Creation of Cellulolytic Communities of Soil Microorganisms-A Search for Optimal Approaches.

For the targeted selection of microbial communities that provide cellulose degradation, soil samples containing cellulolytic microorganisms and specific plant residues as a substrate can be used. The details of this process have not been studied: in particular, whether the use of different soils determines the varying efficiency of communities; whether these established cellulolytic communities will have substrate specificity, and other factors. To answer these questions, four soil microbial communities with different cellulolytic activity (Podzol and the soil of Chernevaya taiga) and substrates (oat straw and hemp shives) with different levels of cellulose availability were used, followed by trained communities that were tested on botrooth substrates (in all possible combinations).

Accurate isoform discovery with IsoQuant using long reads.

Annotating newly sequenced genomes and determining alternative isoforms from long-read RNA data are complex and incompletely solved problems. Here we present IsoQuant-a computational tool using intron graphs that accurately reconstructs transcripts both with and without reference genome annotation. For novel transcript discovery, IsoQuant reduces the false-positive rate fivefold and 2.

MetaGT: A pipeline for assembly of metatranscriptomes with the aid of metagenomic data.

While metagenome sequencing may provide insights on the genome sequences and composition of microbial communities, metatranscriptome analysis can be useful for studying the functional activity of a microbiome. RNA-Seq data provides the possibility to determine active genes in the community and how their expression levels depend on external conditions. Although the field of metatranscriptomics is relatively young, the number of projects related to metatranscriptome analysis increases every year and the scope of its applications expands.

Metagenomic Data Assembly - The Way of Decoding Unknown Microorganisms.

Metagenomics is a segment of conventional microbial genomics dedicated to the sequencing and analysis of combined genomic DNA of entire environmental samples. The most critical step of the metagenomic data analysis is the reconstruction of individual genes and genomes of the microorganisms in the communities using metagenomic assemblers - computational programs that put together small fragments of sequenced DNA generated by sequencing instruments. Here, we describe the challenges of metagenomic assembly, a wide spectrum of applications in which metagenomic assemblies were used to better understand the ecology and evolution of microbial ecosystems, and present one of the most efficient microbial assemblers, SPAdes that was upgraded to become applicable for metagenomics.

Draft genome sequence of strain AHT1, a gram-positive sulfidogenic polyextremophile.

strain AHT1 is an anaerobic, sulfidogenic, moderately salt-tolerant alkaliphilic chemolithotroph isolated from hypersaline soda lake sediments in northeastern Mongolia. It is a Gram-positive bacterium with low GC content, within the phylum . Here we report its draft genome sequence, which consists of 34 contigs with a total sequence length of 3.

Complete genome sequence of Desulfurivibrio alkaliphilus strain AHT2(T), a haloalkaliphilic sulfidogen from Egyptian hypersaline alkaline lakes.

Desulfurivibrio alkaliphilus strain AHT2(T) is a strictly anaerobic sulfidogenic haloalkaliphile isolated from a composite sediment sample of eight hypersaline alkaline lakes in the Wadi al Natrun valley in the Egyptian Libyan Desert. D. alkaliphilus AHT2(T) is Gram-negative and belongs to the family Desulfobulbaceae within the Deltaproteobacteria.

Complete genome sequence of Methanospirillum hungatei type strain JF1.

Methanospirillum hungatei strain JF1 (DSM 864) is a methane-producing archaeon and is the type species of the genus Methanospirillum, which belongs to the family Methanospirillaceae within the order Methanomicrobiales. Its genome was selected for sequencing due to its ability to utilize hydrogen and carbon dioxide and/or formate as a sole source of energy. Ecologically, M.

High quality draft genome sequence of Bacteroides barnesiae type strain BL2(T) (DSM 18169(T)) from chicken caecum.

Bacteroides barnesiae Lan et al. 2006 is a species of the genus Bacteroides, which belongs to the family Bacteroidaceae. Strain BL2(T) is of interest because it was isolated from the gut of a chicken and the growing awareness that the anaerobic microbiota of the caecum is of benefit for the host and may impact poultry farming.

Sequencing, biochemical characterization, crystal structure and molecular dynamics of cellobiohydrolase Cel7A from Geotrichum candidum 3C.

Unlabelled: The ascomycete Geotrichum candidum is a versatile and efficient decay fungus that is involved, for example, in biodeterioration of compact discs; notably, the 3C strain was previously shown to degrade filter paper and cotton more efficiently than several industrial enzyme preparations. Glycoside hydrolase (GH) family 7 cellobiohydrolases (CBHs) are the primary constituents of industrial cellulase cocktails employed in biomass conversion, and feature tunnel-enclosed active sites that enable processive hydrolytic cleavage of cellulose chains. Understanding the structure-function relationships defining the activity and stability of GH7 CBHs is thus of keen interest.

High-Quality Draft Genome Sequence of Desulfovibrio carbinoliphilus FW-101-2B, an Organic Acid-Oxidizing Sulfate-Reducing Bacterium Isolated from Uranium(VI)-Contaminated Groundwater.

Desulfovibrio carbinoliphilus subsp. oakridgensis FW-101-2B is an anaerobic, organic acid/alcohol-oxidizing, sulfate-reducing δ-proteobacterium. FW-101-2B was isolated from contaminated groundwater at The Field Research Center at Oak Ridge National Lab after in situ stimulation for heavy metal-reducing conditions.

Complete genome sequence of Syntrophobacter fumaroxidans strain (MPOB(T)).

Syntrophobacter fumaroxidans strain MPOB(T) is the best-studied species of the genus Syntrophobacter. The species is of interest because of its anaerobic syntrophic lifestyle, its involvement in the conversion of propionate to acetate, H2 and CO2 during the overall degradation of organic matter, and its release of products that serve as substrates for other microorganisms. The strain is able to ferment fumarate in pure culture to CO2 and succinate, and is also able to grow as a sulfate reducer with propionate as an electron donor.

Complete genome sequence and updated annotation of Desulfovibrio alaskensis G20.

Desulfovibrio alaskensis G20 (formerly Desulfovibrio desulfuricans G20) is a Gram-negative mesophilic sulfate-reducing bacterium (SRB), known to corrode ferrous metals and to reduce toxic radionuclides and metals such as uranium and chromium to sparingly soluble and less toxic forms. We present the 3.7-Mb genome sequence to provide insights into its physiology.

Genome sequence of the mercury-methylating strain Desulfovibrio desulfuricans ND132.

Desulfovibrio desulfuricans strain ND132 is an anaerobic sulfate-reducing bacterium (SRB) capable of producing methylmercury (MeHg), a potent human neurotoxin. The mechanism of methylation by this and other organisms is unknown. We present the 3.

A genomic perspective on the potential of Actinobacillus succinogenes for industrial succinate production.

Background: Succinate is produced petrochemically from maleic anhydride to satisfy a small specialty chemical market. If succinate could be produced fermentatively at a price competitive with that of maleic anhydride, though, it could replace maleic anhydride as the precursor of many bulk chemicals, transforming a multi-billion dollar petrochemical market into one based on renewable resources. Actinobacillus succinogenes naturally converts sugars and CO2 into high concentrations of succinic acid as part of a mixed-acid fermentation.

The genome of Syntrophomonas wolfei: new insights into syntrophic metabolism and biohydrogen production.

Syntrophomonas wolfei is a specialist, evolutionarily adapted for syntrophic growth with methanogens and other hydrogen- and/or formate-using microorganisms. This slow-growing anaerobe has three putative ribosome RNA operons, each of which has 16S rRNA and 23S rRNA genes of different length and multiple 5S rRNA genes. The genome also contains 10 RNA-directed, DNA polymerase genes.

Frameshift detection in prokaryotic genomic sequences.

We have developed a new method for frameshift detection, a combination of ab initio and alignment-based algorithms, that can serve as a useful tool for sequencing quality control in the next generation sequencing. We evaluated the method's accuracy on test sets of annotated genomic sequences with artificial frameshifts in protein coding regions. These tests have shown that the new method performs comparably to the earlier developed FrameD.