Open Access
Metatranscriptomics sheds light on the links between the functional traits of fungal guilds and ecological processes in forest soil ecosystems
(Blackwell Scientific Publications Ltd, 2023) Auer, Lucas; Buée, Marc; Fauchery, Laure; Lombard, Vincent; Barry, Kerrie; Clum, Alicia; Copeland, Alex; Daum, Chris; LaButti, Kurt; Singan, Vasanth; Yoshinaga, Yuko; Martineau, Christine; Castillo Martínez, Federico; Alfaro Sánchez, Manuel; Imbert Rodríguez, Bosco; Ramírez Nasto, Lucía; Castanera Andrés, Raúl; Pisabarro de Lucas, Gerardo; Finlay, Roger; Lindahl, Björn D.; Olson, Ake; Séguin, Armand; Kohler, Annegret; Henrissat, Bernard; Grigoriev, Igor V.; Martin, Francis; Agronomía, Biotecnología y Alimentación; Agronomia, Bioteknologia eta Elikadura; Institute for Multidisciplinary Research in Applied Biology - IMAB
Soil fungi belonging to different functional guilds, such as saprotrophs, pathogens, and mycorrhizal symbionts, play key roles in forest ecosystems. To date, no study has compared the actual gene expression of these guilds in different forest soils. We used metatranscriptomics to study the competition for organic resources by these fungal groups in boreal, temperate, and Mediterranean forest soils. Using a dedicated mRNA annotation pipeline combined with the JGI MycoCosm database, we compared the transcripts of these three fungal guilds, targeting enzymes involved in C- and N mobilization from plant and microbial cell walls. Genes encoding enzymes involved in the degradation of plant cell walls were expressed at a higher level in saprotrophic fungi than in ectomycorrhizal and pathogenic fungi. However, ectomycorrhizal and saprotrophic fungi showed similarly high expression levels of genes encoding enzymes involved in fungal cell wall degradation. Transcripts for N-related transporters were more highly expressed in ectomycorrhizal fungi than in other groups. We showed that ectomycorrhizal and saprotrophic fungi compete for N in soil organic matter, suggesting that their interactions could decelerate C cycling. Metatranscriptomics provides a unique tool to test controversial ecological hypotheses and to better understand the underlying ecological processes involved in soil functioning and carbon stabilization.
Open Access
Expansion of the global RNA virome reveals diverse clades of bacteriophages
(Elsevier, 2022) Neri, Uri; Wolf, Yuri I.; Roux, Simon; Camargo, Antonio Pedro; Lee, Benjamin; Kazlauskas, Darius; Chen, I. Min; Ivanova, Natalia; Zeigler Allen, Lisa; Paez-Espino, David; Bryant, Donald A.; Bhaya, Devaki; Krupovic, Mart; Dolja, Valerian V.; Kyrpides, Nikos C.; Koonin, Eugene V.; Gophna, Uri; RNA Virus Discovery Consortium; Narrowe, Adrienne B.; Ramírez Nasto, Lucía; Wang, Zhong; Nusslein, Klaus; Meredith, Laura K.; Buée, Marc; Huntemann, Marcel; Kalyuzhnaya, Marina G.; Waldrop, Mark P.; Sullivan, Matthew B.; Schrenk, Matthew O.; Hess, Matthias; Vega, Michael A.; O’Malley, Michelle A.; Medina, Mónica; Gilbert, Naomi E.; Delherbe, Nathalie; Mason, Olivia U.; Probst, Alexander J.; Sczyrba, Alexander; Kohler, Annegret; Séguin, Armand; Shade, Ashley; Campbell, Barbara J.; Lindahl, Björn D.; Reese, Brandi Kiel; Roque, Breanna M.; DeRito, Christopher; Averill, Colin; Cullen, Daniel; Beck, David A.C.; Walsh, David A.; Ward, David M.; Wu, Dongying; Eloe-Fadrosh, Emiley; Brodie, Eoin L.; Dijkstra, Paul; Chuckran, Peter F.; Baldrian, Petr; Constant, Philippe; Stepanauskas, Ramunas; Daly, Rebecca A.; Lamendella, Regina; Gruninger, Robert J.; McKay, Robert M.; Hylander, Samuel; Lebeis, Sarah L.; Esser, Sarah P.; Acinas, Silvia G.; Young, Erica B.; Lilleskov, Erik A.; Castillo, Federico J.; Martin, Francis; LeCleir, Gary R.; Attwood, Graeme T.; Cadillo-Quiroz, Hinsby; Simon, Holly M.; Hewson, Ian; Grigoriev, Igor V.; Tiedje, James M.; Jansson, Janet K.; Lee, Janey; VanderGheynst, Jean S.; Dangl, Jeff; Bowman, Jeff S.; Blanchard, Jeffrey L.; Bowen, Jennifer L.; Xu, Jiangbing; Banfield, Jillian F.; Deming, Jody W.; Kostka, Joel E.; Gladden, John M.; Rapp, Josephine Z.; Sharpe, Joshua; McMahon, Katherine D.; Treseder, Kathleen K.; Bidle, Kay D.; Wrighton, Kelly C.; Thamatrakoln, Kimberlee; Wilhelm, Steven S.; Singer, Steven W.; Tringe, Susannah S.; Woyke, Tanja; Reddy, T.B.K.; Bell, Terrence H.; Mock, Thomas; McAllister, Tim; Thiel, Vera; Denef, Vincent J.; Liu, Wen-Tso; Martens-Habbena, Willm; Liu, Xiao-Jun Allen; Cooper, Zachary S.; Agronomía, Biotecnología y Alimentación; Agronomia, Bioteknologia eta Elikadura; Institute for Multidisciplinary Research in Applied Biology - IMAB
High-throughput RNA sequencing offers broad opportunities to explore the Earth RNA virome. Mining 5,150 diverse metatranscriptomes uncovered >2.5 million RNA virus contigs. Analysis of >330,000 RNA-dependent RNA polymerases (RdRPs) shows that this expansion corresponds to a 5-fold increase of the known RNA virus diversity. Gene content analysis revealed multiple protein domains previously not found in RNA viruses and implicated in virus-host interactions. Extended RdRP phylogeny supports the monophyly of the five established phyla and reveals two putative additional bacteriophage phyla and numerous putative additional classes and orders. The dramatically expanded phylum Lenarviricota, consisting of bacterial and related eukaryotic viruses, now accounts for a third of the RNA virome. Identification of CRISPR spacer matches and bacteriolytic proteins suggests that subsets of picobirnaviruses and partitiviruses, previously associated with eukaryotes, infect prokaryotic hosts.

Ramírez Nasto, Lucía

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