MlrA, an Essential Enzyme for Microcystins and Nodularin on First Step Biodegradation in Microcystin-Degrading Bacteria.

Microcystin-degrading bacteria first degrade microcystins by microcystinase A (MlrA) to cleave the cyclic structure of microcystins at the Adda-Arg site of microcystin-LR, microcystin-RR, and microcystin-YR, but the cleavage of the other microcystins was not clear. In our study, the microcystin-degrading bacterium Sphingopyxis sp. C-1 as wild type and that of mlrA-disrupting mutant, Sphingopyxis sp. CMS01 were used for microcystins biodegradation. The results showed MlrA degraded microcystin-LA, microcystin-LW, microcystin-LY, microcystin-LF, and nodularin. MlrA could cleave the Adda-L-amino acid site.

Exploring the use of fish as indicators of eicosapentaenoic and docosahexaenoic supply in lake ecosystems.

An adequate supply of food sources with high levels (i.e., weight proportion of total fatty acids) and contents (i.e., absolute amount per mass) of long chain polyunsaturated fatty acids such as eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) are important for ecosystems. Therefore, the supply of EPA and DHA from basal food sources is a useful indicator of ecosystem health. To determine whether EPA and DHA levels and contents in fish can be used as indicators of EPA and DHA supply in lakes, five dominant species of fish and basal food sources (seston and sediment) were collected monthly from June to November from 2016 to 2021 from Lake Hachiro, Japan. Seston and Hypomesus nipponensis were collected from 12 lakes (one collection per lake) with varying seston contents in EPA and DHA. The trends of EPA and DHA in all fish species were similar to those of the basal food sources. Correlation analysis showed that the EPA levels were strongly correlated between fish and seston; moreover, the correlation coefficient increased when a 1- or 2-month moving average was applied to the basal food sources, suggesting that fish represent a time-integrated supply of EPA and DHA. EPA levels of H. nipponensis had the highest correlation coefficients with seston among all fish species. EPA levels of H. nipponensis were significantly correlated with those of seston among lakes. The results of this study suggest that H. nipponensis is a useful indicator of EPA and DHA supplies in lake ecosystems.

Effects of Algal Extracellular Polysaccharides on the Formation of Filamentous Manganese Oxide Particles in the Near-Bottom Layer of Lake Biwa.

Filamentous manganese (Mn) oxide particles, which occur in the suboxic zone of stratified waterbodies, are important drivers of diverse elemental cycles. These particles are considered to be bacteriogenic; despite the importance of biogeochemical implications, however, the environmental factor responsible for their formation has not been identified. The aim of this study was to demonstrate the involvement of algal extracellular polysaccharides in Mn oxide particle formation. Based on this study of laboratory cultures of a model Mn(II)-oxidizing bacterium, the supply of algal extracellular mucilage was shown to stimulate Mn(II) oxidation and thus the production of filamentous Mn oxide particles. This observation was consistent with the results obtained for naturally occurring particles collected from a near-bottom layer (depth of approximately 90 m) in the northern basin of Lake Biwa, Japan, that is, most Mn particles resembling δ-MnO2 were associated with an extracellular mucilage-like gelatinous matrix, which contained dead algal cells and was lectin-stainable. In the lake water column, polysaccharides produced by algal photosynthesis sank to the bottom layer. The analysis of the quality of water samples, which have been collected from the study site for 18 years, reveals that the annual average total phytoplankton biovolume in the surface layer correlates with the density of filamentous Mn particles in the near-bottom layer. Among different phytoplankton species, green algae appeared to be the key species. The results of this study suggest that algal extracellular polysaccharides serve as an important inducer for the formation of filamentous Mn oxide particles in the near-bottom layer of the northern basin of Lake Biwa.

Potential contribution of floral thermogenesis to cold adaptation, distribution pattern, and population structure of thermogenic and non/slightly thermogenic Symplocarpus species.

The genus Symplocarpus in basal Araceae includes both thermogenic and non/slightly thermogenic species that prefer cold environments. If floral thermogenesis of Symplocarpus contributes to cold adaptation, it would be expected that thermogenic species have a larger habitat than non/slightly thermogenic species during an ice age, leading to increased genetic diversity in the current population. To address this question, potential distribution in past environment predicted by ecological niche modeling (ENM), genetic diversity, and population structure of chloroplast and genome-wide single nucleotide polymorphisms were compared between thermogenic Symplocarpus renifolius and non/slightly thermogenic Symplocarpus nipponicus. ENM revealed that the distribution of S. nipponicus decreased, whereas that of S. renifolius expanded in the Last Glacial Maximum. Phylogeographic analyses have shown that the population structures of the two species were genetically segmented and that the genetic diversity of S. renifolius was higher than that of S. nipponicus. The phylogenetic relationship between chloroplast and nuclear DNA is topologically different in the two species, which may be due to the asymmetric gene flow ubiquitously observed in plants. The results of this study imply that floral thermogenesis of Symplocarpus contributes to expanding the distribution during an ice age, resulting in increased genetic diversity due to cold adaptation.

Microcystin-LR incorporated into colonic cells through probenecid-sensitive transporters leads to upregulated MCP-1 expression induced by JNK activation.

Harmful algae that inhabit eutrophic lakes produce cyanotoxic microcystins. Therefore, the relationship between chronic exposure to microcystins via drinking water and organ disorders has been investigated. The present study aimed to determine whether representative microcystin-LR is involved in increased monocyte chemoattractant protein-1 (MCP-1) expression in rat colonic mucosa and enterocyte-like differentiated Caco-2 cells. The mRNA expression of MCP-1 was increased in the colons of rats administered with microcystin-LR, compared with controls. Furthermore, mRNA levels of MCP-1 expression significantly and positively correlated with those of Adhesion G Protein-Coupled Receptor E1 (ADGRE1; EMR1; F4/80), an indicator of macrophage infiltration, suggesting that increased MCP-1 expression induced by microcystin-LR promotes macrophage infiltration into the colon. Microcystin-LR increased MCP-1 expression in enterocyte-like differentiated Caco-2 cells, by activating c-Jun N-terminal kinase (JNK), but not extracellular signal-regulated kinase (ERK) or p38. The findings of transporter inhibitors indicated that microcystin-LR is incorporated into cells via ATP Binding Cassette (ABC) or solute carrier (SLC) transporters other than the organic anion transporting polypeptides (OATPs)1B1, 1B3, 2B1, and 1A2, which this leads to increased MCP-1 expression in the colon through activating JNK. Thus, increased MCP-1 expression induced by microcystin-LR might be a trigger for initiating tumorigenesis with inflammation in the colon because increased MCP-1 expression induces inflammation associated with macrophage infiltration into the colon, and chronic inflammation is associated with the initiation of tumorigenesis.

Mariniplasma anaerobium gen. nov., sp. nov., a novel anaerobic marine mollicute, and proposal of three novel genera to reclassify members of Acholeplasma clusters II-IV.

A novel strictly anaerobic chemoorganotrophic bacterium, designated Mahy22T, was isolated from sulfidic bottom water of a shallow brackish meromictic lake in Japan. Cells of the strain were Gram-stain-negative, non-motile and coccoid in shape with diameters of about 600-800 nm. The temperature range for growth was 15-37 °C, with optimum growth at 30-32 °C. The pH range for growth was pH 6.2-8.9, with optimum growth at pH 7.2-7.4. The strain grew with NaCl concentrations of 5% or below (optimum, 2-3%). Growth of the strain was enhanced by the addition of thiosulfate. The major cellular fatty acids were C16:0 and anteiso-C15:0. Respiratory quinones were not detected. The complete genome sequence of strain Mahy22T possessed a 1 885 846 bp circular chromosome and a 12 782 bp circular genetic element. The G+C content of the genome sequence was 30.1 mol%. Phylogenetic analysis based on the 16S rRNA gene revealed that the novel strain belonged to the family Acholeplasmataceae, class Mollicutes. The closest relative of strain Mahy22T with a validly published name was Acholeplasma palmae J233T with a 16S rRNA gene sequence similarity of 90.5%. Based on the results of polyphasic analysis, the name Mariniplasma anaerobium gen. nov., sp. nov. is proposed to accommodate strain Mahy22T, along with reclassification of some Acholeplasma species into Alteracholeplasma gen. nov., Haploplasma gen. nov. and Paracholeplasma gen. nov.

Dynamics of the prokaryotic and eukaryotic microbial community during a cyanobacterial bloom.

Toxic cyanobacterial blooms frequently develop in eutrophic freshwater bodies worldwide. Microcystis species produce microcystins (MCs) as a cyanotoxin. Certain bacteria that harbor the mlr gene cluster, especially mlrA, are capable of degrading MCs. However, MC-degrading bacteria may possess or lack mlr genes (mlr+ and mlr- genotypes, respectively). In this study, we investigated the genotype that predominantly contributes to biodegradation and cyanobacterial predator community structure with change in total MC concentration in an aquatic environment. The 2 genotypes coexisted but mlr+ predominated, as indicated by the negative correlation between mlrA gene copy abundance and total MC concentration. At the highest MC concentrations, predation pressure by Phyllopoda, Copepoda, and Monogononta (rotifers) was reduced; thus, MCs may be toxic to cyanobacterial predators. The results suggest that cooperation between MC-degrading bacteria and predators may reduce Microcystis abundance and MC concentration.

Variability in deer diet and plant vulnerability to browsing among forests with different establishment years of sika deer.

Increased ungulate browsing alters the composition of plant communities and modifies forest ecosystems worldwide. Ungulates alter their diet following changes in availability of plant species; however, we know little about how browse selection and plant community composition change with different stages of deer establishment. Here, we provide insight into this area of study by combining multiple approaches: comparison of the understory plant community, analysis of records of browsing damage, and DNA barcoding of sika deer feces at 22 sites in forests in northern Japan varying in when deer were first established. The coverage of vegetation and number of plant species were only lower at sites where deer were present for more than 20 years, while the difference in plant coverage among deer establishment years varied among plant species. Deer diet differed across establishment years, but was more affected by the site, thereby indicating that food selection by deer could change over several years after deer establishment. Plant life form and plant architecture explained the difference in plant coverage across establishment years, but large variability was observed in deer diet within the two categories. Integrating these results, we categorized 98 plant taxa into six groups that differed in vulnerability to deer browsing (degree of damage and coverage). The different responses to browsing among plant species inferred from this study could be a first step in predicting the short- and long-term responses of forest plant communities to deer browsing.

Draft Genome Sequence of the Microcystin-Degrading Bacterium Novosphingobium sp. Strain MD-1.

This report describes the whole-genome sequence of a microcystin-degrading bacterium, Novosphingobium sp. strain MD-1, isolated from a lake in Japan. The Novosphingobium sp. strain MD-1 genome had a total length of 4,617,766 bp. Moreover, strain MD-1 showed a conserved microcystin-degrading gene cluster (mlrA to mlrF), similar to Sphingopyxis sp. strain C-1.

Principal Component Analysis applied directly to Sequence Matrix.

Sequence data is now widely used to observe relationships among organisms. However, understanding structure of the qualitative data is challenging. Conventionally, the relationships are analysed using a dendrogram that estimates a tree shape. This approach has difficulty in verifying the appropriateness of the tree shape; rather, horizontal gene transfers and mating can make the shape of the relationship as networks. As a connection-free approach, principal component analysis (PCA) is used to summarize the distance matrix, which records distances between each combination of samples. However, this approach is limited regarding the treatment of information of sequence motifs; distances caused by different motifs are mixed up. This hides clues to figure out how the samples are different. As any bases may change independently, a sequence is multivariate data essentially. Hence, differences among samples and bases that contribute to the difference should be observed coincidentally. To archive this, the sequence matrix is transferred to boolean vector and directly analysed by using PCA. The effects are confirmed in diversity of Asiatic lion and human as well as environmental DNA. Resolution of samples and robustness of calculation is improved. Relationship of a direction of difference and causative nucleotides has become obvious at a glance.

Effects of levofloxacin exposure on sequencing batch reactor (SBR) behavior and microbial community changes.

The adaptation mechanisms of bacterial community for nitrogen removal performance exposed to fluctuated levels of levofloxacin (LVX) during wastewater treatment in SBRs were investigated. Although LVX is completely synthetic, the results of minimum inhibitory concentration (MIC, 32 mg-LVX/L) and minimum bactericidal concentration (MBC, 512 mg-LVX/L) of the sampled sludge showed that the LVX resistance/tolerance for bacterial growth has already existed in the actual wastewater treatment plants (WWTPs). The key bacteria, i.e. Nitrosomonas sp. (ammonia-oxidizing bacteria), Nitrospira sp. (nitrite-oxidizing bacteria) and Thauera sp. (the predominant denitrifiers), decreased with LVX exposure, and the recovery of biological process in the reactor was disturbed due to LVX exposure. However, after stopping exposure their population was quickly increased and thus the performance was recovered. The results of the non-metric multidimensional scaling and microbial community by sequencing showed the LVX concentration was a crucial factor to the change of bacterial communities and controlled the quantitative evolution of the communities in our systems. This effect was more pronounced as the LVX concentration was higher. The results suggested the removal of residual antibiotics to accomplish under no effect concentration before biological treatment is important to suppress emerging and increasing of the antibiotic resistant bacteria in WWTPs.

Transfer of cyanobacterial carbon to a higher trophic-level fish community in a eutrophic lake food web: fatty acid and stable isotope analyses.

The dietary utilization of cyanobacterial carbon by fish communities is poorly understood. We examined the transfer of cyanobacterial carbon to fish in a eutrophic lake using fatty acid biomarkers and measuring the stable carbon isotope ratios of fatty acid and bulk nitrogen. We collected five species of fish (Hypomesus nipponensis, Carassius sp., Cyprinus carpio, Tridentiger brevispinis, and Gymnogobius castaneus) as well as the seston from June to November 2016 from Lake Hachiro, Japan. Cyanobacterial blooms were observed from August to October. From June to August, cyanobacterial fatty acid biomarkers (18:2ω6 and 18:3ω3) accounted for only 1.4-4.3% of total fatty acids in these fish species, indicating a low contribution of cyanobacteria to fish diets during this period. However, the contribution of the cyanobacterial fatty acid biomarkers in these fish species increased sharply in September (10.5-17.1%), except in second-year H. nipponensis. In September, the stable carbon isotope ratios of 18:3ω3 in these fish species were almost equivalent to those in the seston, which was primarily composed of cyanobacteria. The trophic positions of the collected fish species ranged from 1.6 to 3.4, based on their stable nitrogen isotope values, indicating that some fish ingested cyanobacteria directly, while others acquired cyanobacteria indirectly, through the food chain. These findings indicate that cyanobacterial carbon is transferred up the food chain in eutrophic lake ecosystems with cyanobacterial blooms.

Whole-Genome Sequences of Two Manganese(II)-Oxidizing Bacteria, Bosea sp. Strain BIWAKO-01 and Alphaproteobacterium Strain U9-1i.

This report describes the whole-genome sequences of two Mn(II)-oxidizing bacteria, filamentous Mn oxide microparticle-forming Bosea sp. strain BIWAKO-01 and alphaproteobacterium strain U9-1i.

Whole-Genome Sequence of the Microcystin-Degrading Bacterium Sphingopyxis sp. Strain C-1.

This report describes the whole-genome sequence of an alkalitolerant microcystin-degrading bacterium, Sphingopyxis sp. strain C-1, isolated from a lake in China.

Whole Genome Sequence of the Non-Microcystin-Producing Microcystis aeruginosa Strain NIES-44.

Microcystis aeruginosa is a typical algal bloom-forming cyanobacterium. This report describes the whole-genome sequence of a non-microcystin-producing strain of Microcystis aeruginosa, NIES-44, which was isolated from a Japanese lake.

Complete Genome Sequence of the Unclassified Iron-Oxidizing, Chemolithoautotrophic Burkholderiales Bacterium GJ-E10, Isolated from an Acidic River.

Burkholderiales bacterium GJ-E10, isolated from the Tamagawa River in Akita Prefecture, Japan, is an unclassified, iron-oxidizing chemolithoautotrophic bacterium. Its single circular genome, consisting of 3,276,549 bp, was sequenced by using three types of next-generation sequencers and the sequences were then confirmed by PCR-based Sanger sequencing.

Enzymatic pathway for biodegrading microcystin LR in Sphingopyxis sp. C-1.

The mlr gene cluster consisting of mlrA, mlrB, mlrC, and mlrD is involved in the degradation of the cyanobacterial toxin microcystin. However, it is unclear which degradation intermediates are metabolized by MlrB and MlrC. To address these questions, we constructed recombinant Escherichia coli to overproduce MlrB and MlrC from Sphingopyxis sp. C-1, and determined which intermediates were degraded in cell-free extracts. The cell-free extract containing MlrB degraded linearized microcystin-LR, giving rise to a tetrapeptide. The cell-free extract of MlrC degraded linearized microcystin-LR and also degraded the tetrapeptide to the amino acid Adda. These results indicate that linearized microcystin-LR is degraded by both MlrB and MlrC, and tetrapeptide is degraded by specifically by MlrC in Sphingopyxis sp. C-1.

Prevention of Phormidium tenue Biofilm Formation by TiO(2) Photocatalysis.

We showed that the photocatalytic effect of a coating of TiO(2) greatly reduces the formation of a biofilm by Phormidium tenue (P. tenue), a filamentous cyanobacterium, on glass plates. Sample plates were immersed in P. tenue culture solution (OD(730)=0.3) under concurrent illumination with white fluorescent (WF) and UV light (0.3 mW cm(-2), each) for 11 days. TiO(2)-coated glass plates showed greatly reduced adhesion of P. tenue over 11 days compared to bare plates. The number of P. tenue adhering to bare glass plates increased to over 10(6) cells cm(-2) in 6 days. The photocatalytic anti-biofilm effect was also observed under WF light, although it was small and lasted only a few days. The addition of 1 mM mannitol, a scavenger for the hydroxyl radical (·OH), suppressed the effect. The surface of TiO(2)-coated plates was maintained in a highly hydrophilic state for 11 days, regardless of the addition of mannitol. Therefore, we conclude that the photocatalytic oxidation of P. tenue is effective in preventing the formation of a biofilm.

Characteristics of a Microcystin-Degrading Bacterium under Alkaline Environmental Conditions.

The pH of the water associated with toxic blooms of cyanobacteria is typically in the alkaline range; however, previously only microcystin-degrading bacteria growing in neutral pH conditions have been isolated. Therefore, we sought to isolate and characterize an alkali-tolerant microcystin-degrading bacterium from a water bloom using microcystin-LR. Analysis of the 16S rRNA gene sequence revealed that the isolated bacterium belonged to the genus Sphingopyxis, and the strain was named C-1. Sphingopyxis sp. C-1 can grow; at pH 11.0; however, the optimum pH for growth was pH 7.0. The microcystin degradation activity of the bacterium was the greatest between pH 6.52 and pH 8.45 but was also detected at pH 10.0. The mlrA homolog encoding the microcystin-degrading enzyme in the C-1 strain was conserved. We concluded that alkali-tolerant microcystin-degrading bacterium played a key role in triggering the rapid degradation of microcystin, leading to the disappearance of toxic water blooms in aquatic environments.

Detection and sequencing of the microcystin LR-degrading gene, mlrA, from new bacteria isolated from Japanese lakes.

mlrA is the only microcystin-degrading gene detected in Sphingomonas sp. MJ-PV. The gene has an extremely rare nucleotide sequence and homologous genes have not yet been discovered in the DNA database. We discovered the existence of a gene homologous to mlrA in new microcystin-degrading bacteria, MD-1 and Y2. These strains possessed mlrA homologues, and the identities of the genes of MD-1 and Y2 with the corresponding MJ-PV exceeded 98% and 84%, respectively. On the other hand, the mlrA gene was not detected in laboratory strains of the closely related Sphingomonas spp. strains employing hemi-nested polymerase chain reaction detection using two primer sets. Although the microcystin-degrading bacteria were closely related strains, they did not cluster together as the same species. We can conclude that the mlrA gene is conserved in three different bacterial species, and it is unique to microcystin degraders but not to the genus Sphingomonas.