1
|
Ledoux C, Bobée C, Cabet É, David P, Filaine F, Hachimi S, Lalanne C, Ruprich-Robert G, Herbert É, Chapeland-Leclerc F. Characterization of spatio-temporal dynamics of the constrained network of the filamentous fungus Podospora anserina using a geomatics-based approach. PLoS One 2024; 19:e0297816. [PMID: 38319941 PMCID: PMC10846696 DOI: 10.1371/journal.pone.0297816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 01/12/2024] [Indexed: 02/08/2024] Open
Abstract
In their natural environment, fungi are subjected to a wide variety of environmental stresses which they must cope with by constantly adapting the architecture of their growing network. In this work, our objective was to finely characterize the thallus development of the filamentous fungus Podospora anserina subjected to different constraints that are simple to implement in vitro and that can be considered as relevant environmental stresses, such as a nutrient-poor environment or non-optimal temperatures. At the Petri dish scale, the observations showed that the fungal thallus is differentially affected (thallus diameter, mycelium aspect) according to the stresses but these observations remain qualitative. At the hyphal scale, we showed that the extraction of the usual quantities (i.e. apex, node, length) does not allow to distinguish the different thallus under stress, these quantities being globally affected by the application of a stress in comparison with a thallus having grown under optimal conditions. Thanks to an original geomatics-based approach based on the use of automatized Geographic Information System (GIS) tools, we were able to produce maps and metrics characterizing the growth dynamics of the networks and then to highlight some very different dynamics of network densification according to the applied stresses. The fungal thallus is then considered as a map and we are no longer interested in the quantity of material (hyphae) produced but in the empty spaces between the hyphae, the intra-thallus surfaces. This study contributes to a better understanding of how filamentous fungi adapt the growth and densification of their network to potentially adverse environmental changes.
Collapse
Affiliation(s)
- Clara Ledoux
- CNRS, UMR 8236 – LIED, Université Paris Cité, Paris, France
| | - Cécilia Bobée
- CNRS, UMR 8236 – LIED, Université Paris Cité, Paris, France
| | - Éva Cabet
- CNRS, UMR 8236 – LIED, Université Paris Cité, Paris, France
| | - Pascal David
- CNRS, UMR 8236 – LIED, Université Paris Cité, Paris, France
| | | | | | | | | | - Éric Herbert
- CNRS, UMR 8236 – LIED, Université Paris Cité, Paris, France
| | | |
Collapse
|
2
|
Cockx BJR, Foster T, Clegg RJ, Alden K, Arya S, Stekel DJ, Smets BF, Kreft JU. Is it selfish to be filamentous in biofilms? Individual-based modeling links microbial growth strategies with morphology using the new and modular iDynoMiCS 2.0. PLoS Comput Biol 2024; 20:e1011303. [PMID: 38422165 PMCID: PMC10947719 DOI: 10.1371/journal.pcbi.1011303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 03/18/2024] [Accepted: 02/01/2024] [Indexed: 03/02/2024] Open
Abstract
Microbial communities are found in all habitable environments and often occur in assemblages with self-organized spatial structures developing over time. This complexity can only be understood, predicted, and managed by combining experiments with mathematical modeling. Individual-based models are particularly suited if individual heterogeneity, local interactions, and adaptive behavior are of interest. Here we present the completely overhauled software platform, the individual-based Dynamics of Microbial Communities Simulator, iDynoMiCS 2.0, which enables researchers to specify a range of different models without having to program. Key new features and improvements are: (1) Substantially enhanced ease of use (graphical user interface, editor for model specification, unit conversions, data analysis and visualization and more). (2) Increased performance and scalability enabling simulations of up to 10 million agents in 3D biofilms. (3) Kinetics can be specified with any arithmetic function. (4) Agent properties can be assembled from orthogonal modules for pick and mix flexibility. (5) Force-based mechanical interaction framework enabling attractive forces and non-spherical agent morphologies as an alternative to the shoving algorithm. The new iDynoMiCS 2.0 has undergone intensive testing, from unit tests to a suite of increasingly complex numerical tests and the standard Benchmark 3 based on nitrifying biofilms. A second test case was based on the "biofilms promote altruism" study previously implemented in BacSim because competition outcomes are highly sensitive to the developing spatial structures due to positive feedback between cooperative individuals. We extended this case study by adding morphology to find that (i) filamentous bacteria outcompete spherical bacteria regardless of growth strategy and (ii) non-cooperating filaments outcompete cooperating filaments because filaments can escape the stronger competition between themselves. In conclusion, the new substantially improved iDynoMiCS 2.0 joins a growing number of platforms for individual-based modeling of microbial communities with specific advantages and disadvantages that we discuss, giving users a wider choice.
Collapse
Affiliation(s)
- Bastiaan J. R. Cockx
- Department of Environmental and Resource Engineering, Technical University of Demark, DTU Lyngby campus, Kgs. Lyngby, Denmark
| | - Tim Foster
- Centre for Computational Biology & Institute of Microbiology and Infection & School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Robert J. Clegg
- Centre for Computational Biology & Institute of Microbiology and Infection & School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Kieran Alden
- Centre for Computational Biology & Institute of Microbiology and Infection & School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Sankalp Arya
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, United Kingdom
| | - Dov J. Stekel
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, United Kingdom
| | - Barth F. Smets
- Department of Environmental and Resource Engineering, Technical University of Demark, DTU Lyngby campus, Kgs. Lyngby, Denmark
| | - Jan-Ulrich Kreft
- Centre for Computational Biology & Institute of Microbiology and Infection & School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| |
Collapse
|
3
|
Zhang IH, Borer B, Zhao R, Wilbert S, Newman DK, Babbin AR. Uncultivated DPANN archaea are ubiquitous inhabitants of global oxygen deficient zones with diverse metabolic potential. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.30.564641. [PMID: 37961710 PMCID: PMC10634959 DOI: 10.1101/2023.10.30.564641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Archaea belonging to the DPANN superphylum have been found within an expanding number of environments and perform a variety of biogeochemical roles, including contributing to carbon, sulfur, and nitrogen cycling. Generally characterized by ultrasmall cell sizes and reduced genomes, DPANN archaea may form mutualistic, commensal, or parasitic interactions with various archaeal and bacterial hosts, influencing the ecology and functioning of microbial communities. While DPANN archaea reportedly comprise 15-26% of the archaeal community within marine oxygen deficient zone (ODZ) water columns, little is known about their metabolic capabilities in these ecosystems. We report 33 novel metagenome-assembled genomes belonging to DPANN phyla Nanoarchaeota, Pacearchaeota, Woesarchaeota, Undinarchaeota, Iainarchaeota, and SpSt-1190 from pelagic ODZs in the Eastern Tropical North Pacific and Arabian Sea. We find these archaea to be permanent, stable residents of all 3 major ODZs only within anoxic depths, comprising up to 1% of the total microbial community and up to 25-50% of archaea. ODZ DPANN appear capable of diverse metabolic functions, including fermentation, organic carbon scavenging, and the cycling of sulfur, hydrogen, and methane. Within a majority of ODZ DPANN, we identify a gene homologous to nitrous oxide reductase. Modeling analyses indicate the feasibility of a nitrous oxide reduction metabolism for host-attached symbionts, and the small genome sizes and reduced metabolic capabilities of most DPANN MAGs suggest host-associated lifestyles within ODZs.
Collapse
Affiliation(s)
- Irene H. Zhang
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Benedict Borer
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Rui Zhao
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Steven Wilbert
- Divisions of Biology and Biological Engineering and Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
| | - Dianne K. Newman
- Divisions of Biology and Biological Engineering and Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
| | - Andrew R. Babbin
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| |
Collapse
|
4
|
Zhang J, Lin H, Xu J, Zhang M, Ge X, Zhang C, Huang WE, Cheng JX. High-throughput single-cell sorting by stimulated Raman-activated cell ejection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.16.562526. [PMID: 37904930 PMCID: PMC10614813 DOI: 10.1101/2023.10.16.562526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
Single-cell sorting is essential to explore cellular heterogeneity in biology and medicine. Recently developed Raman-activated cell sorting (RACS) circumvents the limitations of fluorescence-activated cell sorting, such as the cytotoxicity of labels. However, the sorting throughputs of all forms of RACS are limited by the intrinsically small cross-section of spontaneous Raman scattering. Here, we report a stimulated Raman-activated cell ejection (S-RACE) platform that enables high-throughput single-cell sorting based on high-resolution multi-channel stimulated Raman chemical imaging, in situ image decomposition, and laser-induced cell ejection. The performance of this platform was illustrated by sorting a mixture of 1 μm polymer beads, where 95% yield, 98% purity, and 14 events per second throughput were achieved. Notably, our platform allows live cell ejection, allowing for the growth of single colonies of bacteria and fungi after sorting. To further illustrate the chemical selectivity, lipid-rich Rhodotorula glutinis cells were successfully sorted from a mixture with Saccharomyces cerevisiae, confirmed by downstream quantitative PCR. Furthermore, by integrating a closed-loop feedback control circuit into the system, we realized real-time single-cell imaging and sorting, and applied this method to precisely eject regions of interest from a rat brain tissue section. The reported S-RACE platform opens exciting opportunities for a wide range of single-cell applications in biology and medicine.
Collapse
Affiliation(s)
- Jing Zhang
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
- Photonics Center, Boston University, Boston, MA 02215, USA
| | - Haonan Lin
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
- Photonics Center, Boston University, Boston, MA 02215, USA
| | - Jiabao Xu
- Division of Biomedical Engineering, James Watt School of Engineering, University of Glasgow, Glasgow, G12 8LT, UK
| | - Meng Zhang
- Photonics Center, Boston University, Boston, MA 02215, USA
- Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215, USA
| | - Xiaowei Ge
- Photonics Center, Boston University, Boston, MA 02215, USA
- Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215, USA
| | - Chi Zhang
- Department of Chemistry, Purdue University, 560 Oval Dr., West Lafayette, IN 47907, USA
| | - Wei E. Huang
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, UK
| | - Ji-Xin Cheng
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
- Photonics Center, Boston University, Boston, MA 02215, USA
- Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215, USA
| |
Collapse
|
5
|
Martínez-Galicia E, Fernanda Flores Enríquez A, Puga A, Gutiérrez-Medina B. Analysis of the emerging physical network in young mycelia. Fungal Genet Biol 2023; 168:103823. [PMID: 37453457 DOI: 10.1016/j.fgb.2023.103823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/21/2023] [Accepted: 07/07/2023] [Indexed: 07/18/2023]
Abstract
Filamentous fungi develop intricate hyphal networks that support mycelial foraging and transport of resources. These networks have been analyzed recently using graph theory, enabling the development of models that seek to predict functional traits. However, attention has focused mainly on mature colonies. Here, we report the extraction and analysis of the graph corresponding to Trichoderma atroviride mycelia only a few hours after conidia germination. To extract the graph for a given mycelium, a mosaic conformed of multiple bright-field, optical microscopy images is digitally processed using freely available software. The resulting graphs are characterized in terms of number of nodes and edges, average edge length, total mycelium length, hyphal growth unit, maximum edge length and mycelium diameter, for colonies between 8 h and 14 h after conidium germination. Our results show that the emerging hyphal network grows first by hyphal elongation and branching, and then it transitions to a stage where hyphal-hyphal interactions become significant. As a tangled hyphal network develops with decreasing hyphal mean length, the mycelium maintains long (∼2 mm) hyphae-a behavior that suggests a combination of aggregated and dispersed architectures to support foraging. Lastly, analysis of early network development in Podospora anserina reveals striking similarity with T. atroviride, suggesting common mechanisms during initial colony formation in filamentous fungi.
Collapse
Affiliation(s)
- Edgar Martínez-Galicia
- Division of Advanced Materials, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José 2055, 78216 San Luis Potosí, Mexico
| | - Ana Fernanda Flores Enríquez
- Division of Advanced Materials, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José 2055, 78216 San Luis Potosí, Mexico
| | - Alejandro Puga
- Unidad Académica de Física, Universidad Autónoma de Zacatecas, Zacatecas, Mexico
| | - Braulio Gutiérrez-Medina
- Division of Advanced Materials, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José 2055, 78216 San Luis Potosí, Mexico.
| |
Collapse
|
6
|
Schaffer‐Morrison SAZ, Zak DR. Mycorrhizal fungal and tree root functional traits: Strategies for integration and future directions. Ecosphere 2023. [DOI: 10.1002/ecs2.4437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2023] Open
Affiliation(s)
| | - Donald R. Zak
- Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor Michigan USA
- School for Environment and Sustainability University of Michigan Ann Arbor Michigan USA
| |
Collapse
|
7
|
Giovannini L, Sbrana C, Giovannetti M, Avio L, Lanubile A, Marocco A, Turrini A. Diverse mycorrhizal maize inbred lines differentially modulate mycelial traits and the expression of plant and fungal phosphate transporters. Sci Rep 2022; 12:21279. [PMID: 36482115 PMCID: PMC9732053 DOI: 10.1038/s41598-022-25834-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
Food production is heavily dependent on soil phosphorus (P), a non-renewable mineral resource essential for plant growth and development. Alas, about 80% is unavailable for plant uptake. Arbuscular mycorrhizal fungi may promote soil P efficient use, although the mechanistic aspects are yet to be completely understood. In this study, plant and fungal variables involved in P acquisition were investigated in maize inbred lines, differing for mycorrhizal responsiveness and low-P tolerance, when inoculated with the symbiont Rhizoglomus irregulare (synonym Rhizophagus irregularis). The expression patterns of phosphate transporter (PT) genes in extraradical and intraradical mycelium (ERM/IRM) and in mycorrhizal and control maize roots were assessed, together with plant growth responses and ERM extent and structure. The diverse maize lines differed in plant and fungal accumulation patterns of PT transcripts, ERM phenotypic traits and plant performance. Mycorrhizal plants of the low-P tolerant maize line Mo17 displayed increased expression of roots and ERM PT genes, compared with the low-P susceptible line B73, which revealed larger ERM hyphal densities and interconnectedness. ERM structural traits showed significant correlations with plant/fungal expression levels of PT genes and mycorrhizal host benefit, suggesting that both structural and functional traits are differentially involved in the regulation of P foraging capacity in mycorrhizal networks.
Collapse
Affiliation(s)
- Luca Giovannini
- grid.5395.a0000 0004 1757 3729Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
| | - Cristiana Sbrana
- grid.5326.20000 0001 1940 4177Institute of Agricultural Biology and Biotechnology, National Research Council of Italy, Via Moruzzi 1, 56124 Pisa, Italy
| | - Manuela Giovannetti
- grid.5395.a0000 0004 1757 3729Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
| | - Luciano Avio
- grid.5395.a0000 0004 1757 3729Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
| | - Alessandra Lanubile
- grid.8142.f0000 0001 0941 3192Department of Sustainable Crop Production, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
| | - Adriano Marocco
- grid.8142.f0000 0001 0941 3192Department of Sustainable Crop Production, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
| | - Alessandra Turrini
- grid.5395.a0000 0004 1757 3729Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
| |
Collapse
|
8
|
Duong HL, Paufler S, Harms H, Schlosser D, Maskow T. Fungal Lignocellulose Utilisation Strategies from a Bioenergetic Perspective: Quantification of Related Functional Traits Using Biocalorimetry. Microorganisms 2022; 10:microorganisms10081675. [PMID: 36014092 PMCID: PMC9415514 DOI: 10.3390/microorganisms10081675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/12/2022] [Accepted: 08/16/2022] [Indexed: 11/16/2022] Open
Abstract
In the present study, we investigated whether a non-invasive metabolic heat flux analysis could serve the determination of the functional traits in free-living saprotrophic decomposer fungi and aid the prediction of fungal influences on ecosystem processes. For this, seven fungi, including ascomycete, basidiomycete, and zygomycete species, were investigated in a standardised laboratory environment, employing wheat straw as a globally relevant lignocellulosic substrate. Our study demonstrates that biocalorimetry can be employed successfully to determine growth-related fungal activity parameters, such as apparent maximum growth rates (AMGR), cultivation times until the observable onset of fungal growth at AMGR (tAMGR), quotients formed from the AMGR and tAMGR (herein referred to as competitive growth potential, CGP), and heat yield coefficients (YQ/X), the latter indicating the degree of resource investment into fungal biomass versus other functional attributes. These parameters seem suitable to link fungal potentials for biomass production to corresponding ecological strategies employed during resource utilisation, and therefore may be considered as fungal life history traits. A close connection exists between the CGP and YQ/X values, which suggests an interpretation that relates to fungal life history strategies.
Collapse
Affiliation(s)
- Hieu Linh Duong
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstraβe 15, 04318 Leipzig, Germany
- Faculty of Engineering, Vietnamese-German University (VGU), Le Lai Street, Hoa Phu Ward, Thủ Dầu Một 7500, Binh Duong, Vietnam
| | - Sven Paufler
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstraβe 15, 04318 Leipzig, Germany
| | - Hauke Harms
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstraβe 15, 04318 Leipzig, Germany
| | - Dietmar Schlosser
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstraβe 15, 04318 Leipzig, Germany
- Correspondence: (D.S.); (T.M.)
| | - Thomas Maskow
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstraβe 15, 04318 Leipzig, Germany
- Correspondence: (D.S.); (T.M.)
| |
Collapse
|