Quantitative PCR for measuring biomass of decomposer fungi in planta

Song, Zewei; Vail, Andrew; Sadowsky, Michael J.; Schilling, Jonathan S.

doi:10.1016/j.funeco.2013.12.004

Cited by 29 publications

(18 citation statements)

References 39 publications

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“…Nevertheless, since proportions of extracted gDNA from a mixed sample do not correspond necessarily to proportions of mixed biomass, results might be biased. On the other hand, there are other authors that have established methods for quantifying specific biomass based on DNA data correction with extraction yield values (Jonkers et al 2012, Song et al 2014, and even correction for substrate interference on these yields (Daly et al 2017). Here, we present a corrected method that accounts not only for inherent differences between species-specific gDNA extraction yields, but also for natural changes in mycelial composition through time, such as melanin deposition and cell wall hardening (Karakousis et al 2006), or secretion of stress-related pigments as a result of mixed culture.…”

Section: Resultsmentioning

confidence: 99%

A simple and accurate method for specific quantification of biomass in mixed cultures of filamentous fungi by quantitative PCR

et al. 2020

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Production of lignocellulolytic enzymes by filamentous fungi have a great potential at industrial level due to their widespread applications. Mixed fungal cultures and particularly mixed fungal biofilms constitute a promising fermentation system for an enhanced enzyme production. However, it has not been addressed how much of this enhancement depends on the mixed biomass proportion. In this sense, the aim of this study was to develop a method to specifically and accurately quantify mixed fungal biomass. For this purpose, mixed biofilm cultures composed of Aspergillus niger and Trichoderma reesei, two filamentous fungi used industrially for cellulase production, were collected from 48 to 120 h of growth; mycelia were pulverized, and DNA was extracted for qPCR assays with specific primers for each fungus. Primers were designed from non-conserved regions of sequences of actin and β-tubulin genes of both A. niger and T. reesei. Specificity of these primers was tested in silico and experimentally. A statistically significant correlation was obtained between qPCR-calculated biomass and dry weight biomass data. By this method, it was possible to detect changes on mycelia proportions in biofilms over time, suggesting a competitive interaction between these two fungi. In conclusion, this method allows a specific and accurate quantification of mixed fungal biomass and could be also applied to different mixed culture systems for studying microbial interactions.

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Section: Resultsmentioning

confidence: 99%

A simple and accurate method for specific quantification of biomass in mixed cultures of filamentous fungi by quantitative PCR

et al. 2020

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“…In recent studies, Song et al (2014) and Wallander et al (2013) identified two main limitations to this method: poor reproducibility in nucleic acid extraction and variation of the conversion factors used to convert genomic DNA quantities to mycelium dry weight between strains. In this study, we optimized fungal cell wall breakage before genomic DNA extraction and determined for each strain the conversion factors necessary to the conversion of genomic DNA quantity to mycelium dry weight.…”

Section: Accepted Manuscriptmentioning

confidence: 99%

“…However, in SSF, quantifying the fungal biomass is a challenge due to partial or complete adhesion of the mycelium to the solid substrate (Steudler and Bley, 2015;Wallander et al, 2013). One limitation of current biomarkers (chitin, ergosterol or phospholipid-derived fatty acids) used to determine fungal biomass is that they rely on conversion factors that vary within a single species due to environmental growth conditions or ageing (Pilgard et al, 2011;Song et al, 2014). In this study, we used the quantification of fungal genomic DNA to assess the fungal biomass during SSF.…”

Section: Introductionmentioning

confidence: 99%

A PCR-based method to quantify fungal growth during pretreatment of lignocellulosic biomass

Zhou

Grisel

Isabelle

et al. 2015

Journal of Microbiological Methods

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“…Traditional methods for identifying wood fungi include isolation of fungi from degrading building timbers and identification of fungal species based on culture characteristics. Several molecular methods based on DNA analyses have been used to provide efficient, sensitive, and rapid diagnostic tools for the detection and identification of wood decay fungi without requiring a prior fungal isolation step [9][10][11][12].…”

Section: Introductionmentioning

confidence: 99%

Analysis of fungal diversity of the rotten wooden pillars of a historic building

Ma¹,

Zhang²,

Liu³

2020

Preprint

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High-throughput sequencing technology was used to analyze the fungal community structure and its association with the cause of decay on the wooden pillars of an ancient archway in Beijing. The dominant fungi on the rotten pillars belonged to Ascomycetes regardless of the sampling position. Compared with the fungal community composition of discolored wood previously studied, the proportion of Basidiomycetes in rotten wood pillars increased at the highest value of 37.9%. High-throughput sequencing showed that the main fungi in the first pillar were Ascomycetes ( Phoma , Lecythophora , and Scedosporium ) and Basidiomycetes (Sporidiobolales). Ascomycetes Lecythophora and Basidiomycetes Cryptcoccus and Postia were the main fungi in pillar 2. Phoma , Trichoderma, and Entoloma were isolated from pillar 1, whereas Alternaria and Phaeosphaeriaceae were obtained from pillar 2 using culture isolation. Traditional isolation failed to obtain all dominant fungi. The importance of high-throughput sequencing technology in ancient wooden structure building biodeterioration analysis was further explained. At the three sampling sites, the contact-ground fungal community composition was similar to that of in-ground wood, whereas above-ground fungal community composition was significantly different from the other two sites. The high moisture content of the wood caused decay. The bottom of the pillar was immersed in groundwater, whereas that cement coating prevents the evaporation of water,cause the wood moisture content to be high. By comparing the fungal diversities of decaying wood and discolored and dry, decayed wood, the relative content of Basidiomycetes may be used as an indicator of wood decay state.

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Quantitative PCR for measuring biomass of decomposer fungi in planta

Cited by 29 publications

References 39 publications

A simple and accurate method for specific quantification of biomass in mixed cultures of filamentous fungi by quantitative PCR

A simple and accurate method for specific quantification of biomass in mixed cultures of filamentous fungi by quantitative PCR

A PCR-based method to quantify fungal growth during pretreatment of lignocellulosic biomass

Analysis of fungal diversity of the rotten wooden pillars of a historic building

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