[ged] Paper for journal club - next Wed, 4/25

[Adina Chuang Howe]

Hi all,

I'll be presenting the attached paper next week at journal club to
show what kind of "real biology" we can learn from sequencing and
analysis efforts of environmental samples.

See ya then (unless I'm called to jury duty),
Adina


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Metatranscriptomics Reveals the Diversity of Genes Expressed by
Eukaryotes in Forest Soils

Coralie Damon1, Fre ́ de ́ ric Lehembre1, Christine Oger-Desfeux2,
Patricia Luis1, Jacques Ranger3, Laurence Fraissinet-Tachet1, Roland
Marmeisse1*

Abstract

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
2610,000 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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