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The genus Vibrio , belonging to Gammaproteobacteria of the phylum Proteobacteria , is a genetically and ecologically diverse group of heterotrophic bacteria, that are ubiquitous in marine environments, especially in coastal areas. In particular, vibrios dominate, i.e. up to 10% of the readily culturable marine bacteria in these habitats. The distribution of Vibrio spp. is shaped by various environmental parameters, notably temperature, salinity and dissolved organic carbon. Vibrio spp. may utilize a wide range of organic carbon compounds, including chitin (this may be metabolized by most Vibrio spp.), alginic acid and agar. Many Vibrio spp. have very short replication times (as short as ~10 min), which could facilitate them developing into high biomass content albeit for relatively short durations. Although Vibrio spp. usually comprise a minor portion (typically ~1% of the total bacterioplankton in coastal waters) of the total microbial population, they have been shown to proliferate explosively in response to various nutrient pulses, e.g., organic nutrients from algae blooms and iron (Fe + ) from Saharan dust. Thus, Vibrio spp. may exert large impacts on marine organic carbon cycling especially in marginal seas. Genomics and related areas of investigation will reveal more about the molecular components and mechanisms involved in Vibrio -mediated biotransformation and remineralization processes.

The biological pump—the transfer of atmospheric carbon dioxide to the ocean interior and marine sediments as organic carbon—plays a critical role in regulating the long-term carbon cycle, atmospheric composition and climate. Despite its centrality in the Earth system, the response of the biological pump to biotic innovation and climatic fluctuations through most stages of Earth’s history has been largely conjectural. Here we use a mechanistic model of the biological carbon pump to revisit the factors controlling the transfer efficiency of carbon from surface waters to the ocean interior and marine sediments. We demonstrate that a shift from bacterioplankton-dominated to more eukaryote-rich ecosystems is unlikely to have considerably impacted the efficiency of Earth’s biological pump. In contrast, the evolution of large zooplankton capable of vertical movement in the water column would have enhanced carbon transfer into the ocean interior. However, the impact of zooplankton on the biological carbon pump is still relatively minor when compared with environmental drivers. In particular, increased ocean temperatures and greater atmospheric oxygen abundance lead to notable decreases in global organic carbon transfer efficiency. Taken together, our results call into question causative links between algal diversification and planetary oxygenation and suggest that climate perturbations in Earth’s history have played an important and underappreciated role in driving both carbon sequestration in the ocean interior and Earth surface oxygenation.Ocean temperature and atmospheric oxygen concentration are key factors in the long-term efficiency of the marine biological carbon pump, according to a mechanistic model of carbon transfer from surface waters to the deep ocean interior.

Conditionally rare bacteria are ubiquitous and perhaps the most diverse of microbial lifeforms, but their temporal dynamics remain largely unknown. High-throughput and deep sequencing of the 16S rRNA gene has allowed us to identify and compare the conditionally rare taxa with other bacterioplankton subcommunities. In this study, we examined the effect of season, water depth, and ecological processes on the fluctuations of bacterial subcommunities (including abundant, conditionally rare, moderate, and rare taxa) from three subtropical reservoirs in China. We discovered that the conditionally rare taxa (CRT) made up 49.7 to 71.8% of the bacterioplankton community richness, and they accounted for 70.6 to 84.4% of the temporal changes in the community composition. Beta-diversity analysis revealed strong seasonal succession patterns among all bacterioplankton subcommunities, suggesting abundant, conditionally rare, moderate, and rare taxa subcommunities have comparable environmental sensitivity. The dominant phyla of CRT were Proteobacteria, Actinobacteria, and Bacteroidetes, whose variations were strongly correlated with environmental variables. Both deterministic and stochastic processes showed strong effect on bacterioplankton community assembly, with deterministic patterns more pronounced for CRT subcommunity. The difference in bacterial community composition was strongly linked with seasonal change rather than water depth. The seasonal patterns of CRT expand our understanding of underlying mechanisms for bacterial community structure and composition. This implies their importance in the function and stability of freshwater ecosystem after environmental disturbance.

Ocean alkalinity enhancement (OAE) is a negative emissions technology (NET) that shows significant potential for climate change mitigation. By increasing the bicarbonate ion concentration in ocean water, OAE could enhance long-term carbon storage and mitigate ocean acidification. However, the side effects and/or potential co-benefits of OAE on natural planktonic communities remain poorly understood. To address this knowledge gap, a mesocosm experiment was conducted in the oligotrophic waters of Gran Canaria. A CO2-equilibrated total alkalinity (TA) gradient was employed in increments of 300 µmol L-1, ranging from ∼ 2400 to ∼ 4800 µmol L-1. This study represents the first attempt to evaluate the potential impacts of OAE on planktonic communities under natural conditions. The results show that net community production (NCP), gross production (GP), community respiration (CR) rates, and the metabolic balance (GP:CR) did not exhibit a linear response to the whole alkalinity gradient. Instead, significant polynomial and linear regression models were observed for all rates up to ΔTA 1800 µmol L-1, in relation to the dissolved inorganic carbon (DIC) concentrations. Notably, the ΔTA 1500 and 1800 µmol L-1 treatments showed peaks in NCP shifting from a heterotrophic to an autotrophic state, with NCP values of 4 and 8 µmol O2 kg-1 d-1, respectively. These peaks and the optimum curve were also reflected in the nanoplankton abundance, size-fractionated chlorophyll a, and 14C uptake data. Furthermore, abiotic precipitation occurred in the highest treatment after day 21, but no impact on the measured parameters was detected. Overall, a damaging effect of CO2-equilibrated OAE in the range applied here on phytoplankton primary production, community metabolism, and composition could not be inferred. In fact, a potential co-benefit to OAE was observed in the form of the positive curvilinear response to the DIC gradient up to the ΔTA 1800 treatment. Further experimental research at this scale is key to gain a better understanding of the short- and long-term effects of OAE on planktonic communities.

The fossil record of marine microplankton provides insights into the evolutionary drivers which led to the origin of modern deep-water plankton, one of the largest components of ocean biomass. We use global abundance and biogeographic data, combined with depth habitat reconstructions, to determine the environmental mechanisms behind speciation in two groups of pelagic microfossils over the past 15 Myr. We compare our microfossil datasets with water column profiles simulated in an Earth system model. We show that deep-living planktonic foraminiferal (zooplankton) and calcareous nannofossil (mixotroph phytoplankton) species were virtually absent globally during the peak of the middle Miocene warmth. The evolution of deep-dwelling planktonic foraminifera started from subpolar–mid-latitude species, during late Miocene cooling, via allopatry. Deep-dwelling species subsequently spread towards lower latitudes and further diversified via depth sympatry, establishing modern communities stratified hundreds of metres down the water column. Similarly, sub-euphotic zone specialist calcareous nannofossils become a major component of tropical and sub-tropical assemblages during the latest Miocene to early Pliocene. Our model simulations suggest that increased organic matter and oxygen availability for planktonic foraminifera, and increased nutrients and light penetration for nannoplankton, favoured the evolution of new deep-water niches. These conditions resulted from global cooling and the associated increase in the efficiency of the biological pump over the last 15 Myr.

Nannoconus (∼ 5–20 µm) was a major planktonic producer in the Early Cretaceous seas (∼ 150–120 Ma). The heavy calcitic skeletons (micaliths; ∼ 200–1400 picogram) of this extinct nannoplankton genus have contributed to massive carbonate accumulations for over ∼ 30 million years. The micalith microstructure is characterized by an interlocking arrangement of calcitic lamellae spanned around a central canal. The biomineralization process involved in producing the sophisticated micalith is investigated for the first time. Ptychography X-ray computed tomography (PXCT) with synchrotron radiation is applied to an isolated micalith, to obtain a 3D set of tomographic images with ∼ 40 nm spatial resolution. This 3D set was processed to virtually segment the individual calcitic lamella and reconstruct the full micalith through constraining different lengths and angles. The lamellae are repetitively stacked in two distinct inclinations, one following the other, and producing segments combined to form the entire micalith. Individual lamellae were calcified in a “template” of organic layer containing amino acid(s)/biomolecule(s), responsible for creating the interlocking arrangement. Our study of Nannoconus provides a simple yet potent approach to the analysis of biomineralized microstructures characterized by the repetitive arrangement of calcitic units as commonly seen in the calcareous nannoplankton.

Throughout the Cenozoic, calcareous nannoplankton and planktonic foraminifera have been the main producers of pelagic carbonate preserved on the seafloor. While past variability in pelagic carbonate production has been previously studied, relatively little is known about the variability in the relative contribution of the two components. This is important because the responses of the two groups to environmental forcing could be different such that they could amplify or reduce the magnitude of fluctuations in total carbonate production. Here we present new data from the tropical Atlantic that allow us to quantify changes in the relative contribution of the two groups to the total pelagic carbonate burial flux on orbital scales and between different climate states since the Miocene. We find that the composition of the deposited pelagic carbonate remained similar on long time scales, with foraminifera making up about 30 % of the deposited carbonate, but varied by up to a factor of two on orbital time scales. We show that the relative contribution of planktonic foraminifera and coccoliths did not correlate with the total pelagic carbonate production, either in the Pliocene, when its dominant cyclicity was in the precession band and in phase with orbital parameters modulations, or in the Miocene, when its predominant cyclicity was in the eccentricity band and in antiphase with orbital parameters modulations. The observed variability in tropical pelagic carbonate productivity between foraminifera and coccolithophores suggests that the two main groups of pelagic calcifiers responded fundamentally differently to orbital forcing and associated oceanographic changes in the tropical ocean, but the resulting changes in their proportions did not drive changes in overall pelagic carbonate deposition on either geological or orbital time scales.

Ulva is a ubiquitous macroalgal genus of commercial interest. Integrated Multi Trophic Aquaculture (IMTA) systems promise large-scale production of macroalgae due to their high productivity and environmental sustainability. Complex host-microbiome interactions play a decisive role in macroalgal development, especially in Ulva spp. due to algal growth- and morphogenesis-promoting factors released by associated bacteria. However, our current understanding of the microbial community assembly and structure in cultivated macroalgae is scant. We aimed to determine (i) to what extent IMTA settings influence the microbiome associated with U. rigida and its rearing water, (ii) to explore the dynamics of beneficial microbes to algal growth and development under IMTA and (iii) to improve current knowledge of host-microbiome interactions. We examined the diversity and taxonomic composition of the prokaryotic communities associated with wild versus IMTA-grown Ulva rigida and surrounding seawater by 16S rRNA gene amplicons. With 3141 Amplicon Sequence Variants (ASVs), the prokaryotic richness was higher in water than in association with U. rigida. Bacterial ASVs were more abundant in aquaculture water samples than water collected from the lagoon. The beta diversity analysis revealed distinct prokaryotic communities associated with Ulva collected in both aquacultures and coastal waters. Aquaculture samples (water and algae) shared 22% of ASVs, whereas natural, coastal lagoon samples only 9%. While cultivated Ulva selected 239 (8%) host-specific ASVs, wild specimens possessed more than twice host-specific ASVs (17%). Cultivated U. rigida specimens enriched the phyla Cyanobacteria, Planctomycetes, Verrucomicrobia, and Proteobacteria. Within the Gammaproteobacteria, while Glaciecola mostly dominated the microbiome in cultivated algae, the genus Granulosicoccus characterized both Ulva microbiomes. In both wild and IMTA settings, the phylum Bacteroidetes was more abundant in the bacterioplankton than in association with U. rigida. However, we observed that the Saprospiraceae family within this phylum was barely present in lagoon water but very abundant in aquaculture water. Aquacultures promoted the presence of known morphogenesis-inducing bacteria in water samples. Our study suggests that IMTA significantly shaped the structure and composition of the microbial community of the rearing water and cultivated U. rigida. Detailed analysis revealed the presence of previously undetected taxa associated with Ulva, possessing potentially unknown functional traits.

Dark CO2 fixation by bacteria is believed to be particularly important in oligotrophic ecosystems. However, only a few studies have characterized the role of bacterial dissolved inorganic carbon (DIC) fixation in global carbon dynamics. Therefore, this study quantified the primary production (PP), total bacteria dark CO2 fixation (TBDIC fixation), and heterotrophic bacterial production (HBP) in the warm and oligotrophic Red Sea using stable-isotope labeling and cavity ring-down spectroscopy (13C–CRDS). Additionally, we assessed the contribution of bacterial DIC fixation (TBDIC %) relative to the total DIC fixation (totalDIC fixation). Our study demonstrated that TBDIC fixation increased the totalDIC fixation from 2.03 to 60.45 µg C L-1 d-1 within the photic zone, contributing 13.18 % to 71.68 % with an average value of 33.95 ± 0.02 % of the photic layer totalDIC fixation. The highest TBDIC fixation values were measured at the surface and deep (400 m) water with an average value of 5.23 ± 0.45 and 4.95 ± 1.33 µg C L-1 d-1, respectively. These findings suggest that the non-photosynthetic processes such as anaplerotic DIC reactions and chemoautotrophic CO2 fixation extended to the entire oxygenated water column. On the other hand, the percent of TBDIC contribution to totalDIC fixation increased as primary production decreased (R2=0.45, p<0.0001), suggesting the relevance of increased dark DIC fixation when photosynthetic production was low or absent, as observed in other systems. Therefore, when estimating the total carbon dioxide production in the ocean, dark DIC fixation must also be accounted for as a crucial component of the carbon dioxide flux in addition to photosynthesis.

Mesoscale eddies modulate the ocean's physical, chemical, and biological properties. In cyclonic eddies (CEs), nutrient upwelling can stimulate primary production by phytoplankton. Yet, how this locally enhanced autotrophic production affects heterotrophy and consequently the metabolic balance between the synthesis and the consumption of dissolved organic matter (DOM) remains largely unknown. To fill this gap, we investigated the horizontal and vertical variability in auto- and heterotrophic microbial activity (biomass production and respiration) within a CE that formed off Mauritania and along the ∼ 900 km zonal corridor between Mauritania and the Cape Verde islands in the Eastern Tropical North Atlantic (ETNA). Our results show how the physical disturbances caused by the CE affected the biomass distribution of phyto- and bacterioplankton and their metabolic activities. The injection of nutrients into the sunlit surface resulted in enhanced autotrophic pico- and nanoplankton abundance and generally increased autotrophic activity as indicated by chlorophyll a (Chl a) concentration, primary production (PP), and extracellular release rates. However, the detailed eddy survey also revealed an uneven distribution of these variables with, for example, the highest Chl a concentrations and PP rates occurring near and just beyond the CE's periphery. The heterotrophic bacterial activity was similarly variable. Optode-based community respiration (CR), bacterial respiration (BR) estimates, and bacterial biomass production (BP) largely followed the trends of PP and Chl a. Thus, a submesoscale spatial mosaic of heterotrophic bacterial abundance and activities occurred within the CE that was closely related to variability in autotrophic production. Consistent with this, we found a significant positive correlation between concentrations of semi-labile dissolved organic carbon (SL-DOC; here the sum of dissolved hydrolysable amino acids and dissolved combined carbohydrates) and BR estimates. Extracellular release of carbon as indicated by primary production of dissolved organic carbon (PPDOC) was variable with depth and laterally and not always sufficient to compensate the bacterial carbon demand (BCD: BR + BP), with PPDOC accounting for between 28 % and 110 % of the BCD. Bacterial growth efficiency (BGE: BP / BCD) ranged between 1.7 % and 18.2 %. We estimated the metabolic state to establish whether the CE was a source or a sink of organic carbon. We showed that the CE carried a strong autotrophic signal in the core (PP / CR > 1). Our results suggest that submesoscale (0–10 km) processes lead to highly variable metabolic activities in both photoautotrophic and heterotrophic microorganisms. Overall, we revealed that the CEs not only trap and transport coastal nutrients and organic carbon to the open ocean but also stimulate phytoplankton growth, generating freshly produced organic matter during westward propagation. This drives heterotrophic processes and may contribute to the previously observed net heterotrophy in open Atlantic surface waters.