Leucine incorporation and its potential as a measure of protein synthesis by bacteria in natural aquatic systems

Effects of bioplastics and their leachates on marine bacterial communities

Biobased biodegradable plastics (bioplastics) are promising alternatives fuel-based plastics. However, higher additive content is generally used to perform similarly to fuel-based materials. Moreover, plastic additives are not covalently bound to carbon chains and can leach into aquatic environments such as seawater, potentially impacting marine biota, though the extent of these effects is not yet fully understood. To evaluate the leaching behaviour in seawater of plastic additives from bioplastics materials and its impact on coastal surface marine bacterial communities, microcosm experiments were conducted using seawater amended with non-aged pellets of polylactic acid (PLA), poly-hydroxybutyrate (PHB), and commercial materials, a knife of PLA and a bag of PLA&PHB, under biotic and abiotic conditions for two months. Samples were taken weekly to study the bacterial abundance, bi-weekly to evaluate the leaching process and potential biodegradation products and, finally, at the end of the experiment to study the microbial communities. Chemical analysis was performed using suspect screening by means of Liquid Chromatography coupled to High-Resolution Mass Spectrometry (LCHRMS) equipped with Electrospray Ionization source working in positive and negative conditions. The experiment showed that 177 compounds were tentatively identified at confidence level 2, including plasticizers, UV filters, flame retardants, and PLA- and PHB-related degradation products, which were detected in similar proportions under abiotic and biotic processes. Bacterial communities exposed to PLA showed higher production and significant differences in the community composition, with PLA degraders being identified in the different plastispheres studied. Leachates impacted differently microbial communities in the free-living fraction, particle-attached fraction and in the plastisphere, indicating taxa-specific responses. To the best of our knowledge, this is the first study providing further insights into the influence of bioplastics and their leachates on marine microbial communities, contributing to our understanding of bioplastics' effects on the global oceans.

Flow of heterotrophic production in oligotrophic ocean waters

In oligotrophic ecosystems, bacterial production (BP) via the microbial loop and grazing processes plays a crucial role in carbon transfer (CT) to higher trophic levels. However, there studies quantifying CT from bacteria to the marine food web are limited. In this study, we used 13C-isotope tracers and cavity ring-down spectroscopy to measure primary production (PP), BP, bacterial respiration (BR), and CT within the microbial food web in oligotrophic waters. Our results revealed that the BP rate, ranging from 0.02 to 4.93 μg C L-1 d-1, was significantly lower than the total PP, which ranged from 2.69 to 16.71 μg C L-1 d-1. Our findings indicate that grazing of bacteria in the Red Sea is substantial. The removal of grazers through prefiltration lead to a 9.5-fold increase in BP rates, rising from 0.37 ± 0.04 μg C L-1 d-1 to 3.52 ± 1.04 μg C L-1 d-1 at the stations analyzed. This significant increase suggests that a large portion of bacterial carbon is rapidly transfer to higher trophic levels via grazing. In addition, carbon transfer (CT) to the food web, measured in size fractions above picoplankton (>1.2 or > 3 μm), accounted for an average of 72.7 ± 4.0% of the net bacterial production (Net BP = BP + CT), underscore the crucial role of grazers in bacterial carbon cycling. This transfer increased significantly with increasing temperatures, highlighting the enhanced role of the microbial loop in CT during warmer conditions. We found that at some stations, a large proportion of the carbon assimilated by bacteria was used for respiration, averaging 1.37 ± 0.54 μg C L-1 d-1. This high respiratory demand of bacterial cells in oligotrophic waters may explain the low bacterial growth efficiency (BGE) of 9.7% ± 1.0% observed in our study, along with the significant correlation between BP and BGE. Our findings demonstrated that BP effectively transfers carbon through the microbial loop to higher trophic levels in the oligotrophic and warm waters of the Red Sea.

Oxidation state of bioavailable dissolved organic matter influences bacterioplankton respiration and growth efficiency

Oxygen consumption by oceanic microbes can predict respiration (CO2 production) but requires an assumed respiratory quotient (RQ; ΔO2/ΔCO2). Measured apparent RQs (ARQs) can be impacted by various processes, including nitrification and changes in dissolved organic matter (DOM) composition, leading to discrepancies between ARQ and actual RQ. In DOM remineralization experiments conducted in the eastern North Atlantic Ocean, ARQs averaged 1.39 ± 0.14, similar to predictions for complete consumption of plankton biomass. DOM removed with an elevated nominal oxidation state (i.e., more oxidized DOM), as detected by liquid chromatography-tandem mass spectrometry, coincided with increased hydrolyzable amino acid removal, increased ARQs and bacterioplankton respiration (BR), and a decreased bacterioplankton growth efficiency (BGE). Across experiments, evidence emerged that nitrification and DOM partial oxidation, driven in part by bacterioplankton members of OM43, SAR92 and Rhodobacteraceae, can elevate BR relative to bacterioplankton consumption of plankton-derived carbon. These rare synoptic measurements of interrelated variables reveal complex biochemical and cellular processes underlying variability in large-scale CO2 production estimates.

Patterns of prokaryotic activity along the marine planktonic matter continuum

Prokaryotic abundance and activity are commonly assessed by dividing them into two size-fractions: free-living and attached to particles. Nevertheless, organic matter, essential for the growth of heterotrophic prokaryotes, is present in the environment in a continuum of sizes, from purely dissolved to large particles. Therefore, defining the activity of the prokaryotic community would be more accurate by considering all the distinct size fractions. To achieve this, we measured prokaryotic abundance (PA), heterotrophic prokaryotic activity (as leucine incorporation) and extracellular enzyme activities at a coastal site in the NW Mediterranean Sea. We conducted measurements in both bulk seawater and size fractionated samples sequentially passing through 5 different filter types: 0.2-0.8-3-5-10 μm pore size. Our results indicate that the fraction <0.8 μm contained the highest percentage of cells (91.6 ± 1.1 %) and leucine incorporation rates (72.2 ± 3.5 %). Most of the extracellular enzyme activity appeared in the dissolved fraction (<0.2 μm; 19.8-79.4 %), yet the specific activity of the enzymes (per cell activity) was 100-1000 times higher in the particulate (>0.8 μm) than in the free-living (0.2-0.8 μm) fraction. The size fraction with highest specific activities for leucine incorporation and most of the enzyme activities (β-glucosidase, esterase, Leu-aminopeptidase and alkaline phosphatase) was the 5-10 μm fraction. In contrast, the higher specific chitobiase activity in the >10 μm fraction, suggests that the prokaryotic community colonizing large particles might be more specialized in the hydrolysis of organic matter of zooplanktonic origin than the community colonizing smaller particles.

Diversity in the utilization of different molecular classes of dissolved organic matter by heterotrophic marine bacteria

Heterotrophic marine bacteria utilize and recycle dissolved organic matter (DOM), impacting biogeochemical cycles. It is currently unclear to what extent distinct DOM components can be used by different heterotrophic clades. Here, we ask how a natural microbial community from the Eastern Mediterranean Sea (EMS) responds to different molecular classes of DOM (peptides, amino acids, amino sugars, disaccharides, monosaccharides, and organic acids) comprising much of the biomass of living organisms. Bulk bacterial activity increased after 24 h for all treatments relative to the control, while glucose and ATP uptake decreased or remained unchanged. Moreover, while the per-cell uptake rate of glucose and ATP decreased, that of Leucin significantly increased for amino acids, reflecting their importance as common metabolic currencies in the marine environment. Pseudoalteromonadaceae dominated the peptides treatment, while different Vibrionaceae strains became dominant in response to amino acids and amino sugars. Marinomonadaceae grew well on organic acids, and Alteromonadaseae on disaccharides. A comparison with a recent laboratory-based study reveals similar peptide preferences for Pseudoalteromonadaceae, while Alteromonadaceae, for example, grew well in the lab on many substrates but dominated in seawater samples only when disaccharides were added. We further demonstrate a potential correlation between the genetic capacity for degrading amino sugars and the dominance of specific clades in these treatments. These results highlight the diversity in DOM utilization among heterotrophic bacteria and complexities in the response of natural communities.

IMPORTANCE

A major goal of microbial ecology is to predict the dynamics of natural communities based on the identity of the organisms, their physiological traits, and their genomes. Our results show that several clades of heterotrophic bacteria each grow in response to one or more specific classes of organic matter. For some clades, but not others, growth in a complex community is similar to that of isolated strains in laboratory monoculture. Additionally, by measuring how the entire community responds to various classes of organic matter, we show that these results are ecologically relevant, and propose that some of these resources are utilized through common uptake pathways. Tracing the path between different resources to the specific microbes that utilize them, and identifying commonalities and differences between different natural communities and between them and lab cultures, is an important step toward understanding microbial community dynamics and predicting how communities will respond to perturbations.

Microbial remineralization processes during postspring-bloom with excess phosphate available in the northern Baltic Sea

The phosphorus (P) concentration is increasing in parts of the Baltic Sea following the spring bloom. The fate of this excess P-pool is an open question, and here we investigate the role of microbial degradation processes in the excess P assimilation phase. During a 17-day-long mesocosm experiment in the southwest Finnish archipelago, we examined nitrogen, phosphorus, and carbon acquiring extracellular enzyme activities in three size fractions (<0.2, 0.2-3, and >3 µm), bacterial abundance, production, community composition, and its predicted metabolic functions. The mesocosms received carbon (C) and nitrogen (N) amendments individually and in combination (NC) to distinguish between heterotrophic and autotrophic processes. Alkaline phosphatase activity occurred mainly in the dissolved form and likely contributed to the excess phosphate conditions together with grazing. At the beginning of the experiment, peptidolytic and glycolytic enzymes were mostly produced by free-living bacteria. However, by the end of the experiment, the NC-treatment induced a shift in peptidolytic and glycolytic activities and degradation of phosphomonoesters toward the particle-associated fraction, likely as a consequence of higher substrate availability. This would potentially promote retention of nutrients in the surface as opposed to sedimentation, but direct sedimentation measurements are needed to verify this hypothesis.

Active microbial communities facilitate carbon turnover in brine pools found in the deep Southeastern Mediterranean Sea

Discharge of gas-rich brines fuels productive chemosynthetic ecosystems in the deep sea. In these salty, methanic and sulfidic brines, microbial communities adapt to specific niches along the physicochemical gradients. However, the molecular mechanisms that underpin these adaptations are not fully known. Using metagenomics, we investigated the dense (∼106 cell ml-1) microbial communities that occupy small deep-sea brine pools found in the Southeastern Mediterranean Sea (1150 m water depth, ∼22 °C, ∼60 PSU salinity, sulfide, methane, ammonia reaching millimolar levels, and oxygen usually depleted), reaching high productivity rates of 685 μg C L-1 d-1 ex-situ. We curated 266 metagenome-assembled genomes of bacteria and archaea from the several pools and adjacent sediment-water interface, highlighting the dominance of a single Sulfurimonas, which likely fuels its autotrophy using sulfide oxidation or inorganic sulfur disproportionation. This lineage may be dominant in its niche due to genome streamlining, limiting its metabolic repertoire, particularly by using a single variant of sulfide: quinone oxidoreductase. These primary producers co-exist with ANME-2c archaea that catalyze the anaerobic oxidation of methane. Other lineages can degrade the necromass aerobically (Halomonas and Alcanivorax), or anaerobically through fermentation of macromolecules (e.g., Caldatribacteriota, Bipolaricaulia, Chloroflexota, etc). These low-abundance organisms likely support the autotrophs, providing energy-rich H2, and vital organics such as vitamin B12.

Reviving Natural Rubber Synthesis via Native/Large Nanodiscs

Natural rubber (NR) is utilized in more than 40,000 products, and the demand for NR is projected to reach $68.5 billion by 2026. The primary commercial source of NR is the latex of Hevea brasiliensis. NR is produced by the sequential cis-condensation of isopentenyl diphosphate (IPP) through a complex known as the rubber transferase (RTase) complex. This complex is associated with rubber particles, specialized organelles for NR synthesis. Despite numerous attempts to isolate, characterize, and study the RTase complex, definitive results have not yet been achieved. This review proposes an innovative approach to overcome this longstanding challenge. The suggested method involves isolating the RTase complex without using detergents, instead utilizing the native membrane lipids, referred to as "natural nanodiscs", and subsequently reconstituting the complex on liposomes. Additionally, we recommend the adaptation of large nanodiscs for the incorporation and reconstitution of the RTase complex, whether it is in vitro transcribed or present within the natural nanodiscs. These techniques show promise as a viable solution to the current obstacles. Based on our experimental experience and insights from published literature, we believe these refined methodologies can significantly enhance our understanding of the RTase complex and its role in in vitro NR synthesis.

Temperature Adaptation of Aquatic Bacterial Community Growth Is Faster in Response to Rising than to Falling Temperature

Bacteria are key organisms in energy and nutrient cycles, and predicting the effects of temperature change on bacterial activity is important in assessing global change effects. A changing in situ temperature will affect the temperature adaptation of bacterial growth in lake water, both long term in response to global change, and short term in response to seasonal variations. The rate of adaptation may, however, depend on whether temperature is increasing or decreasing, since bacterial growth and turnover scale with temperature. Temperature adaptation was studied for winter (in situ temperature 2.5 °C) and summer communities (16.5 °C) from a temperate lake in Southern Sweden by exposing them to a temperature treatment gradient between 0 and 30 °C in ~ 5 °C increments. This resulted mainly in a temperature increase for the winter and a decrease for the summer community. Temperature adaptation of bacterial community growth was estimated as leucine incorporation using a temperature Sensitivity Index (SI, log growth at 35 °C/4 °C), where higher values indicate adaptation to higher temperatures. High treatment temperatures resulted in higher SI within days for the winter community, resulting in an expected level of community adaptation within 2 weeks. Adaptation for the summer community was also correlated to treatment temperature, but the rate of adaption was slower. Even after 5 weeks, the bacterial community had not fully adapted to the lowest temperature conditions. Thus, during periods of increasing temperature, the bacterial community will rapidly adapt to function optimally, while decreasing temperature may result in long periods of non-optimal functioning.

Microbial community composition predicts bacterial production across ocean ecosystems

Microbial ecological functions are an emergent property of community composition. For some ecological functions, this link is strong enough that community composition can be used to estimate the quantity of an ecological function. Here, we apply random forest regression models to compare the predictive performance of community composition and environmental data for bacterial production (BP). Using data from two independent long-term ecological research sites-Palmer LTER in Antarctica and Station SPOT in California-we found that community composition was a strong predictor of BP. The top performing model achieved an R2 of 0.84 and RMSE of 20.2 pmol L-1 hr-1 on independent validation data, outperforming a model based solely on environmental data (R2 = 0.32, RMSE = 51.4 pmol L-1 hr-1). We then operationalized our top performing model, estimating BP for 346 Antarctic samples from 2015 to 2020 for which only community composition data were available. Our predictions resolved spatial trends in BP with significance in the Antarctic (P value = 1 × 10-4) and highlighted important taxa for BP across ocean basins. Our results demonstrate a strong link between microbial community composition and microbial ecosystem function and begin to leverage long-term datasets to construct models of BP based on microbial community composition.

High amino acid osmotrophic incorporation by marine eukaryotic phytoplankton revealed by click chemistry

The osmotrophic uptake of dissolved organic compounds in the ocean is considered to be dominated by heterotrophic prokaryotes, whereas the role of planktonic eukaryotes is still unclear. We explored the capacity of natural eukaryotic plankton communities to incorporate the synthetic amino acid L-homopropargylglycine (HPG, analogue of methionine) using biorthogonal noncanonical amino acid tagging (BONCAT), and we compared it with prokaryotic HPG use throughout a 9-day survey in the NW Mediterranean. BONCAT allows to fluorescently identify translationally active cells, but it has never been applied to natural eukaryotic communities. We found a large diversity of photosynthetic and heterotrophic eukaryotes incorporating HPG into proteins, with dinoflagellates and diatoms showing the highest percentages of BONCAT-labelled cells (49 ± 25% and 52 ± 15%, respectively). Among them, pennate diatoms exhibited higher HPG incorporation in the afternoon than in the morning, whereas small (≤5 μm) photosynthetic eukaryotes and heterotrophic nanoeukaryotes showed the opposite pattern. Centric diatoms (e.g. Chaetoceros, Thalassiosira, and Lauderia spp.) dominated the eukaryotic HPG incorporation due to their high abundances and large sizes, accounting for up to 86% of the eukaryotic BONCAT signal and strongly correlating with bulk 3H-leucine uptake rates. When including prokaryotes, eukaryotes were estimated to account for 19-31% of the bulk BONCAT signal. Our results evidence a large complexity in the osmotrophic uptake of HPG, which varies over time within and across eukaryotic groups and highlights the potential of BONCAT to quantify osmotrophy and protein synthesis in complex eukaryotic communities.

Vertical variation of bacterial production and potential role in oxygen loss in the southern Bay of Bengal

Marine environments wherein long-term microbial oxygen consumption exceeds oxygen replenishment can be associated with oxygen minimum zones (OMZ). The Bay of Bengal OMZ (BOB-OMZ) is one of the most intense OMZs globally. To assess the contribution of bacterial oxygen consumption to oxygen loss in BOB-OMZ, we measured bacterial production (BP), temperature, salinity, and dissolved oxygen (DO) in the whole water column. We then compared the estimated bacterial oxygen demand (BOD) with diapycnal oxygen supply (DOS) at depths of 50-200 m in the southern BOB in January 2020. The average BP was 3.53 ± 3.15 μmol C m-3 h-1 in the upper 200 m of four stations, which was lower than those reported in other tropical waters. The vertical distribution of BP differed between the open ocean and nearshore areas. In the open ocean, temperature and DO were the most important predictors for BP in the whole water column. In the nearshore areas, when DO increased sharply from the suboxic state, extremely high BP occurred at 200 m. The average estimated BOD/DOS could reach up to 153% at depths of 50-200 m, indicating advection and anticyclonic eddies probably are important DO replenishment pathways in the BOB.

Short-Term Effects of Climate Change on Planktonic Heterotrophic Prokaryotes in a Temperate Coastal Lagoon: Temperature Is Good, Ultraviolet Radiation Is Bad, and CO2 Is Neutral

Planktonic heterotrophic prokaryotes (HProks) are a pivotal functional group in marine ecosystems and are highly sensitive to environmental variability and climate change. This study aimed to investigate the short-term effects of increasing carbon dioxide (CO2), ultraviolet radiation (UVR), and temperature on natural assemblages of HProks in the Ria Formosa coastal lagoon during winter. Two multi-stressor microcosm experiments were used to evaluate the isolated and combined effects of these environmental changes on HProk abundance, production, growth, and mortality rates. The isolated and combined effects of increased CO2 on HProks were not significant. However, HProk production, cellular activity, instantaneous growth rate, and mortality rate were negatively influenced by elevated UVR and positively influenced by warming. Stronger effects were detected on HProk mortality in relation to specific growth rate, leading to higher HProk net growth rates and abundance under elevated UVR and lower values under warming conditions.

Tracking nitrogen allocation to proteome biosynthesis in a marine microbial community

Microbial growth in many environments is limited by nitrogen availability, yet there is limited understanding of how complex communities compete for and allocate this resource. Here we develop a broadly applicable approach to track biosynthetic incorporation of ¹⁵N-labelled nitrogen substrates into microbial community proteomes, enabling quantification of protein turnover and N allocation to specific cellular functions in individual taxa. Application to oligotrophic ocean surface water identifies taxa-specific substrate preferences and a distinct subset of protein functions undergoing active biosynthesis. The cyanobacterium Prochlorococcus is the most effective competitor for acquisition of ammonium and urea and shifts its proteomic allocation of N over the day/night cycle. Our approach reveals that infrastructure and protein-turnover functions comprise substantial biosynthetic demand for N in Prochlorococcus and a range of other microbial taxa. The direct interrogation of the proteomic underpinnings of N limitation with ¹⁵N-tracking proteomics illuminates how nutrient stress differentially influences metabolism in co-existing microbes.

A device for assessing microbial activity under ambient hydrostatic pressure: The in situ microbial incubator (ISMI)

Microbes in the dark ocean are exposed to hydrostatic pressure increasing with depth. Activity rate measurements and biomass production of dark ocean microbes are, however, almost exclusively performed under atmospheric pressure conditions due to technical constraints of sampling equipment maintaining in situ pressure conditions. To evaluate the microbial activity under in situ hydrostatic pressure, we designed and thoroughly tested an in situ microbial incubator (ISMI). The ISMI allows autonomously collecting and incubating seawater at depth, injection of substrate and fixation of the samples after a preprogramed incubation time. The performance of the ISMI was tested in a high-pressure tank and in several field campaigns under ambient hydrostatic pressure by measuring prokaryotic bulk 3H-leucine incorporation rates. Overall, prokaryotic leucine incorporation rates were lower at in situ pressure conditions than under to depressurized conditions reaching only about 50% of the heterotrophic microbial activity measured under depressurized conditions in bathypelagic waters in the North Atlantic Ocean off the northwestern Iberian Peninsula. Our results show that the ISMI is a valuable tool to reliably determine the metabolic activity of deep-sea microbes at in situ hydrostatic pressure conditions. Hence, we advocate that deep-sea biogeochemical and microbial rate measurements should be performed under in situ pressure conditions to obtain a more realistic view on deep-sea biotic processes.

Prokaryotic Life in the Deep Ocean's Water Column

The oceanic waters below a depth of 200 m represent, in terms of volume, the largest habitat of the biosphere, harboring approximately 70% of the prokaryotic biomass in the oceanic water column. These waters are characterized by low temperature, increasing hydrostatic pressure, and decreasing organic matter supply with depth. Recent methodological advances in microbial oceanography have refined our view of the ecology of prokaryotes in the dark ocean. Here, we review the ecology of prokaryotes of the dark ocean, present data on the biomass distribution and heterotrophic and chemolithoautotrophic prokaryotic production in the major oceanic basins, and highlight the phylogenetic and functional diversity of this part of the ocean. We describe the connectivity of surface and deep-water prokaryotes and the molecular adaptations of piezophilic prokaryotes to high hydrostatic pressure. We also highlight knowledge gaps in the ecology of the dark ocean's prokaryotes and their role in the biogeochemical cycles in the largest habitat of the biosphere.

Bacterial response to glucose addition: growth and community structure in seawater microcosms from North Pacific Ocean

Onboard microcosm experiments were conducted to assess how bacterial growth pattern and community structure changed by the addition of labile organic compound during the KH-14-2 cruise of R/V Hakuho Maru (Atmosphere and Ocean Research Institute, the University of Tokyo and JAMSTEC) in May-June 2014. Seawater samples were collected from the three diversified oceanic environments, Kuroshio Current, North Pacific Sub-polar Gyre (SPG), and North Pacific Sub-tropical Gyre (STG) in the western North Pacific Ocean, filtered, supplemented with glucose, and incubated at 23 ± 1 °C, ~ 4 °C, and 23 ± 1 °C, respectively. Untreated control microcosms were also maintained for all the sample types. Significant increases in cell counts and cell sizes were observed in Kuroshio Current and STG waters, whereas in SPG neither the counts nor the sizes changed, even after 120 h of incubation. At early stages of incubation, the classes Bacteroidia, Alphaproteobacteria, and Gammaproteobacteria were dominant in the Kuroshio Current and SPG samples, while the phyla Cyanobacteria and Proteobacteria in the STG samples. Over incubation periods between 60 and 96 h, some members of the class Gammaproteobacteria gradually dominated within which the genera Vibrio and Alteromonas became dominant in the Kuroshio Current and STG, respectively. No growth was detected for the microcosms with seawater from SPG, regardless of glucose amendment. It is concluded that depending on the environmental condition, certain different bacterial groups proliferated quickly and modified the community structures. Temperature significantly influenced the growth and succession, and ultimately the community structure of bacteria.

Limited carbon cycling due to high-pressure effects on the deep-sea microbiome

Deep-sea microbial communities are exposed to high-pressure conditions, which has a variable impact on prokaryotes depending on whether they are piezophilic (that is, pressure-loving), piezotolerant or piezosensitive. While it has been suggested that elevated pressures lead to higher community-level metabolic rates, the response of these deep-sea microbial communities to the high-pressure conditions of the deep sea is poorly understood. Based on microbial activity measurements in the major oceanic basins using an in situ microbial incubator, we show that the bulk heterotrophic activity of prokaryotic communities becomes increasingly inhibited at higher hydrostatic pressure. At 4,000 m depth, the bulk heterotrophic prokaryotic activity under in situ hydrostatic pressure was about one-third of that measured in the same community at atmospheric pressure conditions. In the bathypelagic zone-between 1,000 and 4,000 m depth-~85% of the prokaryotic community was piezotolerant and ~5% of the prokaryotic community was piezophilic. Despite piezosensitive-like prokaryotes comprising only ~10% (mainly members of Bacteroidetes, Alteromonas) of the deep-sea prokaryotic community, the more than 100-fold metabolic activity increase of these piezosensitive prokaryotes upon depressurization leads to high apparent bulk metabolic activity. Overall, the heterotrophic prokaryotic activity in the deep sea is likely to be substantially lower than hitherto assumed, with major impacts on the oceanic carbon cycling.

High spatial heterogeneity and low connectivity of bacterial communities along a Mediterranean subterranean estuary

Subterranean estuaries are biogeochemically active coastal sites resulting from the underground mixing of fresh aquifer groundwater and seawater. In these systems, microbial activity can largely transform the chemical elements that may reach the sea through submarine groundwater discharge (SGD), but little is known about the microorganisms thriving in these land-sea transition zones. We present the first spatially-resolved characterization of the bacterial assemblages along a coastal aquifer in the NW Mediterranean, considering the entire subsurface salinity gradient. Combining bulk heterotrophic activity measurements, flow cytometry, microscopy and 16S rRNA gene sequencing we find large variations in prokaryotic abundances, cell size, activity and diversity at both the horizontal and vertical scales that reflect the pronounced physicochemical gradients. The parts of the transect most influenced by freshwater were characterized by smaller cells and lower prokaryotic abundances and heterotrophic production, but some activity hotspots were found at deep low-oxygen saline groundwater sites enriched in nitrite and ammonium. Diverse, heterogeneous and highly endemic communities dominated by Proteobacteria, Patescibacteria, Desulfobacterota and Bacteroidota were observed throughout the aquifer, pointing to clearly differentiated prokaryotic niches across these transition zones and little microbial connectivity between groundwater and Mediterranean seawater habitats. Finally, experimental manipulations unveiled large increases in community heterotrophic activity driven by fast growth of some rare and site-specific groundwater Proteobacteria. Our results indicate that prokaryotic communities within subterranean estuaries are highly heterogeneous in terms of biomass, activity and diversity, suggesting that their role in transforming nutrients will also vary spatially within these terrestrial-marine transition zones.

Role of Bacterial Community Composition as a Driver of the Small-Sized Phytoplankton Community Structure in a Productive Coastal System

We present here the first detailed description of the seasonal patterns in bacterial community composition (BCC) in shelf waters off the Ría de Vigo (Spain), based on monthly samplings during 2 years. Moreover, we studied the relationship between bacterial and small-sized eukaryotic community composition to identify potential biotic interactions among components of these two communities. Bacterial operational taxonomic unit (OTU) richness and diversity systematically peaked in autumn-winter, likely related to low resource availability during this period. BCC showed seasonal and vertical patterns, with Rhodobacteraceae and Flavobacteriaceae families dominating in surface waters, and SAR11 clade dominating at the base of the photic zone (30 m depth). BCC variability was significantly explained by environmental variables (e.g., temperature of water, solar radiation, or dissolved organic matter). Interestingly, a strong and significant correlation was found between BCC and small-sized eukaryotic community composition (ECC), which suggests that biotic interactions may play a major role as structuring factors of the microbial plankton in this productive area. In addition, co-occurrence network analyses revealed strong and significant, mostly positive, associations between bacteria and small-sized phytoplankton. Positive associations likely result from mutualistic relationships (e.g., between Dinophyceae and Rhodobacteraceae), while some negative correlations suggest antagonistic interactions (e.g., between Pseudo-nitzchia sp. and SAR11). These results support the key role of biotic interactions as structuring factors of the small-sized eukaryotic community, mostly driven by positive associations between small-sized phytoplankton and bacteria.

Seasonal variation in temperature sensitivity of bacterial growth in a temperate soil and lake

Faster bacterial biomass turnover is expected in water compared to soil, which would result in more rapid community adaption to changing environmental conditions, including temperature. Bacterial community adaptation for growth is therefore predicted to have larger seasonal amplitudes in lakes than in soil. To test this prediction, we compared the seasonal variation in temperature adaptation of bacterial community growth in a soil and lake in Southern Sweden (Tin situ 0-20°C, mean 10°C) during 1.5 years, based on monthly samplings including two winters and summers. An indicator of community adaptation, minimum temperature for growth (Tmin), was calculated from bacterial growth measurements (Leu incorporation) using the Ratkowsky model. The seasonal variation in Tmin (sinusoidal function, R2 = 0.71) was most pronounced for the lake bacterial community, with an amplitude for Tmin of 3.0°C (-4.5 to -10.5°C) compared to 0.6°C (-7 to -8°C) for the soil. Thus, Tmin in water increased by 0.32°C/degree change of Tin situ. Similar differences were also found when comparing four lakes and soils in the winter and summer (amplitudes 2.9°C and 0.9°C for lakes and soils, respectively). Thus, seasonal variation in temperature adaptation has to be taken into account in lakes, while for soils a constant Tmin can be used.

Phytoplankton Responses to Bacterially Regenerated Iron in a Southern Ocean Eddy

In the Subantarctic sector of the Southern Ocean, vertical entrainment of iron (Fe) triggers the seasonal productivity cycle but diminishing physical supply during the spring to summer transition forces microbial assemblages to rapidly acclimate. Here, we tested how phytoplankton and bacteria within an isolated eddy respond to different dissolved Fe (DFe)/ligand inputs. We used three treatments: one that mimicked the entrainment of new DFe (Fe-NEW), another in which DFe was supplied from bacterial regeneration of particles (Fe-REG), and a control with no addition of DFe (Fe-NO). After 6 days, 3.5 (Fe-NO, Fe-NEW) to 5-fold (Fe-REG) increases in Chlorophyll a were observed. These responses of the phytoplankton community were best explained by the differences between the treatments in the amount of DFe recycled during the incubation (Fe-REG, 15% recycled c.f. 40% Fe-NEW, 60% Fe-NO). This additional recycling was more likely mediated by bacteria. By day 6, bacterial production was comparable between Fe-NO and Fe-NEW but was approximately two-fold higher in Fe-REG. A preferential response of phytoplankton (haptophyte-dominated) relative to high nucleic acid (HNA) bacteria was also found in the Fe-REG treatment while the relative proportion of diatoms increased faster in the Fe-NEW and Fe-NO treatments. Comparisons between light and dark incubations further confirmed the competition between picophytoplankton and HNA for DFe. Overall, our results demonstrate great versatility by microorganisms to use different Fe sources that results in highly efficient Fe recycling within surface waters. This study also encourages future research to further investigate the interactions between functional groups of microbes (e.g. HNA and cyanobacteria) to better constraint modeling in Fe and carbon biogeochemical cycles.

Linking Bacterial Growth Responses to Soil Salinity with Cd Availability

This study investigated the effects of different types of saline stress on the availability of cadmium (Cd) and bacterial growth. Changes in soil physicochemical properties and DTPA-Cd content as well as microbial responses after the addition of salts were measured. The addition of 18 g kg^-1 of salts with NaCl and Na₂SO₄ increased the available Cd content by up to 17.80%-29.79%. Respiration rate, biomass, and relative bacterial growth decreased with increasing salt concentrations. Estimated salinity tolerance of bacterial communities based on pollution-induced community tolerance. The salinity tolerance index EC₅₀ of the bacterial community was estimated by logistic equation and ranged from 4.32-12.63 g kg^-1. Structural equation modeling showed that soil salinity stress significantly affected Cd availability and bacterial community, while bacterial growth characteristics also contributed to reducing available Cd. We conclude that saline stress can alter soil Cd availability in soils by affecting the growth characteristics of soil bacterial communities.

Isotopic Insights into Organic Composition Differences between Supermicron and Submicron Sea Spray Aerosol

To elucidate the seawater biological and physicochemical factors driving differences in organic composition between supermicron and submicron sea spray aerosol (SSA_super and SSA_sub), carbon isotopic composition (δ¹³C) measurements were performed on size-segregated, nascent SSA collected during a phytoplankton bloom mesocosm experiment. The δ¹³C measurements indicate that SSA_super contains a mixture of particulate and dissolved organic material in the bulk seawater. After phytoplankton growth, a greater amount of freshly produced carbon was observed in SSA_super with the proportional contribution being modulated by bacterial activity, emphasizing the importance of the microbial loop in controlling the organic composition of SSA_super. Conversely, SSA_sub exhibited no apparent relationship with biological activity but tracked closely with surface tension measurements probing the topmost ∼0.2-1.5 μm of the sea surface microlayer. This probing depth is similar to a bubble's film thickness at the ocean surface, suggesting that SSA_sub organic composition may be influenced by the presence of surfactants at the air-sea interface that are transferred into SSA_sub by bubble bursting. Our findings illustrate the substantial impact of seawater dynamics on the pronounced organic compositional differences between SSA_super and SSA_sub and demonstrate that these two SSA populations should be considered separately when assessing their contribution to marine aerosols and climate.

Dense macrophyte cover has significant structural and functional influence on planktonic microbial communities leading to bacterial success

We intend to assess how macrophyte cover affects planktonic microbial communities by changing the physical and chemical environment, and how macrophyte-derived DOC affects the balance between autotrophy and heterotrophy/chemoorganotrophy in a shallow lake. The structure and production of phytoplankton and bacterioplankton in the open water of a large shallow lake and in the littoral zone were compared at two sampling stations with different macrophyte cover. According to the obtained results, uncoupling between bacterioplankton and phytoplankton was observed due to the high content of organic carbon of emergent macrophyte origin. While phytoplankton were regulated by TSS, bacterioplankton (in both heterotrophic and photoheterotrophic forms) were determined by dissolved organic carbon. As a result of these processes, the littoral and pelagic zones in the lake are completely separated from each other. In open water the autotrophic processes dominated, but at the sampling stations inside the reed belt, the metabolic processes shifted in the direction of chemoorganotrophy. Our results suggest that increase of macrophyte cover in shallow water bodies will increase the significance of microbe-based carbon pathways and weakens the efficiency of carbon transport from primary producers to higher trophic levels through the planktonic food chain.

Trophic Transfer Efficiency in Lakes

Trophic transfer efficiency (TTE) is usually calculated as the ratio of production rates between two consecutive trophic levels. Although seemingly simple, TTE estimates from lakes are rare. In our review, we explore the processes and structures that must be understood for a proper lake TTE estimate. We briefly discuss measurements of production rates and trophic positions and mention how ecological efficiencies, nutrients (N, P) and other compounds (fatty acids) affect energy transfer between trophic levels and hence TTE. Furthermore, we elucidate how TTE estimates are linked with size-based approaches according to the Metabolic Theory of Ecology, and how food-web models can be applied to study TTE in lakes. Subsequently, we explore temporal and spatial heterogeneity of production and TTE in lakes, with a particular focus on the links between benthic and pelagic habitats and between the lake and the terrestrial environment. We provide an overview of TTE estimates from lakes found in the published literature. Finally, we present two alternative approaches to estimating TTE. First, TTE can be seen as a mechanistic quantity informing about the energy and matter flow between producer and consumer groups. This approach is informative with respect to food-web structure, but requires enormous amounts of data. The greatest uncertainty comes from the proper consideration of basal production to estimate TTE of omnivorous organisms. An alternative approach is estimating food-chain and food-web efficiencies, by comparing the heterotrophic production of single consumer levels or the total sum of all heterotrophic production including that of heterotrophic bacteria to the total sum of primary production. We close the review by pointing to a few research questions that would benefit from more frequent and standardized estimates of TTE in lakes.

Seasonal Dynamics in Carbon Cycling of Marine Bacterioplankton Are Lifestyle Dependent

Although free-living (FL) and particle-attached (PA) bacteria are recognized as ecologically distinct compartments of marine microbial food-webs, few, if any, studies have determined their dynamics in abundance, function (production, respiration and substrate utilization) and taxonomy over a yearly cycle. In the Baltic Sea, abundance and production of PA bacteria (defined as the size-fraction >3.0 μm) peaked over 3 months in summer (6 months for FL bacteria), largely coinciding with blooms of Chitinophagales (Bacteroidetes). Pronounced changes in the growth efficiency (range 0.05–0.27) of FL bacteria (defined as the size-fraction <3.0 μm) indicated the magnitude of seasonal variability of ecological settings bacteria experience. Accordingly, 16S rRNA gene analyses of bacterial community composition uncovered distinct correlations between taxa, environmental variables and metabolisms, including Firmicutes associated with elevated hydrolytic enzyme activity in winter and Verrucomicrobia with utilization of algal-derived substrates during summer. Further, our results suggested a substrate-controlled succession in the PA fraction, from Bacteroidetes using polymers to Actinobacteria and Betaproteobacteria using monomers across the spring to autumn phytoplankton bloom transition. Collectively, our findings emphasize pronounced seasonal changes in both the composition of the bacterial community in the PA and FL size-fractions and their contribution to organic matter utilization and carbon cycling. This is important for interpreting microbial ecosystem function-responses to natural and human-induced environmental changes.

Activity of Ancillary Heterotrophic Community Members in Anaerobic Methane-Oxidizing Cultures

Consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria mediate the anaerobic oxidation of methane (AOM) in marine sediments. However, even sediment-free cultures contain a substantial number of additional microorganisms not directly related to AOM. To track the heterotrophic activity of these community members and their possible relationship with AOM, we amended meso- (37°C) and thermophilic (50°C) AOM cultures (dominated by ANME-1 archaea and their partner bacteria of the Seep-SRB2 clade or Candidatus Desulfofervidus auxilii) with L-leucine-3-¹³C (¹³C-leu). Various microbial lipids incorporated the labeled carbon from this amino acid, independent of the presence of methane as an energy source, specifically bacterial fatty acids, such as iso and anteiso-branched C_15:0 and C_17:0, as well as unsaturated C_18:1ω9 and C_18:1ω7. In natural methane-rich environments, these bacterial fatty acids are strongly ¹³C-depleted. We, therefore, suggest that those fatty acids are produced by ancillary bacteria that grow on ¹³C-depleted necromass or cell exudates/lysates of the AOM core communities. Candidates that likely benefit from AOM biomass are heterotrophic bacterial members of the Spirochetes and Anaerolineae—known to produce abundant branched fatty acids and present in all the AOM enrichment cultures. For archaeal lipids, we observed minor ¹³C-incorporation, but still suggesting some ¹³C-leu anabolism. Based on their relatively high abundance in the culture, the most probable archaeal candidates are Bathyarchaeota, Thermoplasmatales, and Lokiarchaeota. The identified heterotrophic bacterial and archaeal ancillary members are likely key players in organic carbon recycling in anoxic marine sediments.

Viruses affect picocyanobacterial abundance and biogeography in the North Pacific Ocean

The photosynthetic picocyanobacteria Prochlorococcus and Synechococcus are models for dissecting how ecological niches are defined by environmental conditions, but how interactions with bacteriophages affect picocyanobacterial biogeography in open ocean biomes has rarely been assessed. We applied single-virus and single-cell infection approaches to quantify cyanophage abundance and infected picocyanobacteria in 87 surface water samples from five transects that traversed approximately 2,200 km in the North Pacific Ocean on three cruises, with a duration of 2-4 weeks, between 2015 and 2017. We detected a 550-km-wide hotspot of cyanophages and virus-infected picocyanobacteria in the transition zone between the North Pacific Subtropical and Subpolar gyres that was present in each transect. Notably, the hotspot occurred at a consistent temperature and displayed distinct cyanophage-lineage composition on all transects. On two of these transects, the levels of infection in the hotspot were estimated to be sufficient to substantially limit the geographical range of Prochlorococcus. Coincident with the detection of high levels of virally infected picocyanobacteria, we measured an increase of 10-100-fold in the Synechococcus populations in samples that are usually dominated by Prochlorococcus. We developed a multiple regression model of cyanophages, temperature and chlorophyll concentrations that inferred that the hotspot extended across the North Pacific Ocean, creating a biological boundary between gyres, with the potential to release organic matter comparable to that of the sevenfold-larger North Pacific Subtropical Gyre. Our results highlight the probable impact of viruses on large-scale phytoplankton biogeography and biogeochemistry in distinct regions of the oceans.

Photoheterotrophy by aerobic anoxygenic bacteria modulates carbon fluxes in a freshwater lake

Lakes are a significant component of the global carbon cycle. Respiration exceeds net primary production in most freshwater lakes, making them a source of CO₂ to the atmosphere. Driven by heterotrophic microorganisms, respiration is assumed to be unaffected by light, thus it is measured in the dark. However, photoheterotrophs, such as aerobic anoxygenic photoheterotrophic (AAP) bacteria that produce ATP via photochemical reactions, substantially reduce respiration in the light. They are an abundant and active component of bacterioplankton, but their photoheterotrophic contribution to microbial community metabolism remains unquantified. We showed that the community respiration rate in a freshwater lake was reduced by 15.2% (95% confidence interval (CI): 6.6-23.8%) in infrared light that is usable by AAP bacteria but not by primary producers. Moreover, significantly higher assimilation rates of glucose (18.1%; 7.8-28.4%), pyruvate (9.5%; 4.2-14.8%), and leucine (5.9%; 0.1-11.6%) were measured in infrared light. At the ecosystem scale, the amount of CO₂ from respiration unbalanced by net primary production was by 3.69 × 10⁹ g CO₂ lower over these two sampling seasons when measured in the infrared light. Our results demonstrate that dark measurements of microbial activity significantly bias the carbon fluxes, providing a new paradigm for their quantification in aquatic environments.

COVID-19 lockdown moderately increased oligotrophy at a marine coastal site

COVID-19 has led to global population lockdowns that have had indirect effects on terrestrial and marine fauna, yet little is known on their effects on marine planktonic communities. We analysed the effect of the spring 2020 lockdown in a marine coastal area in Blanes Bay, NW Mediterranean. We compared a set of 23 oceanographic, microbial and biogeochemical variables sampled right after the strict lockdown in Spain, with data from the previous 15 years after correcting for long-term trends. Our analysis shows a series of changes in the microbial communities which may have been induced by the combination of the decreased nitrogen atmospheric load, the lower wastewater flux and the reduced fishing activity in the area, among other factors. In particular, we detected a slight decrease beyond the long-term trend in chlorophyll a, in the abundance of several microbial groups (phototrophic nanoflagellates and total prokaryotes) and in prokaryotic activity (heterotrophic prokaryotic production and β-glucosidase activity) which, as a whole, resulted in a moderate increase of oligotrophy in Blanes Bay after the lockdown.

Linkages Among Dissolved Organic Matter Export, Dissolved Metabolites, and Associated Microbial Community Structure Response in the Northwestern Sargasso Sea on a Seasonal Scale

Deep convective mixing of dissolved and suspended organic matter from the surface to depth can represent an important export pathway of the biological carbon pump. The seasonally oligotrophic Sargasso Sea experiences annual winter convective mixing to as deep as 300 m, providing a unique model system to examine dissolved organic matter (DOM) export and its subsequent compositional transformation by microbial oxidation. We analyzed biogeochemical and microbial parameters collected from the northwestern Sargasso Sea, including bulk dissolved organic carbon (DOC), total dissolved amino acids (TDAA), dissolved metabolites, bacterial abundance and production, and bacterial community structure, to assess the fate and compositional transformation of DOM by microbes on a seasonal time-scale in 2016-2017. DOM dynamics at the Bermuda Atlantic Time-series Study site followed a general annual trend of DOC accumulation in the surface during stratified periods followed by downward flux during winter convective mixing. Changes in the amino acid concentrations and compositions provide useful indices of diagenetic alteration of DOM. TDAA concentrations and degradation indices increased in the mesopelagic zone during mixing, indicating the export of a relatively less diagenetically altered (i.e., more labile) DOM. During periods of deep mixing, a unique subset of dissolved metabolites, such as amino acids, vitamins, and benzoic acids, was produced or lost. DOM export and compositional change were accompanied by mesopelagic bacterial growth and response of specific bacterial lineages in the SAR11, SAR202, and SAR86 clades, Acidimicrobiales, and Flavobacteria, during and shortly following deep mixing. Complementary DOM biogeochemistry and microbial measurements revealed seasonal changes in DOM composition and diagenetic state, highlighting microbial alteration of the quantity and quality of DOM in the ocean.

Empirical leucine-to-carbon conversion factors in north-eastern Atlantic waters (50-2000 m) shaped by bacterial community composition and optical signature of DOM

Microbial heterotrophic activity is a major process regulating the flux of dissolved organic matter (DOM) in the ocean, while the characteristics of this DOM strongly influence its microbial utilization and fate in the ocean. In order to broaden the vertical resolution of leucine-to-carbon conversion factors (CFs), needed for converting substrate incorporation into biomass production by heterotrophic bacteria, 20 dilution experiments were performed in the North Atlantic Ocean. We found a depth-stratification in empirical CFs values from epipelagic to bathypelagic waters (4.00 ± 1.09 to 0.10 ± 0.00 kg C mol Leu⁻¹). Our results demonstrated that the customarily used theoretical CF of 1.55 kg C mol Leu⁻¹ in oceanic samples can lead to an underestimation of prokaryotic heterotrophic production in epi- and mesopelagic waters, while it can overestimate it in the bathypelagic ocean. Pearson correlations showed that CFs were related not only to hydrographic variables such as temperature, but also to specific phylogenetic groups and DOM quality and quantity indices. Furthermore, a multiple linear regression model predicting CFs from relatively simple hydrographic and optical spectroscopic measurements was attempted. Taken together, our results suggest that differences in CFs throughout the water column are significantly connected to DOM, and also reflect differences linked to specific prokaryotic groups.

Responses of Coastal Marine Microbiomes Exposed to Anthropogenic Dissolved Organic Carbon

Coastal seawaters receive thousands of organic pollutants. However, we have little understanding of the response of microbiomes to this pool of anthropogenic dissolved organic carbon (ADOC). In this study, coastal microbial communities were challenged with ADOC at environmentally relevant concentrations. Experiments were performed at two Mediterranean sites with different impact by pollutants and nutrients: off the Barcelona harbor ("BCN"), and at the Blanes Bay ("BL"). ADOC additions stimulated prokaryotic leucine incorporation rates at both sites, indicating the use of ADOC as growth substrate. The percentage of "membrane-compromised" cells increased with increasing ADOC, indicating concurrent toxic effects of ADOC. Metagenomic analysis of the BCN community challenged with ADOC showed a significant growth of Methylophaga and other gammaproteobacterial taxa belonging to the rare biosphere. Gene expression profiles showed a taxon-dependent response, with significantly enrichments of transcripts from SAR11 and Glaciecola spp. in BCN and BL, respectively. Further, the relative abundance of transposon-related genes (in BCN) and transcripts (in BL) correlated with the number of differentially abundant genes (in BCN) and transcripts (in BLA), suggesting that microbial responses to pollution may be related to pre-exposure to pollutants, with transposons playing a role in adaptation to ADOC. Our results point to a taxon-specific response to low concentrations of ADOC that impact the functionality, structure and plasticity of the communities in coastal seawaters. This work contributes to address the influence of pollutants on microbiomes and their perturbation to ecosystem services and ocean health.

Microbial Diversity and Activity During the Biodegradation in Seawater of Various Substitutes to Conventional Plastic Cotton Swab Sticks

The European Parliament recently approved a new law banning single-use plastic items for 2021 such as plastic plates, cutlery, straws, cotton swabs, and balloon sticks. Transition to a bioeconomy involves the substitution of these banned products with biodegradable materials. Several materials such as polylactic acid (PLA), polybutylene adipate terephthalate (PBAT), poly(butylene succinate) (PBS), polyhydroxybutyrate-valerate (PHBV), Bioplast, and Mater-Bi could be good candidates to substitute cotton swabs, but their biodegradability needs to be tested under marine conditions. In this study, we described the microbial life growing on these materials, and we evaluated their biodegradability in seawater, compared with controls made of non-biodegradable polypropylene (PP) or biodegradable cellulose. During the first 40 days in seawater, we detected clear changes in bacterial diversity (Illumina sequencing of 16S rRNA gene) and heterotrophic activity (incorporation of ³H-leucine) that coincided with the classic succession of initial colonization, growth, and maturation phases of a biofilm. Biodegradability of the cotton swab sticks was then tested during another 94 days under strict diet conditions with the different plastics as sole carbon source. The drastic decrease of the bacterial activity on PP, PLA, and PBS suggested no bacterial attack of these materials, whereas the bacterial activity in PBAT, Bioplast, Mater-Bi, and PHBV presented similar responses to the cellulose positive control. Interestingly, the different bacterial diversity trends observed for biodegradable vs. non-biodegradable plastics allowed to describe potential new candidates involved in the degradation of these materials under marine conditions. This better understanding of the bacterial diversity and activity dynamics during the colonization and biodegradation processes contributes to an expanding baseline to understand plastic biodegradation in marine conditions and provide a foundation for further decisions on the replacement of the banned single-used plastics.

Mesopelagic microbial carbon production correlates with diversity across different marine particle fractions

The vertical flux of marine snow particles significantly reduces atmospheric carbon dioxide concentration. In the mesopelagic zone, a large proportion of the organic carbon carried by sinking particles dissipates thereby escaping long term sequestration. Particle associated prokaryotes are largely responsible for such organic carbon loss. However, links between this important ecosystem flux and ecological processes such as community development of prokaryotes on different particle fractions (sinking vs. non-sinking) are yet virtually unknown. This prevents accurate predictions of mesopelagic organic carbon loss in response to changing ocean dynamics. Using combined measurements of prokaryotic heterotrophic production rates and species richness in the North Atlantic, we reveal that carbon loss rates and associated microbial richness are drastically different with particle fractions. Our results demonstrate a strong negative correlation between prokaryotic carbon losses and species richness. Such a trend may be related to prokaryotes detaching from fast-sinking particles constantly enriching non-sinking associated communities in the mesopelagic zone. Existing global scale data suggest this negative correlation is a widespread feature of mesopelagic microbes.

Viability and stress state of bacteria associated with primary production or zooplankton-derived suspended particulate matter in summer along a transect in Baffin Bay (Arctic Ocean)

In the framework of the GreenEdge Project (whose the general objective is to understand the dynamic of the phytoplankton spring bloom in Arctic Ocean), lipid composition and viability and stress state of bacteria were monitored in sea ice and suspended particulate matter (SPM) samples collected in 2016 along a transect from sea ice to open water in Baffin Bay (Arctic Ocean). Lipid analyses confirmed the dominance of diatoms in the bottommost layer of ice and suggested (i) the presence of a strong proportion of micro-zooplankton in SPM samples collected at the western ice covered St 403 and St 409 and (ii) a high proportion of macro-zooplankton (copepods) in SPM samples collected at the eastern ice covered St 413 and open water St 418. The use of the propidium monoazide (PMA) method allowed to show a high bacterial mortality in sea ice and in SPM material collected in shallower waters at St 409 and St 418. This mortality was attributed to the release of bactericidal free fatty acids by sympagic diatoms under the effect of light stress. A strong cis-trans isomerization of bacterial MUFAs was observed in the deeper SPM samples collected at the St 403 and St 409. It was attributed to the ingestion of bacteria stressed by salinity in brine channels of ice by sympagic bacterivorous microzooplankton (ciliates) incorporating trans fatty acids of their preys before to be released in the water column during melting. The high trans/cis ratios also observed in SPM samples collected in the shallower waters at St 413 and St 418 suggest the presence of positively or neutrally buoyant extracellular polymeric substances (EPS)-rich particles retained in sea ice and discharged (with bacteria stressed by salinity) in seawater after the initial release of algal biomass. Such EPS particles, which are generally considered as ideal vectors for bacterial horizontal distribution in the Arctic, appeared to contain a high proportion of dead and non-growing bacteria.

Viral-Mediated Microbe Mortality Modulated by Ocean Acidification and Eutrophication: Consequences for the Carbon Fluxes Through the Microbial Food Web

Anthropogenic carbon emissions are causing changes in seawater carbonate chemistry including a decline in the pH of the oceans. While its aftermath for calcifying microbes has been widely studied, the effect of ocean acidification (OA) on marine viruses and their microbial hosts is controversial, and even more in combination with another anthropogenic stressor, i.e., human-induced nutrient loads. In this study, two mesocosm acidification experiments with Mediterranean waters from different seasons revealed distinct effects of OA on viruses and viral-mediated prokaryotic mortality depending on the trophic state and the successional stage of the plankton community. In the winter bloom situation, low fluorescence viruses, the most abundant virus-like particle (VLP) subpopulation comprising mostly bacteriophages, were negatively affected by lowered pH with nutrient addition, while the bacterial host abundance was stimulated. High fluorescence viruses, containing cyanophages, were stimulated by OA regardless of the nutrient conditions, while cyanobacteria of the genus Synechococcus were negatively affected by OA. Moreover, the abundance of very high fluorescence viruses infecting small haptophytes tended to be lower under acidification while their putative hosts' abundance was enhanced, suggesting a direct and negative effect of OA on viral-host interactions. In the oligotrophic summer situation, we found a stimulating effect of OA on total viral abundance and the viral populations, suggesting a cascading effect of the elevated pCO2 stimulating autotrophic and heterotrophic production. In winter, viral lysis accounted for 30 ± 16% of the loss of bacterial standing stock per day (VMMBSS) under increased pCO2 compared to 53 ± 35% in the control treatments, without effects of nutrient additions while in summer, OA had no significant effects on VMMBSS (35 ± 20% and 38 ± 5% per day in the OA and control treatments, respectively). We found that phage production and resulting organic carbon release rates significantly reduced under OA in the nutrient replete winter situation, but it was also observed that high nutrient loads lowered the negative effect of OA on viral lysis, suggesting an antagonistic interplay between these two major global ocean stressors in the Anthropocene. In summer, however, viral-mediated carbon release rates were lower and not affected by lowered pH. Eutrophication consistently stimulated viral production regardless of the season or initial conditions. Given the relevant role of viruses for marine carbon cycling and the biological carbon pump, these two anthropogenic stressors may modulate carbon fluxes through their effect on viruses at the base of the pelagic food web in a future global change scenario.

Enhanced Viral Activity in the Surface Microlayer of the Arctic and Antarctic Oceans

The ocean surface microlayer (SML), with physicochemical characteristics different from those of subsurface waters (SSW), results in dense and active viral and microbial communities that may favor virus–host interactions. Conversely, wind speed and/or UV radiation could adversely affect virus infection. Furthermore, in polar regions, organic and inorganic nutrient inputs from melting ice may increase microbial activity in the SML. Since the role of viruses in the microbial food web of the SML is poorly understood in polar oceans, we aimed to study the impact of viruses on prokaryotic communities in the SML and in the SSW in Arctic and Antarctic waters. We hypothesized that a higher viral activity in the SML than in the SSW in both polar systems would be observed. We measured viral and prokaryote abundances, virus-mediated mortality on prokaryotes, heterotrophic and phototrophic nanoflagellate abundance, and environmental factors. In both polar zones, we found small differences in environmental factors between the SML and the SSW. In contrast, despite the adverse effect of wind, viral and prokaryote abundances and virus-mediated mortality on prokaryotes were higher in the SML than in the SSW. As a consequence, the higher carbon flux released by lysed cells in the SML than in the SSW would increase the pool of dissolved organic carbon (DOC) and be rapidly used by other prokaryotes to grow (the viral shunt). Thus, our results suggest that viral activity greatly contributes to the functioning of the microbial food web in the SML, which could influence the biogeochemical cycles of the water column.

The microbial dimension of submarine groundwater discharge: current challenges and future directions

Despite the relevance of submarine groundwater discharge (SGD) for ocean biogeochemistry, the microbial dimension of SGD remains poorly understood. SGD can influence marine microbial communities through supplying chemical compounds and microorganisms, and in turn, microbes at the land–ocean transition zone determine the chemistry of the groundwater reaching the ocean. However, compared with inland groundwater, little is known about microbial communities in coastal aquifers. Here, we review the state of the art of the microbial dimension of SGD, with emphasis on prokaryotes, and identify current challenges and future directions. Main challenges include improving the diversity description of groundwater microbiota, characterized by ultrasmall, inactive and novel taxa, and by high ratios of sediment-attached versus free-living cells. Studies should explore microbial dynamics and their role in chemical cycles in coastal aquifers, the bidirectional dispersal of groundwater and seawater microorganisms, and marine bacterioplankton responses to SGD. This will require not only combining sequencing methods, visualization and linking taxonomy to activity but also considering the entire groundwater–marine continuum. Interactions between traditionally independent disciplines (e.g. hydrogeology, microbial ecology) are needed to frame the study of terrestrial and aquatic microorganisms beyond the limits of their presumed habitats, and to foster our understanding of SGD processes and their influence in coastal biogeochemical cycles.

Long-term patterns and drivers of microbial organic matter utilization in the northernmost basin of the Mediterranean Sea

Marine heterotrophic prokaryotes degrade, transform, and utilize half of the organic matter (OM) produced by photosynthesis, either in dissolved or particulate form. Microbial metabolic rates are affected by a plethora of different factors, spanning from environmental variables to OM composition. To tease apart the environmental drivers underlying the observed organic matter utilization rates, we analysed a 21 year-long time series from the Gulf of Trieste (NE Adriatic Sea). Heterotrophic carbon production (HCP) time series analysis highlighted a long-term structure made up by three periods of coherent observations (1999-2007; 2008-2011; 2012-2019), shared also by OM concentration time series. Temporal patterns of HCP drivers, extracted with a random forest approach, demonstrated that a period of high salinity anomalies (2002-2008) was the main driver of this structure. The reduced river runoff and the consequent depletion of river-borne inorganic nutrients induced a long-term Chl a decline (2006-2009), followed by a steady increase until 2014. HCP driving features over the three periods substantially changed in their seasonal patterns, suggesting that the years following the draught period represented a transition between two long-term regimes. Overall, temperature and particulate organic carbon concentration were the main factors driving HCP rates. The emergence of these variables highlighted the strong control exerted by the temperature-substrate co-limitation on microbial growth. Further exploration revealed that HCP rates did not follow the Arrhenius' linear response to temperature between 2008 and 2011, demonstrating that microbial growth was substrate-limited following the draught event. By teasing apart the environmental drivers of microbial growth on a long-term perspective, we demonstrated that a substantial change happened in the biogeochemistry of one of the most productive areas of the Mediterranean Sea. As planktonic microbes are the foundation of marine ecosystems, understanding their past dynamics may help to explain present and future changes.

Dissolved organic matter released by two marine heterotrophic bacterial strains and its bioavailability for natural prokaryotic communities

Marine heterotrophic prokaryotes (HP) play a key role in organic matter processing in the ocean; however, the view of HP as dissolved organic matter (DOM) sources remains underexplored. In this study, we quantified and optically characterized the DOM produced by two single marine bacterial strains. We then tested the availability of these DOM sources to in situ Mediterranean Sea HP communities. Two bacterial strains were used: Photobacterium angustum (a copiotrophic gammaproteobacterium) and Sphingopyxis alaskensis (an oligotrophic alphaproteobacterium). When cultivated on glucose as the sole carbon source, the two strains released from 7% to 23% of initial glucose as bacterial derived DOM (B-DOM), the quality of which (as enrichment in humic or protein-like substances) differed between strains. B-DOM induced significant growth and carbon consumption of natural HP communities, suggesting that it was partly labile. However, B-DOM consistently promoted lower prokaryotic growth efficiencies than in situ DOM. In addition, B-DOM changed HP exoenzymatic activities, enhancing aminopeptidase activity when degrading P. angustum DOM, and alkaline phosphatase activity when using S. alaskensis DOM, and promoted differences in HP diversity and composition. DOM produced by HP affects in situ prokaryotic metabolism and diversity, thus changing the pathways for DOM cycling (e.g. respiration over biomass production) in the ocean.

The Toxicity Exerted by the Antibiotic Sulfadiazine on the Growth of Soil Bacterial Communities May Increase over Time

The toxicity exerted by the antibiotic sulfadiazine on the growth of soil bacterial communities was studied in two agricultural soils for a period of 100 days. In the short-term (2 days of incubation), the effect of sulfadiazine on bacterial growth was low (no inhibition or inhibition <32% for a dose of 2000 mg·kg-1). However, sulfadiazine toxicity increased with time, achieving values of 40% inhibition, affecting bacterial growth in both soils after 100 days of incubation. These results, which were here observed for the first time for any antibiotic in soil samples, suggest that long-term experiments would be required for performing an adequate antibiotics risk assessment, as short-term experiments may underestimate toxicity effects.

Changes in Activity and Community Composition Shape Bacterial Responses to Size-Fractionated Marine DOM

To study the response of bacteria to different size-fractions of naturally occurring dissolved organic matter (DOM), a natural prokaryotic community from North Atlantic mesopelagic waters (1000 m depth) was isolated and grown in (i) 0.1-μm filtered seawater (CONTROL), (ii) the low-molecular-weight (<1 kDa) DOM fraction (L-DOM), and (iii) the recombination of high- (>1 kDa) and low-molecular-weight DOM fractions (H + L-DOM), to test the potential effect of ultrafiltration on breaking the DOM size continuum. Prokaryotic abundance and leucine incorporation were consistently higher in the H + L-DOM niche than in the L-DOM and CONTROL treatments, suggesting a different interaction with each DOM fraction and the disruption of the structural DOM continuum by ultrafiltration, respectively. Rhodobacterales (Alphaproteobacteria) and Flavobacteriales (Bacteroidetes) were particularly enriched in L-DOM and closely related to the colored DOM (CDOM) fraction, indicating the tight link between these groups and changes in DOM aromaticity. Conversely, some other taxa that were rare or undetectable in the original bacterial community were enriched in the H + L-DOM treatment (e.g., Alteromonadales belonging to Gammaproteobacteria), highlighting the role of the rare biosphere as a seed bank of diversity against ecosystem disturbance. The relationship between the fluorescence of protein-like CDOM and community composition of populations in the H + L-DOM treatment suggested their preference for labile DOM. Conversely, the communities growing on the L-DOM niche were coupled to humic-like CDOM, which may indicate their ability to degrade more reworked DOM and/or the generation of refractory substrates (as by-products of the respiration processes). Most importantly, L- and/or H + L-DOM treatments stimulated the growth of unique bacterial amplicon sequence variants (ASVs), suggesting the potential of environmental selection (i.e., changes in DOM composition and availability), particularly in the light of climate change scenarios. Taken together, our results suggest that different size-fractions of DOM induced niche-specialization and differentiation of mesopelagic bacterial communities.

Seasonal impact of grazing, viral mortality, resource availability and light on the group-specific growth rates of coastal Mediterranean bacterioplankton

Estimation of prokaryotic growth rates is critical to understand the ecological role and contribution of different microbes to marine biogeochemical cycles. However, there is a general lack of knowledge on what factors control the growth rates of different prokaryotic groups and how these vary between sites and along seasons at a given site. We carried out several manipulation experiments during the four astronomical seasons in the coastal NW Mediterranean in order to evaluate the impact of grazing, viral mortality, resource competition and light on the growth and loss rates of prokaryotes. Gross and net growth rates of different bacterioplankton groups targeted by group-specific CARD-FISH probes and infrared microscopy (for aerobic anoxygenic phototrophs, AAP), were calculated from changes in cell abundances. Maximal group-specific growth rates were achieved when both predation pressure and nutrient limitation were experimentally minimized, while only a minimal effect of viral pressure on growth rates was observed; nevertheless, the response to predation removal was more remarkable in winter, when the bacterial community was not subjected to nutrient limitation. Although all groups showed increases in their growth rates when resource competition as well as grazers and viral pressure were reduced, Alteromonadaceae consistently presented the highest rates in all seasons. The response to light availability was generally weaker than that to the other factors, but it was variable between seasons. In summer and spring, the growth rates of AAP were stimulated by light whereas the growth of the SAR11 clade (likely containing proteorhodopsin) was enhanced by light in all seasons. Overall, our results set thresholds on bacterioplankton group-specific growth and mortality rates and contribute to estimate the seasonally changing contribution of various bacterioplankton groups to the function of microbial communities. Our results also indicate that the least abundant groups display the highest growth rates, contributing to the recycling of organic matter to a much greater extent than what their abundances alone would predict.

Differential recruitment of opportunistic taxa leads to contrasting abilities in carbon processing by bathypelagic and surface microbial communities

Different factors affect the way dissolved organic matter (DOM) is processed in the ocean water column, including environmental conditions and the functional capabilities of the communities. Recent studies have shown that bathypelagic prokaryotes are metabolically flexible, but whether this versatility translates into a higher ability to process DOM has been barely explored. Here we performed a multifactorial transplant experiment to compare the growth, activity and changes in DOM quality in surface and bathypelagic waters inoculated with either surface or bathypelagic prokaryotic communities. The effect of nutrient additions to surface waters was also explored. Despite no differences in the cell abundance of surface and deep ocean prokaryotes were observed in any of the treatments, in surface waters with nutrients the heterotrophic production of surface prokaryotes rapidly decreased. Conversely, bathypelagic communities displayed a sustained production throughout the experiment. Incubations with surface prokaryotes always led to a significant accumulation of recalcitrant compounds, which did not occur with bathypelagic prokaryotes, suggesting they have a higher ability to process DOM. These contrasting abilities could be explained by the recruitment of a comparatively larger number of opportunistic taxa within the bathypelagic assemblages, which likely resulted in a broader community capability of substrate utilization.

Assessing Viral Abundance and Community Composition in Four Contrasting Regions of the Southern Ocean

We explored how changes of viral abundance and community composition among four contrasting regions in the Southern Ocean relied on physicochemical and microbiological traits. During January-February 2015, we visited areas north and south of the South Orkney Islands (NSO and SSO) characterized by low temperature and salinity and high inorganic nutrient concentration, north of South Georgia Island (NSG) and west of Anvers Island (WA), which have relatively higher temperatures and lower inorganic nutrient concentrations. Surface viral abundance (VA) was highest in NSG (21.50 ± 10.70 × 10⁶ viruses mL^-1) and lowest in SSO (2.96 ± 1.48 × 10⁶ viruses mL^-1). VA was positively correlated with temperature, prokaryote abundance and prokaryotic heterotrophic production, chlorophyll a, diatoms, haptophytes, fluorescent organic matter, and isoprene concentration, and was negatively correlated with inorganic nutrients (NO_3-, SiO₄^2-, PO₄^3-), and dimethyl sulfide (DMS) concentrations. Viral communities determined by randomly amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) were grouped according to the sampling location, being more similar within them than among regions. The first two axes of a canonical correspondence analysis, including physicochemical (temperature, salinity, inorganic nutrients-NO_3-, SiO₄^2-, and dimethyl sulfoniopropionate -DMSP- and isoprene concentrations) and microbiological (chlorophyll a, haptophytes and diatom, and prokaryote abundance and prokaryotic heterotrophic production) factors accounted for 62.9% of the variance. The first axis, temperature-related, accounted for 33.8%; the second one, salinity-related, accounted for 29.1%. Thus, different environmental situations likely select different hosts for viruses, leading to distinct viral communities.

Light and Primary Production Shape Bacterial Activity and Community Composition of Aerobic Anoxygenic Phototrophic Bacteria in a Microcosm Experiment

Phytoplankton is a key component of aquatic microbial communities, and metabolic coupling between phytoplankton and bacteria determines the fate of dissolved organic carbon (DOC). Yet, the impact of primary production on bacterial activity and community composition remains largely unknown, as, for example, in the case of aerobic anoxygenic phototrophic (AAP) bacteria that utilize both phytoplankton-derived DOC and light as energy sources. Here, we studied how reduction of primary production in a natural freshwater community affects the bacterial community composition and its activity, focusing primarily on AAP bacteria. The bacterial respiration rate was the lowest when photosynthesis was reduced by direct inhibition of photosystem II and the highest in ambient light condition with no photosynthesis inhibition, suggesting that it was limited by carbon availability. However, bacterial assimilation rates of leucine and glucose were unaffected, indicating that increased bacterial growth efficiency (e.g., due to photoheterotrophy) can help to maintain overall bacterial production when low primary production limits DOC availability. Bacterial community composition was tightly linked to light intensity, mainly due to the increased relative abundance of light-dependent AAP bacteria. This notion shows that changes in bacterial community composition are not necessarily reflected by changes in bacterial production or growth and vice versa. Moreover, we demonstrated for the first time that light can directly affect bacterial community composition, a topic which has been neglected in studies of phytoplankton-bacteria interactions.IMPORTANCE Metabolic coupling between phytoplankton and bacteria determines the fate of dissolved organic carbon in aquatic environments, and yet how changes in the rate of primary production affect the bacterial activity and community composition remains understudied. Here, we experimentally limited the rate of primary production either by lowering light intensity or by adding a photosynthesis inhibitor. The induced decrease had a greater influence on bacterial respiration than on bacterial production and growth rate, especially at an optimal light intensity. This suggests that changes in primary production drive bacterial activity, but the effect on carbon flow may be mitigated by increased bacterial growth efficiencies, especially of light-dependent AAP bacteria. Bacterial activities were independent of changes in bacterial community composition, which were driven by light availability and AAP bacteria. This direct effect of light on composition of bacterial communities has not been documented previously.

Prokaryotic Response to Phytodetritus-Derived Organic Material in Epi- and Mesopelagic Antarctic Waters

Particulate organic matter (POM) export represents the underlying principle of the biological carbon pump, driving the carbon flux from the sunlit to the dark ocean. The efficiency of this process is tightly linked to the prokaryotic community, as >70% of POM respiration is carried out by particle-associated prokaryotes. In the Ross Sea, one of the most productive areas of the Southern Ocean, up to 50% of the surface primary production is exported to the mesopelagic ocean as POM. Recent evidence suggests that a significant fraction of the POM in this area is composed of intact phytoplankton cells. During austral summer 2017, we set up bottle enrichment experiments in which we amended free-living surface and deep prokaryotic communities with organic matter pools generated from native microplankton, mimicking the particle export that may derive from mild (1 μg of Chlorophyll a L-1) and intense (10 μg of Chlorophyll a L-1) phytoplankton bloom. Over a course of 4 days, we followed free-living and particle-attached prokaryotes' abundance, the degradation rates of polysaccharides, proteins and lipids, heterotrophic production as well as inorganic carbon utilization and prokaryotic community structure dynamics. Our results showed that several rare or undetected taxa in the initial community became dominant during the time course of the incubations and that different phytodetritus-derived organic matter sources induced specific changes in microbial communities, selecting for peculiar degradation and utilization processes spectra. Moreover, the features of the supplied detritus (in terms of microplankton taxa composition) determined different colonization dynamics and organic matter processing modes. Our study provides insights into the mechanisms underlying the prokaryotic utilization of phytodetritus, a significant pool of organic matter in the dark ocean.

Inorganic and Organic Carbon Uptake Processes and Their Connection to Microbial Diversity in Meso- and Bathypelagic Arctic Waters (Eastern Fram Strait)

The deep Arctic Ocean is increasingly vulnerable to climate change effects, yet our understanding of its microbial processes is limited. We collected samples from shelf waters, mesopelagic Atlantic Waters (AW) and bathypelagic Norwegian Sea Deep Waters (NSDW) in the eastern Fram Strait, along coast-to-offshore transects off Svalbard during boreal summer. We measured community respiration, heterotrophic carbon production (HCP), and dissolved inorganic carbon utilization (DICu) together with prokaryotic abundance, diversity, and metagenomic predictions. In deep samples, HCP was significantly faster in AW than in NSDW, while we observed no differences in DICu rates. Organic carbon uptake was higher than its inorganic counterpart, suggesting a major reliance of deep microbial Arctic communities on heterotrophic metabolism. Community structure and spatial distribution followed the hydrography of water masses. Distinct from other oceans, the most abundant OTU in our deep samples was represented by the archaeal MG-II. To address the potential biogeochemical role of each water mass-specific microbial community, as well as their link with the measured rates, PICRUSt-based predicted metagenomes were built. The results showed that pathways of auto- and heterotrophic carbon utilization differed between the deep water masses, although this was not reflected in measured DICu rates. Our findings provide new insights to understand microbial processes and diversity in the dark Arctic Ocean and to progress toward a better comprehension of the biogeochemical cycles and their trends in light of climate changes.