Metabolomics analysis of Pseudomonas chlororaphis JK12 algicidal activity under aerobic and micro-aerobic culture condition

A newly identified algicidal bacterium of Pseudomonas fragi YB2: Algicidal compounds and effects

Harmful algal bloom (HAB) is an unresolved existing problem worldwide. Here, we reported a novel algicidal bacterium, Pseudomonas fragi YB2, capable of lysing multiple algal species. To Chlorella vulgaris, YB2 exhibited a maximum algicidal rate of 95.02 % at 120 h. The uniqueness of YB2 lies in its ability to self-produce three algicidal compounds: 2-methyl-1, 3-cyclohexanedione (2-MECHD), N-phenyl-2-naphthylamine, and cyclo (Pro-Leu). The algicidal properties of 2-MECHD have not been previously reported. YB2 significantly affected the chloroplast and mitochondrion, thus decreasing in chlorophyll a by 4.74 times for 120 h and succinate dehydrogenase activity by 103 times for 36 h. These physiological damages disrupted reactive oxygen species and Ca2+ homeostasis at the cellular level, increasing cytosolic superoxide dismutase (23 %), catalase (35 %), and Ca2+ influx. Additionally, the disruption of Ca2+ homeostasis rarely reported in algicidal bacteria-algae interaction was observed using the non-invasive micro-test technology. We proposed a putative algicidal mechanism based on the algicidal outcomes and physiological algicidal effects and explored the potential of YB2 through an algicidal simulation test. Overall, this study is the first to report the algicidal bacterium P. fragi and identify a novel algicidal compound, 2-MECHD, providing new insights and a potent microbial resource for the biocontrol of HAB.

Enhanced inhibitory efficiency against toxic bloom forming Raphidiopsis raciborskii by Streptomyces sp. HY through triple algicidal modes: Direct and indirect attacks combined with bioflocculation

Raphidiopsis raciborskii (R. raciborskii) forms harmful cyanobacterial blooms globally, and poses a great threat to the safety of drinking water and public health. There is a great need to develop eco-friendly biological alternative measures to mitigate mass blooms of R. raciborskii. However, previous rare studies on algicidal microorganisms against R. raciborskii restricted this aim. Recently, an algicidal bacterium Streptomyces sp. HY (designated HY) was identified with flavones producing ability, and could remove up to 98.73 % of R. raciborskii biomass within 48 h by directly attacking the cyanobacterium and release of algicidal substances (i.e., flavonoids) with a inoculum ratio of 5 %. Algicidal rate of HY was enhanced by 88.05 %, 89.33 % under dark and light, and full-light conditions respectively, when compared with the dark condition. Its algicidal substances were stable in a broad range of temperature (-80-55 °C) and pH (3-11) conditions, and all treated groups exhibited ≈ 100 % algicidal rate at day 3. HY treatment disrupted the photosynthesis system and triggered serious oxidative stress resulting in severe morphological injury. Thereby, HY treatment significantly affected expression levels of several essential genes (i.e., psbA, psaB, rbcL, ftsZ, recA, grpE), and simultaneously inhibited the biosynthesis and release of cylindrospermopsin. Yet, HY treatment didn't show any toxicity to zebrafish test embryos. Such results indicate that HY is a promising algicidal candidate strain to control global R. raciborskii blooms, and holds great promises for an effective biological measure to sustain water safety.

Bottom-up construction and screening of algae-bacteria consortia for pollutant biodegradation

Microbial communities have been used as important biological tools for a variety of purposes associated with agriculture, the food industry and human health. Artificial engineering of microbial communities is an emerging field of research motivated by finding stable and efficient microbial systems. However, the successful design of microbial communities with desirable functions not only requires profound understanding of microbial activities, but also needs efficient approaches to piece together the known microbial traits to give rise to more complex systems. This study demonstrates the bottom-up integration of environmentally isolated phototrophic microalgae and chemotrophic bacteria as artificial consortia to bio-degrade selected volatile organic compounds (VOCs). A high throughput screening method based on 96-well plate format was developed for discovering consortia with bioremediation potential. Screened exemplar consortia were verified for VOCs degradation performance, among these, certain robust consortia were estimated to have achieved efficiencies of 95.72% and 92.70% and near 100% removal (7 days) of benzene, toluene, and phenol, respectively, with initial concentrations of 100 mg/L. VOCs degradation by consortia was mainly attributed to certain bacteria including Rhodococcus erythropolis, and Cupriavidus metallidurans, and directly contributed to the growth of microalgae Coelastrella terrestris (R = 0.82, p < 0.001). This work revealed the potential of converting VOCs waste into algal biomass by algae-bacteria consortia constructed through a bottom-up approach. The screening method enables rapid shortlisting of consortia combinatorial scenarios without prior knowledge about the individual strains or the need for interpreting complex microbial interactions.

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.

Citrate Synthase Overexpression of Pseudomonas putida Increases Succinate Production from Acetate in Microaerobic Cultivation

Acetate is an end-product of anaerobic biodegradation and one of the major metabolites of microbial fermentation and lingo-cellulosic hydrolysate. Recently, acetate has been highlighted as a feedstock to produce value-added chemicals. This study examined acetate conversion to succinate by citrate synthase (gltA)-overexpressed Pseudomonas putida under microaerobic conditions. The acetate metabolism is initiated with the gltA enzyme, which converts acetyl-CoA to citrate. gltA-overexpressing P. putida (gltA-KT) showed an ∼50% improvement in succinate production compared to the wild type. Under the optimal pH of 7.5, the accumulation of succinate (4.73 ± 0.6 mM in 36 h) was ∼400% higher than that of the wild type. Overall, gltA overexpression alone resulted in 9.5% of the maximum theoretical yield in a minimal medium with acetate as the sole carbon source. This result shows that citrate synthase is important in acetate conversion to succinate by P. putida under microaerobic conditions.

Algicidal process and mechanisms of Enterobacter hormaechei F2 revealed by an integrated transcriptomic and metabolomic approach

Controlling eutrophication with algicidal bacteria is widely recognized as an effective solution. Here, an integrated transcriptomic and metabolomic approach was used to elucidate the algicidal process of Enterobacter hormaechei F2, which exhibits substantial algicidal activity. At the transcriptome level, RNA sequencing (RNA-seq) identified 1104 differentially expressed genes in the algicidal process of the strain, thus indicating that amino acids, energy metabolism, and signaling-related genes were significantly activated during the algicidal process according to the Kyoto Encyclopedia of Genes and Genomes enrichment analysis. By analyzing the enriched amino acid and energy metabolism pathways using metabolomics, we identified 38 upregulated and 255 downregulated significantly changed metabolites in the algicidal process and an accumulation of B vitamins, peptides, and energy substances. The integrated analysis demonstrated that energy and amino acid metabolism, co-enzymes and vitamins, and bacterial chemotaxis are the most important pathways for the algicidal process of this strain, and metabolites from these pathways, such as thiomethyladenosine, isopentenyl diphosphate, hypoxanthine, xanthine, nicotinamide, and thiamine, all exhibited algicidal activity.

Okara Waste as a Substrate for the Microalgae Phaeodactylum tricornutum Enhances the Production of Algal Biomass, Fucoxanthin, and Polyunsaturated Fatty Acids

Despite the rich nutritional content of okara, the majority remains underutilized and discarded as food waste. In this study, solid-state fermentation of okara with food-grade fungi was performed to extract and solubilize any remnant nutrients locked within the lignocellulosic matrix to produce a nutrient-rich okara fermentate. Fermented okara media (FOM) was used as the sole nutrient source for growing marine diatom, Phaeodactylum tricornutum. Results have shown a two-fold increase in biomass production when grown on FOM (0.52 g L−1) as compared with conventional Guillard’s F/2 media (0.25 g L−1). Furthermore, cellular fucoxanthin content was enhanced significantly by two-fold to reach a final concentration of 15.3 mg g−1 compared to 7.3 mg g−1. Additionally, a significantly higher amount of polyunsaturated fatty acid (PUFA) was produced, particularly eicosapentaenoic acid (EPA) which yield has increased by nearly three-fold. Metabolomics analysis of intracellular contents in fermented okara culture revealed a significantly enhanced accumulation of nitrogenous metabolites, alongside the decrease in sugar metabolites as compared to F/2 culture, thus indicating metabolic flux towards pathways involved in cellular growth. This study demonstrated an innovative and low-cost strategy of using fermented okara as a nutritious substrate for achieving a sustainable media replacement for high density algal growth with a simultaneous enhancement of production in highly valued nutraceuticals, including fucoxanthin and EPA.

Algicidal characteristics of novel algicidal compounds, cyclic lipopeptide surfactins from Bacillus tequilensis strain D8, in eliminating Heterosigma akashiwo blooms

Heterosigma akashiwo blooms have caused severe damage to marine ecosystems, the aquaculture industry and human health worldwide. In this study, Bacillus tequilensis D8 isolated from an H. akashiwo bloom area was found to exert high algicidal activity via extracellular metabolite production. This activity remained stable after exposure to different temperatures and light intensities. Scanning electron microscopy observation and fluorescein diacetate staining indicated that the algicidal substances rapidly destroyed algal plasma membranes and decreased esterase activity. Significant decreases in the maximum photochemical quantum yield and relative electron transfer rate were observed, which indicated photosynthetic membrane destruction. Subsequently, the algicidal compounds were separated and purified by high-performance liquid chromatography and identified as three surfactin homologues by interpreting high-resolution electrospray ionization mass spectrometry and nuclear magnetic resonance spectroscopy data. Among these, surfactin-C13 and surfactin-C14 exhibited strong algicidal activity against three HAB-causing species, namely, H. akashiwo, Skeletonema costatum, and Prorocentrum donghaiense, with 24 h-LC50 values of 1.2-5.31 μg/ml. Surfactin-C15 showed strong algicidal activity against S. costatum and weak algicidal activity against H. akashiwo but little activity against P. donghaiense. The present study illuminates the algicidal characteristics and mechanisms of action of surfactins on H. akashiwo and their potential applicability in controlling harmful algal blooms.

Metabolomic Insights of the Effects of Bacterial Algicide IRI-160AA on Dinoflagellate Karlodinium veneficum

Shewanella sp. IRI-160 is an algicidal bacterium that secretes an algicide, IRI-160AA. This algicide specifically targets dinoflagellates, while having no adverse effects on other algal species tested. Dinoflagellates exposed to IRI-160AA exhibited increased production of reactive oxygen species (ROS), DNA damage, and cell cycle arrest, implying a programmed pathway leading to cell death (PCD). Here, a metabolomic analysis was conducted on dinoflagellate Karlodinium veneficum and a control cryptophyte species Rhodomonas exposed to IRI-160AA to investigate the cellular mechanisms behind the physiological effects and the specificity of this algicide. Results of this research supported previous observations about physiological responses to the algicide. A suite of metabolites was identified that increased in the cell pellets of K. veneficum but not in Rhodomonas, including oxidative stress biomarkers, antioxidants, and compounds involved in DNA damage and PCD. Overall, the results of this study illustrated the metabolomic mechanisms underlying the algicidal effects of IRI-160AA on dinoflagellates. This research also provided insights and future directions for studies on the cellular response of dinoflagellates exposed to antagonistic bacteria in the environment.

Algicidal effect of tryptoline against Microcystis aeruginosa: Excess reactive oxygen species production mediated by photosynthesis

Cyanobacterial blooms significantly decrease water quality and can damage ecosystems and, as such, require efficient control methods. Algicidal bacteria and their associated substances are promising tools for controlling cyanobacterial blooms; however, their specific algicidal mechanisms remain unclear. Therefore, the current study sought to investigate the algicidal mechanism of tryptoline (1,2,3,4-tetrahydro-9 h-pyrido[3,4-b]indole) against Microcystis aeruginosa, with a specific focus on the contribution made by reactive oxygen species (ROS), the underlying mechanisms of ROS increase, as well as the photosystem response. Results show that the algicidal ratio of tryptoline significantly and positively correlates with algal ROS. Moreover, 93.79% of the algicidal ratio variation is attributed to ROS in the tryptoline group, while only 47.75% can be attributed to ROS in the tryptoline + N-acetyl-L-cysteine (NAC) group, where ROS are partially scavenged by NAC. In the presence of tryptoline, algicidal effect and ROS levels were significantly enhanced in the presence of light as compared to those in the dark (P < 0.001). Hence, the increase in ROS production attributed to tryptoline is primarily affected by the presence of light and photosynthesis. Additionally, tryptoline significantly reduces F_v/F_m, PI_ABS, ET_o/RC, and the expression of psaB and psbA genes related to photosynthesis, while increasing V_j and DI_o/RC (P < 0.05). These results suggest that tryptoline hinders algal photosynthesis by significantly decreasing photosynthetic efficiency and carbon assimilation, inhibiting photochemical electron transfer, and increasing closed reaction centers and energy loss. Moreover, following partial blockade of the photosynthetic electron transfer from Q_A to Q_B by diuron (3-(3-4-dichlorophenyl)-1,1-dimethylurea), the ROS of algae exposed to tryptoline is significantly decreased. Thus, tryptoline inhibits electron transfer downstream of Q_A, which increase the number of escaping electron and thereby increase ROS generation. Collectively, this study describes the algicidal mechanism of tryptoline against M. aeruginosa and highlights the critical factors associated with induction of algicidal activity.

Cellular Effects of 2',3'-Cyclic Nucleotide Monophosphates in Gram-Negative Bacteria

Organismal adaptations to environmental stimuli are governed by intracellular signaling molecules such as nucleotide second messengers. Recent studies have identified functional roles for the noncanonical 2',3'-cyclic nucleotide monophosphates (2',3'-cNMPs) in both eukaryotes and prokaryotes. In Escherichia coli, 2',3'-cNMPs are produced by RNase I-catalyzed RNA degradation, and these cyclic nucleotides modulate biofilm formation through unknown mechanisms. The present work dissects cellular processes in E. coli and Salmonella enterica serovar Typhimurium that are modulated by 2',3'-cNMPs through the development of cell-permeable 2',3'-cNMP analogs and a 2',3'-cyclic nucleotide phosphodiesterase. Utilization of these chemical and enzymatic tools, in conjunction with phenotypic and transcriptomic investigations, identified pathways regulated by 2',3'-cNMPs, including flagellar motility and biofilm formation, and by oligoribonucleotides with 3'-terminal 2',3'-cyclic phosphates, including responses to cellular stress. Furthermore, interrogation of metabolomic and organismal databases has identified 2',3'-cNMPs in numerous organisms and homologs of the E. coli metabolic proteins that are involved in key eukaryotic pathways. Thus, the present work provides key insights into the roles of these understudied facets of nucleotide metabolism and signaling in prokaryotic physiology and suggest broad roles for 2',3'-cNMPs among bacteria and eukaryotes. IMPORTANCE Bacteria adapt to environmental challenges by producing intracellular signaling molecules that control downstream pathways and alter cellular processes for survival. Nucleotide second messengers serve to transduce extracellular signals and regulate a wide array of intracellular pathways. Recently, 2',3'-cyclic nucleotide monophosphates (2',3'-cNMPs) were identified as contributing to the regulation of cellular pathways in eukaryotes and prokaryotes. In this study, we define previously unknown cell processes that are affected by fluctuating 2',3'-cNMP levels or RNA oligomers with 2',3'-cyclic phosphate termini in E. coli and Salmonella Typhimurium, providing a framework for studying novel signaling networks in prokaryotes. Furthermore, we utilize metabolomics databases to identify additional prokaryotic and eukaryotic species that generate 2',3'-cNMPs as a resource for future studies.

Effects of two algicidal substances, ortho-tyrosine and urocanic acid, on the growth and physiology of Heterosoigma akashiwo

Heterosigma akashiwo is a commonly found harmful microalgae, however, there are only few studies on its control using algicidal components particularly those identified from algicidal bacteria. In our previous study, ortho-tyrosine and urocanic acid identified from Bacillus sp. B1 showed a significantly high algicidal effect on H. akashiwo. The growth inhibition rates of H. akashiwo after 96 h of treatment with 300 μg/mL o-tyrosine and 500 μg/mL urocanic acid were 91.06% and 88.07%, respectively. Through non-destructive testing by Pulse Amplitude Modulation fluorometry and flow cytometer, the effects of o-tyrosine and urocanic acid on H. akashiwo PS II and physiological parameters (cell volume, mitochondrial membrane potential, and membrane permeability) were estimated. This study shows that o-tyrosine affected the photosynthesis system of H. akashiwo, decreased the mitochondrial membrane potential, and increased the membrane permeability of the algal cells. Treatment with urocanic acid decreased the mitochondrial membrane potential, resulting in the inhibition of algal cell growth and reproduction, but had little effect on membrane permeability and photosynthetic system. Our results may imply that when uridine degrades, surviving H. akashiwo cells may be reactivated. Therefore, o-tyrosine and urocanic acid have the potential to become new biological algicides, which can effectively control the growth of H. akashiwo.

Effects of mycosubtilin homolog algicides from a marine bacterium, Bacillus sp. SY-1, against the harmful algal bloom species Cochlodinium polykrikoides

The marine bacterium, Bacillus sp. SY-1, produced algicidal compounds that are notably active against the bloom-forming alga Cochlodinium polykrikoides. We isolated three algicidal compounds and identified these as mycosubtilins with molecular weights of 1056, 1070, and 1084 (designated MS 1056, 1070, and 1084, respectively), based on amino acid analyses and 1H, 13C, and two-dimensional nuclear magnetic resonance spectroscopy, including 1H-15N heteronuclear multiple bond correlation analysis. MS 1056 contains a β-amino acid residue with an alkyl side chain of C15, which has not previously been seen in known mycosubtilin families. MS 1056, 1070, and 1084 showed algicidal activities against C. polykrikoides with 6-h LC50 values of 2.3 ± 0.4, 0.8 ± 0.2, and 0.6 ± 0.1 μg/ml, respectively. These compounds also showed significant algicidal activities against other harmful algal bloom species. In contrast, MS 1084 showed no significant growth inhibitory effects against other organisms, including bacteria and microalgae, although does inhibit the growth of some fungi and yeasts. These observations imply that the algicidal bacterium Bacillus sp. SY-1 and its algicidal compounds could play an important role in regulating the onset and development of harmful algal blooms in natural environments.

The microbiome of alpine snow algae shows a specific inter-kingdom connectivity and algae-bacteria interactions with supportive capacities

Mutualistic interactions within microbial assemblages provide a survival strategy under extreme conditions; however, little is known about the complexity of interaction networks in multipartite, free-living communities. In the present study, the interplay within algae-dominated microbial communities exposed to harsh environmental influences in the Austrian Alps was assessed in order to reveal the interconnectivity of eukaryotic and prokaryotic inhabitants. All analyzed snowfields harbored distinct microbial communities. Network analyses revealed that mutual exclusion prevailed among microalgae in the alpine environment, while bacteria were mainly positively embedded in the interaction networks. Especially members of Proteobacteria, with a high prevalence of Oxalobacteraceae, Pseudomonadaceae, and Sphingomonadaceae showed genus-specific co-occurrences with distinct microalgae. Co-cultivation experiments with algal and bacterial isolates confirmed beneficial interactions that were predicted based on the bioinformatic analyses; they resulted in up to 2.6-fold more biomass for the industrially relevant microalga Chlorella vulgaris, and up to 4.6-fold increase in biomass for the cryophilic Chloromonas typhlos. Our findings support the initial hypothesis that microbial communities exposed to adverse environmental conditions in alpine systems harbor inter-kingdom supportive capacities. The insights into mutualistic inter-kingdom interactions and the ecology of microalgae within complex microbial communities provide explanations for the prevalence and resilience of such assemblages in alpine environments.

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.