From field sampling to pneumatic bioreactor mycelia production of the ectomycorrhizal mushroom Laccaria trichodermophora

Ángeles-Argáiz, Rodolfo Enrique; Carmona-Reyes, Ilse A.; Quintero‐Corrales, Christian; Medina-Macías, Francisco J.; Blancas-Cabrera, Abel; Valdez‐Cruz, Norma A.; Ulloa, Miguel; Trujillo‐Roldán, Mauricio A.; Garibay‐Orijel, Roberto

doi:10.1016/j.funbio.2020.02.003

Cited by 6 publications

(6 citation statements)

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“…L. trichodermophora was selected due to its cultural and biotechnological importance [27][28][29][30]. This species is a close relative of Laccaria bicolor (Maire) Orton 1960, the genome of which was the first of a mycorrhizal fungus sequenced by cloning in plasmids and fosmids from the monokaryon strain S238N-H82 [31].…”

Section: Strain Origin and Derivationmentioning

confidence: 99%

“…A second genome from Laccaria, that of Laccaria amethystina LaAM-08-1, was obtained with paired-end second-generation sequencing technology, also from a monokaryotic strain [34]. L. bicolor and L. amethystina are host generalists and widely distributed; in contrast, L. trichodermophora is restricted to Northern and Central America, and has a strong preference for pine hosts [27,[35][36][37][38][39][40][41][42][43][44]. However, it can shift hosts when outside of its natural distribution [45][46][47].…”

Section: Strain Origin and Derivationmentioning

confidence: 99%

“…We used previously generated population genomics, and phenotype data for strain selection (Table 1). Ángeles-Argáiz et al [27] reported the field sampling and strain isolation from dikaryotic basidiomata of several L. trichodermophora samples and their culture kinetics. Furthermore, Quintero-Corrales et al [43] found that the genetic diversity and structure in L. trichodermophora populations across the Transmexican Volcanic Belt was determined by geographical distance.…”

Section: Strain Origin and Derivationmentioning

confidence: 99%

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Assembly collapsing versus heterozygosity oversizing: detection of homokaryotic and heterokaryotic Laccaria trichodermophora strains by hybrid genome assembly

Ángeles-Argáiz,

Aguirre-Beltrán,

Hernández-Oaxaca

et al. 2024

Microbial Genomics

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Genome assembly and annotation using short-paired reads is challenging for eukaryotic organisms due to their large size, variable ploidy and large number of repetitive elements. However, the use of single-molecule long reads improves assembly quality (completeness and contiguity), but haplotype duplications still pose assembly challenges. To address the effect of read length on genome assembly quality, gene prediction and annotation, we compared genome assemblers and sequencing technologies with four strains of the ectomycorrhizal fungus Laccaria trichodermophora. By analysing the predicted repertoire of carbohydrate enzymes, we investigated the effects of assembly quality on functional inferences. Libraries were generated using three different sequencing platforms (Illumina Next-Seq, Mi-Seq and PacBio Sequel), and genomes were assembled using single and hybrid assemblies/libraries. Long reads or hybrid assemby resolved the collapsing of repeated regions, but the nuclear heterozygous versions remained unresolved. In dikaryotic fungi, each cell includes two nuclei and each nucleus has differences not only in allelic gene version but also in gene composition and synteny. These heterokaryotic cells produce fragmentation and size overestimation of the genome assembly of each nucleus. Hybrid assembly revealed a wider functional diversity of genomes. Here, several predicted oxidizing activities on glycosyl residues of oligosaccharides and several chitooligosaccharide acetylase activities would have passed unnoticed in short-read assemblies. Also, the size and fragmentation of the genome assembly, in combination with heterozygosity analysis, allowed us to distinguish homokaryotic and heterokaryotic strains isolated from L. trichodermophora fruit bodies.

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Section: Strain Origin and Derivationmentioning

confidence: 99%

Section: Strain Origin and Derivationmentioning

confidence: 99%

Section: Strain Origin and Derivationmentioning

confidence: 99%

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Assembly collapsing versus heterozygosity oversizing: detection of homokaryotic and heterokaryotic Laccaria trichodermophora strains by hybrid genome assembly

Ángeles-Argáiz,

Aguirre-Beltrán,

Hernández-Oaxaca

et al. 2024

Microbial Genomics

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“…The pneumatic bioreactor was a bubble column bioreactor (BCB) designed in-house with a working volume of 5.0 L (using YEG culture medium, initial pH 6.8) and a nominal volume of 6.6 L, in Pyrex glass with stainless-steel top and bottom (Ángeles-Argáiz et al, 2020). In order to evaluate the effect of k L a on the scale-up process in the BCB the airflow was constantly maintained during each culture, and 0.1, 0.3, and 1.0 volume of air per volume of culture medium (vvm) (0.5, 1.5, and 5.0 standard air liters per minute, L min −1 [slpm]) were evaluated.…”

Section: Submerged Cultures In Shake Flasks and Pneumatic Bioreactormentioning

confidence: 99%

Roles of culture media and oxygen transfer in the scale-up from shake flasks to pneumatic bioreactor of the plant growth-promoting bacterium Rhizobium phaseoli

García-Cabrera¹,

Valdez‐Cruz²,

Daniel-Vázquez³

et al. 2021

RMIQ

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“…Various regions of the Peruvian highlands are suitable for afforestation; however, in the definitive field, pine plants have a mortality rate that exceeds 50% [5]; mainly due to the fact that seedlings from nurseries or greenhouses do not have adequate quality for their survival [6]. The adequate humidity affects the different plantations from the germination of the seeds, as is the case of the pine species, which is evidenced in the study carried out by Sevik et al [7] where they found that most pine species are susceptible to water stress below -6 bar, reducing their germination to 30% of the control group.…”

Section: Introductionmentioning

confidence: 99%

Evaluation of the Control of Environmental Variables in a Pine Seedling Greenhouse

Carbajal-Morán¹,

Camarena²,

Galván-Maldonado³

et al. 2023

Pol. J. Environ. Stud.

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The objective of the research was to evaluate the control of environmental variables that allows obtaining a favorable environment inside a greenhouse for the development of Pinus radiata seedlings. A controller was implemented inside the greenhouse to maintain the variables in preset ranges: temperature from 19.0ºC to 25.0ºC; soil humidity from 50% to 100%; ambient humidity from 70% to 90% and illumination at levels greater than 450 lux. The control algorithm was implemented in the PIC 18F4550 microcontroller, as control actuators were used: a fan-exhaust fan and air heater for temperature; solenoid valves for soil and ambient humidity; LED lamps for illumination. As a result, the environmental variables controller, when tested for 24 hours for 10 days, maintained on average: temperature at 21.54ºC; soil humidity at 75.09%; relative humidity at 79.32% and illumination in the absence of sunlight at 451.62 lux. Likewise, it was found that the DQI of Pinus radiata seedlings of the average control group was 0.433 and the experimental group had an average DQI of 0.571; when evaluating the normalized DQI for both groups, a significant difference greater than 5% was obtained, with the t-test for two-tailed independent samples, with the p-value = 0.002, which is less than the significance level alpha = 0.05. Therefore, it is concluded that the controller generated a favorable environment for the development of the Pinus radiata seedlings of the experimental group, having a high possibility of survival when transferred to the final field.

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From field sampling to pneumatic bioreactor mycelia production of the ectomycorrhizal mushroom Laccaria trichodermophora

Cited by 6 publications

References 69 publications

Assembly collapsing versus heterozygosity oversizing: detection of homokaryotic and heterokaryotic Laccaria trichodermophora strains by hybrid genome assembly

Assembly collapsing versus heterozygosity oversizing: detection of homokaryotic and heterokaryotic Laccaria trichodermophora strains by hybrid genome assembly

Roles of culture media and oxygen transfer in the scale-up from shake flasks to pneumatic bioreactor of the plant growth-promoting bacterium Rhizobium phaseoli

Evaluation of the Control of Environmental Variables in a Pine Seedling Greenhouse

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