Biology subjects

Garcia-Pichel, F.

Publications and source records attributed to Garcia-Pichel, F..

6 recordsLinked to original sources

bioRxiv2026

Signaling metabolites spatially organize a multispecies mutualism in the soil microbiome

A plant-independent avenue for N2-fixation takes place in desert topsoils through a "C-for-N" mutualism between heterodiazotrophs and the cyanobacterium Microcoleus vaginatus. These partners come together within a diverse soil microbiome under conditions of N-limitation for the phototroph and C limitation for the heterotrophs. We hypothesized that extracellular chemical signaling might enable partner selection and collocation, though infomolecules shaping inter-microbial architecture were unknown. We show that the complex chemical composition of M. vaginatus exometabolome depends on its N-limitation status, thus potentially offering information to mutualists. In chemotactic assays, the exometabolome effectively repelled most native soil bacteria, particularly intensely when under N-limitation. Bacterial assemblages circumventing the repulsion were enriched in species that are rare in the soil microbiome, and that functionally resemble mutualistic cyanospheres (showing high N2-fixation potential, secretion of urea, and copiotrophy), setting the stage for a working symbiosis. Further, we could reproduce the enrichment of copiotrophs and nitrogen-fixers using mixtures of N-acetylglutamic acid, N-acetylmethionine, indole-3-acetic acid, and 5'-methylthioadenosine, all preferentially released by M. vaginatus under N-limitation. These signaling molecules did not result in an enrichment of urea producers, however. The results demonstrate that trans-species communication through specific infochemicals, together with already known quorum-sensing-like intraspecific communication in M. vaginatus, act as a tool to organize microbiomes spatially and to attain mutualistic partner specificity in an open, crowded background.

microbiology↗

bioRxiv2024

Cyanoexosortase B is essential for motility, biofilm formation and scytonemin production in a filamentous cyanobacterium

Exosortases are involved in trafficking proteins containing PEP-CTERM domains to the exterior of gram-negative bacterial cells. The role of these proteins in cyanobacteria, where such homologs are common, has not been defined. The filamentous cyanobacterium Nostoc punctiforme contains a single putative exosortase, designated cyanoexosortase B (CrtB), implicated by previous work in both the motility, and in the production of the UV-absorbing pigment, scytonemin. To determine the role of crtB in N. punctiforme, a crtB-deletion strain ({Delta}crtB) was generated. {Delta}crtB presented the loss of motility, biofilm formation, and scytonemin production. In the case of motility, the {Delta}crtB mutant exhibited a specific defect in the ability of hormogonia (specialized motile filaments) to adhere to hormogonium polysaccharide (HPS) and several PEP-CTERM proteins expressed in motile hormogonia were differentially abundant in the exoproteome of the wild type compared to the {Delta}crtB strain. These results are consistent with the hypothetical role of CrtB in the processing and export of PEP-CTERM proteins that play a critical role in stabilizing the interaction between the filament surface and HPS to facilitate motility and biofilm formation. In the case of scytonemin, the late biosynthetic steps of which occur in the periplasm and whose operon contains several putative PEP-CTERM proteins, {Delta}crtB failed to produce it. Given the abundance of putative PEP-CTERM proteins encoded in the N. punctiforme genome, and the fact that this study only associates a fraction of them with biological functions, it seems likely that CrtB may play an important role in other biological processes in cyanobacteria. ImportanceIn gram-negative bacteria, exosortases facilitate the trafficking of proteins to the exterior of the cell where they have been implicated in stabilizing the association of extracellular polymeric substances (EPS) with the cell surface to facilitate biofilm formation and flocculation, but the role of exosortases in cyanobacteria has not been explored. Here, we characterize the role of cyanoexosortase B (CrtB) in the filamentous cyanobacterium Nostoc punctiforme, demonstrating that crtB is essential for motility, biofilm formation, and the production of the sunscreen pigment scytonemin. These findings have important implications for understanding motility and biofilm formation in filamentous cyanobacteria as well as efforts toward heterologous production of scytonemin in non-native hosts.

microbiology↗

bioRxiv2023

An evolutionary optimum amid moderate heritability in prokaryotic cell size

We investigated the distribution and evolution of prokaryotic cell size based on a compilation of 5380 species. Size spans four orders of magnitude, from 100 nm (Mycoplasma) to more than 1 cm (Thiomargarita), however most species congregate heavily around the mean. The distribution approximates but is distinct from log-normality. Comparative phylogenetics suggested that size is heritable, yet the phylogenetic signal is moderate, and the degree of heritability is independent of taxonomic scale (i.e. fractal). Evolutionary modeling indicated the presence of an optimal cell size, corresponding to a coccus 0.70 {micro}m in diameter, to which most species gravitate. Analyses of 1361 species with sequenced genomes showed that genomic traits contribute to size evolution moderately and synergistically. In light of our results, scaling theory, and empirical evidence, we discuss potential drivers that may expand or shrink cells around the optimum and propose a stability landscape model for prokaryotic cell size.

evolutionary biology↗

bioRxiv2023

Desiccated cyanobacteria serve as efficient plasmid DNA carrier in space flight

Effective transport of biological systems as cargo during space travel is a critical requirement to use synthetic biology and biomanufacturing in outer space. Bioproduction using microbes will drive the extent to which many human needs can be met in environments with limited resources. Vast repositories of biological parts and strains are available to meet this need, but their on-site availability requires effective transport. Here, we explore an approach that allows DNA plasmids, a ubiquitous synthetic biology part, to be safely transported to the International Space Station and back to the Kennedy Space center, without low-temperature or cryogenic stowage. Our approach relied on the cyanobacterium Nostoc punctiforme PC73102, that is naturally tolerant to prolonged desiccation. Desiccated N. punctiforme was able to carry the non-native pSCR119 plasmid as intracellular cargo safely to space and back. Upon return to the laboratory, the extracted plasmid showed no DNA damage or additional mutations and could be used as intended to transform the model Synbio host Escherichia coli to bestow Kanamycin resistance. This proof-of-concept study provides the foundation for a ruggedized transport host for DNA to environments where there is a need to reduce equipment and infrastructure for biological parts stowage and storage.

microbiology↗

bioRxiv2022

Expanding the pulse-reserve paradigm to microorganisms on the basis of differential reserve management strategies

The pulse-reserve paradigm (PRP) is central in dryland ecology, although traits of microorganisms were not explicitly considered in its inception. We asked if the PRP could be reframed to encompass organisms both large and small. We used a synthetic review of recent advances in arid land microbial autoecology combined with a mathematically explicit theoretical model. Preserving the PRPs original core of adaptations by reserve building, the model considers differential organismal strategies to manage these reserves. It proposes a gradient of organisms according to their reserve strategies, from nimble responders (NIRs) to torpid responders (TORs). It predicts how organismal fitness depends on pulse regimes and reserve strategies thus explaining organismal diversification and distribution. After accounting for scaling phenomena and redefining the microscale meaning of aridity, it becomes patent that the PRP is applicable to microbes, and that this modified PRP represents an inclusive theoretical framework working across life-forms.

ecology↗

bioRxiv2020

Accurate Microbiome Sequencing with Synthetic Long Read Sequencing

The microbiome plays a central role in biochemical cycling and nutrient turnover of most ecosystems. Because it can comprise myriad microbial prokaryotes, eukaryotes and viruses, microbiome characterization requires high-throughput sequencing to attain an accurate identification and quantification of such co-existing microbial populations. Short-read next-generation-sequencing (srNGS) revolutionized the study of microbiomes and remains the most widely used approach, yet read lengths spanning only a few of the nine hypervariable regions of the 16S rRNA gene limit phylogenetic resolution leading to misclassification or failure to classify in a high percentage of cases. Here we evaluate a synthetic long-read (SLR) NGS approach for full-length 16S rRNA gene sequencing that is high-throughput, highly accurate and low-cost. The sequencing approach is amenable to highly multiplexed sequencing and provides microbiome sequence data that surpasses existing short and long-read modalities in terms of accuracy and phylogenetic resolution. We validated this commercially-available technology, termed LoopSeq, by characterizing the microbial composition of well-established mock microbiome communities and diverse real-world samples. SLR sequencing revealed differences in aquatic community complexity associated with environmental gradients, resolved species-level community composition of uterine lavage from subjects with histories of misconception and accurately detected strain differences, multiple copies of the 16S rRNA in a single strains genome, as well as low-level contamination in soil cyanobacterial cultures. This approach has implications for widespread adoption of high-resolution, accurate long-read microbiome sequencing as it is generated on popular short read sequencing platforms without the need for additional infrastructure.

microbiology↗