Interkingdom Cross-Feeding of Ammonium from Marine Methylamine-Degrading Bacteria to the Diatom Phaeodactylum tricornutum

Prospects of formamide as nitrogen source in biotechnological production processes

This review presents an analysis of formamide, focussing on its occurrence in nature, its functional roles, and its promising applications in the context of the bioeconomy. We discuss the utilization of formamide as an innovative nitrogen source achieved through metabolic engineering. These approaches underscore formamide's potential in supporting growth and production in biotechnological processes. Furthermore, our review illuminates formamide's role as a nitrogen source capable of safeguarding cultivation systems against contamination in non-sterile conditions. This attribute adds an extra layer of practicality to its application, rendering it an attractive candidate for sustainable and resilient industrial practices. Additionally, the article unveils the versatility of formamide as a potential carbon source that could be combined with formate or CO2 assimilation pathways. However, its attributes, i.e., enriched nitrogen content and comparatively limited energy content, led to conclude that formamide is more suitable as a co-substrate and that its use as a sole source of carbon for biomass and bio-production is limited. Through our exploration of formamide's properties and its applications, this review underscores the significance of formamide as valuable resource for a large spectrum of industrial applications. KEY POINTS: • Formidases enable access to formamide as source of nitrogen, carbon, and energy • The formamide/formamidase system supports non-sterile fermentation • The nitrogen source formamide supports production of nitrogenous compounds.

Diverse interactions between bacteria and microalgae: A review for enhancing harmful algal bloom mitigation and biomass processing efficiency

The interactions between bacteria and microalgae play pivotal roles in resource allocation, biomass accumulation, nutrient recycling, and species succession in aquatic systems, offering ample opportunities to solve several social problems. The escalating threat of harmful algal blooms (HABs) in the aquatic environment and the lack of cheap and eco-friendly algal-biomass processing methods have been among the main problems, demanding efficient and sustainable solutions. In light of this, the application of algicidal bacteria to control HABs and enhance algal biomass processing has been promoted in the past few decades as potentially suitable mechanisms to solve those problems. Hence, this comprehensive review aims to explore the diverse interaction modes between bacteria and microalgae, ranging from synergistic to antagonistic, and presents up-to-date information and in-depth analysis of their potential biotechnological applications, particularly in controlling HABs and enhancing microalgal biomass processing. For instance, several studies revealed that algicidal bacteria can effectively inhibit the growth of Microcystis aeruginosa, a notorious freshwater HAB species, with an antialgal efficiency of 24.87 %-98.8 %. The review begins with an overview of the mechanisms behind algae-bacteria interactions, including the environmental factors influencing these dynamics and their broader implications for aquatic ecosystems. It then provides a detailed analysis of the role of algicidal bacteria in controlling harmful algal blooms, as well as their role in bioflocculation and the pretreatment of microalgal biomass. Additionally, the review identifies and discusses the constraints and challenges in the biotechnological application of these interactions. By exploring the strategic use of algicidal bacteria, this review not only underscores their importance in maintaining aquatic environmental health but also in enhancing biomass processing efficiency. It offers valuable insights into future research avenues and the potential scalability of these applications, both in situ and at an industrial level.

Phycosphere bacterial composition and function in colony and solitary Phaeocystis globosa strains providing novel insights into the algal blooms

Phycosphere bacteria can regulate the dynamics of different algal blooms that impact marine ecosystems. Phaeocystis globosa can alternate between solitary free-living cells and colonies and the latter morphotype is dominate during blooms. The mechanisms underlying the formation of these blooms have received much attention. High throughput sequencing results showed that the bacterial community composition differed significantly between colony and solitary strains in bacterial composition and function. It was found that the genera SM1A02 and Haliea were detected only among the colony strains and contribute to ammonium accumulation in colonies, and the genus Sulfitobacter was abundant among the colony strains that were excellent at producing DMS. In addition, the bacterial communities of the two colony strains exhibited stronger abilities for carbon and sulfur metabolism, energy metabolism, vitamin B synthesis, and signal transduction, providing inorganic and organic nutrients and facilitating tight communication with the host algae, thereby promoting growth and bloom development.

Impact of host species on assembly, composition, and functional profiles of phycosphere microbiomes

Microalgal microbiomes play vital roles in the growth and health of their host, however, their composition and functions remain only partially characterized, especially across microalgal phyla. In this study, a natural seawater microbiome was introduced to three distinct, axenic species of microalgae, the haptophyte Isochrysis galbana, the chlorophyte Tetraselmis suecica, and the diatom Conticribra weissflogii (previously Thalassiosira), and its divergence and assembly under constant illumination was monitored over 49 days using 16S rRNA amplicon and metagenomic analyses. The microbiomes had a high degree of host specificity in terms of taxonomic composition and potential functions, including CAZymes profiles. Rhodobacteraceae and Flavobacteriaceae families were abundant across all microalgal hosts, but I. galbana microbiomes diverged further from T. suecica and C. weissflogii microbiomes. I. galbana microbiomes had a much higher relative abundance of Flavobacteriaceae, whereas the two other algal microbiomes had higher relative abundances of Rhodobacteraceae. This could be due to the bacterivorous mixotrophic nature of I. galbana affecting the carbohydrate composition available to the microbiomes, which was supported by the CAZymes profile of I. galbana microbiomes diverging further from those of T. suecica and C. weissflogii microbiomes. Finally, the presence of denitrification and other anaerobic pathways was found exclusively in the microbiomes of C. weissflogii, which we speculate could be a result of anoxic microenvironments forming in aggregates formed by this diatom during the experiment. These results underline the significant role of the microalgal host species on microbiome composition and functional profiles along with other factors, such as the trophic mode of the microalgal host.

IMPORTANCE

As the main primary producers of the oceans, microalgae serve as cornerstones of the ecosystems they are part of. Additionally, they are increasingly used for biotechnological purposes such as the production of nutraceuticals, pigments, and antioxidants. Since the bacterial microbiomes of microalgae can affect their hosts in beneficial and detrimental ways, understanding these microbiomes is crucial to both the ecological and applied roles of microalgae. The present study advances the understanding of microalgal microbiome assembly, composition, and functionality across microalgal phyla, which may inform the modeling and engineering of microalgal microbiomes for biotechnological purposes.

Understanding phycosomal dynamics to improve industrial microalgae cultivation

Algal-bacterial interactions are ubiquitous in both natural and industrial systems, and the characterization of these interactions has been reinvigorated by potential applications in biosystem productivity. Different growth conditions can be used for operational functions, such as the use of low-quality water or high pH/alkalinity, and the altered operating conditions likely constrain microbial community structure and function in unique ways. However, research is necessary to better understand whether consortia can be designed to improve the productivity, processing, and sustainability of industrial-scale cultivations through different controls that can constrain microbial interactions for maximal light-driven outputs. The review highlights current knowledge and gaps for relevant operating conditions, as well as suggestions for near-term and longer-term improvements for large-scale cultivation and polyculture engineering.

Cryptic bacterial pathogens of diatoms peak during senescence of a winter diatom bloom

Diatoms are globally abundant microalgae that form extensive blooms in aquatic ecosystems. Certain bacteria behave antagonistically towards diatoms, killing or inhibiting their growth. Despite their crucial implications to diatom blooms and population health, knowledge of diatom antagonists in the environment is fundamentally lacking. We report systematic characterisation of the diversity and seasonal dynamics of bacterial antagonists of diatoms via plaque assay sampling in the Western English Channel (WEC), where diatoms frequently bloom. Unexpectedly, peaks in detection did not occur during characteristic spring diatom blooms, but coincided with a winter bloom of Coscinodiscus, suggesting that these bacteria likely influence distinct diatom host populations. We isolated multiple bacterial antagonists, spanning 4 classes and 10 bacterial orders. Notably, a diatom attaching Roseobacter Ponticoccus alexandrii was isolated multiple times, indicative of a persistent environmental presence. Moreover, many isolates had no prior reports of antagonistic activity towards diatoms. We verified diatom growth inhibitory effects of eight isolates. In all cases tested, these effects were activated by pre-exposure to diatom organic matter. Discovery of widespread 'cryptic' antagonistic activity indicates that bacterial pathogenicity towards diatoms is more prevalent than previously recognised. Finally, examination of the global biogeography of WEC antagonists revealed co-occurrence patterns with diatom host populations in marine waters globally.

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.

Temporal variability of microbiome in the different plankton hosts revealed distinct environmental persistence of Vibrio parahaemolyticus in shrimp farms

Plankton-bacteria interactions may play essential roles in maintaining the persistence of pathogenic Vibrio spp. However, the actual plankton host of the toxigenic Vibrio parahaemolyticus that harbors thermostable direct hemolysin (TDH) and TDH-related hemolysin (TRH) remains unclear. To answer this question, we measured the abundance of toxigenic and nontoxigenic Vibrio parahaemolyticus in different types of plankton by most probable number (MPN)-PCR. We next investigated the dynamics of the microbiomes of rearing water, copepods, Chlorella, four predominant diatom genera (Nitzschia, Melosira, Skeletonema and Chaetoceros) and the gut of the shrimp in two recirculated shrimp farming systems from April to September using high-throughput 16 S rRNA amplicon sequencing. The survival of trh-positive and trh-negative V. parahaemolyticus in seawater and different plankton hosts was examined under low temperature and starvation conditions. The results showed that copepods harbored the highest proportion of trh-positive V. parahaemolyticus, followed by diatoms. Chitinous diatoms (CD) harbored a high proportion of Vibrionaceae, of which a high abundance of V. parahaemolyticus was found in summer. In contrast, Vibrio spp. is rarely found in Chlorella and nonchitinous diatoms. Taxon-specific associations were also observed, including a relatively high abundance of Vibrio and Halodesulfovibrio on copepods and covariation of Aeromonas and Bacillus inside the Chlorella. The survival assays showed that, in comparison to trh-negative V. parahaemolyticus, trh-positive V. parahaemolyticus showed better survival in copepods and CD under starvation conditions and maintained high persistence in the above hosts at low temperature. In conclusion, the results herein suggested that chitinous plankton might provide protection for V. parahaemolyticus, especially trh-positive V. parahaemolyticus, and improve their persistence under harsh conditions. Our study provided in-depth insights into the persistence of V. parahaemolyticus in the environment, which would promote targeted disease prevention measures.

Single-cell isotope tracing reveals functional guilds of bacteria associated with the diatom Phaeodactylum tricornutum

Bacterial remineralization of algal organic matter fuels algal growth but is rarely quantified. Consequently, we cannot currently predict whether some bacterial taxa may provide more remineralized nutrients to algae than others. Here, we quantified bacterial incorporation of algal-derived complex dissolved organic carbon and nitrogen and algal incorporation of remineralized carbon and nitrogen in fifteen bacterial co-cultures growing with the diatom Phaeodactylum tricornutum at the single-cell level using isotope tracing and nanoSIMS. We found unexpected strain-to-strain and cell-to-cell variability in net carbon and nitrogen incorporation, including non-ubiquitous complex organic nitrogen utilization and remineralization. We used these data to identify three distinct functional guilds of metabolic interactions, which we termed macromolecule remineralizers, macromolecule users, and small-molecule users, the latter exhibiting efficient growth under low carbon availability. The functional guilds were not linked to phylogeny and could not be elucidated strictly from metabolic capacity as predicted by comparative genomics, highlighting the need for direct activity-based measurements in ecological studies of microbial metabolic interactions.

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

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

Eliminating the ecological hazards of Heterosigma akashiwo bloom by a microbial algicide: removal of nitrite contamination, redirection of carbon flow and restoration of metabolic generalists

Harmful algal blooms (HABs) attracted much attention due to their extensive ecological hazards and the increasing influences on global biogeochemical cycles with the intensification of human impact and global warming. Lysing algal cells with species-specific microbial algicide seemed to be promising to eliminate HABs, but the potential ecotoxicity was rarely studied. In this study, microcosms simulating Heterosigma akashiwo blooms were established to reveal the influences of a microbial algicide from Streptomyces sp. U3 on the biological, physicochemical parameters and bacterial community. The results showed that H. akashiwo bloom accumulated nitrite to a lethal dose, produced bio-labile DOM with widespread influences and enriched pathogenic Coxiella to a high abundance. Lysing H. akashiwo cells by microbial algicide induced a bacterial bloom, eliminated nitrite contamination, enhanced the recalcitrance of DOM, and restored bacterial population from a Gammaproteobacteria-dominant community during bloom back to an Alphaproteobacteria-dominant community similar to the non-bloom seawater. Succession of bacterial genera further suggested that the variation from algal exudates to lysates promoted the restoration of metabolic generalists, which redirected the carbon flow to a less ecologically impactive path. This study revealed the benefits of using microbial algicide to remediate the ecological hazards of HABs, which provided references for future application.

Microbiomes of bloom-forming Phaeocystis algae are stable and consistently recruited, with both symbiotic and opportunistic modes

Phaeocystis is a cosmopolitan, bloom-forming phytoplankton genus that contributes significantly to global carbon and sulfur cycles. During blooms, Phaeocystis species produce large carbon-rich colonies, creating a unique interface for bacterial interactions. While bacteria are known to interact with phytoplankton-e.g., they promote growth by producing phytohormones and vitamins-such interactions have not been shown for Phaeocystis. Therefore, we investigated the composition and function of P. globosa microbiomes. Specifically, we tested whether microbiome compositions are consistent across individual colonies from four P. globosa strains, whether similar microbiomes are re-recruited after antibiotic treatment, and how microbiomes affect P. globosa growth under limiting conditions. Results illuminated a core colonial P. globosa microbiome-including bacteria from the orders Alteromonadales, Burkholderiales, and Rhizobiales-that was re-recruited after microbiome disruption. Consistent microbiome composition and recruitment is indicative that P. globosa microbiomes are stable-state systems undergoing deterministic community assembly and suggests there are specific, beneficial interactions between Phaeocystis and bacteria. Growth experiments with axenic and nonaxenic cultures demonstrated that microbiomes allowed continued growth when B-vitamins were withheld, but that microbiomes accelerated culture collapse when nitrogen was withheld. In sum, this study reveals symbiotic and opportunistic interactions between Phaeocystis colonies and microbiome bacteria that could influence large-scale phytoplankton bloom dynamics and biogeochemical cycles.

Water masses and their associated temperature and cross-domain biotic factors co-shape upwelling microbial communities

Disentangling the drivers and mechanisms that shape microbial communities in a river-influenced coastal upwelling system requires considering a hydrologic dimension that can drive both deterministic and stochastic community assembly by generating hydrological heterogeneity and dispersal events. Additionally, ubiquitous and complex microbial interactions can play a significant role in community structuring. However, how the hydrology, biotic, and abiotic factors collectively shape microbial distribution in the hydrologically complicated river plume-upwelling coupling system remains unknown. Through underway sampling and daily observations, we employed 16S and 18S ribosomal RNA sequencing to disentangle drivers and mechanisms shaping the protist-bacteria microbiota in a river-influenced coastal upwelling system. Our findings indicate that the composition of microbial communities was water mass specific. Collectively, water mass, local water chemistry (mostly temperature) and biotic interaction (mostly cross-domain biotic interaction) shaped the protistan-bacterial communities. In comparison to protists, bacteria were more influenced by abiotic factors such as temperature than by cross-domain biotic factors, implying a stronger coupling of geochemical cycles. Both deterministic and stochastic processes had an effect on the distribution of microbial communities, but deterministic processes were more important for bacteria and were especially pronounced for upwelling communities. The co-occurrence network revealed strong associations between the protistan assemblages Orchrophyta and Ciliophora and the bacterial assemblages Alphaproteobacteria, Deltaproteobacteria, and Bacteroidetes, which may reflect predation and mutualism interactions. Overall, this study emphasizes the importance of taking water masses, temperature and domains of life into account when seeking to understand the drivers and assemblies of protist-bacteria microbiome dynamics in coastal upwelling systems, which is especially true given the complex and dynamic nature of the coastal ecosystem.

Three Novel Bacteria Associated with Two Centric Diatom Species from the Mediterranean Sea, Thalassiosira rotula and Skeletonema marinoi

Diatoms are a successful group of microalgae at the base of the marine food web. For hundreds of millions of years, they have shared common habitats with bacteria, which favored the onset of interactions at different levels, potentially driving the synthesis of biologically active molecules. To unveil their presence, we sequenced the genomes of bacteria associated with the centric diatom Thalassiosira rotula from the Gulf of Naples. Annotation of the metagenome and its analysis allowed the reconstruction of three bacterial genomes that belong to currently undescribed species. Their investigation showed the existence of novel gene clusters coding for new polyketide molecules, antibiotics, antibiotic-resistance genes and an ectoine production pathway. Real-time PCR was used to investigate the association of these bacteria with three different diatom clones and revealed their preference for T. rotula FE80 and Skeletonema marinoi FE7, but not S. marinoi FE60 from the North Adriatic Sea. Additionally, we demonstrate that although all three bacteria could be detected in the culture supernatant (free-living), their number is up to 45 times higher in the cell associated fraction, suggesting a close association between these bacteria and their host. We demonstrate that axenic cultures of T. rotula are unable to grow in medium with low salinity (<28 ppt NaCl) whereas xenic cultures can tolerate up to 40 ppt NaCl with concomitant ectoine production, likely by the associated bacteria.

Advances in the use of microalgal-bacterial consortia for wastewater treatment: Community structures, interactions, economic resource reclamation, and study techniques

The rise in living standards has generated a demand for higher aquatic environmental quality. The microalgal community and the surrounding organic molecules, environmental factors, and microorganisms, such as bacteria, are together defined as the phycosphere. The bacteria in the phycosphere can form consortia with microalgae through various forms of interaction. The study of the species in these consortia and their relative proportions is of great significance in determining the species and strains of stable algae that can be used in sewage treatment. This article summarizes the following topics: the interactions between microalgae and bacteria that are required to establish consortia; how symbiosis between algae and bacteria is established; microalgal competition with bacteria through inhibition and anti-inhibition strategies; the influence of environmental factors on microalgal-bacterial aggregates, such as illumination conditions, pH, dissolved oxygen, temperature, and nutrient levels; the application of algal-bacterial aggregates to enhance biomass production and nutrient reuse; and techniques for studying the community structure and interactions of algal-bacterial consortia, such as microscopy, flow cytometry, and omics. PRACTITIONER POINTS: Community structures in microalgal-bacterial consortia in wastewater treatment. Interactions between algae and bacteria in wastewater treatment. Effects of ecological factors on the algal-bacterial community in wastewater treatment. Economically recycling resources from algal-bacterial consortia based on wastewater. Technologies for studying microalgal-bacterial consortia in wastewater treatment.

Evidence of Interdomain Ammonium Cross-Feeding From Methylamine- and Glycine Betaine-Degrading Rhodobacteraceae to Diatoms as a Widespread Interaction in the Marine Phycosphere

Dissolved organic nitrogen (DON) compounds such as methylamines (MAs) and glycine betaine (GBT) occur at detectable concentrations in marine habitats and are also produced and released by microalgae. For many marine bacteria, these DON compounds can serve as carbon, energy, and nitrogen sources, but microalgae usually cannot metabolize them. Interestingly though, it was previously shown that Donghicola sp. strain KarMa—a member of the marine Rhodobacteraceae—can cross-feed ammonium such that the ammonium it produces upon degrading monomethylamine (MMA) then serves as nitrogen source for the diatom Phaeodactylum tricornutum; thus, these organisms form a mutual metabolic interaction under photoautotrophic conditions. In the present study, we investigated whether this interaction plays a broader role in bacteria–diatom interactions in general. Results showed that cross-feeding between strain KarMa and P. tricornutum was also possible with di- and trimethylamine as well as with GBT. Further, cross-feeding of strain KarMa was also observed in cocultures with the diatoms Amphora coffeaeformis and Thalassiosira pseudonana with MMA as the sole nitrogen source. Regarding cross-feeding involving other Rhodobacteraceae strains, the in silico analysis of MA and GBT degradation pathways indicated that algae-associated Rhodobacteraceae-type strains likely interact with P. tricornutum in a similar manner as the strain KarMa does. For these types of strains (such as Celeribacter halophilus, Roseobacter denitrificans, Roseovarius indicus, Ruegeria pomeroyi, and Sulfitobacter noctilucicola), ammonium cross-feeding after methylamine degradation showed species-specific patterns, whereas bacterial GBT degradation always led to diatom growth. Overall, the degradation of DON compounds by the Rhodobacteraceae family and the subsequent cross-feeding of ammonium may represent a widespread, organism-specific, and regulated metabolic interaction for establishing and stabilizing associations with photoautotrophic diatoms in the oceans.

Metatranscriptomic Analysis of Oil-Exposed Seawater Bacterial Communities Archived by an Environmental Sample Processor (ESP)

The use of natural marine bacteria as "oil sensors" for the detection of pollution events can be suggested as a novel way of monitoring oil occurrence at sea. Nucleic acid-based devices generically called genosensors are emerging as potentially promising tools for in situ detection of specific microbial marker genes suited for that purpose. Functional marker genes are particularly interesting as targets for oil-related genosensing but their identification remains a challenge. Here, seawater samples, collected in tanks with oil addition mimicking a realistic oil spill scenario, were filtered and archived by the Environmental Sample Processor (ESP), a fully robotized genosensor, and the samples were then used for post-retrieval metatranscriptomic analysis. After extraction, RNA from ESP-archived samples at start, Day 4 and Day 7 of the experiment was used for sequencing. Metatranscriptomics revealed that several KEGG pathways were significantly enriched in samples exposed to oil. However, these pathways were highly expressed also in the non-oil-exposed water samples, most likely as a result of the release of natural organic matter from decaying phytoplankton. Temporary peaks of aliphatic alcohol and aldehyde dehydrogenases and monoaromatic ring-degrading enzymes (e.g., ben, box, and dmp clusters) were observed on Day 4 in both control and oil-exposed and non-exposed tanks. Few alkane 1-monooxygenase genes were upregulated on oil, mostly transcribed by families Porticoccaceae and Rhodobacteraceae, together with aromatic ring-hydroxylating dioxygenases, mostly transcribed by Rhodobacteraceae. Few transcripts from obligate hydrocarbonoclastic genera of Alcanivorax, Oleispira and Cycloclasticus were significantly enriched in the oil-treated exposed tank in comparison to control the non-exposed tank, and these were mostly transporters and genes involved in nitrogen and phosphorous acquisition. This study highlights the importance of seasonality, i.e., phytoplankton occurrence and senescence leading to organic compound release which can be used preferentially by bacteria over oil compounds, delaying the latter process. As a result, such seasonal effect can reduce the sensitivity of genosensing tools employing bacterial functional genes to sense oil. A better understanding of the use of natural organic matter by bacteria involved in oil-biodegradation is needed to develop an array of functional markers enabling the rapid and specific in situ detection of anthropogenic pollution.

Algae-bacteria interactions that balance the planktonic microbiome

Phytoplankton communities within the photic zones of the oceans and lakes are characterised by highly complex assemblages of unicellular microalgae and associated bacteria. The interconnected evolutionary history of algae and bacteria allowed the formation of a wide spectrum of associations defined by orchestrated nutrient exchange, mutual support with growth factors, quorum sensing mediation, and episodic killing of the partners to obtain more resources. In this review, we discuss how these cross-kingdom interactions shape plankton communities that undergo annual, seasonal switching between alternative states with balanced multispecies consortia. We illustrate how these microscopic interactions can have consequences that scale up to influence global element cycling.

Attachment between heterotrophic bacteria and microalgae influences symbiotic microscale interactions

The surface and surroundings of microalgal cells (phycosphere) are critical interaction zones but have been difficult to functionally interrogate due to methodological limitations. We examined effects of phycosphere-associated bacteria for two biofuel-relevant microalgal species (Phaeodactylum tricornutum and Nannochloropsis salina) using stable isotope tracing and high spatial resolution mass spectrometry imaging (NanoSIMS) to quantify elemental exchanges at the single-cell level. Each algal species responded differently to bacterial attachment. In P. tricornutum, a high percentage of cells had attached bacteria (92%-98%, up to eight bacteria per alga) and fixed 64% more carbon with attached bacteria compared to axenic cells. In contrast, N. salina cells were less commonly associated with bacteria (42%-63%), harboured fewer bacteria per alga, and fixed 10% more carbon without attached bacteria compared to axenic cells. An uncultivated bacterium related to Haliscomenobacter sp. was identified as an effective mutualist; it increased carbon fixation when attached to P. tricornutum and incorporated 71% more algal-fixed carbon relative to other bacteria. Our results illustrate how phylogenetic identity and physical location of bacteria and algae facilitate diverse metabolic responses. Phycosphere-mediated, mutualistic chemical exchanges between autotrophs and heterotrophs may be a fruitful means to increase microalgal productivity for applied engineering efforts.

Draft Genome Sequence of Donghicola sp. Strain KarMa, a Model Organism for Monomethylamine-Degrading Nonmethylotrophic Bacteria

The C₁-compound monomethylamine can serve as a nitrogen, carbon, and energy source for heterotrophic bacteria. The marine alphaproteobacterium Donghicola sp. strain KarMa can use monomethylamine as a source only for nitrogen and not for carbon. Its draft genome sequence is presented here and reveals putative gene clusters for the methylamine dehydrogenase and the N-methylglutamate pathways for monomethylamine metabolism.