Microbial Community Structure and Associations During a Marine Dinoflagellate Bloom

Dynamic patterns of carbohydrate metabolism genes in bacterioplankton during marine algal blooms

Carbohydrates play a pivotal role in nutrient recycling and regulation of algal-bacterial interactions. Despite their ecological significance, the intricate molecular mechanisms governing regulation of phycosphere carbohydrates by bacterial taxa linked with natural algal bloom have yet to be fully elucidated. Here, a comprehensive temporal metagenomic analysis was conducted to explore the carbohydrate-active enzyme (CAZyme) genes in two discrete algal bloom microorganisms (Gymnodinium catenatum and Phaeocystis globosa) across three distinct bloom stages: pre-bloom, peak bloom, and post-bloom. Elevated levels of extracellular carbohydrates, primarily rhamnose, galactose, glucose, and arabinose, were observed during the initial and post-peak stages. The prominent CAZyme families identified-glycoside hydrolases (GH) and carbohydrate-binding modules (CBMs)-were present in both algal bloom occurrences. In the G. catenatum bloom, GH23/24 and CBM13/14 were prevalent during the pre-bloom and peak bloom stages, whereas GH2/3/30 and CBM12/24 exhibited increased prevalence during the post-bloom phase. In contrast, the P. globosa bloom had a dominance of GH13/23 and CBM19 in the initial phase, and this was succeeded by GH3/19/24/30 and CBM54 in the later stages. This gene pool variation-observed distinctly in specific genera-highlighted the dynamic structural shifts in functional resources driven by temporal alterations in available substrates. Additionally, ecological linkage analysis underscored a correlation between carbohydrates (or their related genes) and phycospheric bacteria, hinting at a pattern of bottom-up control. These findings contribute to understanding of the dynamic nature of CAZymes, emphasizing the substantial influence of substrate availability on the metabolic capabilities of algal symbiotic bacteria, especially in terms of carbohydrates.

Unveiling the biofloc culture potential: Harnessing immune functions for resilience of shrimp and resistance against AHPND -causing Vibrio parahaemolyticus infection

In shrimp aquaculture, disease mitigation may be accomplished by reducing the virulence of the pathogen or by boosting the shrimp's immunity. Biofloc technology is an innovative system that improves the health and resistance of shrimp to microbial infections while providing a viable option for maintaining the quality of culture water through efficient nutrient recycling. This review aimed at demonstrating the efficacy of the biofloc system in boosting the immune responses and protective processes of shrimp against Vibrio parahaemolyticus infection, which is known to cause Acute Hepatopancreatic Necrosis Disease (AHPND). Numerous studies have revealed that the biofloc system promotes the immunological capability of shrimp by raising multiple immune -related genes e.g. prophenoloxidase, serine proteinase gene, ras-related nuclear gene and penaeidinexpression and cellular and humoral responses such as hyperaemia, prophenoloxidase activity, superoxide dismutase activity, phagocytic activity; the protection and survival of shrimp when faced with a challenge from the V. parahaemolyticus strain have been enhanced. Furthermore, the use of the biofloc system improves water quality parameters and potentially bolstering their immune and overall health to effectively resist diseases; hence, promotes the growth of shrimp. The present review suggests that biofloc can serve as an effective therapy for both preventing and supporting the management of probable AHPND infection in shrimp culture. This approach exhibits potential for the progress of sustainable shrimp farming, higher productivity, and improved shrimp health.

Dinoflagellate-Bacteria Interactions: Physiology, Ecology, and Evolution

Dinoflagellates and heterotrophic bacteria are two major micro-organism groups within marine ecosystems. Their coexistence has led to a co-evolutionary relationship characterized by intricate interactions that not only alter their individual behaviors but also exert a significant influence on the broader biogeochemical cycles. Our review commenced with an analysis of bacterial populations, both free-living and adherent to dinoflagellate surfaces. Members of Alphaproteobacteria, Gammaproteobacteria, and the Cytophaga-Flavobacterium-Bacteroides group are repeatedly found to be associated with dinoflagellates, with representation by relatively few genera, such as Methylophaga, Marinobacter, and Alteromonas. These bacterial taxa engage with dinoflagellates in a limited capacity, involving nutrient exchange, the secretion of pathogenic substances, or participation in chemical production. Furthermore, the genomic evolution of dinoflagellates has been profoundly impacted by the horizontal gene transfer from bacteria. The integration of bacterial genes into dinoflagellates has been instrumental in defining their biological characteristics and nutritional strategies. This review aims to elucidate the nuanced interactions between dinoflagellates and their associated bacteria, offering a detailed perspective on their complex relationship.

Rhodobacteraceae are key players in microbiome assembly of the diatom Asterionellopsis glacialis

The complex interactions between bacterioplankton and phytoplankton have prompted numerous studies that investigate phytoplankton microbiomes with the aim of characterizing beneficial or opportunistic taxa and elucidating core bacterial members. Oftentimes, this knowledge is garnered through 16S rRNA gene profiling of microbiomes from phytoplankton isolated across spatial and temporal scales, yet these studies do not offer insight into microbiome assembly and structuring. In this study, we aimed to identify taxa central to structuring and establishing the microbiome of the ubiquitous diatom Asterionellopsis glacialis. We introduced a diverse environmental bacterial community to A. glacialis in nutrient-rich or nutrient-poor media in a continuous dilution culture setup and profiled the bacterial community over 7 days. 16S rRNA amplicon sequencing showed that cyanobacteria (Coleofasciculaceae) and Rhodobacteraceae dominate the microbiome early on and maintain a persistent association throughout the experiment. Differential abundance, co-abundance networks, and differential association analyses revealed that specific members of the family Rhodobacteraceae, particularly Sulfitobacter amplicon sequence variants, become integral members in microbiome assembly. In the presence of the diatom, Sulfitobacter species and other Rhodobacteraceae developed positive associations with taxa that are typically in high abundance in marine ecosystems (Pelagibacter and Synechococcus), leading to restructuring of the microbiome compared to diatom-free controls. These positive associations developed predominantly under oligotrophic conditions, highlighting the importance of investigating phytoplankton microbiomes in as close to natural conditions as possible to avoid biases that develop under routine laboratory conditions. These findings offer further insight into phytoplankton-bacteria interactions and illustrate the importance of Rhodobacteraceae, not merely as phytoplankton symbionts but as key taxa involved in microbiome assembly.

IMPORTANCE

Most, if not all, microeukaryotic organisms harbor an associated microbial community, termed the microbiome. The microscale interactions that occur between these partners have global-scale consequences, influencing marine primary productivity, carbon cycling, and harmful algal blooms to name but a few. Over the last decade, there has been a growing interest in the study of phytoplankton microbiomes, particularly within the context of bloom dynamics. However, long-standing questions remain regarding the process of phytoplankton microbiome assembly. The significance of our research is to tease apart the mechanism of microbiome assembly with a particular focus on identifying bacterial taxa, which may not merely be symbionts but architects of the phytoplankton microbiome. Our results strengthen the understanding of the ecological mechanisms that underpin phytoplankton-bacteria interactions in order to accurately predict marine ecosystem responses to environmental perturbations.

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.

Influence of phycospheric bacterioplankton disruption or removal on algae growth and survival

Phycospheric bacteria play a crucial role in the survival of microalgae. However, the potential of using the growth regulation and community structure modulation of phycospheric bacteria to prevent the occurrence of blooms is yet to be verified. The phycospheric bacterioplankton of Cyclotella sp. can be categorized into HNA (high nucleic acid) bacteria and LNA (low nucleic acid) bacteria. 16S rRNA sequencing showed that the HNA bacteria exhibited higher α-diversity compared to the LNA bacteria, and the microbial community composition also exhibited variations. Metagenomic sequencing further indicated the distinct ecological functions between HNA and LNA bacteria. Furthermore, the study showcased the restorative capacity of the phycospheric bacterioplankton. Biomass analysis revealed that the recovery of phycospheric bacterioplankton positively influenced the microalgae growth, thus affirming the significance of phycospheric bacterioplankton to microalgae. The community structure of phycospheric bacterioplankton demonstrated a notable decrease in the abundance of restored LNA core bacteria. Additionally, the restored phycospheric bacterioplankton exhibited a more complex co-occurrence network structure, resulting in decreased resistance and sensitivity of microalgae to adverse environments. The presence of phycospheric bacterioplankton provides a protective shield for microalgae, and thus destabilizing or removing phycospheric bacterioplankton may effectively inhibit growth of microalgae.

Microbial metabolomic responses to changes in temperature and salinity along the western Antarctic Peninsula

Seasonal cycles within the marginal ice zones in polar regions include large shifts in temperature and salinity that strongly influence microbial abundance and physiology. However, the combined effects of concurrent temperature and salinity change on microbial community structure and biochemical composition during transitions between seawater and sea ice are not well understood. Coastal marine communities along the western Antarctic Peninsula were sampled and surface seawater was incubated at combinations of temperature and salinity mimicking the formation (cold, salty) and melting (warm, fresh) of sea ice to evaluate how these factors may shape community composition and particulate metabolite pools during seasonal transitions. Bacterial and algal community structures were tightly coupled to each other and distinct across sea-ice, seawater, and sea-ice-meltwater field samples, with unique metabolite profiles in each habitat. During short-term (approximately 10-day) incubations of seawater microbial communities under different temperature and salinity conditions, community compositions changed minimally while metabolite pools shifted greatly, strongly accumulating compatible solutes like proline and glycine betaine under cold and salty conditions. Lower salinities reduced total metabolite concentrations in particulate matter, which may indicate a release of metabolites into the labile dissolved organic matter pool. Low salinity also increased acylcarnitine concentrations in particulate matter, suggesting a potential for fatty acid degradation and reduced nutritional value at the base of the food web during freshening. Our findings have consequences for food web dynamics, microbial interactions, and carbon cycling as polar regions undergo rapid climate change.

Alteration in Community Dynamics of Chaetoceros curvisetus and Bacterioplankton Communities in Response to Surfactin Exposure

The use of surfactin is a promising method to mitigate algal blooms. However, little is known about surfactin toxicity to algae and bacterioplankton. Here, we treated Chaetoceros curvisetus, the dominant species of algal blooms in the East China Sea, with 0, 0.5, 1, 2, 3, and 4 mg/L of surfactin for 96 h to investigate temporal variability. Our results showed that low concentrations of surfactin (<2 mg/L) changed the cell morphology of C. curvisetus, and higher concentrations (>3 mg/L) had lethal effects. Meanwhile, we examined the community dynamics of the free-living (FL, 0.22-5 μm) and particle-attached (PA, >5 μm) bacterioplankton of C. curvisetus in response to different surfactin concentrations and cultivation periods. Both PA and FL bacterioplankton were mainly composed of Proteobacteria, Actinobacteria, and Bacteroidetes, while FL bacterioplankton were more diverse than PA bacterioplankton. The variations of FL and PA bacterioplankton were significantly constrained by the surfactin concentration. Surfactin changed the lifestyle of some bacterioplankton from FL to PA, which mainly belonged to abundant bacterioplankton. Furthermore, we identified some surfactin-sensitive species/taxa. Our study will help enhance the ability to predict marine microbial responses under the effect of surfactin, providing a research foundation for this new harmful algal bloom mitigation method.

Characterization of Silver Carbonate Nanoparticles Biosynthesized Using Marine Actinobacteria and Exploring of Their Antimicrobial and Antibiofilm Activity

Bacterial resistance to different antimicrobial agents is growing with alarming speed, especially when bacterial cells are living in biofilm. Hybrid nanoparticles, synthesized through the green method, hold promise as a potential solution to this challenge. In this study, 66 actinomycete strains were isolated from three distinct marine sources: marine sediment, the algae Codium bursa, and the marine sponge Chondrosia reniformis. From the entirety of the isolated strains, one strain, S26, identified as Saccharopolyspora erythrea, was selected based on its taxonomic position and significant antimicrobial activity. Using the biomass of the selected marine Actinobacteria, the green synthesis of eco-friendly silver carbonate nanoparticles (BioAg2CO3NPs) is reported for the first time in this pioneering study. The BioAg2CO3NPs were characterized using different spectroscopic and microscopic analyses; the synthesized BioAg2CO3NPs primarily exhibit a triangular shape, with an approximate size of 100 nm. Biological activity evaluation indicated that the BioAg2CO3NPs exhibited good antimicrobial activity against all tested microorganisms and were able to remove 58% of the biofilm formed by the Klebsiella pneumoniae kp6 strain.

Harnessing synthetic biology to enhance ocean health

Ocean health is faltering, its capability for regeneration and renewal being eroded by a steady pulse of anthropomorphic impacts. Plastic waste has infiltrated all ocean biomes, climate change threatens coral reefs with extinction, and eutrophication has unleashed vast algal blooms. In the face of these challenges, synthetic biology approaches may hold untapped solutions to mitigate adverse effects, repair ecosystems, and put us on a path towards sustainable stewardship of our planet. Leveraging synthetic biology tools would enable innovative engineering approaches to augment the natural adaptive capacity of ocean biological systems to cope with the swiftness of human-induced change. Here, we present a framework for developing synthetic biology solutions for the challenges of plastic pollution, coral bleaching, and harmful algal blooms.

In Situ Molecular Ecological Analyses Illuminate Distinct Factors Regulating Formation and Demise of a Harmful Dinoflagellate Bloom

The development and demise of a harmful algal bloom (HAB) are generally regulated by multiple processes; identifying specific critical drivers for a specific bloom is important yet challenging. Here, we conducted a whole-assemblage molecular ecological study on a dinoflagellate bloom to address the hypothesis that energy and nutrient acquisition, defense against grazing and microbial attacks, and sexual reproduction are critical to the rise and demise of the bloom. Microscopic and molecular analyses identified the bloom-causing species as Karenia longicanalis and showed that the ciliate Strombidinopsis sp. was dominant in a nonbloom plankton community, whereas the diatom Chaetoceros sp. dominated the after-bloom community, along with remarkable shifts in the community structure for both eukaryotes and prokaryotes. Metatranscriptomic analysis indicated that heightened energy and nutrient acquisition in K. longicanalis significantly contributed to bloom development. In contrast, active grazing by the ciliate Strombidinopsis sp. and attacks by algicidal bacteria (Rhodobacteracea, Cryomorphaceae, and Rhodobacteracea) and viruses prevented (at nonbloom stage) or collapsed the bloom (in after-bloom stage). Additionally, nutrition competition by the Chaetoceros diatoms plausibly contributed to bloom demise. The findings suggest the importance of energy and nutrients in promoting this K. longicanalis bloom and the failure of antimicrobial defense and competition of diatoms as the major bloom suppressor and terminator. This study provides novel insights into bloom-regulating mechanisms and the first transcriptomic data set of K. longicanalis, which will be a valuable resource and essential foundation for further elucidation of bloom regulators of this and related species of Kareniaceae in the future. IMPORTANCE HABs have increasingly occurred and impacted human health, aquatic ecosystems, and coastal economies. Despite great efforts, the factors that drive the development and termination of a bloom are poorly understood, largely due to inadequate in situ data about the physiology and metabolism of the causal species and the community. Using an integrative molecular ecological approach, we determined that heightened energy and nutrient acquisition promoted the bloom, while resource allocation in defense and failure to defend against grazing and microbial attacks likely prevented or terminated the bloom. Our findings reveal the differential roles of multiple abiotic and biotic environmental factors in driving the formation or demise of a toxic dinoflagellate bloom, suggesting the importance of a balanced biodiverse ecosystem in preventing a dinoflagellate bloom. The study also demonstrates the power of whole-assemblage metatranscriptomics coupled to DNA barcoding in illuminating plankton ecological processes and the underlying species and functional diversities.

Microbe, climate change and marine environment: Linking trends and research hotspots

Microbes, or microorganisms, have been the foundation of the biosphere for over 3 billion years and have played an essential role in shaping our planet. The available knowledge on the topic of microbes associated with climate change has the potential to reshape upcoming research trends globally. As climate change impacts the ocean or marine ecosystem, the responses of these "unseen life" will heavily influence the achievement of a sustainable evolutionary environment. The present study aims to identify microbial-related research under changing climate within the marine environment through the mapping of visualized graphs of the available literature. We used scientometric methods to retrieve documents from the Web of Science platform in the Core Collection (WOSCC) database, analyzing a total of 2767 documents based on scientometric indicators. Our findings show that this research area is growing exponentially, with the most influential keywords being "microbial diversity," "bacteria," and "ocean acidification," and the most cited being "microorganism" and "diversity." The identification of influential clusters in the field of marine science provides insight into the hot spots and frontiers of research in this area. Prominent clusters include "coral microbiome," "hypoxic zone," "novel Thermoplasmatota clade," "marine dinoflagellate bloom," and "human health." Analyzing emerging trends and transformative changes in this field can inform the creation of special issues or research topics in selected journals, thus increasing visibility and engagement among the scientific community.

Harmful cyanobacteria-diatom/dinoflagellate blooms and their cyanotoxins in freshwaters: A nonnegligible chronic health and ecological hazard

Human and ecological health depends on the vitality of freshwater systems, but these are increasingly threatened by cyanotoxins released from harmful algal blooms (HABs). Periodic cyanotoxin production, although undesirable, may be tolerable when there is enough time for cyanotoxins to degrade and dissipate in the environment, but the year-round presence of these toxins will be a chronic health for humans and ecosystems. The purpose of this critical review is to document the seasonal shifts of algal species and their ecophysiological acclimatation to dynamic environmental conditions. We discuss how these conditions will create successive occurrences of algal blooms and the release of cyanotoxins into freshwater. We first review the most common cyanotoxins, and evaluate the multiple ecological roles and physiological functions of these toxins for algae. Then, the annual recurring patterns HABs are considered in the context of global change, which demonstrates the capacity for algal blooms to shift from seasonal to year-round growth regimes that are driven by abiotic and biotic factors, leading to chronic loading of freshwaters with cyanotoxins. At last, we illustrate the impacts of HABs on the environment by compiling four health issues and four ecology issues emanating from their presence in the that covers atmosphere, aquatic ecosystems and terrestrial ecosystems. Our study highlights the annual patterns of algal blooms, and proposes that a "perfect storm" of events is lurking that will cause the 'seasonal toxicity' to become a full-blown, 'chronic toxicity' in the context of the deterioration of HABs, highlighting a non-negligible chronic health and ecological hazard.

Multidisciplinary long-term survey of Manila clam grown in farming sites subjected to different environmental conditions

In recent years recurrent bivalve mass mortalities considerably increased around the world, causing the collapse of natural and farmed populations. Venice Lagoon has historically represented one of the major production areas of the Manila clam Ruditapes philippinarum in Europe. However, in the last 20 years a 75 % decrease in the annual production has been experienced. While climate change and anthropogenic interventions may have played a key role in natural and farmed stocks reductions, no studies investigated at multiple levels the environmental stressors affecting farmed Manila clam to date. In this work we carried out a long-term monitoring campaign on Manila clam reared in four farming sites located at different distances from the southern Venice Lagoon inlet, integrating (meta)genomic approaches (i.e. RNA-seq; microbiota characterization), biometric measurements and chemical-physical parameters. Our study allowed to characterize the molecular mechanisms adopted by this species to cope with the different environmental conditions characterizing farming sites and to propose hypotheses to explain mortality events observed in recent years. Among the most important findings, the disruption of clam's immune response, the spread of Vibrio spp., and the up-regulation of molecular pathways involved in xenobiotic metabolism suggested major environmental stressors affecting clams farmed in sites placed close to Chioggia's inlet, where highest mortality was also observed. Overall, our study provides knowledge-based tools for managing Manila clam farming on-growing areas. In addition, the collected data is a snapshot of the time immediately before the commissioning of MoSE, a system of mobile barriers aimed at protecting Venice from high tides, and will represent a baseline for future studies on the effects of MoSE on clams farming and more in general on the ecology of the Venice Lagoon.

Selection processes of Arctic seasonal glacier snowpack bacterial communities

BACKGROUND

Arctic snowpack microbial communities are continually subject to dynamic chemical and microbial input from the atmosphere. As such, the factors that contribute to structuring their microbial communities are complex and have yet to be completely resolved. These snowpack communities can be used to evaluate whether they fit niche-based or neutral assembly theories.

METHODS

We sampled snow from 22 glacier sites on 7 glaciers across Svalbard in April during the maximum snow accumulation period and prior to the melt period to evaluate the factors that drive snowpack metataxonomy. These snowpacks were seasonal, accumulating in early winter on bare ice and firn and completely melting out in autumn. Using a Bayesian fitting strategy to evaluate Hubbell's Unified Neutral Theory of Biodiversity at multiple sites, we tested for neutrality and defined immigration rates at different taxonomic levels. Bacterial abundance and diversity were measured and the amount of potential ice-nucleating bacteria was calculated. The chemical composition (anions, cations, organic acids) and particulate impurity load (elemental and organic carbon) of the winter and spring snowpack were also characterized. We used these data in addition to geographical information to assess possible niche-based effects on snow microbial communities using multivariate and variable partitioning analysis.

RESULTS

While certain taxonomic signals were found to fit the neutral assembly model, clear evidence of niche-based selection was observed at most sites. Inorganic chemistry was not linked directly to diversity, but helped to identify predominant colonization sources and predict microbial abundance, which was tightly linked to sea spray. Organic acids were the most significant predictors of microbial diversity. At low organic acid concentrations, the snow microbial structure represented the seeding community closely, and evolved away from it at higher organic acid concentrations, with concomitant increases in bacterial numbers.

CONCLUSIONS

These results indicate that environmental selection plays a significant role in structuring snow microbial communities and that future studies should focus on activity and growth. Video Abstract.

Unravelling microalgal-bacterial interactions in aquatic ecosystems through 16S rRNA gene-based co-occurrence networks

Interactions between microalgae and bacteria can directly influence the global biogeochemical cycles but the majority of such interactions remain unknown. 16S rRNA gene-based co-occurrence networks have potential to help identify microalgal-bacterial interactions. Here, we used data from 10 Earth microbiome projects to identify potential microalgal-bacterial associations in aquatic ecosystems. A high degree of clustering was observed in microalgal-bacterial modules, indicating densely connected neighbourhoods. Proteobacteria and Bacteroidetes predominantly co-occurred with microalgae and represented hubs of most modules. Our results also indicated that species-specificity may be a global characteristic of microalgal associated microbiomes. Several previously known associations were recovered from our network modules, validating that biologically meaningful results can be inferred using this approach. A range of previously unknown associations were recognised such as co-occurrences of Bacillariophyta with uncultured Planctomycetes OM190 and Deltaproteobacteria order NB1-j. Planctomycetes and Verrucomicrobia were identified as key associates of microalgae due to their frequent co-occurrences with several microalgal taxa. Despite no clear taxonomic pattern, bacterial associates appeared functionally similar across different environments. To summarise, we demonstrated the potential of 16S rRNA gene-based co-occurrence networks as a hypothesis-generating framework to guide more focused research on microalgal-bacterial associations.

Prokaryotic Diversity and Dynamics during Dinoflagellate Bloom Decays in Coastal Tunisian Waters

(1) Background: Harmful algal blooms (HABs) can negatively impact marine ecosystems, but few studies have evaluated the microbial diversity associated with HABs and its potential role in the fates of these proliferations. (2) Methods: Marine prokaryotic diversity was investigated using high-throughput sequencing of the 16S rRNA gene during the bloom declines of two dinoflagellates detected in the summer of 2019 along the northern and southern Tunisian coasts (South Mediterranean Sea). The species Gymnodinium impudicum (Carthage, Tunis Gulf) and Alexandrium minutum (Sfax, Gabes Gulf) were identified using microscopy and molecular methods and were related to physicochemical factors and prokaryotic compositions. (3) Results: The abundance of G. impudicum decreased over time with decreasing phosphate concentrations. During the G. impudicum bloom decay, prokaryotes were predominated by the archaeal MGII group (Thalassarchaeaceae), Pelagibacterales (SAR11), Rhodobacterales, and Flavobacteriales. At Sfax, the abundance of A. minutum declined with decreasing phosphate concentrations and increasing pH. At the A. minutum peak, prokaryotic communities were largely dominated by anoxygenic phototrophic sulfur-oxidizing Chromatiaceae (Gammaproteobacteria) before decreasing at the end of the survey. Both the ubiquitous archaeal MGII group and Pelagibacterales were found in low proportions during the A. minutum decay. Contrary to the photosynthetic Cyanobacteria, the photo-autotrophic and -heterotrophic Rhodobacterales and Flavobacteriales contents remained stable during the dinoflagellate bloom decays. (4) Conclusions: These results indicated changes in prokaryotic community diversity during dinoflagellate bloom decays, suggesting different bacterial adaptations to environmental conditions, with stable core populations that were potentially able to degrade HABs.

Microbial Community Dynamics during a Harmful Chrysochromulina leadbeateri Bloom in Northern Norway

A harmful algal bloom occurred in late spring 2019 across multiple, interconnected fjords and bays in northern Norway. The event was caused by the haptophyte Chrysochromulina leadbeateri and led to severe fish mortality at several salmon aquaculture facilities. This study reports on the spatial and temporal succession dynamics of the holistic marine microbiome associated with this bloom by relating all detectable 18S and 16S rRNA gene amplicon sequence variants to the relative abundance of the C. leadbeateri focal taxon. A k-medoid clustering enabled inferences on how the causative focal taxon cobloomed with diverse groups of bacteria and microeukaryotes. These coblooming patterns showed high temporal variability and were distinct between two geographically separated time series stations during the regional harmful algal bloom. The distinct blooming patterns observed with respect to each station were poorly connected to environmental conditions, suggesting that other factors, such as biological interactions, may be at least as important in shaping the dynamics of this type of harmful algal bloom. A deeper understanding of microbiome succession patterns during these rare but destructive events will help guide future efforts to forecast deviations from the natural bloom cycles of the northern Norwegian coastal marine ecosystems that are home to intensive aquaculture activities. IMPORTANCE The 2019 Chrysochromulina leadbeateri bloom in northern Norway had a major impact on the local economy and society through its devastating effect on the aquaculture industry. However, many fail to remember that C. leadbeateri is, in fact, a common member of the seasonal marine microbiome and the same spring phytoplankton blooms that support the marine ecosystem. It is challenging to draw any conclusions about exact causation behind the harmful bloom of 2019, especially since the natural bloom cycles of C. leadbeateri are not well understood. This study begins to fill major knowledge gaps that may lead to future forecasting abilities, by providing a molecular-based investigation of the destructive 2019 bloom that presents new insights into a seasonal marine microbial ecosystem during one of these sporadically reoccurring events.

Structure-Function Covariation of Phycospheric Microorganisms Associated with the Typical Cross-Regional Harmful Macroalgal Bloom

Unravelling the structure-function variation of phycospheric microorganisms and its ecological correlation with harmful macroalgal blooms (HMBs) is a challenging research topic that remains unclear in the natural dynamic process of HMBs. During the world's largest green tide bloom, causative macroalgae Ulva prolifera experienced dramatic changes in growth state and environmental conditions, providing ideal scenarios for this investment. Here, we assess the phycospheric physicochemical characteristics, the algal host's biology, the phycospheric bacterial constitutive patterns, and the functional potential during the U. prolifera green tide. Our results indicated that (i) variation in the phycosphere nutrient structure was closely related to the growth state of U. prolifera; (ii) stochastic processes govern phycospheric bacterial assembly, and the contribution of deterministic processes to assembly varied among phycospheric seawater bacteria and epiphytic bacteria; (iii) phycospheric seawater bacteria and epiphytic bacteria exhibited significant heterogeneity variation patterns in community composition, structure, and metabolic potential; and (iv) phycospheric bacteria with carbon or nitrogen metabolic functions potentially influenced the nutrient utilization of U. prolifera. Furthermore, the keystone genera play a decisive role in the structure-function covariation of phycospheric bacterial communities. Our study reveals complex interactions and linkages among environment-algae-bacterial communities which existed in the macroalgal phycosphere and highlights the fact that phycospheric microorganisms are closely related to the fate of the HMBs represented by the green tide. IMPORTANCE Harmful macroalgal blooms represented by green tides have become a worldwide marine ecological problem. Unraveling the structure-function variation of phycospheric microorganisms and their ecological correlation with HMBs is challenging. This issue is still unclear in the natural dynamics of HMBs. Here, we revealed the complex interactions and linkages among environment-algae-bacterial communities in the phycosphere of the green macroalgae Ulva prolifera, which causes the world's largest green tides. Our study provides new ideas to increase our understanding of the variation patterns of macroalgal phycospheric bacterial communities and the formation mechanisms and ecological effects of green tides and highlights the importance of phycospheric microorganisms as a robust tool to help understand the fate of HMBs.

Microbial food webs share similar biogeographic patterns and driving mechanisms with depths in oligotrophic tropical western Pacific Ocean

Microbial food web (MFW) dominates the energy flow in oligotrophic tropical open ocean pelagic ecosystems. Understanding biogeographic patterns and driving mechanisms of key components of the MFW is one of the central topics in current marine ecology. Investigations were conducted along an 1,100-km horizontal gradient and in the full-water column vertical gradient of the oligotrophic tropical western Pacific Ocean. High-throughput sequencing and association networking methods were used to analyze the community structure and interspecies interactions of MFW. The structure of MFW significantly differed with depths, but not across horizontal gradients. Bacteria and microeukaryotes were interconnected and had more predominantly positive and negative linkages in the aphotic layers. Key components of MFW exhibited similar biogeographic patterns and driving mechanisms. Geographic distance exerted minimal effects on the distribution patterns of the microbial food web, while environmental factors played more important roles, especially for temperature and inorganic nutrients. Stochastic processes were more important in the microbial food webs of the 5-200  m layer than the >500  m layer, and drift explained the majority of stochastic processes. Moreover, only a weak but not significant driving force for North Equatorial Current on the east-west connectivity of the microbial food web was found in the upper layers. This knowledge is a critical fundamental data for future planning of marine protected areas targeting the protection of tuna fishing in the western Pacific Ocean.

Different Geographic Strains of Dinoflagellate Karlodinium veneficum Host Highly Diverse Fungal Community and Potentially Serve as Possible Niche for Colonization of Fungal Endophytes

In numerous studies, researchers have explored the interactions between fungi and their hosting biota in terrestrial systems, while much less attention has been paid to the counterpart interactions in aquatic, and particularly marine, ecosystems. Despite the growing recognition of the potential functions of fungi in structuring phytoplankton communities, the current insights were mostly derived from phytoplankton hosts, such as diatoms, green microalgae, and cyanobacteria. Dinoflagellates are the second most abundant group of phytoplankton in coastal marine ecosystems, and they are notorious for causing harmful algal blooms (HABs). In this study, we used high-throughput amplicon sequencing to capture global snapshots of specific fungal assemblages associated with laboratory-cultured marine dinoflagellate. We investigated a total of 13 clonal cultures of the dinoflagellate Karlodinium veneficum that were previously isolated from 5 geographic origins and have been maintained in our laboratory from several months to more than 14 years. The total recovered fungal microbiome, which consisted of 349 ASVs (amplicon sequencing variants, sequences clustered at a 100% sequence identity), could be assigned to 4 phyla, 18 classes, 37 orders, 65 families, 97 genera, and 131 species. The fungal consortium displayed high diversity and was dominated by filamentous fungi and ascomycetous and basidiomycetous yeasts. A core set of three genera among all the detected fungi was constitutively present in the K. veneficum strains isolated from geographically distant regions, with the top two most abundant genera, Thyridium and Pseudeurotium, capable of using hydrocarbons as the sole or major source of carbon and energy. In addition, fungal taxa previously documented as endophytes in other hosts were also found in all tested strains of K. veneficum. Because host-endophyte interactions are highly variable and strongly case-dependent, these fungal taxa were not necessarily genuine endosymbionts of K. veneficum; instead, it raised the possibility that dinoflagellates could potentially serve as an alternative ecological niche for the colonization of fungal endophytes. Our findings lay the foundation for further investigations into the potential roles or functions of fungi in the regulation of the growth dynamics and HABs of marine dinoflagellates in the field.

Change of the structure and assembly of bacterial and photosynthetic communities by the ecological engineering practices in Dianchi Lake

Cyanobacterial bloom challenges the aquatic ecosystem and ecological restoration is an effective approach for cyanobacterial bloom control, but the change of aquatic community after ecological restoration is still unclear. Dianchi Lake is an eutrophic lake with frequent cyanobacterial blooms in China, and recent ecological restoration projects in Caohai (north part) have a satisfactory performance. In this study, we collected 249 water samples at 23 sites from Dianchi Lake to explore the relationships between water physicochemical variables and aquatic microbial communities. Water physicochemical variables in Waihai (south part) intensively changed along time, whereas those in Caohai did not. Photoautotrophic communities were significantly divergent between Caohai and Waihai. Waihai had a lower diversity of photoautotrophic community, containing higher abundance of Cyanophyceae (89.9%) than Caohai (42.7%). Nutrient level and Cyanophyceae only exhibited strong correlations in Wahai (p < 0.05). Redundancy analysis and microbial ecological network suggested that microbial communities in Caohai had a higher stability. Deterministic process dominated the microbial assembly (50-80% for bacteria and >90% for photoautotrophs), and particularly in Caohai. Our results unraveled that the structure and assembly of bacterial and photoautotrophic communities significantly changed after ecological restoration, offering valuable suggestions that photosynthetic diversity should be focused for other ecological restoration projects.

The cyanobactericidal bacterium Paucibacter aquatile DH15 caused the decline of Microcystis and aquatic microbial community succession: A mesocosm study

Microcystis blooms pose a major threat to the quality of drinking water. Cyanobactericidal bacteria have attracted much attention in the research community as a vehicle for controlling Microcystis blooms because of their ecological safety. Nonetheless, most studies on cyanobactericidal bacteria have been conducted on a laboratory scale but have not been scaled-up as field experiments. Thus, our understanding of the microbial response to cyanobactericidal bacteria in natural ecosystems remains elusive. Herein, we applied Paucibacter aquatile DH15 to control Microcystis blooms in a 1000 L mesocosm experiment and demonstrated its potential with the following results: (1) DH15 reduced Microcystis cell density by 90.7% within two days; (2) microcystins released by Microcystis death decreased to the control level in four days; (3) during the cyanobactericidal processes, the physicochemical parameters of water quality remained safe for other aquatic organisms; and (4) the cyanobactericidal processes promoted the growth of eukaryotic microalgae, replacing cyanobacteria. The cyanobactericidal processes accelerated turnover rates, decreased stability, and altered the functional profile of the microbial community. Network analysis demonstrated that this process resulted in more complex interactions between microbes. Overall, our findings suggest that strain DH15 could be considered a promising candidate for controlling Microcystis blooms in an eco-friendly manner.

Inherent tendency of Synechococcus and heterotrophic bacteria for mutualism on long-term coexistence despite environmental interference

Mutualism between Synechococcus and heterotrophic bacteria has been found to support their prolonged survival in nutrient-depleted conditions. However, environmental interference on the fate of their mutualism is not understood. Here, we show that exogenous nutrients disrupt their established mutualism. Once the exogenous nutrients were exhausted, Synechococcus and heterotrophic bacteria gradually reestablished their metabolic mutualism during 450 days of culture, which revived unhealthy Synechococcus cells. Using metagenomics, metatranscriptomics, and the ¹⁵N tracer method, we reveal that the associated bacterial nitrogen fixation triggered the reestablishment of the mutualism and revival of Synechococcus health. During this process, bacterial community structure and functions underwent tremendous adjustments to achieve the driving effect, and a cogeneration of nitrogen, phosphorus, iron, and vitamin by the heterotrophic bacteria sustained Synechococcus's prolonged healthy growth. Our findings suggest that Synechococcus and heterotrophic bacteria may have an inherent tendency toward mutualism despite environmental interference. This may exhibit their coevolutionary adaptations in nutrient-deficient environments.

Monitoring harmful microalgal species and their appearance in Tokyo Bay, Japan, using metabarcoding

During the recent decade, high-throughput sequencing (HTS) techniques, in particular, DNA metabarcoding, have facilitated increased detection of biodiversity, including harmful algal bloom (HAB) species. In this study, the presence of HAB species and their appearance patterns were investigated by employing molecular and light microscopy-based monitoring in Tokyo Bay, Japan. The potential co-appearance patterns between the HAB species, as well as with other eukaryotes and prokaryotes were investigated using correlation and association rule-based time-series analysis. In total, 40 unique HAB species were detected, including 12 toxin-producing HAB species previously not reported from the area. More than half of the HAB species were present throughout the sampling season (summer to autumn) and no structuring or succession patterns associated with the environmental conditions could be detected. Statistically significant (p &lt; 0.05, rS ranging from −0.88 to 0.90) associations were found amongst the HAB species and other eukaryotic and prokaryotic species, including genera containing growth-limiting bacteria. However, significant correlations between species differed amongst the years, indicating that variability in environmental conditions between the years may have a stronger influence on the microalgal community structure and interspecies interactions than the variability during the sampling season. The association rule-based time-series analysis allowed the detection of a previously reported negative relationship between Synechococcus sp. and Skeletonema sp. in nature. Overall, the results support the applicability of metabarcoding and HTS-based microalgae monitoring, as it facilitates more precise species identification compared to light microscopy, as well as provides input for investigating potential interactions amongst different species/groups through simultaneous detection of multiple species/genera.

Identification and implications of a core bacterial microbiome in 19 clonal cultures laboratory-reared for months to years of the cosmopolitan dinoflagellate Karlodinium veneficum

Identification of a core microbiome (a group of taxa commonly present and consistently abundant in most samples of host populations) is important to capture the key microbes closely associated with a host population, as this process may potentially contribute to further revealing their spatial distribution, temporal stability, ecological influence, and even impacts on their host’s functions and fitness. The naked dinoflagellate Karlodinium veneficum is a cosmopolitan and toxic species, which is also notorious in forming harmful algal blooms (HABs) and causing massive fish-kills. Here we reported the core microbiome tightly associated with 19 strains of K. veneficum that were originally isolated from 6 geographic locations along the coast of China and from an estuary of Chesapeake Bay, United States, and have been maintained in the laboratory for several months to over 14 years. Using high-throughput metabarcoding of the partial 16S rRNA gene amplicons, a total of 1,417 prokaryotic features were detected in the entire bacterial microbiome, which were assigned to 17 phyla, 35 classes, 90 orders, 273 families, and 716 genera. Although the bacterial communities associated with K. veneficum cultures displayed heterogeneity in feature (sequences clustered at 100% sequence similarity) composition among strains, a core set of 6 genera were found persistent in their phycospheres, which could contribute up to 74.54% of the whole bacterial microbiome. Three γ-proteobacteria members of the “core,” namely, Alteromonas, Marinobacter, and Methylophaga, were the predominant core genera and made up 83.25% of the core bacterial microbiome. The other 3 core genera, Alcanivorax, Thalassospira, and Ponticoccus, are reported to preferably utilize hydrocarbons as sole or major source of carbon and energy, and two of which (Alcanivorax and Ponticoccus) are recognized as obligate hydrocarbonoclastic bacteria (OHCB). Since OHCB generally present in extremely low abundance in marine water and elevate their abundance mostly in petroleum-impacted water, our detection in K. veneficum cultures suggests that the occurrence of obligate and generalist hydrocarbon-degrading bacteria living with dinoflagellates may be more frequent in nature. Our work identified a core microbiome with stable association with the harmful alga K. veneficum and opened a window for further characterization of the physiological mechanisms and ecological implications for the dinoflagellate-bacteria association.

Seasonal Succession and Coherence Among Bacteria and Microeukaryotes in Lake Baikal

Microorganisms exhibit seasonal succession governed by physicochemical factors and interspecies interactions, yet drivers of this process in different environments remain to be determined. We used high-throughput sequencing of 16S rRNA and 18S rRNA genes to study seasonal dynamics of bacterial and microeukaryotic communities at pelagic site of Lake Baikal from spring (under-ice, mixing) to autumn (direct stratification). The microbial community was subdivided into distinctive coherent clusters of operational taxonomic units (OTUs). Individual OTUs were consistently replaced during different seasonal events. The coherent clusters change their contribution to the microbial community depending on season. Changes of temperature, concentrations of silicon, and nitrates are the key factors affected the structure of microbial communities. Functional prediction revealed that some bacterial or eukaryotic taxa that switched with seasons had similar functional properties, which demonstrate their functional redundancy. We have also detected specific functional properties in different coherent clusters of bacteria or microeukaryotes, which can indicate their ability to adapt to seasonal changes of environment. Our results revealed a relationship between seasonal succession, coherency, and functional features of freshwater bacteria and microeukaryotes.

The in-situ release of algal bloom populations and the role of prokaryotic communities in their establishment and growth

Harmful algal blooms (HABs) may quickly travel and inoculate new water bodies via currents and runoff in estuaries. The role of in-situ prokaryotic communities in the re-establishment and growth of inoculated algal blooms remains unknown. A novel on-board incubation experiment was employed to simulate the sudden surge of algal blooms to new estuarine waters and reveal possible outcomes. A dinoflagellate (Amphidinium carterae) and a diatom species (Thalassiosira weissflogii) which had bloomed in the Pearl River Estuary (PRE) area were cultured to bloom densities and reintroduced back into PRE natural seawaters. The diatom showed better adaptation ability to the new environment and increased significantly after the incubation. Simultaneously, particle-attached (PA) prokaryotic community structure was strongly influenced by adding of the diatom, with some opportunistic prokaryotes significantly enhanced in the diatom treatment. Whereas the dinoflagellate population did not increase following incubation, and their PA prokaryotic community showed no significant differences relative to the control. Metagenomic analyzes revealed that labile carbohydrates and organic nitrogen produced by the diatom contributed to the surge of certain PA prokaryotes. Genomic properties of a bacteria strain, which is affiliated with genus GMD16E07 (Planctomycetaceae) and comprised up to 50% of PA prokaryotes in the diatom treatment, was described here for the first time. Notably, the association of Planctomycetaceae and T. weissflogii likely represents symbiotic mutualism, with the diatom providing organic matter for Planctomycetaceae and the bacteria supplying vitamins and detoxifying nitriles and hydrogen peroxides in exchange. Therefore, the close association between Planctomycetaceae and T. weissflogii promoted the growth of both populations, and eventually facilitated the diatom bloom establishment.

Composition and Biogeography of Planktonic Pro- and Eukaryotic Communities in the Atlantic Ocean: Primer Choice Matters

Basin-scale biogeographic observations of marine pelagic pro- and eukaryotic communities are necessary to understand forces driving community composition and for providing a baseline to monitor global change. Deep sequencing of rRNA genes provides community composition at high resolution; yet, it is unclear how the choice of primers affects biogeographic patterns. Here, we re-amplified 16S rRNA genes from DNA sampled during R/V Polarstern Cruise ANT28-5 over a latitudinal transect across the Atlantic Ocean from 52°S to 47°N using universal V4-V5 primers and compared the results with those obtained previously with V5-V6 bacteria-specific primers. For validation of our results, we inferred community composition based on 16S rRNA genes of metagenomes from the same stations and single amplified genomes (SAGs) from the Global Ocean Reference Genome (GORG) database. We found that the universal V4-V5 primers retrieved SAR11 clades with similar relative proportions as those found in the GORG database while the V5-V6 primers recovered strongly diverging clade abundances. We confirmed an inverse bell-shaped distance-decay relationship and a latitudinal diversity gradient that did not decline linearly with absolute latitude in the Atlantic Ocean. Patterns were modified by sampling depth, sequencing depth, choice of primers, and abundance filtering. Especially richness patterns were not robust to methodological change. This study offers a detailed picture of the Atlantic Ocean microbiome using a universal set of PCR primers that allow for the conjunction of biogeographical patterns among organisms from different domains of life.

Variations in Marine Bacterial and Archaeal Communities during an Ulva prolifera Green Tide in Coastal Qingdao Areas

Green tides caused by Ulva prolifera occur annually in the Yellow Sea, potentially influencing the marine microorganisms. Here, we focused on the variations in marine bacterial and archaeal communities during an U. prolifera green tide in coastal Qingdao areas with Illumina high-throughput sequencing analysis. Our results revealed that the diversity and structure of bacterial and archaeal communities, as well as the organization and structure of microbial co-occurrence networks, varied during the green tide. The decline phase may be favorable to the bacterial and archaeal diversity and richness. The bacterial community, as well as the archaeal community, showed clear variations between the outbreak and decline phases. A simpler and less connected microbial co-occurrence network was observed during the outbreak phase compared with the decline phase. Flavobacteriales and Rhodobacterales separately dominated the bacterial community during the outbreak and decline phase, and Marine Group II (MGII) dominated the archaeal community during the green tide. Combined with microbial co-occurrence network analysis, Flavobacteriales, Rhodobacterales and MGII may be important organisms during the green tide. Temperature, chlorophyll a content and salinity may have an important impact on the variations in bacterial and archaeal communities during the green tide.

Towards understanding mechanisms and functional consequences of bacterial interactions with members of various kingdoms in complex biofilms that abound in nature

The microbial world represents a phenomenal diversity of microorganisms from different kingdoms of life which occupy an impressive set of ecological niches. Most, if not all, microorganisms once colonise a surface develop architecturally complex surface-adhered communities which we refer to as biofilms. They are embedded in polymeric structural scaffolds serve as a dynamic milieu for intercellular communication through physical and chemical signalling. Deciphering microbial ecology of biofilms in various natural or engineered settings has revealed co-existence of microorganisms from all domains of life, including Bacteria, Archaea and Eukarya. The coexistence of these dynamic microbes is not arbitrary, as a highly coordinated architectural setup and physiological complexity show ecological interdependence and myriads of underlying interactions. In this review, we describe how species from different kingdoms interact in biofilms and discuss the functional consequences of such interactions. We highlight metabolic advances of collaboration among species from different kingdoms, and advocate that these interactions are of great importance and need to be addressed in future research. Since trans-kingdom biofilms impact diverse contexts, ranging from complicated infections to efficient growth of plants, future knowledge within this field will be beneficial for medical microbiology, biotechnology, and our general understanding of microbial life in nature.

Abundant Species Diversity and Essential Functions of Bacterial Communities Associated with Dinoflagellates as Revealed from Metabarcoding Sequencing for Laboratory-Raised Clonal Cultures

Interactions between algae and bacteria represent an important inter-organism association in aquatic environments, which often have cascading bottom-up influences on ecosystem-scale processes. Despite the increasing recognition of linkages between bacterioplankton and dynamics of dinoflagellate blooms in the field, knowledge about the forms and functions of dinoflagellate-bacteria associations remains elusive, mainly due to the ephemeral and variable conditions in the field. In this study, we characterized the bacterial community associated with laboratory cultures of 144 harmful algal strains, including 130 dinoflagellates (covering all major taxonomic orders of dinoflagellates) and 14 non-dinoflagellates, via high-throughput sequencing for 16S rRNA gene amplicons. A total of 4577 features belonging to bacteria kingdom comprising of 24 phyla, 55 classes, 134 orders, 273 families, 716 genera, and 1104 species were recovered from the algal culture collection, and 3 phyla (Proteobacteria, Bacteroidetes, and Firmicutes) were universally present in all the culture samples. Bacterial communities in dinoflagellates cultures exhibited remarkable conservation across different algal strains, which were dominated by a relatively small number of taxa, most notably the γ-proteobacteria Methylophaga, Marinobacter and Alteromonas. Although the bacterial community composition between dinoflagellates and non-dinoflagellate groups did not show significant difference in general, dinoflagellates harbored a large number of unique features (up to 3811) with relatively low individual abundance and enriched in the potential methylotrophs Methylophaga. While the bacterial assemblages associated with thecate and athecate dinoflagellates displayed no general difference in species composition and functional groups, athecate dinoflagellates appeared to accommodate more aerobic cellulolytic members of Actinobacteria, implying a more possible reliance on cellulose utilization as energy source. The extensive co-occurrence discovered here implied that the relationships between these algal species and the bacterial consortia could be viewed as either bilaterally beneficial (i.e., mutualism) or unilaterally beneficial at least to one party but virtually harmless to the other party (i.e., commensalism), whereas both scenarios support a long-term and stable co-existence rather than an exclusion of one or the other. Our results demonstrated that dinoflagellates-associated bacterial communities were similar in composition, with enrichment of potential uncultured methylotrophs to one-carbon compounds. This work enriches the knowledge about the fundamental functions of bacteria consortia associated with the phycospheres of dinoflagellates and other HABs-forming microalgae.

Zooplankton Population and Community Structure Changes in Response to a Harmful Algal Bloom Caused by Prorocentrum donghaiense in the East China Sea

Blooms of the dinoflagellate Prorocentrum donghaiense have had adverse impacts on marine ecosystems. However, ecological details, particularly the impacts and processes of the P. donghaiense bloom on the zooplankton community structure are poorly known. We investigated the changes of zooplankton communities in situ within the whole process of a P. donghaiense bloom in the coastal waters in southern Zhejiang Province, China, in May 2016. Results showed that ecological changes during the blooms of P. donghaiense could be divided into three major phases, namely the growth, maintenance, and dissipation phases with regard to the cell abundance of P. donghaiense by bottle sampling of plankton. A total of 42 species of zooplankton were identified. The average abundance and species number of zooplankton in the growth phase were significantly higher than those in the maintenance and dissipation phases. It is shown that the top-two highest proportions of zooplankton in the growth phase were small jellyfishes and copepods, while small jellyfishes and chaetognaths, and copepoda larvae and chaetognaths were the top-two highest in the maintenance and dissipation phases respectively. However, the values of biodiversity index have no statistically significant differences between the three phases. The present results suggested that P. donghaiense bloom produced significant negative impacts on the abundance and species composition of zooplankton with particular reference to copepods.

Bacterial diversity in different outdoor pilot plant photobioreactor types during production of the microalga Nannochloropsis sp. CCAP211/78

As large-scale outdoor production cannot be done in complete containment, cultures are (more) open for bacteria, which may affect the productivity and stability of the algae production process. We investigated the bacterial diversity in two indoor reactors and four pilot-scale outdoor reactors for the production of Nannochloropsis sp. CCAP211/78 spanning four months of operation from July to October. Illumina sequencing of 16S rRNA gene amplicons demonstrated that a wide variety of bacteria were present in all reactor types, with predominance of Bacteroidetes and Alphaproteobacteria. Bacterial communities were significantly different between all reactor types (except between the horizontal tubular reactor and the vertical tubular reactor) and also between runs in each reactor. Bacteria common to the majority of samples included one member of the Saprospiraceae family and one of the NS11-12_marine group (both Bacteroidetes). Hierarchical clustering analysis revealed two phases during the cultivation period separated by a major shift in bacterial community composition in the horizontal tubular reactor, the vertical tubular reactor and the raceway pond with a strong decrease of the Saprospiraceae and NS11-12_marine group that initially dominated the bacterial communities. Furthermore, we observed a less consistent pattern of bacterial taxa appearing in different reactors and runs, most of which belonging to the classes Deltaproteobacteria and Flavobacteriia. In addition, canonical correspondence analysis showed that the bacterial community composition was significantly correlated with the nitrate concentration. This study contributes to our understanding of bacterial diversity and composition in different types of outdoor reactors exposed to a range of dynamic biotic and abiotic factors. Key points • Reactor types had significantly different bacterial communities except HT and VT • The inoculum source and physiochemical factors together affect bacterial community • The bacterial family Saprospiraceae is positively correlated to microalgal growth.

Trophic states regulate assembly processes and network structures of small chromophytic phytoplankton communities in estuarine and coastal ecosystem

Small chromophytic phytoplankton (SCP) are anticipated to be more important for a significant proportion of primary production in estuarine-coastal ecosystems. However, responses of SCP community to coastal eutrophication are still unclear. In this study, we investigated diversity, co-occurrence and assembly features of SCP communities, as well as relationship with environmental factors in subtropical Beibu Gulf. The results exhibited that the alpha diversity and beta diversity of SCP communities were significantly different among eutrophic states. Co-occurrence network revealed a complex interaction that most amplicon sequence variants (ASVs) in modules of the network were specific to trophic states. Further, phylogenetic based β-nearest taxon distance analyses revealed that stochastic processes mainly provided 69.26% contribution to SCP community assembly, whereas deterministic processes dominated community assembly in heavy eutrophic state. Overall, our findings elucidate the mechanism of diversity and assembly in SCP community and promote the understanding of SCP ecology related to subtropical coastal eutrophication.

Co-occurrence of chromophytic phytoplankton and the Vibrio community during Phaeocystis globosa blooms in the Beibu Gulf

Accumulating research evidence has revealed that harmful algal blooms (HABs) can substantially affect the community structures of phytoplankton and heterotrophic bacteria in marine ecosystems. However, little is known about their species-specific interactions between phytoplankton and heterotrophic bacteria during the HABs period and about their interaction shifts in response to blooms. From this perspective, we investigated the co-occurrence of chromophytic phytoplankton and Vibrio during Phaeocystis globosa blooms in the Beibu Gulf. The results showed that Vibrio communities were distinct during the blooms, and P. globosa blooms resulted in a decline in phytoplankton alpha diversity, revealing that the blooms could affect their community compositions. The regression lines between the Shannon indices and Bray-Curtis distances of phytoplankton and Vibrio showed positive correlations with each other (p < 0.001), suggesting that they may have intrageneric symbiotic interactions overall. In addition, network analysis further demonstrated that relationships between phytoplankton and Vibrio were dominated by positive correlations, and more interaction modules were observed during the blooms, revealing that the blooms intensified synergistic association and mutual symbiotic interactions between them. Environmental factors (SiO₃^2-, NH₄⁺, NO₃^- and TN,) and P. globosa density more deeply affected network interactions between phytoplankton and Vibrio during the periods of P. globosa blooms than those before the blooms and after the blooms. This study provided new insight to elucidate community structure and interaction relationships between phytoplankton and Vibrio in response to P. globosa blooms and their ecological effects in marine ecosystems.

Diversity pattern of marine culturable heterotrophic bacteria in a region with coexisting upwelling and mud banks in the southeastern Arabian Sea

Mud banks and upwelling are two important oceanographic features occurring along the southwest coast of India during the southwest monsoon period. The study region, Alappuzha lying on the southwest coast of India, is unique due to the co-existence of upwelling and mud banks during the monsoon (MON) season. Water samples were collected from three stations, M1, M2, and M3, from April to September 2014, at weekly/biweekly intervals to determine the total bacterial abundance, viable prokaryotic counts, and total plate counts, along with measurements on physico-chemical parameters. For determining the heterotrophic culturable bacterial diversity, water samples were collected during two seasons, monsoon and pre-monsoon (PRM), from three stations. Water samples were inoculated into two non-selective broths for enrichment, DNA was extracted, and next-generation sequencing analysis was performed using Illumina Miseq sequencing. The sequence analysis revealed that dominant communities were Proteobacteria, followed by Firmicutes and Fusobacteria. Proportions of Fusobacteria increased during monsoon and proportions of Firmicutes were high in premonsoon season. Among Proteobacteria, Gammaproteobacteri is presented more than 99% of all the classes, irrespective of seasons. Vibrio was the most dominant genus during both seasons. The presence of anaerobic genera such as Propionigenium and Cetobacterium at all the stations during MON indicated the presence of upwelled waters. The genus Stenotrophomonas was observed in the M2 station alone. This study provides an overview of the culturable heterotrophic bacterial communities in a region in the southeastern Arabian Sea with coexisting mud banks and upwelling. The results of this study were compared with a published report on culture-independent bacterial diversity (from environmental DNA) from the same region. The study demonstrates that the use of culture media underrepresented the phylogenetic diversity and selectively enriched the class Gammaproteobacteria alone.

How Microbial Food Web Interactions Shape the Arctic Ocean Bacterial Community Revealed by Size Fractionation Experiments

In the Arctic, seasonal changes are substantial, and as a result, the marine bacterial community composition and functions differ greatly between the dark winter and light-intensive summer. While light availability is, overall, the external driver of the seasonal changes, several internal biological interactions structure the bacterial community during shorter timescales. These include specific phytoplankton-bacteria associations, viral infections and other top-down controls. Here, we uncover these microbial interactions and their effects on the bacterial community composition during a full annual cycle by manipulating the microbial food web using size fractionation. The most profound community changes were detected during the spring, with 'mutualistic phytoplankton'-Gammaproteobacteria interactions dominating in the pre-bloom phase and 'substrate-dependent phytoplankton'-Flavobacteria interactions during blooming conditions. Bacterivores had an overall limited effect on the bacterial community composition most of the year. However, in the late summer, grazing was the main factor shaping the community composition and transferring carbon to higher trophic levels. Identifying these small-scale interactions improves our understanding of the Arctic marine microbial food web and its dynamics.

Insight Into Ecology, Metabolic Potential, and the Taxonomic Composition of Bacterial Communities in the Periodic Water Pond on King George Island (Antarctica)

Polar regions contain a wide variety of lentic ecosystems. These include periodic ponds that have a significant impact on carbon and nitrogen cycling in polar environments. This study was conducted to assess the taxonomic and metabolic diversity of bacteria found in Antarctic pond affected by penguins and sea elephants and to define their role in ongoing processes. Metabolic assays showed that of the 168 tested heterotrophic bacteria present in the Antarctic periodic pond, 96% are able to degrade lipids, 30% cellulose, 26% proteins, and 26% starch. The taxonomic classification of the obtained isolates differs from that based on the composition of the 16S rRNA relative abundances in the studied pond. The dominant Actinobacteria constituting 45% of isolates represents a low proportion of the community, around 4%. With the addition of run-off, the proportions of inhabiting bacteria changed, including a significant decrease in the abundance of Cyanobacteria, from 2.38 to 0.33%, increase of Firmicutes from 9.32 to 19.18%, and a decreasing richness (Chao1 index from 1299 to 889) and diversity (Shannon index from 4.73 to 4.20). Comparative studies of communities found in different Antarctic environments indicate a great role for penguins in shaping bacterial populations.

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.

Phylogenetic and Phenogenetic Diversity of Synechococcus along a Yellow Sea Section Reveal Its Environmental Dependent Distribution and Co-Occurrence Microbial Pattern

Synechococcus is a dominant genus of the coastal phytoplankton with an effective contribution to primary productivity. Here, the phylogenetic and phenogenetic composition of Synechococcus in the coastal Yellow Sea was addressed by sequencing marker gene methods. Meanwhile, its co-occurrence pattern with bacterial and eukaryotic microbes was further investigated based on the construction of networks. The result revealed that Synechococcus abundance ranged from 9.8 × 102 cells mL−1 to 1.6 × 105 cells mL−1, which was significantly correlated to sampling depth and nutrient contents of nitrite, ammonia, and dissolved silicon. A total of eight Synechococcus phylogenetic lineages were detected, of which clade III was dominant in most of the samples. Meanwhile, clade I increased along the water column and even reached a maximum value of 76.13% at 20 m of station B. Phenogenetically, Synechococcus PT3 was always the predominant pigment type across the whole study zone. Only salinity was significantly correlated to the phenogenetic constitution. The networks revealed that Synechococcus co-occurred with 159 prokaryotes, as well as 102 eukaryotes including such possible grazers as Gymnodinium clades and Alveolata. Potential function prediction further showed that microbes co-occurring with Synechococcus were associated with diverse element cycles, but the exact mechanism needed further experimentation to verify. This research promotes exploring regularity in the genomic composition and niche position of Synechococcus in the coastal ecosystem and is significant to further discuss its potential participation in materials circulation and bottom-up effects in microbial food webs.

Temporal variability of free-living microbial culturability and community composition after an Akashiwo sanguinea bloom in Shenzhen, China

Dinoflagellate blooms currently caused serious environmental problems in different areas of the world. Recent studies revealed close relationship between dinoflagellate blooms and microbial community dynamics, while less attention has been paid on the bacterial culturability change associated with the bloom. Here, we investigated the temporal variation of microbial community composition and culturability during the decline stage of an Akashiwo sanguinea bloom occurred in Shenzhen, China. The daily microbial community phylogenetic structures in water samples collected during a four-day period after the bloom peak were assessed through 16S rRNA gene amplicons sequencing on the MiSeq (Illumina) platform. The environmental parameters, Chlorophyll a concentrations, and total viable and culturable bacterial densities were also measured. Our results showed that Gamma-proteobacteria comprising mostly of Pseudoalteromonadaceae and Vibrionaceae was the predominant microbial class in the post-bloom samples, except for the second day. During that day, the represented groups switched to Alpha-proteobacteria (Rhizobiales) and Beta-proteobacteria (Comamonadaceae), with the microbial culturability decreased. Total viable bacterial densities reached the maximum value on the third day, with Gamma-proteobacteria regained the dominance till the fourth day. The dramatic microbial community succession and culturability variation observed in this study indicated the complication of algae-bacteria interactions during dinoflagellate bloom.

Water quality drives the regional patterns of an algal metacommunity in interconnected lakes

The metacommunity approach provides insights into how the biological communities are assembled along the environmental variations. The current study presents the importance of water quality on the metacommunity structure of algal communities in six river-connected lakes using long-term (8 years) monitoring datasets. Elements of metacommunity structure were analyzed to evaluate whether water quality structured the metacommunity across biogeographic regions in the riverine ecosystem. The algal community in all lakes was found to exhibit Clementsian or quasi-Clementsian structure properties such as significant turnover, grouped and species sorting indicating that the communities responded to the environmental gradient. Reciprocal averaging clearly classified the lakes into three clusters according to the geographical region in river flow (upstream, midstream, and downstream). The dispersal patterns of algal genera, including Aulacoseira, Cyclotella, Stephanodiscus, and Chlamydomonas across the regions also supported the spatial-based classification results. Although conductivity, chemical oxygen demand, and biological oxygen demand were found to be important variables (loading > |0.5|) of the entire algal community assembly, water temperature was a critical factor in water quality associated with community assembly in each geographical area. These results support the notion that the structure of algal communities is strongly associated with water quality, but the relative importance of variables in structuring algal communities differed by geological regions.

The impacts of straw substrate on biofloc formation, bacterial community and nutrient removal in shrimp ponds

This study explored biofloc technology for shrimp culture based on straw substrates with a size of 40 mu, 80 mu, and 120 mu. Straw substrates utilization stimulated shrimp growth compared to control. Treatment with 40 mu had the best ammonium (71.60%) and nitrite nitrogen (77.78%) removal rates generally. In all biofloc treatments, Proteobacteria (4.10-56.1%) was the most dominant phylum, followed by Bacteroidetes (2.44-38.21%), Planctomycetes (0.45-21.41%), and Verrucomicrobia (1.2-10.30%). Redundancy analysis showed that salinity was a significant factor closely related to the microbial community in biofloc. The environmental parameters (DO > pH > TN > NH₄⁺-N > COD > Salinity > EC), nitrification, and denitrification genes (amoA > napA > nirK) were significant factors that interrelated with the bacterial genus in the network analysis. This study highlighted a novel technology of reusing agricultural waste that transformed inorganic nitrogen using nutrient recycling to control water quality in the culture system and produced microbial proteins that served as a natural nutritional supplement to enhance shrimp growth.

Community composition and functional genes explain different ecological roles of heterotrophic bacteria attached to two bloom-forming cyanobacterial genera

Eutrophication leads to frequent outbreaks of cyanobacterial blooms, however, the effect of heterotrophic bacteria attached to cyanobacterial cells is unclear. Field investigations were carried out to gain a deeper understanding of the community composition and functional role of heterotrophic bacteria attached to Dolichospermum and Microcystins cells. The significantly positive relationships between Dolichospermum density and total nitrogen (TN) and between Microcystins density and particle nitrogen (PN) indicated the strong nitrogen (N) demand of these two species. The lack of functional genes that mediate the nitrification process in bacteria attached to both Microcystins and Dolichospermum cells indicated that these two genera preferred ammonium (NH₄⁺-N). Dolichospermum cells obtained more available N through N₂ fixation, which was expressed by high nitrogenase gene abundance. Bacteria attached to Microcystins cells showed a higher activity of leucine aminopeptidase and a significantly higher abundance of functional genes that mediate dissimilatory nitrate reduction to ammonium (DNRA) than those attached to Dolichospermum cells. The significantly higher abundance of carbon degradation genes and β-glucosidase activity of bacteria attached to Microcystins cells compared with those of bacteria attached to Dolichospermum cells suggested that abundant organic carbon was bound to Microcystins cells, which is a prerequisite for DNRA. In addition, Microcystins cells exhibited a great advantage in soluble reactive phosphorus (SRP) production through high levels of organic phosphorus (P) hydrolysis associated with high levels of phosphatase genes of attached bacteria. In conclusion, bacteria attached to Microcystins cells performed more important functions on NH₄⁺-N and SRP production through ammonification and DNRA, as well as phosphatase hydrolysis respectively, compared to those attached to Dolichospermum. Thus, algal growth is the result of different variables such as nutrient concentration, their ratio and the microbial ability.

Temperature Stress Induces Shift From Co-Existence to Competition for Organic Carbon in Microalgae-Bacterial Photobioreactor Community - Enabling Continuous Production of Microalgal Biomass

To better predict the consequences of environmental change on aquatic microbial ecosystems it is important to understand what enables community resilience. The mechanisms by which a microbial community maintain its overall function, for example, the cycling of carbon, when exposed to a stressor, can be explored by considering three concepts: biotic interactions, functional adaptations, and community structure. Interactions between species are traditionally considered as, e.g., mutualistic, parasitic, or neutral but are here broadly defined as either coexistence or competition, while functions relate to their metabolism (e.g., autotrophy or heterotrophy) and roles in ecosystem functioning (e.g., oxygen production, organic matter degradation). The term structure here align with species richness and diversity, where a more diverse community is though to exhibit a broader functional capacity than a less diverse community. These concepts have here been combined with ecological theories commonly used in resilience studies, i.e., adaptive cycles, panarchy, and cross-scale resilience, that describe how the status and behavior at one trophic level impact that of surrounding levels. This allows us to explore the resilience of a marine microbial community, cultivated in an outdoor photobioreactor, when exposed to a naturally occurring seasonal stress. The culture was monitored for 6weeks during which it was exposed to two different temperature regimes (21 ± 2 and 11 ± 1°C). Samples were taken for metatranscriptomic analysis, in order to assess the regulation of carbon uptake and utilization, and for amplicon (18S and 16S rRNA gene) sequencing, to characterize the community structure of both autotrophs (dominated by the green microalgae Mychonastes) and heterotrophs (associated bacterioplankton). Differential gene expression analyses suggested that community function at warm temperatures was based on concomitant utilization of inorganic and organic carbon assigned to autotrophs and heterotrophs, while at colder temperatures, the uptake of organic carbon was performed primarily by autotrophs. Upon the shift from high to low temperature, community interactions shifted from coexistence to competition for organic carbon. Network analysis indicated that the community structure showed opposite trends for autotrophs and heterotrophs in having either high or low diversity. Despite an abrupt change of temperature, the microbial community as a whole responded in a way that maintained the overall level of diversity and function within and across autotrophic and heterotrophic levels. This is in line with cross-scale resilience theory describing how ecosystems may balance functional overlaps within and functional redundancy between levels in order to be resilient to environmental change (such as temperature).

Loss of Motility as a Non-Lethal Mechanism for Intercolony Inhibition ("Sibling Rivalry") in Marinobacter

Bacteria from the genus Marinobacter are ubiquitous throughout the worlds' oceans as "opportunitrophs" capable of surviving a wide range of conditions, including colonization of surfaces of marine snow and algae. To prevent too many bacteria from occupying this ecological niche simultaneously, some sort of population dependent control must be operative. Here, we show that while Marinobacter do not produce or utilize an acylhomoserine lactone (AHL)-based quorum sensing system, "sibling" colonies of many species of Marinobacter exhibit a form of non-lethal chemical communication that prevents colonies from overrunning each other's niche space. Evidence suggests that this inhibition is the result of a loss in motility for cells at the colony interfaces. Although not the signal itself, we have identified a protein, glycerophosphoryl diester phosphodiesterase, that is enriched in the inhibition zone between the spreading colonies that may be part of the overall response.