The Experts below are selected from a list of 117 Experts worldwide ranked by ideXlab platform
Mary K Firestone - One of the best experts on this subject based on the ideXlab platform.
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metatranscriptomic reconstruction reveals rna viruses with the potential to shape carbon cycling in soil
Proceedings of the National Academy of Sciences of the United States of America, 2019Co-Authors: Evan P. Starr, Erin E. Nuccio, Mary K Firestone, Jillian F Banfield, Jennifer PettridgeAbstract:Viruses impact nearly all organisms on Earth, with ripples of influence in agriculture, health, and biogeochemical processes. However, very little is known about RNA viruses in an environmental context, and even less is known about their diversity and ecology in soil, 1 of the most complex microbial systems. Here, we assembled 48 individual metatranscriptomes from 4 habitats within a planted soil sampled over a 22-d time series: Rhizosphere alone, detritosphere alone, rhizosphere with added root detritus, and unamended soil (4 time points and 3 biological replicates). We resolved the RNA viral community, uncovering a high diversity of viral sequences. We also investigated possible host organisms by analyzing metatranscriptome marker genes. Based on viral phylogeny, much of the diversity was Narnaviridae that may parasitize fungi or Leviviridae, which may infect Proteobacteria. Both host and viral communities appear to be highly dynamic, and rapidly diverged depending on experimental conditions. The viral and host communities were structured based on the presence of root litter. Clear temporal dynamics by Leviviridae and their hosts indicated that viruses were replicating. With this time-resolved analysis, we show that RNA viruses are diverse, abundant, and active in soil. When viral infection causes host cell death, it may mobilize cell carbon in a process that may represent an overlooked component of soil carbon cycling.
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Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil
bioRxiv, 2019Co-Authors: Evan P. Starr, Erin E. Nuccio, Jennifer Pett-ridge, Jillian F Banfield, Mary K FirestoneAbstract:Abstract Viruses impact nearly all organisms on Earth, with ripples of influence in agriculture, health and biogeochemical processes. However, very little is known about RNA viruses in an environmental context, and even less is known about their diversity and ecology in the most complex microbial system, soil. Here, we assembled 48 individual metatranscriptomes from four habitats within a soil sampled over a 22-day time series: rhizosphere alone, detritosphere alone, a combination of the two, and unamended soil (four time points and three biological replicates per time point). We resolved the RNA viral community, uncovering a high diversity of viral sequences. We also investigated possible host organisms by analyzing metatranscriptome marker gene content. Based on viral phylogeny, much of the diversity was Narnaviridae that parasitize fungi or Leviviridae that infect Proteobacteria. Both host and viral communities appear to be highly dynamic, and rapidly diverged depending on experimental conditions. The viral communities were structured based on the presence of litter, while putative hosts appeared to be impacted by both the presence of litter and roots. A clear time signature from Leviviridae and their hosts indicated that viruses were replicating. With this time-resolved analysis, we show that RNA viruses are diverse, abundant and active in soil. Their replication causes host cell death, mobilizing carbon in a process that represents a largely overlooked component of carbon cycling in soil.
Mark Varrelmann - One of the best experts on this subject based on the ideXlab platform.
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Deep Sequencing Analysis Reveals the Mycoviral Diversity of the Virome of an Avirulent Isolate of Rhizoctonia solani AG-2-2 IV
PLOS ONE, 2016Co-Authors: Anika Bartholomäus, Anika Winkler, Andreas Schluter, Daniel Wibberg, Alfred Puhler, Mark VarrelmannAbstract:Rhizoctonia solani represents an important plant pathogenic Basidiomycota species complex and the host of many different mycoviruses, as indicated by frequent detection of dsRNA elements in natural populations of the fungus. To date, eight different mycoviruses have been characterized in Rhizoctonia and some of them have been reported to modulate its virulence. DsRNA extracts of the avirulent R. solani isolate DC17 (AG2-2-IV) displayed a diverse pattern, indicating multiple infections with mycoviruses. Deep sequencing analysis of the dsRNA extract, converted to cDNA, revealed that this isolate harbors at least 17 different mycovirus species. Based on the alignment of the conserved RNA-dependent RNA-polymerase (RdRp) domain, this viral community included putative members of the families Narnaviridae, Endornaviridae, Partitiviridae and Megabirnaviridae as well as of the order Tymovirales. Furthermore, viruses, which could not be assigned to any existing family or order, but showed similarities to so far unassigned species like Sclerotinia sclerotiorum RNA virus L, Rhizoctonia solani dsRNA virus 1, Aspergillus foetidus slow virus 2 or Rhizoctonia fumigata virus 1, were identified. This is the first report of a fungal isolate infected by 17 different viral species and a valuable study case to explore the diversity of mycoviruses infecting R. solani.
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Phylogenetic analysis of the members of the family Narnaviridae.
2016Co-Authors: Anika Bartholomäus, Anika Winkler, Andreas Schluter, Daniel Wibberg, Alfred Puhler, Mark VarrelmannAbstract:An unrooted phylogenetic tree of the Narnaviridae was calculated based on the alignment of the RdRp domain spanning the conserved motifs A to F using the neighbor-joining method with 1000 bootstrap replicates. The scale represents a genetic distance of 0.1 amino acid substitutions per site. Bootstrap values < 50% are not shown. Analyzed species include mitoviruses identified in Rhizoctonia as well as species of the family Narnaviridae recognized by the ICTV. Species identified in this study are marked with dots. Analysis was conducted using MEGA 6.06 and the sequence alignment algorithm MUSCLE [45]. CpMV-1, Cryphonectria parasitica mitovirus (NP_660174.1); OMV-3a, Ophiostoma mitovirus 3a (CAJ32468.1); OMV-4, Ophiostoma mitovirus 4 (NP_660179.1); OMV-5, Ophiostoma mitovirus 5 (NP_660180.1); OMV-6, Ophiostoma mitovirus 6 (NP_660181.1); ScNV-20S, Saccharomyces 20S RNA narnavirus (NP_660178.1); ScNV-23S, Saccharomyces 23S RNA narnavirus (NP_660177.1); RsMV-1, Rhizoctonia solani mitovirus 1 (ALD89121.1); TcMV-1, Thanatephorus cucumeris mitovirus 1 (AAD17381.1); RsMV-2, Rhizoctonia solani mitovirus 2 (ALD89121.1); RsMV-3, Rhizoctonia solani mitovirus 3 (ALD89122.1); RsMV-4, Rhizoctonia solani mitovirus 4 (ALD89123.1); RsMV-5, Rhizoctonia solani mitovirus 5 (ALD89124.1); RsMV-6, Rhizoctonia solani mitovirus 6 (ALD89125.1); RsMV-7, Rhizoctonia solani mitovirus 7 (ALD89126.1); RsMV-8, Rhizoctonia solani mitovirus 8 (ALD89127.1); RsMV-9, Rhizoctonia solani mitovirus 9 (ALD89128.1); RsMV-10, Rhizoctonia solani mitovirus 10 (ALD89102.1); RsMV-11, Rhizoctonia solani mitovirus 11 (ALD89116.1); RsMV-12, Rhizoctonia solani mitovirus 12 (ALD89117.1); RsMV-13, Rhizoctonia solani mitovirus 13 (ALD89118.1); RsMV-14, Rhizoctonia solani mitovirus 14 (ALD89119.1); RsMV-15, Rhizoctonia solani mitovirus 15 (ALD89120.1); RsMV-K1, Rhizoctonia solani mitovirus K1 (ALD60243.1); RcMV, Rhizoctonia cerealis mitovirus (AIT71973.1); RsMV-9, Rhizoctonia solani mitovirus 9 DC17 (KX349058); RsMV-16, Rhizoctonia solani mitovirus 16 (KX349057); RsMV-17, Rhizoctonia solani mitovirus 17 (KX349059); RsMV-18, Rhizoctonia solani mitovirus 18 (KX349060); RsMV-19, Rhizoctonia solani mitovirus 19 (KX349056); RsMV-20, Rhizoctonia solani mitovirus 20 (KX349062).
Robert H A Coutts - One of the best experts on this subject based on the ideXlab platform.
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studies on the virome of the entomopathogenic fungus beauveria bassiana reveal novel dsrna elements and mild hypervirulence
PLOS Pathogens, 2017Co-Authors: Ioly Kottaloizou, Robert H A CouttsAbstract:The entomopathogenic fungus Beauveria bassiana has a wide host range and is used as a biocontrol agent against arthropod pests. Mycoviruses have been described in phytopathogenic fungi while in entomopathogenic fungi their presence has been reported only rarely. Here we show that 21.3% of a collection of B. bassiana isolates sourced from worldwide locations, harbor dsRNA elements. Molecular characterization of these elements revealed the prevalence of mycoviruses belonging to the Partitiviridae and Totiviridae families, the smallest reported virus to date, belonging to the family Narnaviridae, and viruses unassigned to a family or genus. Of particular importance is the discovery of members of a newly proposed family Polymycoviridae in B. bassiana. Polymycoviruses, previously designated as tetramycoviruses, consist of four non-conventionally encapsidated capped dsRNAs. The presence of additional non-homologous genomic segments in B. bassiana polymycoviruses and other fungi illustrates the unprecedented dynamic nature of the viral genome. Finally, a comparison of virus-free and virus-infected isogenic lines derived from an exemplar B. bassiana isolate revealed a mild hypervirulent effect of mycoviruses on the growth of their host isolate and on its pathogenicity against the greater wax moth Galleria mellonella, highlighting for the first time the potential of mycoviruses as enhancers of biocontrol agents.
Anika Bartholomäus - One of the best experts on this subject based on the ideXlab platform.
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Deep Sequencing Analysis Reveals the Mycoviral Diversity of the Virome of an Avirulent Isolate of Rhizoctonia solani AG-2-2 IV
PLOS ONE, 2016Co-Authors: Anika Bartholomäus, Anika Winkler, Andreas Schluter, Daniel Wibberg, Alfred Puhler, Mark VarrelmannAbstract:Rhizoctonia solani represents an important plant pathogenic Basidiomycota species complex and the host of many different mycoviruses, as indicated by frequent detection of dsRNA elements in natural populations of the fungus. To date, eight different mycoviruses have been characterized in Rhizoctonia and some of them have been reported to modulate its virulence. DsRNA extracts of the avirulent R. solani isolate DC17 (AG2-2-IV) displayed a diverse pattern, indicating multiple infections with mycoviruses. Deep sequencing analysis of the dsRNA extract, converted to cDNA, revealed that this isolate harbors at least 17 different mycovirus species. Based on the alignment of the conserved RNA-dependent RNA-polymerase (RdRp) domain, this viral community included putative members of the families Narnaviridae, Endornaviridae, Partitiviridae and Megabirnaviridae as well as of the order Tymovirales. Furthermore, viruses, which could not be assigned to any existing family or order, but showed similarities to so far unassigned species like Sclerotinia sclerotiorum RNA virus L, Rhizoctonia solani dsRNA virus 1, Aspergillus foetidus slow virus 2 or Rhizoctonia fumigata virus 1, were identified. This is the first report of a fungal isolate infected by 17 different viral species and a valuable study case to explore the diversity of mycoviruses infecting R. solani.
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Phylogenetic analysis of the members of the family Narnaviridae.
2016Co-Authors: Anika Bartholomäus, Anika Winkler, Andreas Schluter, Daniel Wibberg, Alfred Puhler, Mark VarrelmannAbstract:An unrooted phylogenetic tree of the Narnaviridae was calculated based on the alignment of the RdRp domain spanning the conserved motifs A to F using the neighbor-joining method with 1000 bootstrap replicates. The scale represents a genetic distance of 0.1 amino acid substitutions per site. Bootstrap values < 50% are not shown. Analyzed species include mitoviruses identified in Rhizoctonia as well as species of the family Narnaviridae recognized by the ICTV. Species identified in this study are marked with dots. Analysis was conducted using MEGA 6.06 and the sequence alignment algorithm MUSCLE [45]. CpMV-1, Cryphonectria parasitica mitovirus (NP_660174.1); OMV-3a, Ophiostoma mitovirus 3a (CAJ32468.1); OMV-4, Ophiostoma mitovirus 4 (NP_660179.1); OMV-5, Ophiostoma mitovirus 5 (NP_660180.1); OMV-6, Ophiostoma mitovirus 6 (NP_660181.1); ScNV-20S, Saccharomyces 20S RNA narnavirus (NP_660178.1); ScNV-23S, Saccharomyces 23S RNA narnavirus (NP_660177.1); RsMV-1, Rhizoctonia solani mitovirus 1 (ALD89121.1); TcMV-1, Thanatephorus cucumeris mitovirus 1 (AAD17381.1); RsMV-2, Rhizoctonia solani mitovirus 2 (ALD89121.1); RsMV-3, Rhizoctonia solani mitovirus 3 (ALD89122.1); RsMV-4, Rhizoctonia solani mitovirus 4 (ALD89123.1); RsMV-5, Rhizoctonia solani mitovirus 5 (ALD89124.1); RsMV-6, Rhizoctonia solani mitovirus 6 (ALD89125.1); RsMV-7, Rhizoctonia solani mitovirus 7 (ALD89126.1); RsMV-8, Rhizoctonia solani mitovirus 8 (ALD89127.1); RsMV-9, Rhizoctonia solani mitovirus 9 (ALD89128.1); RsMV-10, Rhizoctonia solani mitovirus 10 (ALD89102.1); RsMV-11, Rhizoctonia solani mitovirus 11 (ALD89116.1); RsMV-12, Rhizoctonia solani mitovirus 12 (ALD89117.1); RsMV-13, Rhizoctonia solani mitovirus 13 (ALD89118.1); RsMV-14, Rhizoctonia solani mitovirus 14 (ALD89119.1); RsMV-15, Rhizoctonia solani mitovirus 15 (ALD89120.1); RsMV-K1, Rhizoctonia solani mitovirus K1 (ALD60243.1); RcMV, Rhizoctonia cerealis mitovirus (AIT71973.1); RsMV-9, Rhizoctonia solani mitovirus 9 DC17 (KX349058); RsMV-16, Rhizoctonia solani mitovirus 16 (KX349057); RsMV-17, Rhizoctonia solani mitovirus 17 (KX349059); RsMV-18, Rhizoctonia solani mitovirus 18 (KX349060); RsMV-19, Rhizoctonia solani mitovirus 19 (KX349056); RsMV-20, Rhizoctonia solani mitovirus 20 (KX349062).
Ioly Kottaloizou - One of the best experts on this subject based on the ideXlab platform.
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studies on the virome of the entomopathogenic fungus beauveria bassiana reveal novel dsrna elements and mild hypervirulence
PLOS Pathogens, 2017Co-Authors: Ioly Kottaloizou, Robert H A CouttsAbstract:The entomopathogenic fungus Beauveria bassiana has a wide host range and is used as a biocontrol agent against arthropod pests. Mycoviruses have been described in phytopathogenic fungi while in entomopathogenic fungi their presence has been reported only rarely. Here we show that 21.3% of a collection of B. bassiana isolates sourced from worldwide locations, harbor dsRNA elements. Molecular characterization of these elements revealed the prevalence of mycoviruses belonging to the Partitiviridae and Totiviridae families, the smallest reported virus to date, belonging to the family Narnaviridae, and viruses unassigned to a family or genus. Of particular importance is the discovery of members of a newly proposed family Polymycoviridae in B. bassiana. Polymycoviruses, previously designated as tetramycoviruses, consist of four non-conventionally encapsidated capped dsRNAs. The presence of additional non-homologous genomic segments in B. bassiana polymycoviruses and other fungi illustrates the unprecedented dynamic nature of the viral genome. Finally, a comparison of virus-free and virus-infected isogenic lines derived from an exemplar B. bassiana isolate revealed a mild hypervirulent effect of mycoviruses on the growth of their host isolate and on its pathogenicity against the greater wax moth Galleria mellonella, highlighting for the first time the potential of mycoviruses as enhancers of biocontrol agents.