by Davide Ciccarese
Bacterial communities live in a small world where cells fill any available micron. Depending on their location and surrounding environment, they can readily respond to changes by gearing up their gene repertoire to insure their position in a densely packed biofilm. To be able to visualize this concert of gene expression, the unfolding of the kaleidoscopic potential of phenotypic heterogeneity in space and time, is something that many microbiologists dream about. That is why the work of Daniel Dar and colleagues from Dianne Newman's lab is such a mesmerizing achievement. The title of their paper – "Spatial transcriptomics of planktonic and sessile bacterial populations at single-cell resolution" – already conveys great excitement. As they state in their paper, the technique they have developed is like "spying on microbial communities, cell by cell."
Fig. 1. Transcriptome imaging using par-seqFISH reveals the dynamics and spatial organization of transcriptional programs in P. aeruginosa populations at single-cell resolution. Transcriptional states of individual bacterial cells were identified using clustering analysis (left). The detected cellular states are depicted in different colors. Cell metabolic states can be directly mapped to their native biofilm context to identify emerging microenvironment dynamics (right). Source
There is great beauty in the highly diverse bacterial communities, where one can find various metabolisms coexisting and coevolving as part of the emergent landscape selected at the group level. Even within genetically identical populations, individual cells can express different sets of genes in concert depending on the condition of their neighborhood and thus expand their ability to exploit minute differences in micro-niches. Daniel Dar et al., developed a technique they call par-seqFISH (which stands for "parallel sequential fluorescence in situ hybridization) with which they finally make this metabolic multiverse visible. While these authors made the transcriptome visible, recently Geier et al. from Manuel Liebeke's group, made significant advancements in showing the end result of the metabolic activity of bacterial communities by combining different techniques to visualize "spatial metabolomics." They have gone even further and explored the activity of a host in response to its symbionts. They created a pipeline they call metaFISH, which combines fluorescence in situ hybridization (FISH) with high-resolution mass spectrometry. This approach reveals the intimate metabolic interactions between symbiont and host, perhaps revealing a secret metabolic language that we can finally begin to translate.
Fig. 2. Tongue Biofilm Consortia Are Complex and Structurally Organized. The spatial organization of an isolated consortium. Clusters of Rothia, Veillonella, Actinomyces, Neisseria, and Streptococcus cells comprise a large fraction of the consortium's bacterial biomass. Source
These techniques open avenues to keep prokaryotic research up-to-speed and match, to some extent, the ever-growing field of spatial biology in the eukaryotic world. Nevertheless, more will come to broaden our ability to visualize bacterial communities. The fascinating images of the tongue microbiome obtained using CLASI-FISH (combinatorial labelling and spectral imaging FISH), which identified the localization patterns of 17 unique genera, provide evidence that the localization patterns observed in laboratory biofilms with reduced numbers of species are also found in high-order interactions in natural microbial communities. Pushing the boundaries and increasing the number of fluorophores used to barcode individual species, the emergence of the new HiPR-FISH (high phylogenetic resolution FISH) raised the bar even further. In this work the authors identified an astonishing number of 65 genera in the human oral biofilm. All these techniques testify that, in the near future, we will witness continued advancements in imaging, particularly spatial biology, matching the same high throughput of information that we currently observe in the "omics" world. Clearly, the boundary between the two fields of research is becoming thinner.
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Davide Ciccarese is a postdoctoral associate in Jan Roelof van der Meer's lab at the University of Lausanne, within the Swiss NCCR microbiome initiatives. He previously served as a postdoc at the Earth, Atmospheric, and Planetary Sciences Department at MIT. In 2020, he obtained his Ph.D. from ETH, where he worked with David Johnson and Dani Or to study the mechanisms behind microbial spatial self-organization. His current main research focus is on microbiome-driven ecosystem processes across scales.
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