High-resolution and specific detection of bacteria on complex surfaces using nanoparticle probes and electron microscopy

What is slough? Defining the proteomic and microbial composition of slough and its implications for wound healing

Slough is a well-known feature of non-healing wounds. This pilot study aims to determine the proteomic and microbiologic components of slough as well as interrogate the associations between wound slough components and wound healing. Ten subjects with slow-to-heal wounds and visible slough were enrolled. Aetiologies included venous stasis ulcers, post-surgical site infections and pressure ulcers. Patient co-morbidities and wound healing outcome at 3-months post-sample collection was recorded. Debrided slough was analysed microscopically, through untargeted proteomics, and high-throughput bacterial 16S-ribosomal gene sequencing. Microscopic imaging revealed wound slough to be amorphous in structure and highly variable. 16S-profiling found slough microbial communities to associate with wound aetiology and location on the body. Across all subjects, slough largely consisted of proteins involved in skin structure and formation, blood-clot formation and immune processes. To predict variables associated with wound healing, protein, microbial and clinical datasets were integrated into a supervised discriminant analysis. This analysis revealed that healing wounds were enriched for proteins involved in skin barrier development and negative regulation of immune responses. While wounds that deteriorated over time started off with a higher baseline Bates-Jensen Wound Assessment Score and were enriched for anaerobic bacterial taxa and chronic inflammatory proteins. To our knowledge, this is the first study to integrate clinical, microbiome, and proteomic data to systematically characterise wound slough and integrate it into a single assessment to predict wound healing outcome. Collectively, our findings underscore how slough components can help identify wounds at risk of continued impaired healing and serves as an underutilised biomarker.

Chemolithotrophic processes in the bacterial communities on the surface of mineral-enriched biochars

Biochar and mineral-enriched biochar (MEB) have been used as soil amendments to improve soil fertility, sequester carbon and mitigate greenhouse gas emissions. Such beneficial outcomes could be partially mediated by soil bacteria, however little is known about how they directly interact with biochar or MEB. We therefore analyzed the diversity and functions of bacterial communities on the surfaces of one biochar and two different MEBs after a 140-day incubation in soil. The results show that the biochar and the MEBs harbor distinct bacterial communities to the bulk soil. Communities on biochar and MEBs were dominated by a novel Gammaproteobacterium. Genome reconstruction combined with electron microscopy and high-resolution elemental analysis revealed that the bacterium generates energy from the oxidation of iron that is present on the surface. Two other bacteria belonging to the genus Thiobacillus and a novel group within the Oxalbacteraceae were enriched only on the MEBs and they had the genetic capacity for thiosulfate oxidation. All three surface-enriched bacteria also had the capacity to fix carbon dioxide, either in a potentially strictly autotrophic or mixotrophic manner. Our results show the dominance of chemolithotrophic processes on the surface of biochar and MEB that can contribute to carbon sequestration in soil.

Morphological and proteomic analysis of biofilms from the Antarctic archaeon, Halorubrum lacusprofundi

Biofilms enhance rates of gene exchange, access to specific nutrients, and cell survivability. Haloarchaea in Deep Lake, Antarctica, are characterized by high rates of intergenera gene exchange, metabolic specialization that promotes niche adaptation, and are exposed to high levels of UV-irradiation in summer. Halorubrum lacusprofundi from Deep Lake has previously been reported to form biofilms. Here we defined growth conditions that promoted the formation of biofilms and used microscopy and enzymatic digestion of extracellular material to characterize biofilm structures. Extracellular DNA was found to be critical to biofilms, with cell surface proteins and quorum sensing also implicated in biofilm formation. Quantitative proteomics was used to define pathways and cellular processes involved in forming biofilms; these included enhanced purine synthesis and specific cell surface proteins involved in DNA metabolism; post-translational modification of cell surface proteins; specific pathways of carbon metabolism involving acetyl-CoA; and specific responses to oxidative stress. The study provides a new level of understanding about the molecular mechanisms involved in biofilm formation of this important member of the Deep Lake community.