Molecular dynamics and factors governing recalcitrance of dissolved organic matter: Insights from laboratory incubation and ultra-high resolution mass spectrometry

The oceanic dissolved organic matter (DOM) reservoir is one of Earth's largest carbon pools, yet the factors contributing to its recalcitrance and persistence remain poorly understood. Here, we employed ultra-high resolution mass spectrometry (UHRMS) to examine the molecular dynamics of DOM from terrestrial, marine and mixed sources during bio-incubation over weekly, monthly, and one year time spans. Using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), we classified DOM into three distinct categories (Consumed, Resistant and Product) based on their presence or absence at the start and end of the incubation. Our results show that molecular properties, such as hydrogen to carbon ratio (H/C), modified aromaticity index (AImod), and nominal oxidation state of carbon (NOSC), strongly influence DOM lability and its biogeochemical cycling. Interestingly, Product formulas identified in the short-term incubations were often reclassified as Consumed formulas in longer-term incubations, underscoring the importance of incubation time in determining the persistence of DOM formulas. Further, we introduced a Change Ratio (CR) to identify formulas with significantly altered relative abundances. The molecular characteristics of these Increase or Decrease formulas exhibited notable differences, reinforcing their role in determining lability. In seawater samples, Decrease formulas were more abundant than Increase formulas, supporting the dilution hypothesis, which suggests low concentrations contribute to biological recalcitrance. However, the instability of relative abundance differences between Increase and Decrease formulas when CR thresholds were altered, coupled with the robustness of AImod differences, highlights the dominance of molecular properties over concentration in determining DOM lability. Furthermore, the AImod distribution of these Increase and Decrease formulas mirrored deep-enriched and surface-enriched formulas in the open ocean, validating our incubation results with field investigations. Overall, our study demonstrates that combining laboratory incubation with UHRMS advances our molecular-level understanding of DOM recalcitrance and thus global carbon cycling.

A review on amino acids as proxies for organic matter degradation in aquatic ecosystems: implications for nutrient cycling, climate change, and ecosystem management

The fate and degradation of organic matter in aquatic systems is a vital link in nutrient cycling and sedimentation processes influenced by exogenous and endogenous factors, such as inputs from upstream sources, sediment suspension, and the decomposition of aquatic organisms. The interplay of organic carbon, microbes, and environmental factors shapes the distribution and degradation of organic matter. Characterizing the source distribution of sedimentary organic matter in aquatic systems using novel proxies can unravel new insights into the mechanisms that control its dispersal, preservation and fate, which is essential to understanding the global carbon and nitrogen cycles. Therefore, the present review critically investigated amino acids as crucial markers for assessing the degradation status in lacustrine and marine sediments and highlighted the pivotal function of biotic and abiotic determinants that influence the mineralization of organic matter. The review thoroughly discussed studies on the spatio-temporal distribution patterns of amino acids and their bio-refractory nature to overcome the challenges in evaluating sediment organic matter degradation in aquatic systems. Recognizing the paramount impact of climate change on aquatic ecosystems, the review further elucidated how integrating amino acid-based data into climate models is essential for predicting complex interplay between degradation processes and evolving environmental dynamics. Finally, the specific needs for further research and recommendations for developing efficient and sustainable strategies to study organic matter degradation were highlighted. The present review will deliver fresh inferences to researchers, ecologists, and policymakers for a better understanding of source distribution and degradation status of organic matter for evidence-based conservation and management strategies.

Microbial carbon oxidation in seawater below the hypoxic threshold

Global oxygen minimum zones (OMZs) often reach hypoxia but seldom reach anoxia. Recently it was reported that Michaelis Menten constants (Km) of oxidative enzymes are orders of magnitude higher than respiratory Km values, and in the Hypoxic Barrier Hypothesis it was proposed that, in ecosystems experiencing falling oxygen, oxygenase enzyme activities become oxygen-limited long before respiration. We conducted a mesocosm experiment with a phytoplankton bloom as an organic carbon source and controlled dissolved oxygen (DO) concentrations in the dark to determine whether hypoxia slows carbon oxidation and oxygen decline. Total oxygen utilization (TOU) in hypoxic treatment (ca. 7.1 µM O2) was 21.7% lower than the oxic treatment (ca. 245.1 µM O2) over the first 43 days of the experiment. In addition, following the restoration of fully oxic conditions to the hypoxic treatment, TOU accelerated, demonstrating that oxidative processes are sensitive to DO concentrations found in large volumes of the ocean. Microbial amplicon-based community composition diverged between oxic treatments, indicating a specialized microbiome that included Thioglobaceae (SUP05 Gammaproteobacteria), OM190 (Planctomycetota), ABY1 (Patescibacteria), and SAR86 subclade D2472, thrived in the hypoxic treatment, while the genus Candidatus Actinomarina and SAR11 alphaproteobacteria were sharply inhibited. Our findings support the hypothesis that oxygenase kinetics might slow the progression of ocean deoxygenation in oxygen-poor regions and be a factor in the evolution of microbial taxa adapted to hypoxic environments.

Deciphering source, degradation status and temporal trends of organic matter in a himalayan freshwater lake using multiproxy indicators, optically stimulated luminescence dating and time series forecasting

The present study assessed source, degradation status, and temporal trends of organic matter up to ∼3700 years Before Present (BP) in Dal Lake sediment cores using multiproxy indicators, optically stimulated luminescence (OSL) dating, and time series forecasting. Bulk organic parameters such as total organic carbon and total nitrogen indicated their increasing trend in upper sediment layers from ∼476 to ∼73 years BP. Similarly, the C/N ratio revealed varying sources of organic matter with values ranging from 2.26 to 13.05, depicting an increasing trend up to ∼1811 years BP and decreasing significantly from ∼2002 years BP. Amino acid and hexosamine concentrations decreased with depth, dominated by aspartic acid, glycine, glutamic acid, alanine, glucosamine, and galactosamine in recent sediments (∼73 years BP) of the lake. The positive degradation index (DI) confirmed fresh organic matter in top sediment layers (∼396 years BP) of the lake, showing a strong positive correlation with reactivity index (RI) and total organic carbon. However, a negative correlation was observed between DI and RI with Ox/Anox index. Furthermore, the Gluam/Galam, Asp/β-Ala and Glu/γ-Aba ratios revealed enhanced organic matter degradation with age, indicating prokaryotic origins, microbial activity changes, and redox conditions within the lake. Multivariate analysis revealed increasing autochthonous and allochthonous inputs, domestic effluent discharges, agricultural runoff, redox conditions, and microbial processes as the possible contributing factors affecting the dispersal pattern of amino acids and nutrients in Dal Lake. Time series forecasting using the ARIMA model effectively confirmed the future temporal dynamics of amino acids, and organic parameters, indicating potential ecological shifts and external influences affecting the degradation of organic matter in Dal Lake. This work provides novel insights into the diagenetic alterations and biogeochemical processes essential for understanding the organic matter cycling and guiding the conservation efforts for Dal Lake and beyond.

Overlooked Vital Role of Persistent Algae-Bacteria Interaction in Ocean Recalcitrant Carbon Sequestration and Its Response to Ocean Warming

Long-term carbon sequestration by the ocean's recalcitrant dissolved organic carbon (RDOC) pool regulates global climate. Algae and bacteria interactively underpin RDOC formation. However, on the long-term scales, the influence of their persistent interactions close to in situ state on ocean RDOC dynamics and accumulation remains unclear, limiting our understanding of the oceanic RDOC pool formation and future trends under global change. We show that a Synechococcus-bacteria interaction model system viable over 720 days gradually accumulated high DOC concentrations up to 84 mg L-1. Concurrently, the DOC inertness increased with the RDOC ratio reaching > 50%. The identified Synechococcus-bacteria-driven RDOC molecules shared similarity with over half of those from pelagic ocean DOC. Importantly, we provide direct genetic and metabolite evidence that alongside the continuous transformation of algal carbon by bacteria to generate RDOC, Synechococcus itself also directly synthesized and released RDOC molecules, representing a neglected RDOC source with ~0.2-1 Gt y-1 in the ocean. However, we found that although ocean warming (+4°C) can promote algal and bacterial growth and DOC release, it destabilizes and reduces RDOC reservoirs, jeopardizing the ocean's carbon sequestration capacity. This study unveils the previously underestimated yet significant role of algae and long-term algae-bacteria interactions in ocean carbon sequestration and its vulnerability to ocean warming.

Seaweed burial mitigated the release of organic carbon and nutrients by regulating microbial activity

Seaweed debris is susceptible to being buried in sediments due to natural environmental changes and human activities. So far, the effect of buried seaweeds on the environment and its decomposition mechanism remains unclear. This study simulated the decomposition of seaweed Gracilariopsis lemaneiformis for 180 days with different burial depths (0 cm and 10 cm) and burial weights (10 g and 20 g). Our findings revealed that compared with Gracilariopsis decomposition on the sediment surface, the seaweed buried in sediment slowed down the release of N, P, and dissolved organic carbon (DOC) by enhancing the activity of diverse anaerobic microbes (i.e. Draconibacterium, Desulfuromusa, Sediminispirochaeta), which were associated with organic matter decomposition. The enhanced burial quantity of Gracilariopsis resulted in a 3.28 % increase in sediment OC and enriched the humification degree of DOC in seawater. These results highlight the role of seaweed burial in enhancing OC sequestration in marine environments.

Two-Dimensional Liquid Chromatography Tandem Mass Spectrometry Untangles the Deep Metabolome of Marine Dissolved Organic Matter

Dissolved organic matter (DOM) is an ultracomplex mixture that plays a central role in global biogeochemical cycles. Despite its importance, DOM remains poorly understood at the molecular level. Over the last decades, significant efforts have been made to decipher the chemical composition of DOM by high-resolution mass spectrometry (HR-MS) and liquid chromatography (LC) coupled with tandem mass spectrometry (MS/MS). Yet, the complexity and high degree of nonresolved isomers still hamper the full structural analysis of DOM. To address this challenge, we developed an offline two-dimensional (2D) LC approach using two reversed-phase dimensions with orthogonal pH levels, followed by MS/MS data acquisition and molecular networking. 2D-LC-MS/MS reduced the complexity of DOM, enhancing the quality of MS/MS spectra and increasing spectral annotation rates. Applying our approach to analyze coastal-surface DOM from Southern California (USA) and open-ocean DOM from the central North Pacific (Hawaii), we annotated in total more than 600 structures via MS/MS spectrum matching, which was up to 90% more than that in iterative 1D LC-MS/MS analysis with the same total run time. Our data offer unprecedented insights into the molecular composition of marine DOM and highlight the potential of 2D-LC-MS/MS approaches to decipher the chemical composition of ultracomplex samples.

Disentangling drivers of mudflat intertidal DOM chemodiversity using ecological models

Microorganisms consume and transform dissolved organic matter (DOM) into various forms. However, it remains unclear whether the ecological patterns and drivers of DOM chemodiversity are analogous to those of microbial communities. Here, a large-scale investigation is conducted along the Chinese coasts to resolve the intrinsic linkages among the complex intertidal DOM pools, microbial communities and environmental heterogeneity. The abundance of DOM molecular formulae best fits log-normal distribution and follows Taylor's Law. Distance-decay relationships are observed for labile molecular formulae, while latitudinal diversity gradients are noted for recalcitrant molecular formulae. Latitudinal patterns are also observed for DOM molecular features. Negative cohesion, bacterial diversity, and molecular traits are the main drivers of DOM chemodiversity. Stochasticity analyses demonstrate that determinism dominantly shapes the DOM compositional variations. This study unveils the intrinsic mechanisms underlying the intertidal DOM chemodiversity and microbial communities from ecological perspectives, deepening our understanding of microbially driven chemical ecology.

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.

A sonication-filtration method for acquisition of integrated bacterial communities from phycosphere

Bacteria in phycosphere engage in intricate interactions with microalgae by exchanging organic and inorganic matter. However, elucidating the primary roles of bacteria in phycosphere has been a big challenge, due to the lack of adequate methods for separating tightly associated bacteria from microalgal cells. In this study we evaluated several isolation methods including centrifugation, filtration, sonication combined with filtration, and tween lysis followed by sonication and filtration, aiming to efficiently acquire complete bacterial communities from phycosphere. The results demonstrated that the sonication-filtration approach maximally preserves the original characteristics of the bacterial communities. This method will facilitate the acquisition and further analysis of future experimental data.

Algal-bacterial consortium promotes carbon sink formation in saline environment

INTRODUCTION

The level of atmospheric CO2 has continuously been increasing and the resulting greenhouse effects are receiving attention globally. Carbon removal from the atmosphere occurs naturally in various ecosystems. Among them, saline environments contribute significantly to the global carbon cycle. Carbonate deposits in the sediments of salt lakes are omnipresent, and the biological effects, especially driven by halophilic microalgae and bacteria, on carbonate formation remain to be elucidated.

OBJECTIVES

The present study aims to characterize the carbonates formed in saline environments and demonstrate the mechanisms underlying biological-driven CO2 removal via microalgal-bacterial consortium.

METHODS

The carbonates naturally formed in saline environments were collected and analyzed. Two saline representative organisms, the photosynthetic microalga Dunaliella salina and its mutualistic halophilic bacteria Nesterenkonia sp. were isolated from the inhabiting saline environment and co-cultivated to study their biological effects on carbonates precipitation and isotopic composition. During this process, electrochemical parameters and Ca2+ flux, and expression of genes related to CaCO3 formation were analyzed. Genome sequencing and metagenomic analysis were conducted to provide molecular evidence.

RESULTS

The results showed that natural saline sediments are enriched with CaCO3 and enrichment of genes related to photosynthesis and ureolysis. The co-cultivation stimulated 54.54% increase in CaCO3 precipitation and significantly promoted the absorption of external CO2 by 49.63%. A pH gradient was formed between the bacteria and algae culture, creating 150.22 mV of electronic potential, which might promote Ca2+ movement toward D. salina cells. Based on the results of lab-scale induction and 13C analysis, a theoretical calculation indicates a non-negligible amount of 0.16 and 2.3 Tg C/year carbon sequestration in China and global saline lakes, respectively.

CONCLUSION

The combined effects of these two typical representative species have contributed to the carbon sequestration in saline environments, by promoting Ca2+ influx and increase of pH via microalgal and bacterial metabolic processes.

Spatial distribution characteristics of carbazole and polyhalogenated carbazoles in water column and sediments in the open Western Pacific Ocean

Polyhalogenated carbazoles (PHCZs), an emerging persistent halogenated organic pollutant, have been detected in the environment. However, our understanding of PHCZs in the ocean remains limited. In this study, 47 seawater samples (covering 50 - 4000 m) and sediment samples (49 surface and 3 cores) were collected to investigate the occurrence and spatial distribution patterns of carbazole and its halogenated derivants (CZDs) in the Western Pacific Ocean. In seawater, the detection frequencies of CZ (97.87%) and 3-CCZ (57.45%) were relatively high. In addition, the average concentration of ΣPHCZs in the upper water (< 150 m, 0.23 ± 0.21 ng/L) was significantly lower than that in the deep ocean (1000 - 4000 m, 0.65 ± 0.56 ng/L, P < 0.05), which may indicate the vertical transport of PHCZs in the marine environment. The concentration of ΣCZDs in surface sediment ranges from 0.46 to 6.48 ng/g (mean 1.54 ng/g), among which CZ and 36-CCZ were the predominant components. Results from sediment cores demonstrate a noteworthy negative correlation between the concentration of CZDs and depth, indicating the ongoing natural degradation process occurring in sediment cores over a long period. This study offers distinctive insights into the occurrence, composition, and vertical features of CZDs in oceanic environments.

A pilot study suggests the correspondence between SAR202 bacteria and dissolved organic matter in the late stage of a year-long microcosm incubation

SAR202 bacteria are abundant in the marine environment and they have been suggested to contribute to the utilization of recalcitrant organic matter (RDOM) within the ocean's biogeochemical cycle. However, this functional role has only been postulated by metagenomic studies. During a one-year microcosm incubation of an open ocean microbial community with lysed Synechococcus and its released DOM, SAR202 became relatively more abundant in the later stage (after day 30) of the incubation. Network analysis illustrated a high degree of negative associations between SAR202 and a unique group of molecular formulae (MFs) in phase 2 (day 30 to 364) of the incubation, which is empirical evidence that SAR202 bacteria are major consumers of the more oxygenated, unsaturated, and higher-molecular-weight MFs. Further investigation of the SAR202-associated MFs suggested that they were potentially secondary products arising from initial heterotrophic activities following the amendment of labile Synechococcus-derived DOM. This pilot study provided a preliminary observation on the correspondence between SAR202 bacteria and more resistant DOM, further supporting the hypothesis that SAR202 bacteria play important roles in the degradation of RDOM and thus the ocean's biogeochemical cycle.

Spring protistan communities in response to warming in the northeastern East China Sea

The northeastern East China Sea is a highly dynamic marine ecosystem influenced by seasonally varying water mass properties. However, despite being among the world's fastest-warming ocean, there has been limited investigation into the impacts of warming on protistan communities. We collected seawater from two stations (E42 and E46) with different natural protist communities and environmental attributes to investigate the acclimation of the two communities to artificially elevated temperatures (ambient T, +2, and +4 °C). Nutrient and Chl-a conditions reflected oceanographic differences, providing insights into protistan community dynamics. Notably, small-sized autotrophic protists prevailed in the phosphate-deficient E42 community, with mid-incubation heterotrophic conversions. Higher temperatures exacerbated the effects of the P deficiency on the E42 community. While the proportions of Bacillariophyta increased only in the nutrient-balanced E46 communities, those of mixotrophic dinoflagellates increased with elevated temperature, regardless of P deficiency, suggesting that mixotrophy likely aids adaptation in changing marine environments. In summary, the findings of this microcosm study illuminate the potential modulation of spring protistan communities in the northeastern East China Sea under anticipated future warming.

Insight into bacterial role attribution in dissolved organic matter humification during rice straw composting with microbial inoculation

This study aims to investigate the effect of microbial role distribution in microbial carbon pumps on dissolved organic matter (DOM) humification during rice straw composting with microbial inoculation. Three composting groups were designed, named CK (control), B4 (with Bacillus subtilis, OR058594) and Z1 (with Aspergillus fumigatus, AF202956.1). As a result of inoculation, the composition of microbial communities was changed, so that the microorganisms that promoted DOM humification were concentrated in the responders in the microbial carbon pump. DOM was divided into three components in three composting treatments: C1, C2 and C3. After inoculation with Bacillus subtilis, the C2 component was significantly affected, while after inoculation with Aspergillus fumigatus, the C3 component was significantly affected. The results of physicochemical factors affecting the transformation of DOM fluorescence components indicated that C1, C2 and C3 were related to the abundance of the cellulose-degrading enzyme-encoding gene GH7 in CK and B4 composting. However, the C2 was susceptible to organic matter in Z1 composting. This study explored the distribution of microbial communities from a new perspective, which provided new information for analyzing DOM humification and treating agricultural straws to achieve clean conditions for environmental friendliness.

Gene inversion led to the emergence of brackish archaeal heterotrophs in the aftermath of the Cryogenian Snowball Earth

Land-ocean interactions greatly impact the evolution of coastal life on earth. However, the ancient geological forces and genetic mechanisms that shaped evolutionary adaptations and allowed microorganisms to inhabit coastal brackish waters remain largely unexplored. In this study, we infer the evolutionary trajectory of the ubiquitous heterotrophic archaea Poseidoniales (Marine Group II archaea) presently occurring across global aquatic habitats. Our results show that their brackish subgroups had a single origination, dated to over 600 million years ago, through the inversion of the magnesium transport gene corA that conferred osmotic-stress tolerance. The subsequent loss and gain of corA were followed by genome-wide adjustment, characterized by a general two-step mode of selection in microbial speciation. The coastal family of Poseidoniales showed a rapid increase in the evolutionary rate during and in the aftermath of the Cryogenian Snowball Earth (∼700 million years ago), possibly in response to the enhanced phosphorus supply and the rise of algae. Our study highlights the close interplay between genetic changes and ecosystem evolution that boosted microbial diversification in the Neoproterozoic continental margins, where the Cambrian explosion of animals soon followed.

Environment-specific virocell metabolic reprogramming

Viruses impact microbial systems through killing hosts, horizontal gene transfer, and altering cellular metabolism, consequently impacting nutrient cycles. A virus-infected cell, a "virocell," is distinct from its uninfected sister cell as the virus commandeers cellular machinery to produce viruses rather than replicate cells. Problematically, virocell responses to the nutrient-limited conditions that abound in nature are poorly understood. Here we used a systems biology approach to investigate virocell metabolic reprogramming under nutrient limitation. Using transcriptomics, proteomics, lipidomics, and endo- and exo-metabolomics, we assessed how low phosphate (low-P) conditions impacted virocells of a marine Pseudoalteromonas host when independently infected by two unrelated phages (HP1 and HS2). With the combined stresses of infection and nutrient limitation, a set of nested responses were observed. First, low-P imposed common cellular responses on all cells (virocells and uninfected cells), including activating the canonical P-stress response, and decreasing transcription, translation, and extracellular organic matter consumption. Second, low-P imposed infection-specific responses (for both virocells), including enhancing nitrogen assimilation and fatty acid degradation, and decreasing extracellular lipid relative abundance. Third, low-P suggested virocell-specific strategies. Specifically, HS2-virocells regulated gene expression by increasing transcription and ribosomal protein production, whereas HP1-virocells accumulated host proteins, decreased extracellular peptide relative abundance, and invested in broader energy and resource acquisition. These results suggest that although environmental conditions shape metabolism in common ways regardless of infection, virocell-specific strategies exist to support viral replication during nutrient limitation, and a framework now exists for identifying metabolic strategies of nutrient-limited virocells in nature.

Taxon-specific contributions of microeukaryotes to biological carbon pump in the Oyashio region

Microeukaryotes are critical components of sinking particles contributing to carbon export from the surface to deep oceans. However, the knowledge of the sinking microeukaryotic communities and their dynamics is currently limited. In this study, we applied 18S rRNA gene metabarcoding to investigate the microeukaryotic communities in sinking and suspended particles distinguished by marine snow catchers during spring in the Oyashio region. Sinking particles displayed distinct communities and lower diversity than suspended particles. The community compositions of the sinking particles varied with depth, suggesting that microeukaryotes were selectively disaggregated or decomposed during settling. Prymnesiophyceae and diatoms were effectively removed, as indicated by their decreased abundance in sinking particles at increasing depths. Conversely, Dinophyceae maintained a higher abundance in sinking particles across depths, indicating resistance to disaggregation and decomposition. Spirotrichea and heterotrophic Dinophyceae were enriched in sinking particles, while marine stramenopiles groups were enriched in suspended particles. The heterotrophs in the deeper layers were mainly transported from the surface layers by increasing their relative abundance towards deep layers, indicating that they contributed to the transformation processes of sinking particles. Overall, our results demonstrate the functional differences among microeukaryotes in the biological carbon pump.

Vertical connectivity of microbiome and metabolome reveals depth-dependent variations across a deep cold-seep water column

Deciphering the vertical connectivity of oceanic microbiome and metabolome is crucial for understanding the carbon sequestration and achieving the carbon neutrality. However, we lack a systematic view of the interplay among particle transport, microbial community, and metabolic trait across depths. Through integrating the biogeochemical, microbial, and metabolic characteristics of a deep cold-seep water column (∼1989 m), we find the altered connectivity of microbial community and dissolved organic matter (DOM) across depths. Both the microbial communities (bacteria and protists) and DOM show a clear compositional connectivity from surface to the depth of 1000 m, highlighting the controls of sinking particle over microbial connectivity from the epipelagic to mesopelagic zone. However, due to the biological migration and ocean mixing, the fecal-associated bacteria and protistan consumers unexpectedly emerge and the degradation index of DOM substantially alters around 1000-1200 m. Collectively, we unveil the significance of multi-faceted particle dispersion, which supports the connectivity and variability of deep ocean microbial communities.

Selected Bacteria Are Critical for Karst River Carbon Sequestration via Integrating Multi-omics and Hydrochemistry Data

Recalcitrant dissolved organic carbon (RDOC) produced by microbial carbon pumps (MCPs) in the ocean is crucial for carbon sequestration and regulating climate change in the history of Earth. However, the importance of microbes on RDOC formation in terrestrial aquatic systems, such as rivers and lakes, remains to be determined. By integrating metagenomic (MG) and metatranscriptomic (MT) sequencing, we defined the microbial communities and their transcriptional activities in both water and silt of a typical karst river, the Lijiang River, in Southwest China. Betaproteobacteria predominated in water, serving as the most prevalent population remodeling components of dissolved organic carbon (DOC). Binning method recovered 45 metagenome-assembled genomes (MAGs) from water and silt. Functional annotation of MAGs showed Proteobacteria was less versatile in degrading complex carbon, though cellulose and chitin utilization genes were widespread in this phylum, whereas Bacteroidetes had high potential for the utilization of macro-molecular organic carbon. Metabolic remodeling revealed that increased shared metabolites within the bacterial community are associated with increased concentration of DOC, highlighting the significance of microbial cooperation during producing and remodeling of carbon components. Beta-oxidation, leucine degradation, and mevalonate (MVA) modules were significantly positively correlated with the concentration of RDOC. Blockage of the leucine degradation pathway in Limnohabitans and UBA4660-related MAGs were associated with decreased RDOC in the karst river, while the Fluviicola-related MAG containing a complete leucine degradation pathway was positively correlated with RDOC concentration. Collectively, our study revealed the linkage between bacteria metabolic processes and carbon sequestration. This provided novel insights into the microbial roles in karst-rivers carbon sink.

Organic carbon cycling and black shale deposition: an Earth System Science perspective

Earth has a prolonged history characterized by substantial cycling of matter and energy between multiple spheres. The production of organic carbon can be traced back to as early as ∼4.0 Ga, but the frequency and scale of organic-rich shales have varied markedly over geological time. In this paper, we discuss the organic carbon cycle and the development of black shale from the perspective of Earth System Science. We propose that black shale depositions are the results of interactions among lithospheric evolution, orbital forcing, weathering, photosynthesis and degradation. Black shales can record Earth's oxygenation process, provide petroleum and metallic mineral resources and reveal information about the driver, direction and magnitude of climate change. Future research on black shales should be expanded to encompass a more extensive and more multidimensional perspective.

Nutrient-dependent interactions between a marine copiotroph Alteromonas and a diatom Thalassiosira pseudonana

IMPORTANCE

As the major producers and consumers, phytoplankton and bacteria play central roles in marine ecosystems and their interactions show great ecological significance. Whether mutualistic or antagonistic, the interaction between certain phytoplankton and bacterial species is usually seen as a derivative of intrinsic physiological properties and rarely changes. This study demonstrated that the interactions between the ubiquitously co-occurring bacteria and diatom, Alteromonas and Thalassiosira pseudonana, varied with nutrient conditions. They overcame hardship together in oligotrophic seawater but showed antagonistic effects against each other under nutrient amendment. The contact-dependent algicidal behavior of Alteromonas based on protease activity solved the paradox among bacterial proliferation, nutrient viability, and algal demise haunting other known non-contact-dependent algicidal processes and might actually trigger the collapse of algal blooms in situ. The chemotactic and swarming movement of Alteromonas might also contribute greatly to the breakdown of "marine snow," which could redirect the carbon sequestration pathway in the ocean.

Dissolved organic matter defines microbial communities during initial soil formation after deglaciation

Ecosystem succession and pedogenesis reshuffle the composition and turnover of dissolved organic matter (DOM) and its interactions with soil microbiome. The changes of these connections are especially intensive during initial pedogenesis, e.g. in young post-glacial areas. The temporal succession and vertical development of DOM effects on microbial community structure remains elusive. Using Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS), high-throughput sequencing, and molecular ecological networks, we characterized the molecular diversity of water-extractable DOM and identified its links to microbial communities in soil profiles along deglaciation chronosequence (12, 30, 40, 52, 80, and 120 years) in the southeastern Tibetan Plateau. Low-molecular-weight compound content decreased, whereas the mid- and high-molecular-weight compounds increased with succession age and soil depth. This was confirmed by the increase in double bond equivalents and averaged oxygen-to‑carbon ratios (O/C), and decrease in hydrogen-to‑carbon ratios (H/C), which reflect DOM accumulation and stabilization. Microbial community succession shifted towards the dominance of oligotrophic Acidobacteria and saprophytic Mortierellomycota, reflecting the increase of stable DOM components (H/C < 1.5 and wider O/C). Less DOM-bacterial positive networks during the succession reduced specialization of labile DOM production (such as lipid- and protein-like compounds), whereas more DOM-fungal negative networks increased specialization of stable DOM decomposition (such as tannin- and condensed aromatic-like compounds). Consequently, DOM stability is not intrinsic during initial pedogenesis: stable DOM compounds remain after fast bacterial utilization of labile DOM compounds, whereas fungi decompose slowly the remaining DOM pools.

Removable carbon and storage carbon of golden tides

Due to ever-increasing global warming, ocean acidification, and inshore eutrophication, the outbreak of golden tides with Sargassum horneri has increased in the Yellow sea, where the biomass carbon enters three main carbon pathways: a. Removal of carbon from seawater by salvage, known as removable carbon; b. Biomass carbon is deposited to the seafloor through POC and RDOC through Biological Carbon Pump and Microbial Carbon Pump; c. Re-entering the carbon cycle through the food chain or re-entering the atmosphere through the action of microbes. Estimating carbon fixation (removable carbon) and storage (particulate organic carbon (POC) and refractory dissolved organic carbon (RDOC)) is vital in studying the global carbon cycle. In this research, it was observed that the C content of S. horneri was high, and the utilization rate of dissolved organic carbon (DOC), RDOC, and POC was also high in the eutrophication environment, where only 2.71 % of algal biomass carbon was converted to RDOC, and only 0.20 % converted to POC. The C + N + P combination has a restart effect on the seasonal accumulation of RDOC in relevant sea areas. It is suggested that the salvage and resource utilization should be strengthened to effectively control the golden tide and reduce the substantial economic losses to realize the win-win situation of carbon sink and environmental restoration.

Can ocean carbon sink trading achieve economic and environmental benefits? Simulation based on DICE-DSGE model

Low-carbon development requires joint efforts in terms of "carbon reduction" and "carbon sink increase." This study thus proposes a DICE-DSGE model for exploring the environmental and economic benefits of ocean carbon sinks and provides policy suggestions for marine economic development and carbon emission policy choices. The results are as follows: (1) while the economic benefits of heterogeneous technological shocks are apparent, the environmental benefits of carbon tax and carbon quota shocks are significant; (2) increasing the efficiency of ocean carbon sinks improves the environmental benefits of technological shocks as well as the output benefits of emission reduction tools, while increasing the share of marine output can improve both the economic benefits of technological shocks and the environmental benefits of emission reduction tools; and (3) ocean output proportion has the most considerable positive effect on social welfare, followed by marine total factor productivity (TFP). The correlation effect of ocean carbon sink efficiency is negative.

Bacteria and Archaea Regulate Particulate Organic Matter Export in Suspended and Sinking Marine Particle Fractions

The biological carbon pump (BCP) in the Southern Ocean is driven by phytoplankton productivity and is a significant organic matter sink. However, the role of particle-attached (PA) and free-living (FL) prokaryotes (bacteria and archaea) and their diversity in influencing the efficiency of the BCP is still unclear. To investigate this, we analyzed the metagenomes linked to suspended and sinking marine particles from the Sub-Antarctic Southern Ocean Time Series (SOTS) by deploying a Marine Snow Catcher (MSC), obtaining suspended and sinking particulate material, determining organic carbon and nitrogen flux, and constructing metagenome-assembled genomes (MAGs). The suspended and sinking particle-pools were dominated by bacteria with the potential to degrade organic carbon. Bacterial communities associated with the sinking fraction had more genes related to the degradation of complex organic carbon than those in the suspended fraction. Archaea had the potential to drive nitrogen metabolism via nitrite and ammonia oxidation, altering organic nitrogen concentration. The data revealed several pathways for chemoautotrophy and the secretion of recalcitrant dissolved organic carbon (RDOC) from CO₂, with bacteria and archaea potentially sequestering particulate organic matter (POM) via the production of RDOC. These findings provide insights into the diversity and function of prokaryotes in suspended and sinking particles and their role in organic carbon/nitrogen export in the Southern Ocean. IMPORTANCE The biological carbon pump is crucial for the export of particulate organic matter in the ocean. Recent studies on marine microbes have shown the profound influence of bacteria and archaea as regulators of particulate organic matter export. Yet, despite the importance of the Southern Ocean as a carbon sink, we lack comparable insights regarding microbial contributions. This study provides the first insights regarding prokaryotic contributions to particulate organic matter export in the Southern Ocean. We reveal evidence that prokaryotic communities in suspended and sinking particle fractions harbor widespread genomic potential for mediating particulate organic matter export. The results substantially enhance our understanding of the role played by microorganisms in regulating particulate organic matter export in suspended and sinking marine fractions in the Southern Ocean.

Changes of Soil Dissolved Organic Matter and Its Relationship with Microbial Community along the Hailuogou Glacier Forefield Chronosequence

Glacier-retreated areas are ideal areas to study soil biogeochemical processes during vegetation succession, because of the limited effect of other environmental and climatic factors. In this study, the changes of soil dissolved organic matter (DOM) and its relationship with microbial communities along the Hailuogou Glacier forefield chronosequence were investigated. Both microbial diversity and DOM molecular chemodiversity recovered rapidly at the initial stage, indicating the pioneering role of microorganisms in soil formation and development. The chemical stability of soil organic matter enhanced with vegetation succession due to the retaining of compounds with high oxidation state and aromaticity. The molecular composition of DOM affected microbial communities, while microorganisms tended to utilize labile components to form refractory components. This complex relationship network between microorganisms and DOM components played an important role in the development of soil organic matter as well as the formation of stable soil carbon pool in glacier-retreated areas.

Response of dissolved organic matter chemistry to flood control of a large river reservoir during an extreme storm event

With the frequent occurrence of extreme floods under global climate change-induced storm events, reservoir operation has been highlighted for river flood control, complicating the transport and transformation of riverine dissolved organic matter (DOM), one of the largest reactive carbon pools on earth. In particular, the response of riverine DOM chemistry to reservoir flood control during extreme storm events is still unclear. To fill this knowledge gap, the mechanism of DOM variation in Yangtze River with the world's largest Three Gorges Reservoir (TGR) operation during an extreme storm event was explored. Optical and molecular properties of DOM varied significantly from upstream to downstream in non-TGR area, while no significant variation in DOM chemistry was observed in TGR area. The results uncovered a short time transformation of DOM from non-TGR area to TGR area, demonstrating that although storm event induced chemodiversity bloom of riverine DOM, flood control of TGR "re-constrained" DOM to more similar chemistry mainly under the influence of turbidity involved DOM transformation (e.g., adsorption/desorption and flocculation). Furthermore, combined with the hydrological information, we found that although TGR temporarily blocked dissolved organic carbon (DOC) flow during the flood event, the abundance of biologically recalcitrant DOC increased in TGR, which would contribute to its further transportation to downstream watershed. This study emphasizes the impact of TGR on extreme storm event-induced DOM dynamics, which also hints a better understanding of the crucial role of anthropogenic activity in affecting carbon cycling under extreme climate change.

Eco-engineering approaches for ocean negative carbon emission

The goal of achieving carbon neutrality in the next 30-40 years is approaching worldwide consensus and requires coordinated efforts to combat the increasing threat of climate change. Two main sets of actions have been proposed to address this grand goal. One is to reduce anthropogenic CO₂ emissions to the atmosphere, and the other is to increase carbon sinks or negative emissions, i.e., removing CO₂ from the atmosphere. Here we advocate eco-engineering approaches for ocean negative carbon emission (ONCE), aiming to enhance carbon sinks in the marine environment. An international program is being established to promote coordinated efforts in developing ONCE-relevant strategies and methodologies, taking into consideration ecological/biogeochemical processes and mechanisms related to different forms of carbon (inorganic/organic, biotic/abiotic, particulate/dissolved) for sequestration. We focus on marine ecosystem-based approaches and pay special attention to mechanisms that require transformative research, including those elucidating interactions between the biological pump (BP), the microbial carbon pump (MCP), and microbially induced carbonate precipitation (MICP). Eutrophic estuaries, hypoxic and anoxic waters, coral reef ecosystems, as well as aquaculture areas are particularly considered in the context of efforts to increase their capacity as carbon sinks. ONCE approaches are thus expected to be beneficial for both carbon sequestration and alleviation of environmental stresses.

Microbial ecology of the Southern Ocean

The Southern Ocean (SO) distributes climate signals and nutrients worldwide, playing a pivotal role in global carbon sequestration. Microbial communities are essential mediators of primary productivity and carbon sequestration, yet we lack a comprehensive understanding of microbial diversity and functionality in the SO. Here, we examine contemporary studies in this unique polar system, focusing on prokaryotic communities and their relationships with other trophic levels (i.e. phytoplankton and viruses). Strong seasonal variations and the characteristic features of this ocean are directly linked to community composition and ecosystem functions. Specifically, we discuss characteristics of SO microbial communities and emphasise differences from the Arctic Ocean microbiome. We highlight the importance of abundant bacteria in recycling photosynthetically derived organic matter. These heterotrophs appear to control carbon flux to higher trophic levels when light and iron availability favour primary production in spring and summer. Conversely, during winter, evidence suggests that chemolithoautotrophs contribute to prokaryotic production in Antarctic waters. We conclude by reviewing the effects of climate change on marine microbiota in the SO.

Particulate and dissolved fluorescent organic matter fractionation and composition: Abiotic and ecological controls in the Southern Ocean

Phytoplankton-derived organic matter sustains heterotrophic marine life in regions away from terrestrial inputs such as the Southern Ocean. Fluorescence spectroscopy has long been used to characterize the fluorescent organic matter (FOM) pool. However, most studies focus only in the dissolved FOM fraction (FDOM) disregarding the contribution of particles. In order to assess the dynamics and drivers of the dissolved and particulate fractions of FOM, we used a Lagrangian approach to follow the time evolution of phytoplankton proliferations at four different sites in the Southern Ocean and compared the FOM in filtered and unfiltered seawater aliquots. We found that filtration had little effects on FOM visible spectrum fluorescence intensities, implying that most of this signal was due to dissolved fluorophores. On the other hand, protein-like fluorescence was strongly supressed by filtration, with fluorescence of particles accounting for up to 90 % of the total protein-like FOM. Photobleaching was identified as the main driver of visible FDOM composition, which was better described by indices of phytoplankton photoacclimation than by measurements of the incident solar radiation dose. In contrast, protein-like FOM intensity and fractionation were primarily related to abundance, composition and physiological state of phytoplankton proliferations. The chlorophyll a concentration from non-diatom phytoplankton explained 91 % of the particulate protein-like FOM variability. The proportion of protein-like fluorescence found in the dissolved phase was predicted by the combination of potential viral and grazing pressures, which accounted for 51 and 29 % of its variability, respectively. Our results show that comparing FOM measurements from filtered and unfiltered seawater provides relevant information on the taxonomic composition and cell integrity of phytoplankton communities. A better understanding of the commonly overlooked FOM fractionation process is essential for the implementation of in situ fluorescence sensors and will also help us better understand the processes that govern OM cycling in marine systems.

Natural Substrates and Culture Conditions to Produce Pigments from Potential Microbes in Submerged Fermentation

Pigments from bacteria, fungi, yeast, cyanobacteria, and microalgae have been gaining more demand in the food, leather, and textile industries due to their natural origin and effective bioactive functions. Mass production of microbial pigments using inexpensive and ecofriendly agro-industrial residues is gaining more demand in the current research due to their low cost, natural origin, waste utilization, and high pigment stimulating characteristics. A wide range of natural substrates has been employed in submerged fermentation as carbon and nitrogen sources to enhance the pigment production from these microorganisms to obtain the required quantity of pigments. Submerged fermentation is proven to yield more pigment when added with agro-waste residues. Hence, in this review, aspects of potential pigmented microbes such as diversity, natural substrates that stimulate more pigment production from bacteria, fungi, yeast, and a few microalgae under submerged culture conditions, pigment identification, and ecological functions are detailed for the benefit of industrial personnel, researchers, and other entrepreneurs to explore pigmented microbes for multifaceted applications. In addition, some important aspects of microbial pigments are covered herein to disseminate the knowledge.

Microbial and Environmental Processes Shape the Link between Organic Matter Functional Traits and Composition

Dissolved organic matter (DOM) is a large and complex mixture of molecules that fuels microbial metabolism and regulates biogeochemical cycles. Individual DOM molecules have unique functional traits, but how their assemblages vary deterministically under global change remains poorly understood. Here, we examine DOM and associated bacteria in 300 aquatic microcosms deployed on mountainsides that span contrasting temperatures and nutrient gradients. Based on molecular trait dimensions of reactivity and activity, we partition the DOM composition into labile-active, recalcitrant-active, recalcitrant-inactive, and labile-inactive fractions and quantify the relative influences of deterministic and stochastic processes governing the assembly of each. At both subtropical and subarctic study sites, the assembly of labile or recalcitrant molecules in active fractions is primarily governed by deterministic processes, while stochastic processes are more important for the assembly of molecules within inactive fractions. Surprisingly, the importance of deterministic selection increases with global change gradients for recalcitrant molecules in both active and inactive fractions, and this trend is paralleled by changes in the deterministic assembly of microbial communities and environmental filtering, respectively. Together, our results highlight the shift in focus from potential reactivity to realized activity and indicate that active and inactive fractions of DOM assemblages are structured by contrasting processes, and their recalcitrant components are consistently sensitive to global change. Our study partitions the DOM molecular composition across functional traits and links DOM with microbes via a shared ecological framework of assembly processes. This integrated approach opens new avenues to understand the assembly and turnover of organic carbon in a changing world.

Oxygen availability driven trends in DOM molecular composition and reactivity in a seasonally stratified fjord

Ocean deoxygenation could potentially trigger substantial changes in the composition and reactivity of dissolved organic matter (DOM) pool, which plays an important role in the global carbon cycle. To evaluate links between DOM dynamics and oxygen availability, we investigated the DOM composition under varying levels of oxygen in a seasonally hypoxic fjord through a monthly time-series over two years. We used ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) to characterize DOM on a molecular level. We find a clear trend both in diversity and molecular composition of the DOM along the oxygen gradient. As oxygen decreased, the chemodiversity was significantly increased, along with accumulation of relatively high-molecular-weight, reduced and unsaturated compounds enriched with carboxyl-group structures, which were also thermodynamically less favorable to biodegradation. Our results suggested that oxygen depletion selectively protected otherwise bioavailable compounds from decomposition and may promote the accumulation of a larger recalcitrant DOM pool in the global ocean, which could provide negative feedback to the ocean carbon sequestration and climate change.

Effects of Temperature on Transparent Exopolymer Particle Production and Organic Carbon Allocation of Four Marine Phytoplankton Species

Transparent exopolymer particles (TEP) are sticky polymeric substances that are commonly found in the periphery of microbial cells or colonies. They can naturally flocculate smaller suspended particles into larger aggregates and thus play a crucial role in the biological pump and the global carbon cycle. Phytoplankton are the major contributors to marine TEP production, whereas the way TEP production interacts with abiotic factors at the species level is generally unknown but critical for estimating carbon fluxes. In this study, the effects of temperature on TEP production and carbon allocation were studied in two representative diatom species (Nitzschia closterium and Chaetoceros affinis) and two model dinoflagellate species (Prorocentrum micans and Scrippisella trichoidea). The results showed that temperature had a significant impact on TEP production in all species. First, increased temperature promoted the TEP production of all four species. Second, elevated temperature affected the carbon pool allocation, with enhanced dissolved organic carbon (DOC) exudation in the form of TEP in all species. The TEP-C/DOC percentages of N. closterium and P. micans were 93.42 ± 5.88% and 82.03 ± 21.36% at the highest temperature (24 °C), respectively, which was approximately two to five times higher than those percentages at 16 °C. In contrast, TEP’s contribution to the POC pool is lower than that to the DOC pool, ranging from 6.74 ± 0.79% to 28.31 ± 1.79% for all species. Moreover, phytoplankton TEP production may be related to cellular size and physiology. The TEP content produced by the smallest N. closterium (218.96 ± 15.04 fg Xeq./μm3) was ~5 times higher compared to P. micans, S. trichoidea, or C. affinis. In conclusion, TEP production is temperature sensitive and species specific, which should be taken into consideration the regarding TEP-mediated oceanic carbon cycle, particularly in the context of global warming.

Ecological networks of dissolved organic matter and microorganisms under global change

Microbes regulate the composition and turnover of organic matter. Here we developed a framework called Energy-Diversity-Trait integrative Analysis to quantify how dissolved organic matter and microbes interact along global change drivers of temperature and nutrient enrichment. Negative and positive interactions suggest decomposition and production processes of organic matter, respectively. We applied this framework to manipulative field experiments on mountainsides in subarctic and subtropical climates. In both climates, negative interactions of bipartite networks were more specialized than positive interactions, showing fewer interactions between chemical molecules and bacterial taxa. Nutrient enrichment promoted specialization of positive interactions, but decreased specialization of negative interactions, indicating that organic matter was more vulnerable to decomposition by a greater range of bacteria, particularly at warmer temperatures in the subtropical climate. These two global change drivers influenced specialization of negative interactions most strongly via molecular traits, while molecular traits and bacterial diversity similarly affected specialization of positive interactions.

Microbes are intimately linked with the fate of organic matter. Here the authors develop an ecological network framework and show how microbes and dissolved organic matter interact along global change drivers of temperature and nutrient enrichment via manipulative field experiments on mountains.

Bacterial, Phytoplankton, and Viral Distributions and Their Biogeochemical Contexts in Meromictic Lake Cadagno Offer Insights into the Proterozoic Ocean Microbial Loop

Lake Cadagno, a permanently stratified high-alpine lake with a persistent microbial bloom in its chemocline, has long been considered a model for the low-oxygen, high-sulfide Proterozoic ocean. Although the lake has been studied for over 25 years, the absence of concerted study of the bacteria, phytoplankton, and viruses, together with primary and secondary production, has hindered a comprehensive understanding of its microbial food web. Here, the identities, abundances, and productivity of microbes were evaluated in the context of Lake Cadagno biogeochemistry. Photosynthetic pigments together with 16S rRNA gene phylogenies suggest the prominence of eukaryotic phytoplankton chloroplasts, primarily chlorophytes. Chloroplasts closely related to those of high-alpine-adapted Ankyra judayi persisted with oxygen in the mixolimnion, where photosynthetic efficiency was high, while chloroplasts of Closteriopsis-related chlorophytes peaked in the chemocline and monimolimnion. The anoxygenic phototrophic sulfur bacterium Chromatium dominated the chemocline along with Lentimicrobium, a genus of known fermenters. Secondary production peaked in the chemocline, which suggested that anoxygenic primary producers depended on heterotrophic nutrient remineralization. The virus-to-microbe ratio peaked with phytoplankton abundances in the mixolimnion and were at a minimum where Chromatium abundance was highest, trends that suggest that viruses may play a role in the modulation of primary production. Through the combined analysis of bacterial, eukaryotic, viral, and biogeochemical spatial dynamics, we provide a comprehensive synthesis of the Lake Cadagno microbial loop. This study offers a new ecological perspective on how biological and geochemical connections may have occurred in the chemocline of the Proterozoic ocean, where eukaryotic microbial life is thought to have evolved.

The First Cbk-Like Phage Infecting Erythrobacter, Representing a Novel Siphoviral Genus

Erythrobacter is an important and widespread bacterial genus in the ocean. However, our knowledge about their phages is still rare. Here, a novel lytic phage vB_EliS-L02, infecting Erythrobacter litoralis DSM 8509, was isolated and purified from Sanggou Bay seawater, China. Morphological observation revealed that the phage belonged to Cbk-like siphovirus, with a long prolate head and a long tail. The host range test showed that phage vB_EliS-L02 could only infect a few strains of Erythrobacter, demonstrating its potential narrow-host range. The genome size of vB_EliS-L02 was 150,063 bp with a G+C content of 59.43%, encoding 231 putative open reading frames (ORFs), but only 47 were predicted to be functional domains. Fourteen auxiliary metabolic genes were identified, including phoH that may confer vB_EliS-L02 the advantage of regulating phosphate uptake and metabolism under a phosphate-limiting condition. Genomic and phylogenetic analyses indicated that vB_EliS-L02 was most closely related to the genus Lacusarxvirus with low similarity (shared genes < 30%, and average nucleotide sequence identity < 70%), distantly from other reported phages, and could be grouped into a novel viral genus cluster, in this study as Eliscbkvirus. Meanwhile, the genus Eliscbkvirus and Lacusarxvirus stand out from other siphoviral genera and could represent a novel subfamily within Siphoviridae, named Dolichocephalovirinae-II. Being a representative of an understudied viral group with manifold adaptations to the host, phage vB_EliS-L02 could improve our understanding of the virus–host interactions and provide reference information for viral metagenomic analysis in the ocean.

Eutrophication and watershed characteristics shape changes in dissolved organic matter chemistry along two river-estuarine transects

Dissolved organic matter (DOM) plays a crucial role in the coastal carbon cycle. However, eutrophication-induced algal blooms and lateral transport from connected tidal marshes may significantly affect DOM cycling, which remains poorly understood. By combining a suite of bulk and optical techniques, and the Fourier transform ion cyclotron resonance mass spectrometry and ion mobility quadrupole time-of-flight mass spectrometry, we determined DOM concentration and composition along two typical river-estuary transects (namely Liao and Daliao rivers), Northeast China, with contrasting eutrophic state and distribution of tidal marshes. The Daliao River is characterized by a higher eutrophication degree and is surrounded with lower reed coverage than the Liao River. Compared to the Liao River, significantly higher dissolved organic carbon concentrations were observed in the Daliao River, where higher stable carbon isotope (δ13C) values and protein-like fluorescent components, characterized relatively higher autochthonous DOM. Further molecular analysis revealed higher peptide and sugar-like compounds but lower isomeric percentages of several molecular formulas in the Daliao River, suggesting higher molecular lability but lower isomeric complexity than the Liao River. Associations between optical and molecular signatures among all DOM samples revealed that a red-shifted humic-like C3 component was significantly correlated with molecular formulas with lower molecular weight and aromaticity, and higher H/C, indicating that C3 was likely a result of phytoplankton production coupled with further heterotrophic processing. Moreover, we found that reed marshes could introduce to both rivers a series of carboxylic-rich alicyclic compounds, highly unsaturated compounds, and polyphenols with high molecular weight and low H/C. This study suggests that eutrophication and reed marsh affect the DOM quality and can be a potential source of recalcitrant DOM compounds to coastal rivers and estuaries, which warrants further investigations considering the increasing worldwide eutrophication and sea-level rise in coastal delta environments.

Mucospheres produced by a mixotrophic protist impact ocean carbon cycling

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

Inventory of riverine dissolved organic carbon in the Bohai Rim

Riverine carbon (C) composition and export are closely related to changes in the coastal environment and climate. Excessive C inputs from rivers to seas and their subsequent decomposition could result in harmful algal blooms and ecosystem degradation in the coastal sea. In this study, we explored the C transportation and composition in the 24 major rivers of the Bohai Sea (BS) Rim based on the investigation of dissolved organic carbon (DOC), carbon stable isotopes (δ¹³C_DOC) and chromophoric dissolved organic matter (CDOM). The results showed that the riverine DOC concentrations were high (10.6 ± 6.04 mg/L) in the BS Rim compared with the DOC levels in the main rivers in Eastern China (4.98 ± 2.45 mg/L). The δ¹³C_DOC ranged from -28.29‰ to -25.32‰ in the rivers of the BS Rim, suggesting that the DOC mainly originated from riverine plankton, soil organic matter mainly induced by C3 plants, and sewage. The excitation-emission matrix fluorescence spectroscopy of the CDOM indicated that a soluble, microbial by product-like material accounted for the largest proportion (approximately 40%) of CDOM in these rivers and that CDOM mainly originated from autochthonous riverine sources with high protein-like components. The rivers in the BS Rim transported approximately 0.55 Tg C of DOC to the BS each year, with more than 70% of reactive C based on the CDOM composition. The DOC yields in terms of unit drainage area transported from the small rivers to the BS were higher compared to those of the larger rivers in the world, which indicated that the small rivers in the Bohai Rim could be an important source of the C in the BS. This study would enrich our understanding of environmental evolution in coastal areas with numerous small rivers.

Terrestrial lipid biomarkers in marine aerosols over the western North Pacific during 1990-1993 and 2006-2009

Terrestrial lipid biomarkers are one of the key tracers in the studies of atmospheric aerosols. Here, we investigated such organic compounds in marine aerosols collected at Chichijima Island, the western North Pacific for two 4-year periods: 1990-1993 and 2006-2009. A homologous series of lipid biomarkers including C₁₈-C₃₇n-alkanes, C₉-C₃₄ fatty acids, and C₁₄-C₃₅ fatty alcohols were determined by gas chromatography/mass spectrometry (GC/MS). The atmospheric levels of these tracers increased from 1990-1993 to 2006-2009. Their seasonal trends were clearly characterized by winter-spring maxima and summer-fall minima. The relative abundance of the high-molecular-weight (HMW) n-alkanes (C₂₅-C₃₇) and n-alcohols (C₂₀-C₃₅) in total HMW lipids peaked in winter and winter/fall, respectively, whereas those of HMW fatty acids (C₂₀-C₃₄) peaked in summer. Air-mass backward trajectory analyses suggest that the Asian continent, Southeast Asia including tropical regions, and the Central Pacific are the main source regions. The seasonal shift and distribution of the carbon preference index and average chain length for the HMW lipids were controlled by the changes in climatic factors and source regions. The higher abundance of terrestrial lipids during 2006-2009 than 1990-1993 indicates a higher emission from terrestrial plantation in the 2000s than in the early 1990s in upwind regions of East Asia. Furthermore, HMW lipid compounds exhibited much stronger positive correlations with levoglucosan, a biomass-burning tracer, during 2006-2009 than 1990-1993, suggesting that biomass-burning emissions contributed more significantly in this century.

Temporal dynamics of carbon sequestration in coastal North Atlantic fjord system as seen through dissolved organic matter characterisation

Fjord systems in higher latitudes are unique coastal water ecosystems that facilitate the study of dissolved organic matter (DOM) dynamics from surface to deeper waters. The current work was undertaken in the Trondheim fjord characterized by North Atlantic waters, and compared DOM fractions from three depths - surface (3 m), intermediate (225 m) and deep (440 m) in four seasons, from late spring to winter in 2017. The high-resolution mass spectrometry data showed that DOM composition varies significantly in different seasons rather than in different depths in the fjord systems. The bacterial community composition was comparable except at spring surface and summer intermediate depths. Bacterial production was minimal below the euphotic layer, even with sufficient availability of inorganic nutrients. The bacterial production rate in the surface waters was about 7 times and over 50 times higher than that of the aphotic zone in the winter and the summer seasons, respectively. The surface heterotrophic microbial communities might have rapidly consumed the available labile DOM, with the production of more refractory DOM limiting bacterial production in aphotic layers. The greater number of CRAM-like formulas determined in the surface waters compared to other depths supports our hypothesis. The refractory DOM sequestered in the water column may either be exported into sediments attached to particulate matter and marine gels, or may escape into the atmosphere as carbon dioxide/monoxide during the photochemical oxidation pathways, suggesting that it is involved in climate change scenarios.

The ecological impacts of multiple environmental stressors on coastal biofilm bacteria

Ecological communities are increasingly exposed to multiple interacting stressors. For example, warming directly affects the physiology of organisms, eutrophication stimulates the base of the food web, and harvesting larger organisms for human consumption dampens top-down control. These stressors often combine in the natural environment with unpredictable results. Bacterial communities in coastal ecosystems underpin marine food webs and provide many important ecosystem services (e.g. nutrient cycling and carbon fixation). Yet, how microbial communities will respond to a changing climate remains uncertain. Thus, we used marine mesocosms to examine the impacts of warming, nutrient enrichment, and altered top-predator population size structure (common shore crab) on coastal microbial biofilm communities in a crossed experimental design. Warming increased bacterial α-diversity (18% increase in species richness and 67% increase in evenness), but this was countered by a decrease in α-diversity with nutrient enrichment (14% and 21% decrease for species richness and evenness, respectively). Thus, we show some effects of these stressors could cancel each other out under climate change scenarios. Warming and top-predator population size structure both affected bacterial biofilm community composition, with warming increasing the abundance of bacteria capable of increased mineralization of dissolved and particulate organic matter, such as Flavobacteriia, Sphingobacteriia, and Cytophagia. However, the community shifts observed with warming depended on top-predator population size structure, with Sphingobacteriia increasing with smaller crabs and Cytophagia increasing with larger crabs. These changes could alter the balance between mineralization and carbon sequestration in coastal ecosystems, leading to a positive feedback loop between warming and CO₂ production. Our results highlight the potential for warming to disrupt microbial communities and biogeochemical cycling in coastal ecosystems, and the importance of studying these effects in combination with other environmental stressors.

Eukaryotic virus composition can predict the efficiency of carbon export in the global ocean

The biological carbon pump, in which carbon fixed by photosynthesis is exported to the deep ocean through sinking, is a major process in Earth's carbon cycle. The proportion of primary production that is exported is termed the carbon export efficiency (CEE). Based on in-lab or regional scale observations, viruses were previously suggested to affect the CEE (i.e., viral “shunt” and “shuttle”). In this study, we tested associations between viral community composition and CEE measured at a global scale. A regression model based on relative abundance of viral marker genes explained 67% of the variation in CEE. Viruses with high importance in the model were predicted to infect ecologically important hosts. These results are consistent with the view that the viral shunt and shuttle functions at a large scale and further imply that viruses likely act in this process in a way dependent on their hosts and ecosystem dynamics.

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Eukaryotic virus community composition is shown to predict carbon export efficiency

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Tens of viruses are highly important in the prediction of the efficiency

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These viruses are inferred to infect ecologically important hosts

Impact of Terrestrial Input on Deep-Sea Benthic Archaeal Community Structure in South China Sea Sediments

Archaea are widespread in marine sediments and play important roles in the cycling of sedimentary organic carbon. However, factors controlling the distribution of archaea in marine sediments are not well understood. Here we investigated benthic archaeal communities over glacial-interglacial cycles in the northern South China Sea and evaluated their responses to sediment organic matter sources and inter-species interactions. Archaea in sediments deposited during the interglacial period Marine Isotope Stage (MIS) 1 (Holocene) were significantly different from those in sediments deposited in MIS 2 and MIS 3 of the Last Glacial Period when terrestrial input to the South China Sea was enhanced based on analysis of the long-chain n-alkane C₃₁. The absolute archaeal 16S rRNA gene abundance in subsurface sediments was highest in MIS 2, coincident with high sedimentation rates and high concentrations of total organic carbon. Soil Crenarchaeotic Group (SCG; Nitrososphaerales) species, the most abundant ammonia-oxidizing archaea in soils, increased dramatically during MIS 2, likely reflecting transport of terrestrial archaea during glacial periods with high sedimentation rates. Co-occurrence network analyses indicated significant association of SCG archaea with benthic deep-sea microbes such as Bathyarchaeota and Thermoprofundales in MIS 2 and MIS 3, suggesting potential interactions among these archaeal groups. Meanwhile, Thermoprofundales abundance was positively correlated with total organic carbon (TOC), along with n-alkane C₃₁ and sedimentation rate, indicating that Thermoprofundales may be particularly important in processing of organic carbon in deep-sea sediments. Collectively, these results demonstrate that the composition of heterotrophic benthic archaea in the South China Sea may be influenced by terrestrial organic input in tune with glacial-interglacial cycles, suggesting a plausible link between global climate change and microbial population dynamics in deep-sea marine sediments.

Heterotrophy in the earliest gut: a single-cell view of heterotrophic carbon and nitrogen assimilation in sponge-microbe symbioses

Sponges are the oldest known extant animal-microbe symbiosis. These ubiquitous benthic animals play an important role in marine ecosystems in the cycling of dissolved organic matter (DOM), the largest source of organic matter on Earth. The conventional view on DOM cycling through microbial processing has been challenged by the interaction between this efficient filter-feeding host and its diverse and abundant microbiome. Here we quantify, for the first time, the role of host cells and microbial symbionts in sponge heterotrophy. We combined stable isotope probing and nanoscale secondary ion mass spectrometry to compare the processing of different sources of DOM (glucose, amino acids, algal-produced) and particulate organic matter (POM) by a high-microbial abundance (HMA) and low-microbial abundance (LMA) sponge with single-cell resolution. Contrary to common notion, we found that both microbial symbionts and host choanocyte (i.e. filter) cells and were active in DOM uptake. Although all DOM sources were assimilated by both sponges, higher microbial biomass in the HMA sponge corresponded to an increased capacity to process a greater variety of dissolved compounds. Nevertheless, in situ feeding data demonstrated that DOM was the primary carbon source for both the LMA and HMA sponge, accounting for ~90% of their heterotrophic diets. Microbes accounted for the majority (65-87%) of DOM assimilated by the HMA sponge (and ~60% of its total heterotrophic diet) but <5% in the LMA sponge. We propose that the evolutionary success of sponges is due to their different strategies to exploit the vast reservoir of DOM in the ocean.