HyphaTracker: An ImageJ toolbox for time-resolved analysis of spore germination in filamentous fungi

Brunk, Michael G. K.; Sputh, Sebastian; Doose, Sören; Linde, Sebastian van de; Terpitz, Ulrich

doi:10.1038/s41598-017-19103-1

Cited by 32 publications

(30 citation statements)

References 62 publications

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“…The financial and human resources needed to conduct detailed fungal growth analyses prevent the replication of experiments, such that the natural variability of fungal growth is often neglected. In addition, most relevant studies on detailed fungal growth dynamics often focus on small areas (Ramakrishna et al 1993;Gougouli and Koutsoumanis 2013;van Laarhoven et al 2015;Siripatrawan and Makino 2015) or the germination phase (Brunk et al 2018), tracking growth of a few hyphae whose dynamics fail to represent the entire mycelium. Even though several studies compare the effect of environmental conditions on fungal growth over a certain period of time (Etheridge 1957; Magan and Lacey 1984;Pasanen et al 1991;Nielsen et al 2004), no elaborate time series analysis is performed to underpin the comparison.…”

Section: Introductionmentioning

confidence: 99%

Analysis of spatio-temporal fungal growth dynamics under different environmental conditions

et al. 2019

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Traditionally, fungal growth dynamics were assessed manually, limiting the research to a few environmental conditions and/or fungal species. Fortunately, more automated ways of measurement are gaining momentum due to the availability of cheap imaging and processing equipment and the development of dedicated image analysis algorithms. In this paper, we use image analysis to assess the impact of environmental conditions on the growth dynamics of two economically important fungal species, Coniophora puteana and Rhizoctonia solani. Sixteen environmental conditions combining four temperatures (15, 20, 25 and 30°C) and four relative humidity (RH) conditions (65, 70, 75 and 80% RH) were tested. Fungal growth characteristics were extracted from images of the growing fungi, taken at regular points in time. Advanced time series analysis was applied to quantitatively compare the effect of the environmental conditions on these growth characteristics. The evolution of the mycelial area and the number of tips over time resulted in typical sigmoidal growth curves. Other growth characteristics such as the mean hyphal segment length did not vary significantly over time. Temperature and RH usually had a combined effect on the growth dynamics of the mycelial area and the number of tips. When defining optimal growth conditions for a fungus, it is therefore of primordial importance that the effect of temperature and RH is assessed simultaneously. At the most extreme conditions we tested, the mycelium most probably experienced water stress when developing over the inert Petri dish surface. An RH of 65% (independent of temperature) for C. puteana and a temperature of 30°C (independent of RH) for both C. puteana and R. solani therefore always resulted in limited fungal growth, while the optimal growing conditions were at 20°C and 75% RH and at 25°C and 80% RH for R. solani and at 20°C and 75% RH for C. puteana. The method applied in this study offers an updated and broader alternative to classical and narrowly focused studies on fungal growth dynamics, and is well suited to efficiently assess the effect of environmental conditions on fungal growth.

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Section: Introductionmentioning

confidence: 99%

Analysis of spatio-temporal fungal growth dynamics under different environmental conditions

et al. 2019

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“…F. fujikuroi possesses two genes coding for rhodopsins, carO and opsA [ 14 , 23 ]. The carO gene is linked to and co-regulated with genes coding for enzymes for retinal synthesis, whose expression is strongly induced by light, and the CarO protein is an effective proton pump highly expressed in light-exposed conidia, where it slows down their germination [ 8 , 24 ]. On the other hand, the opsA gene is only moderately upregulated by light, and the function of the OpsA rhodopsin is not known.…”

Section: Introductionmentioning

confidence: 99%

Protein Activity of the Fusarium fujikuroi Rhodopsins CarO and OpsA and Their Relation to Fungus–Plant Interaction

Adam

Deimel

Pardo-Medina

et al. 2018

IJMS

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Fungi possess diverse photosensory proteins that allow them to perceive different light wavelengths and to adapt to changing light conditions in their environment. The biological and physiological roles of the green light-sensing rhodopsins in fungi are not yet resolved. The rice plant pathogen Fusarium fujikuroi exhibits two different rhodopsins, CarO and OpsA. CarO was previously characterized as a light-driven proton pump. We further analyzed the pumping behavior of CarO by patch-clamp experiments. Our data show that CarO pumping activity is strongly augmented in the presence of the plant hormone indole-3-acetic acid and in sodium acetate, in a dose-dependent manner under slightly acidic conditions. By contrast, under these and other tested conditions, the Neurospora rhodopsin (NR)-like rhodopsin OpsA did not exhibit any pump activity. Basic local alignment search tool (BLAST) searches in the genomes of ascomycetes revealed the occurrence of rhodopsin-encoding genes mainly in phyto-associated or phytopathogenic fungi, suggesting a possible correlation of the presence of rhodopsins with fungal ecology. In accordance, rice plants infected with a CarO-deficient F. fujikuroi strain showed more severe bakanae symptoms than the reference strain, indicating a potential role of the CarO rhodopsin in the regulation of plant infection by this fungus.

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“…For example, P. anserina, as other fungal species, can express fluorescent proteins that may give access to a three-dimensional imaging of fungal networks in standardized agar media or in opaque structures 16,25 . It may be also coupled with (i) a specific tracking of selected hyphae, as previously described 14,26 , (ii) the study of local behaviors within the thallus, for instance the comparison between the growth front and the central region of the network, and (iii) the global measurement of fungal growth at a macroscale level. Altogether, these observations should give access to a large amount of data allowing the quantitative analysis of fungal growth dynamics and may then be used to develop robust and versatile mathematical models.…”

Section: Discussionmentioning

confidence: 99%

Hyphal network whole field imaging allows for accurate estimation of anastomosis rates and branching dynamics of the filamentous fungus Podospora anserina

Dikec

Olivier

Bobee

et al. 2020

Sci Rep

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The success of filamentous fungi in colonizing most natural environments can be largely attributed to their ability to form an expanding interconnected network, the mycelium, or thallus, constituted by a collection of hyphal apexes in motion producing hyphae and subject to branching and fusion. In this work, we characterize the hyphal network expansion and the structure of the fungus Podospora anserina under controlled culture conditions. To this end, temporal series of pictures of the network dynamics are produced, starting from germinating ascospores and ending when the network reaches a few centimeters width, with a typical image resolution of several micrometers. The completely automated image reconstruction steps allow an easy post-processing and a quantitative analysis of the dynamics. The main features of the evolution of the hyphal network, such as the total length L of the mycelium, the number of "nodes" (or crossing points) N and the number of apexes A, can then be precisely quantified. Beyond these main features, the determination of the distribution of the intrathallus surfaces (S i ) and the statistical analysis of some local measures of N, A and L give new insights on the dynamics of expanding fungal networks. Based on these results, we now aim at developing robust and versatile discrete/continuous mathematical models to further understand the key mechanisms driving the development of the fungus thallus.Due to their paramount role in most ecosystems and in different sectors of human economy, filamentous fungi have attracted a lot of attention in the last decades. Indeed, these organisms are able to grow in complex environments, leading to their ubiquitous occurrence 1,2 . The success of filamentous fungi in colonizing most natural environments can be largely attributed to their ability to form hyphae, whose width typically ranges from 2 to 20 µm, and which are usually composed of multiple cells separated by septa 3 . At the edge of the fungal colony, apical cells explore new territories in search for food and are mainly involved in nutrient acquisition through the production of extracellular enzymes for the decomposition of organic matter, as well as through the sensing of their local environment 4 . Sub-apical cells generate new hyphae by lateral branching, thus increasing the density and surface area of the colony. In ascomycetes and basidiomycetes, the branches also mediate the hyphal fusion events, or anastomosis, that occur in the thallus and appear to be crucial for the exchange of nutrients and signals

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HyphaTracker: An ImageJ toolbox for time-resolved analysis of spore germination in filamentous fungi

Cited by 32 publications

References 62 publications

Analysis of spatio-temporal fungal growth dynamics under different environmental conditions

Analysis of spatio-temporal fungal growth dynamics under different environmental conditions

Protein Activity of the Fusarium fujikuroi Rhodopsins CarO and OpsA and Their Relation to Fungus–Plant Interaction

Hyphal network whole field imaging allows for accurate estimation of anastomosis rates and branching dynamics of the filamentous fungus Podospora anserina

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