Biology subjects

Polz, M. F.

Publications and source records attributed to Polz, M. F..

12 recordsLinked to original sources

bioRxiv2026

Genomically and ecologically cohesive subspecies as biologically meaningful units in the global ocean microbiome

Microbial diversity is organised into operationally defined species. However, it remains unclear whether these, or finer-scale groups represent biologically meaningful units in natural communities. Here, we implement a scalable, cultivation-independent framework to identify 724 genomically discrete and ecologically cohesive subspecies across 270 species in the global ocean microbiome. Their diversification is underpinned by gene-specific, nucleotide-level selection on the core genomic backbone and by variable restructuring of gene content, both of which proceed in a subspecies-specific manner. In over half of the species tested, subspecies were significantly associated with distinct environmental conditions, most frequently temperature. This coupling of genomic discreteness and ecological cohesiveness positions these subspecies as biologically meaningful units, a fundamental level at which ecological and evolutionary processes jointly drive divergence and structure microbial diversity in the oceans.

ecology↗

bioRxiv2025

Single-cell mass accumulation reveals bacterioplankton growth rate in native seawater

AO_SCPLOWBSTRACTC_SCPLOWThe growth of marine microbial communities drives biogeochemical cycling of carbon and other elements, yet the growth rates of individual species within complex ocean ecosystems remain poorly understood. In particular, the coexistence of a large diversity of copiotrophic bacteria, which are capable of fast growth but typically remain at low abundance, has been interpreted as a feast or famine existence. Here we show that contrary to the notion of infrequent growth, Vibrio bacteria exhibited consistent growth rates in coastal ocean samples, despite representing only a small fraction of the total community. These observations were enabled by a suspended microchannel resonator (SMR), which we adapted to function as a single-cell chemostat. By maintaining a continuous supply of native seawater around each trapped cell, we prevented nutrient depletion and used the SMRs high mass precision to resolve growth rates that are otherwise undetectable. Vibrio species displayed significantly larger cell mass and faster growth than other community members across samples collected at different temporal intervals from days to years. Surprisingly, their growth was consistently limited by carbon, contrary to the expectation that heterotrophic bacteria in the euphotic zone would be limited by nitrogen and phosphorus due to competition with algae. The correlation between cell mass and growth rate of Vibrionaceae in seawater followed established growth laws derived from laboratory conditions, suggesting that growth physiology observed in pure cultures is applicable to wild bacterial populations. Overall, our findings suggest that rare species may play a disproportionately large role in the marine carbon cycle, with rapid biomass turnover driven by a combination of high growth rates balanced by intense predation.

microbiology↗

bioRxiv2025

Bacterial peptide deformylase inhibitors induce prophages in competitors

While antibiotics mediate chemical warfare among microbes, their roles in the wild extend beyond direct growth inhibition(1). Some antibiotics have the potential to mediate interference competition by triggering a bacterial stress response that subsequently activates endogenous viruses integrated in bacterial genomes (prophages). Canonically, this activation is regulated by the SOS response upon DNA damage. Here we show that a metabolite produced by natural isolates of Vibrio ordalii circumvents the SOS response by directly triggering prophage induction in other Vibrio species, co-occurring in the same environment. While the metabolite was previously classified as a broad-spectrum antibiotic, we observe how it acts as a peptide deformylase inhibitor that specifically induces certain prophages, even when target bacterial cells carry multiple other prophages. Its biosynthetic gene cluster, or ord cluster, also encodes its own peptide deformylase (OrdE) which provides self-immunity to producer strains. Likewise, among natural Vibrio isolates that carry similar prophages, resistance against the ord metabolite was found in those that had acquired a divergent second peptide deformylase. Finally, we show that prophage induction by the ord cluster prevents slower-growing producer strains from being outcompeted by their otherwise fast-growing competitors if they carry an inducible prophage. Thus, we demonstrate how natural products play additional impactful roles in communities beyond antibiotic activity and that prophage induction serves as an interference competition strategy, sustaining community diversity.

microbiology↗

bioRxiv2025

Fine-scale spatial patterns in hot springs mat bacterial communities

Some of the most widely recognized spatial scaling relationships in ecology include the species-area, the abundance-occupancy, and the community compositional similarity-geographic distance relationships. These patterns have been shown to emerge from common mechanisms, such as habitat heterogeneity and colonization-extinction dynamics, and are predicted by various ecological models and theories, including Island Biogeography, Metapopulation theory, and Neutral Theory of Biodiversity and Biogeography. These patterns have been studied in microbial communities at large-scale, but studies at fine grain and small extent are rare, despite at a fine-scale, emerging patterns can be tested with a higher resolution. In this study, we explored these macroecological patterns in bacterial communities inhabiting hot springs mats, which have been shown to exhibit fine-scale spatial heterogeneity in fundamental environmental parameters such as temperature. In three different localities, we sampled a grid with a heterogeneous temperature at a fine-scale, a small extent (approximately 150 cm2), and fine grain (each containing 30 cells spaced about 1 or 2 cm apart). Our findings revealed sublinear scaling for the species-area relationship, with similar parameters across localities, indicating a low rate of spatial species turnover. For the abundance-occupancy relationship, we observed increasing trends, meaning that species that occupied more patches were, on average, more abundant. Additionally, we identified a decay in community compositional similarity with distance in two of the localities, though with low parameter values, indicating minimal geographic isolation at this scale. These results are consistent with different models that predict that spatial ecological patterns arise from spatial heterogeneity, as different species can partition their niches in space and constitute an example of predictable spatial patterns at a fine scale.

ecology↗

bioRxiv2024

Interpretable machine learning reveals a diverse arsenal of anti-defenses in bacterial viruses

Antagonistic interactions with viruses are an important driver of the ecology and evolution of bacteria, and associating genetic signatures to these interactions is of fundamental importance to predict viral infection success. Recent studies have highlighted that bacteria possess a large, rapidly changing arsenal of defense genes and that viruses can neutralize at least some of these genes with matching anti-defenses. However, a broadly applicable approach for discovering the genetic underpinnings of such interactions is missing since typically used methods such as comparative genomics are limited by the rampant horizontal gene transfer and poor annotation of viral and bacterial genes. Here we show that genes that allow the viruses to overcome bacterial defenses can be systematically identified using an interpretable machine-learning approach even when using diverse bacteria-virus infection data. To verify the predictions, we experimentally characterized eight previously unknown anti-defense proteins in viruses specific for Vibrio bacteria and showed that they counteract a wide range of bacterial immune systems, including AbiH, AbiU, Septu, DRT, CBASS, and Retron. The power of our computational approach is highlighted by the identification of anti-defense proteins that inhibit non-homologous defense systems, which we verify for Retron and AbiH. We suggest that the computational prediction based on experimental interactions offers a promising avenue to unravel the genetic mechanisms of co-evolution between bacteria and their viruses.

microbiology↗

bioRxiv2024

Genome-wide sweeps create fundamental ecological units in the human gut microbiome

The human gut microbiome is shaped by diverse selective forces originating from the host and associated environmental factors, and in turn profoundly influences health and disease. While the association of microbial lineages with various conditions has been shown at different levels of phylogenetic differentiation, it remains poorly understood to what extent unifying adaptive mechanisms sort microbial lineages into ecologically differentiated populations. Here we show that a pervasive mechanism differentiating bacteria in the microbiome are genome-wide selective sweeps, leading to population structure akin to global epidemics across geographically and ethnically diverse human populations. Such sweeps arise when an adaptation allows a clone to outcompete others within its niche followed by re-diversification, and manifest as clusters of closely related genomes on long branches in phylogenetic trees. This structure is revealed by excluding recombination events that mask the clonal descent of the genomes, and we find that genome-wide sweeps originate under a wide regime of recombination rates in at least 66 taxa from 25 bacterial families. Estimated ages of divergence suggest sweep clusters can spread globally within decades, and this process has occurred repeatedly throughout human history. We show, as an example, that the ecological differentiation of sweep clusters forms populations highly associated with age and colorectal cancer. Our analysis elucidates an evolutionary mechanism for the observation of stably inherited strains with differential associations and provides a theoretical foundation for analyzing adaptation among co-occurring microbial populations.

microbiology↗

bioRxiv2024

Mechanism of bacterial predation via ixotrophy

Predation allows bacteria to access alternative substrates in low-nutrient conditions. Ixotrophy has been proposed as a predatory lifestyle of multicellular filamentous bacteria in aquatic environments; however, the molecular mechanism remains unknown. Here we uncover by a multidisciplinary approach that ixotrophy requires the interplay of multiple cellular machineries and a regulatory mechanism. Attacker-prey contacts are established by gliding motility and extracellular grappling hook-like structures that bind prey flagella. Cryo-electron microscopy identifies the grappling hooks as a heptameric assembly of a Type 9 Secretion System substrate. Cryo-electron tomography and functional assays show that killing is mediated by puncturing of the prey cell using a Type 6 Secretion System, possibly triggered by extracellular antennae. Single-cell analyses with stable isotope-labeled prey demonstrate that prey components are taken up by the attacker. Depending on nutrient availability, ixotrophy is switched off by endogenous Insertion Sequence Elements and re-activated through their excision. A marine metagenomic time series provides evidence for coupled dynamics of ixotrophic bacteria and their prey. Our study reveals the complex mechanism of a conserved microbial predatory lifestyle and indicates the need for its regulation in conditions where the expression of costly pathways is dispensable.

microbiology↗

bioRxiv2023

Direct quantification of sinking velocities across unicellular algae

Eukaryotic phytoplankton, also known as algae, form the basis of marine food webs and drive marine carbon sequestration when their biomass sinks to the ocean floor. Algae must regulate their vertical movement, as determined by motility and gravitational sinking, to balance access to light at the surface and nutrients in deeper layers. However, the regulation of gravitational sinking velocities remains largely unknown, especially in motile species. Here, we directly quantify single-cell masses and volumes to calculate sinking velocities according to Stokes law in diverse clades of unicellular marine microalgae. Our results reveal the cell size, light, and nutrient-dependency of sinking velocities. We identify motile dinoflagellate and green algal species that increase their sinking velocity in response to starvation. Mechanistically, this increased cell sinking is achieved by photosynthesis-driven accumulation of carbohydrates, which increases cell mass and density. Moreover, cell sinking velocities correlate inversely with proliferation rates, and the mechanism regulating cell sinking velocities integrates signals from multiple nutrients. Our findings suggest that the regulation of cell composition according to environmental conditions contributes to the vertical movement of motile cells in the oceans. More broadly, our approach for sinking velocity measurements expands the study of gravitational sinking to motile cells and supports the modeling of marine carbon pump and nutrient cycles.

ecology↗

bioRxiv2023

Single-cell mass distributions reveal simple rules for achieving steady-state growth

Optical density is a common method for measuring exponential growth in bacterial batch cultures. However, there is a misconception that such exponential growth is equivalent to steady-state growth, which is a distinct physiological state that improves experimental reproducibility. Determining precisely when steady-state growth occurs is technically challenging and is aided by paired single-cell and population-level measurements. Using microfluidic mass sensors and optical density, we explore when in typical laboratory batch cultures steady-state growth occurs. We show that cell mass increases by an order of magnitude within a few hours of dilution into fresh medium and that steady-state growth is only achieved when cultures are inoculated with high dilutions from overnight stationary phase cultures. At high dilutions, Escherichia coli and Vibrio cyclitrophicus grown in different rich media achieve steady-state growth approximately 4 total biomass doublings after inoculation. We can decompose these dynamics into 3 doublings of average cell mass and 1 doubling of cell number for both species. We also show that batch cultures in rich media depart steady-state growth early in their growth curves at low cell and biomass concentrations. Achieving and maintaining steady-state growth in batch culture is a delicate balancing act, and we provide general guidance for commonly used rich media. Quantifying single-cell mass outside of steady-state growth is an important first step towards understanding how microbes grow in their natural context, where fluctuations pervade at the scale of individual cells. ImportanceMicrobiologists have watched clear liquid turn cloudy for over 100 years. While the cloudiness of a culture is proportional to its total biomass, growth rates using such optical density measurements are challenging to interpret when cells change size. Many bacteria adjust their size at different steady-state growth rates, but also when shifting between starvation and growth. Optical density cannot disentangle how mass is distributed among cells of different sizes, and directly measuring how mass is distributed among cells has been a major challenge. Here we use single-cell mass measurements to demonstrate that a population of cells in batch culture achieves a stable mass distribution for only a short period of time. Achieving steady-state growth in rich medium requires low initial biomass concentrations and enough time for the coordination of individual cell and population growth. Steady-state growth is important for reliable cell mass distributions in a culture and we discuss how mass variation outside of steady-state can impact physiology, ecology, and evolution experiments.

microbiology↗

bioRxiv2021

Resolving the structure of phage-bacteria interactions in the context of natural diversity

Microbial communities are shaped by viral predators1. Yet, resolving which viruses (phages) and bacteria are interacting is a major challenge in the context of natural levels of microbial diversity2. Thus, fundamental features of how phage-bacteria interactions are structured and evolve in "the wild" remain poorly resolved3, 4. Here we use large-scale isolation of environmental marine Vibrio bacteria and their phages to obtain quantitative estimates of strain-level phage predator loads, and use all-by-all host range assays to discover how phage and host genomic diversity shape interactions. We show that killing in environmental interaction networks is sparse - with phage predator loads low for most bacterial strains and phages host-strain-specific in their killing. Paradoxically, we also find that although overlap in killing is generally rare between phages, recombination is common. Together, these results indicate that the number of hosts that phages infect is often larger than the number that they kill and suggest that recombination during cryptic co-infections is an important mode of phage evolution in microbial communities. In the development of phages for bioengineering and therapeutics it will be important to consider that nucleic acids of introduced phages may spread into local phage populations through recombination, and that the likelihood of transfer is not predictable based on killing host range.

microbiology↗

bioRxiv2019

Sympatric and allopatric differentiation delineate population structure in a free-living terrestrial bacterium

In free-living bacteria and archaea, the equivalent of the biological species concept does not exist, creating several barriers to the study of the processes contributing to microbial diversification. As such, microorganisms are often operationally defined using conserved marker genes (i.e., 16S rRNA gene) or whole-genome measurements (i.e., ANI) to interpret intra-specific processes. However, as in eukaryotes, investigations into microbial populations must consider the potential for interacting genotypes among individuals that are subjected to similar environmental selective pressures. Therefore, we isolated 26 strains within a single bacterial ecotype (equivalent to a eukaryotic species definition) from a common habitat (leaf litter) across a regional climate gradient and asked whether the genetic diversity in a free-living soil bacterium (Curtobacterium) was consistent with patterns of allopatric or sympatric differentiation. By examining patterns of gene flow, our results indicate that microbial populations are delineated by gene flow discontinuities and exhibit evidence for population-specific adaptation. We conclude that the genetic structure within this bacterium is due to both adaptation within localized microenvironments (isolation-by-environment) as well as dispersal limitation between geographic locations (isolation-by-distance).

evolutionary biology↗

bioRxiv2018

Interactions in self-assembled microbial communities saturate with diversity

How the diversity of organisms competing for or sharing resources influences community production is an important question in ecology but has rarely been explored in natural microbial communities. These generally contain large numbers of species making it difficult to disentangle how the effects of different interactions scale with diversity. Here, we show that changing diversity affects measures of community function in relatively simple communities but that increasing richness beyond a threshold has little detectable effect. We generated self-assembled communities with a wide range of diversity by growth of cells from serially diluted seawater on brown algal leachate. We subsequently isolated the most abundant taxa from these communities via dilution-to-extinction in order to compare productivity functions of the entire community to those of individual taxa. To parse the effect of different types of organismal interactions, we developed relative total function (RTF) as an index for positive or negative effects of diversity on community function. Our analysis identified three overall regimes with increasing diversity. At low richness (<12 taxa), potential positive and negative effects of interactions are both weak, while at moderate richness (12-20 taxa), community resource uptake increases but the carbon use efficiency decreases. Finally, beyond 20 taxa, there was no net change in community function indicating a saturation of potential interactions. These data suggest that although more diverse communities had overall greater access to resources, individual taxa within these communities had lower resource availability and reduced carbon use efficiency, indicating that competition due to niche overlap increases with diversity but that these interactions saturate at a specific threshold.

ecology↗