Zooming in on the phycosphere: the ecological interface for phytoplankton-bacteria relationships

Life in the PFAS lane: The impact of perfluoroalkyl substances on photosynthesis, cellular exudates, nutrient cycling, and composition of a marine microbial community

Perfluoroalkyl substances (PFAS) are of great ecological concern, however, exploration of their impact on bacteria-phytoplankton consortia is limited. This study employed a bioassay approach to investigate the effect of unary exposures of increasing concentrations of PFAS (perfluorooctane sulfonate (PFOS) and 6:2 fluorotelomer sulfonate (6:2 FTS)) on microbial communities from the northwestern Gulf of Mexico. Each community was examined for changes in growth and photophysiology, exudate production and shifts in community structure (16S and 18S rRNA genes). 6:2 FTS did not alter the growth or health of phytoplankton communities, as there were no changes relative to the controls (no PFOS added). On the other hand, PFOS elicited significant phototoxicity (p < 0.05), altering PSII antennae size, lowering PSII connectivity, and decreasing photosynthetic efficiency over the incubation (four days). PFOS induced a cellular protective response, indicated by significant increases (p < 0.001) in the release of transparent exopolymer particles (TEP) compared to the control. Eukaryotic communities (18S rRNA gene) changed substantially (p < 0.05) and to a greater extent than prokaryotic communities (16S rRNA gene) in PFOS treatments. Community shifts were concentration-dependent for eukaryotes, with the low treatment (5 mg/L PFOS) dominated by Coscinodiscophyceae (40 %), and the high treatment (30 mg/L PFOS) marked by a Trebouxiophyceae (50 %) dominance. Prokaryotic community shifts were not concentration dependent, as both treatment levels became depleted in Cyanobacteriia and were dominated by members of the Bacteroidia, Gammaproteobacteria, and Alphaproteobacteria classes. Further, PFOS significantly decreased (p < 0.05) the Shannon diversity and Pielou's evenness across treatments for eukaryotes, and in the low treatment (5 mg/L PFOS) for prokaryotes. These findings show that photophysiology was not impacted by 6:2 FTS but PFOS elicited toxicity that impacted photosynthesis, exudate release, and community composition. This research is crucial in understanding how PFOS impacts microbial communities.

Algal-bacterial consortium promotes carbon sink formation in saline environment

INTRODUCTION

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

OBJECTIVES

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

METHODS

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

RESULTS

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

CONCLUSION

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

Scarcity of fixed carbon transfer in a model microbial phototroph-heterotroph interaction

Although the green alga Chlamydomonas reinhardtii has long served as a reference organism, few studies have interrogated its role as a primary producer in microbial interactions. Here, we quantitatively investigated C. reinhardtii's capacity to support a heterotrophic microbe using the established coculture system with Mesorhizobium japonicum , a vitamin B 12 -producing α-proteobacterium. Using stable isotope probing and nanoscale secondary ion mass spectrometry (nanoSIMS), we tracked the flow of photosynthetic fixed carbon and consequent bacterial biomass synthesis under continuous and diurnal light with single-cell resolution. We found that more 13 C fixed by the alga was taken up by bacterial cells under continuous light, invalidating the hypothesis that the alga's fermentative degradation of starch reserves during the night would boost M. japonicum heterotrophy. 15 NH 4 assimilation rates and changes in cell size revealed that M. japonicum cells reduced new biomass synthesis in coculture with the alga but continued to divide - a hallmark of nutrient limitation often referred to as reductive division. Despite this sign of starvation, the bacterium still synthesized vitamin B 12 and supported the growth of a B 12 -dependent C. reinhardtii mutant. Finally, we showed that bacterial proliferation could be supported solely by the algal lysis that occurred in coculture, highlighting the role of necromass in carbon cycling. Collectively, these results reveal the scarcity of fixed carbon in this microbial trophic relationship (particularly under environmentally relevant light regimes), demonstrate B 12 exchange even during bacterial starvation, and underscore the importance of quantitative approaches for assessing metabolic coupling in algal-bacterial interactions.

Mitigating salinity stress through interactions between microalgae and different forms (free-living & alginate gel-encapsulated) of bacteria isolated from estuarine environments

Salinity stress in estuarine environments poses a significant challenge for microalgal survival and proliferation. The interaction between microalgae and bacteria shows promise in alleviating the detrimental impacts of salinity stress on microalgae. Our study investigates this interaction by co-cultivating Chlorella sorokiniana, a freshwater microalga, with a marine growth-promoting bacterium Pseudomonas gessardii, both of which were isolated from estuary. In this study, bacteria were encapsulated using sodium alginate microspheres to establish an isolated co-culture system, preventing direct exposure between microalgae and bacteria. We evaluated microalgal responses to different salinities (5 PSU, 15 PSU) and interaction modes (free-living, gel-encapsulated), focusing on growth, photosynthesis, cellular metabolism, and extracellular polymeric substances (EPS) properties. High salinity inhibited microalgal proliferation, while gel-fixed interaction boosted Chlorella growth rate by 50.7 %. Both attached and free-living bacteria restored Chlorella's NPQ to normal levels under salt stress. Microalgae in the free-living interaction group exhibited a significantly lower respiratory rate compared to the pure algae group (-17.2 %). Increased salinity led to enhanced EPS polysaccharide secretion by microalgae, particularly in interaction groups (19.7 %). Both salt stress and interaction increased the proportion of aromatic proteins in microalgae's EPS, enhancing its stability by modulating EPS glycosidic bond C-O-C and protein vibrations. This alteration caused microalgal cells to aggregate, free-living bacteria co-culture group, and fixed co-culture group increasing by 427.5 %, 567.1 %, and 704.1 %, respectively. In gel-fixed bacteria groups, reduced neutral lipids don't accumulate starch instead, carbon redirects to cellular growth, aiding salt stress mitigation. These synergistic activities between salinity and bacterial interactions are vital in mitigating salinity stress, improving the resilience and growth of microalgae in saline conditions. Our research sheds light on the mechanisms of microalgal-bacterial interactions in coping with salt stress, offering insights into the response of estuarine microorganisms to global environmental changes and their ecological stability.

Dissolved organic carbon spurs bacterial-algal competition and phosphorus-paucity adaptation: Boosting Microcystis' phosphorus uptake capacity

Dissolved organic carbon (DOC) can alter the availability of background nutrients by affecting the proliferation of heterotrophic bacteria, which exerts a notable influence on algal growth and metabolism. However, the mechanism of how allochthonous DOC (aDOC) precipitates shifts in bacterial-algal interactions and modulates the occurrence of cyanobacteria blooms remains inadequately elucidated. Therefore, this study investigated the relationship between bacteria and algae under aDOC stimulation. We found that excess aDOC triggered the breakdown and reestablishment of the equilibrium between Microcystis and heterotrophic bacteria. The rapid proliferation of heterotrophic bacteria led to a dramatic decrease in soluble phosphorus and thereby resulted in the inhibition of the Microcystis growth. When the available DOC was depleted, the rapid death of heterotrophic bacteria released large amounts of dissolved phosphorus, which provided sufficient nutrients for the recovery of Microcystis. Notably, Microcystis rejuvenated and showed higher cell density compared to the carbon-absent group. This phenomenon can be ascribed that Microcystis regulated the compositions of extracellular polymeric substances (EPS) and the expression of relevant proteins to adapt to a nutrient-limited environment. Using time of flight secondary ion mass spectrometry (TOF-SIM) and proteomic analysis, we observed an enhancement of the signal of organic matter and metal ions associated with P complexation in EPS. Moreover, Microcystis upregulated proteins related to organic phosphorus transformation to increase the availability of phosphorus in various forms. In summary, this study emphasized the role of DOC in algal blooms, revealing the underestimated enhancement of Microcystis nutrient utilization through DOC-induced heterotrophic competition and providing valuable insights into eutrophication management and control.

Characterizing the Impact of Cyanobacterial Blooms on the Photoreactivity of Surface Waters from New York Lakes: A Combined Statewide Survey and Laboratory Investigation

Cyanobacterial blooms introduce autochthonous dissolved organic matter (DOM) into aquatic environments, but their impact on surface water photoreactivity has not been investigated through collaborative field sampling with comparative laboratory assessments. In this work, we quantified the apparent quantum yields (Φapp,RI) of reactive intermediates (RIs), including excited triplet states of dissolved organic matter (3DOM*), singlet oxygen (1O2), and hydroxyl radicals (•OH), for whole water samples collected by citizen volunteers from more than 100 New York lakes. Multiple comparisons tests and orthogonal partial least-squares analysis identified the level of cyanobacterial chlorophyll a as a key factor in explaining the enhanced photoreactivity of whole water samples sourced from bloom-impacted lakes. Laboratory recultivation of bloom samples in bloom-free lake water demonstrated that apparent increases in Φapp,RI during cyanobacterial growth were likely driven by the production of photoreactive moieties through the heterotrophic transformation of freshly produced labile bloom exudates. Cyanobacterial proliferation also altered the energy distribution of 3DOM* and contributed to the accelerated transformation of protriptyline, a model organic micropollutant susceptible to photosensitized reactions, under simulated sunlight conditions. Overall, our study provides insights into the relationship between the photoreactivity of surface waters and the limnological characteristics and trophic state of lakes and highlights the relevance of cyanobacterial abundance in predicting the photoreactivity of bloom-impacted surface waters.

Unraveling the ecological mechanisms of Aluminum on microbial community succession in epiphytic biofilms on Vallisneria natans leaves: Novel insights from microbial interactions

The extensive use of aluminum (Al) poses an escalating ecological risk to aquatic ecosystems. The epiphytic biofilm on submerged plant leaves plays a crucial role in the regulation nutrient cycling and energy flow within aquatic environments. Here, we conducted a mesocosm experiment aimed at elucidating the impact of different Al concentrations (0, 0.6, 1.2, 2.0 mg/L) on microbial communities in epiphytic biofilms on Vallisneria natans. At 1.2 mg/L, the highest biofilms thickness (101.94 µm) was observed. Al treatment at 2.0 mg/L significantly reduced bacterial diversity, while micro-eukaryotic diversity increased. Pseudomonadota and Bacteroidota decreased, whereas Cyanobacteriota increased at 1.2 mg/L and 2.0 mg/L. At 1.2 and 2.0 mg/L. Furthermore, Al at concentrations of 1.2 and 2.0 mg/L enhanced the bacterial network complexity, while micro-eukaryotic networks showed reduced complexity. An increase in positive correlations among microbial co-occurrence patterns from 49.51% (CK) to 57.05% (2.0 mg/L) was indicative of augmented microbial cooperation under Al stress. The shift in keystone taxa with increasing Al concentration pointed to alterations in the functional dynamics of microbial communities. Additionally, Al treatments induced antioxidant responses in V. natans, elevating leaf reactive oxygen species (ROS) content. This study highlights the critical need to control appropriate concentration Al concentrations to preserve microbial diversity, sustain ecological functions, and enhance lake remediation in aquatic ecosystems.

Metabolic relationships between marine red algae and algae-associated bacteria

Mutualistic interactions between marine phototrophs and associated bacteria are an important strategy for their successful survival in the ocean, but little is known about their metabolic relationships. Here, bacterial communities in the algal sphere (AS) and bulk solution (BS) of nine marine red algal cultures were analyzed, and Roseibium and Phycisphaera were identified significantly more abundantly in AS than in BS. The metabolic features of Roseibium RMAR6-6 (isolated and genome-sequenced), Phycisphaera MAG 12 (obtained by metagenomic sequencing), and a marine red alga, Porphyridium purpureum CCMP1328 (from GenBank), were analyzed bioinformatically. RMAR6-6 has the genetic capability to fix nitrogen and produce B vitamins (B1, B2, B5, B6, B9, and B12), bacterioferritin, dimethylsulfoniopropionate (DMSP), and phenylacetate that may enhance algal growth, whereas MAG 12 may have a limited metabolic capability, not producing vitamins B9 and B12, DMSP, phenylacetate, and siderophores, but with the ability to produce bacitracin, possibly modulating algal microbiome. P. purpureum CCMP1328 lacks the genetic capability to fix nitrogen and produce vitamin B12, DMSP, phenylacetate, and siderophore. It was shown that the nitrogen-fixing ability of RMAR6-6 promoted the growth of P. purpureum, and DMSP reduced the oxidative stress of P. purpureum. The metabolic interactions between strain RMAR6-6 and P. purpureum CCMP1328 were also investigated by the transcriptomic analyses of their monoculture and co-culture. Taken together, potential metabolic relationships between Roseibium and P. purpureum were proposed. This study provides a better understanding of the metabolic relationships between marine algae and algae-associated bacteria for successful growth.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-024-00227-z.

Phycosphere bacterial disturbance of Saccharina japonica caused by white rot disease relates to seawater nutrients

In mid-November 2021, there were large areas of white rot disease on cultivated Saccharina japonica in Rongcheng City, China, and diseases were undetected on Sargassum horneri and Porphyra yezoensis. The disturbance direction of bacterial community in the phycosphere after disease outbreak and the relationship with seawater nutrients remain unclear. Here, in situ studies of bacterial community in the non-diseased and diseased areas (Shawo and Dongchu islands) and seawater nutrient levels were carried out. 16S rRNA sequencing showed that the bacterial richness of the studied seaweeds increased in the diseased area. Only in S. japonica, Algitalea outcompeted abundant primary bacteria with probiotic relationships to the host of the non-diseased area, and dominated in the diseased area (17.6% of the total abundance). Nitrogen and phosphorus levels in seawater were 57.8% and 19.6% higher in the non-diseased area than those in the diseased area, respectively, and were strongly correlated with the phycosphere bacteria at the family level of S. japonica. There was no difference in potential pathogenicity between the two areas, while positive signal communications decreased, and nitrogen cycle, chemoheterotrophy, and cellulolysis increased in the diseased area compared to the non-diseased area. Overall, white rot disease caused a structural disturbance in phycosphere bacterial community of S. japonica that related to seawater nutrient levels. Enriched degraders and altered bacterial community functions may exacerbate the disease. This evaluation will provide information for white rot disease management to prevent and mitigate the occurrence of S. japonica outbreaks.

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

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

Nitrogen and phosphorus limitations promoted bacterial nitrate metabolism and propagation of antibiotic resistome in the phycosphere of Auxenochlorella pyrenoidosa

Despite that nitrogen (N) and phosphorus (P) play critical roles in the lifecycle of microalgae, how N and P further affect the distribution of bacteria and antibiotic resistance genes (ARGs) in the phycosphere is still poorly understood. In this study, the effects of N and P on the distribution of ARGs in the phycosphere of Auxenochlorella pyrenoidosa were investigated. Results showed that the growth and chlorophyll synthesis of microalgae were inhibited when N or P was limited, regardless of the N/P ratios, but the extracellular polymeric substances content and nitrate assimilation efficiency were enhanced in contrast. Metagenomic sequencing revealed that N or P limitation resulted in the recruitment of specific bacteria that highly contribute to the nitrate metabolism in the phycosphere. Besides, N or P limitation promoted the propagation of phycosphere ARGs, primarily through horizontal gene transfer mediated by mobile genetic elements. The enrichment of specific bacteria induced by changes in the algal physiology also contributed to the ARGs proliferation under nutrient limitation. Our results demonstrated that the reduction of algal cells caused by nutrient limitation could promote the propagation of ARGs, which provides new insights into the occurrence and spread of ARGs in the phycosphere.

Microbial community structures and bacteria-Cylindrospermopsis raciborskii interactions in Yilong Lake

Cylindrospermopsis raciborskii-dominated harmful algae blooms have been reported globally in recent years. However, our understanding of the ecology of C. raciborskii in natural conditions is still poor. In this study, we collected the water samples from a C. raciborskii-blooming lake, Yilong Lake, in Yunnan province, China, and used both culture-dependent and culture-independent approaches to investigate their microbial communities and the interactions between C. raciborskii and the other bacteria. The composition and diversity of microbial communities were revealed with 16S rRNA gene high-throughput sequencing data analysis. Microbial co-occurrences analysis suggests C. raciborskii may have complex associations with other bacteria. Based on co-inoculation tests, we obtained 14 strains of bacterial strains from the water samples that exhibited either algicidal or promoting effects on a strain of C. raciborskii. Two bacterial isolates exhibited a consistent performance between co-occurrence analysis and experimental results. Effects of these bacteria-algae interspecies interactions on the bloom event are discussed. All these results may provide new insights into the C. raciborskii-dominated blooms and how its interspecies relationships with other bacteria may influence the bloom events in eutrophic waters throughout the world.

Marine particle microbiomes during a spring diatom bloom contain active sulfate-reducing bacteria

Phytoplankton blooms fuel marine food webs with labile dissolved carbon and also lead to the formation of particulate organic matter composed of living and dead algal cells. These particles contribute to carbon sequestration and are sites of intense algal-bacterial interactions, providing diverse niches for microbes to thrive. We analyzed 16S and 18S ribosomal RNA gene amplicon sequences obtained from 51 time points and metaproteomes from 3 time points during a spring phytoplankton bloom in a shallow location (6-10 m depth) in the North Sea. Particulate fractions larger than 10 µm diameter were collected at near daily intervals between early March and late May in 2018. Network analysis identified two major modules representing bacteria co-occurring with diatoms and with dinoflagellates, respectively. The diatom network module included known sulfate-reducing Desulfobacterota as well as potentially sulfur-oxidizing Ectothiorhodospiraceae. Metaproteome analyses confirmed presence of key enzymes involved in dissimilatory sulfate reduction, a process known to occur in sinking particles at greater depths and in sediments. Our results indicate the presence of sufficiently anoxic niches in the particle fraction of an active phytoplankton bloom to sustain sulfate reduction, and an important role of benthic-pelagic coupling for microbiomes in shallow environments. Our findings may have implications for the understanding of algal-bacterial interactions and carbon export during blooms in shallow-water coastal areas.

Interaction between phytoplankton and heterotrophic bacteria in Arctic fjords during the glacial melting season as revealed by eDNA metabarcoding

The hydrographic variability in the fjords of Svalbard significantly influences water mass properties, causing distinct patterns of microbial diversity and community composition between surface and subsurface layers. However, surveys on the phytoplankton-associated bacterial communities, pivotal to ecosystem functioning in Arctic fjords, are limited. This study investigated the interactions between phytoplankton and heterotrophic bacterial communities in Svalbard fjord waters through comprehensive eDNA metabarcoding with 16S and 18S rRNA genes. The 16S rRNA sequencing results revealed a homogenous community composition including a few dominant heterotrophic bacteria across fjord waters, whereas 18S rRNA results suggested a spatially diverse eukaryotic plankton distribution. The relative abundances of heterotrophic bacteria showed a depth-wise distribution. By contrast, the dominant phytoplankton populations exhibited variable distributions in surface waters. In the network model, the linkage of phytoplankton (Prasinophytae and Dinophyceae) to heterotrophic bacteria, particularly Actinobacteria, suggested the direct or indirect influence of bacterial contributions on the fate of phytoplankton-derived organic matter. Our prediction of the metabolic pathways for bacterial activity related to phytoplankton-derived organic matter suggested competitive advantages and symbiotic relationships between phytoplankton and heterotrophic bacteria. Our findings provide valuable insights into the response of phytoplankton-bacterial interactions to environmental changes in Arctic fjords.

Functional analyses of bacterial genomes found in Symbiodiniaceae genome assemblies

Bacterial-algal interactions strongly influence marine ecosystems. Bacterial communities in cultured dinoflagellates of the family Symbiodiniaceae have been characterized by metagenomics. However, little is known about whole-genome analysis of marine bacteria associated with these dinoflagellates. We performed in silico analysis of four bacterial genomes from cultures of four dinoflagellates of the genera Symbiodinium, Breviolum, Cladocopium and Durusdinium. Comparative analysis showed that the former three contain the alphaproteobacterial family Parvibaculaceae and that the Durusdinium culture includes the family Sphingomonadaceae. There were no large genomic reductions in the alphaproteobacteria with genome sizes of 2.9-3.9 Mb, implying they are not obligate intracellular bacteria. Genomic annotations of three Parvibaculaceae detected the gene for diacetylchitobiose deacetylase (Dac), which may be involved in the degradation of dinoflagellate cell surfaces. They also had metabolic genes for dissimilatory nitrate reduction to ammonium (DNRA) in the nitrogen (N) cycle and cobalamin (vitamin B12 ) biosynthetic genes in the salvage pathway. Those three characters were not found in the Sphingomonadaceae genome. Predicted biosynthetic gene clusters for secondary metabolites indicated that the Parvibaculaceae likely produce the same secondary metabolites. Our study suggests that the Parvibaculaceae is a major resident of Symbiodiniaceae cultures with antibiotics.

Potential gap in understanding cyanoHABs: Light-dependent morphological variations in colonial cyanobacterium Microcystis

Colony formation is a crucial characteristic of Microcystis, a cyanobacterium known for causing cyanobacterial harmful algal blooms (cyanoHABs). It has been observed that as Microcystis colonies grow larger, they often become less densely packed, which correlates with a decrease in light penetration. The objective of this study was to investigate the effects of light limitation on the morphological variations in Microcystis, particularly in relation to the crowded cellular environment. The results indicated that when there was sufficient light (transmittance = 100 %) to support a growth rate of 0.11±0.01 day-1, a significant increase in colony size was found, from 466±15 μm to 1030±111 μm. However, under light limitation (transmittance = 50 % - 1 %) where the growth rate was lower than 0, there was no significant improvement in colony size. Microcystis in the light limitation groups exhibited a loose cell arrangement and even the presence of holes or pores within the colony, confirming the negative correlation between colony size and cell arrangement. This pattern is driven by regional differences in growth within the colony, as internal cells have a significantly lower frequency of division compared to peripheral cells, due to intra-colony self-shading (ICSS). The research demonstrates that Microcystis can adjust its cell arrangement to avoid excessive self-shading, which has implications for predicting and controlling cyanoHABs. These findings also contribute to the understanding of cyanobacterial variations and can potentially inform future research on the diverse phycosphere.

Bacteria contribute exopolysaccharides to an algal-bacterial joint extracellular matrix

Marine ecosystems are influenced by phytoplankton aggregation, which affects processes like marine snow formation and harmful events such as marine mucilage outbreaks. Phytoplankton secrete exopolymers, creating an extracellular matrix (ECM) that promotes particle aggregation. This ECM attracts heterotrophic bacteria, providing a nutrient-rich and protective environment. In terrestrial environments, bacterial colonization near primary producers relies on attachment and the formation of multidimensional structures like biofilms. Bacteria were observed attaching and aggregating within algal-derived exopolymers, but it is unclear if bacteria produce an ECM that contributes to this colonization. This study, using Emiliania huxleyi algae and Phaeobacter inhibens bacteria in an environmentally relevant model system, reveals a shared algal-bacterial ECM scaffold that promotes algal-bacterial aggregation. Algal exudates play a pivotal role in promoting bacterial colonization, stimulating bacterial exopolysaccharide (EPS) production, and facilitating a joint ECM formation. A bacterial biosynthetic pathway responsible for producing a specific EPS contributing to bacterial ECM formation is identified. Genes from this pathway show increased expression in algal-rich environments. These findings highlight the underestimated role of bacteria in aggregate-mediated processes in marine environments, offering insights into algal-bacterial interactions and ECM formation, with implications for understanding and managing natural and perturbed aggregation events.

Assembly dynamics of eukaryotic plankton and bacterioplankton in the Yangtze River estuary: A hybrid community perspective

Estuaries, acting as transitional habitats receiving species introductions from both freshwater and marine sources, undergo significant impacts from global climate changes. Planktonic microorganisms contribute significantly to estuarine biodiversity and ecological stability. These microorganisms primarily fall into three groups: eukaryotic plankton, particle-associated bacteria, and free-living bacteria. Understanding the structural characteristics and interactions within these subcommunities is crucial for comprehending estuarine dynamics. We collected samples from three distinct locations (< 0.1 PSU, 6.6 PSU, and 19 PSU) within the Yangtze River estuary. Samples underwent analysis for physicochemical indicators, while microbial communities were subjected to 16S/18S rRNA amplicon sequencing. Additionally, simulated mixing experiments were conducted using samples of varying salinities. Estuary samples, combined with simulated experiments, were employed to collectively examine the structural characteristics and assembly processes of estuarine microbes. Our research highlights the considerable impact of phylogenetic classification on prokaryotic behavior in these communities. We observed a transition in assembly processes from primarily stochastic for particle-associated bacteria to a predominant influence of homogeneous selection as salinity increased. Particle-associated bacterial communities exhibited a greater influence of stochastic processes compared to free-living bacteria, showcasing higher stability in diversity. The variations in composition and structure of estuarine microbial subcommunities were influenced by diverse environmental factors. Particle-associated bacteria displayed elevated network characterization values and established closer interactions with eukaryotic plankton. Structural equation modeling (SEM) analysis revealed that free-living bacteria displayed a heightened sensitivity to environmental factors and exerted a more significant influence on assembly processes and network characteristics. Simulated mixing in these environments resulted in the loss of species with similar microbial taxonomic relationships. The functioning of bacterioplankton is influenced by salinity and the processes governing their assembly, particularly in relation to different living states. These findings significantly contribute to our understanding of the intricate interplay between prokaryotic and eukaryotic plankton microorganisms in highly dynamic environments, laying a robust foundation for further exploration into the ecological mechanisms governing microbial dynamics in estuaries.

In Situ Formed Microalgae-Integrated Living Hydrogel for Enhanced Tumor Starvation Therapy and Immunotherapy through Photosynthetic Oxygenation

The effectiveness of various cancer therapies for solid tumors is substantially limited by the highly hypoxic tumor microenvironment (TME). Here, a microalgae-integrated living hydrogel (ACG gel) is developed to concurrently enhance hypoxia-constrained tumor starvation therapy and immunotherapy. The ACG gel is formed in situ following intratumoral injection of a biohybrid fluid composed of alginate, Chlorella sorokiniana, and glucose oxidase, facilitated by the crossing-linking between divalent ions within tumors and alginate. The microalgae Chlorella sorokiniana embedded in ACG gel generate abundant oxygen through photosynthesis, enhancing glucose oxidase-catalyzed glucose consumption and shifting the TME from immunosuppressive to immunopermissive status, thus reducing the tumor cell energy supply and boosting antitumor immunity. In murine 4T1 tumor models, the ACG gel significantly suppresses tumor growth and effectively prevents postoperative tumor recurrence. This study, leveraging microalgae as natural oxygenerators, provides a versatile and universal strategy for the development of oxygen-dependent tumor therapies.

Exchange or Eliminate: The Secrets of Algal-Bacterial Relationships

Algae and bacteria have co-occurred and coevolved in common habitats for hundreds of millions of years, fostering specific associations and interactions such as mutualism or antagonism. These interactions are shaped through exchanges of primary and secondary metabolites provided by one of the partners. Metabolites, such as N-sources or vitamins, can be beneficial to the partner and they may be assimilated through chemotaxis towards the partner producing these metabolites. Other metabolites, especially many natural products synthesized by bacteria, can act as toxins and damage or kill the partner. For instance, the green microalga Chlamydomonas reinhardtii establishes a mutualistic partnership with a Methylobacterium, in stark contrast to its antagonistic relationship with the toxin producing Pseudomonas protegens. In other cases, as with a coccolithophore haptophyte alga and a Phaeobacter bacterium, the same alga and bacterium can even be subject to both processes, depending on the secreted bacterial and algal metabolites. Some bacteria also influence algal morphology by producing specific metabolites and micronutrients, as is observed in some macroalgae. This review focuses on algal-bacterial interactions with micro- and macroalgal models from marine, freshwater, and terrestrial environments and summarizes the advances in the field. It also highlights the effects of temperature on these interactions as it is presently known.

The Microcystis-microbiome interactions: origins of the colonial lifestyle

Species of the Microcystis genus are the most common bloom-forming toxic cyanobacteria worldwide. They belong to a clade of unicellular cyanobacteria whose ability to reach high biomasses during blooms is linked to the formation of colonies. Colonial lifestyle provides several advantages under stressing conditions of light intensity, ultraviolet light, toxic substances and grazing. The progression from a single-celled organism to multicellularity in Microcystis has usually been interpreted as individual phenotypic responses of the cyanobacterial cells to the environment. Here, we synthesize current knowledge about Microcystis colonial lifestyle and its role in the organism ecology. We then briefly review the available information on Microcystis microbiome and propose that changes leading from single cells to colonies are the consequence of specific and tightly regulated signals between the cyanobacterium and its microbiome through a biofilm-like mechanism. The resulting colony is a multi-specific community of interdependent microorganisms.

Indole-3-acetic acid promotes growth in bloom-forming Microcystis via an antioxidant response

Interactions between bacteria and phytoplankton in the phycosphere facilitate and constrain biogeochemical cycling in aquatic ecosystems. Indole-3-acetic acid (IAA) is a bacterially produced chemical signal that promotes growth of phytoplankton and plants. Here, we explored the impact of IAA on bloom-forming cyanobacteria and their associated bacteria. Exposure to IAA and its precursor, tryptophan, resulted in a strong growth response in a bloom of the freshwater cyanobacterium, Microcystis. Metatranscriptome analysis revealed the induction of an antioxidant response in Microcystis upon exposure to IAA, potentially allowing populations to increase photosynthetic rate and overcome internally generated reactive oxygen. Our data reveal that co-occurring bacteria within the phycosphere microbiome exhibit a division of labor for supportive functions, such as nutrient mineralization and transport, vitamin synthesis, and reactive oxygen neutralization. These complex dynamics within the Microcystis phycosphere microbiome are an example of interactions within a microenvironment that can have ecosystem-scale consequences.

Algal blooms in the ocean: hot spots for chemically mediated microbial interactions

The cycling of major nutrients in the ocean is affected by large-scale phytoplankton blooms, which are hot spots of microbial life. Diverse microbial interactions regulate bloom dynamics. At the single-cell level, interactions between microorganisms are mediated by small molecules in the chemical crosstalk that determines the type of interaction, ranging from mutualism to pathogenicity. Algae interact with viruses, bacteria, parasites, grazers and other algae to modulate algal cell fate, and these interactions are dependent on the environmental context. Recent advances in mass spectrometry and single-cell technologies have led to the discovery of a growing number of infochemicals - metabolites that convey information - revealing the ability of algal cells to govern biotic interactions in the ocean. The diversity of infochemicals seems to account for the specificity in cellular response during microbial communication. Given the immense impact of algal blooms on biogeochemical cycles and climate regulation, a major challenge is to elucidate how microscale interactions control the fate of carbon and the recycling of major elements in the ocean. In this Review, we discuss microbial interactions and the role of infochemicals in algal blooms. We further explore factors that can impact microbial interactions and the available tools to decipher them in the natural environment.

Communication mediated interaction between bacteria and microalgae advances photogranulation

Recently, photogranules composed of bacteria and microalgae for carbon-negative nitrogen removal receive extensive attention worldwide, yet which type of bacteria is helpful for rapid formation of photogranules and whether they depend on signaling communication remain elusive. Varied signaling communication was analyzed using metagenomic method among bacteria and microalgae in via of two types of experimentally verified signaling molecule from bacteria to microalgae, which include indole-3-acetic acid (IAA) and N-acyl homoserine lactones (AHLs) during the operation of photo-bioreactors. Signaling communication is helpful for the adaptability of bacteria to survive with algae. Compared with non-signaling bacteria, signaling bacteria more easily adapt to the varied conditions, evidenced by the increased abundance in the operated reactors. Signaling bacteria are easier to enter the phycosphere, and they dominate the interactions between bacteria and algae rather than non-signaling bacteria. The co-abundance groups (CAGs) with signaling bacteria possess higher abundance than that without signaling bacteria (22.27 % and 6.67 %). Importantly, signaling bacteria accessibly interact with microalgae, which possess higher degree centralities and 32.50 % of them are keystone nodes in the network, in contrast to only 18.66 % of non-signaling bacteria. Thauera carrying both IAA and AHLs synthase genes are highly enriched and positively correlated with nitrogen removal rate. Our work not only highlights the essential roles of signaling communication between microalgae and bacteria in the development of photogranules, but also enriches our understanding of microbial sociobiology.

Novel functional insights into the microbiome inhabiting marine plastic debris: critical considerations to counteract the challenges of thin biofilms using multi-omics and comparative metaproteomics

BACKGROUND

Microbial functioning on marine plastic surfaces has been poorly documented, especially within cold climates where temperature likely impacts microbial activity and the presence of hydrocarbonoclastic microorganisms. To date, only two studies have used metaproteomics to unravel microbial genotype-phenotype linkages in the marine 'plastisphere', and these have revealed the dominance of photosynthetic microorganisms within warm climates. Advancing the functional representation of the marine plastisphere is vital for the development of specific databases cataloging the functional diversity of the associated microorganisms and their peptide and protein sequences, to fuel biotechnological discoveries. Here, we provide a comprehensive assessment for plastisphere metaproteomics, using multi-omics and data mining on thin plastic biofilms to provide unique insights into plastisphere metabolism. Our robust experimental design assessed DNA/protein co-extraction and cell lysis strategies, proteomics workflows, and diverse protein search databases, to resolve the active plastisphere taxa and their expressed functions from an understudied cold environment.

RESULTS

For the first time, we demonstrate the predominance and activity of hydrocarbonoclastic genera (Psychrobacter, Flavobacterium, Pseudomonas) within a primarily heterotrophic plastisphere. Correspondingly, oxidative phosphorylation, the citrate cycle, and carbohydrate metabolism were the dominant pathways expressed. Quorum sensing and toxin-associated proteins of Streptomyces were indicative of inter-community interactions. Stress response proteins expressed by Psychrobacter, Planococcus, and Pseudoalteromonas and proteins mediating xenobiotics degradation in Psychrobacter and Pseudoalteromonas suggested phenotypic adaptations to the toxic chemical microenvironment of the plastisphere. Interestingly, a targeted search strategy identified plastic biodegradation enzymes, including polyamidase, hydrolase, and depolymerase, expressed by rare taxa. The expression of virulence factors and mechanisms of antimicrobial resistance suggested pathogenic genera were active, despite representing a minor component of the plastisphere community.

CONCLUSION

Our study addresses a critical gap in understanding the functioning of the marine plastisphere, contributing new insights into the function and ecology of an emerging and important microbial niche. Our comprehensive multi-omics and comparative metaproteomics experimental design enhances biological interpretations to provide new perspectives on microorganisms of potential biotechnological significance beyond biodegradation and to improve the assessment of the risks associated with microorganisms colonizing marine plastic pollution. Video Abstract.

Dominance of net autotrophy in arid landscape low relief polar lakes, Nunavut, Canada

The Arctic is the fastest warming biome on the planet, and environmental changes are having striking effects on freshwater ecosystems that may impact the regional carbon cycle. The metabolic state of Arctic lakes is often considered net heterotrophic, due to an assumed supply of allochthonous organic matter that supports ecosystem respiration and carbon mineralization in excess of rates of primary production. However, lake metabolic patterns vary according to regional climatic characteristics, hydrological connectivity, organic matter sources and intrinsic lake properties, and the metabolism of most Arctic lakes is unknown. We sampled 35 waterbodies along a connectivity gradient from headwater to downstream lakes, on southern Victoria Island, Nunavut, in an area characterized by low precipitation, organic-poor soils, and high evaporation rates. We evaluated whether lakes were net autotrophic or heterotrophic during the open water period using an oxygen isotopic mass balance approach. Most of the waterbodies were autotrophic and sites of net organic matter production or close to metabolic equilibrium. Autotrophy was associated with higher benthic primary production, as compared to its pelagic counterpart, due to the high irradiance reaching the bottom and efficient internal carbon and nutrient cycling. Highly connected midstream and downstream lakes showed efficient organic matter cycling, as evidenced by the strong coupling between gross primary production (GPP) and ecosystem respiration, while decoupling was observed in some headwater lakes with significantly higher GPP. The shallow nature of lakes in the flat, arid region of southern Victoria Island supports net autotrophy in most lakes during the open water season. Ongoing climate changes that lengthen the ice-free irradiance period and increase rates of nutrient evapoconcentration may further promote net autotrophy, with uncertain long-term effects for lake functioning.

Epiphytic microorganisms of submerged macrophytes effectively contribute to nitrogen removal

Submerged macrophytes play important roles in nutrient cycling and are widely used in ecological restoration to alleviate eutrophication and improve water quality in lakes. Epiphytic microbial communities on leaves of submerged macrophytes might promote nitrogen cycling, but the mechanisms and quantification of their contributions remain unclear. Here, four types of field zones with different nutrient levels and submerged macrophytes, eutrophic + Vallisneria natans (EV), eutrophic + V. natans + Hydrilla verticillata, mesotrophic + V. natans + H. verticillata, and eutrophic without macrophytes were selected to investigate the microbial communities that involved in nitrification and denitrification. The alpha diversity of bacterial community was higher in the phyllosphere than in the water, and that of H. verticillata was higher compared to V. natans. Bacterial community structures differed significantly between the four zones. The highest relative abundance of dominant bacterioplankton genera involved in nitrification and denitrification was observed in the EV zone. Similarly, the alpha diversity of the epiphytic ammonia-oxidizing archaea and nosZI-type denitrifiers were highest in the EV zone. Consist with the diversity patterns, the potential denitrification rates were higher in the phyllosphere than those in the water. Higher potential denitrification rates in the phyllosphere were also found in H. verticillata than those in V. natans. Anammox was not detected in all samples. Nutrient loads, especially nitrogen concentrations were important factors influencing potential nitrification, denitrification rates, and bacterial communities, especially for the epiphytic nosZI-type taxa. Overall, we observed that the phyllosphere harbors more microbes and promotes higher denitrification rates compared to water, and epiphytic bacterial communities are shaped by nitrogen nutrients and macrophyte species, indicating that epiphytic microorganisms of submerged macrophytes can effectively contribute to the N removal in shallow lakes.

Light-dark fluctuated metabolic features of diazotrophic and non-diazotrophic cyanobacteria and their coexisting bacteria

Cyanobacteria, the most abundant photosynthetic organisms in oceans, are tightly associated with diverse microbiota. However, the relationships between heterotrophic bacteria and cyanobacteria, particularly the diazotrophic group, are not fully understood. Here, we compared diel gene expressions of N2 fixing cyanobacteria Crocosphaera watsonii WH0003 and non-diazotrophic Synechococcus sp. RS9902 and their associated bacteria using metatranscriptomics approach. WH0003 showed significant up-regulation of O2 restriction and oxidative phosphorylation related genes at nighttime due to large carbon and energy investments for active N2 fixation. In contrast, RS9902 had higher expression for those genes at daytime. The two cyanobacteria hosted distinct bacterial communities with clear separate substrate utilization niches to reduce competition. Light-dark partitioning of nutrient acquisition among the dominant bacterial groups likely contributed to the dynamic balance for community coexistence. Moreover, particle-attached (PA) bacteria in RS9902 largely expressed glycoside hydrolases to hydrolyze complex carbohydrate compounds, while free-living (FL) bacteria priorly assimilated soluble, diffusible molecules. Spatial partitioning of nutrient acquisition between PA and FL bacteria implied that location initially influenced metabolic features of host associated bacteria. Our results advance knowledge on light-dark regulated metabolic activities of diazotrophic and non-diazotrophic cyanobacteria, and provide new insights into the coexisting strategies of different bacterial groups.

Genetic evidence for algal auxin production in Chlamydomonas and its role in algal-bacterial mutualism

Interactions between algae and bacteria are ubiquitous and play fundamental roles in nutrient cycling and biomass production. Recent studies have shown that the plant auxin indole acetic acid (IAA) can mediate chemical crosstalk between algae and bacteria, resembling its role in plant-bacterial associations. Here, we report a mechanism for algal extracellular IAA production from L-tryptophan mediated by the enzyme L-amino acid oxidase (LAO1) in the model Chlamydomonas reinhardtii. High levels of IAA inhibit algal cell multiplication and chlorophyll degradation, and these inhibitory effects can be relieved by the presence of the plant-growth-promoting bacterium (PGPB) Methylobacterium aquaticum, whose growth is mutualistically enhanced by the presence of the alga. These findings reveal a complex interplay of microbial auxin production and degradation by algal-bacterial consortia and draws attention to potential ecophysiological roles of terrestrial microalgae and PGPB in association with land plants.

The Evolution, Assembly, and Dynamics of Marine Holobionts

The holobiont concept (i.e., multiple living beings in close symbiosis with one another and functioning as a unit) is revolutionizing our understanding of biology, especially in marine systems. The earliest marine holobiont was likely a syntrophic partnership of at least two prokaryotic members. Since then, symbiosis has enabled marine organisms to conquer all ocean habitats through the formation of holobionts with a wide spectrum of complexities. However, most scientific inquiries have focused on isolated organisms and their adaptations to specific environments. In this review, we attempt to illustrate why a holobiont perspective-specifically, the study of how numerous organisms form a discrete ecological unit through symbiosis-will be a more impactful strategy to advance our understanding of the ecology and evolution of marine life. We argue that this approach is instrumental in addressing the threats to marine biodiversity posed by the current global environmental crisis.

Scarcity of fixed carbon transfer in a model microbial phototroph-heterotroph interaction

Although the green alga Chlamydomonas reinhardtii has long served as a reference organism, few studies have interrogated its role as a primary producer in microbial interactions. Here, we quantitatively investigated C. reinhardtii's capacity to support a heterotrophic microbe using the established coculture system with Mesorhizobium japonicum, a vitamin B12-producing α-proteobacterium. Using stable isotope probing and nanoscale secondary ion mass spectrometry (nanoSIMS), we tracked the flow of photosynthetic fixed carbon and consequent bacterial biomass synthesis under continuous and diurnal light with single-cell resolution. We found that more 13C fixed by the alga was taken up by bacterial cells under continuous light, invalidating the hypothesis that the alga's fermentative degradation of starch reserves during the night would boost M. japonicum heterotrophy. 15NH4 assimilation rates and changes in cell size revealed that M. japonicum cells reduced new biomass synthesis in coculture with the alga but continued to divide-a hallmark of nutrient limitation often referred to as reductive division. Despite this sign of starvation, the bacterium still synthesized vitamin B12 and supported the growth of a B12-dependent C. reinhardtii mutant. Finally, we showed that bacterial proliferation could be supported solely by the algal lysis that occurred in coculture, highlighting the role of necromass in carbon cycling. Collectively, these results reveal the scarcity of fixed carbon in this microbial trophic relationship (particularly under environmentally relevant light regimes), demonstrate B12 exchange even during bacterial starvation, and underscore the importance of quantitative approaches for assessing metabolic coupling in algal-bacterial interactions.

Distinctive chemotactic responses of three marine herbivore protists to DMSP and related compounds

Marine planktonic predator-prey interactions occur in microscale seascapes, where diffusing chemicals may act either as chemotactic cues that enhance or arrest predation, or as elemental resources that are complementary to prey ingestion. The phytoplankton osmolyte dimethylsulfoniopropionate (DMSP) and its degradation products dimethylsulfide (DMS) and acrylate are pervasive compounds with high chemotactic potential, but there is a longstanding controversy over whether they act as grazing enhancers or deterrents. Here, we investigated the chemotactic responses of three herbivorous dinoflagellates to point-sourced, microscale gradients of dissolved DMSP, DMS, and acrylate. We found no evidence for acrylate being a chemotactic repellent and observed a weak attractor role of DMS. DMSP behaved as a strong chemoattractor whose potential for grazing facilitation through effects on swimming patterns and aggregation depends on the grazer's feeding mode and ability to incorporate DMSP. Our study reveals that predation models will fail to predict grazing impacts unless they incorporate chemotaxis-driven searching and finding of prey.

Microbiome processing of organic nitrogen input supports growth and cyanotoxin production of Microcystis aeruginosa cultures

Nutrient-induced blooms of the globally abundant freshwater toxic cyanobacterium Microcystis cause worldwide public and ecosystem health concerns. The response of Microcystis growth and toxin production to new and recycled nitrogen (N) inputs and the impact of heterotrophic bacteria in the Microcystis phycosphere on these processes are not well understood. Here, using microbiome transplant experiments, cyanotoxin analysis, and nanometer-scale stable isotope probing to measure N incorporation and exchange at single cell resolution, we monitored the growth, cyanotoxin production, and microbiome community structure of several Microcystis strains grown on amino acids or proteins as the sole N source. We demonstrate that the type of organic N available shaped the microbial community associated with Microcystis, and external organic N input led to decreased bacterial colonization of Microcystis colonies. Our data also suggest that certain Microcystis strains could directly uptake amino acids, but with lower rates than heterotrophic bacteria. Toxin analysis showed that biomass-specific microcystin production was not impacted by N source (i.e. nitrate, amino acids, or protein) but rather by total N availability. Single-cell isotope incorporation revealed that some bacterial communities competed with Microcystis for organic N, but other communities promoted increased N uptake by Microcystis, likely through ammonification or organic N modification. Our laboratory culture data suggest that organic N input could support Microcystis blooms and toxin production in nature, and Microcystis-associated microbial communities likely play critical roles in this process by influencing cyanobacterial succession through either decreasing (via competition) or increasing (via biotransformation) N availability, especially under inorganic N scarcity.

Taxonomic, Phylogenomic and Bioactivity Profiling of Novel Phycosphere Bacterium from Model Cyanobacterium Synechococcus elongatus PCC 7942

Phycosphere niches host rich microbial consortia that harbor dynamic algae-bacteria interactions with fundamental significance in varied natural ecosystems. Hence, culturing the uncultured microbial majority of the phycosphere microbiota is vital for deep understanding of the intricate mechanisms governing the dynamic interactions, and also to provide novel and rich microbial resources, and to discover new natural bioactive metabolites. Synechococcus elongatus PCC 7942 is a robust model cyanobacterium widely used in environment, synthesis biology, and biotechnology research. To expand the number of novel phycosphere species that were brought into culture and to discover the natural bioactivities, we presented a new yellow-pigmented bacterium named ABI-127-1, which was recovered from the phycosphere of PCC 7942, using an optimized bacterial isolation procedure. Combined polyphasic taxonomic and phylogenomic characterization was performed to confidently identify the new isolate as a potential novel species belonging to the genus Qipengyuania. The observed bioactivity of strain ABI-127-1 with promoting potential towards the growth and CO2 fixation efficiency of the host microalgae was measured. Additionally, the bacterial production of active bioflocculant exopolysaccharides was evaluated after culture optimization. Thus, these findings revealed the potential environmental and biotechnological implications of this new microalgae growth-promoting bacterium isolated from the phycosphere microenvironment.

Temporal variations in reactive oxygen species in biofilms of submerged macrophytes: The key role of microbial metabolism mediated by oxygen fluctuations

Reactive oxygen species (ROS) play a crucial role in the biogeochemistry of aquatic environments, yet their occurrence and accumulation in the biofilm of submerged macrophytes have been poorly documented. Herein, we first investigated the light-dark cycling fluctuations of biofilm microenvironment and the temporal variations of a representative ROS (O2•-) during biofilm succession on the macrophyte leaves and subsequently quantified the photochemical processes in biofilms. The sustained production of O2•- exhibited a distinct rhythmic fluctuation from 32.49 ± 0.56 μmol/kg to 72.56 ± 0.92 μmol/kg FW, which simultaneously fluctuated with the dissolved oxygen, redox potential, and pH, all driven by the alternating oxic-anoxic conditions of biofilms. The intensities of O2•- and ROS firstly increased and then decreased throughout biofilm succession. The O2•- concentrations in biofilms from different waters followed the order of rural river water > landscape lake water > aquaculture pond water, and the leaf photosynthesis and microbial community played a key role. ROS production was significantly associated with Actinobacteria, Proteobacteria and Bacteroidetes, with contributions of 44.6%, 32.8%, and 15.2%, respectively. Partial least squares path modeling structural equation analysis showed that ROS production in leaf biofilms was mainly related to the microenvironment and microbial metabolism. These findings will facilitate the development of ecological restoration strategies in aquatic environments.

Utilization and transformation of Chrysotila dentata-derived dissolved organic matter by phycosphere bacteria Marinobacter hydrocarbonoclasticus and Bacillus firmus

The dissolved organic matter (DOM) released from the cocoolithophores (Chrysotila dentata) was studied in laboratory experiments after co-culturing C. dentata with bacteria. Marinobacter hydrocarbonoclasticus (CA6)-γ-Proteobacteria and Bacillus firmus (CF2) were used to investigate the utilization and processing of the DOM derived from C. dentata, utilizing fluorescence excitation-emission matrix (EEM) combined with parallel factor analysis (EEM-PARAFAC), while measuring algal abundance and photosynthetic parameters. The experimental groups consisted of axenic C. dentata groups, filter cultured with bacteria (CA6 or CF2) groups, C. dentata co-cultured with bacteria (CA6 or CF2) groups and axenic bacteria (CA6 or CF2) groups. We then evaluated the processing of DOM by determining four fluorescence indices. The number of C. dentata cells and the photosynthetic capacity of microalgae were enhanced by CA6 and CF2. The main known fluorophores, including humic-like components and protein-like components, were present in all sample. The protein-like component of algal-bacterial co-cultures was effectively utilized by CA6 and CF2. The humic-like components increased at the end of the culture time for all cultures. Meanwhile, the average fluorescence intensity of protein-like in CA6 co-culture with algae was lower than that in CF2 co-culture with algae over time. On the other hand, the average fluorescence intensity of humic-like in CA6 was higher than CF2. However, the total change in fluorescence in humic-like and protein-like of axenic CF2 cultures was lower than that of CA6. Hence, the ability of CA6 to transform microalgal-derived DOM was superior to that of CF2, and CF2's ability to consume bacterial-derived DOM was superior to that of CA6.

Disentangling microbial networks across pelagic zones in the tropical and subtropical global ocean

Microbial interactions are vital in maintaining ocean ecosystem function, yet their dynamic nature and complexity remain largely unexplored. Here, we use association networks to investigate possible ecological interactions in the marine microbiome among archaea, bacteria, and picoeukaryotes throughout different depths and geographical regions of the tropical and subtropical global ocean. Our findings reveal that potential microbial interactions change with depth and geographical scale, exhibiting highly heterogeneous distributions. A few potential interactions were global, meaning they occurred across regions at the same depth, while 11-36% were regional within specific depths. The bathypelagic zone had the lowest proportion of global associations, and regional associations increased with depth. Moreover, we observed that most surface water associations do not persist in deeper ocean layers despite microbial vertical dispersal. Our work contributes to a deeper understanding of the tropical and subtropical global ocean interactome, which is essential for addressing the challenges posed by global change.

Linking the impact of bacteria on phytoplankton growth with microbial community composition and co-occurrence patterns

The interactions between microalgae and bacteria have recently emerged as key control factors which might contribute to a better understanding on how phytoplankton communities assemble and respond to environmental disturbances. We analyzed partial 16S rRNA and 18S rRNA genes from a total of 42 antibiotic bioassays, where phytoplankton growth was assessed in the presence or absence of an active bacterial community. A significant negative impact of bacteria was observed in 18 bioassays, a significant positive impact was detected in 5 of the cases, and a non-detectable effect occurred in 19 bioassays. Thalasiossira spp., Chlorophytes, Vibrionaceae and Alteromonadales were relatively more abundant in the samples where a positive effect of bacteria was observed compared to those where a negative impact was observed. Phytoplankton diversity was lower when bacteria negatively affect their growth than when the effect was beneficial. The phytoplankton-bacteria co-occurrence subnetwork included many significant Chlorophyta-Alteromonadales and Bacillariophyceae-Alteromonadales positive associations. Phytoplankton-bacteria co-exclusions were not detected in the network, which contrasts with the negative effect of bacteria on phytoplankton growth frequently detected in the bioassays, suggesting strong competitive interactions. Overall, this study adds strong evidence supporting the key role of phytoplankton-bacteria interactions in the microbial communities.

Enhancing organic matter productivity in microalgal-bacterial biofilm using novel bio-coating

Research on renewable energy from microalgae has led to a growing interest in porous substrate photobioreactors, but their widespread adoption is currently limited to pure microalgal biofilm cultures. The behavior of microalgal-bacterial biofilms immobilized on microporous substrates remains as a research challenge, particularly in uncovering their mutualistic interactions in environment enriched with dissolved organic matter. Therefore, this study established a novel culture platform by introducing microalgal-derived bio-coating that preconditioned hydrophilic polyvinylidene fluoride membranes for the microalgal-bacterial biofilm growth of freshwater microalgae, Chlorella vulgaris ESP 31 and marine microalgae, Cylindrotheca fusiformis with bacteria, Escherichia coli. In the attached co-culture mode, the bio-coating we proposed demonstrated the ability to enhance microalgal growth for both studied species by a range of 2.5 % to 19 % starting from day 10 onwards. Additionally, when compared to co-culture on uncoated membranes, the bio-coating exhibited a significant bacterial growth promotion effect, increasing bacterial growth by at least 2.35 times for the C. vulgaris-E. coli co-culture after an initial adaptation phase. A significant increase of at least 72 % in intracellular biochemical compounds (including chlorophyll, polysaccharides, proteins, and lipids) was observed within just five days, primarily due to the high concentration of pre-coated organic matter, mainly sourced from the internal organic matter (IOM) of C. fusiformis. Higher accumulation of organic compounds in the bio-coating indirectly triggers a competition between microalgae and bacteria which potentially stimulate the production of additional intra-/extra-organic substances as a defensive response. In short, insight gained from this study may represent a paradigm shift in the ways that symbiotic interactions are promoted to increase the yield of specific bio-compounds with the presence of bio-coating.

Cyanobacterial bloom-associated lipopolysaccharides induce pro-inflammatory processes in keratinocytes in vitro

Our previous studies have shown that CyanoHAB LPS (lipopolysaccharides) and LPS from cyanobacterial cultures induce pro-inflammatory effects on intestinal epithelial and immune cells in vitro. To expand our understanding, we investigated their impact on human keratinocytes, which are targeted during water recreational activities. LPS samples were isolated from CyanoHAB biomasses dominated by Microcystis, Aphanizomenon, Planktothrix, and Dolichospermum, or from axenic cultures of these genera. We identified two CyanoHAB biomasses containing a high proportion of Gram-negative bacteria, including potentially pathogenic genera. These biomasses showed the highest induction of interleukin (IL) 8, IL-6, C-C motif chemokine ligand (CCL) 2 (also known as MCP-1), and CCL20 production by HaCaT cells. Interestingly, all CyanoHAB-derived LPS and LPS from axenic cultures (except for Microcystis) accelerated cell proliferation and migration. Our findings highlight the role of G- bacteria composition and LPS structural disparities in influencing these effects, with implications for skin health during recreational activities.

Algae communication, conspecific and interspecific: the concepts of phycosphere and algal-bacteria consortia in a photobioreactor (PBR)

Microalgae in the wild often form consortia with other species promoting their own health and resource foraging opportunities. The recent application of microalgae cultivation and deployment in commercial photobioreactors (PBR) so far has focussed on single species of algae, resulting in multi-species consortia being largely unexplored. Reviewing the current status of PBR ecological habitat, this article argues in favor of further investigation into algal communication with conspecifics and interspecifics, including other strains of microalgae and bacteria. These mutualistic species form the 'phycosphere': the microenvironment surrounding microalgal cells, potentiating the production of certain metabolites through biochemical interaction with cohabitating microorganisms. A better understanding of the phycosphere could lead to novel PBR configurations, capable of incorporating algal-microbial consortia, potentially proving more effective than single-species algal systems.

The effect of polyvinyl chloride (PVC) color on biofilm development and biofilm-heavy metal chemodynamics in the aquatic environment

Plastic surfaces are colonized by microorganisms and biofilms are formed in the natural aquatic environment. As the biofilm develops, it changes the density and buoyancy of the plastic-biofilm complex, results in plastic sinking, and increases the heavy metals accumulated by biofilm's mobility and availability in aquatic ecosystems. In this experiment, biofilms were cultured on five colors of polyvinyl chloride (PVC; transparent, green, blue, red, black) in an aquatic environment to investigate the effects of plastic color on biofilm formation and development (Phase 1) and to study the effects of being sunk below the photic zone on biofilm (Phase 2). The PVC color significantly affected the biofilm formation rate but had no impact on the final biofilm biomass. After sinking the biofilm-PVC below the photic zone in Phase 2, the layer of diatoms on the biofilm surface began to disintegrate, and the biomass and Chlorophyll-a (Chla) content of the biofilm decreased, except on the red PVC. Below the photic zone, the microbial community of the biofilm changed from primarily autotrophic microbes to mostly heterotrophic microbes. Microbial diversity increased and extracellular polymeric substances (EPS) content decreased. The primary factor leading to microbial diversity and community structure changes was water depth rather than PVC color. The changes induced in the biofilm led to an increase in the concentration of all heavy metals in the biofilm, related to the increase in microbial diversity. This study provides new insights into the biofilm formation process and the effects on a biofilm when it sinks below the photic zone.

Microbial Diversity and Community Structure of Wastewater-Driven Microalgal Biofilms

Dwindling water sources increase the need for efficient wastewater treatment. Solar-driven algal turf scrubber (ATS) system may remediate wastewater by supporting the development and growth of periphytic microbiomes that function and interact in a highly dynamic manner through symbiotic interactions. Using ITS and 16S rRNA gene amplicon sequencing, we profiled the microbial communities of four microbial biofilms from ATS systems operated with municipal wastewater (mWW), diluted cattle and pig manure (CattleM and PigM), and biogas plant effluent supernatant (BGE) in comparison to the initial inocula and the respective wastewater substrates. The wastewater-driven biofilms differed significantly in their biodiversity and structure, exhibiting an inocula-independent but substrate-dependent establishment of the microbial communities. The prokaryotic communities were comparable among themselves and with other microbiomes of aquatic environments and were dominated by metabolically flexible prokaryotes such as nitrifiers, polyphosphate-accumulating and algicide-producing microorganisms, and anoxygenic photoautotrophs. Striking differences occurred in eukaryotic communities: While the mWW biofilm was characterized by high biodiversity and many filamentous (benthic) microalgae, the agricultural wastewater-fed biofilms consisted of less diverse communities with few benthic taxa mainly inhabited by unicellular chlorophytes and saprophytes/parasites. This study advances our understanding of the microbiome structure and function within the ATS-based wastewater treatment process.

Diatom-Bacteria Interactions in the Marine Environment: Complexity, Heterogeneity, and Potential for Biotechnological Applications

Diatom-bacteria interactions evolved during more than 200 million years of coexistence in the same environment. In this time frame, they established complex and heterogeneous cohorts and consortia, creating networks of multiple cell-to-cell mutualistic or antagonistic interactions for nutrient exchanges, communication, and defence. The most diffused type of interaction between diatoms and bacteria is based on a win-win relationship in which bacteria benefit from the organic matter and nutrients released by diatoms, while these last rely on bacteria for the supply of nutrients they are not able to produce, such as vitamins and nitrogen. Despite the importance of diatom-bacteria interactions in the evolutionary history of diatoms, especially in structuring the marine food web and controlling algal blooms, the molecular mechanisms underlying them remain poorly studied. This review aims to present a comprehensive report on diatom-bacteria interactions, illustrating the different interplays described until now and the chemical cues involved in the communication and exchange between the two groups of organisms. We also discuss the potential biotechnological applications of molecules and processes involved in those fascinating marine microbial networks and provide information on novel approaches to unveiling the molecular mechanisms underlying diatom-bacteria interactions.

A timeline of bacterial and archaeal diversification in the ocean

Microbial plankton play a central role in marine biogeochemical cycles, but the timing in which abundant lineages diversified into ocean environments remains unclear. Here, we reconstructed the timeline in which major clades of bacteria and archaea colonized the ocean using a high-resolution benchmarked phylogenetic tree that allows for simultaneous and direct comparison of the ages of multiple divergent lineages. Our findings show that the diversification of the most prevalent marine clades spans throughout a period of 2.2 Ga, with most clades colonizing the ocean during the last 800 million years. The oldest clades - SAR202, SAR324, Ca. Marinimicrobia, and Marine Group II - diversified around the time of the Great Oxidation Event, during which oxygen concentration increased but remained at microaerophilic levels throughout the Mid-Proterozoic, consistent with the prevalence of some clades within these groups in oxygen minimum zones today. We found the diversification of the prevalent heterotrophic marine clades SAR11, SAR116, SAR92, SAR86, and Roseobacter as well as the Marine Group I to occur near to the Neoproterozoic Oxygenation Event (0.8-0.4 Ga). The diversification of these clades is concomitant with an overall increase of oxygen and nutrients in the ocean at this time, as well as the diversification of eukaryotic algae, consistent with the previous hypothesis that the diversification of heterotrophic bacteria is linked to the emergence of large eukaryotic phytoplankton. The youngest clades correspond to the widespread phototrophic clades Prochlorococcus, Synechococcus, and Crocosphaera, whose diversification happened after the Phanerozoic Oxidation Event (0.45-0.4 Ga), in which oxygen concentrations had already reached their modern levels in the atmosphere and the ocean. Our work clarifies the timing at which abundant lineages of bacteria and archaea colonized the ocean, thereby providing key insights into the evolutionary history of lineages that comprise the majority of prokaryotic biomass in the modern ocean.

Strong chemotaxis by marine bacteria towards polysaccharides is enhanced by the abundant organosulfur compound DMSP

The ability of marine bacteria to direct their movement in response to chemical gradients influences inter-species interactions, nutrient turnover, and ecosystem productivity. While many bacteria are chemotactic towards small metabolites, marine organic matter is predominantly composed of large molecules and polymers. Yet, the signalling role of these large molecules is largely unknown. Using in situ and laboratory-based chemotaxis assays, we show that marine bacteria are strongly attracted to the abundant algal polysaccharides laminarin and alginate. Unexpectedly, these polysaccharides elicited stronger chemoattraction than their oligo- and monosaccharide constituents. Furthermore, chemotaxis towards laminarin was strongly enhanced by dimethylsulfoniopropionate (DMSP), another ubiquitous algal-derived metabolite. Our results indicate that DMSP acts as a methyl donor for marine bacteria, increasing their gradient detection capacity and facilitating their access to polysaccharide patches. We demonstrate that marine bacteria are capable of strong chemotaxis towards large soluble polysaccharides and uncover a new ecological role for DMSP in enhancing this attraction. These navigation behaviours may contribute to the rapid turnover of polymers in the ocean, with important consequences for marine carbon cycling.

Untargeted metabolomics to expand the chemical space of the marine diatom Skeletonema marinoi

Diatoms (Bacillariophyceae) are aquatic photosynthetic microalgae with an ecological role as primary producers in the aquatic food web. They account substantially for global carbon, nitrogen, and silicon cycling. Elucidating the chemical space of diatoms is crucial to understanding their physiology and ecology. To expand the known chemical space of a cosmopolitan marine diatom, Skeletonema marinoi, we performed High-Resolution Liquid Chromatography-Tandem Mass Spectrometry (LC-MS2) for untargeted metabolomics data acquisition. The spectral data from LC-MS2 was used as input for the Metabolome Annotation Workflow (MAW) to obtain putative annotations for all measured features. A suspect list of metabolites previously identified in the Skeletonema spp. was generated to verify the results. These known metabolites were then added to the putative candidate list from LC-MS2 data to represent an expanded catalog of 1970 metabolites estimated to be produced by S. marinoi. The most prevalent chemical superclasses, based on the ChemONT ontology in this expanded dataset, were organic acids and derivatives, organoheterocyclic compounds, lipids and lipid-like molecules, and organic oxygen compounds. The metabolic profile from this study can aid the bioprospecting of marine microalgae for medicine, biofuel production, agriculture, and environmental conservation. The proposed analysis can be applicable for assessing the chemical space of other microalgae, which can also provide molecular insights into the interaction between marine organisms and their role in the functioning of ecosystems.

Insights into the structure of the pelagic microbial food web in the oligotrophic tropical Western Pacific: Examining trophic interactions and relationship with abiotic variables

Microbial food webs (MFW) play an indispensable role in marine pelagic ecosystem, yet their composition and response to abiotic variables were poorly documented in the oligotrophic tropical Western Pacific. During winter of 2015, we conducted a survey to examine key components of MFW, including Synechococcus, Prochlorococcus, picoeukaryotes, heterotrophic prokaryotes (HP), heterotrophic/pigmented nanoflagellates and ciliates, across water column from surface to 2000 m. Each MFW component exhibited unique vertical distribution pattern, with abundance ratio varying over six and three orders of magnitude across Pico/Microplankton (1.6 ± 1.0 × 106) and Nano/Microplankton (3.2 ± 2.8 × 103), respectively. Furthermore, HP was main component for MFW in the bathypelagic (>1000 m) zone. Multivariate biota-environment analysis demonstrated that environmental variables, particularly temperature, significantly impacted MFW composition, suggesting that bottom-up control (resource availability) dominated the water column. Our study provides benchmark information for future environmental dynamics forcing on MFW in the oligotrophic tropical seas.

The diatom Thalassiosira rotula induces distinct growth responses and colonization patterns of Roseobacteraceae, Flavobacteria and Gammaproteobacteria

Diatoms as important phytoplankton components interact with and are colonized by heterotrophic bacteria. This colonization has been studied extensively in the past but a distinction between the bacterial colonization directly on diatom cells or on the aggregated organic material, exopolymeric substances (EPS), was little addressed. Here we show that the diatom Thalassiosira rotula and EPS were differently colonized by strains of Roseobacteraceae and Flavobacteriaceae in two and tree partner treatments and an enriched natural bacterial community as inoculum. In two partner treatments, the algae and EPS were generally less colonized than in the three partner treatments. Two strains benefitted greatly from the presence of another partner as the proportions of their subpopulations colonizing the diatom cell and the EPS were much enhanced relative to their two partner treatments. Highest proportions of bacteria colonizing the diatom and EPS occurred in the treatment inoculated with the enriched natural bacterial community. Dissolved organic carbon, amino acids and carbohydrates produced by T. rotula were differently used by the bacteria in the two and three partner treatments and most efficiently by the enriched natural bacterial community. Our approach is a valid model system to study physico-chemical bacteria-diatom interactions with increasing complexity.

Functional redundancy of seasonal vitamin B12 biosynthesis pathways in coastal marine microbial communities

Vitamin B12 (cobalamin) is a major cofactor required by most marine microbes, but only produced by a few prokaryotes in the ocean, which is globally B12 -depleted. Despite the ecological importance of B12 , the seasonality of B12 metabolisms and the organisms involved in its synthesis in the ocean remain poorly known. Here we use metagenomics to assess the monthly dynamics of B12 -related pathways and the functional diversity of associated microbial communities in the coastal NW Mediterranean Sea over 7 years. We show that genes related to potential B12 metabolisms were characterized by an annual succession of different organisms carrying distinct production pathways. During the most productive winter months, archaea (Nitrosopumilus and Nitrosopelagicus) were the main contributors to B12 synthesis potential through the anaerobic pathway (cbi genes). In turn, Alphaproteobacteria (HIMB11, UBA8309, Puniceispirillum) contributed to B12 synthesis potential in spring and summer through the aerobic pathway (cob genes). Cyanobacteria could produce pseudo-cobalamin from spring to autumn. Finally, we show that during years with environmental perturbations, the organisms usually carrying B12 synthesis genes were replaced by others having the same gene, thus maintaining the potential for B12 production. Such ecological insurance could contribute to the long-term functional resilience of marine microbial communities exposed to contrasting inter-annual environmental conditions.