Metatranscriptomics of eukaryotes in forest soils

Pine needles What would happen if all the leaves fell off the trees and did not rot? We’d be buried under them and all plants would run out of nutrients and die, then we would starve. So the seemingly non-sexy buisness of rotting is rather important when it comes to element and nutrient cycles.

In ecological studies, leaf litter degradation is often estimated by measuring parameters such as soil respiration, litter mass loss or the activities of specific microbial enzymes in soil extracts. In microbiology, the degradation of plant-derived compounds such as lignocellulose has been studied using a few microbial model species and has recently led to the sequencing of the genomes of different saprotrophic fungal species which use different strategies to degrade plant material, thus revealing the full enzymatic machinery implicated in this process. Under natural conditions, litter degradation is generally carried out by consortia of species that either act simultaneously or replace one another on a common piece of plant debris in a sometimes predictable manner and not by a single microbial species. It can therefore be anticipated that the molecular machinery deployed to completely mineralize litter in the field is far more complex and diverse than the machinery observed in a single microbial genome. In addition, it is likely that the diversity of this machinery is partly controlled by litter chemistry and complexity and therefore by plant community composition.

By allowing access to the genome contents of the different microorganisms present in a common environment (metagenomics) or to the set of genes they express (metatranscriptomics), environmental genomics offers a novel opportunity to decipher at the molecular level, complex ecological processes such as plant organic matter degradation, thus bridging the gap between global field measurements and targeted genomic approaches.

 

Metatranscriptomics Reveals the Diversity of Genes Expressed by Eukaryotes in Forest Soils. (2012) PLoS ONE 7(1): e28967. doi:10.1371/journal.pone.0028967
Eukaryotic organisms play essential roles in the biology and fertility of soils. For example the micro and mesofauna contribute to the fragmentation and homogenization of plant organic matter, while its hydrolysis is primarily performed by the fungi. To get a global picture of the activities carried out by soil eukaryotes we sequenced 2×10,000 cDNAs synthesized from polyadenylated mRNA directly extracted from soils sampled in beech (Fagus sylvatica) and spruce (Picea abies) forests. Taxonomic affiliation of both cDNAs and 18S rRNA sequences showed a dominance of sequences from fungi (up to 60%) and metazoans while protists represented less than 12% of the 18S rRNA sequences. Sixty percent of cDNA sequences from beech forest soil and 52% from spruce forest soil had no homologs in the GenBank/EMBL/DDJB protein database. A Gene Ontology term was attributed to 39% and 31.5% of the spruce and beech soil sequences respectively. Altogether 2076 sequences were putative homologs to different enzyme classes participating to 129 KEGG pathways among which several were implicated in the utilisation of soil nutrients such as nitrogen (ammonium, amino acids, oligopeptides), sugars, phosphates and sulfate. Specific annotation of plant cell wall degrading enzymes identified enzymes active on major polymers (cellulose, hemicelluloses, pectin, lignin) and glycoside hydrolases represented 0.5% (beech soil)–0.8% (spruce soil) of the cDNAs. Other sequences coding enzymes active on organic matter (extracellular proteases, lipases, a phytase, P450 monooxygenases) were identified, thus underlining the biotechnological potential of eukaryotic metatranscriptomes. The phylogenetic affiliation of 12 full-length carbohydrate active enzymes showed that most of them were distantly related to sequences from known fungi. For example, a putative GH45 endocellulase was closely associated to molluscan sequences, while a GH7 cellobiohydrolase was closest to crustacean sequences, thus suggesting a potentially significant contribution of non-fungal eukaryotes in the actual hydrolysis of soil organic matter.

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