Relationships between Biovolume and Biomass of Naturally Derived Marine Bacterioplankton

Unveiling Short-Scale Responses: How Pico- and Nanoeukaryotic Plankton Navigate Environmental Variability in a Coastal Upwelling System

For decades, identifying pico- and nanoeukaryotic plankton has been challenging due to their small size, leaving a significant gap in our knowledge of their composition and dynamics in comparison with their larger counterparts. The advent of molecular techniques unlocked new possibilities for exploring this hidden diversity. We applied metabarcoding targeting the V9 region of 18S rDNA to discern the principal taxonomic groups of pico- and nanoeukaryotes in the Ría de Vigo during the upwelling season. Nanoeukaryotes (NE) exhibit greater diversity compared to picoeukaryotes (PE). Specifically, NE were mainly comprised of nano-sized diatoms and dinoflagellates, many of them uncategorized novel species. Within PE, Syndiniales and Marine Stramenopiles (MAST) were the main components identified. We also captured short-term changes in the biomass and composition of PE an NE, with advection emerging as one of the most significant drivers. Most notably was the ocean inflow of unassigned picoeukaryotes into the Ría, likely driven by the negative circulation during downwelling. Moreover, local grazing within the Ría seems to be important enough to alter NE dynamics, but has a minimal effect over PE. Our findings improve the understanding of the small eukaryotic plankton community in coastal upwelling systems, highlighting a significant potential for novel diversity within these environments.

Particle-associated N2 fixation by heterotrophic bacteria in the global ocean

N2-fixing microorganisms (diazotrophs) sustain life on our planet by providing biologically available nitrogen to plants. In the oceans, cyanobacterial diazotrophs, mostly prevalent in warm tropical and subtropical waters, were traditionally considered the sole contributors to marine N2 fixation. Recently, an almost ubiquitous distribution of N2-fixing heterotrophic bacteria has been discovered in the pelagic ocean. However, the mechanisms enabling heterotrophic diazotrophs to thrive in cold high-latitude waters and their contribution to the global nitrogen budget are unknown. Using a data-driven cell-based metabolic model, we show that heterotrophic bacteria inside sinking particles can fix N2 over a wide range of temperatures, explaining their ubiquitous presence in the oceans. We estimate that heterotrophic diazotrophs account for about 10% of global marine N2 fixation, with the highest contribution in oxygen minimum zones. These findings call for a reassessment of the N2 fixation patterns and the biogeochemical cycling of nitrogen in the global ocean.

A dataset on environmental DNA, bacterio-, phyto- and zooplankton from an emerging periglacial lagoon in Svalbard, Arctic

Over the last few decades, climate change in Svalbard (European Arctic) has led to the emergence and growth of periglacial coastal lagoons in the place of retreating glaciers. In these emerging water bodies, new ecosystems are formed, consisting of elements presumably entering the lagoon from the melting glacier, the surrounding tundra water bodies and the coastal ocean. The data presented here were collected from an emerging lagoon in the western region of Spitsbergen, Svalbard, situated between the retreating Eidembreen Glacier and Eidembukta Bay in 2022-2023. The current size of the lagoon area is approximately 6 square kilometers. The sampling was carried out at 26 sites across various sections of the lagoon, spanning from close proximity to the glacier to the furthest point away. The dataset contains the results of bacterioplankton (total cell concentration and carbon biomass), phytoplankton (taxonomic composition, cell size for selected taxa, abundance, biomass and carbon biomass), zooplankton (taxonomic composition, abundance), and environmental DNA (eDNA) metabarcoding. The dataset will be utilized to provide a comprehensive description of the structure of the lagoon ecosystem. It will also facilitate a comparison of its various parts, which vary in terms of their age of origin, i.e., release from the glacier. Additionally, the dataset will aid in the understanding of the intricate interactions between the freshwater and marine elements of the ecosystem. It can be used for comparative analysis of biodiversity assessment using eDNA and traditional microscopy methods in the identification of phyto- and zooplankton. Furthermore, these data can be utilized for environmental monitoring, tracing the temporal shifts and conducting comparative analysis of periglacial lagoons that are emerging in various regions of Svalbard as a result of climate change.

Uneven response of phytoplankton-bacteria coupling under Saharan dust pulse and ultraviolet radiation in the south-western Mediterranean Sea

The microbial carbon (C) flux in the ocean is a key functional process governed by the excretion of organic carbon by phytoplankton (EOC) and heterotrophic bacterial carbon demand (BCD). Ultraviolet radiation (UVR) levels in upper mixed layers and increasing atmospheric dust deposition from arid regions may alter the degree of coupling in the phytoplankton-bacteria relationship (measured as BCD:EOC ratio) with consequences for the C-flux through these compartments in marine oligotrophic ecosystem. Firstly, we performed a field study across the south-western (SW) Mediterranean Sea to assess the degree of coupling (BCD:EOC) and how it may be related to metabolic balance (total primary production: community respiration; PPT:CR). Secondly, we conducted a microcosm experiment in two contrasting areas (heterotrophic nearshore and autotrophic open sea) to test the impact of UVR and dust interaction on microbial C flux. In the field study, we found that BCD was not satisfied by EOC (i.e., BCD:EOC >1; uncoupled phytoplankton-bacteria relationship). BCD:EOC ratio was negatively related to PPT:CR ratio across the SW Mediterranean Sea. A spatial pattern emerged, i.e. in autotrophic open sea stations uncoupling was less severe (BCD:EOC ranged 1-2), whereas heterotrophic nearshore stations uncoupling was more severe (BCD:EOC > 2). In the experimental study, in the seawater both enriched with dust and under UVR, BCD:EOC ratio decreased by stimulating autotrophic processes (particulate primary production (PPP) and EOC) in the heterotrophic nearshore area, whereas BCD:EOC increased by stimulating heterotrophic processes [heterotrophic bacterial production (HBP), bacterial growth efficiency (BGE), bacterial respiration (BR)] in the autotrophic open sea. Our results show that this spatial pattern could be reversed under future UVR × Dust scenario. Overall, the impact of greater dust deposition and higher UVR levels will alter the phytoplankton-bacteria C-flux with consequences for the productivity of both communities, their standing stocks, and ultimately, the ecosystem's metabolic balance at the sea surface.

3D intrusions transport active surface microbial assemblages to the dark ocean

Subtropical oceans contribute significantly to global primary production, but the fate of the picophytoplankton that dominate in these low-nutrient regions is poorly understood. Working in the subtropical Mediterranean, we demonstrate that subduction of water at ocean fronts generates 3D intrusions with uncharacteristically high carbon, chlorophyll, and oxygen that extend below the sunlit photic zone into the dark ocean. These contain fresh picophytoplankton assemblages that resemble the photic-zone regions where the water originated. Intrusions propagate depth-dependent seasonal variations in microbial assemblages into the ocean interior. Strikingly, the intrusions included dominant biomass contributions from nonphotosynthetic bacteria and enrichment of enigmatic heterotrophic bacterial lineages. Thus, the intrusions not only deliver material that differs in composition and nutritional character from sinking detrital particles, but also drive shifts in bacterial community composition, organic matter processing, and interactions between surface and deep communities. Modeling efforts paired with global observations demonstrate that subduction can flux similar magnitudes of particulate organic carbon as sinking export, but is not accounted for in current export estimates and carbon cycle models. Intrusions formed by subduction are a particularly important mechanism for enhancing connectivity between surface and upper mesopelagic ecosystems in stratified subtropical ocean environments that are expanding due to the warming climate.

Coupling of cylindrospermopsin and pho-harboring Verrucomicrobia supports the formation of Raphidiopsis blooms in low-phosphorus waters

Cylindrospermopsin (CYN) can induce phytoplankton community to secrete alkaline phosphatase (ALP), which is one of the important strategies for the bloom-forming cyanobacterium Raphidiopsis to thrive in extremely low-phosphorus (P) waters. However, how bacterioplankton community, another major contributor to ALPs in waters, couples to Raphidiopsis through CYN, and the role of this coupling in supporting the dominance of Raphidiopsis in nature remain largely unknown. Here, we conducted microcosm experiments to address this knowledge gap, using a combination of differential filtration-based and metagenomics-based methods to identify the sources of ALPs. We found that, compared with algal-derived ALPs, bacteria-derived ALPs exhibited a more pronounced and sensitive response to CYN. This response to CYN was enhanced under low-P conditions. Interestingly, we found that Verrucomicrobia made the largest contribution to the total abundance of pho genes, which encode ALPs. Having high gene abundance of the CYN-sensing PI3K-AKT signaling pathway, Verrucomicrobia's proportion increased with higher concentrations of CYN under low-P conditions, thereby explaining the observed increase in pho gene abundance. Compared with other cyanobacterial genera, Raphidiopsis had a higher abundance of the pst gene. This suggests that Raphidiopsis exhibited a greater capacity to uptake the inorganic P generated by ALPs secreted by other organisms. Overall, our results reveal the mechanism of CYN-induced ALP secretion and its impact on planktonic P-cycling, and provide valuable insights into the role of CYN in supporting the formation of Raphidiopsis blooms.

Composition and vertical distribution of organic matter in Central Indian Ocean sediment cores

This study aimed to investigate the quality and quantity of organic matter (OM) using biochemical components (protein, carbohydrate and lipids) in the sediment cores collected from the Central Indian Ocean (CIOB) under the program Equatorial Indian Ocean Process Study Dynamics and Biogeochemistry (EIOPS). Total organic carbon (TOC) and biochemical parameters (carbohydrate, lipid, protein, Tannin and lignin) were determined in core I and core II, respectively. Total carbohydrates varied from 4.66 to 2557.32 mg/kg (average 459.31 mg/kg) and 142.23 to 821.56 mg/kg (average 380.01 mg/kg) in core I and II, respectively. In core I, PRT varied from 70.95 to 107.05 mg/kg, and the minimum and maximum content of CHO was 143.23 and 822.56 mg/kg. The maximum and minimum concentrations of BPC in core II were 786.32 and 381.07 at 0-10 cm depth, respectively, which corresponded to the concentrations of PRT, CHO, LPD, and Tannin. The results showed that PRT was statistically significant with the TOC and negatively correlated with the LPD and CHO, while LPD was highly significant with clay and silt grains. In most of the samples, the ratio of LPD to CHO ratio was > 1, which indicated higher productivity of benthic organisms inhabiting the CIOB.

New chemical and microbial perspectives on vitamin B1 and vitamer dynamics of a coastal system

Vitamin B1 (thiamin, B1) is an essential micronutrient for cells, yet intriguingly in aquatic systems most bacterioplankton are unable to synthesize it de novo (auxotrophy), requiring an exogenous source. Cycling of this valuable metabolite in aquatic systems has not been fully investigated and vitamers (B1-related compounds) have only begun to be measured and incorporated into the B1 cycle. Here, we identify potential key producers and consumers of B1 and gain new insights into the dynamics of B1 cycling through measurements of B1 and vitamers (HMP: 4-amino-5-hydroxymethyl-2-methylpyrimidine, HET: 4-methyl-5-thiazoleethanol, FAMP: N-formyl-4-amino-5-aminomethyl-2-methylpyrimidine) in the particulate and dissolved pool in a temperate coastal system. Dissolved B1 was not the primary limiting nutrient for bacterial production and was relatively stable across seasons with concentrations ranging from 74-117 pM, indicating a balance of supply and demand. However, vitamer concentration changed markedly with season as did transcripts related to vitamer salvage and transport suggesting use of vitamers by certain bacterioplankton, e.g. Pelagibacterales. Genomic and transcriptomic analyses showed that up to 78% of the bacterioplankton taxa were B1 auxotrophs. Notably, de novo B1 production was restricted to a few abundant bacterioplankton (e.g. Vulcanococcus, BACL14 (Burkholderiales), Verrucomicrobiales) across seasons. In summer, abundant picocyanobacteria were important putative B1 sources, based on transcriptional activity, leading to an increase in the B1 pool. Our results provide a new dynamic view of the players and processes involved in B1 cycling over time in coastal waters, and identify specific priority populations and processes for future study.

Suboxic DOM is bioavailable to surface prokaryotes in a simulated overturn of an oxygen minimum zone, Devil's Hole, Bermuda

Oxygen minimum zones (OMZs) are expanding due to increased sea surface temperatures, subsequent increased oxygen demand through respiration, reduced oxygen solubility, and thermal stratification driven in part by anthropogenic climate change. Devil's Hole, Bermuda is a model ecosystem to study OMZ microbial biogeochemistry because the formation and subsequent overturn of the suboxic zone occur annually. During thermally driven stratification, suboxic conditions develop, with organic matter and nutrients accumulating at depth. In this study, the bioavailability of the accumulated dissolved organic carbon (DOC) and the microbial community response to reoxygenation of suboxic waters was assessed using a simulated overturn experiment. The surface inoculated prokaryotic community responded to the deep (formerly suboxic) 0.2 μm filtrate with cell densities increasing 2.5-fold over 6 days while removing 5 μmol L-1 of DOC. After 12 days, the surface community began to shift, and DOC quality became less diagenetically altered along with an increase in SAR202, a Chloroflexi that can degrade recalcitrant dissolved organic matter (DOM). Labile DOC production after 12 days coincided with an increase of Nitrosopumilales, a chemoautotrophic ammonia oxidizing archaea (AOA) that converts ammonia to nitrite based on the ammonia monooxygenase (amoA) gene copy number and nutrient data. In comparison, the inoculation of the deep anaerobic prokaryotic community into surface 0.2 μm filtrate demonstrated a die-off of 25.5% of the initial inoculum community followed by a 1.5-fold increase in cell densities over 6 days. Within 2 days, the prokaryotic community shifted from a Chlorobiales dominated assemblage to a surface-like heterotrophic community devoid of Chlorobiales. The DOM quality changed to less diagenetically altered material and coincided with an increase in the ribulose-1,5-bisphosphate carboxylase/oxygenase form I (cbbL) gene number followed by an influx of labile DOM. Upon reoxygenation, the deep DOM that accumulated under suboxic conditions is bioavailable to surface prokaryotes that utilize the accumulated DOC initially before switching to a community that can both produce labile DOM via chemoautotrophy and degrade the more recalcitrant DOM.

New Insights for the Renewed Phytoplankton-Bacteria Coupling Concept: the Role of the Trophic Web

It is widely accepted that in many aquatic ecosystems bacterioplankton is dependent on and regulated by organic carbon supplied by phytoplankton, leading to coupled algae-bacteria relationship. In this study, an in-depth analysis of this relationship has been carried out by combining two approaches: (i) a correlation analyses between heterotrophic bacterial production (BP) vs. primary production (PP) or algal excretion of organic carbon (EOC), (ii) the balance between bacterial carbon demands (BCD) and the supply of C as EOC, measured as BCD:EOC ratio. During the study period (2013-2016), the algae-bacteria relationship was constantly changing from a coupling in 2013, uncoupling in 2014 and 2015, and an incipient return to coupling (in 2016). Our results show that top-down control (bacterivory) by algal mixotrophy acts as a decoupling force since it provides a fresh C source different to algal EOC to satisfy bacterial carbon demands. Notably, a relationship between the BCD:EOC ratio and the ecosystem metabolic balance (Primary production (PP): respiration (R)) was found, suggesting that PP:R may be a good predictor of the algae-bacteria coupling. This analysis, including the comparison between basal and potential ecosystem metabolic balance, can be a tool to improve knowledge on the interaction between both biotics compartments, which the traditional analyses on coupling may not capture.

Multiyear analysis uncovers coordinated seasonality in stocks and composition of the planktonic food web in the Baltic Sea proper

The planktonic realm from bacteria to zooplankton provides the baseline for pelagic aquatic food webs. However, multiple trophic levels are seldomly included in time series studies, hampering a holistic understanding of the influence of seasonal dynamics and species interactions on food web structure and biogeochemical cycles. Here, we investigated plankton community composition, focusing on bacterio-, phyto- and large mesozooplankton, and how biotic and abiotic factors correlate at the Linnaeus Microbial Observatory (LMO) station in the Baltic Sea from 2011 to 2018. Plankton communities structures showed pronounced dynamic shifts with recurring patterns. Summarizing the parts of the planktonic microbial food web studied here to total carbon, a picture emerges with phytoplankton consistently contributing > 39% while bacterio- and large mesozooplankton contributed ~ 30% and ~ 7%, respectively, during summer. Cyanophyceae, Actinobacteria, Bacteroidetes, and Proteobacteria were important groups among the prokaryotes. Importantly, Dinophyceae, and not Bacillariophyceae, dominated the autotrophic spring bloom whereas Litostomatea (ciliates) and Appendicularia contributed significantly to the consumer entities together with the more traditionally observed mesozooplankton, Copepoda and Cladocera. Our findings of seasonality in both plankton composition and carbon stocks emphasize the importance of time series analyses of food web structure for characterizing the regulation of biogeochemical cycles and appropriately constraining ecosystem models.

On the hidden diversity and niche specialization of the microbial realm of subterranean estuaries

Subterranean estuaries (STEs) modulate the chemical composition of continental groundwater before it reaches the coast, but their microbial community is poorly known. Here, we explored the microbial ecology of two neighbouring, yet contrasting STEs (Panxón and Ladeira STEs; Ría de Vigo, NW Iberian Peninsula). We investigated microbial composition (16S rRNA gene sequencing), abundance, heterotrophic production and their geochemical drivers. A total of 10,150 OTUs and 59 phyla were retrieved from porewater sampled during four surveys covering each STE seepage face. In both STEs, we find a very diverse microbial community composed by abundant cosmopolitans and locally restricted rare taxa. Porewater oxygen and dissolved organic matter are the main environmental predictors of microbial community composition. More importantly, the high variety of benthic microbiota links to biogeochemical processes of different elements in STEs. The oxygen-rich Panxón beach showed strong associations of the ammonium oxidizing archaea Nitrosopumilales with the heterotrophic community, thus acting as a net source of nitrogen to the coast. On the other hand, the prevailing anoxic conditions of Ladeira beach promoted the dominance of anaerobic heterotrophs related to the degradation of complex and aromatic compounds, such as Dehalococcoidia and Desulfatiglans, and the co-occurrence of methane oxidizers and methanogens.

Ecological dynamics and impacts of viruses in Chinese and global estuaries

Estuaries are important ecosystems providing irreplaceable services for humankind and, in turn, are extensively influenced by human activities and climate changes. Microbial processes, which are largely controlled by viruses, are always responsible for the ecological function and environmental problems in estuaries. However, we know little about the ecology and importance of viruses in estuarine systems. Here, we investigated viral ecological dynamics in estuarine systems on local (four largest estuaries in China in different seasons) and global scales. Viral production varied by almost 20-fold in Chinese estuaries with significant seasonality, being responsible for the removal of 1.41%-21.45% of the bacterioplankton standing stock each day, and contributed directly to the organic carbon pool by releasing an average of 3.57 µg of cellular carbon per liter per day. By compiling data from 21 estuaries across the world, we found for the first time that viral population size peaked at mid-latitude and viral production increased towards the equator in estuarine ecosystems. The results indicated the higher viral impact on microbial mortality and dissolved organic matter cycling in tropical estuaries. Our field investigation and global synthesized analysis provide compelling evidence of spatiotemporal variations in estuarine viral dynamics. The global view of viral impacts on estuarine microbial mortality offers important insight for incorporating viruses into ecological models and understanding the environmental implications of the tropicalization of temperate aquatic ecosystems under a scenario of climate warming.

Plankton Community Respiration and Particulate Organic Carbon in the Kuroshio East of Taiwan

Biological organic carbon production and consumption play a fundamental role in the understanding of organic carbon cycling in oceans. However, studies on them in the Kuroshio, the western boundary current in the North Pacific Ocean, are scarce. To better understand the variations of plankton community respiration (CR) and particulate organic carbon (POC), eight cruises. which covered four seasons over a 2-year period, were surveyed across the Kuroshio at the KTV1 transect east of Taiwan. Spatially, a coastal uplift of isotherms (i.e., onshore lifting and offshore deepening) was observed along the KTV1 transect. During the uplift, the cold and nutrient-rich deep waters shoal to shallow water and enhance phytoplankton growth, resulting in higher values of phytoplankton, POC, and plankton CR on the onshore side. In this study, phytoplankton was dominated by picophytoplankton including Prochlorococcus, Synechococcus, and picoeukaryotes. Plankton CR was low, and its mean depth-normalized integrated rate (the upper 100 m water depth) ranged from 7.07 to 22.27 mg C m^-3 d^-1, to which the picophytoplankton and heterotrophic bacteria contributed the most. The mean depth-normalized integrated value of POC ranged from 12.7 to 21.6 μg C L^-1. POC is mainly associated with phytoplankton biomass with a mean carbon ratio of chlorophyll a/POC ≈ 1.03. All results suggest that plankton CR and POC variations may be associated with picoplankton dynamics in the Kuroshio.

Dam-induced flow velocity decrease leads to the transition from heterotrophic to autotrophic system through modifying microbial food web dynamics

The impoundment of reservoirs changes the river from a riverine heterotrophic system to a lacustrine autotrophic system, which could be attributed to the shift of pelagic microbial food webs in response to the dam-induced disturbances. However, little is known about what is the key factor controlling this variation and how different underlying interactions affect the food web dynamics. This study investigated the effects of flow velocity and nutrient supply on microbial plankton using a microcosm experiment. The results showed that flow velocity decrease was the main factor inducing the detritus-based food web transformed to the autotroph-based food web, with heterotrophic bacteria and protozoan dominated at high velocity, whereas phytoplankton and metazoan were prevalent in the lentic environment. The lentic-acclimated genera, such as Chlorella sp., Mallomonas sp. and Microcystis sp., showed hysteresis after the velocity recovery, suggesting the potential of algae bloom in reservoirs and even downstream of dams. We further conducted a flow-velocity manipulating experiment and constructed a multi-trophic nitrogen cycling model to provide a mechanistic explanation for the microbial food web dynamics and the nitrogen transformation performances. As indicated in model prediction and sensitivity analysis, the abiotic and biotic variations were directly or indirectly controlled by nutrient utilization and predator-prey interactions. Quantification of these bottom-up and top-down forces revealed the buffer role of predators in mitigating the positive effects of nutrient availability on autotrophs at low velocity and on heterotrophs at high velocity, respectively. This study highlights the importance of mastering the whole information of different trophic levels, in order to better capture the complex microbial food web interactions and the consequent biogeochemical processes in river-reservoir systems.

Inputs of Terrestrial Dissolved Organic Matter Enhance Bacterial Production and Methylmercury Formation in Oxic Coastal Water

Methylmercury (MeHg) is a potent neurotoxin commonly found in aquatic environments and primarily formed by microbial methylation of inorganic divalent mercury (Hg(II)) under anoxic conditions. Recent evidence, however, points to the production of MeHg also in oxic pelagic waters, but the magnitude and the drivers for this process remain unclear. Here, we performed a controlled experiment testing the hypothesis that inputs of terrestrial dissolved organic matter (tDOM) to coastal waters enhance MeHg formation via increased bacterial activity. Natural brackish seawater from a coastal area of the Baltic Sea was exposed to environmentally relevant levels of Hg(II) and additions of tDOM according to climate change scenarios. MeHg formation was observed to be coupled to elevated bacterial production rates, which, in turn, was linked to input levels of tDOM. The increased MeHg formation was, however, not coupled to any specific change in bacterial taxonomic composition nor to an increased abundance of known Hg(II) methylation genes. Instead, we found that the abundance of genes for the overall bacterial carbon metabolism was higher under increased tDOM additions. The findings of this study may have important ecological implications in a changing global climate by pointing to the risk of increased exposure of MeHg to pelagic biota.

Polycyclic Aromatic Hydrocarbon Degradation in the Sea-Surface Microlayer at Coastal Antarctica

As much as 400 Tg of carbon from airborne semivolatile aromatic hydrocarbons is deposited to the oceans every year, the largest identified source of anthropogenic organic carbon to the ocean. Microbial degradation is a key sink of these pollutants in surface waters, but has received little attention in polar environments. We have challenged Antarctic microbial communities from the sea-surface microlayer (SML) and the subsurface layer (SSL) with polycyclic aromatic hydrocarbons (PAHs) at environmentally relevant concentrations. PAH degradation rates and the microbial responses at both taxonomical and functional levels were assessed. Evidence for faster removal rates was observed in the SML, with rates 2.6-fold higher than in the SSL. In the SML, the highest removal rates were observed for the more hydrophobic and particle-bound PAHs. After 24 h of PAHs exposure, particle-associated bacteria in the SML showed the highest number of significant changes in their composition. These included significant enrichments of several hydrocarbonoclastic bacteria, especially the fast-growing genera Pseudoalteromonas, which increased their relative abundances by eightfold. Simultaneous metatranscriptomic analysis showed that the free-living fraction of SML was the most active fraction, especially for members of the order Alteromonadales, which includes Pseudoalteromonas. Their key role in PAHs biodegradation in polar environments should be elucidated in further studies. This study highlights the relevant role of bacterial populations inhabiting the sea-surface microlayer, especially the particle-associated habitat, as relevant bioreactors for the removal of aromatic hydrocarbons in the oceans.

Pelagic Bacteria and Viruses in a High Arctic Region: Environmental Control in the Autumn Period

In the marine environment, bacteria and viruses play a significant role in carbon fluxes, remineralization processes, and the infection of various organisms. We performed a survey in the northeastern Barents Sea, a region adjacent to the Arctic Ocean, to investigate spatial patterns of microbial plankton, after the main productive period, in October 2020. Two main water masses occurred in the study region—colder Arctic Water and warmer Barents Sea Water, representing transformed Atlantic Water. Multivariate analyses detected patchiness in the horizontal distribution of bacteria and viruses, and their abundances showed no clear association with the water masses. There was an obvious vertical pattern in microbial concentration, with the highest estimates in the upper layers. Surface viral and bacterial abundance varied in a wide range (2.20 × 105−10.7 × 105 cells·mL−1 and 0.86 × 106−14.98 × 106 particles·mL−1, respectively) and were correlated with each other. Bacterioplankton was dominated by small-sized cells (<2 μm, 0.04−0.06 µm3), and the average volume of bacterial cells tended to increase toward the seafloor. The ratio of viral to bacterial abundance (VBR) was 11 ± 1 and did not differ between water masses and depth layers. VBR were higher, compared to summer values, suggesting a strong impact of viruses on bacterioplankton, after the main productive season. Redundancy and correlation analyses showed that inorganic nutrients (nitrate and phosphate) and organic carbon from zooplankton were most responsible for the total variability in the microbial parameters. Water temperature and salinity, also, had a measurable impact, but their influence was lower. Bacterial abundance was lower than in other seasons and regions of the Barents Sea, while viral abundance was comparable, suggesting a stronger viral impact on Arctic marine bacteria in the autumn season.

Linking Microbial Population Succession and DOM Molecular Changes in Synechococcus-Derived Organic Matter Addition Incubation

The molecular-level interactions between phytoplankton-derived dissolved organic matter (DOM) and heterotrophic prokaryotes represent a fundamental and yet poorly understood component of the marine elemental cycle. Here, we investigated the degradation of Synechococcus-derived organic matter (SynOM) by coastal microorganisms using spectroscopic and ultrahigh-resolution mass spectrometry analyses coupled with high-throughput sequencing. The added SynOM showed a spectrum of reactivity during a 180-day dark incubation experiment. Along with the decrease in DOM bioavailability, the chemical properties of DOM molecules overall showed increases in oxidation state and aromaticity. Both the microbial community and DOM molecular compositions became more homogeneous toward the end of the incubation. The experiment was partitioned into three phases (I, II, and III) based on the total organic carbon consumption rates from 7.0 ± 1.0 to 1.0 ± 0.1 and to 0.1 ± 0.0 μmol C L-1 day-1, respectively. Diverse generalists with low abundance were present in all three phases of the experiment, while a few abundant specialists dominated specific phases, suggesting their diverse roles in the transformation of DOM molecules from labile and semilabile to recalcitrant. The changes of organic molecules belonging to CHO, CHNO, and CHOS containing formulas were closely associated with specific microbial populations, suggesting close interactions between the different bacterial metabolic potential for substrates and DOM molecular compositional characteristics. This study sheds light on the interactions between microbial population succession and DOM molecular changes processes and collectively advances our understanding of microbial processing of the marine elemental cycle. IMPORTANCE Phytoplankton are a major contributor of labile dissolved organic matter (DOM) in the upper ocean, fueling tremendous marine prokaryotic activity. Interactions between microorganisms and algae-derived DOM regulate biogeochemical cycles in the ocean, but key aspects of their interactions remain poorly understood. Under global warming and eutrophication scenarios, Synechococcus blooms are commonly observed in coastal seawaters, and they significantly influence the elemental biogeochemistry cycling in eutrophic ecosystems. To understand the interactions between Synechococcus-derived DOM and heterotrophic prokaryotes as well as their influence on the coastal environment, we investigated the degradation of DOM by coastal microbes during a 180-day dark incubation. We showed substantial DOM compositional changes that were closely linked to the developments of microbial specialists and generalists. Our study provides information on the interactions between microbial population succession and DOM molecular changes, thereby advancing our understanding of microbial processing of the marine DOM pool under the influence of climate change.

The ProkaBioDen database, a global database of benthic prokaryotic biomasses and densities in the marine realm

Benthic prokaryotes include Bacteria and Archaea and dominate densities of marine benthos. They play major roles in element cycles and heterotrophic, chemoautotrophic, and phototrophic carbon production. To understand how anthropogenic disturbances and climate change might affect these processes, better estimates of prokaryotic biomasses and densities are required. Hence, I developed the ProkaBioDen database, the largest open-access database of benthic prokaryotic biomasses and densities in marine surface sediments. In total, the database comprises 1,089 georeferenced benthic prokaryotic biomass and 1,875 density records extracted from 85 and 112 studies, respectively. I identified all references applying the procedures for systematic reviews and meta analyses and report prokaryotic biomasses as g C cm⁻³ sediment, g C g⁻¹ sediment, and g C m⁻². Density records are presented as cell cm⁻³ sediment, cell g⁻¹ sediment/ sulfide/ vent precipitate, and cell m⁻². This database should serve as reference to close sampling gaps in the future.

Measurement(s)	prokaryotic benthic biomass • prokaryotic benthic density
Technology Type(s)	PLFA • microscopy • ATP
Sample Characteristic - Organism	unclassified Bacteria
Sample Characteristic - Environment	marine sediment • deep marine sediment • shallow marine sediment
Sample Characteristic - Location	Pacific Ocean • Atlantic Ocean • Indian Ocean • Southern Ocean • Arctic Ocean

Quantification of Biologically and Chemically Bound Phosphorus in Activated Sludge from Full-Scale Plants with Biological P-Removal

Phosphorus (P) is present in activated sludge from wastewater treatment plants in the form of metal salt precipitates, extracellular polymeric substances, or bound into the biomass, for example, as intracellular polyphosphate (poly-P). Several methods for a reliable quantification of the different P-fractions have recently been developed, and this study combines them to obtain a comprehensive P mass-balance of activated sludge from four enhanced biological phosphate removal (EBPR) plants. Chemical characterization by ICP-OES and sequential P fractionation showed that chemically bound P constituted 38-69% of total P, most likely in the form of Fe, Mg, or Al minerals. Raman microspectroscopy, solution state ³¹P NMR, and ³¹P MAS NMR spectroscopy applied before and after anaerobic P-release experiments, were used to quantify poly-P, which constituted 22-54% of total P and was found in approximately 25% of all bacterial cells. Raman microspectroscopy in combination with fluorescence in situ hybridization was used to quantify poly-P in known polyphosphate-accumulating organisms (PAO) (Tetrasphaera, Candidatus Accumulibacter, and Dechloromonas) and other microorganisms known to possess high level of poly-P, such as the filamentous Ca. Microthrix. Interestingly, only 1-13% of total P was stored by unidentified PAO, highlighting that most PAOs in the full-scale EBPR plants investigated are known.

The "Regulator" Function of Viruses on Ecosystem Carbon Cycling in the Anthropocene

Viruses act as "regulators" of the global carbon cycle because they impact the material cycles and energy flows of food webs and the microbial loop. The average contribution of viruses to the Earth ecosystem carbon cycle is 8.6‰, of which its contribution to marine ecosystems (1.4‰) is less than its contribution to terrestrial (6.7‰) and freshwater (17.8‰) ecosystems. Over the past 2,000 years, anthropogenic activities and climate change have gradually altered the regulatory role of viruses in ecosystem carbon cycling processes. This has been particularly conspicuous over the past 200 years due to rapid industrialization and attendant population growth. The progressive acceleration of the spread and reproduction of viruses may subsequently accelerate the global C cycle.

Microbial plankton responses to multiple environmental drivers in marine ecosystems with different phosphorus limitation degrees

Multiple drivers are threatening the functioning of the microbial food webs and trophic interactions. Our understanding about how temperature, CO₂, nutrient inputs, and solar ultraviolet radiation (UVR) availability interact to alter ecosystem functioning is scarce because research has focused on single and double interactions. Moreover, the role that the degree of in situ nutrient limitation could play in the outcome of these interactions has been largely neglected, despite it is predominant in marine ecosystems. We address these uncertainties by combining remote-sensing analyses, and a collapsed experimental design with natural microbial communities from Mediterranean Sea and Atlantic Ocean exposed to temperature, nutrients, CO₂, and UVR interactions. At the decade scale, we found that more intense and frequent (and longer lasting) Saharan dust inputs (and marine heatwaves) were only coupled with reduced phytoplankton biomass production. When microbial communities were concurrently exposed to future temperature, CO₂, nutrient, and UVR conditions (i.e. the drivers studied over long-term scales), we found shifts from net autotrophy [primary production:respiration (PP:R) ratio > 1] towards a metabolic equilibrium (PP:R ratio ~ 1) or even a net heterotrophy (PP:R ratio < 1), as P-limitation degree was higher (i.e. Atlantic Ocean). These changes in the metabolic balance were coupled with a weakened phytoplankton-bacteria interaction (i.e. bacterial carbon demand exceeded phytoplankton carbon supply. Our work reveals that an accentuated in situ P limitation may promote reductions both in carbon uptake and fluxes between trophic levels in microbial plankton communities under global-change conditions. We show that considering long-term series can aid in identifying major local environmental drivers (i.e. temperature and nutrients in our case), easing the design of future global-change studies, but also that the abiotic environment to which microbial plankton communities are acclimated should be taken into account to avoid biased predictions concerning the effects of multiple interacting global-change drivers on marine ecosystems.

Mucospheres produced by a mixotrophic protist impact ocean carbon cycling

Mixotrophic protists (unicellular eukaryotes) that engage in both phototrophy (photosynthesis) and phago-heterotrophy (engulfment of particles)—are predicted to contribute substantially to energy fluxes and marine biogeochemical cycles. However, their impact remains largely unquantified. Here we describe the sophisticated foraging strategy of a widespread mixotrophic dinoflagellate, involving the production of carbon-rich ‘mucospheres’ that attract, capture, and immobilise microbial prey facilitating their consumption. We provide a detailed characterisation of this previously undescribed behaviour and reveal that it represents an overlooked, yet quantitatively significant mechanism for oceanic carbon fluxes. Following feeding, the mucospheres laden with surplus prey are discarded and sink, contributing an estimated 0.17–1.24 mg m−2 d−1 of particulate organic carbon, or 0.02–0.15 Gt to the biological pump annually, which represents 0.1–0.7% of the estimated total export from the euphotic zone. These findings demonstrate how the complex foraging behaviour of a single species of mixotrophic protist can disproportionally contribute to the vertical flux of carbon in the ocean.

An integrated multiple driver mesocosm experiment reveals the effect of global change on planktonic food web structure

Global change puts coastal marine systems under pressure, affecting community structure and functioning. Here, we conducted a mesocosm experiment with an integrated multiple driver design to assess the impact of future global change scenarios on plankton, a key component of marine food webs. The experimental treatments were based on the RCP 6.0 and 8.5 scenarios developed by the IPCC, which were Extended (ERCP) to integrate the future predicted changing nutrient inputs into coastal waters. We show that simultaneous influence of warming, acidification, and increased N:P ratios alter plankton dynamics, favours smaller phytoplankton species, benefits microzooplankton, and impairs mesozooplankton. We observed that future environmental conditions may lead to the rise of Emiliania huxleyi and demise of Noctiluca scintillans, key species for coastal planktonic food webs. In this study, we identified a tipping point between ERCP 6.0 and ERCP 8.5 scenarios, beyond which alterations of food web structure and dynamics are substantial.

Implications of bacterial mineralisation in aquatic ecosystem response models

Widespread wastewater pollution is a major barrier to the sustainable management of freshwater and coastal marine ecosystems worldwide. Integrated multi-disciplinary studies are necessary to improve waterway management and protect ecosystem integrity. This study used the Generalised Likelihood Uncertainty Estimation (GLUE) methodology to link microbial community ecotoxicology laboratory data to a mechanistic aquatic ecosystem response model. The generic model provided good predictive skill for major water quality constituents, including heterotrophic bacteria dynamics (r2 = 0.91). The model was validated against observed data across a gradient of effluent concentrations from community whole effluent toxicity (WET) laboratory tests. GLUE analysis revealed that a combined likelihood measure increased confidence in the predictive capability of the model. This study highlights the importance of calibrating aquatic ecosystem response models with net growth rates (i.e., sum of the growth minus loss rate parameter terms) of biological functional groups. The final calibrated net growth rate value of heterotrophic bacteria determined using the GLUE analysis was selected to be 0.58, which was significantly greater than the average literature value of -0.15. This finding demonstrated that use of literature parameter values without a good understanding of the represented processes could create misleading outputs and result in unsatisfactory conclusions. Further, fixed bulk mineralisation rate literature values are typically higher than realistically required in aquatic ecosystem response models. This indicates that explicitly including bacterial mineralisation is crucial to represent microbial ecosystem functioning more accurately. Our study suggests that improved data collection and modelling efforts in real-world management applications are needed to better address nutrients released into the natural environment. Future studies should aim to better understand the sensitivity of aquatic ecosystem response models to bacterial mineralisation rates.

Contrasting land-uses in two small river basins impact the colored dissolved organic matter concentration and carbonate system along a river-coastal ocean continuum

Human activities have led to an increase in land use change, with effects on the structure and functioning of ecosystems. The impact of contrasting land uses along river basins on the concentration of colored dissolved organic matter (CDOM) reaching the coastal zone, and its relationship with the carbonate system of the adjacent coastal ocean, is poorly known. To understand the relationship between land use change, CDOM and its influence on the carbonate system, two watersheds with contrasting land uses in southern Chile were studied. The samples were collected at eight stations between river and adjacent coastal areas, during three sampling campaigns in the austral summer and spring. Chemical and biological samples were analyzed in the laboratory according to standard protocols. Landsat 8 satellite images of the study area were used for identification and supervised classification using remote sensing tools. The Yaldad River basin showed 82% of native forest and the Colu River basin around 38% of grassland (agriculture). Low total alkalinity (A_T) and Dissolved Inorganic Carbon (DIC), but high CDOM proportions were typically observed in freshwater. A higher CDOM and humic-like compounds concentration was observed along the river-coastal ocean continuum in the Yaldad basin, characterized by a predominance of native forests. In contrast, nutrient concentrations, A_T and DIC, were higher in the Colu area. Low CaCO₃ saturation state (Ω_Ar < 2) and even undersaturation conditions were observed at the coastal ocean at Yaldad. A strong negative correlation between A_T, DIC and Ω_Ar with CDOM/fDOM, suggested the influence of terrestrial material on the seawater carbon chemistry. Our results provide robust evidence that land uses in river basins can influence CDOM/fDOM proportion and its influence on the carbonate chemistry of the adjacent coastal, with potential implications for the shellfish farming activity in this region.

Bacterial Indicators Are Ubiquitous Members of Pelagic Microbiome in Anthropogenically Impacted Coastal Ecosystem

Coastal zones are exposed to various anthropogenic impacts, such as different types of wastewater pollution, e.g., treated wastewater discharges, leakage from sewage systems, and agricultural and urban runoff. These various inputs can introduce allochthonous organic matter and microbes, including pathogens, into the coastal marine environment. The presence of fecal bacterial indicators in the coastal environment is usually monitored using traditional culture-based methods that, however, fail to detect their uncultured representatives. We have conducted a year-around in situ survey of the pelagic microbiome of the dynamic coastal ecosystem, subjected to different anthropogenic pressures to depict the seasonal and spatial dynamics of traditional and alternative fecal bacterial indicators. To provide an insight into the environmental conditions under which bacterial indicators thrive, a suite of environmental factors and bacterial community dynamics were analyzed concurrently. Analyses of 16S rRNA amplicon sequences revealed that the coastal microbiome was primarily structured by seasonal changes regardless of the distance from the wastewater pollution sources. On the other hand, fecal bacterial indicators were not affected by seasons and accounted for up to 34% of the sequence proportion for a given sample. Even more so, traditional fecal indicator bacteria (Enterobacteriaceae) and alternative wastewater-associated bacteria (Lachnospiraceae, Ruminococcaceae, Arcobacteraceae, Pseudomonadaceae and Vibrionaceae) were part of the core coastal microbiome, i.e., present at all sampling stations. Microbial source tracking and Lagrangian particle tracking, which we employed to assess the potential pollution source, revealed the importance of riverine water as a vector for transmission of allochthonous microbes into the marine system. Further phylogenetic analysis showed that the Arcobacteraceae in our data set was affiliated with the pathogenic Arcobacter cryaerophilus, suggesting that a potential exposure risk for bacterial pathogens in anthropogenically impacted coastal zones remains. We emphasize that molecular analyses combined with statistical and oceanographic models may provide new insights for environmental health assessment and reveal the potential source and presence of microbial indicators, which are otherwise overlooked by a cultivation approach.

The Effect of Salmon Food-Derived DOM and Glacial Melting on Activity and Diversity of Free-Living Bacterioplankton in Chilean Patagonian Fjords

Fjord ecosystems cycle and export significant amounts of carbon and appear to be extremely sensitive to climate change and anthropogenic perturbations. To identify patterns of microbial responses to ongoing natural and human-derived changes in the fjords of Chilean Patagonia, we examined the effect of organic enrichment associated with salmon aquaculture and freshening produced by glacial melting on bacterial production (BP), extracellular enzymatic activity (EEA), and community diversity of free-living bacterioplankton. We assayed the effects of salmon food-derived dissolved organic matter (SF-DOM) and meltwaters through microcosm experiments containing waters from Puyuhuapi Fjord and the proglacial fjords of the Southern Patagonia Icefield, respectively. Rates of BP and EEA were 2 times higher in the presence of SF-DOM than in controls, whereas the addition of autochthonous organic matter derived from diatoms (D-DOM) resulted in rates of BP and EEA similar to those measured in the controls. The addition of SF-DOM also reduced species richness and abundance of a significant fraction of the representative taxa of bacterioplankton of Puyuhuapi Fjord. In the proglacial fjords, bacterioplankton diversity was reduced in areas more heavily influenced by meltwaters and was accompanied by moderate positive changes in BP and EEA. Our findings strongly suggest that SF-DOM is highly reactive, promoting enhanced rates of microbial activity while could be influencing the diversity of bacterioplankton communities in Patagonian fjords with a strong salmon farming activity. These findings challenge the traditional view of phytoplankton production as the primary source of labile DOM that fuels heterotrophic activity in coastal ecosystems impacted by anthropogenic organic enrichment. Given the intensive local production of salmon, we analyze the significance of this emerging source of rich "allochthonous" organic substrates for autotrophic/heterotrophic balance, carbon exportation, and hypoxia in Patagonian fjords. The effect of human DOM enrichment can be enhanced in proglacial fjords, where progressive glacial melting exerts additional selective pressure on bacterioplankton diversity.

All-In-One: Microbial Response to Natural and Anthropogenic Forcings in a Coastal Mediterranean Ecosystem, the Syracuse Bay (Ionian Sea, Italy)

Bacterial and phytoplankton communities are known to be in close relationships, but how natural and anthropogenic stressors can affect their dynamics is not fully understood. To study the response of microbial communities to environmental and human-induced perturbations, phytoplankton and bacterial communities were seasonally monitored in a Mediterranean coastal ecosystem, Syracuse Bay, where multiple conflicts co-exist. Quali-quantitative, seasonal surveys of the phytoplankton communities (diatoms, dinoflagellates and other taxa), the potential microbial enzymatic activity rates (leucine aminopeptidase, beta-glucosidase and alkaline phosphatase) and heterotrophic culturable bacterial abundance, together with the thermohaline structure and trophic status in terms of nutrient concentrations, phytoplankton biomass (as Chlorophyll-a), and total suspended and particulate organic matter, were carried out. The aim was to integrate microbial community dynamics in the context of the environmental characterization and disentangle microbial patterns related to natural changes from those driven by the anthropic impact on this ecosystem. In spite of the complex relationships between the habitat characteristics, microbial community abundance and metabolic potential, in Syracuse Bay, the availability of organic substrates differently originated by the local conditions appeared to drive the distribution and activity of microbial assemblage. A seasonal pattern of microbial abundances was observed, with the highest concentrations of phytoplankton in spring and low values in winter, whereas heterotrophic bacteria were more abundant during the autumn period. The autumn peaks of the rates of enzymatic activities suggested that not only phytoplankton-derived but also allochthonous organic polymers strongly stimulated microbial metabolism. Increased microbial response in terms of abundance and metabolic activities was detected especially at the sites directly affected by organic matter inputs related to agriculture or aquaculture activities. Nitrogen salts such as nitrate, rather than orthophosphate, were primary drivers of phytoplankton growth. This study also provides insights on the different seasonal scenarios of water quality in Syracuse Bay, which could be helpful for management plans of this Mediterranean coastal environment.

Effects of seawater scrubbing on a microplanktonic community during a summer-bloom in the Baltic Sea

The International Maritime Organization (IMO) has gradually applied stricter regulations on the maximum sulphur content permitted in marine fuels and from January 1, 2020, the global fuel sulphur limit was reduced from 3.5% to 0.5%. An attractive option for shipowners is to install exhaust gas cleaning systems, also known as scrubbers, and continue to use high sulphur fuel oil. In the scrubber, the exhausts are led through a fine spray of water, in which sulphur oxides are easily dissolved. The process results in large volumes of acidic discharge water, but while regulations are focused on sulphur oxides removal and acidification, other pollutants e.g. polycyclic aromatic hydrocarbons, metals and nitrogen oxides can be transferred from the exhausts to the washwater and discharged to the marine environment. The aim of the current study was to investigate how different treatments of scrubber discharge water (1, 3 and 10%) affect a natural Baltic Sea summer microplanktonic community. To resolve potential contribution of acidification from the total effect of the scrubber discharge water, "pH controls" were included where the pH of natural sea water was reduced to match the scrubber treatments. Biological effects (e.g. microplankton species composition, biovolume and primary productivity) and chemical parameters (e.g. pH and alkalinity) were monitored and analysed during 14 days of exposure. Significant effects were observed in the 3% scrubber treatment, with more than 20% increase in total biovolume of microplankton compared to the control group, and an even greater effect in the 10% scrubber treatment. Group-specific impacts were recorded where diatoms, flagellates incertae sedis, chlorophytes and ciliates increased in biovolume with increasing concentrations of scrubber water while no effect was recorded for cyanobacteria. In contrast, these effects was not observed in the "pH controls", a suggestion that other parameters/stressors in the scrubber water were responsible for the observed effects.

The global ocean size spectrum from bacteria to whales

It has long been hypothesized that aquatic biomass is evenly distributed among logarithmic body mass size classes. Although this community structure has been observed regionally, mostly among plankton groups, its generality has never been formally tested across all marine life over the global ocean, nor have the impacts of humans on it been globally assessed. Here, we bring together data at the global scale to test the hypothesis from bacteria to whales. We find that biomass within most order of magnitude size classes is indeed remarkably constant, near 1 gigatonne (Gt) wet weight (10¹⁵ g), but bacteria and large marine mammals are markedly above and below this value, respectively. Furthermore, human impacts appear to have significantly truncated the upper one-third of the spectrum. This dramatic alteration to what is possibly life’s largest-scale regularity underscores the global extent of human activities.

Spatio-temporal variation in number and production of neustonic and planktonic bacteria inhabiting polluted estuarine harbour channel

The aim of this paper was to determine the abundance and secondary production by bacteria inhabiting the surface microlayer and subsurface water in a specific water basin, i.e., polluted estuarine harbour channel. In a 3-year seasonal cycle, the total number of bacteria and their biomass were higher in the surface microlayer (SML) 7.57 × 108cells dm-3 and 15.86 µg C dm-3 than in the subsurface water (SSW) 4.25 × 108cells dm-3 and 9.11 µg C dm-3 of the studied channel. The opposite relationship was noted in the level of the secondary production (SML-37.16 μg C dm-3 h-1, SSW-60.26 μg C dm-3 h-1) in this water basin. According to the analysed microbiological parameters, the total number of bacteria and secondary production varied along the horizontal profile in the water of the studied channel. The total number of bacteria and their secondary production showed the seasonal variation as well.

Relationships of pelagic ciliates with the microbial food web components at a coastal station in the oligotrophic Eastern Mediterranean Sea: temporal and vertical variability

The annual/temporal and vertical dynamics of the microbial food web (MFW) was studied in a coastal station of the oligotrophic Eastern Mediterranean Sea. The present study analyzed the changes of all components of the MFW with a specific focus on the relationships between different size classes of heterotrophic and mixotrophic ciliates with their potential prey. The MFW was dominated by heterotrophic picoplankton in all months and depths analyzed, whereas autotrophic nanoplankton took advantage in cold months with higher nutrient availability. On the other hand, mixotrophic microplankton biomass was higher in summer when nutrients and chlorophyll-a were scarce. As part of the mixotrophic biomass, mixotrophic ciliates were correlated with their "potential" prey at the surface and deep chlorophyll maximum. Large mixotrophic ciliates (L. strobila) were more selective in terms of potential prey, showing a correlation with Synechococcus. On the other hand, mixotrophic nanociliates (Strombidium dalum) were correlated differently with different potential prey according to depth, supporting the idea that nanociliates could be more generalists in terms of prey selection. Because the relationships between mixotrophic ciliates and their potential prey are still poorly studied, this work represents the start for further investigation.

Effect of East Asian atmospheric particulate matter deposition on bacterial activity and community structure in the oligotrophic Northwest Pacific

Large amounts of anthropogenic East Asian (EA) particulate matters (PM), containing inorganic nutrients and organic matter, are deposited in the oligotrophic Northwest Pacific Ocean. However, the effects of such deposition on marine microbes remain unclear. In this study, the effect of EA PM deposition on marine bacteria was assessed by five on-board microcosm experiments, conducted in oligotrophic basins of the South China Sea. The addition of EA PM to the sampling water induced a clear shift in bacterial community composition from prevailing oligotrophs (i.e., SAR 11 clade, Prochlorococcus, AEGEAN-169 marine group) to less common copiotrophs (i.e., Alteromonas, Ruegeria, Flavobacteriaceae) and thus a slight increase in bacterial diversity. The shift to more active community composition, as well as stimulation of PM nutrients, resulted in a large increase in cell-specific and bulk bacterial production. In contrast, there were only minor changes in bacterial abundance, possibly due to increased top-down mortality. The EA PM also exhibited a stronge toxic effect on pico-cyanobacteria, leading to a significant decrease in their proportion. Moreover, the responses of bacterial metabolism and community composition exhibited significant relationships with the hydrographic condition of the locations. Stronger promotion effects of the EA PM on bacterial production and community shift from oligotrophs to copiotrophs was demonstrated at the more oligotrophic sites with lower chlorophyll a concentrations. These results suggest that PM deposition from polluted areas has the potential to alter the typical oligotrophic microbiomes and change the net metabolic balance of the bacterial community. These will then influence the dynamics of carbon flow in microbial food webs and biogeochemical cycles, especially with the trend of global warming and expansion of low-chlorophyll regions.

Storage and export of microbial biomass across the western Greenland Ice Sheet

The Greenland Ice Sheet harbours a wealth of microbial life, yet the total biomass stored or exported from its surface to downstream environments is unconstrained. Here, we quantify microbial abundance and cellular biomass flux within the near-surface weathering crust photic zone of the western sector of the ice sheet. Using groundwater techniques, we demonstrate that interstitial water flow is slow (~10⁻² m d⁻¹), while flow cytometry enumeration reveals this pathway delivers 5 × 10⁸ cells m⁻² d⁻¹ to supraglacial streams, equivalent to a carbon flux up to 250 g km⁻² d⁻¹. We infer that cellular carbon accumulation in the weathering crust exceeds fluvial export, promoting biomass sequestration, enhanced carbon cycling, and biological albedo reduction. We estimate that up to 37 kg km⁻² of cellular carbon is flushed from the weathering crust environment of the western Greenland Ice Sheet each summer, providing an appreciable flux to support heterotrophs and methanogenesis at the bed.

Microbes that colonise ice sheet surfaces are important to the carbon cycle, but their biomass and transport remains unquantified. Here, the authors reveal substantial microbial carbon fluxes across Greenland’s ice surface, in quantities that may sustain subglacial heterotrophs and fuel methanogenesis.

The Seasonal Flux and Fate of Dissolved Organic Carbon Through Bacterioplankton in the Western North Atlantic

The oceans teem with heterotrophic bacterioplankton that play an appreciable role in the uptake of dissolved organic carbon (DOC) derived from phytoplankton net primary production (NPP). As such, bacterioplankton carbon demand (BCD), or gross heterotrophic production, represents a major carbon pathway that influences the seasonal accumulation of DOC in the surface ocean and, subsequently, the potential vertical or horizontal export of seasonally accumulated DOC. Here, we examine the contributions of bacterioplankton and DOM to ecological and biogeochemical carbon flow pathways, including those of the microbial loop and the biological carbon pump, in the Western North Atlantic Ocean (∼39-54°N along ∼40°W) over a composite annual phytoplankton bloom cycle. Combining field observations with data collected from corresponding DOC remineralization experiments, we estimate the efficiency at which bacterioplankton utilize DOC, demonstrate seasonality in the fraction of NPP that supports BCD, and provide evidence for shifts in the bioavailability and persistence of the seasonally accumulated DOC. Our results indicate that while the portion of DOC flux through bacterioplankton relative to NPP increased as seasons transitioned from high to low productivity, there was a fraction of the DOM production that accumulated and persisted. This persistent DOM is potentially an important pool of organic carbon available for export to the deep ocean via convective mixing, thus representing an important export term of the biological carbon pump.

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.

Grazing Pressure Is Independent of Prey Size in a Generalist Herbivorous Protist: Insights from Experimental Temperature Gradients

Grazing by herbivorous protists contributes to structuring plankton communities through its effect on the growth, biomass, and competitiveness of prey organisms and also impacts the transfer of primary production towards higher trophic levels. Previous evidence shows that heterotrophic processes (grazing rates, g) are more sensitive to temperature than autotrophic ones (phytoplankton growth rates, μ) and also that small cells tend to be more heavily predated than larger ones; however, it remains unresolved how the interplay between changes in temperature and cell size modulates grazing pressure (i.e., g:μ ratio). We addressed this problem by conducting an experiment with four phytoplankton populations, from pico- to microphytoplankton, over a 12 °C gradient and in the presence/absence of a generalist herbivorous protist, Oxyrrhis marina. We found that highest g rates coincided with highest μ rates, which corresponded to intermediate cell sizes. There were no significant differences in either μ or g between the smallest and largest cell sizes considered. The g:μ ratio was largely independent of cell size and C:N ratios, and its thermal dependence was low although species-specific differences were large. We suggest that the similar g:μ found could be the consequence that the energetic demand imposed by rising temperatures would be a more important issue than the mechanical constriction to ingestion derived from prey cell size. Despite the difficulty of quantifying μ and g in natural planktonic communities, we suggest that the g:μ ratio is a key response variable to evaluate thermal sensitivity of food webs because it gives a more integrative view of trophic functioning than both rates separately.

The potential of viruses to influence the magnitude of greenhouse gas emissions in an inland wetland

Wetlands are among the earth's most efficient ecosystems for carbon sequestration, but can also emit potent greenhouse gases (GHGs) depending on how they are managed. Global management strategies have sought to maximize carbon drawdown by wetlands by manipulating wetland hydrology to inhibit bacterially-mediated emissions. However, it has recently been hypothesized within wetlands that viruses have the potential to dictate the magnitude and direction of GHG emissions by attacking prokaryotes involved in the carbon cycle. Here we tested this hypothesis in a whole-ecosystem manipulation by hydrologically-restoring a degraded wetland ('rewetting') and investigated the changes in GHG emissions, prokaryotes, viruses, and virus-host interactions. We found that hydrological restoration significantly increased prokaryotic diversity, methanogenic Methanomicrobia, as well as putative iron/sulfate-cyclers (Geobacteraceae), nitrogen-cyclers (Nitrosomonadaceae), and fermentative bacteria (Koribacteraceae). These results provide insights into successional microbial community shifts during rehabilitation. Additionally, in response to watering, viral-induced prokaryotic mortality declined by 77%, resulting in limited carbon released by viral shunt that was significantly correlated with the 2.8-fold reduction in wetland carbon emissions. Our findings highlight, for the first time, the potential implications of viral infections in soil prokaryotes on wetland greenhouse gas dynamics and confirm the importance of wetland rehabilitation as a tool to offset carbon emissions.

Dominant protozoan species in rhizosphere soil over growth of Beta vulgaris L. in Northeast China

This paper identified the dominant protozoan species in the four layers of rhizosphere soil during the six growth stages of Beta vulgaris L. and analyzed the correlations of the abundance and diversity of the dominant protozoan species with soil properties at different growth stages and soil depth. A total of 15 species of protozoa were identified; among them, Colpoda sp., Bodo sp., two kinds of Oxytricha sp., and Tachysoma sp. were the most dominant species of Beta vulgaris L. rhizosphere soil. The Colpoda sp. was eurytopic species in the Beta vulgaris L. rhizosphere soil and Tachysoma sp., Vorticella sp., Colpoda sp., Oxytricha sp.1, and Oxytricha sp. 2 were noted closely related to the acceleration function of circulation of N and P elements in soils. These dominant protozoan species were proposed to play a significant role of fertilization on N supply in rhizosphere soil during the initial growth of Beta vulgaris L.

Metabolomics-derived marker metabolites to characterize Phaeocystis pouchetii physiology in natural plankton communities

Phaeocystis pouchetii (Hariot) Lagerheim, 1893 regularly dominates phytoplankton blooms in higher latitudes spanning from the English Channel to the Arctic. Through zooplankton grazing and microbial activity, it is considered to be a key resource for the entire marine food web, but the actual relevance of biomass transfer to higher trophic levels is still under discussion. Cell physiology and algal nutritional state are suggested to be major factors controlling the observed variability in zooplankton grazing. However, no data have so far yielded insights into the metabolic state of Phaeocystis populations that would allow testing this hypothesis. Therefore, endometabolic markers of different growth phases were determined in laboratory batch cultures using comparative metabolomics and quantified in different phytoplankton blooms in the field. Metabolites, produced during exponential, early and late stationary growth of P. pouchetii, were profiled using gas chromatography-mass spectrometry. Then, metabolites were characterized that correlate with the growth phases using multivariate statistical analysis. Free amino acids characterized the exponential growth, whereas the early stationary phase was correlated with sugar alcohols, mono- and disaccharides. In the late stationary phase, free fatty acids, sterols and terpenes increased. These marker metabolites were then traced in Phaeocystis blooms during a cruise in the Barents Sea and North Norwegian fjords. About 50 endometabolites of P. pouchetii were detected in natural phytoplankton communities. Mannitol, scyllo-inositol, 24-methylcholesta-5,22-dien-3β-ol, and several free fatty acids were characteristic for Phaeocystis-dominated blooms but showed variability between them. Distinct metabolic profiles were detected in the nutrient-depleted community in the inner Porsangerfjord (< 0.5 µM NO₃^-, < 0.1 µM PO ₄ ^3- ), with high relative amounts of free mono- and disaccharides indicative for a limited culture. This study thereby shows how the variable physiology of phytoplankton can alter the metabolic landscape of entire plankton communities.

Microbial Processing of Jellyfish Detritus in the Ocean

When jellyfish blooms decay, sinking jellyfish detrital organic matter (jelly-OM), rich in proteins and characterized by a low C:N ratio, becomes a significant source of OM for marine microorganisms. Yet, the key players and the process of microbial jelly-OM degradation and the consequences for marine ecosystems remain unclear. We simulated the scenario potentially experienced by the coastal pelagic microbiome after the decay of a bloom of the cosmopolitan Aurelia aurita s.l. We show that about half of the jelly-OM is instantly available as dissolved organic matter and thus, exclusively and readily accessible to microbes. During a typical decay of an A. aurita bloom in the northern Adriatic Sea about 100 mg of jelly-OM L-1 becomes available, about 44 μmol L-1 as dissolved organic carbon (DOC), 13 μmol L-1 as total dissolved nitrogen, 11 μmol L-1 of total hydrolyzable dissolved amino acids (THDAA) and 0.6 μmol L-1 PO4 3-. The labile jelly-OM was degraded within 1.5 days (>98% of proteins, ∼70% of THDAA, 97% of dissolved free amino acids and the entire jelly-DOC pool) by a consortium of Pseudoalteromonas, Alteromonas, and Vibrio. These bacteria accounted for >90% of all metabolically active jelly-OM degraders, exhibiting high bacterial growth efficiencies. This implies that a major fraction of the detrital jelly-OM is rapidly incorporated into biomass by opportunistic bacteria. Microbial processing of jelly-OM resulted in the accumulation of tryptophan, dissolved combined amino acids and inorganic nutrients, with possible implications for biogeochemical cycles.

Microbial Abundance and Enzyme Activity Patterns: Response to Changing Environmental Characteristics along a Transect in Kongsfjorden (Svalbard Islands)

Svalbard archipelago is experiencing the effects of climate changes (i.e., glaciers’ thickness reduction and glacier front retreat), but how ice melting affects water biogeochemistry is still unknown. Microbial communities often act as environmental sentinels, modulating their distribution and activity in response to environmental variability. To assess microbial response to climate warming, within the ARctic: present Climatic change and pAst extreme events (ARCA) project, a survey was carried out along a transect in Konsfjorden from off-shore stations towards the Kronebreen glacier. Total bacterial abundance and the fraction of actively respiring cells (labelled by cyanotetrazolium chloride, CTC), cultivable heterotrophic bacterial abundance, and extracellular enzymatic activities (leucine aminopeptidase (LAP), beta-glucosidase (GLU), and alkaline phosphatase (AP)) were measured. In addition, water temperature, salinity, dissolved oxygen, turbidity, total suspended matter (TSM), particulate and chromophoric dissolved organic matter (CDOM), chlorophyll-a (Chl-a), and inorganic compounds were determined, in order to evaluate whether variations in microbial abundance and metabolism were related with changes in environmental variables. Colder waters at surface (3.5–5 m) depths and increased turbidity, TSM, and inorganic compounds found at some hydrological stations close to the glacier were signals of ice melting. CDOM absorption slope values (275–295 nm) varied from 0.0077 to 0.0109 nm−1, and total bacterial cell count and cultivable heterotrophic bacterial abundance were in the order of 106 cells/mL and 103 colony forming units/mL, respectively. Enzymatic rates <1.78, 1.25, and 0.25 nmol/L/h were recorded for AP, LAP, and GLU, respectively. Inorganic compounds, TSM, and turbidity correlated inversely with temperature; AP was significantly related with CDOM absorption spectra and heterotrophic bacteria (r = 0.59, 0.71, p < 0.05); and LAP with Chl-a, Particulate Organic Carbon (POC) and Particulate Organic Nitrogen (PON) (0.97, 0.780, 0.734, p < 0.01), suggesting that fresh material from ice melting stimulated the metabolism of the cultivable fraction.

Use of organic exudates from two polar diatoms by bacterial isolates from the Arctic Ocean

Global warming affects primary producers in the Arctic, with potential consequences for the bacterial community composition through the consumption of microalgae-derived dissolved organic matter (DOM). To determine the degree of specificity in the use of an exudate by bacterial taxa, we used simple microalgae-bacteria model systems. We isolated 92 bacterial strains from the sea ice bottom and the water column in spring-summer in the Baffin Bay (Arctic Ocean). The isolates were grouped into 42 species belonging to Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes. Forty strains were tested for their capacity to grow on the exudate from two Arctic diatoms. Most of the strains tested (78%) were able to grow on the exudate from the pelagic diatom Chaetoceros neogracilis, and 33% were able to use the exudate from the sea ice diatom Fragilariopsis cylindrus. 17.5% of the strains were not able to grow with any exudate, while 27.5% of the strains were able to use both types of exudates. All strains belonging to Flavobacteriia (n = 10) were able to use the DOM provided by C. neogracilis, and this exudate sustained a growth capacity of up to 100 times higher than diluted Marine Broth medium, of two Pseudomonas sp. strains and one Sulfitobacter strain. The variable bioavailability of exudates to bacterial strains highlights the potential role of microalgae in shaping the bacterial community composition. This article is part of the theme issue 'The changing Arctic Ocean: consequences for biological communities, biogeochemical processes and ecosystem functioning'.

Microbial carrying capacity and carbon biomass of plastic marine debris

Trillions of plastic debris fragments are floating at sea, presenting a substantial surface area for microbial colonization. Numerous cultivation-independent surveys have characterized plastic-associated microbial biofilms, however, quantitative studies addressing microbial carbon biomass are lacking. Our confocal laser scanning microscopy data show that early biofilm development on polyethylene, polypropylene, polystyrene, and glass substrates displayed variable cell size, abundance, and carbon biomass, whereas these parameters stabilized in mature biofilms. Unexpectedly, plastic substrates presented lower volume proportions of photosynthetic cells after 8 weeks, compared to glass. Early biofilms displayed the highest proportions of diatoms, which could influence the vertical transport of plastic debris. In total, conservative estimates suggest 2.1 × 10²¹ to 3.4 × 10²¹ cells, corresponding to about 1% of the microbial cells in the ocean surface microlayer (1.5 × 10³ to 1.1 × 10⁴ tons of carbon biomass), inhabit plastic debris globally. As an unnatural addition to sea surface waters, the large quantity of cells and biomass carried by plastic debris has the potential to impact biodiversity, autochthonous ecological functions, and biogeochemical cycles within the ocean.

Spatial and Temporal Patterns of δ13C and δ15N of Suspended Particulate Organic Matter in Maryland Coastal Bays, USA

The suspended particulate organic matter (SPOM) in transitional waters such as the Maryland Coastal Bays (MCBs) is derived from allochthonous and autochthonous sources. Little is known, however, about the contribution of terrestrially derived organic matter to SPOM in the MCBs. The sources of SPOM in the MCBs were evaluated using stable isotope ratios of nitrogen (δ15N) and carbon (δ13C), and C/N molar ratios. The values of SPOM δ15N, δ13C and C/N ratios from samples collected seasonally (July 2014 to October 2017) at 13 sites ranged from −0.58 to 10.51‰, −26.85 to −20.33‰, and 1.67 to 11.36, respectively, indicating a mixture of terrestrial SPOM transported by tributaries, marine organic matter from phytoplankton, and sewage. SPOM δ13C levels less than −24‰, suggesting the dominance of terrestrially derived carbon, occurred mainly at sites close to the mouths of tributaries, and were less depleted at sites near the ocean. The mean value of SPOM δ13C was higher in October 2014 (−22.76‰) than in October 2015 (−24.65‰) and 2016 (−24.57‰) likely due to differences in river discharge. Much lower values (<4‰) of δ15N observed in February 2016 coincided with a high freshwater inflow that accompanied a major storm, indicating a strong influence of untreated sewage. Results from a two end-member mixing model suggest that on average, the SPOM in the MCBs is composed of 44% terrestrial materials with the highest percent contributions in October 2015 and 2016 (61%), and lowest (28%) in July 2015. The contribution of terrestrial materials to the SPOM was highest (58%) near the mouth of St. Martin River and lowest (25%) near the Ocean City inlet. SPOM composition and distribution in MCBs are, therefore, a function of land use, freshwater inflow, and water circulation that influence in situ phytoplankton production, and the transport and distribution of terrestrially derived materials.

Phenotypic Variations of Oleispira antarctica RB-8(T) in Different Growth Conditions

The peculiar biotechnological applications of Oleispira spp. in the natural cleansing of oil-polluted marine systems stimulated the study of the phenotypic characteristics of the Oleispira antarctica RB-8(T) strain and modifications of these characteristics in relation to different growth conditions. Bacterial abundance, cell size and morphology variations (by image analysis) and hydrocarbon degradation (by gas chromatography with flame ionization detection, GC-FID) were analysed in different cultures of O. antarctica RB-8(T). The effects of six different hydrocarbon mixtures (diesel, engine oil, naval oil waste, bilge water, jet fuel and oil) used as a single carbon source combined with two different growth temperatures (4° and 15 °C) were analysed (for 22 days). The data obtained showed that the mean cell volume decreased with increasing experimental temperature. Three morphological bacterial shapes were identified: spirals, rods and cocci. Morphological transition from spiral to rod and coccoid shapes in relation to the different substrates (oil mixtures) and/or growth temperatures was observed, except for one experimental condition (naval oil waste) in which spiral bacteria were mostly dominant. Phenotypic traits and physiological status of hydrocarbon-degrading bacteria showed important modifications in relation to culture conditions. These findings suggest interesting potential for strain RB-8(T) for ecological and applicative purposes.

Coupling Between Carbon and Nitrogen Metabolic Processes Mediated by Coastal Microbes in Synechococcus-Derived Organic Matter Addition Incubations

Phytoplankton are major contributors to labile organic matter in the upper ocean. Diverse heterotrophic bacteria successively metabolize these labile compounds and drive elemental biogeochemical cycling. We investigated the bioavailability of Synechococcus-derived organic matter (SOM) by estuarine and coastal microbes during 180-day dark incubations. Variations in organic carbon, inorganic nutrients, fluorescent dissolved organic matter (FDOM), and total/active microbial communities were monitored. The entire incubations could be partitioned into three phases (labeled I, II, and III) based on the total organic carbon (TOC) consumption rates of 6.38–7.01, 0.53–0.64, and 0.10–0.13 μmol C L^–1 day^–1, respectively. This corresponded with accumulation processes of NH₄⁺, NO₂^–, and NO₃^–, respectively. One tryptophan-like (C1) and three humic-like (C2, C3, and C4) FDOM components were identified. The intensity variation of C1 followed bacterial growth activities, and C2, C3, and C4 displayed labile, semi-labile, and refractory DOM characteristics, respectively. Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes, and Actinobacteria dominated the quickly consumed process of SOM (phase I) coupled with a substantial amount of NH₄⁺ generation. Thaumarchaeota became an abundant population with the highest activities in phase II, especially in the free-living size-fraction, and these organisms could perform chemoautotroph processes through the ammonia oxidation. Microbial populations frequently found in the dark ocean, even the deep sea, became abundant during phase III, in which Nitrospinae/Nitrospirae obtained energy through nitrite oxidation. Our results shed light on the transformation of different biological availability of organic carbon by coastal microorganisms which coupled with the regeneration of different form of inorganic nitrogen.