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

Stable isotope probing and oligotyping reveal the impact of organophosphorus pesticides on the carbon fixation related bacterioplankton lineage

Freshwater bacterioplankton communities play a pivotal role in global carbon fixation and energy exchange. However, establishing direct linkages between environmental stressors like organophosphorus pesticides (OPPs) and the ecological functions, such as carbon-fixing related microorganisms (CFMs), remains challenging. This study investigated the effects of four OPPs - two phosphates (dichlorvos, monocrotophos) and two phosphorothioates (omethoate, parathion) - on bacterioplankton communities using stable isotope probing, high-throughput sequencing and oligotyping analysis. Seven CFMs were identified. All OPPs significantly reduced total biomass (from 7.87 ×104 to 2.30-4.11 ×104 cells/mL) but stimulated CFMs proliferation. Notably, phosphorothioates induced a greater increase in CFMs abundance (36.84 %-57.18 %, up from 21.1 %) compared to phosphates (23.85 %-37.10 %; p < 0.05). Principal coordinate analysis (PCoA) revealed that phosphorothioates exerted stronger effects on microbial community and CFMs oligotypes structure compared to phosphates (p < 0.05). Variance partitioning analysis (VPA) identified pesticide type as the dominant driver of community structure. PICRUSt2 prediction demonstrated that OPPs suppressed oxidoreductase pathways linked to energy metabolism while activating transferase pathways associated with microbial stress resistance. Phosphorothioates depleted 64 pathways and enhanced 208 pathways, far exceeding phosphate impacts (2 depleted, 22 enhanced), indicating the phosphorothioates played a more important role on bacterioplankton communities than phosphate. Additionally, OPPs exposure reduced functional redundancy and destabilized community stability in bacterioplankton, potentially granting CFMs a long-term competitive advantage and elevating algal bloom risks. These findings provide insights into active CFMs in aquatic systems and their responses to diverse OPPs, offering new perspectives for managing organophosphorus pesticide contamination.

Risk-reward trade-off during carbon starvation generates dichotomy in motility endurance among marine bacteria

Copiotrophic marine bacteria contribute to the control of carbon storage in the ocean by remineralizing organic matter. Motility presents copiotrophs with a risk-reward trade-off: it is highly beneficial in seeking out sparse nutrient hotspots, but energetically costly. Here we studied the motility endurance of 26 marine isolates, representing 18 species, using video microscopy and cell tracking over 2 days of carbon starvation. We found that the trade-off results in a dichotomy among marine bacteria, in which risk-averse copiotrophs ceased motility within hours ('limostatic'), whereas risk-prone copiotrophs converted ~9% of their biomass per day into energy to retain motility for the 2 days of observation ('limokinetic'). Using machine learning classifiers, we identified a genomic component associated with both strategies, sufficiently robust to predict the response of additional species with 86% accuracy. This dichotomy can help predict the prevalence of foraging strategies in marine microbes and inform models of ocean carbon cycles.

Chemodiversity and molecular traits of dissolved organic matter driven by cascade reservoirs regulations in the upper Yangtze River

Dissolved organic matter (DOM) plays a fundamental role in biogeochemical cycles within riverine ecosystems. However, the construction and impoundment of dams disrupt the natural biophysical gradients in rivers, potentially leading to alterations and turnover of DOM compositions. This research investigated the composition and chemodiversity of DOM in the cascade reservoirs along the upper Yangtze River. Our findings reveal that DOM in the cascade reservoirs are predominantly composed of lignin-like, lipid-like, and protein-like compounds. The DOM chemodiversity exhibited a significant decrease during the flood season, but recovered during the dry season. Additionally, a general decline in DOM chemodiversity was observed along the longitudinal gradient in the cascade reservoirs. The molecular traits of DOM results indicated high bioavailability and lability of DOM molecules during the flood season. A random forest analysis identified physicochemical indicators as the most important factor influencing DOM chemodiversity. During the flood season, the selected variables were mostly strongly correlated with DOM molecular traits and categories. Specifically, Qin and Qout showed significant negative correlations with easily degradable compounds such as carbohydrates and lipids, as well as with molecular traits. Conversely, during the dry season, few physicochemical indicators and hydrological parameters show significant correlations with proteins and aromatic compounds. Structural equation model further demonstrated that hydrological parameters exert a strong positive influence on DOM molecular categories. This study provides a foundational framework for further evaluation cascade damming effects on DOM biogeochemical processes.

Biogel scavenging slows the sinking of organic particles to the ocean depths

One of Earth's largest carbon fluxes is driven by particles made from photosynthetically fixed matter, which aggregate and sink into the deep ocean. While biodegradation is known to reduce this vertical flux, the biophysical processes that control particle sinking speed are not well understood. Here, we use a vertical millifluidic column to video-track single particles and find that biogels scavenged by particles during sinking significantly reduce the particles' sinking speed, slowing them by up to 45% within one day. Combining observations with a mathematical model, we determine that the mechanism for this slowdown is a combination of increased drag due to the formation of biogel tendrils and increased buoyancy due to the biogel's low density. Because biogels are pervasive in the ocean, we propose that by slowing the sinking of organic particles they attenuate the vertical carbon flux in the ocean.

Clostridium sediminicola sp. nov., a crude oil aggregation-forming anaerobic bacterium isolated from marine sediment

A crude oil aggregation-forming, strictly anaerobic, Gram-stain-positive, spore-forming, rod-shaped, motile and mesophilic bacterium, named strain SH18-2T, was isolated from marine sediment near Sado Island in the Sea of Japan. The temperature, salinity and pH ranges of this strain for the growth were 15-40 °C (optimum 35 °C), 0.5-6.0% NaCl (w/v; optimum 2.0%) and pH 6.0-8.0 (optimum 7.5), respectively. A phylogenetic analysis of the 16S rRNA gene sequence showed that this strain belongs to the genus Clostridium. It was most closely related to Clostridium grantii A-1T (97.02% homology). The draft genome size was 5616089 bp, with a G+C content of 29.7 mol%. The digital DNA-DNA hybridization values determined using the Genome-to-Genome Distance Calculator and the average nucleotide identity between this strain and C. grantii A-1T were 20.30 and 78.24%, respectively. Whole-organism hydrolysates of strain SH18-2T contained meso-diaminopimelic acid; the major fatty acid was C16:0, and the polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol, glycolipid and three unidentified polar lipids. From the results of genotypic, phenotypic and chemotaxonomic analyses, SH18-2T (=NBRC 116030T=DSM 115762T) is the type strain and represents a novel species of the genus Clostridium, and the name Clostridium sediminicola sp. nov. is proposed.

Metabolic Flux Modeling in Marine Ecosystems

Ocean metabolism constitutes a complex, multiscale ensemble of biochemical reaction networks harbored within and between the boundaries of a myriad of organisms. Gaining a quantitative understanding of how these networks operate requires mathematical tools capable of solving in silico the resource allocation problem each cell faces in real life. Toward this goal, stoichiometric modeling of metabolism, such as flux balance analysis, has emerged as a powerful computational tool for unraveling the intricacies of metabolic processes in microbes, microbial communities, and multicellular organisms. Here, we provide an overview of this approach and its applications, future prospects, and practical considerations in the context of marine sciences. We explore how flux balance analysis has been employed to study marine organisms, help elucidate nutrient cycling, and predict metabolic capabilities within diverse marine environments, and highlight future prospects for this field in advancing our knowledge of marine ecosystems and their sustainability.

Macroscale vertical power-law distribution of bacteria in dark oceans can emerge from microscale bacteria-particle interactions

Microbes in the dark oceans are a key determinant of remineralization of sinking carbon particles. However, most marine ecosystem models overlook how microbes aggregate on particles and the microscale interactions between particle-associated microbes, making it difficult to obtain mechanistic insights on their vertical power-law decay pattern. Here, we present a spatial population model where the attachment and detachment processes of bacterial cells depend on local density of particle-associated bacteria. We show that the power-law relationship can emerge when the non-random aggregated distribution of bacteria is considered without any depth-specific environmental parameters. Furthermore, the comparison between model behavior and empirical patterns in the Pacific and Southern Ocean indicated that temperature-dependent hydrolysis rate and nutrient-dependent sinking rate of particles are key parameters to explain the regional variations of the power-law exponent. The mechanistic approach developed here provides a pathway to link micro-scale interactions between individuals to macro-scale food chain structures and carbon cycle.

Bacterial clustering amplifies the reshaping of eutrophic plumes around marine particles: A hybrid data-driven model

Multifaceted interactions between marine bacteria and particulate matter exert a major control over the biogeochemical cycles in the oceans. At the microbial scale, free-living bacteria benefit from encountering and harnessing the plumes around nutrient-releasing particles, like phyto-plankton and organic aggregates. However, our understanding of the bacterial potential to reshape these eutrophic microhabitats remains poor, in part because of the traditional focus on fast-moving particles that generate ephemeral plumes with lifetime shorter than the uptake timescale. Here we develop a novel hybrid model to assess the impacts of nutrient uptake by clustered free-living bacteria on the nutrient field around slow-moving particles. We integrate a physics-based nutrient transport model with data-derived bacterial distributions at the single-particle level. We inferred the functional form of the bacterial distribution and extracted parameters from published datasets of in vitro and in silico microscale experiments. Based on available data, we find that exponential radial distribution functions properly represent bacterial microzones, but also capture the trend and variation for the exposure of bacteria to nutrients around sinking particles. Our computational analysis provides fundamental insight into the conditions under which free-living bacteria may significantly reshape plumes around marine aggregates in terms of the particle size and sinking velocity, the nutrient diffusivity, and the bacterial trophic lifestyle (oligotrophs < mesotrophs < copiotrophs). A high potential is predicted for chemotactic copiotrophs like Vibrio sp. that achieve fast uptake and strong clustering. This microscale phenomenon can be critical for the microbiome and nutrient cycling in marine ecosystems, especially during particulate blooms.

The hidden acceleration pump uncovers the role of shellfish in oceanic carbon sequestration

Whether shellfish mariculture should be included in the blue carbon profile as a strategy to combat climate change has been controversial. It is highly demanding not only to provide calibration quantitation, but also to provide an ecosystem-based mechanism. In this study, we chose mussel farms as a case study to evaluate their contributions to carbon sinks and their responses to sedimentary carbon fixation and sequestration. First, we quantified the air-sea CO2 flux in the mussel aquacultural zone and observed a weak carbon sink (-0.15 ± 0.07 mmol·m-2·d-1) during spring. Next, by analyzing the carbon composition in the sediment, we recorded a noticeable and unexpected increase in the sedimentary recalcitrant carbon (RC) content in the mussel farming case. To address this surprising sedimentary phenomenon, a long-term indoor experimental test was conducted to distinguish the consequences of mussel engagement with sedimentary RC. Our observational data support the idea that mussel engagement promotes accumulation of RC in sediments by 2.5-fold. Furthermore, the relative intensity of carboxylic-rich alicyclic molecule (CRAM)-like compounds (recalcitrant dissolved organic matter (RDOM)) increased by 451.4 % in the mussel-engaged sedimentary dissolved organic matter (DOM) in comparison to the initial state. Mussel engagement had a significantly positive effect on the abundance of sedimentary carbon-fixing genes. Therefore, we definitively conclude that mussel farming is blue carbon positive and propose a new alternative theory that mussel farming areas may have high carbon sequestration potential via an ecologically integrated "3 M" (microalgae-mussel-microbiota) consortium. The "mussel pump" accelerates carbon sequestration and enhances climate-related ecosystem services.

Metabolic Plasticity Shapes Microbial Communities across a Temperature Gradient

AbstractA central challenge in community ecology is understanding and predicting the effects of abiotic factors on community assembly. In particular, microbial communities play a central role in the ecosystem, but we do not understand how changing factors like temperature are going to affect community composition or function. In this article, we studied the self-assembly of multiple communities in synthetic environments to understand changes in microbial community composition based on metabolic responses of different functional groups along a temperature gradient. In many microbial communities, different microbial functional groups coexist through the partitioning of carbon sources in an emergent trophic structure (cross-feeding). In this system, respirofermentative bacteria display a preference for the sugars supplied as the only carbon source but secrete secondary carbon sources (organic acids) that are more efficiently consumed by obligate respirators. As a consequence of this trophic structure, the metabolic plasticity of the respirofermenters has downstream consequences for the relative abundance of respirators across temperatures. We found that the effects of different temperatures on microbial composition can largely be described by an increase in fermentation by-products with increasing temperatures from the respirofermentative bacteria. This research highlights the importance of metabolic plasticity and metabolic trade-offs in predicting species interactions and community dynamics across abiotic gradients.

Microbial dietary preference and interactions affect the export of lipids to the deep ocean

Lipids comprise a significant fraction of sinking organic matter in the ocean and play a crucial role in the carbon cycle. Despite this, our understanding of the processes that control lipid degradation is limited. We combined nanolipidomics and imaging to study the bacterial degradation of diverse algal lipid droplets and found that bacteria isolated from marine particles exhibited distinct dietary preferences, ranging from selective to promiscuous degraders. Dietary preference was associated with a distinct set of lipid degradation genes rather than with taxonomic origin. Using synthetic communities composed of isolates with distinct dietary preferences, we showed that lipid degradation is modulated by microbial interactions. A particle export model incorporating these dynamics indicates that metabolic specialization and community dynamics may influence lipid transport efficiency in the ocean's mesopelagic zone.

Decoding drivers of carbon flux attenuation in the oceanic biological pump

The biological pump supplies carbon to the oceans' interior, driving long-term carbon sequestration and providing energy for deep-sea ecosystems1,2. Its efficiency is set by transformations of newly formed particles in the euphotic zone, followed by vertical flux attenuation via mesopelagic processes3. Depth attenuation of the particulate organic carbon (POC) flux is modulated by multiple processes involving zooplankton and/or microbes4,5. Nevertheless, it continues to be mainly parameterized using an empirically derived relationship, the 'Martin curve'6. The derived power-law exponent is the standard metric used to compare flux attenuation patterns across oceanic provinces7,8. Here we present in situ experimental findings from C-RESPIRE9, a dual particle interceptor and incubator deployed at multiple mesopelagic depths, measuring microbially mediated POC flux attenuation. We find that across six contrasting oceanic regimes, representing a 30-fold range in POC flux, degradation by particle-attached microbes comprised 7-29 per cent of flux attenuation, implying a more influential role for zooplankton in flux attenuation. Microbial remineralization, normalized to POC flux, ranged by 20-fold across sites and depths, with the lowest rates at high POC fluxes. Vertical trends, of up to threefold changes, were linked to strong temperature gradients at low-latitude sites. In contrast, temperature played a lesser role at mid- and high-latitude sites, where vertical trends may be set jointly by particle biochemistry, fragmentation and microbial ecophysiology. This deconstruction of the Martin curve reveals the underpinning mechanisms that drive microbially mediated POC flux attenuation across oceanic provinces.

Fragmented micro-growth habitats present opportunities for alternative competitive outcomes

Bacteria in nature often thrive in fragmented environments, like soil pores, plant roots or plant leaves, leading to smaller isolated habitats, shared with fewer species. This spatial fragmentation can significantly influence bacterial interactions, affecting overall community diversity. To investigate this, we contrast paired bacterial growth in tiny picoliter droplets (1-3 cells per 35 pL up to 3-8 cells per species in 268 pL) with larger, uniform liquid cultures (about 2 million cells per 140 µl). We test four interaction scenarios using different bacterial strains: substrate competition, substrate independence, growth inhibition, and cell killing. In fragmented environments, interaction outcomes are more variable and sometimes even reverse compared to larger uniform cultures. Both experiments and simulations show that these differences stem mostly from variation in initial cell population growth phenotypes and their sizes. These effects are most significant with the smallest starting cell populations and lessen as population size increases. Simulations suggest that slower-growing species might survive competition by increasing growth variability. Our findings reveal how microhabitat fragmentation promotes diverse bacterial interaction outcomes, contributing to greater species diversity under competitive conditions.

Investigation of the marine bacterial community along the coastline of the Gulf of Thailand

The Gulf of Thailand provides many services to the Thai population, and human activities may influence the diversity of microorganisms in the seawater. Information of the microorganisms' profile which inhabit the coastline can be used to monitor the water quality. This study aimed to investigate the bacterial community in the waters along the coastline provinces, including Rayong, Chonburi, Prachuap Kiri Khan, and Nakhon Sri Thammarat. Seawater samples were collected at each site, and the conductivity, pH, salinity, temperature, and turbidity were measured. The samples were subjected to whole DNA extraction, 16S rRNA amplification, next-generation sequencing, and statistical analysis to identify the bacterial diversity and analyse the effects of water parameters on the bacterial community. The dominant bacterial phyla found were Proteobacteria, Bacteroidota, and Cyanobacteria. Spearman rank correlation analysis revealed a high correlation of Pseudoalteromonas, the NS5 marine group, Lachnospiraceae, Marinobacterium, Mariviven, and Vibrio with the seawater parameters. The predatory bacteria Peredibacter and Halobacteriovorax were reported among these bacterial communities for the first time in the Gulf of Thailand. Interestingly, Akkermansia, a novel candidate for next-generation probiotics to improve human health, was also found in the sample from Nakhon Sri Thammarat Province. Although the rich-ness and diversity of the bacterial communities differed among sampling sites, it is a possible source of many valuable bacteria for future use.

Microfluidic approaches in microbial ecology

Microbial life is at the heart of many diverse environments and regulates most natural processes, from the functioning of animal organs to the cycling of global carbon. Yet, the study of microbial ecology is often limited by challenges in visualizing microbial processes and replicating the environmental conditions under which they unfold. Microfluidics operates at the characteristic scale at which microorganisms live and perform their functions, thus allowing for the observation and quantification of behaviors such as growth, motility, and responses to external cues, often with greater detail than classical techniques. By enabling a high degree of control in space and time of environmental conditions such as nutrient gradients, pH levels, and fluid flow patterns, microfluidics further provides the opportunity to study microbial processes in conditions that mimic the natural settings harboring microbial life. In this review, we describe how recent applications of microfluidic systems to microbial ecology have enriched our understanding of microbial life and microbial communities. We highlight discoveries enabled by microfluidic approaches ranging from single-cell behaviors to the functioning of multi-cellular communities, and we indicate potential future opportunities to use microfluidics to further advance our understanding of microbial processes and their implications.

Slow closure of Earth's carbon cycle

Carbon near the Earth's surface cycles between the production and consumption of organic carbon; the former sequesters carbon dioxide while the latter releases it. Microbes attempt to close the loop, but the longer organic matter survives, the slower microbial degradation becomes. This aging effect leaves observable quantitative signatures: Organic matter decays at rates that are inversely proportional to its age, while microbial populations and concentrations of organic carbon in ocean sediments decrease at distinct powers of age. Yet mechanisms that predict this collective organization remain unknown. Here, I show that these and other observations follow from the assumption that the decay of organic matter is limited by progressively rare extreme fluctuations in the energy available to microbes for decomposition. The theory successfully predicts not only observed scaling exponents but also a previously unobserved scaling regime that emerges when microbes subsist on the minimum energy flux required for survival. The resulting picture suggests that the carbon cycle's age-dependent dynamics are analogous to the slow approach to equilibrium in disordered systems. The impact of these slow dynamics is profound: They preclude complete oxidation of organic carbon in sediments, thereby freeing molecular oxygen to accumulate in the atmosphere.

Efficient biological carbon export to the mesopelagic ocean induced by submesoscale fronts

Oceanic submesoscale processes are ubiquitous in the North Pacific Subtropical Gyre (NPSG), where the biological carbon pump is generally ineffective. Due to difficulties in collecting continuous observations, however, it remains uncertain whether episodic submesoscale processes can drive significant changes in particulate organic carbon (POC) export into the mesopelagic ocean. Here we present observations from high-frequency Biogeochemical-Argo floats in the NPSG, which captured the enhanced POC export fluxes during the intensifying stages of a submesoscale front and a cyclonic eddy compared to their other life stages. A higher percentage of POC export flux was found to be transferred to the base of mesopelagic layer at the front compared to that at the intensifying eddy and the mean of previous studies (37% vs. ~10%), suggesting that the POC export efficiency was significantly strengthened by submesoscale dynamics. Such findings highlight the importance of submesoscale fronts for carbon export and sequestration in subtropical gyres.

Iron limitation of heterotrophic bacteria in the California Current System tracks relative availability of organic carbon and iron

Iron is an essential nutrient for all microorganisms of the marine environment. Iron limitation of primary production has been well documented across a significant portion of the global surface ocean, but much less is known regarding the potential for iron limitation of the marine heterotrophic microbial community. In this work, we characterize the transcriptomic response of the heterotrophic bacterial community to iron additions in the California Current System, an eastern boundary upwelling system, to detect in situ iron stress of heterotrophic bacteria. Changes in gene expression in response to iron availability by heterotrophic bacteria were detected under conditions of high productivity when carbon limitation was relieved but when iron availability remained low. The ratio of particulate organic carbon to dissolved iron emerged as a biogeochemical proxy for iron limitation of heterotrophic bacteria in this system. Iron stress was characterized by high expression levels of iron transport pathways and decreased expression of iron-containing enzymes involved in carbon metabolism, where a majority of the heterotrophic bacterial iron requirement resides. Expression of iron stress biomarkers, as identified in the iron-addition experiments, was also detected insitu. These results suggest iron availability will impact the processing of organic matter by heterotrophic bacteria with potential consequences for the marine biological carbon pump.

Direct observations of microbial community succession on sinking marine particles

Microbial community dynamics on sinking particles control the amount of carbon that reaches the deep ocean and the length of time that carbon is stored, with potentially profound impacts on Earth's climate. A mechanistic understanding of the controls on sinking particle distributions has been hindered by limited depth- and time-resolved sampling and methods that cannot distinguish individual particles. Here, we analyze microbial communities on nearly 400 individual sinking particles in conjunction with more conventional composite particle samples to determine how particle colonization and community assembly might control carbon sequestration in the deep ocean. We observed community succession with corresponding changes in microbial metabolic potential on the larger sinking particles transporting a significant fraction of carbon to the deep sea. Microbial community richness decreased as particles aged and sank; however, richness increased with particle size and the attenuation of carbon export. This suggests that the theory of island biogeography applies to sinking marine particles. Changes in POC flux attenuation with time and microbial community composition with depth were reproduced in a mechanistic ecosystem model that reflected a range of POC labilities and microbial growth rates. Our results highlight microbial community dynamics and processes on individual sinking particles, the isolation of which is necessary to improve mechanistic models of ocean carbon uptake.

The active free-living bathypelagic microbiome is largely dominated by rare surface taxa

A persistent microbial seed bank is postulated to sustain the marine biosphere, and recent findings show that prokaryotic taxa present in the ocean's surface dominate prokaryotic communities throughout the water column. Yet, environmental conditions exert a tight control on the activity of prokaryotes, and drastic changes in these conditions are known to occur from the surface to deep waters. The simultaneous characterization of the total (DNA) and active (i.e. with potential for protein synthesis, RNA) free-living communities in 13 stations distributed across the tropical and subtropical global ocean allowed us to assess their change in structure and diversity along the water column. We observed that active communities were surprisingly more similar along the vertical gradient than total communities. Looking at the vertical connectivity of the active vs. the total communities, we found that taxa detected in the surface sometimes accounted for more than 75% of the active microbiome of bathypelagic waters (50% on average). These active taxa were generally rare in the surface, representing a small fraction of all the surface taxa. Our findings show that the drastic vertical change in environmental conditions leads to the inactivation and disappearance of a large proportion of surface taxa, but some surface-rare taxa remain active (or with potential for protein synthesis) and dominate the bathypelagic active microbiome.

Growth rates of marine prokaryotes are extremely diverse, even among closely related taxa

Marine prokaryotes play crucial roles in ocean biogeochemical cycles, being their contribution strongly influenced by their growth rates. Hence, elucidating the variability and phylogenetic imprint of marine prokaryotes' growth rates are crucial for better determining the role of individual taxa in biogeochemical cycles. Here, we estimated prokaryotic growth rates at high phylogenetic resolution in manipulation experiments using water from the northwestern Mediterranean Sea. Experiments were run in the four seasons with different treatments that reduced growth limiting factors: predators, nutrient availability, viruses, and light. Single-amplicon sequence variants (ASVs)-based growth rates were calculated from changes in estimated absolute abundances using total prokaryotic abundance and the proportion of each individual ASV. The trends obtained for growth rates in the different experiments were consistent with other estimates based on total cell-counts, catalyzed reporter deposition fluorescence in situ hybridization subcommunity cell-counts or metagenomic-operational taxonomic units (OTUs). Our calculations unveil a broad range of growth rates (0.3-10 d-1) with significant variability even within closely related ASVs. Likewise, the impact of growth limiting factors changed over the year for individual ASVs. High numbers of responsive ASVs were shared between winter and spring seasons, as well as throughout the year in the treatments with reduced nutrient limitation and viral pressure. The most responsive ASVs were rare in the in situ communities, comprising a large pool of taxa with the potential to rapidly respond to environmental changes. Essentially, our results highlight the lack of phylogenetic coherence in the range of growth rates observed, and differential responses to the various limiting factors, even for closely related taxa.

Hydrodynamic Treadmill Reveals Reduced Rising Speeds of Oil Droplets Deformed by Marine Bacteria

In marine environments, microscopic droplets of oil can be transported over large distances in the water column. Bacterial growth on the droplets' surface can deform the oil-water interface to generate complex shapes and significantly enlarge droplets. Understanding the fate of spilled oil droplets requires bridging these length scales and determining how microscale processes affect the large-scale transport of oil. Here, we describe an experimental setup, the hydrodynamic treadmill, developed to keep rising oil droplets stationary in the lab frame for continuous and direct observation. Oil droplets with radii 10 < R < 100 μm were colonized and deformed by bacteria over several days before their effective rising speeds were measured. The rising speeds of deformed droplets were significantly slower than those of droplets without bacteria. This decrease in rising speed is understood by an increase in drag force and a decrease in buoyancy as a result of bio-aggregate formation at the droplet surface. Additionally, we found sinking bio-aggregate particles of oil and bacterial biofilms and quantified their composition using fluorescence microscopy. Our experiments can be adapted to further study the interactions between oil droplets and marine organisms and could significantly improve our understanding of the transport of hydrocarbons and complex aggregates.

Inherited chitinases enable sustained growth and rapid dispersal of bacteria from chitin particles

Many biogeochemical functions involve bacteria utilizing solid substrates. However, little is known about the coordination of bacterial growth with the kinetics of attachment to and detachment from such substrates. In this quantitative study of Vibrio sp. 1A01 growing on chitin particles, we reveal the heterogeneous nature of the exponentially growing culture comprising two co-existing subpopulations: a minority replicating on chitin particles and a non-replicating majority which was planktonic. This partition resulted from a high rate of cell detachment from particles. Despite high detachment, sustained exponential growth of cells on particles was enabled by the enrichment of extracellular chitinases excreted and left behind by detached cells. The 'inheritance' of these chitinases sustains the colonizing subpopulation despite its reduced density. This simple mechanism helps to circumvent a trade-off between growth and dispersal, allowing particle-associated marine heterotrophs to explore new habitats without compromising their fitness on the habitat they have already colonized.

Unsupervised machine learning model to predict cognitive impairment in subcortical ischemic vascular disease

INTRODUCTION

It is challenging to predict which patients who meet criteria for subcortical ischemic vascular disease (SIVD) will ultimately progress to subcortical vascular cognitive impairment (SVCI).

METHODS

We collected clinical information, neuropsychological assessments, T1 imaging, diffusion tensor imaging, and resting-state functional magnetic resonance imaging from 83 patients with SVCI and 53 age-matched patients with SIVD without cognitive impairment. We built an unsupervised machine learning model to isolate patients with SVCI. The model was validated using multimodal data from an external cohort comprising 45 patients with SVCI and 32 patients with SIVD without cognitive impairment.

RESULTS

The accuracy, sensitivity, and specificity of the unsupervised machine learning model were 86.03%, 79.52%, and 96.23% and 80.52%, 71.11%, and 93.75% for internal and external cohort, respectively.

DISCUSSION

We developed an accurate and accessible clinical tool which requires only data from routine imaging to predict patients at risk of progressing from SIVD to SVCI.

HIGHLIGHTS

Our unsupervised machine learning model provides an accurate and accessible clinical tool to predict patients at risk of progressing from subcortical ischemic vascular disease (SIVD) to subcortical vascular cognitive impairment (SVCI) and requires only data from imaging routinely used during the diagnosis of suspected SVCI. The model yields good accuracy, sensitivity, and specificity and is portable to other cohorts and to clinical practice to distinguish patients with SIVD at risk for progressing to SVCI. The model combines assessment of diffusion tensor imaging and functional magnetic resonance imaging measures in patients with SVCI to analyze whether the "disconnection hypothesis" contributes to functional and structural changes and to the clinical presentation of SVCI.

The Role of Bacteria in the Formation and Migration of Oil-Particle Aggregates (OPAs) after Marine Oil Spills and the Associated Mechanism

Oil spills interact with mineral particles to form oil-particle aggregates (OPAs), which promotes the oil's natural diffusion and biodegradation. We investigated the effect of bacteria on the formation and vertical migration of OPAs under different concentrations and types of particles and proposed and elucidated an oil-particle-bacteria coupling mechanism. The depth of particle penetration into oil droplets (13-17 μm) was more than twice that of the nonbacterial group. Oil that remained in the water column and deposited to the bottom decreased from 87% to 49% and increased from 14% to 15% at high/low concentration, respectively. Interestingly, the median droplet diameter showed a negative correlation (R² = 0.83) and positive correlation (R² = 0.60) at high/low concentration, respectively, with the relative penetration depth first proposed. We further demonstrated that bacteria increased the penetrating depth by a combination of reducing/increasing the interfacial tension, reducing the oil amount (C₁₇-C₃₈) in the OPAs, and increasing the particle width. These effects reduced the droplet size and ultimately changed the vertical migration of OPAs. Finally, we provided a simple assessment of the vertical distribution of OPAs in nearshore environments based on experimental data and suggested that the role of bacteria in increasing the depth of particles penetrating into the oil droplets should not be ignored. These findings will broaden the research perspective of marine oil spill migration.

Respiration rate scales inversely with sinking speed of settling marine aggregates

Sinking marine aggregates have been studied for a long time to understand their role in carbon sequestration. Traditionally, sinking speed and respiration rates have been treated as independent variables, but two recent papers suggest that there is a connection albeit in contrasting directions. Here we collected recently formed (<2 days old) aggregates from sediment traps mounted underneath mesocosms during two different experiments. The mesocosms were moored off Gran Canaria, Spain (~ 27.9 N; 15.4 E) in a coastal, sub-tropical and oligotrophic ecosystem. We determined the respiration rates of organisms (mainly heterotrophic prokaryotes) attached to aggregates sinking at different velocities. The average respiration rate of fast sinking aggregates (>100 m d-1) was 0.12 d-1 ± 0.08 d-1 (SD). Slower sinking aggregates (<50 m d-1) had on average higher (p <0.001) and more variable respiration rates (average 0.31 d-1 ± 0.16 d-1, SD). There was evidence that slower sinking aggregates had higher porosity than fast sinking aggregates, and we hypothesize that higher porosity increase the settlement area for bacteria and the respiration rate. These findings provide insights into the efficiency of the biological carbon pump and help resolve the apparent discrepancy in the recent studies of the correlation between respiration and sinking speed.

Fungal parasitism on diatoms alters formation and bio-physical properties of sinking aggregates

Phytoplankton forms the base of aquatic food webs and element cycling in diverse aquatic systems. The fate of phytoplankton-derived organic matter, however, often remains unresolved as it is controlled by complex, interlinked remineralization and sedimentation processes. We here investigate a rarely considered control mechanism on sinking organic matter fluxes: fungal parasites infecting phytoplankton. We demonstrate that bacterial colonization is promoted 3.5-fold on fungal-infected phytoplankton cells in comparison to non-infected cells in a cultured model pathosystem (diatom Synedra, fungal microparasite Zygophlyctis, and co-growing bacteria), and even ≥17-fold in field-sampled populations (Planktothrix, Synedra, and Fragilaria). Additional data obtained using the Synedra-Zygophlyctis model system reveals that fungal infections reduce the formation of aggregates. Moreover, carbon respiration is 2-fold higher and settling velocities are 11-48% lower for similar-sized fungal-infected vs. non-infected aggregates. Our data imply that parasites can effectively control the fate of phytoplankton-derived organic matter on a single-cell to single-aggregate scale, potentially enhancing remineralization and reducing sedimentation in freshwater and coastal systems.

Impact of particle flux on the vertical distribution and diversity of size-fractionated prokaryotic communities in two East Antarctic polynyas

Antarctic polynyas are highly productive open water areas surrounded by ice where extensive phytoplankton blooms occur, but little is known about how these surface blooms influence carbon fluxes and prokaryotic communities from deeper waters. By sequencing the 16S rRNA gene, we explored the vertical connectivity of the prokaryotic assemblages associated with particles of three different sizes in two polynyas with different surface productivity, and we linked it to the magnitude of the particle export fluxes measured using thorium-234 (²³⁴Th) as particle tracer. Between the sunlit and the mesopelagic layers (700 m depth), we observed compositional changes in the prokaryotic communities associated with the three size-fractions, which were mostly dominated by Flavobacteriia, Alphaproteobacteria, and Gammaproteobacteria. Interestingly, the vertical differences between bacterial communities attached to the largest particles decreased with increasing ²³⁴Th export fluxes, indicating a more intense downward transport of surface prokaryotes in the most productive polynya. This was accompanied by a higher proportion of surface prokaryotic taxa detected in deep particle-attached microbial communities in the station with the highest ²³⁴Th export flux. Our results support recent studies evidencing links between surface productivity and deep prokaryotic communities and provide the first evidence of sinking particles acting as vectors of microbial diversity to depth in Antarctic polynyas, highlighting the direct influence of particle export in shaping the prokaryotic communities of mesopelagic waters.

Porous marine snow differentially benefits chemotactic, motile, and nonmotile bacteria

Particulate organic carbon settling through the marine water column is a key process that regulates the global climate by sequestering atmospheric carbon. The initial colonization of marine particles by heterotrophic bacteria represents the first step in recycling this carbon back to inorganic constituents-setting the magnitude of vertical carbon transport to the abyss. Here, we demonstrate experimentally using millifluidic devices that, although bacterial motility is essential for effective colonization of a particle leaking organic nutrients into the water column, chemotaxis specifically benefits at intermediate and higher settling velocities to navigate the particle boundary layer during the brief window of opportunity provided by a passing particle. We develop an individual-based model that simulates the encounter and attachment of bacterial cells with leaking marine particles to systematically evaluate the role of different parameters associated with bacterial run-and-tumble motility. We further use this model to explore the role of particle microstructure on the colonization efficiency of bacteria with different motility traits. We find that the porous microstructure facilitates additional colonization by chemotactic and motile bacteria, and fundamentally alters the way nonmotile cells interact with particles due to streamlines intersecting with the particle surface.