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  • Diel investments in metabolite production and consumption in a model microbial system

    Uchimiya M, Schroer W, Olofsson M, Edison AS, and Moran MA

    , 2022, ISME Journal, 16: 1306–1317

    Organic carbon transfer between surface ocean photosynthetic and heterotrophic microbes is a central but poorly understood process in the global carbon cycle. In a model community in which diatom extracellular release of organic molecules sustained growth of a co-cultured bacterium, we determined quantitative changes in the diatom endometabolome and the bacterial uptake transcriptome over two diel cycles. Of the nuclear magnetic resonance (NMR) peaks in the diatom endometabolites, 38% had diel patterns with noon or mid-afternoon maxima; the remaining either increased (36%) or decreased (26%) through time. Of the genes in the bacterial uptake transcriptome, 94% had a diel pattern with a noon maximum; the remaining decreased over time (6%). Eight diatom endometabolites identified with high confidence were matched to the bacterial genes mediating their utilization. Modeling of these coupled inventories with only diffusion-based phytoplankton extracellular release could not reproduce all the patterns. Addition of active release mechanisms for physiological balance and bacterial recognition significantly improved model performance. Estimates of phytoplankton extracellular release range from only a few percent to nearly half of annual net primary production. Improved understanding of the factors that influence metabolite release and consumption by surface ocean microbes will better constrain this globally significant carbon flux.

  • Controls on the relative abundances and rates of nitrifying microorganisms in the ocean

    Zakem EJ, Bayer B, Qin W, Santoro AE, Zhang Y, and Levine NM

    , 2022, Biogeosciences, 19(23): 5401–5418

    Nitrification controls the oxidation state of bioavailable nitrogen. Distinct clades of chemoautotrophic microorganisms – predominantly ammonia-oxidizing archaea (AOA) and nitrite-oxidizing bacteria (NOB) – regulate the two steps of nitrification in the ocean, but explanations for their observed relative abundances and nitrification rates remain incomplete and their contributions to the global marine carbon cycle via carbon fixation remain unresolved. Using a mechanistic microbial ecosystem model with nitrifying functional types, we derive simple expressions for the controls on AOA and NOB in the deep, oxygenated open ocean. The relative biomass yields, loss rates, and cell quotas of AOA and NOB control their relative abundances, though we do not need to invoke a difference in loss rates to explain the observed relative abundances. The supply of ammonium, not the traits of AOA or NOB, controls the relatively equal ammonia and nitrite oxidation rates at steady state. The relative yields of AOA and NOB alone set their relative bulk carbon fixation rates in the water column. The quantitative relationships are consistent with multiple in situ datasets. In a complex global ecosystem model, nitrification emerges dynamically across diverse ocean environments, and ammonia and nitrite oxidation and their associated carbon fixation rates are decoupled due to physical transport and complex ecological interactions in some environments. Nevertheless, the simple expressions capture global patterns to first order. The model provides a mechanistic upper estimate on global chemoautotrophic carbon fixation of 0.2–0.5 Pg C yr−1, which is on the low end of the wide range of previous estimates. Modeled carbon fixation by AOA (0.2–0.3 Pg C yr−1) exceeds that of NOB (about 0.1 Pg C yr−1) because of the higher biomass yield of AOA. The simple expressions derived here can be used to quantify the biogeochemical impacts of additional metabolic pathways (i.e., mixotrophy) of nitrifying clades and to identify alternative metabolisms fueling carbon fixation in the deep ocean.

  • Microbial population dynamics decouple growth response from environmental nutrient concentration

    Fink JW, Held NA, and Manhart M

    , 2022, PNAS, 120 (2): e2207295120

    How the growth rate of a microbial population responds to the environmental availability of chemical nutrients and other resources is a fundamental question in microbiology. Models of this response, such as the widely used Monod model, are generally characterized by a maximum growth rate and a half-saturation concentration of the resource. What values should we expect for these half-saturation concentrations, and how should they depend on the environmental concentration of the resource? We survey growth response data across a wide range of organisms and resources. We find that the half-saturation concentrations vary across orders of magnitude, even for the same organism and resource. To explain this variation, we develop an evolutionary model to show that demographic fluctuations (genetic drift) can constrain the adaptation of half-saturation concentrations. We find that this effect fundamentally differs depending on the type of population dynamics: Populations undergoing periodic bottlenecks of fixed size will adapt their half-saturation concentrations in proportion to the environmental resource concentrations, but populations undergoing periodic dilutions of fixed size will evolve half-saturation concentrations that are largely decoupled from the environmental concentrations. Our model not only provides testable predictions for laboratory evolution experiments, but it also reveals how an evolved half-saturation concentration may not reflect the organism’s environment. In particular, this explains how organisms in resource-rich environments can still evolve fast growth at low resource concentrations. Altogether, our results demonstrate the critical role of population dynamics in shaping fundamental ecological traits.

  • Community instability in the microbial world

    Huelsmann M and Ackermann M

    , 2022, Science, 378:6615

    No abstract available.

  • The ecological roles of bacterial chemotaxis

    Keegstra JM, Carrara F, and Stocker R

    , 2022, Nature Reviews Microbiology, 20(8): 401-504

    How bacterial chemotaxis is performed is much better understood than why.
    Traditionally, chemotaxis has been understood as a foraging strategy by which bacteria enhance
    their uptake of nutrients and energy, yet it has remained puzzling why certain less nutritious
    compounds are strong chemoattractants and vice versa. Recently, we have gained increased
    understanding of alternative ecological roles of chemotaxis, such as navigational guidance
    in colony expansion, localization of hosts or symbiotic partners and contribution to microbial
    diversity by the generation of spatial segregation in bacterial communities. Although bacterial
    chemotaxis has been observed in a wide range of environmental settings, insights into the
    phenomenon are mostly based on laboratory studies of model organisms. In this Review, we
    highlight how observing individual and collective migratory behaviour of bacteria in different
    settings informs the quantification of trade-offs, including between chemotaxis and growth.
    We argue that systematically mapping when and where bacteria are motile, in particular by
    transgenerational bacterial tracking in dynamic environments and in situ approaches from guts
    to oceans, will open the door to understanding the rich interplay between metabolism and
    growth and the contribution of chemotaxis to microbial life

  • Unique mobile elements and scalable gene flow at the prokaryote–eukaryote boundary revealed by circularized Asgard archaea genomes

    Wu F, Speth DR, Philosoph A, Crémière A, Narayanan A, Barco RA, Connon SA, Amend JP, Antoschechkin IA, and Orphan VJ

    , 2022, Nature Microbiololgy, 7: 200-212

    Eukaryotic genomes are known to have garnered innovations from both archaeal and bacterial domains but the sequence of events that led to the complex gene repertoire of eukaryotes is largely unresolved. Here, through the enrichment of hydrothermal vent microorganisms, we recovered two circularized genomes of Heimdallarchaeum species that belong to an Asgard archaea clade phylogenetically closest to eukaryotes. These genomes reveal diverse mobile elements, including an integrative viral genome that bidirectionally replicates in a circular form and aloposons, transposons that encode the 5,000 amino acid-sized proteins Otus and Ephialtes. Heimdallaechaeal mobile elements have garnered various genes from bacteria and bacteriophages, likely playing a role in shuffling functions across domains. The number of archaea- and bacteria-related genes follow strikingly different scaling laws in Asgard archaea, exhibiting a genome size-dependent ratio and a functional division resembling the bacteria- and archaea-derived gene repertoire across eukaryotes. Bacterial gene import has thus likely been a continuous process unaltered by eukaryogenesis and scaled up through genome expansion. Our data further highlight the importance of viewing eukaryogenesis in a pan-Asgard context, which led to the proposal of a conceptual framework, that is, the Heimdall nucleation–decentralized innovation–hierarchical import model that accounts for the emergence of eukaryotic complexity.

  • Random encounters and amoeba locomotion drive the predation of Listeria monocytogenes by Acanthamoeba castellanii

    De Schaetzen F, Fan M, Alcolombri U, Peaudecerf FJ, Drissner D, Loessner MJ, Stocker R, and Schuppler M

    , 2022, PNAS, 119(32): e2122659119

    Predatory protozoa play an essential role in shaping microbial populations. Among these protozoa, Acanthamoeba are ubiquitous in the soil and aqueous environments inhabited by Listeria monocytogenes. Observations of predator–prey interactions between these two microorganisms revealed a predation strategy in which Acanthamoeba castellanii assemble L. monocytogenes in aggregates, termed backpacks, on their posterior. The rapid formation and specific location of backpacks led to the assumption that A. castellanii may recruit L. monocytogenes by releasing an attractant. However, this hypothesis has not been validated, and the mechanisms driving this process remained unknown. Here, we combined video microscopy, microfluidics, single-cell image analyses, and theoretical modeling to characterize predator–prey interactions of A. castellanii and L. monocytogenes and determined whether bacterial chemotaxis contributes to the backpack formation. Our results indicate that L. monocytogenes captures are not driven by chemotaxis. Instead, random encounters of bacteria with amoebae initialize bacterial capture and aggregation. This is supported by the strong correlation between experimentally derived capture rates and theoretical encounter models at the single-cell level. Observations of the spatial rearrangement of L. monocytogenes trapped by A. castellanii revealed that bacterial aggregation into backpacks is mainly driven by amoeboid locomotion. Overall, we show that two nonspecific, independent mechanisms, namely random encounters enhanced by bacterial motility and predator surface-bound locomotion, drive backpack formation, resulting in a bacterial aggregate on the amoeba ready for phagocytosis. Due to the prevalence of these two processes in the environment, we expect this strategy to be widespread among amoebae, contributing to their effectiveness as predators.

  • Single-cell stable isotope probing in microbial ecology

    Alcolombri U, Pioli R, Stocker R, and Berry D

    , 2022, ISME Communications, 2

    Environmental and host-associated microbiomes are typically diverse assemblages of organisms performing myriad activities and engaging in a network of interactions that play out in spatially structured contexts. As the sum of these activities and interactions give rise to overall microbiome function, with important consequences for environmental processes and human health, elucidating specific microbial activities within complex communities is a pressing challenge. Single-cell stable isotope probing (SC-SIP) encompasses multiple techniques that typically utilize Raman microspectroscopy or nanoscale secondary ion mass spectrometry (NanoSIMS) to enable spatially resolved tracking of isotope tracers in cells, cellular components, and metabolites. SC-SIP techniques are uniquely suited for illuminating single-cell activities in microbial communities and for testing hypotheses about cellular functions generated for example from meta-omics datasets. Here, we illustrate the insights enabled by SC-SIP techniques by reviewing selected applications in microbiology and offer a perspective on their potential for future research.

  • Bacterial growth in multicellular aggregates leads to the emergence of complex life cycles

    Schwartzman JA, Ebrahimi A, Chadwick G, Sato Y, Roller BRK, Orphan VJ, and Cordero OX

    , 2022, Current Biololgy 32 (14): 3059-3069

    Facultative multicellular behaviors expand the metabolic capacity and physiological resilience of bacteria. Despite their ubiquity in nature, we lack an understanding of how these behaviors emerge from cellular-scale phenomena. Here, we show how the coupling between growth and resource gradient formation leads to the emergence of multicellular lifecycles in a marine bacterium. Under otherwise carbon-limited growth conditions, Vibrio splendidus 12B01 forms clonal multicellular groups to collectively harvest carbon from soluble polymers of the brown-algal polysaccharide alginate. As they grow, groups phenotypically differentiate into two spatially distinct sub-populations: a static ‘‘shell’’ surrounding a motile, carbon-storing ‘‘core.’’ Differentiation of these two sub-populations coincides with the formation of a gradient in nitrogen-source availability within clusters. Additionally, we find that populations of cells containing a high proportion of carbon-storing individuals propagate and form new clusters more readily on alginate than do populations with few carbonstoring cells. Together, these results suggest that local metabolic activity and differential partitioning of resources leads to the emergence of reproductive cycles in a facultatively multicellular bacterium.

  • Turnover in Life-Strategies Recapitulates Marine Microbial Succession Colonizing Model Particles

    Pascual-Garcia A, Schwartzman J, Enke T, Iffland-​Stettner A, Cordero O, and Bonhoeffer S

    , 2022, Frontiers Microbiololgy, 13: 812116

    Particulate organic matter (POM) in the ocean sustains diverse communities of bacteria that mediate the remineralization of organic complex matter. However, the variability of these particles and of the environmental conditions surrounding them present a challenge to the study of the ecological processes shaping particle-associated communities and their function. In this work, we utilize data from experiments in which coastal water communities are grown on synthetic particles to ask which are the most important ecological drivers of their assembly and associated traits. Combining 16S rRNA amplicon sequencing with shotgun metagenomics, together with an analysis of the full genomes of a subset of isolated strains, we were able to identify two-to-three distinct community classes, corresponding to early vs. late colonizers. We show that these classes are shaped by environmental selection (early colonizers) and facilitation (late colonizers) and find distinctive traits associated with each class. While early colonizers have a larger proportion of genes related to the uptake of nutrients, motility, and environmental sensing with few pathways enriched for metabolism, late colonizers devote a higher proportion of genes for metabolism, comprising a wide array of different pathways including the metabolism of carbohydrates, amino acids, and xenobiotics. Analysis of selected pathways suggests the existence of a trophic-chain topology connecting both classes for nitrogen metabolism, potential exchange of branched chain amino acids for late colonizers, and differences in bacterial doubling times throughout the succession. The interpretation of these traits suggests a distinction between early and late colonizers analogous to other classifications found in the literature, and we discuss connections with the classical distinction between r- and K-strategists.

  • Transport of Pseudomonas aeruginosa in Polymer Solutions

    Savorana G, Geisel S, Cen T, Ling Y, Stocker R, Rusconi R, and Secchi E

    , 2022, Frontiers Physiology, 10:910882

    Bacteria often live surrounded by polymer solutions, such as in animal respiratory, gastrointestinal, and reproductive tracts. In these systems, polymer solutions are often exposed to fluid flow, and their complex rheology can affect the transport of chemical compounds and microorganisms. Recent studies have focused on the effect of polymer solutions on the motility of bacteria in the absence of fluid flow. However, flow can be a game-changer on bacterial transport, as demonstrated by the depletion of motile bacteria from the low-shear regions and trapping in the high-shear regions in simple fluids, even for flows as simple as the Poiseuille one. Despite the relevance of polymer solutions in many bacterial habitats, the effect of their complex rheology on shear-induced trapping and bacterial transport in flow has remained unexplored. Using microfluidic experiments and numerical modeling, we studied how the shear rate and the rheological behavior of Newtonian and non-Newtonian polymer solutions affect the transport of motile, wild-type Pseudomonas aeruginosa in a Poiseuille flow. Our results show that, in Newtonian solutions, an increase in viscosity reduces bacterial depletion in the low-shear regions at the microchannel center, due to a reduction in the bacterial swimming velocity. Conversely, in the non-Newtonian solution, we observed a depletion comparable to the buffer case, despite its zero-shear viscosity being two orders of magnitude higher. In both cases, bacterial swimming and polymer fluid rheology control the magnitude of bacterial depletion and its shear-rate dependence. Our observations underscore the importance of the rheological behavior of the carrier fluid in controlling bacterial transport, in particular, close to surfaces giving rise to velocity gradients, with potential consequences on surface colonization and biofilm formation in many naturally relevant microbial habitats.

  • Elongation enhances encounter rates between phytoplankton in turbulence

    Argueidas-Leiva J-A, Slomka J, Lalescu CC, Stocker R, and Wilczek M

    , 2022, PNAS, 119 (32): e2203191119

    Phytoplankton come in a stunning variety of shapes but elongated morphologies dominate—typically 50% of species have aspect ratio above 5, and bloom-forming species often form chains whose aspect ratios can exceed 100. How elongation affects encounter rates between phytoplankton in turbulence has remained unknown, yet encounters control the formation of marine snow in the ocean. Here, we present simulations of encounters among elongated phytoplankton in turbulence, showing that encounter rates between neutrally buoyant elongated cells are up to 10-fold higher than for spherical cells and even higher when cells sink. Consequently, we predict that elongation can significantly speed up the formation of marine snow compared to spherical cells. This unexpectedly large effect of morphology in driving encounter rates among plankton provides a potential mechanistic explanation for the rapid clearance of many phytoplankton blooms.

  • Bacterial chemotaxis to saccharides is governed by a trade-off between sensing and uptake

    Norris N, Alcolombri U, Keegstra JM, Yawata Y, Menolascina F, Frazzoli E, Levine NM, Fernandez VI, and Stocker R

    , 2022, Biophysical Journal, 121(11): 2046-2059

    To swim up gradients of nutrients, E. coli senses nutrient concentrations within its periplasm. For small nutrient molecules, periplasmic concentrations typically match extracellular concentrations. However, this is not necessarily the case for saccharides, such as maltose, which are transported into the periplasm via a specific porin. Previous observations have shown that, under various conditions, E. coli limits maltoporin abundance so that, for extracellular micromolar concentrations of maltose, there are predicted to be only nanomolar concentrations of free maltose in the periplasm. Thus, in the micromolar regime, the total uptake of maltose from the external environment into the cytoplasm is limited not by the abundance of cytoplasmic transport proteins but by the abundance of maltoporins. Here, we present results from experiments and modeling suggesting that this porin-limited transport enables E. coli to sense micromolar gradients of maltose despite having a high-affinity ABC transport system that is saturated at these micromolar levels. We used microfluidic assays to study chemotaxis of E. coli in various gradients of maltose and methyl-aspartate and leveraged our experimental observations to develop a mechanistic transport-and-sensing chemotaxis model. Incorporating this model into agent-based simulations, we discover a trade-off between uptake and sensing: although high-affinity transport enables higher uptake rates at low nutrient concentrations, it severely limits the range of dynamic sensing. We thus propose that E. coli may limit periplasmic uptake to increase its chemotactic sensitivity, enabling it to use maltose as an environmental cue.

  • A microfluidic platform for characterizing the structure and rheology of biofilm streamers

    Savorana G, Slomka J, Stocker R, Rusconi R, and Secchi E

    , 2022, Soft Matter, 18: 3878-3890

    Biofilm formation is the most successful survival strategy for bacterial communities. In the biofilm lifestyle, bacteria embed themselves in a self-secreted matrix of extracellular polymeric substances (EPS), which acts as a shield against mechanical and chemical insults. When ambient flow is present, this viscoelastic scaffold can take a streamlined shape, forming biofilm filaments suspended in flow, called streamers. Streamers significantly disrupt the fluid flow by causing rapid clogging and affect transport in aquatic environments. Despite their relevance, the structural and rheological characterization of biofilm streamers is still at an early stage. In this work, we present a microfluidic platform that allows the reproducible growth of biofilm streamers in controlled physico-chemical conditions and the characterization of their biochemical composition, morphology, and rheology in situ. We employed isolated micropillars as nucleation sites for the growth of single biofilm streamers under the continuous flow of a diluted bacterial suspension. By combining fluorescent staining of the EPS components and epifluorescence microscopy, we were able to characterize the biochemical composition and morphology of the streamers. Additionally, we optimized a protocol to perform hydrodynamic stress tests in situ, by inducing controlled variations of the fluid shear stress exerted on the streamers by the flow. Thus, the reproducibility of the formation process and the testing protocol make it possible to perform several consistent experimental replicates that provide statistically significant information. By allowing the systematic investigation of the role of biochemical composition on the structure and rheology of streamers, this platform will advance our understanding of biofilm formation.

  • Historical contingencies and phage induction diversify bacterioplankton communities at the microscale

    Szabo RE, Pontrelli S, Grilli J, Schwartzman JA, Pollak S, Sauer U, and Cordero OX

    , 2022, PNAS, 119(30): e2117748119

    In many natural environments, microorganisms decompose microscale resource patches made of complex organic matter. The growth and collapse of populations on these resource patches unfold within spatial ranges of a few hundred micrometers or less, making such microscale ecosystems hotspots of heterotrophic metabolism. Despite the potential importance of patch-level dynamics for the large-scale functioning of heterotrophic microbial communities, we have not yet been able to delineate the ecological processes that control natural populations at the microscale. Here, we address this challenge by characterizing the natural marine communities that assembled on over 1,000 individual microscale particles of chitin, the most abundant marine polysaccharide. Using low-template shotgun metagenomics and imaging, we find significant variation in microscale community composition despite the similarity in initial species pools across replicates. Chitin-degrading taxa that were rare in seawater established large populations on a subset of particles, resulting in a wide range of predicted chitinolytic abilities and biomass at the level of individual particles. We show, through a mathematical model, that this variability can be attributed to stochastic colonization and historical contingencies affecting the tempo of growth on particles. We find evidence that one biological process leading to such noisy growth across particles is differential predation by temperate bacteriophages of chitin-degrading strains, the keystone members of the community. Thus, initial stochasticity in assembly states on individual particles, amplified through ecological interactions, may have significant consequences for the diversity and functionality of systems of microscale patches.

  • Simultaneous visualization of flow fields and oxygen concentrations to unravel transport and metabolic processes in biological systems

    Ahmerkamp S, Jalaluddin FM, Cui Y, Brumley DR, Pacherres CO, Berg JS, Stocker R, Kuypers MMM, Koren K, and Behrendt L

    , 2022, Cells Report Methods, 2(5): 100216

    From individual cells to whole organisms, O2 transport unfolds across micrometer- to millimeter-length scales and can change within milliseconds in response to fluid flows and organismal behavior. The spatiotemporal complexity of these processes makes the accurate assessment of O2 dynamics via currently available methods difficult or unreliable. Here, we present “sensPIV,” a method to simultaneously measure O2 concentrations and flow fields. By tracking O2-sensitive microparticles in flow using imaging technologies that allow for instantaneous referencing, we measured O2 transport within (1) microfluidic devices, (2) sinking model aggregates, and (3) complex colony-forming corals. Through the use of sensPIV, we find that corals use ciliary movement to link zones of photosynthetic O2 production to zones of O2 consumption. SensPIV can potentially be extendable to study flow-organism interactions across many life-science and engineering applications.

  • Diauxic lags explain unexpected coexistence in multi-resource environments

    Bloxham B, Lee H, and Gore J

    , 2022, Molecular System Biology, 18(5): e10630

    How the coexistence of species is affected by the presence of multiple resources is a major question in microbial ecology. We experimentally demonstrate that differences in diauxic lags, which occur as species deplete their own environments and adapt their metabolisms, allow slow-growing microbes to stably coexist with faster-growing species in multi-resource environments despite being excluded in single-resource environments. In our focal example, an Acinetobacter species (Aci2) competitively excludes Pseudomonas aurantiaca (Pa) on alanine and on glutamate. However, they coexist on the combination of both resources. Experiments reveal that Aci2 grows faster but Pa has shorter diauxic lags. We establish a tradeoff between Aci2’s fast growth and Pa’s short lags as their mechanism for coexistence. We model this tradeoff to accurately predict how environmental changes affect community composition. We extend our work by surveying a large set of competitions and observe coexistence nearly four times as frequently when the slow-grower is the fast-switcher. Our work illustrates a simple mechanism, based entirely on supplied-resource growth dynamics, for the emergence of multi-resource coexistence.

  • Microbial metabolites in the marine carbon cycle

    Moran MA, Kujawinski EB, Schroer WF, Amin SA, Bates NR, Bertrand EM, Braackman R, Brown CT, Covert MW, and Doney SC

    , 2022, Nature Microbiology, 7: 508-523

    One-quarter of photosynthesis-derived carbon on Earth rapidly cycles through a set of short-lived seawater metabolites that are generated from the activities of marine phytoplankton, bacteria, grazers and viruses. Here we discuss the sources of microbial metabolites in the surface ocean, their roles in ecology and biogeochemistry, and approaches that can be used to analyse them from chemistry, biology, modelling and data science. Although microbial-derived metabolites account for only a minor fraction of the total reservoir of marine dissolved organic carbon, their flux and fate underpins the central role of the ocean in sustaining life on Earth.

  • Sulfate differentially stimulates but is not respired by diverse anaerobic methanotrophic archaea

    Yu H, Skennerton CT, Chadwick GL, Leu AO, Aoki M, Tyson GW, and Orphan V

    , 2022, ISME Journal, 16: 168-177

    Sulfate-coupled anaerobic oxidation of methane (AOM) is a major methane sink in marine sediments. Multiple lineages of anaerobic methanotrophic archaea (ANME) often coexist in sediments and catalyze this process syntrophically with sulfate-reducing bacteria (SRB), but the potential differences in ANME ecophysiology and mechanisms of syntrophy remain unresolved. A humic acid analog, anthraquinone 2,6-disulfonate (AQDS), could decouple archaeal methanotrophy from bacterial sulfate reduction and serve as the terminal electron acceptor for AOM (AQDS-coupled AOM). Here in sediment microcosm experiments, we examined variations in physiological response between two co-occurring ANME-2 families (ANME-2a and ANME-2c) and tested the hypothesis of sulfate respiration by ANME-2. Sulfate concentrations as low as 100 µM increased AQDS-coupled AOM nearly 2-fold matching the rates of sulfate-coupled AOM. However, the SRB partners remained inactive in microcosms with sulfate and AQDS and neither ANME-2 families respired sulfate, as shown by their cellular sulfur contents and anabolic activities measured using nanoscale secondary ion mass spectrometry. ANME-2a anabolic activity was significantly higher than ANME-2c, suggesting that ANME-2a was primarily responsible for the observed sulfate stimulation of AQDS-coupled AOM. Comparative transcriptomics showed significant upregulation of ANME-2a transcripts linked to multiple ABC transporters and downregulation of central carbon metabolism during AQDS-coupled AOM compared to sulfate-coupled AOM. Surprisingly, genes involved in sulfur anabolism were not differentially expressed during AQDS-coupled AOM with and without sulfate amendment. Collectively, this data indicates that ANME-2 archaea are incapable of respiring sulfate, but sulfate availability differentially stimulates the growth and AOM activity of different ANME lineages.

  • Growth-stage-related shifts in diatom endometabolome composition set the stage for bacterial heterotrophy

    Olofsson M, Ferrer-González FX, Uchimiya M, Schreier JE, Holderman NR, Smith CB, Edison AS, Moran MA

    , 2022, ISME Communications, 2:28

    Phytoplankton-derived metabolites fuel a large fraction of heterotrophic bacterial production in the global ocean, yet methodological challenges have limited our understanding of the organic molecules transferred between these microbial groups. In an experimental bloom study consisting of three heterotrophic marine bacteria growing together with the diatom Thalassiosira pseudonana, we concurrently measured diatom endometabolites (i.e., potential exometabolite supply) by nuclear magnetic resonance (NMR) spectroscopy and bacterial gene expression (i.e., potential exometabolite uptake) by metatranscriptomic sequencing. Twenty-two diatom endometabolites were annotated, with nine increasing in internal concentration in the late stage of the bloom, eight decreasing, and five showing no variation through the bloom progression. Some metabolite changes could be linked to shifts in diatom gene expression, as well as to shifts in bacterial community composition and their expression of substrate uptake and catabolism genes. Yet an overall low match indicated that endometabolome concentration was not a good predictor of exometabolite availability, and that complex physiological and ecological interactions underlie metabolite exchange. Six diatom endometabolites accumulated to higher concentrations in the bacterial co-cultures compared to axenic cultures, suggesting a bacterial influence on rates of synthesis or release of glutamate, arginine, leucine, 2,3-dihydroxypropane-1-sulfonate, glucose, and glycerol-3-phosphate. Better understanding of phytoplankton metabolite production, release, and transfer to assembled bacterial communities is key to untangling this nearly invisible yet pivotal step in ocean carbon cycling.

  • The Ocean’s labile DOC supply chain

    Moran MA, Ferrer-Gonzalez FX, Fu H, Nowinski B, Olofsson M, Powers MA, Schreier JE, Smith CB, and Uchimiya M

    , 2022, Limnology and Oceanography, 67: 1007–1021

    Microbes of the surface ocean release, consume, and exchange labile metabolites at time scales of minutes to days. The details of this important step in the global carbon cycle remain poorly resolved, largely due to the methodological challenges of studying a diverse pool of metabolites that are produced and consumed nearly simultaneously. In this perspective, a new compilation of published data builds on previous studies to obtain an updated estimate of the fraction of marine net primary production that passes through the labile dissolved organic carbon (DOC) pool. In agreement with previous studies, our data mining and modeling approaches hypothesize that about half of ocean net primary production is processed through the labile DOC pool. The fractional contributions from three major sources are estimated at 0.4 for living phytoplankton, 0.4 for dead and dying phytoplankton, and 0.2 for heterotrophic microbes and mesoplankton.

  • A tradeoff between physical encounters and consumption determines an optimal droplet size for microbial degradation of dispersed oil

    Fernandez VI, Stocker R, and Juarez G

    , 2022, Scientific Reports, 12:4734

    Immiscible hydrocarbons occur in the ocean water column as droplets of varying diameters. Although microbial oil degradation is a central process in the remediation of hydrocarbon pollution in marine environments, the relationship between droplet size distribution and oil degradation rates by bacteria remains unclear, with a conflicting history of laboratory studies. Despite this knowledge gap, the use of chemical dispersants in oil spill response and mitigation is based on the rationale that increasing the surface-area-to-volume ratio of droplets will enhance net bacterial biodegradation rates. We demonstrate that this intuitive argument does not apply to most natural marine environments, where the abundance of oil droplets is much lower than in laboratory experiments and droplet-bacteria encounters are the limiting factor. We present a mechanistic encounter-consumption model to predict the characteristic time for oil degradation by marine bacteria as a function of the initial oil concentration, the distribution of droplet sizes, and the initial abundance of oil-degrading bacteria. We find that the tradeoff between the encounter time and the consumption time leads to an optimal droplet size larger than the average size generated by the application of dispersants. Reducing droplet size below this optimum can increase the persistence of oil droplets in the environment from weeks to years. The new perspective granted by this biophysical model of biodegradation that explicitly accounts for oil-microbe encounters changes our understanding of biodegradation particularly in the deep ocean, where droplets are often small and oil concentrations low, and explains degradation rate discrepancies between laboratory and field studies.

  • The structural role of bacterial eDNA in the formation of biofilm streamers

    Secchi E, Savorana G, Vitale A, Eberl L, Stocker R, and Rusconi R

    , 2022, PNAS, 119 (12): e2113723119

    Across diverse habitats, bacteria are mainly found as biofilms, surface-attached communities embedded in a self-secreted matrix of extracellular polymeric substances (EPS), which enhance bacterial recalcitrance to antimicrobial treatment and mechanical stresses. In the presence of flow and geometric constraints such as corners or constrictions, biofilms can take the form of long, suspended filaments (streamers), which bear important consequences in industrial and clinical settings by causing clogging and fouling. The formation of streamers is thought to be driven by the viscoelastic nature of the biofilm matrix. Yet, little is known about the structural composition of streamers and how it affects their mechanical properties. Here, using a microfluidic platform that allows growing and precisely examining biofilm streamers, we show that extracellular DNA (eDNA) constitutes the backbone and is essential for the mechanical stability of Pseudomonas aeruginosa streamers. This finding is supported by the observations that DNA-degrading enzymes prevent the formation of streamers and clear already formed ones and that the antibiotic ciprofloxacin promotes their formation by increasing the release of eDNA. Furthermore, using mutants for the production of the exopolysaccharide Pel, an important component of P. aeruginosa EPS, we reveal an concurring role of Pel in tuning the mechanical properties of the streamers. Taken together, these results highlight the importance of eDNA and of its interplay with Pel in determining the mechanical properties of P. aeruginosa streamers and suggest that targeting the composition of streamers can be an effective approach to control the formation of these biofilm structures.

  • Particle foraging strategies promote microbial diversity in marine environments

    Ebrahimi A, Goyal A, and Cordero OX

    , 2022, eLife, 11:e73948

    Microbial foraging in patchy environments, where resources are fragmented into particles or pockets embedded in a large matrix, plays a key role in natural environments. In the oceans and freshwater systems, particle-associated bacteria can interact with particle surfaces in different ways: some colonize only during short transients, while others form long-lived, stable colonies. We do not yet understand the ecological mechanisms by which both short- and long-term colonizers can coexist. Here, we address this problem with a mathematical model that explains how marine populations with different detachment rates from particles can stably coexist. In our model, populations grow only while on particles, but also face the increased risk of mortality by predation and sinking. Key to coexistence is the idea that detachment from particles modulates both net growth and mortality, but in opposite directions, creating a trade-off between them. While slow-detaching populations show the highest growth return (i.e., produce more net offspring), they are more susceptible to suffer higher rates of mortality than fast-detaching populations. Surprisingly, fluctuating environments, manifesting as blooms of particles (favoring growth) and predators (favoring mortality) significantly expand the likelihood that populations with different detachment rates can coexist. Our study shows how the spatial ecology of microbes in the ocean can lead to a predictable diversification of foraging strategies and the coexistence of multiple taxa on a single growth-limiting resource.

  • Microbes contribute to setting the ocean carbon flux by altering the fate of sinking particulates

    Nguyen TTH, Zakem EJ, Ebrahimi A, Schwartzman J, Caglar T, Amarnath K, Alcolombri U, Peaudecerf FJ, Hwa T, Stocker R, Cordero OX, and Levine NM

    , 2022, Nature Communications, 13:165

    Sinking particulate organic carbon out of the surface ocean sequesters carbon on decadal to millennial timescales. Predicting the particulate carbon flux is therefore critical for understanding both global carbon cycling and the future climate. Microbes play a crucial role in particulate organic carbon degradation, but the impact of depth-dependent microbial dynamics on ocean-scale particulate carbon fluxes is poorly understood. Here we scale-up essential features of particle-associated microbial dynamics to understand the large-scale vertical carbon flux in the ocean. Our model provides mechanistic insight into the microbial contribution to the particulate organic carbon flux profile. We show that the enhanced transfer of carbon to depth can result from populations struggling to establish colonies on sinking particles due to diffusive nutrient loss, cell detachment, and mortality. These dynamics are controlled by the interaction between multiple biotic and abiotic factors. Accurately capturing particle-microbe interactions is essential for predicting variability in large-scale carbon cycling.

  • Interactions between strains govern the eco-evolutionary dynamics of microbial communities

    Goyal A, Blitteston LS, Leventhal GE, Lu L, and Cordero OX

    , 2022, eLife, 11:e74987

    Genomic data has revealed that genotypic variants of the same species, that is, strains, coexist and are abundant in natural microbial communities. However, it is not clear if strains are ecologically equivalent, and at what characteristic genetic distance they might exhibit distinct interactions and dynamics. Here, we address this problem by tracking 10 taxonomically diverse microbial communities from the pitcher plant Sarracenia purpurea in the laboratory for more than 300 generations. Using metagenomic sequencing, we reconstruct their dynamics over time and across scales, from distant phyla to closely related genotypes. We find that most strains are not ecologically equivalent and exhibit distinct dynamical patterns, often being significantly more correlated with strains from another species than their own. Although even a single mutation can affect laboratory strains, on average, natural strains typically decouple in their dynamics beyond a genetic distance of 100 base pairs. Using mathematical consumer-resource models, we show that these taxonomic patterns emerge naturally from ecological interactions between community members, but only if the interactions are coarse-grained at the level of strains, not species. Finally, by analyzing genomic differences between strains, we identify major functional hubs such as transporters, regulators, and carbohydrate-catabolizing enzymes, which might be the basis for strain-specific interactions. Our work suggests that fine-scale genetic differences in natural communities could be created and stabilized via the rapid diversification of ecological interactions between strains.

  • Metabolic cross-feeding structures the assembly of polysaccharide degrading communities

    Pontrelli S, Szabo R, Pollak S, Schwartzman J, Ledezma-Tejeida D, Cordero OX, and Sauer U

    , 2022, Science Advances, 8(8)

    Metabolic processes that fuel the growth of heterotrophic microbial communities are initiated by specialized biopolymer degraders that decompose complex forms of organic matter. It is unclear, however, to what extent degraders structure the downstream assembly of the community that follows polymer breakdown. Investigating a model marine microbial community that degrades chitin, we show that chitinases secreted by different degraders produce oligomers of specific chain lengths that not only select for specialized consumers but also influence the metabolites secreted by these consumers into a shared resource pool. Each species participating in the breakdown cascade exhibits unique hierarchical preferences for substrates, which underlies the sequential colonization of metabolically distinct groups as resource availability changes over time. By identifying the metabolic underpinnings of microbial community assembly, we reveal a hierarchical cross-feeding structure that allows biopolymer degraders to shape the dynamics of community assembly.

  • Dynamic diel proteome and daytime nitrogenase activity supports buoyancy in the cyanobacterium Trichodesmium

    Held NA, Waterbury JB, and Webb EA

    , 2022, Nature Microbiololgy, 7: 300–311

    Cyanobacteria of the genus Trichodesmium provide about 80 Tg of fixed nitrogen to the surface ocean per year and contribute to marine biogeochemistry, including the sequestration of carbon dioxide. Trichodesmium fixes nitrogen in the daylight, despite the incompatibility of the nitrogenase enzyme with oxygen produced during photosynthesis. While the mechanisms protecting nitrogenase remain unclear, all proposed strategies require considerable resource investment. Here we identify a crucial benefit of daytime nitrogen fixation in Trichodesmium spp. that may counteract these costs. We analysed diel proteomes of cultured and field populations of Trichodesmium in comparison with the marine diazotroph Crocosphaera watsonii WH8501, which fixes nitrogen at night. Trichodesmium’s proteome is extraordinarily dynamic and demonstrates simultaneous photosynthesis and nitrogen fixation, resulting in balanced particulate organic carbon and particulate organic nitrogen production. Unlike Crocosphaera, which produces large quantities of glycogen as an energy store for nitrogenase, proteomic evidence is consistent with the idea that Trichodesmium reduces the need to produce glycogen by supplying energy directly to nitrogenase via soluble ferredoxin charged by the photosynthesis protein PsaC. This minimizes ballast associated with glycogen, reducing cell density and decreasing sinking velocity, thus supporting Trichodesmium’s niche as a buoyant, high-light-adapted colony forming cyanobacterium. To occupy its niche of simultaneous nitrogen fixation and photosynthesis, Trichodesmium appears to be a conspicuous consumer of iron, and has therefore developed unique iron-acquisition strategies, including the use of iron-rich dust. Particle capture by buoyant Trichodesmium colonies may increase the residence time and degradation of mineral iron in the euphotic zone. These findings describe how cellular biochemistry defines and reinforces the ecological and biogeochemical function of these keystone marine diazotrophs.

  • Settling of highly porous and impermeable particles in linear stratification: implications for marine aggregates

    Ahmerkamp S, Liu B, Kindler K, Maerz J, Stocker R, Kuypers MMM, and Khalili A

    , 2022, Journal of Fluid Mechanics, 931: A9

    The settling velocity of porous particles in linear stratification is affected by the diffusive exchange between interstitial and ambient water. The extent to which buoyancy and interstitial mass adaptation alters the settling velocity depends on the ratio of the diffusive and viscous time scales. We conducted schlieren experiments and lattice Boltzmann simulations for highly porous (95 %) but impermeable spheres settling in linear stratification. For a parameter range that resembles marine porous particles, ‘marine aggregates’, i.e. low Reynolds numbers (0.05≤Re≤10), intermediate Froude numbers (0.1≤Fr≤100) and Schmidt number of salt (Sc=700), we observe delayed mass adaptation of the interstitial fluid due to lower-density fluid being dragged by a particle that forms a density boundary layer around the particle. The boundary layer buffers the diffusive exchange of stratifying agent with the ambient fluid, leading to an enhanced density contrast of the interstitial pore fluid. Stratification-related drag enhancement by means of additional buoyancy of dragging lighter fluid and buoyancy-induced vorticity resembles earlier findings for solid spheres. However, the exchange between density boundary layer and pore fluid substantially increases stratification drag for small Fr. To estimate the effect of stratification on marine aggregates settling in the ocean, we derived scaling laws and show that small particles (≤0.5 mm) experience enhanced drag which increases retention times by 10 % while larger porous particle (>0.5 mm) settling is dominated by delayed mass adaptation that diminishes settling velocity by 10 % up to almost 100 %. The derived relationships facilitate the integration of stratification-dependent settling velocities into biogeochemical models.