmental stress compared to endophyte-free tall fescue. Whether this enhanced performance of tall fescue exclusively results from the grass–fungus symbiosis, or this symbiosis additionally results in the recruitment of soil microbes in the rhizosphere that in turn promote plant growth, remain a question. We investigated the soil bacterial and fungal community composition in iron-rich soil in the southeastern USA, and possible community shifts in soil microbial populations based on endophyte infection in tall fescue by analyzing the 16s rRNA gene and ITS specific region. Our data revealed that plant-available phosphorus (P) was significantly (p < 0.05) influenced by endophyte infection in tall fescue. While the prominent soil bacterial phyla were similar, a clear fungal community shift was observed between endophyte-infected (E+) and endophyte-free (E−) tall fescue soil at the phylum level. Moreover, compared to E− soil, E+ soil showed a greater fungal diversity at the genus level. Our results, thus, indicate a possible three-way interaction between tall fescue, fungal endophyte, and soil fungal communities resulting in improved tall fescue performance.

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Section: Methodsmentioning

confidence: 99%

Influence of Tall Fescue Epichloë Endophytes on Rhizosphere Soil Microbiome

et al. 2021

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“…For the fungal data analysis, we followed the ITS-speci c variation of the DADA2 package. In the fungal DADA2 work ow, after orienting the primers, we used a specialized primer/adapter removal tool "cutadapt" [53]. After primer removal, the steps are quality ltering, dereplication, inferring ASVs after error learning, and nally removing chimeras.…”

Section: Discussionmentioning

confidence: 99%

Influence of Tall Fescue Epichloë endophytes on Rhizosphere Soil Microbiome

Mahmud

Lee

Hill

et al. 2021

Preprint

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Background Tall fescue (Lolium arundinaceum (Schreb.) S.J. Darbyshire) is a popular perennial grass species for livestock production and amenities in the United States. Tall fescue often forms a symbiotic relationship with fungal endophytes (Epichloë coenophiala) which provides increased plant tolerance to environmental stress compared to endophyte-free plants. However, whether this improved plant performance is the sole result of the unique relationship between the grass and the shoot-dwelling fungal endophyte of rhizosphere origin remains a question. This symbiosis possibly regulates the recruitment of beneficial soil microbial communities in endophyte-infected tall fescue rhizosphere and may offer enhanced nutrients and water acquisition, thereby, providing the plant with an increased tolerance level against environmental stresses. We compared the soil bacterial and fungal community composition and investigated possible community shifts in soil microbial populations based on endophyte infection in tall fescue by analyzing the 16s rRNA gene and ITS specific region. Results Our data revealed that bacterial community richness and the evenness indicated by Shannon Diversity Index (SDI) was greater than 4 in both endophyte-infected and endophyte-free tall fescue soil. In both types tall fescue soil, the prominent bacterial families were Planctomycetaceae, Balstocatellaceae_(subgroup_4), Chitinophagaceae, and Bacillaceae. In the case of soil fungal diversity, the SDI was overall low and ranged between 1.21 for endophyte-free and 1.27 for endophyte-infected tall fescue soil. The prominent fungal phyla were Basidiomycota and Ascomycota, and we observed a clear fungal community difference between endophyte-infected and endophyte-free soil at the phylum level. Moreover, endophyte-infected tall fescue soil showed a greater diversity at the genus level compared to endophyte-free tall fescue soil. In addition, plant-available soil phosphorus (P) is also influenced by the presence of endophytes in tall fescue. Conclusion Our results indicate that there is a tripartite relationship between tall fescue, the presence of fungal endophyte in the tall fescue, and the below-ground soil fungal communities. The dynamic of this three-way interaction perhaps contributes to the nutrient acquisition and stress tolerance by tall fescue possibly by recruiting a diverse array of potentially beneficial soil microbes.

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“…The libraries were denatured using Denature and Dilute Libraries for HiSeq Clustering protocol and sequenced in Rapid Run mode by Genotek (Russia) using Illumina HiSeq 2500 (Illumina, USA) at a read length of 150 paired-end bp. Adaptors and nucleotides with a Phred score <30 were removed using Cutadapt v2.10 (error-rate = 0.1). Clean reads were mapped to the genome of R. rhodochrous M8 (GCF_001890475.2 in RefSeq database) using BWA-MEM v 0.7.17 (− k = 30).…”

Section: Methodsmentioning

confidence: 99%

A Set of Active Promoters with Different Activity Profiles for Superexpressing Rhodococcus Strain

et al. 2021

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Rhodococcus bacteria are a promising platform for biodegradation, biocatalysis, and biosynthesis, but the use of rhodococci is hampered by the insufficient number of both platform strains for expression and promoters that are functional and thoroughly studied in these strains. To expand the list of such strains and promoters, we studied the expression capability of the Rhodococcus rhodochrous M33 strain, and the functioning of a set of recombinant promoters in it. We showed that the strain supports superexpression of the target enzyme (nitrile hydratase) using alternative inexpensive feedingsacetate and ureawithout growth factor supplementation, thus being a suitable expression platform. The promoter set included P tuf (elongation factor Tu) and P sod (superoxide dismutase) from Corynebacterium glutamicum ATCC13032, P cpi (isocitrate lyase) from Rhodococcus erythropolis PR4, and P nh (nitrile hydratase) from R. rhodochrous M8. Activity levels, regulation possibilities, and growth-phase-dependent activity profiles of these promoters were studied in derivatives of the M33 strain. The activities of the promoters were significantly different (P cpi < P sod ≪ P tuf < P nh ), covering 10 3 -fold range, and the most active P nh and P tuf produced up to a 30−50% portion of target protein in soluble intracellular proteins. On the basis of the mRNA quantification and amount of target protein, the production level of P nh was positioned close to the theoretical upper limit of expression in a bacterial cell. A selection method for the laboratory evolution of such active promoters directly in Rhodococcus was also proposed. Concerning regulation, P tuf could not be regulated (2-fold change), while others were tunable (6-fold for P sod , 79-fold for P nh , and 44-fold for P cpi ). The promoters possessed four different activity profiles, including three with peak of activity at different growth phases and one with constant activity throughout the growth phases. P tuf and P cpi did not change their activity profile under different growth conditions, whereas the P sod and P nh profiles changed depending on the growth media. The results allow flexible construction of Rhodococcus strains using the studied promoters, and demonstrate a valuable approach for complex characterization of promoters intended for biotechnological strain construction.

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BioQuery-ASP: querying biomedical databases and ontologies using answer set programming

Cited by 5 publications

References 81 publications

Influence of Tall Fescue Epichloë Endophytes on Rhizosphere Soil Microbiome

Influence of Tall Fescue Epichloë Endophytes on Rhizosphere Soil Microbiome

Influence of Tall Fescue Epichloë endophytes on Rhizosphere Soil Microbiome

A Set of Active Promoters with Different Activity Profiles for Superexpressing Rhodococcus Strain

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