Complete Genome Sequence of Pelosinus fermentans JBW45, a Member of a Remarkably Competitive Group of Negativicutes in the Firmicutes Phylum

Towards passive bioremediation of dye-bearing effluents using hydrous ferric oxide wastes: Mechanisms, products and microbiology

A novel, circular economy-inspired approach for the "passive" (non-powered and reagent-free) treatment of dye-bearing effluent is presented. The treatment utilises the biogeochemical interaction of dye-bearing wastewater with hydrous ferric oxide (HFO) bearing sludges. The work presented demonstrates for the first time the reuse of HFO-rich waste sludges from potable water and mine water treatment. The waste was used directly without modification or reagent addition, as media/substrate in simple flow-through reactors for the decolourisation and biodegradation of methyl orange (MO) and mixed dyes textile effluent. Three phases of exploratory proof of concept work were undertaken. Columns containing HFO sludges were challenged with solution of MO, and MO amended with glycerol (Phase I), MO in a synthetic textile effluent recipe (Phase II), and real mixed textile effluent containing a mixture of dyes (Phase III). After an initial lag period extensive decolourisation of dye was observed in all cases at rates comparable with pure strains and engineered bioreactor processes, with evidence of biodegradation beyond simple cleavage of the mono azo chromophore and mineralisation. The microbiology of the initial sludge samples in both cases exhibited a diverse range of iron oxidising and reducing bacteria. However, post experiment the microbiology of sludge evolved from being dominated by Proteobacteria to being dominated by Firmicutes. Distinct changes in the microbial community structure were observed in post-treatment MWTS and WTWS where genera capable of iron and sulphate reduction and/or aromatic amine degradation were identified. Average nitrogen removal rates for the columns ranged from 27.8 to 194 g/m³/day which is higher than engineered sequential anaerobic-aerobic bioreactor. Postulated mechanisms for the fast anaerobic decolourisation, biodegradation, and mineralisation of the dyes (as well nitrogen transformations) include various direct and indirect enzymatic and metabolic reactions, as well as reductive attack by continuously regenerated reductants such as Fe(II), HFO bound Fe(II), FeS, and HS^-. The ability of iron reducers to degrade aromatic rings is also considered important in the further biodegradation and complete mineralisation of organic carbon. The study reveals that abundant and ubiquitous HFO-rich waste sludges, can be used without amendment, as a substrate in simple flow-through bioremediation system for the decolourisation and partial biodegradation of dyes in textile effluent.

A Case Study into Microbial Genome Assembly Gap Sequences and Finishing Strategies

This study characterized regions of DNA which remained unassembled by either PacBio and Illumina sequencing technologies for seven bacterial genomes. Two genomes were manually finished using bioinformatics and PCR/Sanger sequencing approaches and regions not assembled by automated software were analyzed. Gaps present within Illumina assemblies mostly correspond to repetitive DNA regions such as multiple rRNA operon sequences. PacBio gap sequences were evaluated for several properties such as GC content, read coverage, gap length, ability to form strong secondary structures, and corresponding annotations. Our hypothesis that strong secondary DNA structures blocked DNA polymerases and contributed to gap sequences was not accepted. PacBio assemblies had few limitations overall and gaps were explained as cumulative effect of lower than average sequence coverage and repetitive sequences at contig termini. An important aspect of the present study is the compilation of biological features that interfered with assembly and included active transposons, multiple plasmid sequences, phage DNA integration, and large sequence duplication. Our targeted genome finishing approach and systematic evaluation of the unassembled DNA will be useful for others looking to close, finish, and polish microbial genome sequences.

Application of Long Sequence Reads To Improve Genomes for Clostridium thermocellum AD2, Clostridium thermocellum LQRI, and Pelosinus fermentans R7

We and others have shown the utility of long sequence reads to improve genome assembly quality. In this study, we generated PacBio DNA sequence data to improve the assemblies of draft genomes for Clostridium thermocellum AD2, Clostridium thermocellum LQRI, and Pelosinus fermentans R7.

Near-Complete Genome Sequence of the Cellulolytic Bacterium Bacteroides (Pseudobacteroides) cellulosolvens ATCC 35603

We report the single-contig genome sequence of the anaerobic, mesophilic, cellulolytic bacterium, Bacteroides cellulosolvens. The bacterium produces a particularly elaborate cellulosome system, wherein the types of cohesin-dockerin interactions are opposite of other known cellulosome systems: cell-surface attachment is thus mediated via type-I interactions, whereas enzymes are integrated via type-II interactions.