Influence of nutrient supply on plankton microbiome biodiversity and distribution in a coastal upwelling region

Recurring seasonality exposes dominant species and niche partitioning strategies of open ocean picoeukaryotic algae

Ocean spring phytoplankton blooms are dynamic periods important to global primary production. We document vertical patterns of a diverse suite of eukaryotic algae, the prasinophytes, in the North Atlantic Subtropical Gyre with monthly sampling over four years at the Bermuda Atlantic Time-series Study site. Water column structure was used to delineate seasonal stability periods more ecologically relevant than seasons defined by calendar dates. During winter mixing, tiny prasinophytes dominated by Class II comprise 46  ±  24% of eukaryotic algal (plastid-derived) 16S rRNA V1-V2 amplicons, specifically Ostreococcus Clade OII, Micromonas commoda, and Bathycoccus calidus. In contrast, Class VII are rare and Classes I and VI peak during warm stratified periods when surface eukaryotic phytoplankton abundances are low. Seasonality underpins a reservoir of genetic diversity from multiple prasinophyte classes during warm periods that harbor ephemeral taxa. Persistent Class II sub-species dominating the winter/spring bloom period retreat to the deep chlorophyll maximum in summer, poised to seed the mixed layer upon winter convection, exposing a mechanism for initiating high abundances at bloom onset. Comparisons to tropical oceans reveal broad distributions of the dominant sub-species herein. This unparalleled window into temporal and spatial niche partitioning of picoeukaryotic primary producers demonstrates how key prasinophytes prevail in warm oceans.

Influence of oceanic mesoscale eddies on the deep chlorophyll maxima

The deployment of the biogeochemical Argo network significantly enhances our understanding of the ecological effects of mesoscale eddies at different ocean depths. In this study, satellite data and more than one hundred thousand biogeochemical Argo float profiles were used to analyze the responses of the deep chlorophyll maximum (DCM) to mesoscale eddies. The DCM profiles were categorized into two types: DAM (adaptation maximum) and DBM (biomass maximum), based on their adaptation to light and maximum biomass characteristics. The variabilities in the DCM profiles in terms of latitude, seasonality, and their response to mesoscale eddies were subsequently investigated on a global scale. Our analysis demonstrates that light and nutrient availability explain a significant portion of the variability in the phytoplankton distribution across different regions and seasons. Statistical analysis reveals that cyclonic (anticyclonic) eddies enhance (weaken) the intensity of the DCM. The magnitude of this enhancement or weakening exhibits regional differences. Specifically, high-latitude regions are more influenced by eddies in terms of light-adapted DCM intensity, while in mid-latitude regions, eddies exhibit a stronger effect on the maximum biomass-driven DCM intensity. Moreover, our findings suggest that eddies in the North Atlantic Subtropical Gyre contribute to a downward shift in the euphotic zone depth, leading to an increased DCM depth and strengthened DCM intensity. However, in the equatorial region, eddies impact the DCM depth by influencing the nitracline (a layer in a body of water in which the nitrate concentration changes rapidly with depth). Similar patterns are frequently observed in different regions at the same latitude, providing a foundation for further detailed investigations of the DCM in specific areas.

Distinct Assembly Processes Structure Planktonic Bacterial Communities Among Near- and Offshore Ecosystems in the Yangtze River Estuary

The estuarine system functions as natural filters due to its ability to facilitate material transformation, planktonic bacteria play a crucial role in the cycling of complex nutrients and pollutants within estuaries, and understanding the community composition and assembly therein is crucial for comprehending bacterial ecology within estuaries. Despite extensive investigations into the composition and community assembly of two bacterial fractions (free-living, FLB; particle-attached, PAB), the process by which bacterioplankton communities in these two habitats assemble in the nearshore and offshore zones of estuarine ecosystems remains poorly understood. In this study, we conducted sampling in the Yangtze River Estuary (YRE) to investigate potential variations in the composition and community assembly of FLB and PAB in nearshore and offshore regions. We collected 90 samples of surface, middle, and bottom water from 16 sampling stations and performed 16S rRNA gene amplicon analysis along with environmental factor measurements. The results unveiled that the nearshore communities demonstrated significantly greater species richness and Chao1 indices compared to the offshore communities. In contrast, the nearshore communities had lower values of Shannon and Simpson indices. When compared to the FLB, the PAB exhibit a higher level of biodiversity and abundance. However, no distinct alpha and beta diversity differences were observed between the bottom, middle, and surface water layers. The community assembly analysis indicated that nearshore communities are predominantly shaped by deterministic processes, particularly due to heterogeneous selection of PAB; In contrast, offshore communities are governed more by stochastic processes, largely due to homogenizing dispersal of FLB. Consequently, the findings of this study demonstrate that nearshore and PAB communities exhibit higher levels of species diversity, while stochastic and deterministic processes exert distinct influences on communities among near- and offshore regions. This study further sheds new light on our understanding of the mechanisms governing bacterial communities in estuarine ecosystems.

A marine heatwave drives significant shifts in pelagic microbiology

Marine heatwaves (MHWs) cause disruption to marine ecosystems, deleteriously impacting macroflora and fauna. However, effects on microorganisms are relatively unknown despite ocean temperature being a major determinant of assemblage structure. Using data from thousands of Southern Hemisphere samples, we reveal that during an "unprecedented" 2015/16 Tasman Sea MHW, temperatures approached or surpassed the upper thermal boundary of many endemic taxa. Temperate microbial assemblages underwent a profound transition to niche states aligned with sites over 1000 km equatorward, adapting to higher temperatures and lower nutrient conditions bought on by the MHW. MHW conditions also modulate seasonal patterns of microbial diversity and support novel assemblage compositions. The most significant affects of MHWs on microbial assemblages occurred during warmer months, when temperatures exceeded the upper climatological bounds. Trends in microbial response across several MHWs in different locations suggest these are emergent properties of temperate ocean warming, which may facilitate monitoring, prediction and adaptation efforts.

Machine learning modeling for the prediction of phosphorus and nitrogen removal efficiency and screening of crucial microorganisms in wastewater treatment plants

The effectiveness of wastewater treatment plants (WWTPs) is largely determined by the microbial community structure in their activated sludge (AS). Interactions among microbial communities in AS systems and their indirect effects on water quality changes are crucial for WWTP performance. However, there is currently no quantitative method to evaluate the contribution of microorganisms to the operating efficiency of WWTPs. Traditional assessments of WWTP performance are limited by experimental conditions, methods, and other factors, resulting in increased costs and experimental pollutants. Therefore, an effective method is needed to predict WWTP efficiency based on AS community structure and quantitatively evaluate the contribution of microorganisms in the AS system. This study evaluated and compared microbial communities and water quality changes from WWTPs worldwide by meta-analysis of published high-throughput sequencing data. Six machine learning (ML) models were utilized to predict the efficiency of phosphorus and nitrogen removal in WWTPs; among them, XGBoost showed the highest prediction accuracy. Cross-entropy was used to screen the crucial microorganisms related to phosphorus and nitrogen removal efficiency, and the modeling confirmed the reasonableness of the results. Thirteen genera with nitrogen and phosphorus cycling pathways obtained from the screening were considered highly appropriate for the simultaneous removal of phosphorus and nitrogen. The results showed that the microbes Haliangium, Vicinamibacteraceae, Tolumonas, and SWB02 are potentially crucial for phosphorus and nitrogen removal, as they may be involved in the process of phosphorus and nitrogen removal in sewage treatment plants. Overall, these findings have deepened our understanding of the relationship between microbial community structure and performance of WWTPs, indicating that microbial data should play a critical role in the future design of sewage treatment plants. The ML model of this study can efficiently screen crucial microbes associated with WWTP system performance, and it is promising for the discovery of potential microbial metabolic pathways.

Oligotrophic waters of the Northwest Atlantic support taxonomically diverse diatom communities that are distinct from coastal waters

Diatoms are important components of the marine food web and one of the most species-rich groups of phytoplankton. The diversity and composition of diatoms in eutrophic nearshore habitats have been well documented due to the outsized influence of diatoms on coastal ecosystem functioning. In contrast, patterns of both diatom diversity and community composition in offshore oligotrophic regions where diatom biomass is low have been poorly resolved. To compare the diatom diversity and community composition in oligotrophic and eutrophic waters, diatom communities were sampled along a 1,250 km transect from the oligotrophic Sargasso Sea to the coastal waters of the northeast US shelf. Diatom community composition was determined by amplifying and sequencing the 18S rDNA V4 region. Of the 301 amplicon sequence variants (ASVs) identified along the transect, the majority (70%) were sampled exclusively from oligotrophic waters of the Gulf Stream and Sargasso Sea and included the genera Bacteriastrum, Haslea, Hemiaulus, Pseudo-nitzschia, and Nitzschia. Diatom ASV richness did not vary along the transect, indicating that the oligotrophic Sargasso Sea and Gulf Stream are occupied by a diverse diatom community. Although ASV richness was similar between oligotrophic and coastal waters, diatom community composition in these regions differed significantly and was correlated with temperature and phosphate, two environmental variables known to influence diatom metabolism and geographic distribution. In sum, oligotrophic waters of the western North Atlantic harbor diverse diatom assemblages that are distinct from coastal regions, and these open ocean diatoms warrant additional study, as they may play critical roles in oligotrophic ecosystems.

Short-term acidification promotes diverse iron acquisition and conservation mechanisms in upwelling-associated phytoplankton

Coastal upwelling regions are among the most productive marine ecosystems but may be threatened by amplified ocean acidification. Increased acidification is hypothesized to reduce iron bioavailability for phytoplankton thereby expanding iron limitation and impacting primary production. Here we show from community to molecular levels that phytoplankton in an upwelling region respond to short-term acidification exposure with iron uptake pathways and strategies that reduce cellular iron demand. A combined physiological and multi-omics approach was applied to trace metal clean incubations that introduced 1200 ppm CO2 for up to four days. Although variable, molecular-level responses indicate a prioritization of iron uptake pathways that are less hindered by acidification and reductions in iron utilization. Growth, nutrient uptake, and community compositions remained largely unaffected suggesting that these mechanisms may confer short-term resistance to acidification; however, we speculate that cellular iron demand is only temporarily satisfied, and longer-term acidification exposure without increased iron inputs may result in increased iron stress.

Symbiotic UCYN-A strains co-occurred with El Niño, relaxed upwelling, and varied eukaryotes over 10 years off Southern California

Biological nitrogen fixation, the conversion of N2 gas into a bioavailable form, is vital to sustaining marine primary production. Studies have shifted beyond traditionally studied tropical diazotrophs. Candidatus Atelocyanobacterium thalassa (or UCYN-A) has emerged as a focal point due to its streamlined metabolism, intimate partnership with a haptophyte host, and broad distribution. Here, we explore the environmental parameters that govern UCYN-A's presence at the San Pedro Ocean Time-series (SPOT), its host specificity, and statistically significant interactions with non-host eukaryotes from 2008-2018. 16S and 18S rRNA gene sequences were amplified by "universal primers" from monthly samples and resolved into Amplicon Sequence Variants, allowing us to observe multiple UCYN-A symbioses. UCYN-A1 relative abundances increased following the 2015-2016 El Niño event. This "open ocean ecotype" was present when coastal upwelling declined, and Ekman transport brought tropical waters into the region. Network analyses reveal all strains of UCYN-A co-occur with dinoflagellates including Lepidodinium, a potential predator, and parasitic Syndiniales. UCYN-A2 appeared to pair with multiple hosts and was not tightly coupled to its predominant host, while UCYN-A1 maintained a strong host-symbiont relationship. These biological relationships are particularly important to study in the context of climate change, which will alter UCYN-A distribution at regional and global scales.

From the Sunlit to the Aphotic Zone: Assembly Mechanisms and Co-Occurrence Patterns of Protistan-Bacterial Microbiotas in the Western Pacific Ocean

We know little about the assembly processes and association patterns of microbial communities below the photic zone. In marine pelagic systems, there are insufficient observational data regarding why and how the microbial assemblies and associations vary from photic to aphotic zones. In this study, we investigated size-fractionated oceanic microbiotas, specifically free-living (FL; 0.22 to 3 μm) and particle-associated (PA; >3 μm) bacteria and protists (0.22 to 200 μm) collected from the surface to 2,000 m in the western Pacific Ocean, to see how assembly mechanisms and association patterns changed from photic to aphotic zones. Taxonomic analysis revealed a distinct community composition between photic and aphotic zones that was largely driven by biotic associations rather than abiotic factors. Aphotic community co-occurrence was less widespread and robust than its photic counterparts, and biotic associations were crucial in microbial co-occurrence, having a higher influence on photic than aphotic co-occurrences. The decrease in biotic associations and the increase in dispersal limitation from the photic to the aphotic zone affect the deterministic-stochastic balance, leading to a more stochastic-process-driven community assembly for all three microbial groups in the aphotic zone. Our findings significantly contribute to our understanding of how and why microbial assembly and co-occurrence vary from photic to aphotic zones, offering insight into the dynamics of the protistan-bacterial microbiota in the western Pacific's photic and aphotic zones. IMPORTANCE We know little about the assembly processes and association patterns of microbial communities below the photic zone in marine pelagic systems. We discovered that community assembly processes differed between photic and aphotic zones, with all three microbial groups studied (protists and FL and PA bacteria) being more influenced by stochastic processes than in the photic zone. The decrease in organismic associations and the increase in dispersal limitation from the photic to the aphotic zone both have an impact on the deterministic-stochastic balance, resulting in a more stochastic process-driven community assembly for all three microbial groups in the aphotic zone. Our findings significantly contribute to the understanding of how and why microbial assembly and co-occurrence change between photic and aphotic zones, offering insight into the dynamics of the protist-bacteria microbiota in the western Pacific oceans.

Predictable Changes in Eelgrass Microbiomes with Increasing Wasting Disease Prevalence across 23° Latitude in the Northeastern Pacific

Predicting outcomes of marine disease outbreaks presents a challenge in the face of both global and local stressors. Host-associated microbiomes may play important roles in disease dynamics but remain understudied in marine ecosystems. Host–pathogen–microbiome interactions can vary across host ranges, gradients of disease, and temperature; studying these relationships may aid our ability to forecast disease dynamics. Eelgrass, Zostera marina, is impacted by outbreaks of wasting disease caused by the opportunistic pathogen Labyrinthula zosterae. We investigated how Z. marina phyllosphere microbial communities vary with rising wasting disease lesion prevalence and severity relative to plant and meadow characteristics like shoot density, longest leaf length, and temperature across 23° latitude in the Northeastern Pacific. We detected effects of geography (11%) and smaller, but distinct, effects of temperature (30-day max sea surface temperature, 4%) and disease (lesion prevalence, 3%) on microbiome composition. Declines in alpha diversity on asymptomatic tissue occurred with rising wasting disease prevalence within meadows. However, no change in microbiome variability (dispersion) was detected between asymptomatic and symptomatic tissues. Further, we identified members of Cellvibrionaceae, Colwelliaceae, and Granulosicoccaceae on asymptomatic tissue that are predictive of wasting disease prevalence across the geographic range (3,100 kilometers). Functional roles of Colwelliaceae and Granulosicoccaceae are not known. Cellvibrionaceae, degraders of plant cellulose, were also enriched in lesions and adjacent green tissue relative to nonlesioned leaves. Cellvibrionaceae may play important roles in disease progression by degrading host tissues or overwhelming plant immune responses. Thus, inclusion of microbiomes in wasting disease studies may improve our ability to understand variable rates of infection, disease progression, and plant survival.

IMPORTANCE The roles of marine microbiomes in disease remain poorly understood due, in part, to the challenging nature of sampling at appropriate spatiotemporal scales and across natural gradients of disease throughout host ranges. This is especially true for marine vascular plants like eelgrass (Zostera marina) that are vital for ecosystem function and biodiversity but are susceptible to rapid decline and die-off from pathogens like eukaryotic slime-mold Labyrinthula zosterae (wasting disease). We link bacterial members of phyllosphere tissues to the prevalence of wasting disease across the broadest geographic range to date for a marine plant microbiome-disease study (3,100 km). We identify Cellvibrionaceae, plant cell wall degraders, enriched (up to 61% relative abundance) within lesion tissue, which suggests this group may be playing important roles in disease progression. These findings suggest inclusion of microbiomes in marine disease studies will improve our ability to predict ecological outcomes of infection across variable landscapes spanning thousands of kilometers.