Nutrient-dependent interactions between a marine copiotroph Alteromonas and a diatom Thalassiosira pseudonana.

IMPORTANCE: As the major producers and consumers, phytoplankton and bacteria play central roles in marine ecosystems and their interactions show great ecological significance. Whether mutualistic or antagonistic, the interaction between certain phytoplankton and bacterial species is usually seen as a derivative of intrinsic physiological properties and rarely changes. This study demonstrated that the interactions between the ubiquitously co-occurring bacteria and diatom, Alteromonas and Thalassiosira pseudonana, varied with nutrient conditions. They overcame hardship together in oligotrophic seawater but showed antagonistic effects against each other under nutrient amendment. The contact-dependent algicidal behavior of Alteromonas based on protease activity solved the paradox among bacterial proliferation, nutrient viability, and algal demise haunting other known non-contact-dependent algicidal processes and might actually trigger the collapse of algal blooms in situ. The chemotactic and swarming movement of Alteromonas might also contribute greatly to the breakdown of "marine snow," which could redirect the carbon sequestration pathway in the ocean.

Mangrove Sediment Microbiome: Adaptive Microbial Assemblages and Their Routed Biogeochemical Processes in Yunxiao Mangrove National Nature Reserve, China.

Microorganisms play important roles in mangrove ecosystems. However, we know little about the ecological implications of mangrove microbiomes for high productivity and the efficient circulation of elements in mangrove ecosystems. Here, we focused on mangrove sediments located at the Yunxiao National Mangrove Reserve in southeast China, uncovering the mangrove microbiome using the 16S rRNA gene and shotgun metagenome sequencing approaches. Physicochemical assays characterized the Yunxiao mangrove sediments as carbon (C)-rich, sulfur (S)-rich, and nitrogen (N)-limited environment. Then phylogenetic analysis profiling a distinctive microbiome with an unexpected high frequency of Chloroflexi and Nitrospirae appeared to be an adaptive characteristic of microbial structure in S-rich habitat. Metagenome sequencing analysis revealed that the metabolic pathways of N and S cycling at the community-level were routed through ammonification and dissimilatory nitrate reduction to ammonium for N conservation in this N-limited habitat, and dissimilatory sulfate reduction along with polysulfide formation for generating bioavailable S resource avoiding the biotoxicity of sulfide in mangrove sediments. In addition, methane metabolism acted as a bridge to connect C cycling to N and S cycling. Further identification of possible biogeochemical linkers suggested Syntrophobacter, Sulfurovum, Nitrospira, and Anaerolinea potentially drive the coupling of C, N, and S cycling. These results highlighting the adaptive routed metabolism flow, a previously undescribed property of mangrove sediment microbiome, appears to be a defining characteristic of this habitat and may significantly contribute to the high productivity of mangrove ecosystems, which could be used as indicators for the health and biodiversity of mangrove ecosystems.

Flocculating properties and potential of Halobacillus sp. strain H9 for the mitigation of Microcystis aeruginosa blooms.

Microcystis aeruginosa can cause harmful algal blooms in freshwaters worldwide. It has already seriously affected human lives and prevented the use of water resources. Therefore, there is an urgent need to develop ecofriendly and effective methods to control and eliminate M. aeruginosa in aquatic environments. In this study, Halobacillus sp. strain H9, a bacterium that showed high M. aeruginosa flocculation activity, was isolated and selected to assess its potential for the removal of M. aeruginosa. The analyses of flocculation activity and mode indicated that the strain H9 induced M. aeruginosa flocculation by secreting active flocculating substance rather than by directly contacting algal cells. A 5% concentration of the H9 supernatant could efficiently flocculate M. aeruginosa cells with a density of up to 5 × 107 cells/mL. Dramatic increases in the zeta potential indicated that charge neutralization could be the mechanism of the flocculation process. The strain H9 flocculated M. aeruginosa with no damage to the algal cell membrane, and did not result in microcystin being released into the surrounding environment. The flocculated algal culture was less toxic to zebrafish larvae, suggesting an environmentally friendly benefit of the H9 supernatant. In addition to M. aeruginosa, the H9 strain was also able to flocculate two other species causing harmful algal blooms, Phaeocystis globose and Heterosigma akashiwo. Furthermore, the flocculation activity of the H9 supernatant was stable at different temperatures and over a wide pH range. These characteristics give the H9 strain great potential for mitigating the influences of harmful algal blooms.

Flocculation characteristics of a bioflocculant produced by the actinomycete Streptomyces sp. hsn06 on microalgae biomass.

BACKGROUND: Microbial flocculation is a good choice for harvest of microalgae biomass, which has gained extensive attention. There have been carried out massive studies in bacterial flocculation, many bacterial strains with flocculation activity were isolated and different types of bioflocculants were produced. However, harvest of algal biomass by bioflocculants which produced from actinomycete are deficiency. In this study, the bioflocculant from an actinomycete Streptomyces sp. hsn06 could be used to harvest Chlorella vulgaris biomass. RESULTS: Consecutive treatment with 20 mg·L- 1 bioflocculant and 5 mM CaCl2 for 5 min showed the highest flocculating activity. The bioflocculant was a nonprotein substance with thermal stability and pH stability, which can be used in comprehensive applications. Chemical analysis of the bioflocculant indicated that it is a small molecule substance of moderate polarity with containing triple bond and cumulated double bonds. Algal temperature, pH, and metal ions showed great effects on the flocculation efficiency of the bioflocculant. CONCLUSIONS: The bioflocculant produced by Streptomyces sp. hsn06 possesses the potential to harvest algal biomass with high-efficiency.

Effective harvesting of the marine microalga Thalassiosira pseudonana by Marinobacter sp. FL06.

In this study, Marinobacter sp. FL06 was used to effectively harvest the energy-producing microalga Thalassiosira pseudonana through direct flocculation. Strain FL06 showed 92.7% flocculating efficiency against T. pseudonana, and no metal ion was added for the flocculation process, resulting in a more environmentally friendly process. The flocculation efficiency of FL06 was stable over a wide range of pH values and temperatures, indicating that the application of this bacteria has potential advantages under various conditions. Strain FL06 also exhibited flocculation activity against different microalgae, indicating that the strain can be used to harvest multiple types of microalgae. Strain FL06 showed high chemotactic ability toward algal cells, suggesting that chemotaxis is important for flocculation. This study provides the first demonstration that the Marinobacter genus could be used to harvest T. pseudonana biomass. In summary, the results showed that FL06 has the potential for effective harvesting of microalgal biomass.

Algicidal Activity of Novel Marine Bacterium Paracoccus sp. Strain Y42 against a Harmful Algal-Bloom-Causing Dinoflagellate, Prorocentrum donghaiense.

Prorocentrum donghaiense blooms occur frequently in the Yangtze River estuary and the adjacent East China Sea. These blooms have damaged marine ecosystems and caused enormous economic losses over the past 2 decades. Thus, highly efficient, low-cost, ecofriendly approaches must be developed to control P. donghaiense blooms. In this study, a bacterial strain (strain Y42) was identified as Paracoccus sp. and was used to lyse P. donghaiense The supernatant of the strain Y42 culture was able to lyse P. donghaiense, and the algicidal activity of this Y42 supernatant was stable with different temperatures and durations of light exposure and over a wide pH range. In addition to P. donghaiense, Y42 showed high algicidal activity against Alexandrium minutum, Scrippsiella trochoidea, and Skeletonema costatum, suggesting that it targets primarily Pyrrophyta. To clarify the algicidal effects of Y42, we assessed algal lysis and determined the chlorophyll a contents, photosynthetic activity, and malondialdehyde contents of P. donghaiense after exposure to the Y42 supernatant. Scanning electron microscopy and transmission electron microscopy analyses showed that the Y42 supernatant disrupted membrane integrity and caused algal cell breakage at the megacytic zone. Photosynthetic pigment loss and significant declines in both photosynthetic efficiency and the electron transport rate indicated that the Y42 supernatant damaged the photosynthetic system of P. donghaiense Malondialdehyde overproduction indicated that the Y42 supernatant caused lipid peroxidation and oxidative damage to membrane systems in the algal cell, ultimately leading to death. The findings of this study reveal the potential of Y42 to remove algal cells from P. donghaiense blooms.IMPORTANCEP. donghaiense is one of the most common dinoflagellate species that form harmful algal blooms, which frequently cause serious ecological pollution and pose health hazards to humans and other animals. Screening for bacteria with high algicidal activity against P. donghaiense and studying their algicidal processes and characteristics will contribute to an understanding of their algicidal effects and provide a theoretical basis for preventing algal blooms and reducing their harm to the environment. This study reports the algicidal activity and characteristics of Paracoccus against P. donghaiense The stability of the algicidal activity of Paracoccus in different environments (including different temperature, pH, and sunlight conditions) indicates its potential for use in the control of P. donghaiense blooms.

Soil Bacterial Diversity Is Associated with Human Population Density in Urban Greenspaces.

Urban greenspaces provide extensive ecosystem services, including pollutant remediation, water management, carbon maintenance, and nutrient cycling. However, while the urban soil microbiota underpin these services, we still have limited understanding of the factors that influence their distribution. We characterized soil bacterial communities from turf-grasses associated with urban parks, streets, and residential sites across a major urban environment, including a gradient of human population density. Bacterial diversity was significantly positively correlated with the population density; and species diversity was greater in park and street soils, compared to residential soils. Population density and greenspace type also led to significant differences in the microbial community composition that was also significantly correlated with soil pH, moisture, and texture. Co-occurrence network analysis revealed that microbial guilds in urban soils were well correlated. Abundant soil microbes in high density population areas had fewer interactions, while abundant bacteria in high moisture soils had more interactions. These results indicate the significant influence of changes in urban demographics and land-use on soil microbial communities. As urbanization is rapidly growing across the planet, it is important to improve our understanding of the consequences of urban zoning on the soil microbiota.

Molecular and stable isotopic evidence for the occurrence of nitrite-dependent anaerobic methane-oxidizing bacteria in the mangrove sediment of Zhangjiang Estuary, China.

Nitrite-dependent anaerobic methane oxidation (n-damo), which is mediated by "Candidatus Methylomirabilis oxyfera-like" bacteria, is unique in linking the carbon and nitrogen cycles. However, the niche and activity of n-damo bacteria in the mangrove ecosystem have not been confirmed. Here, we report the occurrence of the n-damo process in the mangrove wetland of the Zhangjiang Estuary, China. The widespread occurrence of n-damo bacteria in mangrove wetland was confirmed using real-time quantitative polymerase chain reaction (qPCR) assay, which showed that the abundance of Methylomirabilis oxyfera-like bacterial 16S rRNA and pmoA genes ranged from 2.43 × 106 to 2.09 × 107 and 2.07 × 106 to 3.38 × 107copies per gram of dry soil in the examined sediment cores. The highest amount of targeting genes was all detected in the upper layer (0-20 cm). Phylogenetic analyses of n-damo bacterial 16S rRNA and pmoA genes illustrated the depth-specific distribution and high diversity of n-damo bacteria in the mangrove wetland. Stable isotope experiments further confirmed the occurrence of n-damo in the examined mangrove sediments, and the potential n-damo rates ranged from 25.93 to 704.08 nmol CO2 per gram of dry soil per day at different depths of the sediment cores, with the n-damo being more active in the upper layer of the mangrove sediments. These results illustrate the existence of active M. oxyfera-like bacteria and indicate that the n-damo process is a previously overlooked microbial methane sink in the mangrove wetlands.

Fast-growing algicidal Streptomyces sp. U3 and its potential in harmful algal bloom controls.

To find the potential algicidal microorganisms and apply them to prevent and terminate harmful algal blooms (HABs), we isolated an actinomycete U3 from Mangrove, which had a potent algicidal effect on the harmful alga Heterosigma akashiwo. It could completely lyse the algal cells by producing active compounds, which were highly sensitive to high temperature and strong alkaline, but resistant to acid. One µg/mL of crude extract of the fermentation supernatant could kill 70% of H. akashiwo cells in 3 d. Unlike most of the other known algicidal Streptomyces, U3 showed strong ability of proliferation with the algal inclusion as the nutrient source. The washed mycelial pellets also gradually exhibited significant algicidal effect during the visible growth in the algal culture. It suggests that U3 could efficiently absorb nutrients from algal culture to support its growth and produce algicidal compounds that might cause the autophagy of algal cells. Therefore, applying U3, as a long-term and environmentally friendly bio-agent to control the harmful blooms of H. akashiwo, would be effective and promising. And the decrease of bioavailable DOM and increase of bio-refractory DOM during the algicidal process of U3 provided new insights into the ecological influence of algicial microorganisms on marine ecosystem.

Amino acids in cell wall of Gram-positive bacterium Micrococcus sp. hsn08 with flocculation activity on Chlorella vulgaris biomass.

The aim of this work was to investigate the flocculation mechanism by Gram-positive bacterium, Micrococcus sp. hsn08 as a means for harvesting Chlorella vulgaris biomass. Bacterial cells of Micrococcus sp. hsn08 were added into algal culture to harvest algal cells through direct contacting with algae to form flocs. Viability dependence test confirmed that flocculation activity does not depend on live bacteria, but on part of the peptidoglycan. The further investigation has determined that amino acids in cell wall play an important role to flocculate algal cells. Positively charged calcium can combine bacterial and algal cells together, and form a bridge between them, thereby forming the flocs, suggesting that ions bridging is the main flocculation mechanism. These results suggest that bacterial cells of Micrococcus sp. hsn08 can be applied to harvest microalgae biomass with the help of amino acids in cell wall.

Mangrovitalea sediminis gen. nov., sp. nov., a member of the family Alteromonadaceae isolated from mangrove sediment.

A Gram-stain-negative, facultative anaerobic and oligotrophic, rod-shaped, and motile with single polar flagellum bacterial strain, designed M11-4T was isolated from mangrove sediment in Yunxiao Mangrove National Nature Reserve, China. Growth was observed at temperatures from 10 to 40 °C (optimum 30 °C), at salinities from 0.5 to 6 % (optimum 2-3 %), and at pH from 5 to 8 (optimum 6). Phylogenetic analysis based on 16S rRNA gene sequence revealed that strain M11-4T shared highest sequence similarity with the genus Marinobacter(92.5-95.0 %) and represented a distinct phylogenetic lineage in the family Alteromonadaceae. The G+C content of the genomic DNA was 58.2 mol%. The dominant fatty acids were C16 : 0, C16 : 0 N-alcohol, summed feature 9 (comprising iso-C17 : 1ω9c and/or C16 : 0 10-methyl) and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c). The predominant respiratory quinone was ubiquinone-9 and the major polar lipids were diphosphatidylglycerol; phosphatidylethanolamine; phosphatidylglycerol and an unidentified aminophospholipid. According to its morphology, physiology, fatty acid composition and 16S rRNA gene sequence analysis, the strain M11-4T should be assigned as a novel species of a novel genus for which the name Mangrovitalea sediminis gen. nov., sp. nov. is proposed. The type strain of Mangrovitalea sediminis is M11-4T (=MCCC 1K03312T=JCM 32104T).

The algicidal mechanism of prodigiosin from Hahella sp. KA22 against Microcystis aeruginosa.

In recent years, Microcystis aeruginosa blooms have occurred throughout the world, causing huge economic losses and destroying aquatic ecosystems. It is necessary to develop effective and ecofriendly methods to control M. aeruginosa blooms. Here, we report a high algicidal activity of prodigiosin (PG) against M. aeruginosa as well as the algicidal mechanism. PG showed high algicidal activity against M. aeruginosa, with a 50% lethal dose (LD50) of 5.87 µg/mL in 72 h. A combination of methods, including propidium iodide and Annexin V-fluorescein staining assays and light and electron microscopy indicated the existence of two modes of cell death with features similar to those in eukaryotic programmed cell death: necrotic-like and apoptotic-like. Biochemical and physiological analyses showed that PG generates reactive oxygen species (ROS), which induce lipid peroxidation, damage the membrane system and destroy the function of the photosystem. A proteomics analysis revealed that many proteins were differentially expressed in response to PG stress and that most of these proteins were involved in important metabolic processes, which may trigger necrotic-like or apoptotic-like cell death. The present study sheds light on the multiple toxicity mechanisms of PG on M. aeruginosa and its potential for controlling the occurrence of M. aeruginosa blooms in lakes.

LSU rDNA based RFLP assays for the routine identification of Gambierdiscus species.

The Gambierdiscus genus is a group of benthic dinoflagellates commonly associated with ciguatera fish poisoning (CFP), which is generally found in tropical or sub-tropical regions around the world. Morphologically similar species within the genus can vary in toxicity; however, species identifications are difficult or sometimes impossible using light microscopy. DNA sequencing of ribosomal RNA genes (rDNA) is thus often used to identify and describe Gambierdiscus species and ribotypes, but the expense and time can be prohibitive for routine culture screening and/or large-scale monitoring programs. This study describes a restriction fragment length polymorphism (RFLP) typing method based on analysis of the large subunit rDNA that can successfully identify at least nine of the described Gambierdiscus species and two Fukuyoa species. The software programs DNAMAN 6.0 and Restriction Enzyme Picker were used to identify a set of restriction enzymes (SpeI, HpyCH4IV, and TaqαI) capable of distinguishing most of the known Gambierdiscus species for which DNA sequences were available. This assay was tested using in silico analysis and cultured isolates, and species identifications of isolates assigned by RFLP typing were confirmed by DNA sequencing. To verify the assay and assess intra-specific heterogeneity in RFLP patterns, identifications of 63 Gambierdiscus isolates comprising ten Gambierdiscus species, one ribotype, and two Fukuyoa species were confirmed using RFLP typing, and this method was subsequently employed in the routine identification of isolates collected from the Caribbean Sea. The RFLP assay presented here reduces the time and cost associated with morphological identification via scanning electron microscopy and/or DNA sequencing, and provides a phylogenetically sensitive method for routine Gambierdiscus species assignment.

Toxic Effects of Prodigiosin Secreted by Hahella sp. KA22 on Harmful Alga Phaeocystis globosa.

Application of algicidal compounds secreted by bacteria is a promising and environmentally friendly strategy to control harmful algal blooms (HABs). Years ago prodigiosin was described as an efficient algicidal compound, but the details about the effect of prodigiosin on algal cells are still elusive. Prodigiosin shows high algicidal activity on Phaeocystis globosa, making it a potential algicide in HAB control. When P. globosa were treated with prodigiosin at 5 µg/mL, algae cells showed cytoplasmic hypervacuolization, chloroplast and nucleus rupture, flagella missing, and cell fracture, when observed by scanning electron microscope and transmission electron microscopy. Prodigiosin induced a reactive oxygen species (ROS) burst in P. globosa at 2 h, which could result in severe oxidative damage to algal cells. Chlorophyll a (Chl a) fluorescence decreased significantly after prodigiosin treatment; about 45.3 and 90.0% of algal cells lost Chl a fluorescence at 24 and 48 h. The Fv/Fm value, reflecting the status of the photosystem II electron flow also decreased after prodigiosin treatment. Quantitative polymerase chain reaction (PCR) analysis psbA and rbcS expression indicated that photosynthesis process was remarkably inhibited by prodigiosin. The results indicated that the inhibition of photosynthesis may produce excessive ROS causing cell necrosis. This study is the first report about algal lysis mechanism of prodigiosin on harmful algae. Our results could increase our knowledge on the interaction between algicidal compounds and harmful algae, which could lead to further studies in the microcosm.

Flocculation mechanism of the actinomycete Streptomyces sp. hsn06 on Chlorella vulgaris.

In this study, an actinomycete Streptomyces sp. hsn06 with the ability to harvest Chlorella vulgaris biomass was used to investigate the flocculation mechanism. Streptomyces sp. hsn06 exhibited flocculation activity on algal cells through mycelial pellets with adding calcium. Calcium was determined to promote flocculation activity of mycelial pellets as a bridge binding with mycelial pellets and algal cells, which implied that calcium bridging is the main flocculation mechanism for mycelial pellets. Characteristics of flocculation activity confirmed proteins in mycelial pellets involved in flocculation procedure. The morphology and structure of mycelial pellets also caused dramatic effects on flocculation activity of mycelial pellets. According to the results, Streptomyces sp. hsn06 can be used as a novel flocculating microbial resource for high-efficiency harvesting of microalgae biomass.

Changes in land use driven by urbanization impact nitrogen cycling and the microbial community composition in soils.

Transition of populations from rural to urban living causes landscape changes and alters the functionality of soil ecosystems. It is unclear how this urbanization disturbs the microbial ecology of soils and how the disruption influences nitrogen cycling. In this study, microbial communities in turfgrass-grown soils from urban and suburban areas around Xiamen City were compared to microbial communities in the soils from rural farmlands. The potential N2O emissions, potential denitrification activity, and abundances of denitrifiers were higher in the rural farmland soils compared with the turfgrass soils. Ammonia oxidizing archaea (AOA) were more abundant than ammonia oxidizing bacteria (AOB) in turfgrass soils. Within turfgrass soils, the potential nitrification activities and AOA abundances were higher in the urban than in the suburban soils. These results indicate a more pivotal role of AOA in nitrification, especially in urban soils. Microbial community composition was distinctly grouped along urbanization categories (urban, suburban, and rural) classified according to the population density, which can in part be attributed to the differences in soil properties. These observed changes could potentially have a broader impact on soil nutrient availability and greenhouse gas emissions.

Trace metals in sediments and benthic animals from aquaculture ponds near a mangrove wetland in Southern China.

In this study, we measured the concentrations of trace metals (Cr, Cu, Zn, As, Cd, Pb and Hg) in typical cultured animals (crabs, clams, and shrimps) and sediments from aquaculture ponds nearby mangrove wetlands in Zhangjiang estuary, China. The contents of Cr, Cu, Cd, and Pb in mangrove sediments were significantly higher than those in pond sediments, while an inverse distribution was observed for Zn, As, and Hg. Significantly higher concentrations of trace metals were found in clams from the mangrove mudflats compared to those from the aquaculture ponds. The sources of trace metals in the clams were primarily from organic fertilizer, whereas those in the shrimp were from contaminated sediment. The results of geo-accumulation index and the ecological risk assessment indicated that the aquaculture ponds near the mangrove wetlands in this subtropical estuary posed a special risk of endogenous and exogenous trace metal pollution to nearby systems.

[Chemotaxis and characteristics of chemotactic genes in Novosphingobium strains].

Objective: The present study aims to analyze the chemotaxis genes and proteins of several PAH-degrading Novosphingobium strains, and the chemotaxis of these strains toward aromatic compounds and intermediates. Methods: Based on genome comparative analysis, we identified the chemotaxis genes organization and proteins distribution. We used drop and swarm plate assays to detect the chemotaxis of these strains toward aromatic compounds and intermediates of TCA cycle. Results: We found that all these Novosphingobium strains showed chemotaxis, but the chemotatic ability varied. The completed genome sequenced strains N. pentaromativorans F2, N. pentaromativorans US6-1, N. pentaromativorans PP1Y, Novosphingobium sp. AP12, Novosphingobium sp. Rr 2-17, and Novosphingobium nitrogenifigens DSM 19370 contained MCP, CheW, CheA, CheB, CheR and CheY. Strain F2, US6-1 and PP1Y, shared a consistent order of chemotaxis genes in "che" cluster. The chemotatic system of these Novosphingobium strains belonged to the Fla chemotactic system. Conclusion: These strains all contained a complete chmotaxis pathway. Their chemotactic ability toward aromatic compounds and intermediates varied, and the chemotaxis of US6-1 was obvious.

Lytic and Chemotactic Features of the Plaque-Forming Bacterium KD531 on Phaeodactylum tricornutum.

Phaeodactylum tricornutum is a dominant bloom forming species and potential biofuel feedstock. To control P. tricornutum bloom or to release lipids from P. tricornutum, we previously screened and identified the lytic bacterium Labrenzia sp. KD531 toward P. tricornutum. In the present study, we evaluated the lytic activity of Labrenzia sp. KD531 on microalgae and investigated its lytic mechanism. The results indicated that the lytic activity of KD531 was temperature- and pH-dependent, but light-independent. In addition to P. tricornutum, KD531 also showed lytic activity against other algal species, especially green algae. A quantitative analysis of algal cellular protein, carbohydrate and lipid content together with measurements of dry weight after exposure to bacteria-infected algal lysate indicated that the bacterium KD531 influenced the algal biomass by disrupting the algal cells. Both chemotactic analysis and microscopic observations of subsamples from different regions of formed plaques showed that KD531 could move toward and then directly contact algal cells. Direct contact between P. tricornutum and KD531 cells was essential for the lytic process.