Modelling phytoplankton-virus interactions: phytoplankton blooms and lytic virus transmission.

A dynamic reaction-diffusion model of four variables is proposed to describe the spread of lytic viruses among phytoplankton in a poorly mixed aquatic environment. The basic ecological reproductive index for phytoplankton invasion and the basic reproduction number for virus transmission are derived to characterize the phytoplankton growth and virus transmission dynamics. The theoretical and numerical results from the model show that the spread of lytic viruses effectively controls phytoplankton blooms. This validates the observations and experimental results of Emiliana huxleyi-lytic virus interactions. The studies also indicate that the lytic virus transmission cannot occur in a low-light or oligotrophic aquatic environment.

Clustering evaluation of water quality for various classes of in-flow rivers in connected brackish lakes.

Brackish waters and estuaries at the lower reaches of rivers accumulate organic matter and nutrients from various sources in the watershed. Sufficient light and shallow water depth stimulate phytoplankton growth, resulting in a more diversified ecosystem with higher trophic levels. For effective watershed management, it is crucial to characterize the water quality of all rivers, including small and medium-sized ones. Our field survey assessed water quality parameters in 26 inflow rivers surrounding Lakes Shinji and Nakaumi, two consolidated brackish lakes in Japan. The parameters included water temperature, salinity, chlorophyll-a, and nutrients. The study used hierarchical clustering. The Silhouette Index was used to assess clustering outcomes and identify any difficulties in dispersion across clusters. The 26 rivers surrounding Lakes Shinji and Nakaumi were classified into six groups based on their water quality characteristics. This classification distinguishes itself from earlier subjective methods that relied on geographical factors. The new approach identifies a need for improved management of river water quality. The results of the cluster analysis provide valuable insights for future management initiatives. It is important to consider these findings alongside established watershed criteria.

Land use change and coastal water darkening drive synchronous dynamics in phytoplankton and fish phenology on centennial timescales.

At high latitudes, the suitable window for timing reproductive events is particularly narrow, promoting tight synchrony between trophic levels. Climate change may disrupt this synchrony due to diverging responses to temperature between, for example, the early life stages of higher trophic levels and their food resources. Evidence for this is equivocal, and the role of compensatory mechanisms is poorly understood. Here, we show how a combination of ocean warming and coastal water darkening drive long-term changes in phytoplankton spring bloom timing in Lofoten Norway, and how spawning time of Northeast Arctic cod responds in synchrony. Spring bloom timing was derived from hydrographical observations dating back to 1936, while cod spawning time was estimated from weekly fisheries catch and roe landing data since 1877. Our results suggest that land use change and freshwater run-off causing coastal water darkening has gradually delayed the spring bloom up to the late 1980s after which ocean warming has caused it to advance. The cod appear to track phytoplankton dynamics by timing gonadal development and spawning to maximize overlap between offspring hatch date and predicted resource availability. This finding emphasises the importance of land-ocean coupling for coastal ecosystem functioning, and the potential for fish to adapt through phenotypic plasticity.

Atlas of phytoplankton phenology indices in selected Eastern Mediterranean marine ecosystems.

Phytoplankton is a fundamental component of marine food webs and play a crucial role in marine ecosystem functioning. The phenology (timing of growth) of these microscopic algae is an important ecological indicator that can be utilized to observe its seasonal dynamics, and assess its response to environmental perturbations. Ocean colour remote sensing is currently the only means of obtaining synoptic estimates of chlorophyll-a (a proxy of phytoplankton biomass) at high temporal and spatial resolution, enabling the calculation of phenology metrics. However, ocean colour observations have acknowledged weaknesses compromising its reliability, while the scarcity of long-term in situ data has impeded the validation of satellite-derived phenology estimates. To address this issue, we compared one of the longest available in situ time series (20 years) of chlorophyll-a concentrations in the Eastern Mediterranean Sea (EMS), along with concurrent remotely-sensed observations. The comparison revealed a marked coherence between the two datasets, indicating the capability of satellite-based measurements in accurately capturing the phytoplankton seasonality and phenology metrics (i.e., timing of initiation, duration, peak and termination) in the studied area. Furthermore, by studying and validating these metrics we constructed a satellite-derived phytoplankton phenology atlas, reporting in detail the seasonal patterns in several sub-regions in coastal and open seas over the EMS. The open waters host higher concentrations from late October to April, with maximum levels recorded during February and lowest during the summer period. The phytoplankton growth over the Northern Aegean Sea appeared to initiate at least a month later than the rest of the EMS (initiating in late November and terminating in late May). The coastal waters and enclosed gulfs (such as Amvrakikos and Maliakos), exhibit a distinct seasonal pattern with consistently higher levels of chlorophyll-a and prolonged growth period compared to the open seas. The proposed phenology atlas represents a useful resource for monitoring phytoplankton growth periods in the EMS, supporting water quality management practices, while enhancing our current comprehension on the relationships between phytoplankton biomass and higher trophic levels (as a food source).

Long-term declines in chlorophyll a and variable phenology revealed by a 60-year estuarine plankton time series.

Long-term ecological time series provide a unique perspective on the emergent properties of ecosystems. In aquatic systems, phytoplankton form the base of the food web and their biomass, measured as the concentration of the photosynthetic pigment chlorophyll a (chl a), is an indicator of ecosystem quality. We analyzed temporal trends in chl a from the Long-Term Plankton Time Series in Narragansett Bay, Rhode Island, USA, a temperate estuary experiencing long-term warming and changing anthropogenic nutrient inputs. Dynamic linear models were used to impute and model environmental variables (1959 to 2019) and chl a concentrations (1968 to 2019). A long-term chl a decrease was observed with an average decline in the cumulative annual chl a concentration of 49% and a marked decline of 57% in winter-spring bloom magnitude. The long-term decline in chl a concentration was directly and indirectly associated with multiple environmental factors that are impacted by climate change (e.g., warming temperatures, water column stratification, reduced nutrient concentrations) indicating the importance of accounting for regional climate change effects in ecosystem-based management. Analysis of seasonal phenology revealed that the winter-spring bloom occurred earlier, at a rate of 4.9 ± 2.8 d decade-1. Finally, the high degree of temporal variation in phytoplankton biomass observed in Narragansett Bay appears common among estuaries, coasts, and open oceans. The commonality among these marine ecosystems highlights the need to maintain a robust set of phytoplankton time series in the coming decades to improve signal-to-noise ratios and identify trends in these highly variable environments.

Local intraspecific aggregation in phytoplankton model communities: spatial scales of occurrence and implications for coexistence.

The coexistence of multiple phytoplankton species despite their reliance on similar resources is often explained with mean-field models assuming mixed populations. In reality, observations of phytoplankton indicate spatial aggregation at all scales, including at the scale of a few individuals. Local spatial aggregation can hinder competitive exclusion since individuals then interact mostly with other individuals of their own species, rather than competitors from different species. To evaluate how microscale spatial aggregation might explain phytoplankton diversity maintenance, an individual-based, multispecies representation of cells in a hydrodynamic environment is required. We formulate a three-dimensional and multispecies individual-based model of phytoplankton population dynamics at the Kolmogorov scale. The model is studied through both simulations and the derivation of spatial moment equations, in connection with point process theory. The spatial moment equations show a good match between theory and simulations. We parameterized the model based on phytoplankters' ecological and physical characteristics, for both large and small phytoplankton. Defining a zone of potential interactions as the overlap between nutrient depletion volumes, we show that local species composition-within the range of possible interactions-depends on the size class of phytoplankton. In small phytoplankton, individuals remain in mostly monospecific clusters. Spatial structure therefore favours intra- over inter-specific interactions for small phytoplankton, contributing to coexistence. Large phytoplankton cell neighbourhoods appear more mixed. Although some small-scale self-organizing spatial structure remains and could influence coexistence mechanisms, other factors may need to be explored to explain diversity maintenance in large phytoplankton.

Natural iron fertilization by shallow hydrothermal sources fuels diazotroph blooms in the ocean.

Iron is an essential nutrient that regulates productivity in ~30% of the ocean. Compared with deep (>2000 meter) hydrothermal activity at mid-ocean ridges that provide iron to the ocean's interior, shallow (<500 meter) hydrothermal fluids are likely to influence the surface's ecosystem. However, their effect is unknown. In this work, we show that fluids emitted along the Tonga volcanic arc (South Pacific) have a substantial impact on iron concentrations in the photic layer through vertical diffusion. This enrichment stimulates biological activity, resulting in an extensive patch of chlorophyll (360,000 square kilometers). Diazotroph activity is two to eight times higher and carbon export fluxes are two to three times higher in iron-enriched waters than in adjacent unfertilized waters. Such findings reveal a previously undescribed mechanism of natural iron fertilization in the ocean that fuels regional hotspot sinks for atmospheric CO2.

Coastal phytoplankton blooms expand and intensify in the 21st century.

Phytoplankton blooms in coastal oceans can be beneficial to coastal fisheries production and ecosystem function, but can also cause major environmental problems1,2-yet detailed characterizations of bloom incidence and distribution are not available worldwide. Here we map daily marine coastal algal blooms between 2003 and 2020 using global satellite observations at 1-km spatial resolution. We found that algal blooms occurred in 126 out of the 153 coastal countries examined. Globally, the spatial extent (+13.2%) and frequency (+59.2%) of blooms increased significantly (P < 0.05) over the study period, whereas blooms weakened in tropical and subtropical areas of the Northern Hemisphere. We documented the relationship between the bloom trends and ocean circulation, and identified the stimulatory effects of recent increases in sea surface temperature. Our compilation of daily mapped coastal phytoplankton blooms provides the basis for global assessments of bloom risks and benefits, and for the formulation or evaluation of management or policy actions.

Elongation enhances encounter rates between phytoplankton in turbulence.

Phytoplankton come in a stunning variety of shapes but elongated morphologies dominate-typically 50% of species have aspect ratio above 5, and bloom-forming species often form chains whose aspect ratios can exceed 100. How elongation affects encounter rates between phytoplankton in turbulence has remained unknown, yet encounters control the formation of marine snow in the ocean. Here, we present simulations of encounters among elongated phytoplankton in turbulence, showing that encounter rates between neutrally buoyant elongated cells are up to 10-fold higher than for spherical cells and even higher when cells sink. Consequently, we predict that elongation can significantly speed up the formation of marine snow compared to spherical cells. This unexpectedly large effect of morphology in driving encounter rates among plankton provides a potential mechanistic explanation for the rapid clearance of many phytoplankton blooms.

Sustained stoichiometric imbalance and its ecological consequences in a large oligotrophic lake.

Considerable attention is given to absolute nutrient levels in lakes, rivers, and oceans, but less is paid to their relative concentrations, their nitrogen:phosphorus (N:P) stoichiometry, and the consequences of imbalanced stoichiometry. Here, we report 38 y of nutrient dynamics in Flathead Lake, a large oligotrophic lake in Montana, and its inflows. While nutrient levels were low, the lake had sustained high total N: total P ratios (TN:TP: 60 to 90:1 molar) throughout the observation period. N and P loading to the lake as well as loading N:P ratios varied considerably among years but showed no systematic long-term trend. Surprisingly, TN:TP ratios in river inflows were consistently lower than in the lake, suggesting that forms of P in riverine loading are removed preferentially to N. In-lake processes, such as differential sedimentation of P relative to N or accumulation of fixed N in excess of denitrification, likely also operate to maintain the lake's high TN:TP ratios. Regardless of causes, the lake's stoichiometric imbalance is manifested in P limitation of phytoplankton growth during early and midsummer, resulting in high C:P and N:P ratios in suspended particulate matter that propagate P limitation to zooplankton. Finally, the lake's imbalanced N:P stoichiometry appears to raise the potential for aerobic methane production via metabolism of phosphonate compounds by P-limited microbes. These data highlight the importance of not only absolute N and P levels in aquatic ecosystems, but also their stoichiometric balance, and they call attention to potential management implications of high N:P ratios.

Phytoplankton dynamics in Louisiana estuaries: Building a baseline to understand current and future change.

Louisiana estuaries are important habitats in the northern Gulf of Mexico, a region undergoing significant and sustained human- and climate-driven changes. This paper synthesizes data collected over multiple years from four Louisiana estuaries - Breton Sound, Terrebonne Bay, the Atchafalaya River Delta Estuary, and Vermilion Bay - to characterize trends in phytoplankton biomass, community composition, and the environmental factors influencing them. Results highlight similarities in timing and composition of maximum chlorophyll, with salinity variability often explaining biomass trends. Distinct drivers for biomass versus community structure were observed in all four estuarine systems. Systems shared a lack of significant correlation between river discharge and overall phytoplankton biomass, while discharge was important for understanding community composition. Temperature was a significant explanatory variable for both biomass and community composition in only one system. These results provide a regional view of phytoplankton dynamics in Louisiana estuaries critical to understanding and predicting the effects of ongoing change.

Enhancement of diatom growth and phytoplankton productivity with reduced O2 availability is moderated by rising CO2.

Many marine organisms are exposed to decreasing O2 levels due to warming-induced expansion of hypoxic zones and ocean deoxygenation (DeO2). Nevertheless, effects of DeO2 on phytoplankton have been neglected due to technical bottlenecks on examining O2 effects on O2-producing organisms. Here we show that lowered O2 levels increased primary productivity of a coastal phytoplankton assemblage, and enhanced photosynthesis and growth in the coastal diatom Thalassiosira weissflogii. Mechanistically, reduced O2 suppressed mitochondrial respiration and photorespiration of T. weissflogii, but increased the efficiency of their CO2 concentrating mechanisms (CCMs), effective quantum yield and improved light use efficiency, which was apparent under both ambient and elevated CO2 concentrations leading to ocean acidification (OA). While the elevated CO2 treatment partially counteracted the effect of low O2 in terms of CCMs activity, reduced levels of O2 still strongly enhanced phytoplankton primary productivity. This implies that decreased availability of O2 with progressive DeO2 could boost re-oxygenation by diatom-dominated phytoplankton communities, especially in hypoxic areas, with potentially profound consequences for marine ecosystem services in coastal and pelagic oceans.

Growth at the limits: comparing trace metal limitation of a freshwater cyanobacterium (Dolichospermum lemmermannii) and a freshwater diatom (Fragilaria crotonensis).

Freshwater phytoplankton blooms are increasing in prevalence and there are conflicting views on whether trace metals limit growth of key species and thus bloom formation. The Taupo Volcanic Zone (TVZ), New Zealand, was formed by multiple eruptions of a super-volcano which emitted rhyolitic tephra leaving lakes depleted in trace metals. This provides an opportunity to test the potential of trace metal limitation on freshwater phytoplankton growth under nanomolar concentrations. Growth responses of two algal species isolated from Lake Taupo, Dolichospermum lemmermannii (cyanobacteria) and Fragilaria crotonensis (diatom), to six biologically important trace metals (manganese, iron, zinc, cobalt, copper and molybdenum) were examined in culture experiments. These were conducted at three trace metal concentrations: (1) ambient, (2) two-times ambient, and (3) ten-times ambient concentrations in Lake Taupo. Elevated concentrations of iron significantly increased growth rates and maximum cell densities in D. lemmermannii, whereas no significant concentration dependence was observed for other trace metals. Fragilaria crotonensis showed no significant growth response to elevated concentrations of trace metals. These results highlight the importance of iron as a growth limiting nutrient for cyanobacteria and indicate that even small (twofold) increases in Fe concentrations could enhance cyanobacteria growth rates in Lake Taupo, potentially causing cyanobacterial blooms.

Geologic controls on phytoplankton elemental composition.

Planktonic organic matter forms the base of the marine food web, and its nutrient content (C:N:Porg) governs material and energy fluxes in the ocean. Over Earth history, C:N:Porg had a crucial role in marine metazoan evolution and global biogeochemical dynamics, but the geologic history of C:N:Porg is unknown, and it is often regarded constant at the "Redfield" ratio of ∼106:16:1. We calculated C:N:Porg through Phanerozoic time by including nutrient- and temperature-dependent C:N:Porg parameterizations in a model of the long-timescale biogeochemical cycles. We infer a decrease from high Paleozoic C:Porg and N:Porg to present-day ratios, which stems from a decrease in the global average temperature and an increase in seawater phosphate availability. These changes in the phytoplankton's growth environment were driven by various Phanerozoic events: specifically, the middle to late Paleozoic expansion of land plants and the Triassic breakup of the supercontinent Pangaea, which increased continental weatherability and the fluxes of weathering-derived phosphate to the oceans. The resulting increase in the nutrient content of planktonic organic matter likely impacted the evolution of marine fauna and global biogeochemistry.

Environmental control of marine phytoplankton stoichiometry in the North Atlantic Ocean.

The stoichiometric coupling of carbon to limiting nutrients in marine phytoplankton regulates the magnitude of biological carbon sequestration in the ocean. While clear links between plankton C:N ratios and environmental drivers have been identified, the nature and direction of these links, as well as their underlying physiological and ecological controls, remain uncertain. We show, with a well-constrained mechanistic model of plankton ecophysiology, that while nitrogen availability and temperature emerge as the main drivers of phytoplankton C:N stoichiometry in the North Atlantic, the biological mechanisms involved vary depending on the spatiotemporal scale and region considered. We find that phytoplankton C:N stoichiometry is overall controlled by nitrogen availability below 40° N, predominantly driven by ecoevolutionary shifts in the functional composition of the phytoplankton communities, while phytoplankton stoichiometric plasticity in response to dropping temperatures and increased grazing pressure dominates at higher latitudes. Our findings highlight the potential of "organisms-to-ecosystems" modeling approaches based on mechanistic models of plankton biology accounting for physiology, ecology, and trait evolution to explore and explain complex observational data and ultimately improve the predictions of global ocean models.

Geologic controls on phytoplankton elemental composition.

Planktonic organic matter forms the base of the marine food web, and its nutrient content (C:N:Porg) governs material and energy fluxes in the ocean. Over Earth history, C:N:Porg had a crucial role in marine metazoan evolution and global biogeochemical dynamics, but the geologic history of C:N:Porg is unknown, and it is often regarded constant at the "Redfield" ratio of ∼106:16:1. We calculated C:N:Porg through Phanerozoic time by including nutrient- and temperature-dependent C:N:Porg parameterizations in a model of the long-timescale biogeochemical cycles. We infer a decrease from high Paleozoic C:Porg and N:Porg to present-day ratios, which stems from a decrease in the global average temperature and an increase in seawater phosphate availability. These changes in the phytoplankton's growth environment were driven by various Phanerozoic events: specifically, the middle to late Paleozoic expansion of land plants and the Triassic breakup of the supercontinent Pangaea, which increased continental weatherability and the fluxes of weathering-derived phosphate to the oceans. The resulting increase in the nutrient content of planktonic organic matter likely impacted the evolution of marine fauna and global biogeochemistry.

Increased adoption of best practices in ecological forecasting enables comparisons of forecastability.

Near-term iterative forecasting is a powerful tool for ecological decision support and has the potential to transform our understanding of ecological predictability. However, to this point, there has been no cross-ecosystem analysis of near-term ecological forecasts, making it difficult to synthesize diverse research efforts and prioritize future developments for this emerging field. In this study, we analyzed 178 near-term (≤10-yr forecast horizon) ecological forecasting papers to understand the development and current state of near-term ecological forecasting literature and to compare forecast accuracy across scales and variables. Our results indicated that near-term ecological forecasting is widespread and growing: forecasts have been produced for sites on all seven continents and the rate of forecast publication is increasing over time. As forecast production has accelerated, some best practices have been proposed and application of these best practices is increasing. In particular, data publication, forecast archiving, and workflow automation have all increased significantly over time. However, adoption of proposed best practices remains low overall: for example, despite the fact that uncertainty is often cited as an essential component of an ecological forecast, only 45% of papers included uncertainty in their forecast outputs. As the use of these proposed best practices increases, near-term ecological forecasting has the potential to make significant contributions to our understanding of forecastability across scales and variables. In this study, we found that forecastability (defined here as realized forecast accuracy) decreased in predictable patterns over 1-7 d forecast horizons. Variables that were closely related (i.e., chlorophyll and phytoplankton) displayed very similar trends in forecastability, while more distantly related variables (i.e., pollen and evapotranspiration) exhibited significantly different patterns. Increasing use of proposed best practices in ecological forecasting will allow us to examine the forecastability of additional variables and timescales in the future, providing a robust analysis of the fundamental predictability of ecological variables.

Variability in spring phytoplankton blooms associated with ice retreat timing in the Pacific Arctic from 2003-2019.

The Arctic is experiencing rapid changes in sea-ice seasonality and extent, with significant consequences for primary production. With the importance of accurate monitoring of spring phytoplankton dynamics in a changing Arctic, this study further examines the previously established critical relationship between spring phytoplankton bloom types and timing of the sea-ice retreat for broader temporal and spatial coverages, with a particular focus on the Pacific Arctic for 2003-2019. To this end, time-series of satellite-retrieved phytoplankton biomass were modeled using a parametric Gaussian function, as an effective approach to capture the development and decay of phytoplankton blooms. Our sensitivity analysis demonstrated accurate estimates of timing and presence/absence of peaks in phytoplankton biomass even with some missing values, suggesting the parametric Gaussian function is a powerful tool for capturing the development and decay of phytoplankton blooms. Based on the timing and presence/absence of a peak in phytoplankton biomass and following the classification developed by the previous exploratory work, spring bloom types are classified into three groups (under-ice blooms, probable under-ice blooms, and marginal ice zone blooms). Our results showed that the proportion of under-ice blooms was higher in the Chukchi Sea than in the Bering Sea. The probable under-ice blooms registered as the dominant bloom types in a wide area of the Pacific Arctic, whereas the marginal ice zone bloom was a relatively minor bloom type across the Pacific Arctic. Associated with a shift of sea-ice retreat timing toward earlier dates, we confirmed previous findings from the Chukchi Sea of recent shifts in phytoplankton bloom types from under-ice blooms to marginal ice zone blooms and demonstrated that this pattern holds for the broader Pacific Arctic sector for the time period 2003-2019. Overall, the present study provided additional evidence of the changing sea-ice retreat timing that can drive variations in phytoplankton bloom dynamics, which contributes to addressing the detection and consistent monitoring of the biophysical responses to the changing environments in the Pacific Arctic.

A novel random forest approach to revealing interactions and controls on chlorophyll concentration and bacterial communities during coastal phytoplankton blooms.

Increasing occurrence of harmful algal blooms across the land-water interface poses significant risks to coastal ecosystem structure and human health. Defining significant drivers and their interactive impacts on blooms allows for more effective analysis and identification of specific conditions supporting phytoplankton growth. A novel iterative Random Forests (iRF) machine-learning model was developed and applied to two example cases along the California coast to identify key stable interactions: (1) phytoplankton abundance in response to various drivers due to coastal conditions and land-sea nutrient fluxes, (2) microbial community structure during algal blooms. In Example 1, watershed derived nutrients were identified as the least significant interacting variable associated with Monterey Bay phytoplankton abundance. In Example 2, through iRF analysis of field-based 16S OTU bacterial community and algae datasets, we independently found stable interactions of prokaryote abundance patterns associated with phytoplankton abundance that have been previously identified in laboratory-based studies. Our study represents the first iRF application to marine algal blooms that helps to identify ocean, microbial, and terrestrial conditions that are considered dominant causal factors on bloom dynamics.

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

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