Picocyanobacteria and deep-ocean fluorescent dissolved organic matter share similar optical properties

Aggregating Synechococcus contributes to particle organic carbon export in coastal estuarine waters: Its lineage features and assembly processes

The release and deposition of phytoplankton-derived particulate organic matter is crucial in marine carbon export, yet the roles of picoplankton in these processes were seldom considered. Therefore, this study aimed to shed light on the matter by investigating the aggregating (AG) lifestyle of Synechococcus, a main group of picoplankton, in the coastal waters of the Yellow River Estuary with ample sediments acting as ballast minerals. We revealed that AG Synechococcus constituted a substantial portion, maximally reaching up to 85.4 %, of the total Synechococcus population. Pearson correlations and random forest (RF) regression analyses found significant connections (p < 0.01) between AG Synechococcus and the content of particulate organic carbon (POC), which emphasized its underlying role in facilitating POC export in this region. Furthermore, by employing high-throughput sequencing of the RNA polymerase gene (rpoC1), it was demonstrated that S5.1 clade I exhibited a significantly higher proportion in the AG fraction than in the free-living (FL) fraction (p < 0.05). This suggests distinct inclinations in the phylogenetic preference for different Synechococcus lineages between different lifestyles in the studied area. Finally, we ascertained "small-world" and higher robustness attributes of aggregates formed through the co-occurrence construction between Synechococcus and heterotrophic bacteria, likely facilitated by the reciprocal exchange of carbon and nitrogen elements. Overall, these findings have implications for our understanding of the role of Synechococcus in the ecology and biogeochemistry of marine ecosystems, and they are significant for more accurately evaluating the contribution of picophytoplankton in ocean carbon export.

The microbial carbon pump and climate change

The ocean has been a regulator of climate change throughout the history of Earth. One key mechanism is the mediation of the carbon reservoir by refractory dissolved organic carbon (RDOC), which can either be stored in the water column for centuries or released back into the atmosphere as CO2 depending on the conditions. The RDOC is produced through a myriad of microbial metabolic and ecological processes known as the microbial carbon pump (MCP). Here, we review recent research advances in processes related to the MCP, including the distribution patterns and molecular composition of RDOC, links between the complexity of RDOC compounds and microbial diversity, MCP-driven carbon cycles across time and space, and responses of the MCP to a changing climate. We identify knowledge gaps and future research directions in the role of the MCP, particularly as a key component in integrated approaches combining the mechanisms of the biological and abiotic carbon pumps for ocean negative carbon emissions.

Terrigenous humic substances regulate the concentrations of dissolved Fe and Cu (but not Al, Mn, Ni or Zn) in the Gaoping River plume

The small mountainous rivers of Oceania discharge a large fraction of their dissolved and particulate load of materials within a very small percentage of the time. As a result, the yearly inputs and physicochemical forms of dissolved metals exported to the ocean by these rivers are poorly quantified. We investigated the wet-season distribution patterns of metals and fluorescent organic substances in the surface waters of the Gaoping River plume, SW Taiwan, under both moderate (Sep 2020) and strong flow conditions (Aug 2021). The mixing behaviour of both soluble (<5 kDa) and colloidal (>5 kDa) metals and fluorescent components was examined over the salinity range 3.0-32.2 in 2020 and 5.8-31.1 in 2021. We detected two humic-like and one protein-like fluorescent components, the same on both surveys. The humic-like components, C1 and C3, originated from the Gaoping River and correlated strongly with Cu and Fe, respectively. Component C3 showed a greater enrichment relative to C1 in the colloidal (C3/C1 > 0.8) than in the soluble phase (C3/C1 = 0.4). The protein-like component, C2, came from both terrestrial and marine sources and displayed a more complex mixing behaviour than the other two. One striking result was that the effective zero-salinity concentrations of Fe (∼300 nM) and Cu (∼23 nM) did not change significantly in response to a 10-fold increase in river discharge between Sep 2020 and Aug 2021. Similarly to Fe and Cu, the distribution patterns of Components C1 and C3 did not change significantly between the moderate and the strong plume, and C3 and C1 correlated strongly with Fe and Cu, respectively. We conclude that subtropical mountainous rivers can provide soil-derived humic substances which facilitate and regulate the delivery of Fe and Cu to the ocean, provided mountain forests are preserved.

Diversity, composition and ecological networks of bacterial communities in response to a full cultivation cycle of the seaweed, Gracilariopsis lemaneiformis

Cultivation of the seaweed, Gracilariopsis lemaneiformis, supports environmental bioremediation and the aquaculture economy in coastal ecosystems, and microorganisms play important roles during the cultivation process. In this study, we aimed to understand the response of bacterial communities through a full cultivation cycle of G. lemaneiformis. We analyzed the bacterial communities using 16S rRNA gene amplicon sequencing and defined the environmental factors of 144 water samples from the Nan'ao Island, South China Sea. Community diversity, keystone species and ecological networks of bacterial communities shifted markedly in the cultivation zone largely due to changes in the environmental factors, seaweed biomass and cultivation stages. The bacterial communities at the seaweed zone have lower species richness, more seaweed-associated taxa and simpler but more stable co-occurrence networks compared to the control zone. Persistent microbial groups such as Aquimarina, Formosa, Glaciecola and Marinobacter exhibited a strong association with seaweed during the growth and maturity stages. We describe a conceptual model to summarize the changes in the bacterial community composition, its diversity and the ecological networks in seaweed cultivation zone. Overall, this study provides new perspectives on the dynamic interaction of seaweed cultivation, bacterial communities and environment factors and their potential ecosystem services as observed in the example of the G. lemaneiformis cultivation ecosystem.

Bottom-up and top-down controls on Alteromonas macleodii lead to different dissolved organic matter compositions

The effects of both bottom-up (e.g. substrate) and top-down (e.g. viral lysis) controls on the molecular composition of dissolved organic matter have not been investigated. In this study, we investigated the dissolved organic matter composition of the model bacterium Alteromonas macleodii ATCC 27126 growing on different substrates (glucose, laminarin, extracts from a Synechococcus culture, oligotrophic seawater, and eutrophic seawater), and infected with a lytic phage. The ultra-high resolution mass spectrometry analysis showed that when growing on different substrates Alteromonas macleodii preferred to use reduced, saturated nitrogen-containing molecules (i.e. O4 formula species) and released or preserved oxidized, unsaturated sulfur-containing molecules (i.e. O7 formula species). However, when infected with the lytic phage, Alteromonas macleodii produced organic molecules with higher hydrogen saturation, and more nitrogen- or sulfur-containing molecules. Our results demonstrate that bottom-up (i.e. varying substrates) and top-down (i.e. viral lysis) controls leave different molecular fingerprints in the produced dissolved organic matter.

Dominant heterocyclic composition of dissolved organic nitrogen in the ocean: A new paradigm for cycling and persistence

Marine dissolved organic nitrogen (DON) is one of the planet's largest reservoirs of fixed N, which persists even in the N-limited oligotrophic surface ocean. The vast majority of the ocean's total DON reservoir is refractory (RDON), primarily composed of low molecular weight (LMW) compounds in the subsurface and deep sea. However, the composition of this major N pool, as well as the reasons for its accumulation and persistence, are not understood. Past characterization of the analytically more tractable, but quantitatively minor, high molecular weight (HMW) DON fraction revealed a functionally simple amide-dominated composition. While extensive work in the past two decades has revealed enormous complexity and structural diversity in LMW dissolved organic carbon, no efforts have specifically targeted LMW nitrogenous molecules. Here, we report the first coupled isotopic and solid-state NMR structural analysis of LMW DON isolated throughout the water column in two ocean basins. Together these results provide a first view into the composition, potential sources, and cycling of this dominant portion of marine DON. Our data indicate that RDON is dominated by 15N-depleted heterocyclic-N structures, entirely distinct from previously characterized HMW material. This fundamentally new view of marine DON composition suggests an important structural control for RDON accumulation and persistence in the ocean. The mechanisms of production, cycling, and removal of these heterocyclic-N-containing compounds now represents a central challenge in our understanding of the ocean's DON reservoir.

Photochemical behaviors of dissolved organic matter in aquatic environment: Generation, characterization, influencing factors and practical application

Dissolved organic matter (DOM) widely exists in aquatic environment and plays a critical role in environmental photochemical reaction. The photochemical behaviors of DOM in sunlit surface waters have received widely attention because its photochemical effects for some coexisted substances in aquatic environment, especially for organic micropollutants degradation. Therefore, to gain a comprehensive understanding of the photochemical properties and environmental effects of DOM, we reviewed the influence of sources on the structure and composition of DOM with relevant identified techniques to analysis functional groups. Additionally, identification and quantification for reactive intermediates are discussed with a focus on influencing factors to produce reactive intermediates by DOM under solar irradiation. These reactive intermediates can promote the photodegradation of organic micropollutants in the environmental system. In future, attention should be paid to the photochemical properties of DOM and environmental effects in real environmental system and development of advanced techniques to study DOM.

Viral lysing can alleviate microbial nutrient limitations and accumulate recalcitrant dissolved organic matter components in soil

Viruses are critical for regulating microbial communities and biogeochemical processes affecting carbon/nutrient cycling. However, the role of soil phages in controlling microbial physiological traits and intrinsic dissolved organic matter (DOM) properties remains largely unknown. Herein, microcosm experiments with different soil phage concentrates (including no-added phages, inactive phages, and three dilutions of active phages) at two temperatures (15 °C and 25 °C) were conducted to disclose the nutrient and DOM dynamics associated with viral lysing. Results demonstrated three different phases of viral impacts on CO₂ emission at both temperatures, and phages played a role in maintaining Q₁₀ within bounds. At both temperatures, microbial nutrient limitations (especially P limitation) were alleviated by viral lysing as determined by extracellular enzyme activity (decreased V_angle with active phages). Additionally, the re-utilization of lysate-derived DOM by surviving microbes stimulated an increase of microbial metabolic efficiency and recalcitrant DOM components (e.g., SUV254, SUV260 and HIX). This research provides direct experimental evidence that the "viral shuttle" exists in soils, whereby soil phages increase recalcitrant DOM components. Our findings advance the understanding of viral controls on soil biogeochemical processes, and provide a new perspective for assessing whether soil phages provide a net "carbon sink" vs. "carbon source" in soils.

Direct Production of Bio-Recalcitrant Carboxyl-Rich Alicyclic Molecules Evidenced in a Bacterium-Induced Steroid Degradation Experiment

Carboxyl-rich alicyclic molecules (CRAM) are highly unsaturated compounds extensively distributed throughout aquatic environments and sediments. This molecular group is widely referred to as a major proxy of recalcitrant organic materials, but its direct biosynthesis remains unclear. Steroids are a typical anthropogenic contaminant and have been previously suggested to be precursors of CRAM; however, experimental evidence to support this hypothesis is lacking. Here, a steroid-degrading bacterium, Comamonas testosteroni ATCC 11996, was incubated in a liquid medium supplemented with testosterone (a typical steroid) as the sole carbon source for 90 days. Testosterone-induced metabolites (TIM) were extracted for molecular characterization and to examine the bioavailability during an additional 90-day incubation after inoculation with a natural coastal microbial assemblage. The results showed that 1,775 molecular formulas (MFs) were assigned to TIM using ultrahigh-resolution mass spectrometry, with 66.99% categorized as CRAM-like constituents. A large fraction of TIM was respired or transformed during the additional 90-day seawater incubation; nevertheless, 638 MFs of the TIM persisted or increased during incubation. Among the 638 MFs, 394 were commonly assigned in natural deep seawater samples (depths of 500 to 2,000 m) from the South China Sea. Compared to the catabolites of the well-established testosterone degradation pathway, we compiled a list of bio-refractory MFs and potential chemical structures, some of which shared structural homology with CRAM. These results demonstrated direct microbial production of bio-refractory CRAM from steroid hormones and indicated that some of the biogenic CRAM resisted microbial decomposition, potentially contributing to the aquatic refractory dissolved organic matter (DOM) pool. IMPORTANCE CRAM are an operationally defined DOM group comprising a complex mixture of carboxylated and fused alicyclic structures. This DOM group is majorly characterized as refractory DOM in the marine environment. However, the origins of the complex CRAM remain unclear. In this study, we demonstrated that testosterone (a typical steroid) could be transformed into bio-refractory CRAM by a single bacterial strain and observed that some of the CRAM highly resisted microbial degradation. Through molecular comparison and screening, potential chemical structures of steroid-induced CRAM were suggested. This study established the biological connection between steroids and bio-refractory CRAM, and it provides a novel perspective explaining the fate of terrestrial contaminants in aquatic environments.

Regulatory and metabolic adaptations in the nitrogen assimilation of marine picocyanobacteria

Prochlorococcus and Synechococcus are the two most abundant photosynthetic organisms on Earth, with a strong influence on the biogeochemical carbon and nitrogen cycles. Early reports demonstrated the streamlining of regulatory mechanisms in nitrogen metabolism and the removal of genes not strictly essential. The availability of a large series of genomes, and the utilization of latest generation molecular techniques have allowed elucidating the main mechanisms developed by marine picocyanobacteria to adapt to the environments where they thrive, with a particular interest in the strains inhabiting oligotrophic oceans. Given that nitrogen is often limited in those environments, a series of studies have explored the strategies utilized by Prochlorococcus and Synechococcus to exploit the low concentrations of nitrogen-containing molecules available in large areas of the oceans. These strategies include the reduction in the GC and the cellular protein contents; the utilization of truncated proteins; a reduced average amount of N in the proteome; the development of metabolic mechanisms to perceive and utilize nanomolar nitrate concentrations; and the reduced responsiveness of key molecular regulatory systems such as NtcA to 2-oxoglutarate. These findings are in sharp contrast with the large body of knowledge obtained in freshwater cyanobacteria. We will outline the main discoveries, stressing their relevance to the ecological success of these important microorganisms.

Growth dynamics and transcriptional responses of a Red Sea Prochlorococcus strain to varying temperatures

Prochlorococcus play a crucial role in the ocean's biogeochemical cycling, but it remains controversial how they will respond to global warming. Here we assessed the response to temperature (22-30°C) of the growth dynamics and gene expression profiles of a Red Sea Prochlorococcus strain (RSP50) in a non-axenic culture. Both the specific growth rate (0.55-0.80 day^-1 ) and cell size (0.04-0.07 μm³ ) of Prochlorococcus increased significantly with temperature. The primary production released extracellularly ranged from 20% to 34%, with humic-like fluorescent compounds increasing up to fivefold as Prochlorococcus reached its maximum abundance. At 30°C, genes involved in carbon fixation such as CsoS2 and CsoS3 and photosynthetic electron transport including PTOX were downregulated, suggesting a cellular homeostasis and energy saving mechanism response. In contrast, PTOX was found upregulated at 22°C and 24°C. Similar results were found for transaldolase, related to carbon metabolism, and citrate synthase, an important enzyme in the TCA cycle. Our data suggest that in spite of the currently warm temperatures of the Red Sea, Prochlorococcus can modulate its gene expression profiles to permit growth at temperatures lower than its optimum temperature (28°C) but is unable to cope with temperatures exceeding 30°C.

Mechanistic insights into the generation and control of Cl-DBPs during wastewater sludge chlorination disinfection process

Chlorination disinfection has been widely used to kill the pathogenic microorganisms in wastewater sludge during the special Covid-19 period, but sludge chlorination might cause the generation of harmful disinfection byproducts (DBPs). In this work, the transformation of extracellular polymeric substance (EPS) and mechanisms of Cl-DBPs generation during sludge disinfection by sodium hypochlorite (NaClO) were investigated using multispectral analysis in combination with Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS). The microorganism Escherichia coli (E. coli) was effectively inactivated by active chlorine generated from NaClO. However, a high diversity of Cl-DBPs were produced with the addition of NaClO into sludge, causing the increase of acute toxicity on Q67 luminous bacteria of chlorinated EPS. A variety of N-containing molecular formulas were produced after chlorination, but N-containing DBPs were not detected, which might be the indicative of the dissociation of -NH₂ groups after Cl-DBPs generated. Additionally, the release of N-containing compounds was increased in alkaline environment caused by NaClO addition, resulted in more Cl-DBPs generation via nucleophilic substitutions. Whereas, less N-compounds and Cl-DBPs were detected after EPS chlorination under acidic environment, leading to lower cell cytotoxicity. Therefore, N-containing compounds of lignin derivatives in sludge were the major Cl-DBPs precursors, and acidic environment could control the release of N-compounds by eliminating the dissociation of functional groups in lignin derivatives, consequently reducing the generation and cytotoxicity of Cl-DBPs. This study highlights the importance to control the alkalinity of sludge to reduce Cl-DBPs generation prior to chlorination disinfection process, and ensure the safety of subsequential disposal for wastewater sludge.

Metagenomic evidence for the microbial transformation of carboxyl-rich alicyclic molecules: A long-term macrocosm experiment

Carboxyl-rich alicyclic molecules (CRAMs) widely exist in the ocean and constitute the central part of the refractory dissolved organic matter (RDOM) pool. Although a consensus has been reached that microbial activity forms CRAMs, the detailed molecular mechanisms remain largely unexplored. To better understand the underlying genetic mechanisms driving the microbial transformation of CRAM, a long-term macrocosm experiment spanning 220 days was conducted in the Aquatron Tower Tank at Dalhousie University, Halifax, Canada, with the supply of diatom-derived DOM as a carbon source. The DOM composition, community structure, and metabolic pathways were characterised using multi-omics approaches. The addition of diatom lysate introduced a mass of labile DOM into the incubation seawater, which led to a low degradation index (I_DEG) and refractory molecular lability boundary (RMLB) on days 1 and 18. The molecular compositions of the DOM molecules in the later incubation period (from day 120 to day 220) were more similar in composition to those on day 0, suggesting a rapid turnover of phytoplankton debris by microbial communities. Taxonomically, while Alpha proteobacteria dominated during the entire incubation period, Gamma proteobacteria became more sensitive and abundant than the other bacterial groups on days 1 and 18. Recalcitrant measurements such as I_DEG and RMLB were closely related to the DOM molecules, bacterial community, and Kyoto encyclopaedia of Genes and Genomes (KEGG) modules, suggesting close associations between RDOM accumulation and microbial metabolism. KEGG modules that showed strong positive correlation with CRAMs were identified using a microbial ecological network approach. The identified KEGG modules produced the substrates, such as the acetyl-CoA or 3‑hydroxy-3-methylglutaryl-CoA, which could participate in the mevalonate pathway to generate the precursor of CRAM analogues, isopentenyl-PP, suggesting a potential generation pathway of CRAM analogues in bacteria and archaea. This study revealed the potential genetic and molecular processes involved in the microbial origin of CRAM analogues, and thus indicated a vital ecological role of bacteria and archaea in RDOM production. This study also offered new perspectives on the carbon sequestration in the ocean.

New Perspectives on the Marine Carbon Cycle-The Marine Dissolved Organic Matter Reactivity Continuum

This perspective challenges our current understanding of the marine carbon cycle, including an alternative explanation of bulk 14C-DOM measurements. We propose the adoption of the carbon reactivity continuum concept previously established for lakes and sediments for the oceans using kinetic data and term this the marine DOM reactivity continuum. We need to gain a fundamental understanding of the biogeochemical drivers of surface water DOM concentrations and reactivity, biological carbon pump efficiency, and the autotrophic communities that are the ultimate but variable sources of marine DOM. This perspective is intended to shift our focus to a more inclusive kinetic model and may lead us to a more accurate assessment of the active and dynamic role marine DOM plays in the global carbon cycle. Currently, the kinetic data to establish and validate such a marine DOM reactivity continuum model are still lacking, and their resolution depends on the discovery of new organic tracers that span large differences in reactivity and microbial degradation rates. We may need to refocus our efforts in deciphering the structure and reactivity of marine organic molecules in a kinetic context, including the microbial and physicochemical constraints on molecular reactivity that are present in the deep ocean.

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.

Isolation and Characterization of a Novel Cyanophage Encoding Multiple Auxiliary Metabolic Genes

As significant drivers of cyanobacteria mortality, cyanophages have been known to regulate the population dynamics, metabolic activities, and community structure of this most important marine autotrophic picoplankton and, therefore, influence the global primary production and biogeochemical cycle in aquatic ecosystems. In the present study, a lytic Synechococcus phage, namely S-SZBM1, was isolated and identified. Cyanophage S-SZBM1 has a double-stranded DNA genome of 177,834 bp with a G+C content of 43.31% and contains a total of 218 predicted ORFs and six tRNA genes. Phylogenetic analysis and nucleotide-based intergenomic similarity suggested that cyanophage S-SZBM1 belongs to a new genus under the family Kyanoviridae. A variety of auxiliary metabolic genes (AMGs) that have been proved or speculated to relate to photosynthesis, carbon metabolism, nucleotide synthesis and metabolism, cell protection, and other cell metabolism were identified in cyanophage S-SZBM1 genome and may affect host processes during infection. In addition, 24 of 32 predicted structural proteins were identified by a high-throughput proteome analysis which were potentially involved in the assembly processes of virion. The genomic and proteomic analysis features of cyanophage S-SZBM1 offer a valuable insight into the interactions between cyanophages and their hosts during infection.

Temperature Rise Increases the Bioavailability of Marine Synechococcus-Derived Dissolved Organic Matter

Synechococcus is one group of main primary producers and plays a key role in oceanic carbon fixation and transformation. To explore how the temperature rise affects the bioavailability of Synechococcus-derived dissolved organic matter (SOM) and whether this effect would be altered by the involvement of heterotrophic bacteria, we compared the optical and molecular properties of the SOM of axenic Synechococcus sp. PCC7002 culture (Syn) to that with associated heterotrophic bacteria (SynB) under 15, 18, and 21°C growth temperatures at exponential and decay growth phases. Our results showed that the temperature rise increased the bioavailability of the SOM of both Syn and SynB cultures by lowering the proportion of the hydrogen-poor and double-bond structure-rich humus-like components and highly unsaturated substances, as indicated by the increase of spectral slope ratio (S R ) and biological index (BIX) and decrease of humification index (HIX). Moreover, the involvement of heterotrophic bacteria modified the Synechococcus-derived SOM, together with its intracellular dissolved organic matter (DOM) excludes, lowering the SOM bioavailability. Our results indicated that the warming in climate change scenario may enhance the bioavailability of the Synechococcus-derived SOM although it may be tempered by the involvement of heterotrophic bacteria, providing an insight for preservation of the organic carbon pool in global oceans.

Improved water quality monitoring indicators may increase carbon storage in the oceans

Indicators related to organic matter are important when assessing aquatic environment quality. The chemical oxygen demand (COD) is widely used as a water quality reference. However, oxidizing agents used to determine the COD can oxidize refractory organic matter that is not pollutant and can persist in the ocean for thousands of years. This means the COD can misrepresent the water quality. The actual water quality can be indicated better by the biochemical oxygen demand (BOD) than the COD, but determining the BOD is time-consuming and gives variable results. In this study, the optical properties of dissolved organic matter in water samples from the Chinese coast that had been incubated for a long time or directly oxidized using COD oxidant were analyzed. The results indicated that the oxidizing agent rapidly oxidized 22.93% ± 4.96% of refractory dissolved organic matter (RDOM) that was resistant to microbial degradation, implying that RDOM made a marked contribution to the COD. Meanwhile, size-fractional fluorescence spectroscopy and COD measurements indicated that the COD of the >0.7 μm fraction and the fluorescence intensity of the protein-like component significantly positively correlated with the BOD of the bulk sample. This indicated that, for monitoring organic pollutants in coastal waters, the COD of the >0.7 μm fraction could be used as a proxy for the standard COD and that the fluorescence intensity of the protein-like component could be used as a convenient proxy for the BOD. The method can help retain recalcitrant organic matter in seawater to act as a carbon sink.

Empirical estimation of marine phytoplankton assemblages in coastal and offshore areas using an in situ multi-wavelength excitation fluorometer

Phytoplankton assemblages are essential for understanding the quality of primary production in marine ecosystems. Here, we describe the development of a methodology for monitoring marine phytoplankton assemblages using an in situ multi-wavelength excitation fluorometer (MEX). The MEX recorded the fluorescence excited with nine light-emitting diodes, temperature, and sensor depth. We prepared reference datasets comprising MEX fluorescence and plant pigment-based phytoplankton assemblages of nine chemotaxonomy groups (diatoms, dinoflagellates, cryptophytes, chlorophytes, haptophytes type 3, haptophytes type 4, prasinophytes, cyanophytes, and prochlorophytes). Conversions from the MEX fluorescence to the phytoplankton assemblages were conducted with two processes. First, target MEX fluorescence was decomposed using a linear inverse model for calculating coefficients. Second, pigment-based chemotaxonomy of the target MEX fluorescence was reconstructed using the coefficients and the chemotaxonomy assemblages of the reference data. Cross-validation analyses indicated good estimation of the proportion of diatoms, dinoflagellates, cryptophytes, cyanophytes, and prochlorophytes with MEX, and when chlorophytes, haptophytes and prasinophytes were summarized as other eukaryotes, the positive correlation was seen between proportions estimated with MEX and pigments as same as other five chemotaxonomy groups. Repeated MEX observations were conducted in the Kuroshio, the Sea of Japan, the Oyashio, and the Okhotsk Sea. The water-column integrated biomass indicated that the diatoms were an important primary producer in the Oyashio and the Okhotsk Sea, while eukaryotes were important in the Sea of Japan and prochlorophytes were important in the Kuroshio. Our method with the MEX will be a powerful tool to understand and estimate the chemotaxonomy-level assemblages and biomass in the ocean.

Heterogeneous viral contribution to dissolved organic matter processing in a long-term macrocosm experiment

Viruses saturate environments throughout the world and play key roles in microbial food webs, yet how viral activities affect dissolved organic matter (DOM) processing in natural environments remains elusive. We established a large-scale long-term macrocosm experiment to explore viral dynamics and their potential impacts on microbial mortality and DOM quantity and quality in starved and stratified ecosystems. High viral infection dynamics and the virus-induced cell lysis (6.23-64.68% d^-1) was found in the starved seawater macrocosm, which contributed to a significant transformation of microbial biomass into DOM (0.72-5.32 μg L^-1 d^-1). In the stratified macrocosm, a substantial amount of viral lysate DOM (2.43-17.87 μg L^-1 d^-1) was released into the upper riverine water, and viral lysis and DOM release (0.35-5.75 μg L^-1 d^-1) were reduced in the mixed water layer between riverine water and seawater. Viral lysis was stimulated at the bottom of stratified macrocosm, potentially fueled by the sinking of particulate organic carbon. Significant positive and negative associations between lytic viral production and different fluorescent DOM components were found in the starved and stratified macrocosm, indicating the potentially complex viral impacts on the production and utilization of DOM. Results also revealed the significant viral contribution to pools of both relatively higher molecular weight labile DOM and lower molecular weight recalcitrant DOM. Our study suggests that viruses have heterogeneous impact on the cycling and fate of DOM in aquatic environments.

Distinct metabolic strategies of the dominant heterotrophic bacterial groups associated with marine Synechococcus

The marine Synechococcus is a major primary producer in the global oceans. It is phylogenetically highly diverse, and its major phylogenetic lineages display clear spatial segregation among different marine environments. Here, we showed that the composition of the associated bacterial communities was related to the geographic origin of the different Synechococcus strains, and it was stable during long-term lab incubation. Of all the Synechococcus cultures investigated, the Rhodobacteraceae had a relatively high abundance and was the core bacterial family of the associated bacterial communities. In contrast, the Flavobacteriaceae were only abundant in the cultures collected from the South China Sea (which is warm and oligotrophic), whereas those of the Alteromonadaceae were abundant in the cultures from the coastal waters off Hong Kong and Xiamen. We also found that the Rhodobacteraceae had more ABC transporters and utilized a wider spectrum of carbon sources than did the Flavobacteriaceae and Alteromonadaceae. Moreover, the Alteromonadaceae had more transporters for importing phosphate and amino acids, but fewer transporters for importing oligosaccharides, polyol, and lipid, than the Flavobacteriaceae. Furthermore, metagenomic analysis demonstrated that bacteria involved in nitrate-ammonification prevailed in all the cultures. These results imply that networks formed by phytoplankton and heterotrophic bacteria might vary across habitats, and that different dominant bacterial groups play different roles in the phycosphere. This study provides new insight into the unique interactive and interdependent bond between phytoplankton and their associated microbiome, which may enhance our understanding of carbon and nutrient cycling in marine environments.

Epiphytic Bacteria Are Essential for the Production and Transformation of Algae-Derived Carboxyl-Rich Alicyclic Molecule (CRAM)-like DOM

The microbial carbon pump (MCP) provides a mechanistic illustration of transformation of recalcitrant dissolved organic matter (DOM) in the ocean. Here, we explored and demonstrated the key roles of algae-associated microorganisms (mainly heterotrophic bacteria) in the production and transformation of carboxyl-rich alicyclic molecule (CRAM)-like DOM through a laboratory experiment involving cultures of Skeletonema dohrnii. Without the participation of the associated bacteria, CRAM-like DOM molecules were not detected via Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS) in algal cultures treated with antibiotics. Similarly, CRAM-like DOM were not detected in cultures of bacteria alone. Our experimental results showed that algae-associated bacteria are important in the process of converting algal-derived organic matter into CRAM-like DOM during S. dohrnii culture. Bacteroidetes (mainly Flavobacteriia) dominated the bacterial community in the stationary and degradation phases, where the predicted metabolic pathways for bacterial assemblages were mainly involved in biosynthesis, metabolism, and degradation. Facilitated by these heterotrophic bacteria, the amount and the chemodiversity of CRAM-like DOM derived from algae varied during the growth and decomposition of algal cells, and CRAM-like DOM were enriched at the later growth stage. The properties and characteristics of these CRAM-like DOM, including molecular weight, double bond equivalent, hydrogen-carbon ratio, carbon-nitrogen ratio, carbon-sulfur ratio, and modified aromaticity index increased with the growth and decay of algal cells, indicating the transformation from active to recalcitrant DOM. In contrast, the organic matter in axenic cultures of S. dohrnii mainly existed in the form of particulate organic matters (POM), and small amounts of CRAM-like DOM were detected. This study provides the first laboratory evidence to reveal and confirm the direct involvement of algae-associated microbiomes in the production and transformation of algae-derived refractory DOM, highlighting the significance of these epiphytic bacteria in marine carbon sequestration and global carbon cycling.

IMPORTANCE Dissolved organic matter (DOM) serves as a major carbon and nutrient pool in oceans, and recalcitrant DOM are the primary sources for carbon sequestration in depths. Here, we demonstrate the critical roles of algae-associated microorganisms (mainly heterotrophic bacteria) in the transformation of recalcitrant dissolved organic matter through laboratory cultures of a model diatom, Skeletonema dohrnii. Our experimental results showed that in addition to affecting the growth and the physiology of S. dohrnii, algae-associated bacteria are important in processing and converting algal DOM into CRAM-like DOM. Facilitated by the associated bacteria, the amount and the chemodiversity of DOM derived from algae varied during the growth and decomposition of algal cells, and enriched recalcitrant DOM formed in the later growth stage. The properties and diversity of DOM increased with the growth and decay of algal cells, indicating the transformation from active DOM to inert organic matter. Our results confirmed that the direct involvement of algae-associated microbes in the production of CRAM-like DOM. Detailed community structure analysis of the algae-associated bacterial community and its predicted functions confirmed the involvement of certain bacterial groups (e.g., Flavobacteriia) in biosynthesis, metabolism, and degradation.

Fluorescent dissolved organic matter facilitates the phytoavailability of copper in the coastal wetlands influenced by artificial topography

Dissolved organic matter (DOM) is a crucial driver in ecosystem services and a central part of the carbon transport and biological cycle in land-sea interaction. DOM exhibits characteristic environmental behavior in the coastal zone, but its sustainability is affected by expanding artificial topography (AT) construction. It requires combining analyses on AT-induced response of field fluorescent DOM (fDOM) and its quenching pattern under metal-complexation. Herein, we conducted systemic investigations into the spatiotemporal dynamics of fDOM compositions with further in-lab verification to study its Cu-binding capacity. We detected three humid-like fDOM components sensitive to AT. The total fDOM intensity was positively correlated with low molecular weight organic acid (LMWOA) extractable Cu and the Cu pools in above-ground biomass. The enriched fDOM serves as an ecological engineer by increasing the Cu mobility, confirmed by an in-lab fluorescence titration. The application of LMWOA greatly enhanced the intensity of one fDOM component, elevated its conditional stability constant, and decreased its quenched proportion, implying that LMWOA might extract part of Cu from fDOM complexation. The present work provides an "fDOM-LMWOA pump" explanation to suggest that fDOM is a novel ecological regulator on vegetation growth under the AT-induced matter accumulation.

Ultrafast Energy Transfer Determines the Formation of Fluorescence in DOM and Humic Substances

Humification is a ubiquitous natural process of biomass degradation that creates multicomponent systems of nonliving organic matter, including dissolved organic matter (DOM) and humic substances (HS) in water environments, soils, and organic rocks. Despite significant differences in molecular composition, the optical properties of DOM and HS are remarkably similar, and the reason for this remains largely unknown. Here, we employed fluorescence spectroscopy with (sub)picosecond resolution to elucidate the role of electronic interactions within DOM and HS. We revealed an ultrafast decay component with a characteristic decay lifetime of 0.5-1.5 ps and spectral diffusion originating from excitation energy transfer (EET) in the system. The rate of EET was positively correlated to the fraction of aromatic species and tightness of aromatic species packing. Diminishing the number of EET donor-acceptor pairs by reduction with NaBH₄ (decrease of the acceptor number), decrease of pH (decrease of the electron-donating ability), or decrease of the average particle size by filtration (less donor-acceptor pairs within a particle) resulted in a lower impact of the ultrafast component on fluorescence decay. Our results uncover the role of electronic coupling among fluorophores in the formation of DOM and HS optical properties and provide a framework for studying photophysical processes in heterogeneous systems of natural fluorophores.

Microbial transformation of distinct exogenous substrates into analogous composition of recalcitrant dissolved organic matter

Oceanic dissolved organic matter (DOM) comprises a complex molecular mixture which is typically refractory and homogenous in the deep layers of the ocean. Though the refractory nature of deep-sea DOM is increasingly attributed to microbial metabolism, it remains unexplored whether ubiquitous microbial metabolism of distinct carbon substrates could lead to similar molecular composition of refractory DOM. Here, we conducted microbial incubation experiments using four typically bioavailable substrates (L-alanine, trehalose, sediment DOM extract, and diatom lysate) to investigate how exogenous substrates are transformed by a natural microbial assemblage. The results showed that although each-substrate-amendment induced different changes in the initial microbial assemblage and the amended substrates were almost depleted after 90 days of dark incubation, the bacterial community compositions became similar in all incubations on day 90. Correspondingly, revealed by ultra-high resolution mass spectrometry, molecular composition of DOM in all incubations became compositionally consistent with recalcitrant DOM and similar toward that of DOM from the deep-sea. These results indicate that while the composition of natural microbial communities can shift with substrate exposures, long-term microbial transformation of distinct substrates can ultimately lead to a similar refractory DOM composition. These findings provide an explanation for the homogeneous and refractory features of deep-sea DOM.

Water quality assessment of the Ganges River during COVID-19 lockdown

Ganges River water quality was assessed to record the changes due to the nation-wide pandemic lockdown. Satellite-based (Sentinel-2) water quality analysis before and during lockdown was performed for seven selected locations spread across the entire stretch of the Ganges (Rishikesh-Dimond Harbour). Results revealed that due to the lockdown, the water quality of the Ganges improved with reference to specific water quality parameters, but the improvements were region specific. Along the entire stretch of Ganges, only the Haridwar site showed improvement to an extent of being potable as per the threshold set by the Central Pollution Control Board, New Delhi, India. A 55% decline in turbidity at that site during the lockdown was attributed to the abrupt halt in pilgrimage activities. Absorption by chromophoric dissolved organic matter which is an indicator of organic pollution declined all along the Ganges stretch with a maximum decline at the downstream location of Diamond Harbour. Restricted discharge of industrial effluent, urban pollution, sewage from hotels, lodges, and spiritual dwellings along the Ganges are some of the reasons behind such declines. No significant change in the geographic trend of chlorophyll-a was observed. The findings of this study highlight the importance of regular monitoring of the changes in the Ganges water quality using Sentinel-2 data to further isolate the anthropogenic impact, as India continues the phase-wise opening amidst the pandemic.

Advances in the characterization and monitoring of natural organic matter using spectroscopic approaches

Natural organic matter (NOM) is ubiquitous in environment and plays a fundamental role in the geochemical cycling of elements. It is involved in a wide range of environmental processes and can significantly affect the environmental fates of exogenous contaminants. Understanding the properties and environmental behaviors of NOM is critical to advance water treatment technologies and environmental remediation strategies. NOM is composed of characteristic light-absorbing/emitting functional groups, which are the "identification card" of NOM and susceptive to ambient physiochemical changes. These groups and their variations can be captured through optical sensing. Therefore, spectroscopic techniques are elegant tools to track the sources, features, and environmental behaviors of NOM. In this work, the most recent advances in molecular spectroscopic techniques, including UV-Vis, fluorescence, infrared, and Raman spectroscopy, for the characterization, measurement, and monitoring of NOM are reviewed, and the state-of-the-art innovations are highlighted. Furthermore, the limitations of current spectroscopic approaches for the exploration of NOM-related environmental processesand how these weaknesses/drawbacks can be addressed are explored. Finally, suggestions and directions are proposed to advance the development of spectroscopic methods in analyzing and elucidating the properties and behaviors of NOM in natural and engineered environments.

Viral Lysis Alters the Optical Properties and Biological Availability of Dissolved Organic Matter Derived from Prochlorococcus Picocyanobacteria

Phytoplankton contribute almost half of the world's total primary production. The exudates and viral lysates of phytoplankton are two important forms of dissolved organic matter (DOM) in aquatic environments and fuel heterotrophic prokaryotic metabolism. However, the effect of viral infection on the composition and biological availability of phytoplankton-released DOM is poorly understood. Here, we investigated the optical characteristics and microbial utilization of the exudates and viral lysates of the ecologically important unicellular picophytoplankton Prochlorococcus Our results showed that Prochlorococcus DOM produced by viral lysis (Pro-vDOM) with phages of three different morphotypes (myovirus P-HM2, siphovirus P-HS2, and podovirus P-SSP7) had higher humic-like fluorescence intensities, lower absorption coefficients, and higher spectral slopes than DOM exuded by Prochlorococcus (Pro-exudate). The results indicate that viral infection altered the composition of Prochlorococcus-derived DOM and might contribute to the pool of oceanic humic-like DOM. Incubation with Pro-vDOM resulted in a greater dissolved organic carbon (DOC) degradation rate and lower absorption spectral slope and heterotrophic bacterial growth rate than incubation with Pro-exudate, suggesting that Pro-vDOM was more bioavailable than Pro-exudate. In addition, the stimulated microbial community succession trajectories were significantly different between the Pro-exudate and Pro-vDOM treatments, indicating that viral lysates play an important role in shaping the heterotrophic bacterial community. Our study demonstrated that viral lysis altered the chemical composition and biological availability of DOM derived from Prochlorococcus, which is the numerically dominant phytoplankton in the oligotrophic ocean.IMPORTANCE The unicellular picocyanobacterium Prochlorococcus is the numerically dominant phytoplankton in the oligotrophic ocean, contributing to the vast majority of marine primary production. Prochlorococcus releases a significant fraction of fixed organic matter into the surrounding environment and supports a vital portion of heterotrophic bacterial activity. Viral lysis is an important biomass loss process of Prochlorococcus However, little is known about whether and how viral lysis affects Prochlorococcus-released dissolved organic matter (DOM). Our paper shows that viral infection alters the optical properties (such as the absorption coefficients, spectral slopes, and fluorescence intensities) of released DOM and might contribute to a humic-like DOM pool and carbon sequestration in the ocean. Meanwhile, viral lysis also releases various intracellular labile DOM, including amino acids, protein-like DOM, and lower-molecular-weight DOM, increases the bioavailability of DOM, and shapes the successive trajectory of the heterotrophic bacterial community. Our study highlights the importance of viruses in impacting the DOM quality in the ocean.

Evaluation of the Production of Dissolved Organic Matter by Three Marine Bacterial Strains

A large part of marine dissolved organic matter (DOM) is considered to be recalcitrant DOM (RDOM) produced by marine bacteria. However, it is still unclear whether differences in bacterial species and/or physiology control the efficiency of RDOM production. Here, batch culture experiments with glucose as the sole carbon source were carried out using three model marine bacterial strains, namely, Alteromonas macleodii (Alt), Vibrio splendidus (Vib), and Phaeobacter gallaeciensis (Pha). Dissolved organic carbon (DOC) concentrations drastically decreased during the exponential growth phases of these bacteria due to the consumption of glucose. The efficiency of bacterial DOC production at the end of incubation was largely different among the strains and was higher for Vib (20%) than for the other two strains (Alt, 4%; Pha, 6%). All strains produced fluorescent DOM (FDOM), including humic-like FDOM which is considered as recalcitrant component in the ocean, even though the composition of bacterial FDOM was also different among the strains. The efficiency of humic-like FDOM production during the exponential growth phase was different among the bacterial strains; that is, Pha produced humic-like FDOM efficiently compared with the other two species. The efficiency of humic-like FDOM production with mineralization of organic matter was lower during the exponential growth phase than during the stationary phase of Alt and Pha. Four processes for the production of bacterially derived recalcitrant humic-like FDOM are suggested from this study: (1) production during active growing (in all strains), (2) production with the reutilization of bacterial DOM (Alt), (3) production with the consumption of cellular materials (Pha), and (4) release from lysis (Vib). Our results suggest that bacterial species and physiology can regulate RDOM production and accumulation in the ocean.

Quantitative determination of redox-active carbonyls of natural dissolved organic matter

Natural dissolved organic matter (DOM) is ubiquitous in environment and plays an important role in numerous environmental processes. Although the molecular basis of the reactivity of DOM remains poorly understood due to its extreme complexity, redox-active carbonyls (aromatic ketones/aldehydes and quinones) within DOM are believed vitally important. Except the rough determination of total carbonyls (including non-redox active -COOR) based on inflexible ¹³C chemical shift range by expensive and time-consuming solid-state nuclear magnetic resonance (NMR), there is no ready method to quantify redox-active carbonyls in DOM. Here we show that after treatment with sodium borohydride (NaBH₄) by selectively eliminating redox-active carbonyls, quenched fluorescence of carbon quantum dots (CD) by DOM recovered dramatically, and displayed a good linear relationship between redox-active carbonyls detected and DOM concentration (R² ≥ 0.977), thus allowing first quantitative determination of the redox-active carbonyls of DOM. Eight DOM isolates present 0.59%-0.90% redox-active carbonyls by the current method. And this method is robust from coexisting proteins and salts. This method could provide better or equal instructive results compared with solid-state NMR for total carbonyls or electrochemical method for electron-accepting capacities (EAC). Our results provide the underlying structural basis of many important geochemical processes that mediated by DOM. We posit that this method could apply to other complex molecular systems such as the atmospheric aerosols and extracellular polymeric substances (EPS), too.

DOC dynamics and bacterial community succession during long-term degradation of Ulva prolifera and their implications for the legacy effect of green tides on refractory DOC pool in seawater

Under climate warming and coastal eutrophication, outbreaks of green tides have increased in recent decades; e.g., the world's largest green tide caused by Ulva prolifera has occurred in the Yellow Sea for 13 consecutive years. The massive assemblage of macroalgae absorbs large amounts of atmospheric CO₂ and converts it into biomass. After the green tide, millions of tons of the macroalgal biomass sink to the seabed to be degraded eventually; this inevitably has a significant impact on the coastal organic carbon pool and microbial community. However, this impact is poorly understood. Here, the degradation of Ulva prolifera over 520 days revealed that relatively sufficient degradation of the macroalgae occurred at ca. 7 months. The rapid release of dissolved organic carbon (DOC) mainly occurred in the first week, which not only increased the size and diversity of the DOC pool in a short time but also promoted the rapid growth of bacteria and led to hypoxia and acidification of the seawater. After that, the labile portion of DOC was gradually used up by bacteria within one month, while the degradation of semi-labile or semi-refractory DOC occurred in half a year. The remaining DOC existed in the form of refractory DOC (RDOC), resisting bacterial consumption and remaining stable for 10 months. During the long-term degradation process, bacterial community structure and metabolic function showed obvious successional characteristics, driving the gradual transformation of DOC from labile to refractory through the microbial carbon pump mechanism. After the long-term degradation, the remaining RDOC accounted for approximately 1.6% of the macroalgal carbon biomass. As RDOC can maintain long-term stability, we propose that the frequent outbreaks of green tides not only affect microbial processes but also may have an important cumulative effect on the coastal RDOC pool.

Optical characteristics of colored dissolved organic matter during blooms of Trichodesmium in the coastal waters off Goa

Trichodesmium, a marine cyanobacterium, plays a significant role in the global nitrogen cycle due to its nitrogen fixing ability. Large patches of Trichodesmium blooms were observed in the coastal waters, off Goa during spring intermonsoon (SIM) of 2014-2018. Zeaxanthin was the dominant pigment in the bloom region. Here, we present the spectral absorption and fluorescence characteristics of colored dissolved organic matter (CDOM) during these blooms. CDOM concentration was much higher in the bloom patches as compared with nonbloom regions. During the bloom spectral CDOM absorption had distinct peaks in the UV region due to the presence of UV-absorbing/screening compounds, mycosporine-like amino acids (MAAs) and in the visible region due to phycobiliproteins (PBPs). The spectral fluorescence signatures by the traditional peak picking method exhibited three peaks, one was protein-like, and the other two were humic-like. Apart from these, Trichodesmium exhibited strong protein-like fluorescence with 370/460 nm (Ex/Em), which is a signature of cyanobacteria. A parallel factor analysis (PARAFAC) on the fluorescence excitation-emission matrix (EEM) of Trichodesmium dataset fitted a 3-component model of which one was protein-like, and two were humic-like. The fluorescence index (FI) values during Trichodesmium bloom was very high (~ 3) compared with the typical range of 1.2-1.8 observed for the natural waters. Bloom degradation experiments proved that increase in tryptophan fluorescence enhances the CDOM absorption. Our study indicates that Trichodesmium blooms provide a rich source of organic matter in the coastal waters and long-term monitoring of these blooms is essential for understanding the health of ecosystem.

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.

Small Phytoplankton Shapes Colored Dissolved Organic Matter Dynamics in the North Atlantic Subtropical Gyre

The North Atlantic subtropical gyre (NASTG) is a model of the future ocean under climate change. Ocean warming signals are hidden within the blue color of these clear waters and can be tracked by understanding the dynamics among phytoplankton chlorophyll ([Chl]) and colored dissolved organic matter (CDOM). In NASTG, [Chl] and CDOM are strongly correlated. Yet, this unusual correlation for open oceans remains unexplained. Here, we test main hypotheses by analyzing high spatiotemporal resolution data collected by Biogeochemical-Argo floats between 2012 and 2018. The direct production of CDOM via phytoplankton metabolism is the main occurring mechanism. More importantly, CDOM dynamics strongly depend on the abundance of picophytoplankton. Our findings thus highlight the critical role of these small organisms under the ocean warming scenario. Picophytoplankton will enhance the production of colored dissolved compounds and, ultimately, impact on the ocean carbon cycle.

DOM as an indicator of occurrence and risks of antibiotics in a city-river-reservoir system with multiple pollution sources

Multiple sources contribute to the presence of antibiotic residues in water environments, and the environmental risks caused by antibiotics were paid more and more attention. This work aims to establish a relationship between optical properties of dissolved organic matter (DOM) and sources and risks of antibiotics. Occurrence of antibiotics and DOM in a city-river-reservoir freshwater system containing distinct antibiotic sources was investigated during three seasons using LC-MS and fluorescence excitation-emission matrix coupled with parallel factor analysis (EEM-PARAFAC), respectively. The results showed that antibiotics and DOM in the water had trends of increasing levels from the upstream to the midstream in the system. Five classes of antibiotics had statistically significant correlations with the humic-like component (C3) in the water (Pearson, p < 0.05). Especially, norfloxacin (NFX), which was dominant in the aquaculture source, significantly increased the fluorescence of C3 according to the fluorescence titration (R² = 0.86, p < 0.01). Furthermore, fluorescence signature in the aquaculture pond posed broad humic acid-like peaks with relatively higher abundances compared to other areas. These results suggested that C3 could be recognized as an indicator of NFX from aquaculture sources. Meanwhile, C3 can largely account for ecological risks of tetracyclines according to the results of redundancy analysis. This work highlights the roles of EEM-PARAFAC on tracing the source of antibiotics and the correlations between environmental risks of antibiotics and DOM in the aquatic environment.

Synergistic effects of urban tributary mixing on dissolved organic matter biodegradation in an impounded river system

Dams and wastewater may greatly perturb riverine fluxes of dissolved organic matter (DOM) and CO₂, yet little is known about the relationships between altered DOM quality and CO₂ emission in eutrophic impounded river systems. A basin-wide field survey of surface water CO₂ and dissolved organic carbon (DOC) was combined with laboratory incubations to examine how dams and urban tributaries delivering treated wastewater influence longitudinal patterns in DOM properties and CO₂ along the impounded Han River traversing Seoul metropolitan area. Fluorescent DOM indices including parallel factor analysis (PARAFAC) components were used to characterize DOM in relation to biodegradable DOC (BDOC). Compared with distinct downstream increases in DOC and CO₂, BDOC concentration and its proportion in DOC (%BDOC) were highly variable along the mainstem and peaked at urban tributaries. Longitudinal increases in fluorescence index (FI), biological index (BIX), and two PARAFAC components (C2 and C3) contrasted with general decreases in humification index (HIX) and C1, reflecting increasing downstream inputs of anthropogenic DOM. During a 5-day incubation employing continuous CO₂ measurements, the cumulative production of CO₂ in the mainstem water mixed with urban tributary water was significantly higher than the level expected for conservative mixing of the two samples, indicating a synergistic enhancement of DOM biodegradation. Molecular formulas identified by Fourier transform-ion cyclotron resonance-mass spectrometry (FT-ICR-MS) revealed more consumed molecules in the mainstem water and more newly produced molecules in the tributary water over the 5-day incubation, implying abundant labile components in the mainstem water discharged from the upstream dam and highly processed tributary DOM limited in immediately biodegradable organic materials. Downstream increases in CO₂ and DOC along the Han River, combined with the synergistic effect observed in the mixed water, suggest that mixing wastewater-derived DOM with labile autochthonous DOM can enhance CO₂ production in the river system perturbed by impoundment and wastewater.

Microbial transformation of virus-induced dissolved organic matter from picocyanobacteria: coupling of bacterial diversity and DOM chemodiversity

Picocyanobacteria make up half of the ocean's primary production, and they are subjected to frequent viral infection. Viral lysis of picocyanobacteria is a major driving force converting biologically fixed carbon into dissolved organic carbon (DOC). Viral-induced dissolved organic matter (vDOM) released from picocyanobacteria provides complex organic matter to bacterioplankton in the marine ecosystem. In order to understand how picocyanobacterial vDOM are transformed by bacteria and the impact of this process on bacterial community structure, viral lysate of picocyanobacteria was incubated with coastal seawater for 90 days. The transformation of vDOM was analyzed by ultrahigh-resolution mass spectrometry and the shift of bacterial populations analyzed using high-throughput sequencing technology. Addition of picocyanobacterial vDOM introduced abundant nitrogen components into the coastal water, which were largely degraded during the 90 days' incubation period. However, some DOM signatures were accumulated and the total assigned formulae number increased over time. In contrast to the control (no addition of vDOM), bacterial community enriched with vDOM changed markedly with increased biodiversity indices. The network analysis showed that key bacterial species formed complex relationship with vDOM components, suggesting the potential correspondence between bacterial populations and DOM molecules. We demonstrate that coastal bacterioplankton are able to quickly utilize and transform lysis products of picocyanobacteria, meanwhile, bacterial community varies with changing chemodiverisity of DOM. vDOM released from picocyanobacteria generated a complex labile DOM pool, which was converted to a rather stable DOM pool after microbial processing in the time frame of days to weeks.

Molecular characteristics of microbially mediated transformations of Synechococcus-derived dissolved organic matter as revealed by incubation experiments

In this study, we investigated the microbially mediated transformation of labile Synechococcus-derived DOM to RDOM using a 60-day experimental incubation system. Three phases of TOC degradation activity (I, II and III) were observed following the addition of Synechococcus-derived DOM. The phases were characterized by organic carbon consumption rates of 8.77, 1.26 and 0.16 μmol L^-1 day^-1 , respectively. Excitation emission matrix analysis revealed the presence of three FDOM components including tyrosine-like, fulvic acid-like, and humic-like molecules. The three components also exhibited differing biological availabilities that could be considered as labile DOM (LDOM), semi-labile DOM (SLDOM) and RDOM, respectively. DOM molecular composition was also evaluated using FT-ICR MS. Based on differing biological turnover rates and normalized intensity values, a total of 1704 formulas were identified as candidate LDOM, SLDOM and RDOM molecules. Microbial transformation of LDOM to RDOM tended to proceed from high to low molecular weight, as well as from molecules with high to low double bond equivalent (DBE) values. Relatively higher aromaticity was observed in the formulas of RDOM molecules relative to those of LDOM molecules. FDOM components provide valuable proxy information to investigate variation in the bioavailability of DOM. These results suggest that coordinating fluorescence spectroscopy and FT-ICR MS of DOM, as conducted here, is an effective strategy to identify and characterize LDOM, SLDOM and RDOM molecules in incubation experiments emulating natural systems. The results described here provide greater insight into the metabolism of phytoplankton photosynthate by heterotrophic bacteria in marine environments.

The chemodiversity of algal dissolved organic matter from lysed Microcystis aeruginosa cells and its ability to form disinfection by-products during chlorination

Algal-derived dissolved organic matter (ADOM) originating from lysed Microcystis aeruginosa cells was investigated as precursor material to form disinfection by-products upon disinfection with free chlorine. Non-targeted ultrahigh resolution 12 T negative mode electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) revealed high molecular diversity in solid-phase extracted and ionizable components of Microcystis aeruginosa ADOM. The toxin microcystin LR was effectively degraded by free chlorine, which was expected. However, we found a high diversity of disinfection by-products associated with the addition of free chlorine to the water-soluble and solid-phase extractable fraction of ADOM and of double-bond moieties in abundant and known unsaturated fatty acids. Aromatic DOM precursors were absent from known metabolites of Microcystis aeruginosa and no evidence for aromatic disinfection by-products (DBPs) was found, despite N-containing compounds. A large diversification of N-containing molecular formulas was observed after chlorination, which seems indicative for the breakdown and oxidation of larger peptides. Additionally, a diverse group of N-compounds with presumed chloramine functional groups was observed. This study highlights the importance to evaluate ADOM and its ability to form different DBPs when compared to allochthonous or terrestrially-derived DOM.

Dissolved organic carbon contribution to oxygen respiration in the central Red Sea

In oligotrophic waters, dissolved organic carbon (DOC) is mostly produced in the surface layers by phytoplankton and remineralized by heterotrophic prokaryotes throughout the water column. DOC surface excess is subducted and exported to deeper layers where a semi-labile fraction is further processed contributing to oxygen consumption. How this cycling of DOC occurs in the Red Sea, one of the warmest oligotrophic marine basins, is virtually unknown. We examined DOC vertical and seasonal variability in a mesopelagic station (ca. 700 m depth) of the central Red Sea performing monthly profile samplings over a two-year period. Together with DOC vertical and seasonal distribution we evaluated the interaction with heterotrophic prokaryotes and contribution to oxygen respiration. DOC values ranged from 41.4 to 95.4 µmol C L⁻¹, with concentrations in the epipelagic (70.0 ± 7.5 µmol C L⁻¹) 40% higher on average than in the mesopelagic (50.7 ± 4.1 µmol C L⁻¹). Subduction of seasonally accumulated semi-labile DOC was estimated to be responsible for ∼20% of the oxygen consumption mostly occurring at the low epipelagic-upper mesopelagic boundary layer. Variability in mesopelagic waters was higher than expected (ca. 20 µmol C L⁻¹) evidencing a more active realm than previously thought, with consequences for carbon sequestration.

The mesopelagic anoxic Black Sea as an unexpected habitat for Synechococcus challenges our understanding of global "deep red fluorescence"

The Black Sea is the largest meromictic sea with a reservoir of anoxic water extending from 100 to 1000 m depth. These deeper layers are characterised by a poorly understood fluorescence signal called “deep red fluorescence”, a chlorophyll a- (Chl a) like signal found in deep dark oceanic waters. In two cruises, we repeatedly found up to 10³ cells ml⁻¹ of picocyanobacteria at 750 m depth in these waters and isolated two phycoerythrin-rich Synechococcus sp. strains (BS55D and BS56D). Tests on BS56D revealed its high adaptability, involving the accumulation of Chl a in anoxic/dark conditions and its capacity to photosynthesise when re-exposed to light. Whole-genome sequencing of the two strains showed the presence of genes that confirms the putative ability of our strains to survive in harsh mesopelagic environments. This discovery provides new evidence to support early speculations associating the “deep red fluorescence” signal to viable picocyanobacteria populations in the deep oxygen-depleted oceans, suggesting a reconsideration of the ecological role of a viable stock of Synechococcus in dark deep waters.

Transcriptomic responses of the marine cyanobacterium Prochlorococcus to viral lysis products

Viral infection of marine phytoplankton releases a variety of dissolved organic matter (DOM). The impact of viral DOM (vDOM) on the uninfected co-occurring phytoplankton remains largely unknown. Here, we conducted transcriptomic analyses to study the effects of vDOM on the cyanobacterium Prochlorococcus, which is the most abundant photosynthetic organism on Earth. Using Prochlorococcus MIT9313, we showed that its growth was not affected by vDOM, but many tRNAs increased in abundance. We tested tRNA-gly and found that its abundance increased upon addition of glycine. The decreased transcript abundances of N metabolism genes also suggested that Prochlorococcus responded to organic N compounds in vDOM. Addition of vDOM to Prochlorococcus reduced the maximum photochemical efficiency of photosystem II and CO₂ fixation while increasing its respiration rate, consistent with differentially abundant transcripts related to photosynthesis and respiration. One of the highest positive fold-changes was observed for the 6S RNA, a noncoding RNA functioning as a global transcriptional regulator in bacteria. The high level of 6S RNA might be responsible for some of the observed transcriptional responses. Taken together, our results revealed the transcriptional regulation of Prochlorococcus in response to viral lysis products and suggested its metabolic potential to utilize organic N compounds.

Impacts of maricultural activities on characteristics of dissolved organic carbon and nutrients in a typical raft-culture area of the Yellow Sea, North China

Ailian Bay is an integrated multi-trophic aquaculture bay with approximately 60 years maricultural activities in North China. The floating raft culture of kelp and shellfish is the unique mariculture mode. In this study, the impacts of intensive mariculture activities on seasonal carbon and nutrient dynamics in Ailian Bay were systematically analysed via seasonal surveys between 2015 and 2016. The dissolved inorganic nitrogen and silicon reached the maximum concentrations during summer, which were mainly attributed to the release of shellfish metabolic by-products and their filter-feeding effects on diatoms. Dissolved organic carbon (DOC) concentrations were significantly elevated when kelps were rotting in summer and kelp seeding were occurring in winter. Meanwhile, the fluorescence intensity of humic-like chromophoric dissolved organic matter was relatively high in kelp mariculture zone. As most humic-like DOC are potentially refractory substances, we propose that kelp mariculture would contribute importantly to the increase of refractory DOC pool in oceans.

Chemical transfer of dissolved organic matter from surface seawater to sea spray water-soluble organic aerosol in the marine atmosphere

It is critical to understand how variations in chemical composition in surface seawater (SSW) affect the chemistry of marine atmospheric aerosols. We investigated the sea-to-air transfer of dissolved organic carbon (DOC) via cruise measurements of both ambient aerosols and SSW in the Oyashio and its coastal regions, the western subarctic Pacific during early spring. Sea spray aerosols (SSAs) were selected based on the stable carbon isotope ratio of water-soluble organic carbon (WSOC) (δ¹³C_WSOC) and concentrations of glucose as a molecular tracer in marine aerosols together with local surface wind speed data. For both SSA and SSW samples, excitation-emission matrices were obtained to examine the transfer of fluorescent organic material. We found that the ratios of fluorescence intensity of humic-like and protein-like substances in the submicrometer SSAs were significantly larger than those in the bulk SSW (~63%). This ratio was also larger for the supermicrometer SSAs than for the SSW. The results suggest significant decomposition of protein-like DOC on a timescale of <12-24 h and/or preferential production of humic-like substances in the atmospheric aerosols regardless of the particle size. This study provides unique insights into the complex transfer of DOC from the ocean surface to the atmosphere.

Sources and coastal distribution of dissolved organic matter in the Gulf of Cadiz

Dissolved organic matter (DOM) is a major component of the organic matter pool, playing a key role in the global ocean functioning. However, studies on DOM in waters of many ocean regions, such as the Gulf of Cadiz (GoC), are poorly known. Advanced aquatic sensors enable autonomous for long-term deployments in situ collection of high frequency DOM data using fluorescent dissolved organic matter (FDOM) as a proxy. The present study evaluates the relevance of FDOM, the estuarine influence and the environmental factors that determine its spatial distribution in the GoC. Our results suggest that the GoC water mass, under the estuarine influence of three main rivers, is receiving large amounts of DOM transported mainly by Guadalquivir and Guadiana rivers and much less from Tinto-Odiel. Salinity is the main factor explaining the FDOM variability within the Guadalquivir and Guadiana rivers and in the inner shelf of the GoC. In the outer shelf of the GoC, plankton-produced DOM could explain the persistent spatial pattern of FDOM, playing an important role in the dynamics of FDOM from the North area of the GoC through the persistent low-salinity Eastern North Atlantic Central Water. The oceanographic dynamics and the spatial pattern of FDOM concentration in the continental shelf of the GoC suggest a net transport of FDOM through the GCC (Gulf of Cadiz Current) to the Mediterranean Sea.

Evolving paradigms in biological carbon cycling in the ocean

Carbon is a keystone element in global biogeochemical cycles. It plays a fundamental role in biotic and abiotic processes in the ocean, which intertwine to mediate the chemistry and redox status of carbon in the ocean and the atmosphere. The interactions between abiotic and biogenic carbon (e.g. CO2, CaCO3, organic matter) in the ocean are complex, and there is a half-century-old enigma about the existence of a huge reservoir of recalcitrant dissolved organic carbon (RDOC) that equates to the magnitude of the pool of atmospheric CO2. The concepts of the biological carbon pump (BCP) and the microbial loop (ML) shaped our understanding of the marine carbon cycle. The more recent concept of the microbial carbon pump (MCP), which is closely connected to those of the BCP and the ML, explicitly considers the significance of the ocean's RDOC reservoir and provides a mechanistic framework for the exploration of its formation and persistence. Understanding of the MCP has benefited from advanced ‘omics’ and novel research in biological oceanography and microbial biogeochemistry. The need to predict the ocean's response to climate change makes an integrative understanding of the BCP, ML and MCP a high priority. In this review, we summarize and discuss progress since the proposal of the MCP in 2010 and formulate research questions for the future.

Efficient dissolved organic carbon production and export in the oligotrophic ocean

Biologically fixed carbon is transferred from the surface to deep ocean as sinking particles or dissolved organic carbon (DOC). DOC is estimated to account for ~20% of global export production, but the degree to which this varies regionally has not been assessed at a global scale. Here we present the first observationally based global-scale assessment of DOC production and export, obtained by combining an artificial neural network estimate of the global DOC distribution, and a data-constrained ocean circulation model. Our results demonstrate that the efficiency of DOC production and export varies more than threefold across oceanographic regions. DOC production and export display a pronounced peak in the oligotrophic subtropical oceans, where DOC accounts for roughly half of the total organic carbon export. These stratified nutrient-depleted regions are expected to expand with future warming, amplifying the role of DOC in the biological pump, and magnifying the need to improve DOC cycling in climate models.