A Bacterial Quorum-Sensing Precursor Induces Mortality in the Marine Coccolithophore, Emiliania huxleyi

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.

Succession of microbial community composition and secondary metabolism during marine biofilm development

In nature, secondary metabolites mediate interactions between microorganisms residing in complex microbial communities. However, the degree to which community dynamics can be linked to secondary metabolite potential remains largely unknown. In this study, we address the relationship between community succession and secondary metabolism variation. We used 16S and 18S rRNA gene and adenylation domain amplicon sequencing, genome-resolved metagenomics, and untargeted metabolomics to track the taxons, biosynthetic gene clusters, and metabolome dynamics in situ of microorganisms during marine biofilm succession over 113 days. Two phases were identified during the community succession, with a clear shift around Day 29, where the alkaloid secondary metabolites, pseudanes, were also detected. The microbial secondary metabolite potential changed between the phases, and only a few community members, including Myxococotta spp., were responsible for the majority of the biosynthetic gene cluster potential in the early succession phase. In the late phase, bryozoans and benthic copepods were detected, and the microbial nonribosomal peptide potential drastically decreased in association with a reduction in the relative abundance of the prolific secondary metabolite producers. Conclusively, this study provides evidence that the early succession of the marine biofilm community favors prokaryotes with high nonribosomal peptide synthetase potential. In contrast, the late succession is dominated by multicellular eukaryotes and a reduction in bacterial nonribosomal peptide synthetase potential.

A bacterial quorum sensing signal is a potent inhibitor of de novo pyrimidine biosynthesis in the globally abundant Emiliania huxleyi

Interactions between marine phytoplankton, viruses, and bacteria drive biogeochemical cycling, shape marine trophic structures, and impact global climate. Microbially produced compounds have emerged as key players in influencing eukaryotic organismal physiology, and in turn, remodel microbial community structure. This work aimed to reveal the molecular mechanism by which the bacterial quorum sensing molecule 2-heptyl-4-quinolone (HHQ), produced by the marine gammaproteobacterium Pseudoalteromonas spp., arrests cell division and confers protection from virus-induced mortality in the bloom-forming coccolithophore Emiliania huxleyi. Previous work has established alkylquinolones as inhibitors of dihydroorotate dehydrogenase (DHODH), a fundamental enzyme catalyzing the fourth step in pyrimidine biosynthesis and a potential antiviral drug target. An N-terminally truncated version of E. huxleyi DHODH was heterologously expressed in E. coli, purified, and kinetically characterized. Here, we show HHQ is a potent inhibitor (Ki of 2.3 nM) of E. huxleyi DHODH. E. huxleyi cells exposed to brequinar, the canonical human DHODH inhibitor, experienced immediate, yet reversible cellular arrest, an effect which mirrors HHQ-induced cellular stasis previously observed. However, brequinar treatment lacked other notable effects observed in HHQ-exposed E. huxleyi including significant changes in cell size, chlorophyll fluorescence, and protection from virus-induced lysis, indicating HHQ has additional as yet undiscovered physiological targets. Together, these results suggest a novel and intricate role of bacterial quorum sensing molecules in tripartite interdomain interactions in marine ecosystems, opening new avenues for exploring the role of microbial chemical signaling in algal bloom regulation and host-pathogen dynamics.

Abundant Sulfitobacter marine bacteria protect Emiliania huxleyi algae from pathogenic bacteria

Emiliania huxleyi is a unicellular micro-alga that forms massive oceanic blooms and plays key roles in global biogeochemical cycles. Mounting studies demonstrate various stimulatory and inhibitory influences that bacteria have on the E. huxleyi physiology. To investigate these algal-bacterial interactions, laboratory co-cultures have been established by us and by others. Owing to these co-cultures, various mechanisms of algal-bacterial interactions have been revealed, many involving bacterial pathogenicity towards algae. However, co-cultures represent a significantly simplified system, lacking the complexity of bacterial communities. In order to investigate bacterial pathogenicity within an ecologically relevant context, it becomes imperative to enhance the microbial complexity of co-culture setups. Phaeobacter inhibens bacteria are known pathogens that cause the death of E. huxleyi algae in laboratory co-culture systems. The bacteria depend on algal exudates for growth, but when algae senesce, bacteria switch to a pathogenic state and induce algal death. Here we investigate whether P. inhibens bacteria can induce algal death in the presence of a complex bacterial community. We show that an E. huxleyi-associated bacterial community protects the alga from the pathogen, although the pathogen occurs within the community. To study how the bacterial community regulates pathogenicity, we reduced the complex bacterial community to a five-member synthetic community (syncom). The syncom is comprised of a single algal host and five isolated bacterial species, which represent major bacterial groups that are naturally associated with E. huxleyi. We discovered that a single bacterial species in the reduced community, Sulfitobacter pontiacus, protects the alga from the pathogen. We further found that algal protection from P. inhibens pathogenicity is a shared trait among several Sulfitobacter species. Algal protection by bacteria might be a common phenomenon with ecological significance, which is overlooked in reduced co-culture systems.

Temporal variability in the growth-enhancing effects of different bacteria within the microbiome of the diatom Actinocyclus sp

Reciprocal metabolite exchanges between diatoms and bacteria can enhance the growth of both partners and therefore fundamentally influence aquatic ecosystem productivity. Here, we examined the growth-promoting capabilities of 15 different bacterial isolates from the bacterial community associated with the marine diatom Actinocyclus sp. and investigated the magnitude and timing of their effect on the growth of this diatom. In the presence of its microbiome, Actinocyclus sp. growth was significantly enhanced relative to axenic cultures. Co-culture with each of the 15 bacterial isolates examined here (seven Rhodobacteraceae, four Vibrionaceae, two Pseudoalteromonadaceae, one Oceanospirillaceae and one Alteromonadaceae) increased the growth of the diatom host, with four isolates inducing rates of growth that were similar to those delivered by the diatom's full microbiome. However, the timing and duration of this effect differed between the different bacteria tested. Indeed, one Rhodobacteraceae and one Alteromonadaceae enhanced Actinocyclus sp. cell numbers between days 0-6 after co-incubation, five other Rhodobacteraceae promoted diatom cell numbers the most between days 8-12, whilst four Vibrionaceae, one Oceanospirillaceae and one Rhodobacteraceae enhanced Actinocyclus sp. cell abundance between days 14-16. These results are indicative of a succession of the growth-enhancing effects delivered by diverse bacteria throughout the Actinocyclus sp. life cycle, which will likely deliver sustained growth benefits to the diatom when its full microbiome is present.

A review on microalgal-bacterial co-culture: The multifaceted role of beneficial bacteria towards enhancement of microalgal metabolite production

Mass microalgal-bacterial co-cultures have come to the fore of applied physiological research, in particularly for the optimization of high-value metabolite from microalgae. These co-cultures rely on the existence of a phycosphere which harbors unique cross-kingdom associations that are a prerequisite for the cooperative interactions. However, detailed mechanisms underpinning the beneficial bacterial effects onto microalgal growth and metabolic production are rather limited at the moment. Hence, the main purpose of this review is to shed light on how bacteria fuels microalgal metabolism or vice versa during mutualistic interactions, building upon the phycosphere which is a hotspot for chemical exchange. Nutrients exchange and signal transduction between two not only increase the algal productivity, but also facilitate in the degradation of bio-products and elevate the host defense ability. Main chemical mediators such as photosynthetic oxygen, N-acyl-homoserine lactone, siderophore and vitamin B12 were identified to elucidate beneficial cascading effects from the bacteria towards microalgal metabolites. In terms of applications, the enhancement of soluble microalgal metabolites is often associated with bacteria-mediated cell autolysis while bacterial bio-flocculants can aid in microalgal biomass harvesting. In addition, this review goes in depth into the discussion on enzyme-based communication via metabolic engineering such as gene modification, cellular metabolic pathway fine-tuning, over expression of target enzymes, and diversion of flux toward key metabolites. Furthermore, possible challenges and recommendations aimed at stimulating microalgal metabolite production are outlined. As more evidence emerges regarding the multifaceted role of beneficial bacteria, it will be crucial to incorporate these findings into the development of algal biotechnology.

Aerobic bacteria produce nitric oxide via denitrification and promote algal population collapse

Microbial interactions govern marine biogeochemistry. These interactions are generally considered to rely on exchange of organic molecules. Here we report on a novel inorganic route of microbial communication, showing that algal-bacterial interactions between Phaeobacter inhibens bacteria and Gephyrocapsa huxleyi algae are mediated through inorganic nitrogen exchange. Under oxygen-rich conditions, aerobic bacteria reduce algal-secreted nitrite to nitric oxide (NO) through denitrification, a well-studied anaerobic respiratory mechanism. The bacterial NO is involved in triggering a cascade in algae akin to programmed cell death. During death, algae further generate NO, thereby propagating the signal in the algal population. Eventually, the algal population collapses, similar to the sudden demise of oceanic algal blooms. Our study suggests that the exchange of inorganic nitrogen species in oxygenated environments is a potentially significant route of microbial communication within and across kingdoms.

Malformation in coccolithophores in low pH waters: evidences from the eastern Arabian Sea

Oceanic calcifying plankton such as coccolithophores is expected to exhibit sensitivity to climate change stressors such as warming and acidification. Observational studies on coccolithophore communities along with carbonate chemistry provide important perceptions of possible adaptations of these organisms to ocean acidification. However, this phytoplankton group remains one of the least studied in the northern Indian Ocean. In 2017, the biogeochemistry group at the Council for Scientific and Industrial Research-National Institute of Oceanography (CSIR-NIO) initiated a coccolithophore monitoring study in the eastern Arabian Sea (EAS). Here, we document for the first time a detailed spatial and seasonal distribution of coccolithophores and their controlling factors from the EAS, which is a well-known source of CO₂ to the atmosphere. To infer the seasonality, data collected at three transects (Goa, Mangalore, and Kochi) during the Southwest Monsoon (SWM) of 2018 was compared with that of the late SWM of 2017. Apart from this, the abundance of coccolithophores was studied at the Candolim Time Series (CaTS) transect, off Goa during the Northeast Monsoon (NEM). The most abundant coccolithophore species found in the study region was Gephyrocapsa oceanica. A high abundance of G. oceanica (1800 × 10³cells L^-1) was observed at the Mangalore transect during the late SWM despite experiencing low pH and can be linked to nitrogen availability. The high abundance of G. oceanica at Mangalore was associated with high dimethylsulphide (DMS). Particulate inorganic carbon (PIC) and scattering coefficient retrieved from satellites also indicated a high abundance of coccolithophores off Mangalore during the late SWM of 2017. Interestingly, G. oceanica showed malformation during the late SWM in low pH waters. Malformation in coccolithophores could have a far-reaching impact on the settling fluxes of organic matter and also on the emissions of climatically important gases such as DMS and CO₂, thus influencing atmospheric chemistry. The satellite data for PIC in the EAS indicates a high abundance of coccolithophore in recent years, especially during the warm El Nino years (2015 and 2018). This warrants the need for a better assessment of the fate of coccolithophores in high-CO₂ and warmer oceans.

Coccolith Sr/Ca is a robust temperature and growth rate indicator that withstands dynamic microbial interactions

Coccolithophores are a diverse group of calcifying microalgae that have left a prominent fossil record on Earth. Various coccolithophore relics, both organic and inorganic, serve as proxies for reconstruction of past oceanic conditions. Emiliania huxleyi is the most widely distributed representative of the coccolithophores in modern oceans and is known to engage in dynamic interactions with bacteria. Algal-bacterial interactions influence various aspects of algal physiology and alter algal alkenone unsaturation (U^K'₃₇ ), a frequently used organic coccolithophore-derived paleo-temperature proxy. Whether algal-bacterial interactions influence inorganic coccolithophore-derived paleo-proxies is yet unknown. A commonly used inorganic proxy for past productivity and sea surface temperature is the Sr/Ca ratio of the coccolith calcite. Interestingly, during interactions between bacteria and a population of calcifying algae, bacteria were shown to physically attach only to non-calcified algal cells, suggesting an influence on algal calcification. In this study, we explore the effects of algal-bacterial interactions on calcification and coccolith Sr/Ca ratios. We find that while bacteria attach only to non-calcified algal cells, coccolith cell coverage and overall calcite production in algal populations with and without bacteria is similar. Furthermore, we find that Sr/Ca values are impacted only by water temperature and algal growth rate, regardless of bacterial influences on algal physiology. Our observations reinforce the robustness of coccolith Sr/Ca ratios as a paleo-proxy independent of microbial interactions and highlight a fundamental difference between organic and inorganic paleo-proxies.

Algicidal Bacteria: A Review of Current Knowledge and Applications to Control Harmful Algal Blooms

Interactions between bacteria and phytoplankton in aqueous ecosystems are both complex and dynamic, with associations that range from mutualism to parasitism. This review focuses on algicidal interactions, in which bacteria are capable of controlling algal growth through physical association or the production of algicidal compounds. While there is some evidence for bacterial control of algal growth in the field, our understanding of these interactions is largely based on laboratory culture experiments. Here, the range of these algicidal interactions is discussed, including specificity of bacterial control, mechanisms for activity, and insights into the chemical and biochemical analysis of these interactions. The development of algicidal bacteria or compounds derived from bacteria for control of harmful algal blooms is reviewed with a focus on environmentally friendly or sustainable methods of application. Potential avenues for future research and further development and application of bacterial algicides for the control of algal blooms are presented.

Microbial metabolites in the marine carbon cycle

One-quarter of photosynthesis-derived carbon on Earth rapidly cycles through a set of short-lived seawater metabolites that are generated from the activities of marine phytoplankton, bacteria, grazers and viruses. Here we discuss the sources of microbial metabolites in the surface ocean, their roles in ecology and biogeochemistry, and approaches that can be used to analyse them from chemistry, biology, modelling and data science. Although microbial-derived metabolites account for only a minor fraction of the total reservoir of marine dissolved organic carbon, their flux and fate underpins the central role of the ocean in sustaining life on Earth.

Resolving the microalgal gene landscape at the strain level: A novel hybrid transcriptome of Emiliania huxleyi CCMP3266

Microalgae are key ecological players with a complex evolutionary history. Genomic diversity, in addition to limited availability of high-quality genomes, challenge studies that aim to elucidate molecular mechanisms underlying microalgal ecophysiology. Here, we present a novel and comprehensive transcriptomic hybrid approach to generate a reference for genetic analyses, and resolve the microalgal gene landscape at the strain level. The approach is demonstrated for a strain of the coccolithophore microalga Emiliania huxleyi, which is a species complex with considerable genome variability. The investigated strain is commonly studied as a model for algal-bacterial interactions, and was therefore sequenced in the presence of bacteria to elicit the expression of interaction-relevant genes. We applied complementary PacBio Iso-Seq full-length cDNA, and poly(A)-independent Illumina total RNA sequencing, which resulted in a de novo assembled, near complete hybrid transcriptome. In particular, hybrid sequencing improved the reconstruction of long transcripts and increased the recovery of full-length transcript isoforms. To use the resulting hybrid transcriptome as a reference for genetic analyses, we demonstrate a method that collapses the transcriptome into a genome-like dataset, termed "synthetic genome" (sGenome). We used the sGenome as a reference to visually confirm the robustness of the CCMP3266 gene assembly, to conduct differential gene expression analysis, and to characterize novel E. huxleyi genes. The newly-identified genes contribute to our understanding of E. huxleyi genome diversification, and are predicted to play a role in microbial interactions. Our transcriptomic toolkit can be implemented in various microalgae to facilitate mechanistic studies on microalgal diversity and ecology. Importance Microalgae are key players in the ecology and biogeochemistry of our oceans. Efforts to implement genomic and transcriptomic tools in laboratory studies involving microalgae suffer from the lack of published genomes. In the case of coccolithophore microalgae, the problem has long been recognized; the model species Emiliania huxleyi is a species complex with genomes composed of a core, and a large variable portion. To study the role of the variable portion in niche adaptation, and specifically in microbial interactions, strain-specific genetic information is required. Here we present a novel transcriptomic hybrid approach, and generated strain-specific genome-like information. We demonstrate our approach on an E. huxleyi strain that is co-cultivated with bacteria. By constructing a "synthetic genome", we generated comprehensive gene annotations that enabled accurate analyses of gene expression patterns. Importantly, we unveiled novel genes in the variable portion of E. huxleyi that play putative roles in microbial interactions.

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

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

Genomic signatures of Lake Erie bacteria suggest interaction in the Microcystis phycosphere

Microbial interactions in harmful algal bloom (HAB) communities have been examined in marine systems, but are poorly studied in fresh waters. To investigate HAB-microbe interactions, we isolated bacteria with close associations to bloom-forming cyanobacteria, Microcystis spp., during a 2017 bloom in the western basin of Lake Erie. The genomes of five isolates (Exiguobacterium sp. JMULE1, Enterobacter sp. JMULE2, Deinococcus sp. JMULE3, Paenibacillus sp. JMULE4, and Acidovorax sp. JMULE5.) were sequenced on a PacBio Sequel system. These genomes ranged in size from 3.1 Mbp (Exiguobacterium sp. JMULE1) to 5.7 Mbp (Enterobacter sp. JMULE2). The genomes were analyzed for genes relating to critical metabolic functions, including nitrogen reduction and carbon utilization. All five of the sequenced genomes contained genes that could be used in potential signaling and nutrient exchange between the bacteria and cyanobacteria such as Microcystis. Gene expression signatures of algal-derived carbon utilization for two isolates were identified in Microcystis blooms in Lake Erie and Lake Tai (Taihu) at low levels, suggesting these organisms are active and may have a functional role during Microcystis blooms in aggregates, but were largely missing from whole water samples. These findings build on the growing evidence that the bacterial microbiome associated with bloom-forming algae have the functional potential to contribute to nutrient exchange within bloom communities and interact with important bloom formers like Microcystis.

How Do Quorum-Sensing Signals Mediate Algae-Bacteria Interactions?

Quorum sensing (QS) describes a process by which bacteria can sense the local cell density of their own species, thus enabling them to coordinate gene expression and physiological processes on a community-wide scale. Small molecules called autoinducers or QS signals, which act as intraspecies signals, mediate quorum sensing. As our knowledge of QS has progressed, so too has our understanding of the structural diversity of QS signals, along with the diversity of bacteria conducting QS and the range of ecosystems in which QS takes place. It is now also clear that QS signals are more than just intraspecies signals. QS signals mediate interactions between species of prokaryotes, and between prokaryotes and eukaryotes. In recent years, our understanding of QS signals as mediators of algae-bacteria interactions has advanced such that we are beginning to develop a mechanistic understanding of their effects. This review will summarize the recent efforts to understand how different classes of QS signals contribute to the interactions between planktonic microalgae and bacteria in our oceans, primarily N-acyl-homoserine lactones, their degradation products of tetramic acids, and 2-alkyl-4-quinolones. In particular, this review will discuss the ways in which QS signals alter microalgae growth and metabolism, namely as direct effectors of photosynthesis, regulators of the cell cycle, and as modulators of other algicidal mechanisms. Furthermore, the contribution of QS signals to nutrient acquisition is discussed, and finally, how microalgae can modulate these small molecules to dampen their effects.

Identification and analysis of the biological activity of the new strain of Pseudoalteromonas piscicida isolated from the hemal fluid of the bivalve Modiolus kurilensis (F. R. Bernard, 1983)

A cultivated form of bacteria (strain 2202) was isolated from the hemal fluid of the bivalve mollusk Modiolus kurilensis. Based on the set of data collected by genetic and physiological/biochemical analyses, the strain was identified as the species Pseudoalteromonas piscicida. Strain 2202 exhibits antimicrobial activity against Staphylococcus aureus, Candida albicans, and Bacillus subtilis but not against Escherichia coli and Pseudomonas aeruginosa. These activities characterize the behavior of strain 2202 as predator-like and classify it as a facultative predator. Being part of the normal microflora in the hemolymph of M. kurilensis, when external conditions change, strain 2202 shows features of opportunistic microflora. The strain 2202 exhibits selective toxicity towards larvae of various invertebrates: it impairs the early development of Mytilus edulis, but not of Strongylocentrotus nudus. Thus, the selective manner in which P. piscicida strains interact with various species of microorganisms and eukaryotes should be taken into consideration when using their biotechnological potential as a probiotic in aquaculture, source of antimicrobial substances, and factors that prevent fouling.

Bacterial Quorum-Sensing Signal Arrests Phytoplankton Cell Division and Impacts Virus-Induced Mortality

Bacteria and phytoplankton form close associations in the ocean that are driven by the exchange of chemical compounds. The bacterial signal 2-heptyl-4-quinolone (HHQ) slows phytoplankton growth; however, the mechanism responsible remains unknown.

Interactions between phytoplankton and heterotrophic bacteria fundamentally shape marine ecosystems by controlling primary production, structuring marine food webs, mediating carbon export, and influencing global climate. Phytoplankton-bacterium interactions are facilitated by secreted compounds; however, linking these chemical signals, their mechanisms of action, and their resultant ecological consequences remains a fundamental challenge. The bacterial quorum-sensing signal 2-heptyl-4-quinolone (HHQ) induces immediate, yet reversible, cellular stasis (no cell division or mortality) in the coccolithophore Emiliania huxleyi; however, the mechanism responsible remains unknown. Using transcriptomic and proteomic approaches in combination with diagnostic biochemical and fluorescent cell-based assays, we show that HHQ exposure leads to prolonged S-phase arrest in phytoplankton coincident with the accumulation of DNA damage and a lack of repair despite the induction of the DNA damage response (DDR). While this effect is reversible, HHQ-exposed phytoplankton were also protected from viral mortality, ascribing a new role of quorum-sensing signals in regulating multitrophic interactions. Furthermore, our data demonstrate that in situ measurements of HHQ coincide with areas of enhanced micro- and nanoplankton biomass. Our results suggest bacterial communication signals as emerging players that may be one of the contributing factors that help structure complex microbial communities throughout the ocean.

IMPORTANCE Bacteria and phytoplankton form close associations in the ocean that are driven by the exchange of chemical compounds. The bacterial signal 2-heptyl-4-quinolone (HHQ) slows phytoplankton growth; however, the mechanism responsible remains unknown. Here, we show that HHQ exposure leads to the accumulation of DNA damage in phytoplankton and prevents its repair. While this effect is reversible, HHQ-exposed phytoplankton are also relieved of viral mortality, elevating the ecological consequences of this complex interaction. Further results indicate that HHQ may target phytoplankton proteins involved in nucleotide biosynthesis and DNA repair, both of which are crucial targets for viral success. Our results support microbial cues as emerging players in marine ecosystems, providing a new mechanistic framework for how bacterial communication signals mediate interspecies and interkingdom behaviors.

Signal Synthase-Type versus Catabolic Monooxygenases: Retracing 3-Hydroxylation of 2-Alkylquinolones and Their N-Oxides by Pseudomonas aeruginosa and Other Pulmonary Pathogens

The multiple biological activities of 2-alkylquinolones (AQs) are crucial for virulence of Pseudomonas aeruginosa, conferring advantages during infection and in polymicrobial communities. Whereas 2-heptyl-3-hydroxyquinolin-4(1H)-one (the "Pseudomonas quinolone signal" [PQS]) is an important quorum sensing signal molecule, 2-alkyl-1-hydroxyquinolin-4(1H)-ones (also known as 2-alkyl-4-hydroxyquinoline N-oxides [AQNOs]) are antibiotics inhibiting respiration. Hydroxylation of the PQS precursor 2-heptylquinolin-4(1H)-one (HHQ) by the signal synthase PqsH boosts AQ quorum sensing. Remarkably, the same reaction, catalyzed by the ortholog AqdB, is used by Mycobacteroides abscessus to initiate degradation of AQs. The antibiotic 2-heptyl-1-hydroxyquinolin-4(1H)-one (HQNO) is hydroxylated by Staphylococcus aureus to the less toxic derivative PQS-N-oxide (PQS-NO), a reaction probably also catalyzed by a PqsH/AqdB ortholog. In this study, we provide a comparative analysis of four AQ 3-monooxygenases of different organisms. Due to the major impact of AQ/AQNO 3-hydroxylation on the biological activities of the compounds, we surmised adaptations on the enzymatic and/or physiological level to serve either the producer or target organisms. Our results indicate that all enzymes share similar features and are incapable of discriminating between AQs and AQNOs. PQS-NO, hence, occurs as a native metabolite of P. aeruginosa although the unfavorable AQNO 3-hydroxylation is minimized by export as shown for HQNO, involving at least one multidrug efflux pump. Moreover, M. abscessus is capable of degrading the AQNO heterocycle by concerted action of AqdB and dioxygenase AqdC. However, S. aureus and M. abscessus orthologs disfavor AQNOs despite their higher toxicity, suggesting that catalytic constraints restrict evolutionary adaptation and lead to the preference of non-N-oxide substrates by AQ 3-monooxygenases.IMPORTANCE Pseudomonas aeruginosa, Staphylococcus aureus, and Mycobacteroides abscessus are major players in bacterial chronic infections and particularly common colonizers of cystic fibrosis (CF) lung tissue. Whereas S. aureus is an early onset pathogen in CF, P. aeruginosa establishes at later stages. M. abscessus occurs at all stages but has a lower epidemiological incidence. The dynamics of how these pathogens interact can affect survival and therapeutic success. 2-Alkylquinolone (AQ) and 2-alkylhydroxyquinoline N-oxide (AQNO) production is a major factor of P. aeruginosa virulence. The 3-position of the AQ scaffold is critical, both for attenuation of AQ toxicity or degradation by competitors, as well as for full unfolding of quorum sensing. Despite lacking signaling functionality, AQNOs have the strongest impact on suppression of Gram-positives. Because evidence for 3-hydroxylation of AQNOs has been reported, it is desirable to understand the extent by which AQ 3-monooxygenases contribute to manipulation of AQ/AQNO equilibrium, resistance, and degradation.

Attenuation of quorum sensing mediated virulence factors production and biofilm formation in Pseudomonas aeruginosa PAO1 by Colletotrichum gloeosporioides HM3

Signal dependent microbial communication in Pseudomonas aeruginosa PAO1 is a typical phenomenon mediated by acyl homo-serine lactone molecules that helps in developing biofilm and enhance antibiotic resistance. Microbial sources provide insight to the hidden treasure of secondary metabolites, and these structurally diversified chemical motifs can be used as antimicrobial and anti-infective agents. In the present study, endophytic fungus, Colletotrichum gloeosporioides HM3 isolated from Carica papaya leaves was explored for anti-infective potential against P. aeruginosa PAO1. The crude extract of C. gloeosporioides HM3 displayed bacteriostatic effect on P. aeruginosa PAO1 growth at 750 μg/ml concentration. A significant decline was observed in the production of quorum sensing regulated virulence factors, i.e. 56.32%, 62.54%, and 66.67% of pyocyanin, chitinase, and elastase enzyme, respectively. A drastic reduction in pathogenic determinant behaviour after treatment with crude extract of C. gloeosporioides HM3 i.e. EPS, rhamnolipid, and HCN production was noted. Light microscopy and CLSM analysis revealed that fungal extract treatment has reduced bacterial ability to form dense biofilm architecture. In silico analysis demonstrated the binding efficiency of bioactive compound, 4-(2,3-dimethoxybenzylidene)-3-methyl-1-(4-nitrophenyl)-2-pyrazolin-5-one, which is equipotent to the natural ligand and displayed a docking score of -5.436 kcal/mol with QS transcriptional regulator (LasR). Whereas the compound Acetamide, n-[tetrahydro-3-(phenylmethyl) thieno [3,4-d]thiazol-2 (3 h)-ylidene]-, s,s-dioxide exhibits a docking score of -4.088 kcal/mol (LasR) and -1.868 kcal/mol (RhlR) with cognate receptor proteins. Henceforth, the research report suggests C. gloeosporioides HM3 derived metabolites could be considered as a potential inhibitors of QS regulated virulence factors and biofilm production in P. aeruginosa PAO1.

Production of the antimicrobial compound tetrabromopyrrole and the Pseudomonas quinolone system precursor, 2-heptyl-4-quinolone, by a novel marine species Pseudoalteromonas galatheae sp. nov

Novel antimicrobials are urgently needed due to the rapid spread of antibiotic resistant bacteria. In a genome-wide analysis of Pseudoalteromonas strains, one strain (S4498) was noticed due to its potent antibiotic activity. It did not produce the yellow antimicrobial pigment bromoalterochromide, which was produced by several related type strains with which it shared less than 95% average nucleotide identity. Also, it produced a sweet-smelling volatile not observed from other strains. Mining the genome of strain S4498 using the secondary metabolite prediction tool antiSMASH led to eight biosynthetic gene clusters with no homology to known compounds, and synteny analyses revealed that the yellow pigment bromoalterochromide was likely lost during evolution. Metabolome profiling of strain S4498 using HPLC-HRMS analyses revealed marked differences to the type strains. In particular, a series of quinolones known as pseudanes were identified and verified by NMR. The characteristic odor of the strain was linked to the pseudanes. The highly halogenated compound tetrabromopyrrole was detected as the major antibacterial component by bioassay-guided fractionation. Taken together, the polyphasic analysis demonstrates that strain S4498 belongs to a novel species within the genus Pseudoalteromonas, and we propose the name Pseudoalteromonas galatheae sp. nov. (type strain S4498T = NCIMB 15250T = LMG 31599T).

An α/β-Hydrolase Fold Subfamily Comprising Pseudomonas Quinolone Signal-Cleaving Dioxygenases

The quinolone ring is a common core structure of natural products exhibiting antimicrobial, cytotoxic, and signaling activities. A prominent example is the Pseudomonas quinolone signal (PQS), a quorum-sensing signal molecule involved in the regulation of virulence of Pseudomonas aeruginosa The key reaction to quinolone inactivation and biodegradation is the cleavage of the 3-hydroxy-4(1H)-quinolone ring, catalyzed by dioxygenases (HQDs), which are members of the α/β-hydrolase fold superfamily. The α/β-hydrolase fold core domain consists of a β-sheet surrounded by α-helices, with an active site usually containing a catalytic triad comprising a nucleophilic residue, an acidic residue, and a histidine. The nucleophile is located at the tip of a sharp turn, called the "nucleophilic elbow." In this work, we developed a search workflow for the identification of HQD proteins from databases. Search and validation criteria include an [H-x(2)-W] motif at the nucleophilic elbow, an [HFP-x(4)-P] motif comprising the catalytic histidine, the presence of a helical cap domain, the positioning of the triad's acidic residue at the end of β-strand 6, and a set of conserved hydrophobic residues contributing to the substrate cavity. The 161 candidate proteins identified from the UniProtKB database originate from environmental and plant-associated microorganisms from all domains of life. Verification and characterization of HQD activity of 9 new candidate proteins confirmed the reliability of the search strategy and suggested residues correlating with distinct substrate preferences. Among the new HQDs, PQS dioxygenases from Nocardia farcinica, N. cyriacigeorgica, and Streptomyces bingchenggensis likely are part of a catabolic pathway for alkylquinolone utilization.IMPORTANCE Functional annotation of protein sequences is a major requirement for the investigation of metabolic pathways and the identification of sought-after biocatalysts. To identify heterocyclic ring-cleaving dioxygenases within the huge superfamily of α/β-hydrolase fold proteins, we defined search and validation criteria for the primarily motif-based identification of 3-hydroxy-4(1H)-quinolone 2,4-dioxygenases (HQD). HQDs are key enzymes for the inactivation of metabolites, which can have signaling, antimicrobial, or cytotoxic functions. The HQD candidates detected in this study occur particularly in environmental and plant-associated microorganisms. Because HQDs active toward the Pseudomonas quinolone signal (PQS) likely contribute to interactions within microbial communities and modulate the virulence of Pseudomonas aeruginosa, we analyzed the catalytic properties of a PQS-cleaving subset of HQDs and specified characteristics to identify PQS-cleaving dioxygenases within the HQD family.

Functional profiles of phycospheric microorganisms during a marine dinoflagellate bloom

Harmful algal blooms (HABs) are an ecological concern but relatively few studies have investigated the functional potential of bacterioplankton over a complete algal bloom cycle, which is critical for determining their contribution to the fate of algal blooms. To address this point, we carried out a time-series metagenomic analysis of the functional features of microbial communities at three different Gymnodinium catenatum bloom stages (pre-, peak-, and post-bloom). Different microbial composition were observed during the blooming stages. The environmental parameters and correlation networks co-contribute to microbial variability, and the former explained 38.4% of total variations of the bacterioplankton community composition. Functionally, a range of pathways involved in carbon, nitrogen, phosphorus and sulfur cycling were significantly different during the various HAB stages. Genes associated with carbohydrate-active enzymes, denitrification, and iron oxidation were enriched at the pre-bloom stage; genes involved in reductive citrate cycle for carbon fixation, carbon degradation, nitrification and phosphate transport were enhanced at the peak stage; and relative gene abundance related to sulfur oxidation, vitamin synthesis, and iron transport and storage was increased at the post-bloom stage. The ecological linkage analysis has shown that microbial functional potential especially the C/P/Fe metabolism were significantly linked to the fate of the algal blooms. Taken together, our results demonstrated that microorganisms displayed successional patterns not only at the community level, but also in the metabolic potential on HAB's progression. This work contributes to a growing understanding of microbial structural elasticity and functional plasticity and shed light on the potential mechanisms of microbial-mediated HAB trajectory.

Physiological response and morphological changes of Heterosigma akashiwo to an algicidal compound prodigiosin

Harmful algal blooms (HABs) occur all over the world, producing severely negative effects on human life as well as on marine ecosystems. The algicidal compound, prodigiosin, secreted by algicidal bacteria Hahella sp. KA22 can lyse the harmful alga Heterosigma akashiwo. This study is aimed to investigate the algicidal mechanism of prodigiosin against H. akashiwo by detecting physiological and morphological responses of H. akashiwo to presence of prodigiosin. The results indicated that prodigiosin showed strong algicidal effects on H. akashiwo at the concentration of 3 μg/mL. Chlorophyll a and protein levels of the microalgae decreased significantly while malonaldehyde levels increased at this concentration. Contents of ascorbic acid and activities of superoxide dismutase and peroxidase increased fast with the quick decrease of the reactive oxygen species (ROS). For the 3 μg/mL prodigiosin treatment group, transcription of genes related to photosynthesis and respiration were significantly inhibited at 12 h while respiration related genes increased at 24 h. Collectively, the results indicated that prodigiosin could kill the microalgae by inducing ROS overproduction which could destroy the cell integrity and change the antioxidant system levels and functional gene expression. Our results demonstrated that prodigiosin is an effective algicide for the control of harmful algae.

The Multifaceted Inhibitory Effects of an Alkylquinolone on the Diatom Phaeodactylum tricornutum

The mechanisms underlying interactions between diatoms and bacteria are crucial to understand diatom behaviour and proliferation, and can result in far‐reaching ecological consequences. Recently, 2‐alkyl‐4‐quinolones have been isolated from marine bacteria, both of which (the bacterium and isolated chemical) inhibited growth of microalgae, suggesting these compounds could mediate diatom–bacteria interactions. The effects of several quinolones on three diatom species have been investigated. The growth of all three was inhibited, with half‐maximal inhibitory concentrations reaching the sub‐micromolar range. By using multiple techniques, dual inhibition mechanisms were uncovered for 2‐heptyl‐4‐quinolone (HHQ) in Phaeodactylum tricornutum. Firstly, photosynthetic electron transport was obstructed, primarily through inhibition of the cytochrome b₆f complex. Secondly, respiration was inhibited, leading to repression of ATP supply to plastids from mitochondria through organelle energy coupling. These data clearly show how HHQ could modulate diatom proliferation in marine environments.

The complete genome sequence of the algicidal bacterium Bacillus subtilis strain JA and the use of quorum sensing to evaluate its antialgal ability

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B. subtilis strain JA exhibit strong algicidal effects on algae with the inhibition rate exceeding 80 % within 48 h.

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The algicidal activity is regulated by AI-2 type quorum sensing.

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The complete genome information is provided for developing novel chemical-ecological methods to control harmful algae.

We describe the isolation of Bacillus subtilis strain JA and demonstrate that this bacterium exhibited strong algicidal effects on the algae Alexandrium minutum with an inhibition rate exceeding 80 % within 48 h. B. subtilis JA significantly reduced the photosynthetic efficiency of A. minutum and caused extensive morphological damage to the algae. Genomic analysis of B. subtilis JA demonstrated that a putative AI-2 type quorum sensing (QS) gene (LuxS) is present in its genome cluster, which is regulate pheromone biosynthesis. Interestingly, the exogenous addition of a QS-oligopeptide (ComX-pheromone) improved the algicidal efficiency of B. subtilis JA, thus indicating that the algicidal activity of this bacterium is potentially regulated by QS. Collectively, our data describe a potential antialgal bacterium and speculated that its behavior can be modulated by QS signal. B. subtilis JA may therefore represent a valuable tool for the development of novel chemical-ecological methods with which to control harmful algae.

Bacterial alkylquinolone signaling contributes to structuring microbial communities in the ocean

BACKGROUND

Marine bacteria form complex relationships with eukaryotic hosts, from obligate symbioses to pathogenic interactions. These interactions can be tightly regulated by bioactive molecules, creating a complex system of chemical interactions through which these species chemically communicate thereby directly altering the host's physiology and community composition. Quorum sensing (QS) signals were first described in a marine bacterium four decades ago, and since then, we have come to discover that QS mediates processes within the marine carbon cycle, affects the health of coral reef ecosystems, and shapes microbial diversity and bacteria-eukaryotic host relationships. Yet, only recently have alkylquinolone signals been recognized for their role in cell-to-cell communication and the orchestration of virulence in biomedically relevant pathogens. The alkylquinolone, 2-heptyl-4-quinolone (HHQ), was recently found to arrest cell growth without inducing cell mortality in selected phytoplankton species at nanomolar concentrations, suggesting QS molecules like HHQ can influence algal physiology, playing pivotal roles in structuring larger ecological frameworks.

RESULTS

To understand how natural communities of phytoplankton and bacteria respond to HHQ, field-based incubation experiments with ecologically relevant concentrations of HHQ were conducted over the course of a stimulated phytoplankton bloom. Bulk flow cytometry measurements indicated that, in general, exposure to HHQ caused nanoplankton and prokaryotic cell abundances to decrease. Amplicon sequencing revealed HHQ exposure altered the composition of particle-associated and free-living microbiota, favoring the relative expansion of both gamma- and alpha-proteobacteria, and a concurrent decrease in Bacteroidetes. Specifically, Pseudoalteromonas spp., known to produce HHQ, increased in relative abundance following HHQ exposure. A search of representative bacterial genomes from genera that increased in relative abundance when exposed to HHQ revealed that they all have the genetic potential to bind HHQ.

CONCLUSIONS

This work demonstrates HHQ has the capacity to influence microbial community organization, suggesting alkylquinolones have functions beyond bacterial communication and are pivotal in driving microbial community structure and phytoplankton growth. Knowledge of how bacterial signals alter marine communities will serve to deepen our understanding of the impact these chemical interactions have on a global scale.

Bromination of alkyl quinolones by Microbulbifer sp. HZ11, a marine Gammaproteobacterium, modulates their antibacterial activity

Alkyl quinolones (AQs) are multifunctional bacterial secondary metabolites generally known for their antibacterial and algicidal properties. Certain representatives are also employed as signalling molecules of Burkholderia strains and Pseudomonas aeruginosa. The marine Gammaproteobacterium Microbulbifer sp. HZ11 harbours an AQ biosynthetic gene cluster with unusual topology but does not produce any AQ-type metabolites under laboratory conditions. In this study, we demonstrate the potential of strain HZ11 for AQ production by analysing intermediates and key enzymes of the pathway. Moreover, we demonstrate that exogenously added AQs such as 2-heptyl-1(H)-quinolin-4-one (referred to as HHQ) or 2-heptyl-1-hydroxyquinolin-4-one (referred to as HQNO) are brominated by a vanadium-dependent haloperoxidase (V-HPO_HZ11 ), which preferably is active towards AQs with C5-C9 alkyl side chains. Bromination was specific for the third position and led to 3-bromo-2-heptyl-1(H)-quinolin-4-one (BrHHQ) and 3-bromo-2-heptyl-1-hydroxyquinolin-4-one (BrHQNO), both of which were less toxic for strain HZ11 than the respective parental compounds. In contrast, BrHQNO showed increased antibiotic activity against Staphylococcus aureus and marine isolates. Therefore, bromination of AQs by V-HPO_HZ11 can have divergent consequences, eliciting a detoxifying effect for strain HZ11 while simultaneously enhancing antibiotic activity against other bacteria.

Chemical ecology of the marine plankton

A review of chemically mediated interactions in planktonic marine environments covering new studies from January 2015 to December 2017.

The chemical cue tetrabromopyrrole induces rapid cellular stress and mortality in phytoplankton

Eukaryotic phytoplankton contribute to the flow of elements through marine food webs, biogeochemical cycles, and Earth's climate. Therefore, how phytoplankton die is a critical determinate of the flow and fate of nutrients. While heterotroph grazing and viral infection contribute to phytoplankton mortality, recent evidence suggests that bacteria-derived cues also control phytoplankton lysis. Here, we report exposure to nanomolar concentrations of 2,3,4,5-tetrabromopyrrole (TBP), a brominated chemical cue synthesized by marine γ-proteobacteria, resulted in mortality of seven phylogenetically-diverse phytoplankton species. A comparison of nine compounds of marine-origin containing a range of cyclic moieties and halogenation indicated that both a single pyrrole ring and increased bromination were most lethal to the coccolithophore, Emiliania huxleyi. TBP also rapidly induced the production of reactive oxygen species and the release of intracellular calcium stores, both of which can trigger the activation of cellular death pathways. Mining of the Ocean Gene Atlas indicated that TBP biosynthetic machinery is globally distributed throughout the water column in coastal areas. These findings suggest that bacterial cues play multiple functions in regulating phytoplankton communities by inducing biochemical changes associated with cellular death. Chemically-induced lysis by bacterial infochemicals is yet another variable that must be considered when modeling oceanic nutrient dynamics.

Bacterial virulence against an oceanic bloom-forming phytoplankter is mediated by algal DMSP

Emiliania huxleyi is a bloom-forming microalga that affects the global sulfur cycle by producing large amounts of dimethylsulfoniopropionate (DMSP) and its volatile metabolic product dimethyl sulfide. Top-down regulation of E. huxleyi blooms has been attributed to viruses and grazers; however, the possible involvement of algicidal bacteria in bloom demise has remained elusive. We demonstrate that a Roseobacter strain, Sulfitobacter D7, that we isolated from a North Atlantic E. huxleyi bloom, exhibited algicidal effects against E. huxleyi upon coculturing. Both the alga and the bacterium were found to co-occur during a natural E. huxleyi bloom, therefore establishing this host-pathogen system as an attractive, ecologically relevant model for studying algal-bacterial interactions in the oceans. During interaction, Sulfitobacter D7 consumed and metabolized algal DMSP to produce high amounts of methanethiol, an alternative product of DMSP catabolism. We revealed a unique strain-specific response, in which E. huxleyi strains that exuded higher amounts of DMSP were more susceptible to Sulfitobacter D7 infection. Intriguingly, exogenous application of DMSP enhanced bacterial virulence and induced susceptibility in an algal strain typically resistant to the bacterial pathogen. This enhanced virulence was highly specific to DMSP compared to addition of propionate and glycerol which had no effect on bacterial virulence. We propose a novel function for DMSP, in addition to its central role in mutualistic interactions among marine organisms, as a mediator of bacterial virulence that may regulate E. huxleyi blooms.

Pelagibaca bermudensis promotes biofuel competence of Tetraselmis striata in a broad range of abiotic stressors: dynamics of quorum-sensing precursors and strategic improvement in lipid productivity

BACKGROUND

Amelioration of biofuel feedstock of microalgae using sustainable means through synthetic ecology is a promising strategy. The co-cultivation model (Tetraselmis striata and Pelagibaca bermudensis) was evaluated for the robust biofuel production under varying stressors as well as with the selected two-stage cultivation modes. In addition, the role of metabolic exudates including the quorum-sensing precursors was assessed.

RESULTS

The co-cultivation model innovated in this study supported the biomass production of T. striata in a saline/marine medium at a broad range of pH, salinity, and temperature/light conditions, as well as nutrient limitation with a growth promotion of 1.2-3.6-fold. Hence, this developed model could contribute to abiotic stress mitigation of T. striata. The quorum-sensing precursor dynamics of the growth promoting bacteria P. bermudensis exhibited unique pattern under varying stressors as revealed through targeted metabolomics (using liquid chromatography-mass spectrometry, LC-MS). P. bermudensis and its metabolic exudates mutually promoted the growth of T. striata, which elevated the lipid productivity. Interestingly, hydroxy alkyl quinolones independently showed growth inhibition of T. striata on elevated concentration. Among two-stage cultivation modes (low pH, elevated salinity, and nitrate limitation), specifically, nitrate limitation induced a 1.5 times higher lipid content (30-31%) than control in both axenic and co-cultivated conditions.

CONCLUSION

Pelagibaca bermudensis is established as a potential growth promoting native phycospheric bacteria for robust biomass generation of T. striata in varying environment, and two-stage cultivation using nitrate limitation strategically maximized the biofuel precursors for both axenic and co-cultivation conditions (T and T-PB, respectively). Optimum metabolic exudate of P. bermudensis which act as a growth substrate to T. striata surpasses the antagonistic effect of excessive hydroxy alkyl quinolones [HHQ, 4-hydroxy-2-alkylquinolines and PQS (pseudomonas quorum signal), 2-heptyl-3-hydroxy-4(1H)-quinolone].

Synergy and Target Promiscuity Drive Structural Divergence in Bacterial Alkylquinolone Biosynthesis

Microbial natural products are genetically encoded by dedicated biosynthetic gene clusters (BGCs). A given BGC usually produces a family of related compounds that share a core but contain variable substituents. Though common, the reasons underlying this divergent biosynthesis are in general unknown. Herein, we have addressed this issue using the hydroxyalkylquinoline (HAQ) family of natural products synthesized by Burkholderia thailandensis. Investigations into the detailed functions of two analogs show that they act synergistically in inhibiting bacterial growth. One analog is a nanomolar inhibitor of pyrimidine biosynthesis and at the same time disrupts the proton motive force. A second analog inhibits the cytochrome bc₁ complex as well as pyrimidine biogenesis. These results provide a functional rationale for the divergent nature of HAQs. They imply that synergy and target promiscuity are driving forces for the evolution of tailoring enzymes that diversify the products of the HAQ biosynthetic pathway.

NprR-NprX Quorum-Sensing System Regulates the Algicidal Activity of Bacillus sp. Strain S51107 against Bloom-Forming Cyanobacterium Microcystis aeruginosa

Harmful cyanobacterial blooms have severely impaired freshwater quality and threatened human health worldwide. Here, a Gram-positive bacterium, Bacillus sp. strain S51107, which exhibits strong algicidal activity against Microcystis aeruginosa, was isolated from Lake Taihu. We found that the algicidal activity of strain S51107 was regulated primarily by NprR-NprX quorum sensing (QS), in which the mature form of the signaling peptide NprX was identified as the SKPDIVG heptapeptide. Disruption of the nprR-nprX cassette markedly decreased the algicidal activity, and complemented strains showed significantly recovered algicidal activity. Strain S51107 produced low-molecular-weight algicidal compounds [indole-3-carboxaldehyde and cyclo(Pro-Phe)] and high-molecular-weight algicidal substance(s) (>3 kDa). Moreover, the production of high-molecular-weight algicidal substance(s) was regulated by NprR-NprX QS, but the production of low-molecular-weight algicidal compounds was not. High-molecular-weight algicidal substance(s) played a more important role than low-molecular-weight algicidal compounds in the algicidal activity of strain S51107. The results of this study could increase our knowledge about algicidal characteristics of a potential algicidal bacterium, Bacillus sp. strain S51107, and provide the first evidence that the algicidal activity of Gram-positive algicidal bacteria is regulated by QS, which will greatly enhance our understanding of the interactions between algae and indigenous algicidal bacteria, thereby providing aid in the design and optimization of strategies to control harmful algae blooms.

Fungal community dynamics during a marine dinoflagellate (Noctiluca scintillans) bloom

Contamination and eutrophication have caused serious ecological events (such as algal bloom) in coastal area. During this ecological process, microbial community structure is critical for algal bloom succession. The diversity and composition of bacteria and archaea communities in algal blooms have been widely investigated; however, those of fungi are poorly understood. To fill this gap, we used pyrosequencing and correlation approaches to assess fungal patterns and associations during a dinoflagellate (Noctiluca scintillans) bloom. Phylum level fungal types were predominated by Ascomycota, Chytridiomycota, Mucoromycotina, and Basidiomycota. At the genus level drastic changes were observed with Hysteropatella, Malassezia and Saitoella dominating during the initial bloom stage, while Malassezia was most abundant (>50%) during onset and peak-bloom stages. Saitoella and Lipomyces gradually became more abundant and, in the decline stage, contributed almost 70% of sequences. In the terminal stage of the bloom, Rozella increased rapidly to a maximum of 50-60%. Fungal population structure was significantly influenced by temperature and substrate (N and P) availability (P < 0.05). Inter-specific network analyses demonstrated that Rozella and Saitoella fungi strongly impacted the ecological trajectory of N. scintillans. The functional prediction show that symbiotrophic fungi was dominated in the onset stage; saprotroph type was the primary member present during the exponential growth period; whereas pathogentroph type fungi enriched in decline phase. Overall, fungal communities and functions correlated significantly with N. scintillans processes, suggesting that they may regulate dinoflagellate bloom fates. Our results will facilitate deeper understanding of the ecological importance of marine fungi and their roles in algal bloom formation and collapse.

Bacterial transcriptome remodeling during sequential co-culture with a marine dinoflagellate and diatom

In their role as primary producers, marine phytoplankton modulate heterotrophic bacterial activities through differences in the types and amounts of organic matter they release. This study investigates the transcriptional response of bacterium Ruegeria pomeroyi, a member of the Roseobacter clade known to affiliate with diverse phytoplankton groups in the ocean, during a shift in phytoplankton taxonomy. The bacterium was initially introduced into a culture of the dinoflagellate Alexandrium tamarense, and then experienced a change in phytoplankton community composition as the diatom Thalassiosira pseudonana gradually outcompeted the dinoflagellate. Samples were taken throughout the 30-day experiment to track shifts in bacterial gene expression informative of metabolic and ecological interactions. Transcriptome data indicate fundamental differences in the exometabolites released by the two phytoplankton. During growth with the dinoflagellate, gene expression patterns indicated that the main sources of carbon and energy for R. pomeroyi were dimethysulfoniopropionate (DMSP), taurine, methylated amines, and polyamines. During growth with the diatom, dihydroxypropanesulfonate (DHPS), xylose, ectoine, and glycolate instead appeared to fuel the bulk of bacterial metabolism. Expression patterns of genes for quorum sensing, gene transfer agent, and motility suggest that bacterial processes related to cell communication and signaling differed depending on which phytoplankton species dominated the co-culture. A remodeling of the R. pomeroyi transcriptome implicating more than a quarter of the genome occurred through the change in phytoplankton regime.

Dynamic metabolic exchange governs a marine algal-bacterial interaction

Emiliania huxleyi is a model coccolithophore micro-alga that generates vast blooms in the ocean. Bacteria are not considered among the major factors influencing coccolithophore physiology. Here we show through a laboratory model system that the bacterium Phaeobacter inhibens, a well-studied member of the Roseobacter group, intimately interacts with E. huxleyi. While attached to the algal cell, bacteria initially promote algal growth but ultimately kill their algal host. Both algal growth enhancement and algal death are driven by the bacterially-produced phytohormone indole-3-acetic acid. Bacterial production of indole-3-acetic acid and attachment to algae are significantly increased by tryptophan, which is exuded from the algal cell. Algal death triggered by bacteria involves activation of pathways unique to oxidative stress response and programmed cell death. Our observations suggest that bacteria greatly influence the physiology and metabolism of E. huxleyi. Coccolithophore-bacteria interactions should be further studied in the environment to determine whether they impact micro-algal population dynamics on a global scale.

DOI:http://dx.doi.org/10.7554/eLife.17473.001

Microscopic algae that live in the ocean release countless tons of oxygen into the atmosphere each year. Widespread algae – known as coccolithophores – surround their little plant-like body with a mineral shell made of a material similar to chalk. These microscopic algae form seasonal blooms. Over several weeks in early summer, the algae grow to enormous numbers and cover hundreds of thousands of square kilometers in the ocean. These blooms become so vast that satellites can detect them. However, suddenly the blooms collapse; the algae die and their chalky shells sink to the bottom of the ocean where they have been accumulating for millions of years.

More and more evidence suggests that these tiny algae interact with bacteria in various ways. However, so far, no one had documented a direct interaction between bacteria and a member of this key group of algae.

Now, in a controlled laboratory environment, Segev et al. show that marine bacteria from the Roseobacter group physically attach onto a tiny coccolithophore alga called Emiliania huxleyi. While the bacteria are attached to their algal host, they enjoy a supply of nutrients that trickles from the algal cell. Unexpectedly, Segev et al. also discovered that the algae grow better in the presence of the bacteria. It turns out that the bacteria use a molecule that they obtain from their algal hosts to produce a small hormone-like molecule that in turn enhances the growth of the algae. However, after three weeks of growing together, the bacteria produce so much of the growth-enhancing molecule – which is harmful in higher concentrations – that they actually kill their algal host.

These findings suggest that the bacteria first promote the alga’s growth to boost their supply of nutrients. But as algae grow older, the bacteria harvest the algae to enjoy a last pulse of nutrients and allow their offspring to swim away and attach to younger algae.

The next challenge will be to link these laboratory observations to the actual microbial interactions in the ocean. It will also be important to explore whether other algae and bacteria interact in similar ways and if bacteria contribute to the sudden collapse of algal blooms by killing the algae.

DOI:http://dx.doi.org/10.7554/eLife.17473.002

Quorum Sensing and Quorum Quenching in the Phycosphere of Phytoplankton: a Case of Chemical Interactions in Ecology

The interactions between bacteria and phytoplankton regulate many important biogeochemical reactions in the marine environment, including those in the global carbon, nitrogen, and sulfur cycles. At the microscopic level, it is now well established that important consortia of bacteria colonize the phycosphere, the immediate environment of phytoplankton cells. In this microscale environment, abundant bacterial cells are organized in a structured biofilm, and exchange information through the diffusion of small molecules called semiochemicals. Among these processes, quorum sensing plays a particular role as, when a sufficient abundance of cells is reached, it allows bacteria to coordinate their gene expression and physiology at the population level. In contrast, quorum quenching mechanisms are employed by many different types of microorganisms that limit the coordination of antagonistic bacteria. This review synthesizes quorum sensing and quorum quenching mechanisms evidenced to date in the phycosphere, emphasizing the implications that these signaling systems have for the regulation of bacterial communities and their activities. The diversity of chemical compounds involved in these processes is examined. We further review the bacterial functions regulated in the phycosphere by quorum sensing, which include biofilm formation, nutrient acquisition, and emission of algaecides. We also discuss quorum quenching compounds as antagonists of quorum sensing, their function in the phycosphere, and their potential biotechnological applications. Overall, the current state of the art demonstrates that quorum sensing and quorum quenching regulate a balance between a symbiotic and a parasitic way of life between bacteria and their phytoplankton host.