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Rescooped by Srini Chaluvadi from Genomics and metagenomics of microbes
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The ISME Journal - Estimating coverage in metagenomic data sets and why it matters

The ISME Journal - Estimating coverage in metagenomic data sets and why it matters | Metagenome | Scoop.it

A ‘metagenome’ is the theoretical collection of genomes from all members of a given microbial community, and a ‘metagenomic data set’ is the subset captured in a given sequencing event. Although these terms are often used interchangeably and metagenomic data sets are regularly called metagenomes by synecdoche, their relationship is analogous to sample and population in statistics. The fraction of the metagenome represented in the metagenomic data set, termed coverage (not to be confused with the repetition of features, termed sequencing depth), is of key importance in assessing statistical significance of features sampled (taxa, genes and so on). However, quantitative computational methods to assess the level of coverage are limited, a problem we have recently attempted to solve. In extreme cases, where small data sets are used to characterize complex communities, misleading inferences can arise. For instance, random variation can be frequently mistaken for real differences in comparisons of metagenomic data sets with extreme differences in coverage. Further, insufficient coverage also reduces the detection limits and statistical power of the comparisons, hiding real, ecologically relevant trends and differences (Figure 1). We demonstrate here how available solutions can determine the level of sequencing coverage obtained by metagenomic data sets and thus, guide their robust analysis and comparison.


Via Francis Martin, Bradford Condon
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Rescooped by Srini Chaluvadi from MycorWeb Plant-Microbe Interactions
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Communities of Endophytic Sebacinales Associated with Roots of Herbaceous Plants in Agricultural and Grassland Ecosystems Are Dominated by Serendipita herbamans sp. nov

Communities of Endophytic Sebacinales Associated with Roots of Herbaceous Plants in Agricultural and Grassland Ecosystems Are Dominated by Serendipita herbamans sp. nov | Metagenome | Scoop.it
Endophytic fungi are known to be commonly associated with herbaceous plants, however, there are few studies focusing on their occurrence and distribution in plant roots from ecosystems with different land uses. To explore the phylogenetic diversity and community structure of Sebacinales endophytes from agricultural and grassland habitats under different land uses, we analysed the roots of herbaceous plants using strain isolation, polymerase chain reaction (PCR), transmission electron microscopy (TEM) and co-cultivation experiments. A new sebacinoid strain named Serendipita herbamans belonging to Sebacinales group B was isolated from the roots of Bistorta vivipara, which is characterized by colourless monilioid cells (chlamydospores) that become yellow with age. This species was very common and widely distributed in association with a broad spectrum of herbaceous plant families in diverse habitats, independent of land use type. Ultrastructurally, the presence of S. herbamans was detected in the cortical cells of Plantago media, Potentilla anserina and Triticum aestivum. In addition, 13 few frequent molecular operational taxonomic units (MOTUs) or species were found across agricultural and grassland habitats, which did not exhibit a distinctive phylogenetic structure. Laboratory-based assays indicate that S. herbamans has the ability to colonize fine roots and stimulate plant growth. Although endophytic Sebacinales are widely distributed across agricultural and grassland habitats, TEM and nested PCR analyses reinforce the observation that these microorganisms are present in low quantity in plant roots, with no evidence of host specificity.

Via Steve Marek, Håvard Kauserud, Stéphane Hacquard, Francis Martin
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Rescooped by Srini Chaluvadi from MycorWeb Plant-Microbe Interactions
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When Maverick Mycorrhizae debunks the Scientific Orthodoxy

When Maverick Mycorrhizae debunks the Scientific Orthodoxy | Metagenome | Scoop.it
 Sorry, I couldn't resist. In most of the text books and literature promoting the wonders of mycorrhizal fungi, both Ecto (EM) & Endo (AM) Mycorrhizae generally are categorized into lists that  highlight the main types of plants which both these differing fungi will supposedly ONLYcolonize. The lists are almost a sort of etched in stone scriptural text that cannot be altered without facing some sort of backlash from the established Orthodoxy. Frankly, the Natural World couldn't care less what the research membership club may assume to be the prevailing consensus. Take for example the Chaparral Plant Community. The conventional thinking is that aside from Scrub Oak, Manzanita and a handful of other plants, most shrubs are Endomycorrhizal . 

Via Jean-Michel Ané, Francis Martin
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Jean-Michel Ané's curator insight, June 9, 11:26 PM

The style is a bit aggressive but it's interesting

Rescooped by Srini Chaluvadi from Genomics and metagenomics of microbes
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Tackling soil diversity with the assembly of large, complex metagenomes

Tackling soil diversity with the assembly of large, complex metagenomes | Metagenome | Scoop.it

Abstract

The large volumes of sequencing data required to sample deeply the microbial communities of complex environments pose new challenges to sequence analysis. De novo metagenomic assembly effectively reduces the total amount of data to be analyzed but requires substantial computational resources. We combine two preassembly filtering approaches—digital normalization and partitioning—to generate previously intractable large metagenome assemblies. Using a human-gut mock community dataset, we demonstrate that these methods result in assemblies nearly identical to assemblies from unprocessed data. We then assemble two large soil metagenomes totaling 398 billion bp (equivalent to 88,000 Escherichia coligenomes) from matched Iowa corn and native prairie soils. The resulting assembled contigs could be used to identify molecular interactions and reaction networks of known metabolic pathways using the Kyoto Encyclopedia of Genes and Genomes Orthology database. Nonetheless, more than 60% of predicted proteins in assemblies could not be annotated against known databases. Many of these unknown proteins were abundant in both corn and prairie soils, highlighting the benefits of assembly for the discovery and characterization of novelty in soil biodiversity. Moreover, 80% of the sequencing data could not be assembled because of low coverage, suggesting that considerably more sequencing data are needed to characterize the functional content of soil.


Via Bradford Condon
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Rescooped by Srini Chaluvadi from MycorWeb Plant-Microbe Interactions
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Symbiotic root fungus promotes growth in plants

Symbiotic root fungus promotes growth in plants | Metagenome | Scoop.it
Researchers at the University of Tübingen have discovered a microscopic fungus which promotes growth in certain plants. "This fungus, native to Europe, is an organic fertilizer with the potential to increase yields of crops such as wheat and maize," says Sigisfredo Garnica of the Institute of Evolution and Ecology.

Read more at: http://phys.org/news/2014-06-symbiotic-root-fungus-growth.html#jCp

Via Jean-Michel Ané, Francis Martin
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Jean-Michel Ané's curator insight, June 8, 8:15 PM

Commentary on Kai Riess, Franz Oberwinkler, Robert Bauer, Sigisfredo Garnica (2014): "Communities of endophytic Sebacinales associated with roots of herbaceous plants in agricultural and grassland ecosystems are dominated by Serendipita herbamans sp. nov." PLoS ONE 9(4): e94676.