- Volume 165, Issue 12, 2019

The rationale of our bioprospecting campaigns is that the extremobiosphere, particularly the deep sea and hyper-arid deserts, harbours undiscovered biodiversity that is likely to express novel chemistry and biocatalysts thereby providing opportunities for therapeutic drug and industrial process development. We have focused on actinobacteria because of their frequent role as keystone species in soil ecosystems and their unrivalled track record as a source of bioactive compounds. Population numbers and diversity of actinobacteria in the extremobiosphere are traditionally considered to be low, although they often comprise the dominant bacterial biota. Recent metagenomic evaluation of ‘the uncultured microbial majority’ has now revealed enormous taxonomic diversity among ‘dark’ and ‘rare’ actinobacteria in samples as diverse as sediments from the depths of the Mariana Trench and soils from the heights of the Central Andes. The application of innovative culture and screening options that emphasize rigorous dereplication at each stage of the analysis, and strain prioritization to identify ‘gifted’ organisms, have been deployed to detect and characterize bioactive hit compounds and sought-after catalysts from this hitherto untapped resource. The rewards include first-in-a-class chemical entities with novel modes of action, as well as a growing microbial seed bank that represents a potentially enormous source of biotechnological and therapeutic innovation.

Platinum and palladium are much sought-after metals of critical global importance in terms of abundance and availability. At the nano-scale these metals are of even higher value due to their catalytic abilities for industrial applications. Desulfovibrio alaskensis is able to capture ionic forms of both of these metals, reduce them and synthesize elemental nanoparticles. Despite this ability, very little is known about the biological pathways involved in the formation of these nanoparticles. Proteomic analysis of D. alaskensis in response to platinum and palladium has highlighted those proteins involved in both the reductive pathways and the wider stress-response system. A core set of 13 proteins was found in both treatments and consisted of proteins involved in metal transport and reduction. There were also seven proteins that were specific to either platinum or palladium. Overexpression of one of these platinum-specific genes, a NiFe hydrogenase small subunit (Dde_2137), resulted in the formation of larger nanoparticles. This study improves our understanding of the pathways involved in the metal resistance mechanism of Desulfovibrio and is informative regarding how we can tailor the bacterium for nanoparticle production, enhancing its application as a bioremediation tool and as a way to capture contaminant metals from the environment.

Extracellular vesicle release is a wide-spread and broadly important phenomenon in bacteria. However, not much is known about the mechanism of vesicle release in Gram-positive bacteria. Observations of polarly growing Streptomyces venezuelae by live cell time-lapse imaging reveal release of extracellular membrane vesicles from tips of vegetative hyphae. Vesicle extrusion is associated with spontaneous growth arrests, but often the apical cell survives and can re-initiate growth by forming new hyphal branches. Treatment with vancomycin to block peptidoglycan synthesis leads to a high frequency of lysis and vesicle extrusion, where some hyphae can survive growth arrest and vesicle extrusion and reinitiate growth after antibiotic is washed away. The extruded vesicles do not contain nucleoids and do not appear able to proliferate. Vesicle extrusion is not affected by the Ser/Thr protein kinase AfsK that phosphorylates the DivIVA at hyphal tips, nor is it affected by the intermediate filament-like protein FilP that localizes in gradient-like structures at hyphal tips. Notably, hyphae of a scy mutant, which has an unstable apical polarisome structure, are prone to spontaneous growth arrests and vesicle extrusion even in the absence of antibiotic treatment, supporting the idea that the nature of the growth zone at the hyphal tips is important for this route of extracellular vesicle formation. We speculate that the propensity for vesicle extrusion is a direct consequence of how polar growth is organized at hyphal tips in Streptomyces , with the cell-wall sacculus being weak and susceptible to bursting at the apical zones of growth where peptidoglycan synthesis is primarily taking place.

The presence and diversity of mycobacteria that are capable of survival in a harsh and adverse condition, such as hospital environments, have not been comprehensively studied. This study aimed to assess the frequency and diversity of mycobacteria in hospital soil and dust of a developing country using a combination of molecular and conventional methods. A total of 318 hospital dust and soil samples collected from 38 hospitals were analysed using standard protocols for characterization of mycobacteria. The conventional tests were used for preliminary identification and Runyon’s classification, the PCR amplification of the hsp65 gene and sequence analyses of 16SrRNA were applied for genus and species identification. In total, 28 samples (8.8 %) were positive for mycobacteria. The isolates included 33 mycobacteria species including 19 rapidly growing and 14 slowly growing organisms. The most prevalent species were M. setense and M. lentiflavum, five isolates (15.1 %) each, M. fortuitum, four isolates (12.12 %) and M. kumamotonense and M. massiliense/abscessus complex three isolates (9.1 %) each, M. arupense and M. frederiksbergense, two isolates (6 %) each. The remaining isolates consisted the single strains of eight various mycobacterium species, the results of our study revealed that soil and dust in hospitals can be the reservoir of mycobacteria. This reaffirms the fact that these organisms due to intrinsic resistance can persist in hospitals and create a threat to patient’s health, in particular to those who suffer from weakness of immunity.

Bacteria affiliated with the phylum Gemmatimonadetes are found in high abundance in many terrestrial and aquatic environments, yet little is known about their metabolic capabilities. Difficulty in their cultivation has prompted interest in identifying better growth conditions for metabolic studies, especially related to their ability to reduce N2O, a potent greenhouse gas. T-27 Gemmatimonas aurantiaca is one of few cultivated strains of Gemmatimonadetes available for physiological studies. Our objective was to test this organism’s ability to use nitrite, nitrate, and N2O, and mineral forms of assimilable NH4 + at concentrations not typically used in tests for compound utilization. Cultures incubated under anaerobic conditions with nitrate, nitrite or N2O failed to grow or show depletion of these substrates. Nitrate and nitrite (1 mM) were not used even when cells were grown aerobically with the O2 allowed to deplete first. N2O reduction only commenced in the presence of O2 and continued to be depleted when refed to the culture under anaerobic, microaerobic and aerobic atmospheres. Carbon mineralization was coupled to the electron-accepting processes, with higher reducing equivalents needed for N2O utilization under aerobic atmospheres. N2O was reduced to N2 in the presence of 20% O2, however the rate of this reaction is reduced in the presence of high O2 concentration. This study demonstrated that G. aurantiaca T-27 possesses unique characteristics for assimilative and dissimilative N processes with new implications for cultivation strategies to better assess the metabolic abilities of Gemmatimonadetes.

DNA replication is controlled mostly at the initiation step. In bacteria, replication of the chromosome starts at a single origin of replication called oriC. The initiator protein, DnaA, binds to specific sequences (DnaA boxes) within oriC and assembles into a filament that promotes DNA double helix opening within the DNA unwinding element (DUE). This process has been thoroughly examined in model bacteria, including Escherichia coli and Bacillus subtilis, but we have a relatively limited understanding of chromosomal replication initiation in other species. Here, we reveal new details of DNA replication initiation in Streptomyces , a group of Gram-positive soil bacteria that possesses a long linear (8–10 Mbps) and GC-rich chromosome with a centrally positioned oriC. We used comprehensive in silico, in vitro and in vivo analyses to better characterize the structure of Streptomyces oriC. We identified 14 DnaA-binding motifs and determined the consensus sequence of the DnaA box. Unexpectedly, our in silico analysis using the WebSIDD algorithm revealed the presence of two putative Streptomyces DUEs (DUE1 and DUE2) located very near one another toward the 5′ end of the oriC region. In vitro P1 nuclease assay revealed that DNA unwinding occurs at both of the proposed sites, but using an in vivo replication initiation point mapping, we were able to confirm only one of them (DUE2). The previously observed transcriptional activity of the Streptomyces oriC region may help explain the current results. We speculate that transcription itself could modulate oriC activity in Streptomyces by determining whether DNA unwinding occurs at DUE1 or DUE2.