Draft Genome Sequence of an Anaerobic and Extremophilic Bacterium, Caldanaerobacter yonseiensis, Isolated from a Geothermal Hot Stream

Caldanaerobacter subterraneus subsp. keratinolyticus subsp. nov., a Novel Feather-Degrading Anaerobic Thermophile

Caldanaerobacter subterraneus subsp. keratinolyticus subsp. nov. strain KAk was isolated from a geothermal hot spring located in Kazakhstan. Growth occurred at temperatures ranging from 50 to 80 °C, with approximately 70 °C as optimum. It also thrived in pH conditions ranging from 4.0 to 9.0, with the best growth occurring at 6.8. Under optimal conditions in a glucose-containing medium, the cells were predominantly observed singly, in pairs, or less frequently in chains, and did not form endospores. However, under conditions involving growth with merino wool or feathers, or under suboptimal conditions, the cells of strain KAk exhibited a notably elongated and thinner morphology, with lengths ranging from 5 to 8 µm, and spores were observed. The KAk strain exhibited efficient degradation of feather keratin and merino wool at temperatures ranging from 65 to 70 °C. Analysis of the 16S rRNA gene sequence placed KAk within the genus Caldanaerobacter, family Thermoanaerobacteraceae, with the highest similarity to C. subterraneus subsp. tengcongensis MB4T (98.84% sequence identity). Furthermore, our analysis of the draft genome sequence indicated a genome size of 2.4 Mbp, accompanied by a G+C value of 37.6 mol%. This study elucidated the physiological and genomic characteristics of strain KAk, highlighting its keratinolytic capabilities and distinctiveness compared to other members of the genus Caldanaerobacter.

Combination of sequencing batch reactor activated sludge process with sludge lysis using thermophilic bacterial community for minimizing excess sludge

Sludge reduction is a major challenge in biological wastewater treatment. Hydrolytic enzymes secreted by thermophilic bacteria can lyse sludge and thus achieve sludge reduction, and the indigenous thermophilic community in sludge can lyse sludge more effectively. In this study, the feasibility of combining a sludge lysis reactor based on thermophilic bacteria community (LTBC reactor, 75 °C) with a conventional sequencing batch activated sludge reactor (SBR) for sludge reduction (i.e., LTBC-SBR process) was systematically investigated first time. The effect of lysed sludge returning to the biochemical tank on pollutant removal efficiency, sludge flocculation, sludge settling, and microbial community and function of the LTBC-SBR process was studied. In the LTBC1-SBR process, a sludge growth rate of 0.71 g TSS/day was observed when the lysed sludge reflux ratio (LRR) was 1, and the sludge generation was reduced by 81.5% compared to the conventional SBR reactor. In the LTBC1-SBR process, the removal efficiencies of chemical oxygen demand and total nitrogen were 94.0% and 80.5%, respectively. There was no significant difference in the sludge volume index from the SBR to the LTBC1-SBR stage, however, the effluent suspended solids concentration increased from 35.2 ± 2.1 mg/L to 80.1 ± 5.3 mg/L. This was attributed to the reflux of sludge lysate. In addition, the changes in extracellular polymers content and composition resulted in poor sludge flocculation performance. Heterotrophic bacteria associated with Actinobacteria and Patescibacteria enriched in LTBC1-SBR with relative abundance of 28.51 ± 1.25% and 20.01 ± 1.21%, respectively, which decomposed the macromolecules in the refluxed lysed sludge and contributed to the sludge reduction. Furthermore, due to the inhibition of nitrite-oxidizing bacteria, the nitrite concentration in the effluent of the LTBC1-SBR system reached 4.7 ± 1.1 mg/L, and part of the denitrification process was achieved by short-cut nitrification and simultaneous denitrification. These results indicate that in-situ sludge reduction technology based on lyse sludge lysing by thermophilic community has considerable potential to be widely used in wastewater treatment.

Mining for novel cyclomaltodextrin glucanotransferases unravels the carbohydrate metabolism pathway via cyclodextrins in Thermoanaerobacterales

Carbohydrate metabolism via cyclodextrins (CM-CD) is an uncommon starch-converting pathway that thoroughly depends on extracellular cyclomaltodextrin glucanotransferases (CGTases) to transform the surrounding starch substrate to α-(1,4)-linked oligosaccharides and cyclodextrins (CDs). The CM-CD pathway has emerged as a convenient microbial adaptation to thrive under extreme temperatures, as CDs are functional amphipathic toroids with higher heat-resistant values than linear dextrins. Nevertheless, although the CM-CD pathway has been described in a few mesophilic bacteria and archaea, it remains obscure in extremely thermophilic prokaryotes (Topt ≥ 70 °C). Here, a new monophyletic group of CGTases with an exceptional three-domain ABC architecture was detected by (meta)genome mining of extremely thermophilic Thermoanaerobacterales living in a wide variety of hot starch-poor environments on Earth. Functional studies of a representative member, CldA, showed a maximum activity in a thermoacidophilic range (pH 4.0 and 80 °C) with remarkable product diversification that yielded a mixture of α:β:γ-CDs (34:62:4) from soluble starch, as well as G3-G7 linear dextrins and fermentable sugars as the primary products. Together, comparative genomics and predictive functional analysis, combined with data of the functionally characterized key proteins of the gene clusters encoding CGTases, revealed the CM-CD pathway in Thermoanaerobacterales and showed that it is involved in the synthesis, transportation, degradation, and metabolic assimilation of CDs.

Genomic insights of aromatic hydrocarbon degrading Klebsiella pneumoniae AWD5 with plant growth promoting attributes: a paradigm of soil isolate with elements of biodegradation

This research employs draft genome sequence data of Klebsiella pneumoniae AWD5 to explore genes that contribute to the degradation of polyaromatic hydrocarbon (PAH) and stimulate plant growth, for rhizosphere-mediated bioremediation. Annotation analysis suggests that the strain AWD5 not only possess gene clusters for PAH utilization, but also for utilization of benzoate, fluorobenzoate, phenylacetate (paa), hydroxyphenylacetic acid (hpa), 3-hydroxyphenyl propionate (mhp). A comparative genome analysis revealed that the genome of AWD5 was highly similar with genomes of environmental as well as clinical K. pneumoniae isolates. The artemis output confirmed that there are 139 different genes present in AWD5 which were absent in genome of clinical strain K. pneumoniae ATCC BAA-2146, and 25 genes were identified to be present in AWD5 genome but absent in genome of environmental strain K. pneumoniae KP-1. Pathway analyzed using Kyoto Encyclopedia of Genes and Genomes enzyme database revealed the presence of gene clusters that code for enzymes to initiate the opening of aromatic rings. The polyaromatic hydrocarbon and benzoate degradation were found to be metabolized through ortho-cleavage pathway, mineralizing the compounds to TCA cycle intermediates. Genes for plant growth promoting attributes such as Indole acetic acid (IAA) synthesis, siderophore production, and phosphate solubilization were detected in the genome. These attributes were verified in vitro, including IAA (14.75 µg/ml), siderophore production (13.56%), phosphate solubilization (198.28 ng/ml), and ACC deaminase (0.118 mM α-ketobutyrate/mg) in the presence of pyrene, and also compared with results obtained in glucose amended medium. K. pneumoniae AWD5 enhanced the growth of Jatropha curcas in the presence of pyrene-contaminated soil. Moreover, AWD5 harbors heavy metal resistance genes indicating adaptation to contaminants. The study revealed the genomic attributes of K. pneumoniae AWD5 for its catabolic characteristics for different aromatic compounds, which makes it suitable for rhizoremediation of PAH-contaminated soil.

Analysis of three genomes within the thermophilic bacterial species Caldanaerobacter subterraneus with a focus on carbon monoxide dehydrogenase evolution and hydrolase diversity

Background

The Caldanaerobacter subterraneus species includes thermophilic fermentative bacteria able to grow on carbohydrates substrates with acetate and L-alanine as the main products. In this study, comprehensive analysis of three genomes of C. subterraneus subspecies was carried in order to identify genes encoding key metabolic enzymes and to document the genomic basis for the evolution of these organisms.

Methods

Average nucleotide identity and in silico DNA relatedness were estimated for the studied C. subterraneus genomes. Genome synteny was evaluated using R2CAT software. Protein conservation was analyzed using mGenome Subtractor. Horizontal gene transfer was predicted through the GOHTAM pipeline (using tetranucleotide composition) and phylogenetic analyses (by maximum likelihood). Hydrolases were identified through the MEROPS and CAZy platforms.

Results

The three genomes of C. subterraneus showed high similarity, although there are substantial differences in their gene composition and organization. Each subspecies possesses a gene cluster encoding a carbon monoxide dehydrogenase (CODH) and an energy converting hydrogenase (ECH). The CODH gene is associated with an operon that resembles the Escherichia coli hydrogenase hyc/hyf operons, a novel genetic context distinct from that found in archetypical hydrogenogenic carboxydotrophs. Apart from the CODH-associated hydrogenase, these bacteria also contain other hydrogenases, encoded by ech and hyd genes. An Mbx ferredoxin:NADP oxidoreductase homolog similar to that originally described in the archaeon Pyrococcus furiosus was uniquely encoded in the C. subterraneus subsp. yonseiensis genome. Compositional analysis demonstrated that some genes of the CODH-ECH and mbx operons present distinct sequence patterns in relation to the majority of the other genes of each genome. Phylogenetic reconstructions of the genes from these operons and those from the ech operon are incongruent to the species tree. Notably, the cooS gene of C. subterraneus subsp. pacificus and its homologs in C. subterraneus subsp. tengcongensis and C. subterraneus subsp. yonseiensis form distinct clades. The strains have diverse hydrolytic enzymes and they appear to be proteolytic and glycolytic. Divergent glycosidases from 14 families, among them amylases, chitinases, alpha-glucosidases, beta-glucosidases, and cellulases, were identified. Each of the three genomes also contains around 100 proteases from 50 subfamilies, as well about ten different esterases.

Conclusions

Genomic information suggests that multiple horizontal gene transfers conferred the adaptation of C. subterraneus subspecies to extreme niches throughout the carbon monoxide utilization and hydrogen production. The variety of hydrolases found in their genomes indicate the versatility of the species in obtaining energy and carbon from diverse substrates, therefore these organisms constitute a remarkable resource of enzymes with biotechnological potential.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1955-9) contains supplementary material, which is available to authorized users.