Characterization of Fungal Morphology using Digital Image Analysis Techniques

Abstract

The use of filamentous fungi for the production of commercially important products is old but keeps increasing during the last decades. New classes of compounds are being added in the list of products of fungal fermentations as a result of progress in methodologies and applications of biotechnology. Fungi are morphologically complex organisms that differ in structure throughout their life cycle. In submerged fermentation fungal morphology may take distinct forms ranging from dispersed filaments to densely interwoven masses of mycelium known as pellets. Each morphological form has each own characteristics that have a critical impact on the overall process outcome. Dispersed growth results in highly viscous broths with pseudoplastic behavior that have a negative impact on mass and energy transfer rates resulting in higher energy input requirements. Due to the high industrial relevance of fungal morphology there has been a substantial development of tools and techniques to characterize morphology and extract quantitative information that can be used in process control and optimization studies. Digital image analysis is the state of the art method to characterize and quantify fungal morphology in the developmental process from spores to filamentous structures to pellets. The progress made in the area since the 1990s, when the first image analysis methods were reported, is discussed in detail throughout the review.

Warming weakens facilitative interactions between decomposers and detritivores, and modifies freshwater ecosystem functioning

“…T A B L E 2 Permutational multivariate analysis of variance (PERMANOVA) comparing the difference in bacterial community structure (DGGE band profiles) between temperature (ambient and warmed), treatment of organisms (control, "bacteria," "bacteria + macroinvertebrates"), and interaction between temperature and organisms. 2014;Inselsbacher et al, 2007), conditioning organic matter (Gessner et al, 2010;Webster & Benfield, 1986), and facilitating digestion in the intestines of many animals (Canhoto & Grac ßa, 2006;Wolf, Zwick, & Marxsen, 1997). Although the opposite, i.e., detritivores facilitating bacteria, might be common in nature, few studies have investigated such mechanism (Harris, 1993;Hoekman, Winston, & Mitchell, 2009;Treplin & Zimmer, 2012).…”

“…The degree of hyphal branching and the number of tips are morphological characters that correlate positively with the number of cells and biomass of fungi [more details in Barry (); Cox et al. (); Papagianni ()]. We established four levels of fungi biomass based on Barry (), which are as follows: (1) absent—with no fungus on the sample, (2) low—freely dispersed fungi with at least five hyphal ramification points (Figure S8a), (3) moderate—mycelial clumps with more than five ramification points (Figure S8b), and (4) high—presence of pellets which comprises of a dense mycelium with uncountable ramification points and hyphal overlap (Figure S8c).…”

“…Our fungi samples were mostly constituted by filamentous fungi (Figure S8). We estimated fungi biomass through image analysis of hyphal branching (number of hyphal ramifications) and number of tips(Barry, Chan, & Williams, 2009;Cox, Paul, & Thomas, 1998;Papagianni, 2014). The degree of hyphal branching and the number of tips are morphological characters that correlate positively with the number of cells and biomass of fungi [more details in Barry (2010); Cox et al (1998); Papagianni…”

Fungal Feature Tracker (FFT): A tool for quantitatively characterizing the morphology and growth of filamentous fungi

“…Fortunately, fungi grow at a spatial and time scale that can be easily captured using basic imaging devices. Thus, together with the increasing availability of new technologies, this feature has resulted in the development of image analysis techniques to characterize different aspects of fungal biology (19), including programs to characterize germination of fungal spores (20), differentiation of aerial spore types (21), and measurement of the area of fungal cultures (22). However, these tools are often developed for very specific experimental setups and require prior image analysis or programming experience, limiting their accessibility to fungal biologists.…”

SParticle, an algorithm for the analysis of filamentous microorganisms in submerged cultures

“…Sufficient resolution is required to allow reliable image analysis, but higher magnification limits the number of particles that can be captured (Barry and Williams 2011;Papagianni 2014;Hardy 2017). Various methods have been tried to increase the sample size in image analysis methods (Cox and Thomas 1992;Packer and Thomas 1990).…”