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Zhang F, Yang YQ, Zhou FP, Xiao W, Boonmee S, Yang XY. Multilocus Phylogeny and Characterization of Five Undescribed Aquatic Carnivorous Fungi ( Orbiliomycetes). J Fungi (Basel) 2024; 10:81. [PMID: 38276027 PMCID: PMC10817524 DOI: 10.3390/jof10010081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/18/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
The diversity of nematode-trapping fungi (NTF) holds significant theoretical and practical implications in the study of adaptive evolution and the bio-control of harmful nematodes. However, compared to terrestrial ecosystems, research on aquatic NTF is still in its early stages. During a survey of NTF in six watersheds in Yunnan Province, China, we isolated 10 taxa from freshwater sediment. Subsequent identification based on morphological and multigene (ITS, TEF1-α, and RPB2) phylogenetic analyses inferred they belong to five new species within Arthrobotrys. This paper provides a detailed description of these five novel species (Arthrobotrys cibiensis, A. heihuiensis, A. jinshaensis, A. yangbiensis, and A. yangjiangensis), contributing novel insights for further research into the diversity of NTF and providing new material for the biological control of aquatic harmful nematodes. Additionally, future research directions concerning aquatic NTF are also discussed.
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Affiliation(s)
- Fa Zhang
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali 671003, China; (F.Z.); (Y.-Q.Y.); (F.-P.Z.); (W.X.)
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Yao-Quan Yang
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali 671003, China; (F.Z.); (Y.-Q.Y.); (F.-P.Z.); (W.X.)
| | - Fa-Ping Zhou
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali 671003, China; (F.Z.); (Y.-Q.Y.); (F.-P.Z.); (W.X.)
| | - Wen Xiao
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali 671003, China; (F.Z.); (Y.-Q.Y.); (F.-P.Z.); (W.X.)
- The Provincial Innovation Team of Biodiversity Conservation and Utility of the Three Parallel Rivers Region, Dali University, Dali 671003, China
- Yunling Back-and-White Snub-Nosed Monkey Observation and Research Station of Yunnan Province, Dali 671003, China
| | - Saranyaphat Boonmee
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Xiao-Yan Yang
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali 671003, China; (F.Z.); (Y.-Q.Y.); (F.-P.Z.); (W.X.)
- The Provincial Innovation Team of Biodiversity Conservation and Utility of the Three Parallel Rivers Region, Dali University, Dali 671003, China
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Chou MY, Andersen TB, Mechan Llontop ME, Beculheimer N, Sow A, Moreno N, Shade A, Hamberger B, Bonito G. Terpenes modulate bacterial and fungal growth and sorghum rhizobiome communities. Microbiol Spectr 2023; 11:e0133223. [PMID: 37772854 PMCID: PMC10580827 DOI: 10.1128/spectrum.01332-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 07/05/2023] [Indexed: 09/30/2023] Open
Abstract
Terpenes are among the oldest and largest class of plant-specialized bioproducts that are known to affect plant development, adaptation, and biological interactions. While their biosynthesis, evolution, and function in aboveground interactions with insects and individual microbial species are well studied, how different terpenes impact plant microbiomes belowground is much less understood. Here we designed an experiment to assess how belowground exogenous applications of monoterpenes (1,8-cineole and linalool) and a sesquiterpene (nerolidol) delivered through an artificial root system impacted its belowground bacterial and fungal microbiome. We found that the terpene applications had significant and variable impacts on bacterial and fungal communities, depending on terpene class and concentration; however, these impacts were localized to the artificial root system and the fungal rhizosphere. We complemented this experiment with pure culture bioassays on responsive bacteria and fungi isolated from the sorghum rhizobiome. Overall, higher concentrations (200 µM) of nerolidol were inhibitory to Ferrovibrium and tested Firmicutes. While fungal isolates of Penicillium and Periconia were also more inhibited by higher concentrations (200 µM) of nerolidol, Clonostachys was enhanced at this higher level and together with Humicola was inhibited by the lower concentration tested (100 µM). On the other hand, 1,8-cineole had an inhibitory effect on Orbilia at both tested concentrations but had a promotive effect at 100 µM on Penicillium and Periconia. Similarly, linalool at 100 µM had significant growth promotion in Mortierella, but an inhibitory effect for Orbilia. Together, these results highlight the variable direct effects of terpenes on single microbial isolates and demonstrate the complexity of microbe-terpene interactions in the rhizobiome. IMPORTANCE Terpenes represent one of the largest and oldest classes of plant-specialized metabolism, but their role in the belowground microbiome is poorly understood. Here, we used a "rhizobox" mesocosm experimental set-up to supply different concentrations and classes of terpenes into the soil compartment with growing sorghum for 1 month to assess how these terpenes affect sorghum bacterial and fungal rhizobiome communities. Changes in bacterial and fungal communities between treatments belowground were characterized, followed by bioassays screening on bacterial and fungal isolates from the sorghum rhizosphere against terpenes to validate direct microbial responses. We found that microbial growth stimulatory and inhibitory effects were localized, terpene specific, dose dependent, and transient in time. This work paves the way for engineering terpene metabolisms in plant microbiomes for improved sustainable agriculture and bioenergy crop production.
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Affiliation(s)
- Ming-Yi Chou
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan, USA
- Department of Plant Biology, Rutgers University, New Brunswick, New Jersey, USA
| | - Trine B. Andersen
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Marco E. Mechan Llontop
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Nick Beculheimer
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Alassane Sow
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Nick Moreno
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Ashley Shade
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
- Research Group on Bacterial Efflux and Environmental Resistance, CNRS, INRAe, École Nationale Véterinaire de Lyon and Université Lyon 1, Université de Lyon, Villeurbanne, France
| | - Bjoern Hamberger
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Gregory Bonito
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
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Zhang F, Yang YQ, Zhou FP, Xiao W, Boonmee S, Yang XY. Morphological and Phylogenetic Characterization of Five Novel Nematode-Trapping Fungi (Orbiliomycetes) from Yunnan, China. J Fungi (Basel) 2023; 9:735. [PMID: 37504724 PMCID: PMC10381634 DOI: 10.3390/jof9070735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 07/29/2023] Open
Abstract
Nematode-trapping fungi are widely studied due to their unique morphological structure, survival strategy, and potential value in the biological control of harmful nematodes. During the identification of carnivorous fungi preserved in our laboratory, five novel nematode-trapping fungi were established and placed in the genera Arthrobotrys and Drehslerella based on morphological and multigene (ITS, TEF, and RPB2) phylogenetic analyses. A. hengjiangensis sp. nov. and A. weixiensis sp. nov. are characterized by producing adhesive networks to catch nematodes. Dr. pengdangensis sp. nov., Dr. tianchiensis sp. nov., and Dr. yunlongensis sp. nov. are characterized by producing constricting rings. Morphological descriptions, illustrations, taxonomic notes, and phylogenetic analysis are provided for all new taxa; a key for Drechslerella species is listed; and some deficiencies in the taxonomy and evolution study of nematode-trapping fungi are also discussed herein.
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Affiliation(s)
- Fa Zhang
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali 671003, China
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Yao-Quan Yang
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali 671003, China
| | - Fa-Ping Zhou
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali 671003, China
| | - Wen Xiao
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali 671003, China
- The Provincial Innovation Team of Biodiversity Conservation and Utility of the Three Parallel Rivers Region, Dali University, Dali 671003, China
- Yunling Back-and-White Snub-Nosed Monkey Observation and Research Station of Yunnan Province, Dali 671003, China
| | - Saranyaphat Boonmee
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Xiao-Yan Yang
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali 671003, China
- The Provincial Innovation Team of Biodiversity Conservation and Utility of the Three Parallel Rivers Region, Dali University, Dali 671003, China
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Qu L, Dai K, Wang J, Cao L, Rao Z, Han R. Microbial landscapes of the rhizosphere soils and roots of Luffa cylindrica plant associated with Meloidogyne incognita. Front Microbiol 2023; 14:1168179. [PMID: 37303801 PMCID: PMC10247985 DOI: 10.3389/fmicb.2023.1168179] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/02/2023] [Indexed: 06/13/2023] Open
Abstract
Introduction The root-knot nematodes (RKN), especially Meloidogyne spp., are globally emerging harmful animals for many agricultural crops. Methods To explore microbial agents for biological control of these nematodes, the microbial communities of the rhizosphere soils and roots of sponge gourd (Luffa cylindrica) infected and non-infected by M. incognita nematodes, were investigated using culture-dependent and -independent methods. Results Thirty-two culturable bacterial and eight fungal species, along with 10,561 bacterial and 2,427 fungal operational taxonomic units (OTUs), were identified. Nine culturable bacterial species, 955 bacterial and 701 fungal OTUs were shared in both four groups. More culturable bacterial and fungal isolates were detected from the uninfected soils and roots than from the infected soils and roots (except no fungi detected from the uninfected roots), and among all samples, nine bacterial species (Arthrobacter sp., Bacillus sp., Burkholderia ambifaria, Enterobacteriaceae sp., Fictibacillus barbaricus, Microbacterium sp., Micrococcaceae sp., Rhizobiaceae sp., and Serratia sp.) were shared, with Arthrobacter sp. and Bacillus sp. being dominant. Pseudomonas nitroreducens was exclusively present in the infested soils, while Mammaliicoccus sciuri, Microbacterium azadirachtae, and Priestia sp., together with Mucor irregularis, Penicillium sp., P. commune, and Sordariomycetes sp. were found only in the uninfected soils. Cupriavidus metallidurans, Gordonia sp., Streptomyces viridobrunneus, and Terribacillus sp. were only in the uninfected roots while Aspergillus sp. only in infected roots. After M. incognita infestation, 319 bacterial OTUs (such as Chryseobacterium) and 171 fungal OTUs (such as Spizellomyces) were increased in rhizosphere soils, while 181 bacterial OTUs (such as Pasteuria) and 166 fungal OTUs (such as Exophiala) rose their abundance in plant roots. Meanwhile, much more decreased bacterial or fungal OTUs were identified from rhizosphere soils rather than from plant roots, exhibiting the protective effects of host plant on endophytes. Among the detected bacterial isolates, Streptomyces sp. TR27 was discovered to exhibit nematocidal activity, and B. amyloliquefaciens, Bacillus sp. P35, and M. azadirachtae to show repellent potentials for the second stage M. incognita juveniles, which can be used to develop RKN bio-control agents. Discussion These findings provided insights into the interactions among root-knot nematodes, host plants, and microorganisms, which will inspire explorations of novel nematicides.
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Zhang F, Boonmee S, Yang YQ, Zhou FP, Xiao W, Yang XY. Arthrobotrys blastospora sp. nov. (Orbiliomycetes): A Living Fossil Displaying Morphological Traits of Mesozoic Carnivorous Fungi. J Fungi (Basel) 2023; 9:jof9040451. [PMID: 37108905 PMCID: PMC10144811 DOI: 10.3390/jof9040451] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 03/29/2023] [Accepted: 04/03/2023] [Indexed: 04/29/2023] Open
Abstract
The evolution of carnivorous fungi in deep time is still poorly understood as their fossil record is scarce. The approximately 100-million-year-old Cretaceous Palaeoanellus dimorphus is the earliest fossil of carnivorous fungi ever discovered. However, its accuracy and ancestral position has been widely questioned because no similar species have been found in modern ecosystems. During a survey of carnivorous fungi in Yunnan, China, two fungal isolates strongly morphologically resembling P. dimorphus were discovered and identified as a new species of Arthrobotrys (Orbiliaceae, Orbiliomycetes), a modern genus of carnivorous fungi. Phylogenetically, Arthrobotrys blastospora sp. nov. forms a sister lineage to A. oligospora. A. blastospora catches nematodes with adhesive networks and produces yeast-like blastospores. This character combination is absent in all other previously known modern carnivorous fungi but is strikingly similar to the Cretaceous P. dimorphus. In this paper, we describe A. blastospora in detail and discuss its relationship to P. dimorphus.
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Affiliation(s)
- Fa Zhang
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali 671003, China
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Saranyaphat Boonmee
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Yao-Quan Yang
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali 671003, China
| | - Fa-Ping Zhou
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali 671003, China
| | - Wen Xiao
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali 671003, China
- Key Laboratory of Yunnan State Education Department on Er'hai Lake Basin Protection and the Sustainable Development Research, Dali University, Dali 671003, China
- The Provincial Innovation Team of Biodiversity Conservation and Utility of the Three Parallel Rivers from Dali University, Dali University, Dali 671003, China
- Yunling Black-and-White Snub-Nosed Monkey Observation and Research Station of Yunnan Province, Dali 671003, China
| | - Xiao-Yan Yang
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali 671003, China
- Key Laboratory of Yunnan State Education Department on Er'hai Lake Basin Protection and the Sustainable Development Research, Dali University, Dali 671003, China
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Zhang F, Boonmee S, Monkai J, Yang XY, Xiao W. Drechslerelladaliensis and D.xiaguanensis (Orbiliales, Orbiliaceae), two new nematode-trapping fungi from Yunnan, China. Biodivers Data J 2022; 10:e96642. [PMID: 36761641 PMCID: PMC9836436 DOI: 10.3897/bdj.10.e96642] [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: 10/23/2022] [Accepted: 12/02/2022] [Indexed: 12/23/2022] Open
Abstract
Background Nematode-trapping fungi are a highly specialised group in fungi and are essential regulators of natural nematode populations. At present, more than 130 species have been discovered in Zygomycota (Zoopagaceae), Basidiomycota (Nematoctonus), and Ascomycota (Orbiliaceae). Amongst them, nematode-trapping fungi in Orbiliaceae have become the research focus of carnivorous fungi due to their abundant species. During the investigation of carnivorous fungi in Yunnan, China, four fungal strains isolated from burned forest soil were identified as two new nematode-trapping species in Drechslerella (Orbiliaceae), based on multigene phylogenetic analysis and morphological characters. New information Drechslerelladaliensis sp. nov. is characterised by its ellipsoid, 1-2-septate macroconidia, clavate or bottle-shaped, 0-1-septate microconidia and unbranched, simple conidiophores. D.xiaguanensis sp. nov. is characterised by fusiform or spindle-shaped, 2-4-septate conidia and unbranched, simple conidiophores. Both of them produce constricting rings to capture nematodes. The phylogenetic analysis, based on combined ITS, TEF1-α and RPB2 sequences, determined their placement in Drechslerella. D.daliensis forms a basal lineage closely nested with D.hainanensis (YMF1.03993). D.xiaguanensis forms a sister lineage with D.bembicodes (1.01429), D.aphrobrocha (YMF1.00119) and D.coelobrocha (FWY03-25-1).
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Affiliation(s)
- Fa Zhang
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, ThailandCenter of Excellence in Fungal Research, Mae Fah Luang UniversityChiang RaiThailand,Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali, ChinaInstitute of Eastern-Himalaya Biodiversity Research, Dali UniversityDaliChina,School of Science, Mae Fah Luang University, Chiang Rai, ThailandSchool of Science, Mae Fah Luang UniversityChiang RaiThailand
| | - Saranyaphat Boonmee
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, ThailandCenter of Excellence in Fungal Research, Mae Fah Luang UniversityChiang RaiThailand,School of Science, Mae Fah Luang University, Chiang Rai, ThailandSchool of Science, Mae Fah Luang UniversityChiang RaiThailand
| | - Jutamart Monkai
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, ThailandCenter of Excellence in Fungal Research, Mae Fah Luang UniversityChiang RaiThailand
| | - Xiao-Yan Yang
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali, ChinaInstitute of Eastern-Himalaya Biodiversity Research, Dali UniversityDaliChina,Key Laboratory of Yunnan State Education Department on Er’hai Lake Basin Protection and the Sustainable Development Research, Dali University, Dali, ChinaKey Laboratory of Yunnan State Education Department on Er’hai Lake Basin Protection and the Sustainable Development Research, Dali UniversityDaliChina,The provincial innovation team of biodiversity conservation and utility of the three parallel rivers from Dali University, Dali University, Dali, ChinaThe provincial innovation team of biodiversity conservation and utility of the three parallel rivers from Dali University, Dali UniversityDaliChina
| | - Wen Xiao
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali, ChinaInstitute of Eastern-Himalaya Biodiversity Research, Dali UniversityDaliChina,Key Laboratory of Yunnan State Education Department on Er’hai Lake Basin Protection and the Sustainable Development Research, Dali University, Dali, ChinaKey Laboratory of Yunnan State Education Department on Er’hai Lake Basin Protection and the Sustainable Development Research, Dali UniversityDaliChina,The provincial innovation team of biodiversity conservation and utility of the three parallel rivers from Dali University, Dali University, Dali, ChinaThe provincial innovation team of biodiversity conservation and utility of the three parallel rivers from Dali University, Dali UniversityDaliChina
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Banos S, Gysi DM, Richter-Heitmann T, Glöckner FO, Boersma M, Wiltshire KH, Gerdts G, Wichels A, Reich M. Seasonal Dynamics of Pelagic Mycoplanktonic Communities: Interplay of Taxon Abundance, Temporal Occurrence, and Biotic Interactions. Front Microbiol 2020; 11:1305. [PMID: 32676057 PMCID: PMC7333250 DOI: 10.3389/fmicb.2020.01305] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 05/22/2020] [Indexed: 12/14/2022] Open
Abstract
Marine fungi are an important component of pelagic planktonic communities. However, it is not yet clear how individual fungal taxa are integrated in marine processes of the microbial loop and food webs. Most likely, biotic interactions play a major role in shaping the fungal community structure. Thus, the aim of our work was to identify possible biotic interactions of mycoplankton with phytoplankton and zooplankton groups and among fungi, and to investigate whether there is coherence between interactions and the dynamics, abundance and temporal occurrence of individual fungal OTUs. Marine surface water was sampled weekly over the course of 1 year, in the vicinity of the island of Helgoland in the German Bight (North Sea). The mycoplankton community was analyzed using 18S rRNA gene tag-sequencing and the identified dynamics were correlated to environmental data including phytoplankton, zooplankton, and abiotic factors. Finally, co-occurrence patterns of fungal taxa were detected with network analyses based on weighted topological overlaps (wTO). Of all abundant and persistent OTUs, 77% showed no biotic relations suggesting a saprotrophic lifestyle. Of all other fungal OTUs, nearly the half (44%) had at least one significant negative relationship, especially with zooplankton and other fungi, or to a lesser extent with phytoplankton. These findings suggest that mycoplankton OTUs are embedded into marine food web chains via highly complex and manifold relationships such as parasitism, predation, grazing, or allelopathy. Furthermore, about one third of all rare OTUs were part of a dense fungal co-occurrence network probably stabilizing the fungal community against environmental changes and acting as functional guilds or being involved in fungal cross-feeding. Placed in an ecological context, strong antagonistic relationships of the mycoplankton community with other components of the plankton suggest that: (i) there is a top-down control by fungi on zooplankton and phytoplankton; (ii) fungi serve as a food source for zooplankton and thereby transfer nutrients and organic material; (iii) the dynamics of fungi harmful to other plankton groups are controlled by antagonistic fungal taxa.
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Affiliation(s)
- Stefanos Banos
- Molecular Ecology Group, University of Bremen, Bremen, Germany
| | - Deisy Morselli Gysi
- Department of Computer Science, Interdisciplinary Center of Bioinformatics, University of Leipzig, Leipzig, Germany.,Swarm Intelligence and Complex Systems Group, Faculty of Mathematics and Computer Science, University of Leipzig, Leipzig, Germany.,Center for Complex Networks Research, Northeastern University, Boston, MA, United States
| | | | - Frank Oliver Glöckner
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany.,Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Bremen, Germany.,MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Maarten Boersma
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Biologische Anstalt Helgoland, Helgoland, Germany.,FB2, University of Bremen, Bremen, Germany
| | - Karen H Wiltshire
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Biologische Anstalt Helgoland, Helgoland, Germany.,Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Wattenmeerstation, List, Germany
| | - Gunnar Gerdts
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Biologische Anstalt Helgoland, Helgoland, Germany
| | - Antje Wichels
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Biologische Anstalt Helgoland, Helgoland, Germany
| | - Marlis Reich
- Molecular Ecology Group, University of Bremen, Bremen, Germany
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Zhang Y, Yang G, Fang M, Deng C, Zhang KQ, Yu Z, Xu J. Comparative Analyses of Mitochondrial Genomes Provide Evolutionary Insights Into Nematode-Trapping Fungi. Front Microbiol 2020; 11:617. [PMID: 32351475 PMCID: PMC7174627 DOI: 10.3389/fmicb.2020.00617] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 03/19/2020] [Indexed: 01/10/2023] Open
Abstract
Predatory fungi in Orbiliaceae (Ascomycota) have evolved a diversity of trapping devices that enable them to trap and kill nematodes, other small animals, and protozoans. These trapping devices include adhesive hyphae, adhesive knobs, adhesive networks, constricting rings, and non-constricting rings. Their diversity and practical importance have attracted significant attention from biologists, making them excellent model organisms for studying adaptative evolution and as biological control agents against parasitic nematodes. The putative origins and evolutionary relationships among these carnivorous fungi have been investigated using nuclear protein-encoding genes, but their patterns of mitogenome relationships and divergences remain unknown. Here we analyze and compare the mitogenomes of 12 fungal strains belonging to eight species, including six species representing all four types of nematode trapping devices and two from related but non-predatory fungi. All 12 analyzed mitogenomes were of circular DNA molecules, with lengths ranging from 146,101 bp to 280,699 bp. Gene synteny analysis revealed several gene rearrangements and intron transfers among the mitogenomes. In addition, the number of protein coding genes (PCGs), GC content, AT skew, and GC skew varied among these mitogenomes. The increased number and total size of introns were the main contributors to the length differences among the mitogenomes. Phylogenetic analyses of the protein-coding genes indicated that mitochondrial and nuclear genomes evolved at different rates, and signals of positive selection were found in several genes involved in energy metabolism. Our study provides novel insights into the evolution of nematode-trapping fungi and shall facilitate further investigations of this ecologically and agriculturally important group of fungi.
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Affiliation(s)
- Ying Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
| | - Guangzhu Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
| | - Meiling Fang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
| | - Chu Deng
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
| | - Ke-Qin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
| | - Zefen Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
| | - Jianping Xu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
- Department of Biology, McMaster University, Hamilton, ON, Canada
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9
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Xie M, Bai N, Yang J, Jiang K, Zhou D, Zhao Y, Li D, Niu X, Zhang KQ, Yang J. Protein Kinase Ime2 Is Required for Mycelial Growth, Conidiation, Osmoregulation, and Pathogenicity in Nematode-Trapping Fungus Arthrobotrys oligospora. Front Microbiol 2020; 10:3065. [PMID: 31993040 PMCID: PMC6971104 DOI: 10.3389/fmicb.2019.03065] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Accepted: 12/18/2019] [Indexed: 11/26/2022] Open
Abstract
Inducer of meiosis 2 (Ime2), a protein kinase that has been identified in diverse fungal species, functions in the regulation of various cellular processes, such as ascospore formation, pseudohyphal growth, and sexual reproduction. In this study, AoIme2, an ortholog of Saccharomyces cerevisiae Ime2, was characterized in the nematode-trapping fungus Arthrobotrys oligospora. Disruption of the gene Aoime2 caused defective growth, with slower mycelial growth in ΔAoime2 mutants than the wild type (WT) strain, and in the mutants, the number of hyphal septa in mycelia was higher and the number of cell nuclei in mycelia and conidia was considerably lower than in the WT strain. The conidial yields of the ΔAoime2 mutants were decreased by ∼33% relative to the WT strain, and the transcription of several sporulation-related genes, including abaA, fluG, rodA, aspB, velB, and vosA, was markedly downregulated during the conidiation stage. The ΔAoime2 mutants were highly sensitive to the osmotic stressors NaCl and sorbitol, and the cell wall of partial hyphae in the mutants was deformed. Further examination revealed that the cell wall of the traps produced by ΔAoime2 mutants became loose, and that the electron-dense bodies in trap cells were also few than in the WT strain. Moreover, Aoime2 disruption caused a reduction in trap formation and serine-protease production, and most hyphal traps produced by ΔAoime2 mutants did not form an intact hyphal loop; consequently, substantially fewer nematodes were captured by the mutants than by the WT strain. In summary, an Ime2-MAPK is identified here for the first time from a nematode-trapping fungus, and the kinase is shown to be involved in the regulation of mycelial growth and development, conidiation, osmolarity, and pathogenicity in A. oligospora.
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Affiliation(s)
- Meihua Xie
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China.,School of Life Sciences, Yunnan University, Kunming, China.,Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, China.,Department of Chemistry and Life Science, Chuxiong Normal University, Chuxiong, China
| | - Na Bai
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China.,School of Life Sciences, Yunnan University, Kunming, China.,Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, China
| | - Jiangliu Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China.,School of Life Sciences, Yunnan University, Kunming, China.,Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, China
| | - Kexin Jiang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China.,School of Life Sciences, Yunnan University, Kunming, China.,Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, China
| | - Duanxu Zhou
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China.,School of Life Sciences, Yunnan University, Kunming, China.,Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, China
| | - Yining Zhao
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China.,School of Life Sciences, Yunnan University, Kunming, China.,Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, China
| | - Dongni Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China.,School of Life Sciences, Yunnan University, Kunming, China.,Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, China
| | - Xuemei Niu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China.,School of Life Sciences, Yunnan University, Kunming, China.,Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, China
| | - Ke-Qin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China.,School of Life Sciences, Yunnan University, Kunming, China.,Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, China
| | - Jinkui Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China.,School of Life Sciences, Yunnan University, Kunming, China.,Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, China
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10
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Zhou S, Chen G, Huang G. Design, synthesis and biological evaluation of imidazo[1,2-a]pyridine analogues or derivatives as anti-helmintic drug. Chem Biol Drug Des 2018; 93:503-510. [PMID: 30427117 DOI: 10.1111/cbdd.13441] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 10/12/2018] [Accepted: 10/31/2018] [Indexed: 11/28/2022]
Abstract
The Albendazole was used as the lead compound, which was modified by structural transformation and with alkyl groups. A total of 18 compounds (4a-4r) were designed and synthesized. The in vitro experiment results showed that compounds 4e, 4f, 4k, 4l, 4q and 4r had good inhibitory effect on egg and imago of roundworm. IC50 of compound 4l to anti-egg of roundworm was 0.65 ± 0.01 μmol/L and to anti-imago of roundworm was 1.04 ± 0.01 μmol/L. At the same time, it showed that compound 4l had the best effect in vivo, and the rate of anti-helmintic could reach more than 99%. The results of acute toxicity tests indicated that these compounds were with LD50 > 2100 mg/kg by oral administration, so they were low toxicity compounds. In a word, compound 4l was most likely to be a new anti-helmintic drug through screening in vitro and in vivo.
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Affiliation(s)
- Shiyang Zhou
- College of Chemistry and Chemical Engineering, Hainan Normal University, Hainan, China.,Key Laboratory of Tropical Medicinal Plant Chemistry of Ministry of Education, Hainan Normal University, Hainan, China
| | - Guangying Chen
- College of Chemistry and Chemical Engineering, Hainan Normal University, Hainan, China.,Key Laboratory of Tropical Medicinal Plant Chemistry of Ministry of Education, Hainan Normal University, Hainan, China
| | - Gangliang Huang
- Active Carbohydrate Research Institute, Chongqing Key Laboratory of Green Synthesis and Application, Chongqing Normal University, Chongqing, China
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11
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Kirker GT, Bishell AB, Jusino MA, Palmer JM, Hickey WJ, Lindner DL. Amplicon-Based Sequencing of Soil Fungi from Wood Preservative Test Sites. Front Microbiol 2017; 8:1997. [PMID: 29093702 PMCID: PMC5651271 DOI: 10.3389/fmicb.2017.01997] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 09/28/2017] [Indexed: 12/22/2022] Open
Abstract
Soil samples were collected from field sites in two AWPA (American Wood Protection Association) wood decay hazard zones in North America. Two field plots at each site were exposed to differing preservative chemistries via in-ground installations of treated wood stakes for approximately 50 years. The purpose of this study is to characterize soil fungal species and to determine if long term exposure to various wood preservatives impacts soil fungal community composition. Soil fungal communities were compared using amplicon-based DNA sequencing of the internal transcribed spacer 1 (ITS1) region of the rDNA array. Data show that soil fungal community composition differs significantly between the two sites and that long-term exposure to different preservative chemistries is correlated with different species composition of soil fungi. However, chemical analyses using ICP-OES found levels of select residual preservative actives (copper, chromium and arsenic) to be similar to naturally occurring levels in unexposed areas. A list of indicator species was compiled for each treatment-site combination; functional guild analyses indicate that long-term exposure to wood preservatives may have both detrimental and stimulatory effects on soil fungal species composition. Fungi with demonstrated capacity to degrade industrial pollutants were found to be highly correlated with areas that experienced long-term exposure to preservative testing.
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Affiliation(s)
- Grant T. Kirker
- FPL, United States Department of Agriculture-Forest Service (USDA-FS), Durability and Wood Protection, Madison, WI, United States
| | - Amy B. Bishell
- FPL, United States Department of Agriculture-Forest Service (USDA-FS), Durability and Wood Protection, Madison, WI, United States
| | - Michelle A. Jusino
- NRS, United States Department of Agriculture-Forest Service (USDA-FS), Center for Forest Mycology Research, Madison, WI, United States
| | - Jonathan M. Palmer
- NRS, United States Department of Agriculture-Forest Service (USDA-FS), Center for Forest Mycology Research, Madison, WI, United States
| | - William J. Hickey
- Department of Soil Science, University of Wisconsin-Madison, Madison, WI, United States
| | - Daniel L. Lindner
- NRS, United States Department of Agriculture-Forest Service (USDA-FS), Center for Forest Mycology Research, Madison, WI, United States
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12
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Meyer SL, Carta LK, Rehner SA. Morphological variability and molecular phylogeny of the nematophagous fungusMonacrosporium drechsleri. Mycologia 2017. [DOI: 10.1080/15572536.2006.11832816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | - Lynn K. Carta
- USDA ARS Nematology Laboratory, Building 011A, Room 165B, BARC-West, 10300 Baltimore Avenue, Beltsville, Maryland 20705-2350
| | - Stephen A. Rehner
- USDA ARS Insect Biocontrol Laboratory, Building 011A, Room 214, BARC-West, 10300 Baltimore Avenue, Beltsville, Maryland 20705-2350
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13
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Li Y, Hyde KD, Jeewon R, Cai L, Vijaykrishna D, Zhang K. Phylogenetics and evolution of nematode-trapping fungi (Orbiliales) estimated from nuclear and protein coding genes. Mycologia 2017. [DOI: 10.1080/15572536.2006.11832753] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Yan Li
- Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming 650091, Yunnan Province, PR China
| | | | | | | | - Dhanasekaran Vijaykrishna
- Centre for Research in Fungal Diversity, Department of Ecology & Biodiversity, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, PR China
| | - Keqin Zhang
- Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming 650091, Yunnan Province, PR China
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14
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Phylogenic analysis of adhesion related genes Mad1 revealed a positive selection for the evolution of trapping devices of nematode-trapping fungi. Sci Rep 2016; 6:22609. [PMID: 26941065 PMCID: PMC4778117 DOI: 10.1038/srep22609] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 02/17/2016] [Indexed: 12/27/2022] Open
Abstract
Adhesions, the major components of the extracellular fibrillar polymers which accumulate on the outer surface of adhesive traps of nematode-trapping fungi, are thought to have played important roles during the evolution of trapping devices. Phylogenetic analyses based on the genes related to adhesive materials can be of great importance for understanding the evolution of trapping devices. Recently, AoMad1, one homologous gene of the entomopathogenic fungus Metarhizium anisopliae cell wall protein MAD1, has been functionally characterized as involved in the production of adhesions in the nematode-trapping fungus Arthrobotrys oligospora. In this study, we cloned Mad1 homologous genes from nematode-trapping fungi with various trapping devices. Phylogenetic analyses suggested that species which formed nonadhesive constricting ring (CR) traps more basally placed and species with adhesive traps evolved along two lineages. Likelihood ratio tests (LRT) revealed that significant positive selective pressure likely acted on the ancestral trapping devices including both adhesive and mechanical traps, indicating that the Mad1 genes likely played important roles during the evolution of nematode-trapping fungi. Our study provides new insights into the evolution of trapping devices of nematode-trapping fungi and also contributes to understanding the importance of adhesions during the evolution of nematode-trapping fungi.
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15
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Degenkolb T, Vilcinskas A. Metabolites from nematophagous fungi and nematicidal natural products from fungi as an alternative for biological control. Part I: metabolites from nematophagous ascomycetes. Appl Microbiol Biotechnol 2015; 100:3799-812. [PMID: 26715220 PMCID: PMC4824826 DOI: 10.1007/s00253-015-7233-6] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Revised: 11/29/2015] [Accepted: 12/02/2015] [Indexed: 11/29/2022]
Abstract
Plant-parasitic nematodes are estimated to cause global annual losses of more than US$ 100 billion. The number of registered nematicides has declined substantially over the last 25 years due to concerns about their non-specific mechanisms of action and hence their potential toxicity and likelihood to cause environmental damage. Environmentally beneficial and inexpensive alternatives to chemicals, which do not affect vertebrates, crops, and other non-target organisms, are therefore urgently required. Nematophagous fungi are natural antagonists of nematode parasites, and these offer an ecophysiological source of novel biocontrol strategies. In this first section of a two-part review article, we discuss 83 nematicidal and non-nematicidal primary and secondary metabolites found in nematophagous ascomycetes. Some of these substances exhibit nematicidal activities, namely oligosporon, 4',5'-dihydrooligosporon, talathermophilins A and B, phomalactone, aurovertins D and F, paeciloxazine, a pyridine carboxylic acid derivative, and leucinostatins. Blumenol A acts as a nematode attractant. Other substances, such as arthrosporols and paganins, play a decisive role in the life cycle of the producers, regulating the formation of reproductive or trapping organs. We conclude by considering the potential applications of these beneficial organisms in plant protection strategies.
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Affiliation(s)
- Thomas Degenkolb
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Andreas Vilcinskas
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany. .,Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Winchester Strasse 2, 35394, Giessen, Germany.
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16
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Andersson KM, Kumar D, Bentzer J, Friman E, Ahrén D, Tunlid A. Interspecific and host-related gene expression patterns in nematode-trapping fungi. BMC Genomics 2014; 15:968. [PMID: 25384908 PMCID: PMC4237727 DOI: 10.1186/1471-2164-15-968] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 09/24/2014] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Nematode-trapping fungi are soil-living fungi that capture and kill nematodes using special hyphal structures called traps. They display a large diversity of trapping mechanisms and differ in their host preferences. To provide insights into the genetic basis for this variation, we compared the transcriptome expressed by three species of nematode-trapping fungi (Arthrobotrys oligospora, Monacrosporium cionopagum and Arthrobotrys dactyloides, which use adhesive nets, adhesive branches or constricting rings, respectively, to trap nematodes) during infection of two different plant-pathogenic nematode hosts (the root knot nematode Meloidogyne hapla and the sugar beet cyst nematode Heterodera schachtii). RESULTS The divergence in gene expression between the fungi was significantly larger than that related to the nematode species being infected. Transcripts predicted to encode secreted proteins and proteins with unknown function (orphans) were overrepresented among the highly expressed transcripts in all fungi. Genes that were highly expressed in all fungi encoded endopeptidases, such as subtilisins and aspartic proteases; cell-surface proteins containing the carbohydrate-binding domain WSC; stress response proteins; membrane transporters; transcription factors; and transcripts containing the Ricin-B lectin domain. Differentially expressed transcripts among the fungal species encoded various lectins, such as the fungal fruit-body lectin and the D-mannose binding lectin; transcription factors; cell-signaling components; proteins containing a WSC domain; and proteins containing a DUF3129 domain. A small set of transcripts were differentially expressed in infections of different host nematodes, including peptidases, WSC domain proteins, tyrosinases, and small secreted proteins with unknown function. CONCLUSIONS This is the first study on the variation of infection-related gene expression patterns in nematode-trapping fungi infecting different host species. A better understanding of these patterns will facilitate the improvements of these fungi in biological control programs, by providing molecular markers for screening programs and candidates for genetic manipulations of virulence and host preferences.
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Affiliation(s)
- Karl-Magnus Andersson
- />Department of Biology, Microbial Ecology Group, Lund University, Ecology Building, 223 62 Lund, Sweden
| | - Dharmendra Kumar
- />Department of Genetics and Plant Breeding, College of Agriculture, Narendra Deva University of Agriculture and Technology, Kumarganj, Faizabad, 224229 Uttar Pradesh (U.P.) India
| | - Johan Bentzer
- />Department of Biology, Microbial Ecology Group, Lund University, Ecology Building, 223 62 Lund, Sweden
| | - Eva Friman
- />Department of Biology, Microbial Ecology Group, Lund University, Ecology Building, 223 62 Lund, Sweden
| | - Dag Ahrén
- />Department of Biology, BILS Bioinformatics Infrastructure for Life Sciences, Lund University, Ecology Building, 223 62 Lund, Sweden
| | - Anders Tunlid
- />Department of Biology, Microbial Ecology Group, Lund University, Ecology Building, 223 62 Lund, Sweden
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17
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Meerupati T, Andersson KM, Friman E, Kumar D, Tunlid A, Ahrén D. Genomic mechanisms accounting for the adaptation to parasitism in nematode-trapping fungi. PLoS Genet 2013; 9:e1003909. [PMID: 24244185 PMCID: PMC3828140 DOI: 10.1371/journal.pgen.1003909] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 09/09/2013] [Indexed: 01/12/2023] Open
Abstract
Orbiliomycetes is one of the earliest diverging branches of the filamentous ascomycetes. The class contains nematode-trapping fungi that form unique infection structures, called traps, to capture and kill free-living nematodes. The traps have evolved differently along several lineages and include adhesive traps (knobs, nets or branches) and constricting rings. We show, by genome sequencing of the knob-forming species Monacrosporium haptotylum and comparison with the net-forming species Arthrobotrys oligospora, that two genomic mechanisms are likely to have been important for the adaptation to parasitism in these fungi. Firstly, the expansion of protein domain families and the large number of species-specific genes indicated that gene duplication followed by functional diversification had a major role in the evolution of the nematode-trapping fungi. Gene expression indicated that many of these genes are important for pathogenicity. Secondly, gene expression of orthologs between the two fungi during infection indicated that differential regulation was an important mechanism for the evolution of parasitism in nematode-trapping fungi. Many of the highly expressed and highly upregulated M. haptotylum transcripts during the early stages of nematode infection were species-specific and encoded small secreted proteins (SSPs) that were affected by repeat-induced point mutations (RIP). An active RIP mechanism was revealed by lack of repeats, dinucleotide bias in repeats and genes, low proportion of recent gene duplicates, and reduction of recent gene family expansions. The high expression and rapid divergence of SSPs indicate a striking similarity in the infection mechanisms of nematode-trapping fungi and plant and insect pathogens from the crown groups of the filamentous ascomycetes (Pezizomycotina). The patterns of gene family expansions in the nematode-trapping fungi were more similar to plant pathogens than to insect and animal pathogens. The observation of RIP activity in the Orbiliomycetes suggested that this mechanism was present early in the evolution of the filamentous ascomycetes.
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Affiliation(s)
- Tejashwari Meerupati
- Microbial Ecology Group, Department of Biology, Lund University, Ecology Building, Lund, Sweden
| | - Karl-Magnus Andersson
- Microbial Ecology Group, Department of Biology, Lund University, Ecology Building, Lund, Sweden
| | - Eva Friman
- Microbial Ecology Group, Department of Biology, Lund University, Ecology Building, Lund, Sweden
| | - Dharmendra Kumar
- Microbial Ecology Group, Department of Biology, Lund University, Ecology Building, Lund, Sweden
- Department of Genetics and Plant Breeding, N.D. University of Agriculture and Technology, Faizabad, India
| | - Anders Tunlid
- Microbial Ecology Group, Department of Biology, Lund University, Ecology Building, Lund, Sweden
| | - Dag Ahrén
- Microbial Ecology Group, Department of Biology, Lund University, Ecology Building, Lund, Sweden
- BILS Bioinformatics Infrastructure for Life Sciences, Department of Biology, Lund University, Ecology Building, Lund, Sweden
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18
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Andersson KM, Meerupati T, Levander F, Friman E, Ahrén D, Tunlid A. Proteome of the nematode-trapping cells of the fungus Monacrosporium haptotylum. Appl Environ Microbiol 2013; 79:4993-5004. [PMID: 23770896 PMCID: PMC3754708 DOI: 10.1128/aem.01390-13] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 06/07/2013] [Indexed: 01/08/2023] Open
Abstract
Many nematophagous fungi use morphological structures called traps to capture nematodes by adhesion or mechanically. To better understand the cellular functions of adhesive traps, the trap cell proteome of the fungus Monacrosporium haptotylum was characterized. The trap of M. haptotylum consists of a unicellular structure called a knob that develops at the apex of a hypha. Proteins extracted from knobs and mycelia were analyzed using SDS-PAGE and liquid chromatography-tandem mass spectrometry (LC-MS-MS). The peptide sequences were matched against predicted gene models from the recently sequenced M. haptotylum genome. In total, 336 proteins were identified, with 54 expressed at significantly higher levels in the knobs than in the mycelia. The upregulated knob proteins included peptidases, small secreted proteins with unknown functions, and putative cell surface adhesins containing carbohydrate-binding domains, including the WSC domain. Phylogenetic analysis showed that all upregulated WSC domain proteins belonged to a large, expanded cluster of paralogs in M. haptotylum. Several peptidases and homologs of experimentally verified proteins in other pathogenic fungi were also upregulated in the knob proteome. Complementary profiling of gene expression at the transcriptome level showed poor correlation between the upregulation of knob proteins and their corresponding transcripts. We propose that the traps of M. haptotylum contain many of the proteins needed in the early stages of infection and that the trap cells can tightly control the translation and degradation of these proteins to minimize the cost of protein synthesis.
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Affiliation(s)
| | | | - Fredrik Levander
- Bioinformatics Infrastructure for Life Sciences, Department of Immunotechnology, Lund University, Lund, Sweden
| | - Eva Friman
- Microbial Ecology, Department of Biology, Lund University, Lund, Sweden
| | - Dag Ahrén
- Microbial Ecology, Department of Biology, Lund University, Lund, Sweden
- Bioinformatics Infrastructure for Life Sciences, Department of Biology, Lund University, Lund, Sweden
| | - Anders Tunlid
- Microbial Ecology, Department of Biology, Lund University, Lund, Sweden
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19
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Zhang Y, Qiao M, Xu J, Cao Y, Zhang KQ, Yu ZF. Genetic diversity and recombination in natural populations of the nematode-trapping fungus Arthrobotrys oligospora from China. Ecol Evol 2013; 3:312-25. [PMID: 23467563 PMCID: PMC3586641 DOI: 10.1002/ece3.450] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2012] [Revised: 11/12/2012] [Accepted: 11/15/2012] [Indexed: 11/09/2022] Open
Abstract
Nematophagous fungi can trap and capture nematodes and other small invertebrates. This unique ability has made them ideal organisms from which to develop biological control agents against plant- and animal-parasitic nematodes. However, effective application of biocontrol agents in the field requires a comprehensive understanding about the ecology and population genetics of the nematophagous fungi in natural environments. Here, we genotyped 228 strains of the nematode-trapping fungus Arthrobotrys oligospora using 12 single nucleotide polymorphic markers located on eight random DNA fragments. The strains were from different ecological niches and geographical regions from China. Our analyses identified that ecological niche separations contributed significantly, whereas geographic separation contributed relatively little to the overall genetic variation in our samples of A. oligospora. Interestingly, populations from stressful environments seemed to be more variable and showed more evidence for recombination than those from benign environments at the same geographic areas. We discussed the implications of our results to the conservation and biocontrol application of A. oligospora in agriculture and forestry.
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Affiliation(s)
- Ying Zhang
- Laboratory for Conservation and Utilization of Bio-resources, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan UniversityKunming, Yunnan, 650091, China
| | - Min Qiao
- Laboratory for Conservation and Utilization of Bio-resources, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan UniversityKunming, Yunnan, 650091, China
| | - Jianping Xu
- Laboratory for Conservation and Utilization of Bio-resources, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan UniversityKunming, Yunnan, 650091, China
- Department of Biology, McMaster University1280 Main Street West, Hamilton, Ontario, Canada, L8S 4K1
| | - Yang Cao
- Laboratory for Conservation and Utilization of Bio-resources, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan UniversityKunming, Yunnan, 650091, China
| | - Ke-Qin Zhang
- Laboratory for Conservation and Utilization of Bio-resources, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan UniversityKunming, Yunnan, 650091, China
| | - Ze-Fen Yu
- Laboratory for Conservation and Utilization of Bio-resources, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan UniversityKunming, Yunnan, 650091, China
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20
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Yang E, Xu L, Yang Y, Zhang X, Xiang M, Wang C, An Z, Liu X. Origin and evolution of carnivorism in the Ascomycota (fungi). Proc Natl Acad Sci U S A 2012; 109:10960-5. [PMID: 22715289 PMCID: PMC3390824 DOI: 10.1073/pnas.1120915109] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Carnivorism is one of the basic life strategies of fungi. Carnivorous fungi possess the ability to trap and digest their preys by sophisticated trapping devices. However, the origin and development of fungal carnivorism remains a gap in evolution biology. In this study, five protein-encoding genes were used to construct the phylogeny of the carnivorous fungi in the phylum Ascomycota; these fungi prey on nematodes by means of specialized trapping structures such as constricting rings and adhesive traps. Our analysis revealed a definitive pattern of evolutionary development for these trapping structures. Molecular clock calibration based on two fossil records revealed that fungal carnivorism diverged from saprophytism about 419 Mya, which was after the origin of nematodes about 550-600 Mya. Active carnivorism (fungi with constricting rings) and passive carnivorism (fungi with adhesive traps) diverged from each other around 246 Mya, shortly after the occurrence of the Permian-Triassic extinction event about 251.4 Mya. The major adhesive traps evolved around 198-208 Mya, which was within the time frame of the Triassic-Jurassic extinction event about 201.4 Mya. However, no major carnivorous ascomycetes divergence was correlated to the Cretaceous-Tertiary extinction event, which occurred more recently (about 65.5 Mya). Therefore, a causal relationship between mass extinction events and fungal carnivorism evolution is not validated in this study. More evidence including additional fossil records is needed to establish if fungal carnivorism evolution was a response to mass extinction events.
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Affiliation(s)
- Ence Yang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Lingling Xu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Biotechnology, Xi'an University of Arts and Science, Xi'an 710065, China
| | - Ying Yang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xinyu Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Meichun Xiang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chengshu Wang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; and
| | - Zhiqiang An
- Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030
| | - Xingzhong Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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Fekete C, Tholander M, Rajashekar B, Ahrén D, Friman E, Johansson T, Tunlid A. Paralysis of nematodes: shifts in the transcriptome of the nematode-trapping fungus Monacrosporium haptotylum during infection of Caenorhabditis elegans. Environ Microbiol 2007; 10:364-75. [PMID: 18028414 DOI: 10.1111/j.1462-2920.2007.01457.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The transcriptional response in the parasitic fungus Monacrosporium haptotylum and its nematode host Caenorhabditis elegans were analysed during infection using cDNA microarrays. The array contained 2684 fungal and 372 worm gene reporters. Dramatic shifts occurred in the transcriptome of M. haptotylum during the different stages of the infection. An initial transcriptional response was recorded after 1 h of infection when the traps adhered to the cuticle, but before immobilization of the captured nematodes. Among the differentially expressed genes were two serine protease genes (spr1 and spr2), and several homologues to genes known to be regulated in other pathogenic fungi. After 4 h, when approximately 40% of the nematodes were paralysed, we identified an upregulated cluster of 372 fungal genes which were not regulated during the other phases of the infection. This cohort contained a large proportion (79%) of genes that appear to be specific for M. haptotylum and closely related species. These genes were of two different classes: those translating into presumably functional peptides and those with no apparent protein coding potential (non-coding RNAs). Among the infection-induced C. elegans genes were those encoding antimicrobial peptides, protease inhibitors and lectins.
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Affiliation(s)
- Csaba Fekete
- Department of Microbial Ecology, Lund University, Ecology Building, SE-223 62 Lund, Sweden
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Yang Y, Yang E, An Z, Liu X. Evolution of nematode-trapping cells of predatory fungi of the Orbiliaceae based on evidence from rRNA-encoding DNA and multiprotein sequences. Proc Natl Acad Sci U S A 2007; 104:8379-84. [PMID: 17494736 PMCID: PMC1895958 DOI: 10.1073/pnas.0702770104] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2006] [Indexed: 11/18/2022] Open
Abstract
Among fungi, the basic life strategies are saprophytism, parasitism, and predation. Fungi in Orbiliaceae (Ascomycota) prey on animals by means of specialized trapping structures. Five types of trapping devices are recognized, but their evolutionary origins and divergence are not well understood. Based on comprehensive phylogenetic analysis of nucleotide sequences of three protein-coding genes (RNA polymerase II subunit gene, rpb2; elongation factor 1-alpha gene, ef1-alpha; and ss tubulin gene, bt) and ribosomal DNA in the internal transcribed spacer region, we have demonstrated that the initial trapping structure evolved along two lineages yielding two distinct trapping mechanisms: one developed into constricting rings and the other developed into adhesive traps. Among adhesive trapping devices, the adhesive network separated from the others early and evolved at a steady and gentle speed. The adhesive knob evolved through stalk elongation, with a final development of nonconstricting rings. Our data suggest that the derived adhesive traps are at a highly differentiated stage. The development of trapping devices is felicitous proof of adaptive evolution.
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Affiliation(s)
- Ying Yang
- Key Laboratory of Systematic Mycology and Lichenology, Institute of Microbiology, Chinese Academy of Sciences 3A Datun Rd, Chaoyang District, Beijing 100101, China
- Graduate University of Chinese Academy of Sciences, Beijing 100049, China; and
| | - Ence Yang
- Key Laboratory of Systematic Mycology and Lichenology, Institute of Microbiology, Chinese Academy of Sciences 3A Datun Rd, Chaoyang District, Beijing 100101, China
- Graduate University of Chinese Academy of Sciences, Beijing 100049, China; and
| | - Zhiqiang An
- Merck Research Laboratories, WP26A-4000, 770 Sumneytown Pike, West Point, PA 19486-0004
| | - Xingzhong Liu
- Key Laboratory of Systematic Mycology and Lichenology, Institute of Microbiology, Chinese Academy of Sciences 3A Datun Rd, Chaoyang District, Beijing 100101, China
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