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Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines

Soda lakes are salt lakes with a naturally alkaline pH due to evaporative concentration of sodium carbonates in the absence of major divalent cations. Hypersaline soda brines harbor microbial communities with a high species- and strain-level archaeal diversity and a large proportion of still uncultured poly-extremophiles compared to neutral brines of similar salinities. We present… [Read More]

Complementary microorganisms in highly corrosive biofilms from an offshore oil production facility

Offshore oil production facilities are frequently victims of internal piping corrosion, potentially leading to human and environmental risks and significant economic losses. Microbially influenced corrosion (MIC) is believed to be an important factor in this major problem for the petroleum industry. However, knowledge of the microbial communities and metabolic processes leading to corrosion is still… [Read More]

Early-branching gut fungi possess a large, comprehensive array of biomass-degrading enzymes

The fungal kingdom is the source of almost all industrial enzymes in use for lignocellulose bioprocessing. We developed a systems-level approach that integrates transcriptomic sequencing (RNA-Seq), proteomics, phenotype and biochemical studies of relatively unexplored basal fungi. Anaerobic gut fungi isolated from herbivores produce a large array of biomass-degrading enzymes that synergistically degrade crude, untreated plant… [Read More]

Genetic analysis of Physcomitrella patens identifies ABSCISIC ACID NON-RESPONSIVE (ANR), a regulator of ABA responses unique to basal land plants and required for desiccation tolerance

The anatomically simple plants that first colonised land must have acquired molecular and biochemical adaptations to drought stress. Abscisic acid (ABA) coordinates responses leading to desiccation tolerance in all land plants. We identified ABA non-responsive mutants in the model bryophyte Physcomitrella patens and genotyped a segregating population to map and identify the ABA NON-RESPONSIVE (ANR)… [Read More]

Genome analysis of ‘Candidatus Ancillula trichonymphae’, first representative of a deep-branching clade of Bifidobacteriales, strengthens evidence for convergent evolution in flagellate endosymbionts

The flagellate protists in the hindgut of lower termites play an essential role in the digestion of lignocellulose. Most flagellate species are associated with host-specific symbionts from various bacterial lineages, which typically lack cultured representatives. In this study, we analyzed the genome of ‘Candidatus Ancillula trichonymphae’, an endosymbiont of Trichonympha flagellates from dry-wood termites, which… [Read More]

Description of Trichococcus ilyis sp. nov. by combined physiological and in silico genome hybridization analyses

Trichococcus species share high similarity of their 16S rRNA gene sequences (> 99%). Digital DNA-DNA hybridization values (dDDH) among all described Trichococcus species (T. flocculiformis DSM 2094T, T. pasteurii DSM 2381T, T. collinsii DSM 14526T, T. palustris DSM 9172T, and T. patagoniensis DSM 18806T) indicated that Trichococcus sp. strain R210T represents a novel species of… [Read More]

The Sphagnum Genome Project: A New Model for Ecological and Evolutionary Genomics

The inception of the Sphagnum (peat moss) genome project marks the first plant-based sequencing project aimed specifically at carbon cycling genomics in a plant system relevant to ecological and evolutionary genomics. Sphagnum provides considerable intra-and interspecific variation at the nucleotide level, and in physiology, morphology, net production, decomposition and carbon accumulation (peat formation). Because of… [Read More]

Performance evaluation and tuning of BioPig for genomic analysis

In this study, we aim to optimize Hadoop parameters to improve the performance of BioPig on Amazon Web Service (AWS). BioPig is a toolkit for large-scale sequencing data analysis and is built on Hadoop and Pig that enables easy parallel programming and scaling to datasets of terabyte sizes. AWS is the most popular cloud-computing platform… [Read More]

High-resolution phylogenetic microbial community profiling

Over the past decade, high-throughput short-read 16S rRNA gene amplicon sequencing has eclipsed clone-dependent long-read Sanger sequencing for microbial community profiling. The transition to new technologies has provided more quantitative information at the expense of taxonomic resolution with implications for inferring metabolic traits in various ecosystems. We applied single-molecule real-time sequencing for microbial community profiling,… [Read More]