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

[Jason Pell]

Hi everyone,

Adina will be presenting the paper below tomorrow for journal club at
11am in 2228. Hope to see you then.

Jason

On Tue, Apr 17, 2012 at 2:08 PM, Adina Chuang Howe
<adina.chuang at gmail.com> wrote:
> 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
>
>
> ======
> 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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