Viral particles are abundant in aquatic and soil environments and are operationally defined as part of dissolved organic matter (DOM) in nature. Virions are known to contain rich nitrogen, phosphorus, and sulfur, and they represent a special pool of DOM. Little is known about whether bacteria can use virion DOM to support their growth. In this study, we added purified phage particles to three non-host marine bacterial cultures to investigate how marine bacteria respond to the addition of purified virions. Upon adding virions, we monitored bacterial and viral abundance, bacterial extracellular enzymatic activities, and the composition of virion DOM. Bacterial growth increased with the addition of purified virions, and a large portion of the virions was degraded in the three bacterial cultures within 6 days of incubation. High activities of exocellular alkaline phosphatase and leucine aminopeptidase suggest these exoenzymes are involved in virion degradation. Using an ultra-high-resolution mass spectrometer, we obtained the first van Krevelen diagram of virion DOM molecules. A total of 508 DOM molecules derived from virions were detected, and 77 virion DOM molecules shared across all three bacterial cultures were not detected after 6 days. Together, our results show that bacteria tend to utilize nitrogen-, phosphorus-, and sulfur-rich DOM molecules resulting from virions. This study provides direct evidence that purified virions can serve as a DOM source to support bacterial growth, implying that viruses in the natural environment are a unique source of DOM, which would exert profound impacts on marine food webs and biogenic element cycling.

Mixotrophic-continuous culture integration presents a promising approach for algal-based renewable energy and nutraceuticals. To fully understand the biomass accumulation patterns and underlying mechanisms, chemostats of mixotrophic Auxenochlorella pyrenoidosa were maintained stably for 80 days for 4 stages and 3 dilution rates, enabling precise nutrient (glucose) control by adjusting dilution rates. Although intracellular pigment content (chlorophyll a, b, and carotenoids) decreased, the biomass, free fatty acid, and amino acid levels increased by up to 9.1-fold, 4.6-fold, and 1.7-fold, respectively, compared to the autotrophy. High phosphate and glucose utilization were observed, with glucose significantly enhancing nitrate utilization. Low dilution rates promoted the accumulation of pigments and total fatty acids for reserve, whereas higher dilution rates favored unsaturated fatty acids (over 52%) and growth-related molecules such as amino acids (max 53.87%) with a well-balanced profile. Chlorophyll fluorescence revealed that the more active initial slope (alpha), maximum relative electron transfer rate (rETRmax), and enhanced minimal saturated light intensity (Ik) during mixotrophy were consistent with biomass and bioactive compound accumulation, particularly supporting algae under high growth rates. Although urea supplementation caused the maximum photochemical quantum yield (Fv/Fm) decline transiently, it significantly enhanced amino acid content and carotenoids with antioxidant benefits under low dilution rate. Throughout mixotrophy, glucose was fully consumed with markedly improved nitrogen assimilation efficiency. Principal component analysis (PCA) further elucidated that bioactive compound accumulation correlated with rETRmax and Ik. This study demonstrates efficient bioconversion of carbohydrate, providing a viable approach for sustainable production and monitoring of microalgae-derived amino-acid-rich products with potential health applications.

Estuaries are dynamic processing hubs for dissolved organic matter (DOM), and bacteria play key roles in DOM transformation. However, the processes and drivers of estuarine bacteria-mediated DOM transformation remain poorly understood. We investigated the DOM composition, bacterial communities, and environmental factors across four geographically distinct estuaries: Jiaozhou Bay (JZB), Xiamen Bay (XMB), Chesapeake Bay (CB), and Mission-Aransas Estuary (MAE). During the sampling period, JZB and XMB were enriched in autochthonous DOM, while CB and MAE were dominated by terrestrial DOM. Bacterial diversity was significantly greater in JZB and XMB than in CB and MAE. Co-occurrence networks showed that Proteobacteria (41.4% ± 9.8%) were extensively involved in estuarine DOM metabolism; bacterial communities exhibited a metabolic preference for carboxyl-rich alicyclic molecules (71.7% ± 7.1%) in all estuaries, and more complex communities had greater capacity to degrade recalcitrant DOM. Structural equation modeling further indicated that bacterial-mediated DOM transformation in all estuaries was regulated by similar environmental factors (temperature and dissolved inorganic nitrogen). Warming and nitrogen limitation could reduce bacterial diversity and promote the accumulation of recalcitrant DOM. Overall, this study explored estuarine bacteria-mediated DOM transformation at the molecular level and identified common environmental drivers, providing deeper insight into the fate of estuarine DOM.

Tiny unicellular cyanobacteria or picocyanobacteria (0.5–3 µm) are important due to their ecological significance. Chesapeake Bay is a temperate estuary that contains abundant and diverse picocyanobacteria. Studies of Chesapeake Bay picocyanobacteria in the past 20 years led to the finding of new members of subcluster 5.2 Synechococcus. They laid the foundation for revealing the ecophysiology, biogeography, genomics, and molecular evolution of picocyanobacterial in the Chesapeake Bay and other coastal estuaries. The Bay picocyanobacteria are known to better tolerate the changes in temperature, salinity, and heavy metals compared to their coastal and open-ocean counterparts. Many picocyanobacteria isolated from the Bay contain rich toxin–antitoxin (TA) genes, suggesting that the TA system may provide them with a genetic advance to cope with variable estuarine environments. Distinct winter and summer picocyanobacteria are present in the Bay, suggesting a dynamic seasonal shift of the picocyanobacterial community in the temperate estuary. While the Bay contains subcluster 5.2 Synechococcus, it also contains freshwater Synechococcus, Cyanobium, and marine Synechococcus due to river influx and the ocean’s tidal influence. Some Chesapeake Bay picocyanobacterial clades were found in the Bering Sea and Chukchi Sea, showing a link between the Bay and polar picocyanobacteria. Genomic sequences of estuarine picocyanobacteria provide new insight into the taxonomy and evolution of freshwater, estuarine, and marine unicellular cyanobacteria. Estuaries connect freshwater and marine ecosystems. This overview attempts to extend what we learned from Chesapeake Bay picocyanobacteria to picocyanobacteria in freshwater and marine waters.

Glyphosate, a commonly utilized herbicide in agriculture, poses significant threats to microbial diversity, soil fertility, human health, and agricultural productivity due to its frequent and intensive application. To mitigate these challenges, we investigated the potential of plant growth-promoting rhizobacterial strains tolerant to glyphosate (GLY) to alleviate its toxicity and enhance maize growth. Eleven pre-isolated bacterial strains were assessed for their ability to promote maize growth and reduce phytotoxicity at 100 and 200 mg kg− 1 GLY in soil. Among them, five GLY-tolerant bacterial strains (E. cloacae, E. ludwigii, K. variicola, P. aeruginosa and S. liquefaciens) exhibited notable resistance. These strains exhibited positive qualitative characteristics, including 1-aminocyclopropane 1-carboxylate (ACC) deaminase activity, oxidase and catalase production, indole-3-acetic acid synthesis, and siderophore production. Moreover, these five GLY-tolerant strains reduced the toxicity and improved the biological traits of the maize plants. Inoculated plants average improved chlorophyll SPAD value by 43

Aggregation and co-occurrence patterns of microbial communities are the key scientific issues in lake ecology. To explore the mechanisms of microbial ecological assembly and community succession in this unique habitat, 16 samples were collected from eight sites in Wuliangsuhai Lake. Second-generation DNA sequencing was applied to reveal the spatial dynamics of the bacterial community structure and distribution across two environmental media in this nutrient-rich shallow grassland lake and to elucidate the characteristics of the co-occurrence network. This study also examined the effects of environmental filtering and biological interactions on the formation and maintenance of the community composition and diversity. The results highlight habitat heterogeneity in microbial community composition, with no discernible latitudinal diversity patterns. The causal analysis identified electrical conductivity, pH, total nitrogen, and phosphorus as the primary factors driving changes in the bacterial community structure in the water and sediment of grass-type lakes, with TN being the key environmental driver. CL500-3 was identified as a pollution-tolerant species in aquatic environments. g__norank_f_Verrucomicrobiaceae was identified as a pollution-tolerant species in sediment environments. The bacterial communities exhibited a significant distance decay pattern, with a higher spatial turnover rate in water than in sediment. Co-occurrence network analysis revealed greater complexity and stability in the sediment bacterial communities, with three potential keystone species, than in water. The neutral and null model results indicated that the water bacterial communities were more susceptible to dispersal limitation, whereas more complex interactions in sediment increased the role of deterministic processes in community construction. This study proposed the division of aquatic plant regions in freshwater lakes and demonstrated the community characteristics of different habitat types, contributing to a comprehensive understanding of shallow-water bacterial diversity and community structure.

During the bloom season, the colonial cyanobacterium Microcystis forms complex aggregates which include a diverse microbiome within an exopolymer matrix. Early research postulated a simple mutualism existing with bacteria benefitting from the rich source of fixed carbon and Microcystis receiving recycled nutrients. Researchers have since hypothesized that Microcystis aggregates represent a community of synergistic and interacting species, an interactome, each with unique metabolic capabilities that are critical to the growth, maintenance, and demise of Microcystis blooms. Research has also shown that aggregate-associated bacteria are taxonomically different from free-living bacteria in the surrounding water. Moreover, research has identified little overlap in functional potential between Microcystis and members of its microbiome, further supporting the interactome concept. However, we still lack verification of general interaction and know little about the taxa and metabolic pathways supporting nutrient and metabolite cycling within Microcystis aggregates. During a 7-month study of bacterial communities comparing free-living and aggregate-associated bacteria in Lake Taihu, China, we found that aerobic anoxygenic phototrophic (AAP) bacteria were significantly more abundant within Microcystis aggregates than in free-living samples, suggesting a possible functional role for AAP bacteria in overall aggregate community function. We then analyzed gene composition in 102 high-quality metagenome-assembled genomes (MAGs) of bloom-microbiome bacteria from 10 lakes spanning four continents, compared with 12 complete Microcystis genomes which revealed that microbiome bacteria and Microcystis possessed complementary biochemical pathways that could serve in C, N, S, and P cycling. Mapping published transcripts from Microcystis blooms onto a comprehensive AAP and non-AAP bacteria MAG database (226 MAGs) indicated that observed high levels of expression of genes involved in nutrient cycling pathways were in AAP bacteria. Our results provide strong corroboration of the hypothesized Microcystis interactome and the first evidence that AAP bacteria may play an important role in nutrient cycling within Microcystis aggregate microbiomes.

Synechococcus is ubiquitous and diverse in marine environments and contributes significantly to primary productivity in the ocean. The genetic diversity of the genus Synechococcus has been extensively explored based on the 16S-23S rRNA internal transcribed spacer (ITS) region. However, accurate identification of Synechococcus ITS from large sequencing datasets is challenging owing to the absence of a standardized taxonomy and to ambiguous clade boundaries. To address these limitations, we developed Syn_Tool, a deep-learning-based framework integrating a curated Synechococcus ITS database for sequence identification, classification and novel clade discovery. Analysing 1 087 323 ITS sequences from the coastal water of China-the largest Synechococcus dataset to date-Syn_Tool classified them into 42 clades, including 28 known and 14 newly defined clades. Biogeographical analyses revealed a latitudinal diversity gradient driven by temperature, with 12 newly defined clades (clades CSII-IV, CSVI-XIV) primarily found in estuarine regions where rapid diversification may promote the emergence of novel genotypes. This study demonstrates the application of deep learning in classifying Synechococcus and understanding their ecological roles in dynamic marine ecosystems.

Marine viral communities harbor an astounding diversity of phages infecting diverse marine bacteria. The double-stranded DNA phage family Autographiviridae is among the most abundant phage families in the ocean. However, the current understanding of marine Autographiviridae phages is predominantly derived from isolates infecting cyanobacteria, SAR11, and Roseobacter. To achieve a more comprehensive understanding of the diversity, ecological traits, and functional profiles of this phage family, we recovered 1253 complete marine Autographiviridae uncultivated viral genomes (UViGs). Comparative genomic analysis showed that marine-derived Autographiviridae phages display genome synteny and share a conserved core of seven genes. The core gene-based phylogenomic analysis classified them into 14 groups, 6 of which were previously undescribed. These groups varied in G + C content, genome size, and presence of specific genes. Metagenomic recruitment analysis demonstrated that Autographiviridae phages are globally distributed and enriched in the upper ocean layers of tropical and temperate zones. The differential distribution patterns among these groups mirror the ecological niches of their potential hosts, emphasizing the top-down control these phages exert on their host populations. Collectively, our study substantially expands knowledge regarding the diversity, potential hosts, functional capacity, and ecological distribution of Autographiviridae phages in the ocean, emphasizing their ecological implications in marine environments.

SAR202 bacteria are a diverse group of bacteria in the ocean. The SAR202 lineages dominate the bacterial community and evolve specialized metabolisms for oxidizing recalcitrant organic compounds in the dark ocean. SAR202 bacteria are also present in the euphotic oceans; however, their ecological roles and metabolic potential remain poorly understood. In this study, we collected 392 non-redundant metagenome-assembled genomes from different oceans, with 18% of these SAR202 genomes characterized by small genome sizes (<2 Mbp), low GC content (<40%), and high gene density. The 70 genome-streamlined SAR202 bacteria constitute more than an average of 90% of SAR202 in the euphotic zone and exhibit streamlined metabolic features compared to the dark ocean SAR202. Genome-streamlined SAR202 is distributed in many major SAR202 lineages (i.e. I, II, III, and VI). Phylogenomic analysis shows that the genome-streamlined SAR202 clades diverged from the non-genome-streamlined SAR202 lineages and evolved independently within the same clades. Certain genes are enriched in genome-streamlined SAR202, such as proteorhodopsin genes and the coding genes of major facilitator superfamily transporters, nucleoside transporters, and deoxyribodipyrimidine photo-lyase, indicating their adaptation to sunlit oligotrophic water. A detailed comparison between genome-streamlined SAR202 and non-genome-streamlined SAR202 was made to illustrate their distinct niche distribution and metabolic buildup. In addition, the metatranscriptomic analysis supports that genome-streamlined SAR202 bacteria are active in the upper ocean. This study represents a systematic study of streamlined SAR202 bacteria that occupy the euphotic ocean and provides a comprehensive view of the ecological roles of SAR202 bacteria in the ocean.

Temperature is a key factor influencing coastal carbon pools, yet the effects of warming on dissolved organic carbon (DOC) transformations and associated microbial processes remain poorly understood. Through bioassay experiments across a wide temperature gradient (7.6-35.9 °C), three critical thresholds (15.6, 24.6, and 29.9 °C) are identified that delineate distinct regimes of microbial DOC utilization with contrasting carbon fates. Below 15.6 °C, DOC characterized the most unique molecules, and their transformations are governed by bacteria whose relative abundance decreased with warming; hereafter warming-resistant microbes dominated accompanied by DOC molecular signatures that changed till 24.6 °C. Limited substrate availability constrained microbial remineralization rates in these two stages. Once temperatures surpassed 24.6 °C, thermal-favored microbes prevailed but taxa changed after 29.9 °C, DOC accumulated, and a larger fraction of recalcitrant DOC is retained, thereby enhancing carbon sequestration. Network analysis further revealed complex many-one-many resource-consumer-excretion linkages between bacteria and individual DOC molecules, underscoring the tangled nature of microbial DOC processing. The findings demonstrate that coastal DOC cycling responds to warming in a strongly non-linear, threshold-controlled manner, providing critical insights for predicting the behavior of coastal carbon sinks under ongoing climate change.

Genome foundation models hold transformative potential for precision medicine, drug discovery, and understanding complex biological systems. However, existing models are often inefficient, constrained by suboptimal tokenization and architectural design, and biased toward reference genomes, limiting their representation of low-abundance, uncultured microbes in the rare biosphere. To address these challenges, we developed GenomeOcean, a 4-billion-parameter generative genome foundation model trained on over 600 Gbp of high-quality contigs derived from 220 TB of metagenomic datasets collected from diverse habitats across Earth's ecosystems. A key innovation of GenomeOcean is training directly on large-scale co-assemblies of metagenomic samples, enabling enhanced representation of rare microbial species and improving generalizability beyond genome-centric approaches. We implemented a byte-pair encoding (BPE) tokenization strategy for genome sequence generation, alongside architectural optimizations, achieving up to 150× faster sequence generation while maintaining high biological fidelity. GenomeOcean excels in representing microbial species and generating protein-coding genes constrained by evolutionary principles. Additionally, its fine-tuned model demonstrates the ability to discover novel biosynthetic gene clusters (BGCs) in natural genomes and perform zero-shot synthesis of biochemically plausible, complete BGCs. GenomeOcean sets a new benchmark for metagenomic research, natural product discovery, and synthetic biology, offering a robust foundation for advancing these fields.

Certain microalgal species can grow with different trophic strategies depending on the availability of nutrient resources. They can use the energy from light or an organic substrate, or both, and can therefore be called autotrophs, heterotrophs, or mixotrophs. We recently isolated a microalgal strain from the microplastic biofilm, which was identified as Auxenochlorella protothecoides, AS-1. Strain AS-1 grew rapidly in bacterial culture media and exhibited different growth rates and cell sizes under different trophic conditions. We compared the growth performance of AS-1 under the three different trophic modes. AS-1 reached a high biomass (>4 g/L) in 6 days under mixotrophic growth conditions with a few organic carbons as a substrate. In contrast, poor autotrophic growth was observed for AS-1. Different cell sizes, including daughter and mother cells, were observed under the different growth modes. We applied a Coulter Counter to measure the size distribution patterns of AS-1 under different trophic modes. We showed that the cell size distribution of AS-1 was affected by different growth modes. Compared to the auto-, hetero- and mixotrophic modes, AS-1 achieved higher biomass productivity by increasing cell number and cell size in the presence of organic substrate. The mechanisms and advantages of having more mother cells with organic substrates are still unclear and warrant further investigations. The work here provides the growth information of a newly isolated A. protothecoides AS-1 which will be beneficial to future downstream applications.

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.

Glyphosate (GLX) is a crucial organophosphonate herbicide applied to eliminate unwanted, grasses and herbaceous plants in various vegetation management situations. Its widespread and consequently application is causing environmental pollution, there is a need to remove it from the environment using an eco-friendly and cost-effective method. Biodegradation is an effective method for the removal of GLX. But various environmental factor effecting is degradation after its applications such as aerobic and anaerobic environment, different pH and temperature, soil water contents and soil textures. Glyphosate resistant bacterial strains have been isolated from GLX-contaminated soil which were proficient to utilize GLX as a carbon source. High Pressure Liquid Chromatography instrument was used to determine the rate of GLX biodegradation in liquid media and soil under different environmental conditions. The five out of eleven strains such as WAG2 (Serratia liquefaciens), WAG4 (Klebsiella variicola), WAG45 (Enterobacter cloacae), WAG9 (Pseudomonas aeruginosa), and WAG11 (Enterobacter ludwigii) were proficient in average degraded 95 to 98 mg kg(-1) glyphosate in soil followed by liquid media 93 to 96 mg kg(-1) within 28 days of incubation in different environmental factors. The optimal circumstances for the degradation of GLX were found to be aerobic, pH 7, 40(degrees)C, soil water content at 10% and sandy loam texture showed maximum degradation at 100 mg kg-1 compared to 200 mg kg-1 concentration of GLX. This study demonstrates the potential of isolated bacterial strains for efficient degradation of GLX, which can be exploited for remediation of GLX in contaminated soil.

ABSTRACT Gene transfer agents (GTAs) are phage-like entities that package and transfer random host genome fragments between prokaryotes. RcGTA, produced by Rhodobacter capsulatus , is hypothesized to originate from a prophage ancestor. Most of the evidence supporting this hypothesis came from the finding of RcGTA-like genes in phages. More than 75% of the RcGTA genes have a phage homolog. However, only a few RcGTA homologs have been identified in a (pro)phage genome, leaving the hypothesis that GTAs evolved from prophages through gene loss with only weak evidence. We herein report the discovery of an inducible prophage (vB_MseS-P1) from a Mesorhizobium sediminum strain that contains the largest number (12) of RcGTA homologs found in a phage genome to date. We also identified three putative prophages and two prophage remnants harboring 12–14 RcGTA homologs in a Methylobacterium nodulans strain. The protein remote homology detection also revealed more RcGTA homologs from other phages than we previously thought. Moreover, the head–tail gene architecture of these newly discovered prophage-related elements closely resembles that of RcGTA. Furthermore, vB_MseS-P1 virions have structural proteins similar to RcGTA particles. Close phylogenetic relationships between certain prophage genes and RcGTA-like genes in Alphaproteobacteria further support the shared ancestry between RcGTA and prophages. Our findings provide new relatively direct evidence of the origin of RcGTA from a prophage progenitor. IMPORTANCE GTAs are important genetic elements in certain groups of bacteria and contribute to the genetic diversification, evolution, and ecological adaptation of bacteria. RcGTA, a common type of GTA, is known to package and transfer random fragments of the bacterial genome to recipient cells. However, the origin of RcGTA is still elusive. It has been hypothesized that RcGTA evolved from a prophage ancestor through gene loss. However, the few RcGTA homologs identified in a (pro)phage genome leave the hypothesis lacking direct evidence. This study uncovers the presence of a large number of RcGTA homologs in an inducible prophage and several putative prophages. The similar head–tail gene architecture and structural protein compositions of these newly discovered prophage-related elements and RcGTA further demonstrate an unprecedentedly observed close evolutionary relationship between prophages and RcGTA. Together, our findings provide more direct evidence supporting the origin of RcGTA from prophage.

SAR202 bacteria in the Chloroflexota phylum are abundant and widely distributed in the ocean. Their genome coding capacities indicate their potential roles in degrading complex and recalcitrant organic compounds in the ocean. However, our understanding of their genomic diversity, vertical distribution, and depth-related metabolisms is still limited by the number of assembled SAR202 genomes. In this study, we apply deep metagenomic sequencing (180 Gb per sample) to investigate microbial communities collected from six representative depths at the Bermuda Atlantic Time Series (BATS) station. We obtain 173 SAR202 metagenome-assembled genomes (MAGs). Intriguingly, 154 new species and 104 new genera are found based on these 173 SAR202 genomes. We add 12 new subgroups to the current SAR202 lineages. The vertical distribution of 20 SAR202 subgroups shows their niche partitioning in the euphotic, mesopelagic, and bathypelagic oceans, respectively. Deep-ocean SAR202 bacteria contain more genes and exhibit more metabolic potential for degrading complex organic substrates than those from the euphotic zone. With deep metagenomic sequencing, we uncover many new lineages of SAR202 bacteria and their potential functions which greatly deepen our understanding of their diversity, vertical profile, and contribution to the ocean's carbon cycling, especially in the deep ocean. The authors apply deep metagenomic sequencing to analyze six depth samples at the BATS station. They identify novel SAR202 groups/subgroups in the ocean to understand their vertical distribution, metabolic diversity, unique ecological niches.

The ubiquitous and abundant marine phages play critical roles in shaping the composition and function of bacterial communities, impacting biogeochemical cycling in marine ecosystems. Autographiviridae is among the most abundant and ubiquitous phage families in the ocean. However, studies on the diversity and ecology of Autographiviridae phages in marine environments are restricted to isolates that infect SAR11 bacteria and cyanobacteria. In this study, ten new roseophages that infect marine Roseobacter strains were isolated from coastal waters. These new roseophages have a genome size ranging from 38 917 to 42 634 bp and G+C content of 44.6–50 %. Comparative genomics showed that they are similar to known Autographiviridae phages regarding gene content and architecture, thus representing the first Autographiviridae roseophages. Phylogenomic analysis based on concatenated conserved genes showed that the ten roseophages form three distinct subgroups within the Autographiviridae, and sequence analysis revealed that they belong to eight new genera. Finally, viromic read-mapping showed that these new Autographiviridae phages are widely distributed in global oceans, mostly inhabiting polar and estuarine locations. This study has expanded the current understanding of the genomic diversity, evolution and ecology of Autographiviridae phages and roseophages. We suggest that Autographiviridae phages play important roles in the mortality and community structure of roseobacters, and have broad ecological applications.

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.

ABSTRACT Phytoplankton are important drivers of aquatic ecosystem function and environmental health. Their community compositions and distributions are directly impacted by environmental processes and human activities, including in the largest estuary in North America, the Chesapeake Bay. It is crucial to uncover how planktonic eukaryotes play fundamental roles as primary producers and trophic links and sustain estuarine ecosystems. In this study, we investigated the detailed community structure and spatiotemporal variations of planktonic eukaryotes in the Chesapeake Bay across space and time for three consecutive years. A clear seasonal and spatial shift of total, abundant, and rare planktonic eukaryotes was evident, and the pattern recurred interannually. Multiple harmful algal species have been identified in the Bay with varied distribution patterns, such as Karlodinium, Heterosigma akashiwo, Protoperidinium sp., etc. Compared to abundant taxa, rare subcommunities were more sensitive to environmental disturbance in terms of richness, diversity, and distribution. The combined effects of temporal variation (13.3%), nutrient availability (10.0%), and spatial gradients (8.8%) structured the distribution of eukaryotic microbial communities in the Bay. Similar spatiotemporal patterns between planktonic prokaryotes and eukaryotes suggest common mechanisms of adjustment, replacement, and species interaction for planktonic microbiomes under strong estuarine gradients. To our best knowledge, this work represents the first systematic study on planktonic eukaryotes in the Bay. A comprehensive view of the distribution of planktonic microbiomes and their interactions with environmental processes is critical in understanding the underlying microbial mechanisms involved in maintaining the stability, function, and environmental health of estuarine ecosystems. IMPORTANCE Deep sequencing analysis of planktonic eukaryotes in the Chesapeake Bay reveals high community diversity with many newly recognized phytoplankton taxa. The Chesapeake Bay planktonic eukaryotes show distinct seasonal and spatial variability, with recurring annual patterns of total, abundant, and rare groups. Rare taxa mainly contribute to eukaryotic diversity compared to abundant groups, and they are more sensitive to spatiotemporal variations and environmental filtering. Temporal variations, nutrient availability, and spatial gradients significantly affect the distribution of eukaryotic microbial communities. Similar spatiotemporal patterns in prokaryotes and eukaryotes suggest common mechanisms of adjustment, substitution, and species interactions in planktonic microbiomes under strong estuarine gradients. Interannually recurring patterns demonstrate that diverse eukaryotic taxa have well adapted to the estuarine environment with a long residence time. Further investigations of how human activities impact estuarine planktonic eukaryotes are critical in understanding their essential ecosystem roles and in maintaining environmental safety and public health.