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Diversity of glycosyl hydrolases from cellulose-depleting communities enriched from casts of two earthworm species.

ABSTRACT: The guts and casts of earthworms contain microbial assemblages that process large amounts of organic polymeric substrates from plant litter and soil; however, the enzymatic potential of these microbial communities remains largely unexplored. In the present work, we retrieved carbohydrate-modifying enzymes through the activity screening of metagenomic fosmid libraries from cellulose-depleting microbial communities established with the fresh casts of two earthworm species, Aporrectodea caliginosa and Lumbricus terrestris, as inocula. Eight glycosyl hydrolases (GHs) from the A. caliginosa-derived community were multidomain endo-beta-glucanases, beta-glucosidases, beta-cellobiohydrolases, beta-galactosidase, and beta-xylosidases of known GH families. In contrast, two GHs derived from the L. terrestris microbiome had no similarity to any known GHs and represented two novel families of beta-galactosidases/alpha-arabinopyranosidases. Members of these families were annotated in public databases as conserved hypothetical proteins, with one being structurally related to isomerases/dehydratases. This study provides insight into their biochemistry, domain structures, and active-site architecture. The two communities were similar in bacterial composition but significantly different with regard to their eukaryotic inhabitants. Further sequence analysis of fosmids and plasmids bearing the GH-encoding genes, along with oligonucleotide usage pattern analysis, suggested that those apparently originated from Gammaproteobacteria (pseudomonads and Cellvibrio-like organisms), Betaproteobacteria (Comamonadaceae), and Alphaproteobacteria (Rhizobiales).

SUBMITTER: Beloqui A

PROVIDER: S-EPMC2935051 | biostudies-literature | 2010 Sep

REPOSITORIES: biostudies-literature

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Diversity of glycosyl hydrolases from cellulose-depleting communities enriched from casts of two earthworm species.

Beloqui Ana A Nechitaylo Taras Y TY López-Cortés Nieves N Ghazi Azam A Guazzaroni María-Eugenia ME Polaina Julio J Strittmatter Axel W AW Reva Oleg O Waliczek Agnes A Yakimov Michail M MM Golyshina Olga V OV Ferrer Manuel M Golyshin Peter N PN

Applied and environmental microbiology 20100709 17

The guts and casts of earthworms contain microbial assemblages that process large amounts of organic polymeric substrates from plant litter and soil; however, the enzymatic potential of these microbial communities remains largely unexplored. In the present work, we retrieved carbohydrate-modifying enzymes through the activity screening of metagenomic fosmid libraries from cellulose-depleting microbial communities established with the fresh casts of two earthworm species, Aporrectodea caliginosa ...[more]

PMID: 20622123

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Project description:The microbial populations in no-till agricultural soil and casts of the earthworm Lumbricus rubellus were examined by culturing and molecular methods. Clone libraries of the 16S rRNA genes were prepared from DNA isolated directly from the soil and earthworm casts. Although no single phylum dominated the soil library of 95 clones, the largest numbers of clones were from Acidobacteria (14%), Cytophagales (13%), Chloroflexi (8%), and gamma-Proteobacteria (8%). While the cast clone library of 102 clones was similar to the soil library, the abundances of several taxa were different. Representatives of the Pseudomonas genus as well as the Actinobacteria and Firmicutes increased in number, and one group of unclassified organisms found in the soil library was absent in the cast library. Likewise, soil and cast archaeal 16S rRNA gene libraries were similar, although the abundances of some groups were different. Two hundred and thirty aerobic bacteria were also isolated on general heterotrophic media from casts, burrows, and soil. The cast isolates were both phenotypically and genotypically different from the soil isolates. The cast isolates were more likely to reduce nitrate, grow on acetate and Casamino Acids, and utilize fewer sugars than the soil isolates. On the basis of their ribotypes, the cast isolates were dominated by Aeromonas spp. (28%), which were not found in the soil isolates, and other gamma-Proteobacteria (49%). In contrast, the soil isolates were mostly Actinobacteria (53%), Firmicutes (16%), and gamma-Proteobacteria (19%). Isolates obtained from the sides of earthworm burrows were not different from the soil isolates. Diversity indices for the collections of isolates as well as rRNA gene libraries indicated that the species richness and evenness were decreased in the casts from their levels in the soil. These results were consistent with a model where a large portion of the microbial population in soil passes through the gastrointestinal tract of the earthworm unchanged while representatives of some phyla increase in abundance.

Project description:Biodiversity is a major driver of numerous ecosystem functions. However, consequences of changes in forest biodiversity remain difficult to predict because of limited knowledge about how tree diversity influences ecosystem functions. Litter decomposition is a key process affecting nutrient cycling, productivity, and carbon storage and can be influenced by plant biodiversity. Leaf litter species composition, environmental conditions, and the detritivore community are main components of the decomposition process, but their complex interactions are poorly understood. In this study, we tested the effect of tree functional diversity (FD) on litter decomposition in a field experiment manipulating tree diversity and partitioned the effects of litter physiochemical diversity and the detritivore community. We used litterbags with different mesh sizes to separate the effects of microorganisms and microfauna, mesofauna, and macrofauna and monitored soil fauna using pitfall traps and earthworm extractions. We hypothesized that higher tree litter FD accelerates litter decomposition due to the availability of complementary food components and higher activity of detritivores. Although we did not find direct effects of tree FD on litter decomposition, we identified key litter traits and macrodetritivores that explained part of the process. Litter mass loss was found to decrease with an increase in leaf litter carbon:nitrogen ratio. Moreover, litter mass loss increased with an increasing density of epigeic earthworms, with most pronounced effects in litterbags with a smaller mesh size, indicating indirect effects. Higher litter FD and litter nutrient content were found to increase the density of surface-dwelling macrofauna and epigeic earthworm biomass. Based on structural equation modeling, we conclude that tree FD has a weak positive effect on soil surface litter decomposition by increasing the density of epigeic earthworms and that litter nitrogen-related traits play a central role in tree composition effects on soil fauna and decomposition.

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Dataset Information

Diversity of glycosyl hydrolases from cellulose-depleting communities enriched from casts of two earthworm species.

Publications

Diversity of glycosyl hydrolases from cellulose-depleting communities enriched from casts of two earthworm species.

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