scholarly journals Early Transcriptome Response of Trichoderma virens to Colonization of Maize Roots

2021 ◽  
Vol 2 ◽  
Author(s):  
James T. Taylor ◽  
Ken-Der Wang ◽  
Benjamin Horwitz ◽  
Michael Kolomiets ◽  
Charles M. Kenerley
Keyword(s):  
Gene Clustering ◽  
Deletion Mutants ◽  
Post Inoculation ◽  
Trichoderma Virens ◽  
Plant Host ◽  
Network Analyses ◽  
Maize Roots ◽  
Transduction Mechanisms ◽  
Colonization Process ◽  
Colonization Time

Trichoderma virens is a well-known mycoparasitic fungal symbiont that is valued for its biocontrol capabilities. T. virens initiates a symbiotic relationship with a plant host through the colonization of its roots. To achieve colonization, the fungus must communicate with the host and evade its innate defenses. In this study, we explored the genes involved with the host communication and colonization process through transcriptomic profiling of the wild-type fungus and selected deletion mutants as they colonized maize roots. Transcriptome profiles of the T. virens colonization of maize roots over time revealed that 24 h post inoculation appeared to be a key time for plant-microbe communication, with many key gene categories, including signal transduction mechanisms and carbohydrate transport and metabolism, peaking in expression at this early colonization time point. The transcriptomic profiles of Sm1 and Sir1 deletion mutants in the presence of plants demonstrated that Sir1, rather than Sm1, appears to be the key regulator of the fungal response to maize, with 64% more unique differentially expressed genes compared to Sm1. Additionally, we developed a novel algorithm utilizing gene clustering and coexpression network analyses to select potential colonization-related gene targets for characterization. About 40% of the genes identified by the algorithm would have been missed using previous methods for selecting gene targets.

A paralog of the proteinaceous elicitor SM1 is involved in colonization of maize roots by Trichoderma virens

2015 ◽  
Vol 119 (6) ◽  
pp. 476-486 ◽  
Author(s):  
Frankie K. Crutcher ◽  
Maria E. Moran-Diez ◽  
Shengli Ding ◽  
Jinggao Liu ◽  
Benjamin A. Horwitz ◽  
...  
Keyword(s):  
Trichoderma Virens ◽  
Maize Roots

scholarly journals Comparative Genomic Analysis of Third-Generation-Cephalosporin-Resistant Escherichia coli Harboring the blaCMY-2-Positive IncI1 Group, IncB/O/K/Z, and IncC Plasmids Isolated from Healthy Broilers in Japan

2020 ◽  
Vol 64 (7) ◽  
Author(s):  
Takahiro Shirakawa ◽  
Tsuyoshi Sekizuka ◽  
Makoto Kuroda ◽  
Satowa Suzuki ◽  
Manao Ozawa ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Phylogenetic Analysis ◽  
Gene Clustering ◽  
Comparative Genomic ◽  
Third Generation ◽  
Chromosomal Dna ◽  
In Ovo ◽  
Content Type ◽  
E Coli ◽  
Network Analyses

ABSTRACT The off-label use of third-generation cephalosporins (3GCs) during in ovo vaccination or vaccination of newly hatched chicks has been a common practice worldwide. CMY-2-producing Escherichia coli strains have been disseminated in broiler chicken production. The objective of this study was to determine the epidemiological linkage of blaCMY-2-positive plasmids among broilers both within and outside Japan, because the grandparent stock and parent stock were imported into Japan. We examined the whole-genome sequences of 132 3GC-resistant E. coli isolates collected from healthy broilers during 2002 to 2014. The predominant 3GC resistance gene was blaCMY-2, which was detected in the plasmids of 87 (65.9%) isolates. The main plasmid replicon types were IncI1-Iγ (n = 21; 24.1%), IncI (n = 12; 13.8%), IncB/O/K/Z (n = 28; 32.2%), and IncC (n = 22; 25.3%). Those plasmids were subjected to gene clustering, network analyses, and plasmid multilocus sequence typing (pMLST). The chromosomal DNA of isolates was subjected to MLST and single-nucleotide variant (SNV)-based phylogenetic analysis. MLST and SNV-based phylogenetic analysis revealed high diversity of E. coli isolates. The sequence type 429 (ST429) cluster harboring blaCMY-2-positive IncB/O/K/Z was closely related to isolates from broilers in Germany harboring blaCMY-2-positive IncB/O/K/Z. pST55-IncI, pST12-IncI1-Iγ, and pST3-IncC were prevalent in western Japan. pST12-IncI1-Iγ and pST3-IncC were closely related to plasmids detected in E. coli isolates from chickens in North America, whereas 26 IncB/O/K/Z types were related to those in Europe. These data will be useful to reveal the whole picture of transmission of CMY-2-producing bacteria inside and outside Japan.

scholarly journals Comparative Analysis of Transcriptome and sRNAs Expression Patterns in the Brachypodium distachyon— Magnaporthe oryzae Pathosystems

2021 ◽  
Vol 22 (2) ◽  
pp. 650
Author(s):  
Silvia Zanini ◽  
Ena Šečić ◽  
Tobias Busche ◽  
Matteo Galli ◽  
Ying Zheng ◽  
...  
Keyword(s):  
Magnaporthe Oryzae ◽  
Brachypodium Distachyon ◽  
Expression Patterns ◽  
Critical Role ◽  
Differentially Expressed ◽  
Post Inoculation ◽  
Plant Host ◽  
Fungal Cell ◽  
Fungal Virulence ◽  
Leaves And Roots

The hemibiotrophic fungus Magnaporthe oryzae (Mo) is the causative agent of rice blast and can infect aerial and root tissues of a variety of Poaceae, including the model Brachypodium distachyon (Bd). To gain insight in gene regulation processes occurring at early disease stages, we comparatively analyzed fungal and plant mRNA and sRNA expression in leaves and roots. A total of 310 Mo genes were detected consistently and differentially expressed in both leaves and roots. Contrary to Mo, only minor overlaps were observed in plant differentially expressed genes (DEGs), with 233 Bd-DEGs in infected leaves at 2 days post inoculation (DPI), compared to 4978 at 4 DPI, and 138 in infected roots. sRNA sequencing revealed a broad spectrum of Mo-sRNAs that accumulated in infected tissues, including candidates predicted to target Bd mRNAs. Conversely, we identified a subset of potential Bd-sRNAs directed against fungal cell wall components, virulence genes and transcription factors. We also show a requirement of operable RNAi genes from the DICER-like (DCL) and ARGONAUTE (AGO) families for fungal virulence. Overall, our work elucidates the extensive reprogramming of transcriptomes and sRNAs in both plant host (Bd) and fungal pathogen (Mo), further corroborating the critical role played by sRNA species in the establishment of the interaction and its outcome.

scholarly journals Evaluation of Antifusarium and Auxin Production of Trichoderma virens InaCC F1030 Isolated from Rhizosphere of Banana

2020 ◽  
Vol 2 (1) ◽  
pp. 31-39
Author(s):  
Toga Pangihotan Napitupulu
Keyword(s):  
Culture Collection ◽  
Trichoderma Virens ◽  
Plant Host ◽  
Trichoderma Species ◽  
Auxin Production ◽  
Volatile Organic ◽  
Plant Growth Promoting ◽  
Growth Promoting ◽  
Indole 3 Acetic Acid

Banana rhizosphere harbors a unique diversity of microbes including fungi that play critical roles in the growth of the plant host as well as might be important for biologically controlling the fungal soil-borne pathogens particularly Fusarium oxysporum f.sp. cubense (Foc), the causing agent of devastating Panama wilt. Among other fungi, we have succeeded to isolate a Trichoderma species from rhizosphere of healthy banana. Molecular identification revealed the isolate as Trichoderma virens InaCC F1030 (being collection of Indonesian Culture Collection or InaCC). Therefore, the aim of this study was to investigate the biological control of our isolate against Foc as well as plant growth promoting ability through its ability to produce auxin (indole-3-acetic acid/IAA). Two approaches were employed to evaluate the antagonism of our isolate against Foc, through direct confrontation test and volatile organic compounds (VOCs) producing. We found that our isolate was considered as antagonistic to the Foc, but not highly antagonistic according to direct confrontation assay. It was also revealed that our isolate produces the VOCs that inhibited around 50% of the mycelial growth of the test pathogen after six to seven days of exposure. Our isolate was able to produce the IAA in axenic submerged fermentation condition particularly in the presence of the precursor L-tryptophan. IAA production ability as well as the mycelial biomass of fungus were increased approximately 17% and 120% respectively as the effect of supplementation of 0.1% of L-tryptophan. These in vitro bioassays lead us to conclude that somehow our isolate T. virens InaCC F1030 has potency to be utilized as biocontrol and biofertilizer agent.

scholarly journals The Apoplastic Secretome of Trichoderma virens During Interaction With Maize Roots Shows an Inhibition of Plant Defence and Scavenging Oxidative Stress Secreted Proteins

2018 ◽  
Vol 9 ◽  
Author(s):  
Guillermo Nogueira-Lopez ◽  
David R. Greenwood ◽  
Martin Middleditch ◽  
Christopher Winefield ◽  
Carla Eaton ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Plant Defence ◽  
Secreted Proteins ◽  
Trichoderma Virens ◽  
Maize Roots

scholarly journals Microbiome Networks: A Systems Framework for Identifying Candidate Microbial Assemblages for Disease Management

2016 ◽  
Vol 106 (10) ◽  
pp. 1083-1096 ◽  
Author(s):  
R. Poudel ◽  
A. Jumpponen ◽  
D. C. Schlatter ◽  
T. C. Paulitz ◽  
B. B. McSpadden Gardener ◽  
...  
Keyword(s):  
Network Analysis ◽  
Disease Management ◽  
A Priori ◽  
Network Models ◽  
Disease Suppression ◽  
Plant Host ◽  
Network Analyses ◽  
General Network ◽  
Positive Direct ◽  
Systems Framework

Network models of soil and plant microbiomes provide new opportunities for enhancing disease management, but also challenges for interpretation. We present a framework for interpreting microbiome networks, illustrating how observed network structures can be used to generate testable hypotheses about candidate microbes affecting plant health. The framework includes four types of network analyses. “General network analysis” identifies candidate taxa for maintaining an existing microbial community. “Host-focused analysis” includes a node representing a plant response such as yield, identifying taxa with direct or indirect associations with that node. “Pathogen-focused analysis” identifies taxa with direct or indirect associations with taxa known a priori as pathogens. “Disease-focused analysis” identifies taxa associated with disease. Positive direct or indirect associations with desirable outcomes, or negative associations with undesirable outcomes, indicate candidate taxa. Network analysis provides characterization not only of taxa with direct associations with important outcomes such as disease suppression, biofertilization, or expression of plant host resistance, but also taxa with indirect associations via their association with other key taxa. We illustrate the interpretation of network structure with analyses of microbiomes in the oak phyllosphere, and in wheat rhizosphere and bulk soil associated with the presence or absence of infection by Rhizoctonia solani.

scholarly journals Broccoli: combining phylogenetic and network analyses for orthology assignment

2019 ◽  
Author(s):  
Romain Derelle ◽  
Hervé Philippe ◽  
John K. Colbourne
Keyword(s):  
Learning Algorithm ◽  
Phylogenetic Analyses ◽  
Gene Clustering ◽  
Comparative Genomic ◽  
Orthology Assignment ◽  
Bioinformatic Tools ◽  
Network Analyses ◽  
Benchmark Datasets ◽  
Genomic Studies ◽  
High Level

AbstractOrthology assignment is a key step of comparative genomic studies, for which many bioinformatic tools have been developed. However, all gene clustering pipelines are based on the analysis of protein distances, which are subject to many artefacts. In this paper we introduce Broccoli, a user-friendly pipeline designed to infer, with high precision, orthologous groups and pairs of proteins using a phylogeny-based approach. Briefly, Broccoli performs ultra-fast phylogenetic analyses on most proteins and builds a network of orthologous relationships. Orthologous groups are then identified from the network using a parameter-free machine learning algorithm. Broccoli is also able to detect chimeric proteins resulting from gene-fusion events and to assign these proteins to the corresponding orthologous groups. Tested on two benchmark datasets, Broccoli outperforms current orthology pipelines. In addition, Broccoli is scalable, with runtimes similar to those of recent distance-based pipelines. Given its high level of performance and efficiency, this new pipeline represents a suitable choice for comparative genomic studies.Broccoli is freely available at https://github.com/rderelle/Broccoli.

scholarly journals Influence of plant host and organ, management strategy, and spore traits on microbiome composition

2020 ◽  
Author(s):  
Kristi Gdanetz ◽  
Zachary Noel ◽  
Frances Trail
Keyword(s):  
Microbial Communities ◽  
Bacterial Communities ◽  
Life Histories ◽  
Management Strategies ◽  
Alpha Diversity ◽  
Fungal Spore ◽  
Organ Specificity ◽  
Growth Stages ◽  
Plant Host ◽  
Network Analyses

ABSTRACTMicrobiomes from maize and soybean were characterized in a long-term three-crop rotation research site, under four different land management strategies, to begin unraveling the effects of common farming practices on microbial communities. The fungal and bacterial communities of leaves, stems, and roots in host species were characterized across the growing season using amplicon sequencing and compared with the results of a similar study on wheat. Communities differed across hosts, and among plant growth stages and organs, and these effects were most pronounced in the bacterial communities of the wheat and maize phyllosphere. Roots consistently showed the highest number of bacterial OTUs compared to above-ground organs, whereas the alpha diversity of fungi was similar between above- and below-ground organs. Network analyses identified putatively influential members of the microbial communities of the three host plant species. The fungal taxa specific to roots, stems, or leaves were examined to determine if the specificity reflected their life histories based on previous studies. The analysis suggests that fungal spore traits are drivers of organ specificity in the fungal community. Identification of influential taxa in the microbial community and understanding how community structure of specific crop organs is formed, will provide a critical resource for manipulations of microbial communities. The ability to predict how organ specific communities are influenced by spore traits will enhance our ability to introduce them sustainably.

scholarly journals A class I hydrophobin in Trichoderma virens influences plant-microbe interactions through enhancement of enzyme activity and MAMP recognition

2021 ◽  
Author(s):  
James T Taylor ◽  
Inna V Krieger ◽  
Frankie K Crutcher ◽  
Pierce Jamieson ◽  
Benjamin A Horwitz ◽  
...  
Keyword(s):  
Enzyme Activity ◽  
Class I ◽  
Systemic Resistance ◽  
Trichoderma Virens ◽  
Colletotrichum Graminicola ◽  
Cell Wall Degrading Enzymes ◽  
Plant Host ◽  
Trichoderma Spp ◽  
Plant Symbiont ◽  
Molecular Pattern

The filamentous fungus, Trichoderma virens, is a well-known mycoparasitic plant symbiont, valued for its biocontrol capabilities. T. virens initiates a symbiotic relationship with a plant host through the colonization of its roots. To achieve colonization, the fungus must communicate with the host and evade its innate defenses. Hydrophobins from Trichoderma spp. have previously been demonstrated to be involved in colonization of host roots. In this study, the class I hydro-phobin, HFB9A from T. virens was characterized for a potential role in root colonization. Δhfb9a gene deletion mutants colonized less than the wild-type strain, were unable to induce systemic resistance against Colletotrichum graminicola, and showed a reduction in the activity of its cell wall degrading enzymes. The purified HFB9A protein was able to complement the enzyme activity of mutant culture filtrates as well as enhance the activity of commercially sourced cellulase. When exogenously applied to Arabidopsis plants, HFB9A protein induced phosphorylation of AtMAPK3/6, suggesting that it functions as a microbe-associated molecular pattern.

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