Dataset Information

Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation.

ABSTRACT: The moose (Alces alces) is a ruminant that harvests energy from fiber-rich lignocellulose material through carbohydrate-active enzymes (CAZymes) produced by its rumen microbes. We applied shotgun metagenomics to rumen contents from six moose to obtain insights into this microbiome. Following binning, 99 metagenome-assembled genomes (MAGs) belonging to 11 prokaryotic phyla were reconstructed and characterized based on phylogeny and CAZyme profile. The taxonomy of these MAGs reflected the overall composition of the metagenome, with dominance of the phyla Bacteroidetes and Firmicutes. Unlike in other ruminants, Spirochaetes constituted a significant proportion of the community and our analyses indicate that the corresponding strains are primarily pectin digesters. Pectin-degrading genes were also common in MAGs of Ruminococcus, Fibrobacteres and Bacteroidetes and were overall overrepresented in the moose microbiome compared with other ruminants. Phylogenomic analyses revealed several clades within the Bacteriodetes without previously characterized genomes. Several of these MAGs encoded a large numbers of dockerins, a module usually associated with cellulosomes. The Bacteroidetes dockerins were often linked to CAZymes and sometimes encoded inside polysaccharide utilization loci, which has never been reported before. The almost 100 CAZyme-annotated genomes reconstructed in this study provide an in-depth view of an efficient lignocellulose-degrading microbiome and prospects for developing enzyme technology for biorefineries.

SUBMITTER: Svartstrom O

PROVIDER: S-EPMC5648042 | biostudies-literature | 2017 Nov

REPOSITORIES: biostudies-literature

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Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation.

Svartström Olov O Alneberg Johannes J Terrapon Nicolas N Lombard Vincent V de Bruijn Ino I Malmsten Jonas J Dalin Ann-Marie AM El Muller Emilie E Shah Pranjul P Wilmes Paul P Henrissat Bernard B Aspeborg Henrik H Andersson Anders F AF

The ISME journal 20170721 11

The moose (Alces alces) is a ruminant that harvests energy from fiber-rich lignocellulose material through carbohydrate-active enzymes (CAZymes) produced by its rumen microbes. We applied shotgun metagenomics to rumen contents from six moose to obtain insights into this microbiome. Following binning, 99 metagenome-assembled genomes (MAGs) belonging to 11 prokaryotic phyla were reconstructed and characterized based on phylogeny and CAZyme profile. The taxonomy of these MAGs reflected the overall ...[more]

PMID: 28731473

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Project description:Given recent and abrupt declines in the abundance of moose (Alces alces) throughout parts of Minnesota and elsewhere in North America, accurately estimating statewide population trends and demographic parameters is a high priority for their continued management and conservation. Statistical population reconstruction using integrated population models provides a flexible framework for combining information from multiple studies to produce robust estimates of population abundance, recruitment, and survival. We used this framework to combine aerial survey data and survival data from telemetry studies to recreate trends and demographics of moose in northeastern Minnesota, USA, from 2005 to 2020. Statistical population reconstruction confirmed the sharp decline in abundance from an estimated 7,841 (90% CI = 6,702-8,933) in 2009 to 3,386 (90% CI = 2,681-4,243) animals in 2013, but also indicated that abundance has remained relatively stable since then, except for a slight decline to 3,163 (90% CI = 2,403-3,718) in 2020. Subsequent stochastic projection of the population from 2021 to 2030 suggests that this modest decline will continue for the next 10 years. Both annual adult survival and per-capita recruitment (number of calves that survived to 1 year per adult female alive during the previous year) decreased substantially in years 2005 and 2019, from 0.902 (SE = 0.043) to 0.689 (SE = 0.061) and from 0.386 (SE = 0.030) to 0.303 (SE = 0.051), respectively. Sensitivity analysis revealed that moose abundance was more sensitive to fluctuations in adult survival than recruitment; thus, we conclude that the steep decline in 2013 was driven primarily by decreasing adult survival. Our analysis demonstrates the potential utility of using statistical population reconstruction to monitor moose population trends and to identify population declines more quickly. Future studies should focus on providing better estimates of per-capita recruitment, using pregnancy rates and calf survival, which can then be incorporated into reconstruction models to help improve estimates of population change through time.

Dataset Information

Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation.

Publications

Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation.

Similar Datasets

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