Wide Distribution of Phage That Infect Freshwater SAR11 Bacteria

Chen, Lin-Xing; Zhao, Yanlin; McMahon, Katherine D.; Mori, Jiro F.; Jessen, Gerdhard L; Nelson, Tara Colenbrander; Warren, Lesley A.; Banfield, Jillian F.

doi:10.1128/msystems.00410-19

Cited by 16 publications

(12 citation statements)

References 54 publications

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“…One possibility is as an effective defense mechanism against abundant viruses. Viruses infecting SAR11 have been shown to be extremely abundant in both marine ( 90 , 91 ) and freshwater ( 92 ) systems. Indeed, the paradox of high viral abundances and high host abundances in SAR11 has led to a refining of negative density-dependent selection through Lokta-Volterra predator-prey dynamics ( 93 ) to include heterogeneous susceptibility at the strain level ( 94 , 95 ) and positive density-dependent selection through intraspecific proliferation of defense mechanisms ( 96 ).…”

Section: Discussionmentioning

confidence: 99%

Expanding the Diversity of Bacterioplankton Isolates and Modeling Isolation Efficacy with Large-Scale Dilution-to-Extinction Cultivation

Henson

Lanclos

Pitre

et al. 2020

Appl Environ Microbiol

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Cultivated bacterioplankton representatives from diverse lineages and locations are essential for microbiology, but the large majority of taxa either remain uncultivated or lack isolates from diverse geographic locales. We paired large scale dilution-to-extinction (DTE) cultivation with microbial community analysis and modeling to expand the phylogenetic and geographic diversity of cultivated bacterioplankton and to evaluate DTE cultivation success. Here, we report results from 17 DTE experiments totaling 7,820 individual incubations over three years, yielding 328 repeatably transferable isolates. Comparison of isolates to microbial community data of source waters indicated that we successfully isolated 5% of the observed bacterioplankton community throughout the study. 43% and 26% of our isolates matched operational taxonomic units and amplicon single nucleotide variants, respectively, within the top 50 most abundant taxa. Isolates included those from previously uncultivated clades such as SAR11 LD12 and Actinobacteria acIV, as well as geographically novel members from other ecologically important groups like SAR11 subclade IIIa, SAR116, and others; providing isolates in eight putatively new genera and seven putatively new species. Using a newly developed DTE cultivation model, we evaluated taxon viability by comparing relative abundance with cultivation success. The model i) revealed the minimum attempts required for successful isolation of taxa amenable to growth on our media, and ii) identified possible subpopulation viability variation in abundant taxa such as SAR11 that likely impacts cultivation success. By incorporating viability in experimental design, we can now statistically constrain the effort necessary for successful cultivation of specific taxa on a defined medium. Importance Even before the coining of the term “great plate count anomaly” in the 1980s, scientists had noted the discrepancy between the number of microorganisms observed under the microscope and the number of colonies that grew on traditional agar media. New cultivation approaches have reduced this disparity, resulting in the isolation of some of the “most wanted” bacterial lineages. Nevertheless, the vast majority of microorganisms remain uncultured, hampering progress towards answering fundamental biological questions about many important microorganisms. Furthermore, few studies have evaluated the underlying factors influencing cultivation success, limiting our ability to improve cultivation efficacy. Our work details the use of dilution-to-extinction (DTE) cultivation to expand the phylogenetic and geographic diversity of available axenic cultures. We also provide a new model of the DTE approach that uses cultivation results and natural abundance information to predict taxon-specific viability and iteratively constrain DTE experimental design to improve cultivation success.

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Section: Discussionmentioning

confidence: 99%

Expanding the Diversity of Bacterioplankton Isolates and Modeling Isolation Efficacy with Large-Scale Dilution-to-Extinction Cultivation

Henson

Lanclos

Pitre

et al. 2020

Appl Environ Microbiol

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“…Given currently available tools, it is probably wise to choose a bin with no more than 10 pieces (Fig. 5, step 4), although a MAG (Chen et al 2019). The best possible case is when the genome is de novo assembled into a single piece.…”

Section: From High-quality Draft Sequences To Complete Genomes From Mmentioning

confidence: 99%

Accurate and complete genomes from metagenomes

et al. 2020

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Genomes are an integral component of the biological information about an organism; thus, the more complete the genome, the more informative it is. Historically, bacterial and archaeal genomes were reconstructed from pure (monoclonal) cultures, and the first reported sequences were manually curated to completion. However, the bottleneck imposed by the requirement for isolates precluded genomic insights for the vast majority of microbial life. Shotgun sequencing of microbial communities, referred to initially as community genomics and subsequently as genome-resolved metagenomics, can circumvent this limitation by obtaining metagenome-assembled genomes (MAGs); but gaps, local assembly errors, chimeras, and contamination by fragments from other genomes limit the value of these genomes. Here, we discuss genome curation to improve and, in some cases, achieve complete (circularized, no gaps) MAGs (CMAGs). To date, few CMAGs have been generated, although notably some are from very complex systems such as soil and sediment. Through analysis of about 7000 published complete bacterial isolate genomes, we verify the value of cumulative GC skew in combination with other metrics to establish bacterial genome sequence accuracy. The analysis of cumulative GC skew identified potential misassemblies in some reference genomes of isolated bacteria and the repeat sequences that likely gave rise to them. We discuss methods that could be implemented in bioinformatic approaches for curation to ensure that metabolic and evolutionary analyses can be based on very high-quality genomes.

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“…For example, most ASVs of clade alfV-A, tribe LD12, decreased while one increased from highlight to low-light years. These bacteria are aerobic heterotrophs occurring during summer in the epilimnion (Salcher et al, 2011), are adapted to oligotrophic conditions (Henson et al, 2018), require certain amino acids and vitamins from external sources (Henson et al, 2018), and are controlled by phage infection (Chen et al, 2019). Thus, their decline was related to unfavourable under-ice conditions while a temperature-dependent ecotype diversification within LD12 (Henson et al, 2018) might apply to the single exception.…”

Section: Under-ice Bacterial Communitiesmentioning

confidence: 99%

Temporal and spatial differences of the under-ice microbiome are linked to light transparency and chlorophyll-a

Obertegger

2022

Hydrobiologia

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Under-ice community dynamics are barely understood. Temporal and spatial studies are needed to fully understand the consequences of a declining ice cover on microbial biodiversity. Here, bacterial communities of different years (2015, 2017–2021) and layers (upper and lower euphotic layer, euphotic layer, hypolimnion) were assessed by Illumina sequencing of the 16S rRNA gene. Alpha- and beta-diversity of summer and under-ice hypolimnetic communities were similar, and a seasonal difference was found only when excluding summer hypolimnetic communities. Similarly, in non-metric multidimensional scaling (NMDS), summer and under-ice communities were different even though hypolimnetic communities were similar. Investigating under-ice conditions, the year 2017 showed highest under-ice light and chlorophyll-a while 2021 showed no under-ice light and lowest chlorophyll-a. Under-ice communities were not linked to layer differences implying that a spatial distinction under ice was less important than in summer, especially in years with little or no under-ice light. Most under-ice bacterial classes and ASVs showed direct and indirect dependencies on light availability and primary production. Similarly in NMDS with only under-ice communities, light transparency and primary production were important. In the future, ice conditions with less snow cover might lead to bacterial communities similar to that of high-light years (2017, 2018, 2020).

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Wide Distribution of Phage That Infect Freshwater SAR11 Bacteria

Cited by 16 publications

References 54 publications

Expanding the Diversity of Bacterioplankton Isolates and Modeling Isolation Efficacy with Large-Scale Dilution-to-Extinction Cultivation

Expanding the Diversity of Bacterioplankton Isolates and Modeling Isolation Efficacy with Large-Scale Dilution-to-Extinction Cultivation

Accurate and complete genomes from metagenomes

Temporal and spatial differences of the under-ice microbiome are linked to light transparency and chlorophyll-a

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