Revealing ecologically coherent population structure of uncultivated bacterioplankton with POGENOM

Sjöqvist, Conny; Zambrano, Luis Fernando Delgado; Alneberg, Johannes; Andersson, Anders F.

doi:10.1101/2020.03.25.999755

“…The completeness of the metagenome assemblies was checked with Quast 71 , mOTU2 72 and Busco 73 . pN/pS ratio was calculated with POGENOM 74 . The assemblies were submitted to NCBI and annotated with PGAP 75 .…”

Section: Raw Read Analysis and Reference Genome Analysismentioning

confidence: 99%

Functional strain redundancy and persistent phage infection in Swiss hard cheese starter cultures

Somerville

¹

,

Berthoud

²

,

Schmidt

³

et al. 2021

Preprint

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Undefined starter cultures are poorly characterized bacterial communities from environmental origin used in cheese making. They are phenotypically stable and have evolved through domestication by repeated propagation in closed and highly controlled environments over centuries. This makes them interesting for understanding eco-evolutionary dynamics governing microbial communities. While cheese starter cultures are known to be dominated by a few bacterial species, little is known about the composition, functional relevance, and temporal dynamics of strain-level diversity. Here, we applied shotgun metagenomics to an important Swiss cheese starter culture and analyzed historical and experimental samples reflecting 82 years of starter culture propagation. We found that the bacterial community is highly stable and dominated by only a few coexisting strains of Streptococcus thermophilus and Lactobacillus delbrueckii subsp. lactis. Genome sequencing, metabolomics analysis, and co-culturing experiments of 43 isolates show that these strains are functionally redundant, but differ tremendously in their phage resistance potential. Moreover, we identified two highly abundant Streptococcus phages that seem to stably coexist in the community without any negative impact on bacterial growth or strain persistence, and despite the presence of a large and diverse repertoire of matching CRISPR spacers. Our findings show that functionally equivalent strains can coexist in domesticated microbial communities and highlight an important role of bacteria-phage interactions that are different from kill-the-winner dynamics.

show abstract

Functional strain redundancy and persistent phage infection in Swiss hard cheese starter cultures

Somerville

¹

,

Berthoud

²

,

Schmidt

³

et al. 2021

View full text Add to dashboard Cite

Undefined starter cultures are poorly characterized bacterial communities from environmental origin used in cheese making. They are phenotypically stable and have evolved through domestication by repeated propagation in closed and highly controlled environments over centuries. This makes them interesting for understanding eco-evolutionary dynamics governing microbial communities. While cheese starter cultures are known to be dominated by a few bacterial species, little is known about the composition, functional relevance, and temporal dynamics of strain-level diversity. Here, we applied shotgun metagenomics to an important Swiss cheese starter culture and analyzed historical and experimental samples reflecting 82 years of starter culture propagation. We found that the bacterial community is highly stable and dominated by only a few coexisting strains of Streptococcus thermophilus and Lactobacillus delbrueckii subsp. lactis. Genome sequencing, metabolomics analysis, and co-culturing experiments of 43 isolates show that these strains are functionally redundant, but differ tremendously in their phage resistance potential. Moreover, we identified two highly abundant Streptococcus phages that seem to stably coexist in the community without any negative impact on bacterial growth or strain persistence, and despite the presence of a large and diverse repertoire of matching CRISPR spacers. Our findings show that functionally equivalent strains can coexist in domesticated microbial communities and highlight an important role of bacteria-phage interactions that are different from kill-the-winner dynamics.

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Geographic population structure and distinct population dynamics of globally abundant freshwater bacteria

Hoetzinger

¹

,

Hahn

²

,

Andersson

³

et al. 2023

Preprint

0

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Geographic separation is a principal factor for structuring populations of macroorganisms, with important consequences for evolution, by means of processes such as allopatric speciation. For free-living prokaryotes, implications of geographic separation on their evolution are more unclear. The limited phylogenetic resolution of commonly used markers such as 16S rRNA gene sequences have since long impeded prokaryotic population genetics. However, the vast amount of metagenome sequencing data generated during the last decades from various habitats around the world, now provides an excellent opportunity for such investigations. Here we exploited publicly available and new freshwater metagenomes in combination with genomes of abundant freshwater bacteria to study the impact of geographic separation on population structure. We focused on species that were detected across broad geographic ranges at high enough sequence coverage for meaningful population genomic analyses, i.e. members of the predominant freshwater taxa acI, LD12, Polynucleobacter and Ca. Methylopumilus. Population differentiation increased significantly with spatial distance in all species, but notable dispersal barriers (e.g. oceanic) were not apparent. Yet, the different species showed contrasting rates of geographic divergence and strikingly different population dynamics in time series within individual lakes. While certain populations hardly diverged over several years, others displayed high divergence after merely a few months, similar in scale to populations separated by thousands of kilometers. We speculate that populations with higher strain diversity evolve more monotonously, while low strain diversity enables more drastic clonal expansion of genotypes which will be reflected in strong but transient differentiation between temporally or spatially adjacent populations.

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Revealing ecologically coherent population structure of uncultivated bacterioplankton with POGENOM

Cited by 3 publications

References 76 publications

Functional strain redundancy and persistent phage infection in Swiss hard cheese starter cultures

Functional strain redundancy and persistent phage infection in Swiss hard cheese starter cultures

Functional strain redundancy and persistent phage infection in Swiss hard cheese starter cultures

Geographic population structure and distinct population dynamics of globally abundant freshwater bacteria

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