Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/032169

Latitude delineates patterns of biogeography in terrestrial Streptomyces

Mallory J Choudoir·James R Doroghazi·Daniel H Buckley
View original source ↗Export metadata ↓

Abstract

We examined the biogeography of Streptomyces at regional spatial scales to identify factors that govern patterns of microbial diversity. Streptomyces are spore forming filamentous bacteria which are widespread in soil. Streptomyces strains were isolated from perennial grass habitats sampled across a spatial scale of more than 6,000 km. Previous analysis of this geographically explicit culture collection provided evidence for a latitudinal diversity gradient in Streptomyces species. Here we evaluate the hypothesis that this latitudinal diversity gradient is a result of evolutionary dynamics associated with historical demographic processes. Historical demographic phenomena have genetic consequences that can be evaluated through analysis of population genetics. We applied population genetic approaches to analyze population structure in six of the most numerically abundant and geographically widespread Streptomyces phylogroups from our culture collection. Streptomyces population structure varied at regional spatial scales and allelic diversity correlated with geographic distance. In addition, allelic diversity and gene flow are partitioned by latitude. Finally, we found that nucleotide diversity within phylogroups is negatively correlated with latitude. These results indicate that phylogroup diversification is constrained by dispersal limitation at regional spatial scales and they are consistent with the hypothesis that historical demographic processes have influenced the contemporary biogeography of Streptomyces.\n\nOriginality-Significance StatementWe provide the first population genetic evidence that patterns of Streptomyces biogeography, which manifest in geographically explicit patterns of gene flow and a latitudinal gradient of nucleotide diversity, result from dispersal limitation and regional diversification due to drift. This contribution elucidates evolutionary processes that underlie patterns of microbial biogeography.

Source connections

Explore related subjects

MicrobiologyPreprint

Keep this discovery

BibTeXRIS

Mallory J Choudoir, James R Doroghazi, Daniel H Buckley. 2015-11-18. Latitude delineates patterns of biogeography in terrestrial Streptomyces. https://doi.org/10.1101/032169

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2016

In vivo bioluminescent imaging reveals temporal and spatial dynamics of giardiasis

Giardia lamblia is the most prevalent protistan parasite, causing acute and chronic diarrheal disease in over one billion people worldwide. Vertebrate hosts ingest Giardia cysts from contaminated sources, and these cysts excyst in the gut to become motile trophozoites. Trophozoites colonize the small intestine by attaching to the intestinal villi and later differentiate into infectious cysts that are released into the environment, completing Giardias life cycle. Due to the limited accessibility of the gastrointestinal tract, our understanding of in in vivo temporal and spatial dynamics of giardiasis is largely inferred from parasite physiology in laboratory culture. Yet parasite growth under in vitro culture conditions may not mirror in vivo parasite physiology in the host. Here we develop bioluminescent imaging (BLI) methods to directly interrogate the temporal and spatial dynamics of giardiasis in mice, providing an improved animal model for the evaluation of anti-Giardia drugs. This non-invasive method of imaging giardiasis allows unprecedented and precise quantification of in vivo temporal and spatial patterns of infection. By infecting mice with parasites expressing constitutive or encystation-specific luciferase bioreporters, we show that parasite colonization of the gut is not uniform. Metabolically active parasites primarily colonize the proximal small intestine in \"hot spots\"--high density foci of infection that likely result in localized pathology to the gut epithelium. Using in vivo and ex vivo BLI of encystation-specific bioreporters, we show that encystation initiates shortly after inoculation and parasites encyst throughout the entire duration of infection. We also find that encystation is initiated in high density foci in the proximal small intestine, rather than the colon as has been previously assumed, and show that the initiation of encystation is magnified in parasites incubated at high density in laboratory culture. Prior models have suggested that chemical cues cause parasites to encyst as they are dislodged from the upper gut and travel to more distal regions of the gastrointestinal tract. We suggest a model of encystation in which parasites reach a threshold density that results the induction of encystation due to local nutrient depletion. The in vivo imaging of giardiasis has redefined the dynamics of the Giardia life cycle in the host, paving the way for future mechanistic studies of density-dependent processes in this highly prevalent, yet understudied parasite.

Microbiology↗
bioRxiv2016

A bacterial chaperone is required for plastid function in malaria parasites

Apicomplexan parasites such as Plasmodium falciparum, the causative agent of malaria, contain a non-photosynthetic plastid known as the apicoplast that functions to produce essential metabolic compounds. It was previously reported that several members of the Clp family of chaperones and proteases localize to the apicoplast. In bacteria and in chloroplasts these proteins form complexes that degrade proteins in a proteasome-like manner to regulate key cellular processes, but their function in the apicoplast is completely unknown. In this study, we generated a conditional mutant of the P. falciparum apicoplast-targeted pfclpc gene and found that under normal conditions it localizes to the apicoplast. Knockdown of PfClpC results in growth inhibition and morphological defects, indicating that PfClpC is essential for parasite viability. Upon inhibition, PfClpC loses its apicoplast localization and appears in vesicle-like structures. Other apicoplast-targeted proteins also localize to these structures, suggesting that organelle integrity is compromised. Addition of isopentynyl pyrophosphate completely rescued the growth inhibition, indicating that the only essential function of PfClpC is related to the apicoplast. Moreover, cellular assays suggest that PfClpC inhibition interferes with the ability of the schizont-stage parasites to properly sort functional apicoplast organelles into daughter-merozoites. These data show that PfClpC is an essential gene that functions to maintain apicoplast integrity.\n\nAuthor SummaryThe deadly human malaria parasite, Plasmodium falciparum, contains a unique organelle called the apicoplast, a non-photosynthetic plastid that produces vital metabolites. Members of the prokaryotic-derived Clp family were previously reported to localize to the apicoplast. In bacteria and plant chloroplasts, Clp homologs form a proteasome-like complex that degrade proteins but their function in parasite biology is unknown. Here we took a conditional knockdown approach to study an apicoplast localized Clp proteins, PfClpC, which we found to be essential for parasite viability. Inhibition of PfClpC results in a growth arrest phenotype that correlates with a reduced replication rate. We observed that PfClpC localizes to the apicoplast, however upon inhibition it is found dispersed in vesicle-like structures suggesting a complete breakdown of organelle integrity. Our ability to rescue the phenotype by adding an essential apicoplast-derived metabolite proved that the only essential function of PfClpC is linked to apicoplast function. Furthermore, we have found evidence supporting a role for PfClpC in apicoplast sorting into daughter cells. Therefore, we propose PfClpC as a potential drug target due to its essentiality, prokaryotic origin and absence from the human host.

Microbiology↗
bioRxiv2016

Functional analysis of a biosynthetic cluster essential for production of 4-formylaminooxyvinylglycine, a germination-arrest factor from Pseudomonas fluorescens WH6

Rhizosphere-associated Pseudomonas fluorescens WH6 produces the germination-arrest factor, 4-formylaminooxyvinylglycine (FVG). FVG has previously been shown to both arrest the germination of weedy grasses and to inhibit the growth of the bacterial plant pathogen Erwinia amylovora. Very little is known about the mechanism by which FVG is produced. Although a previous study identified a region of the genome that may be involved in FVG biosynthesis, it has not yet been determined which genes within that region are sufficient and necessary for FVG production. In the current study, we explored the role of each of the putative genes encoded in that region by constructing deletion mutations. Mutant strains were assayed for their ability to produce FVG with a combination of biological assays and thin-layer chromatographic analyses. This work defined the core FVG biosynthetic gene cluster and revealed several interesting characteristics of FVG production. We determined that FVG biosynthesis requires two small open reading frames of less than 150 nucleotides and that multiple transporters have overlapping but distinct functionality. In addition, two genes in the center of the biosynthetic gene cluster are not required for FVG production, suggesting that additional products may be produced from the cluster. Transcriptional analysis indicated that at least three active promoters play a role in the expression of genes within this cluster. The results of this study enrich our knowledge regarding the diversity of mechanisms by which bacteria produce non-proteinogenic amino acids like vinylglycines.

Microbiology↗