Paucibacter toxinivorans gen. nov., sp. nov., a bacterium that degrades cyclic cyanobacterial hepatotoxins microcystins and nodularin

Paucibacter sediminis sp. nov., isolated from sediment in a freshwater pond

A Gram-stain-negative, aerobic, oxidase-positive, weakly catalase-positive, motile by means of a single polar flagellum, rod-shaped bacterium designated as strain S2-9T was isolated from sediment sampled in Wiyang pond, Republic of Korea. Growth of this strain was observed at 10-40 °C (optimum, 35 °C) and pH 5.5-9.5 (optimum, pH 7.0-8.0) and in the presence of 0-0.5 % NaCl in Reasoner's 2A broth. The major fatty acids (>10 %) of strain S2-9T were C16 : 0 and summed feature 3 (comprising a mixture of C16 : 1  ω7c and/or C16 : 1  ω6c). Ubiquinone-8 was detected as the respiratory quinone. The major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. Strain S2-9T showed the highest 16S rRNA gene sequence similarity to Paucibacter oligotrophus CHU3T (98.7 %), followed by 'Paucibacter aquatile' CR182 (98.4 %), all type strains of Pelomonas species (98.1-98.3 %), Mitsuaria chitosanitabida NBRC 102408T (97.9 %), Kinneretia asaccharophila KIN192T (97.8 %), Mitsuaria chitinivorans HWN-4T (97.4 %), and Paucibacter toxinivorans 2C20T (97.4 %). Phylogenetic trees based on the 16S rRNA gene and whole-genome sequences showed that strain S2-9T formed a tight phylogenetic lineage with Paucibacter species (CHU3T, CR182, and 2C20T). Average nucleotide identity and digital DNA-DNA hybridization values between strain S2-9T and Paucibacter strains were 76.6-79.3% and 19.5-21.5 %, respectively. The genomic DNA G+C content of strain S2-9T was 68.3 mol%. Notably, genes responsible for both sulphur oxidation and reduction and denitrification were found in the genome of strain S2-9T, suggesting that strain S2-9T is involved in the nitrogen and sulphur cycles in pond ecosystems. Based on the polyphasic taxonomic results, strain S2-9T represents a novel species of the genus Paucibacter, for which the name Paucibacter sediminis sp. nov. is proposed. The type strain is S2-9T (= KACC 22267T= JCM 34541T).

Microcystin influence on soil-plant microbiota: Unraveling microbiota modulations and assembly processes in the rhizosphere of Vicia faba

Microcystins (MCs) are frequently detected in cyanobacterial bloom-impacted waterbodies and introduced into agroecosystems via irrigation water. They are widely known as phytotoxic cyanotoxins, which impair the growth and physiological functions of crop plants. However, their impact on the plant-associated microbiota is scarcely tackled and poorly understood. Therefore, we aimed to investigate the effect of MCs on microbiota-inhabiting bulk soil (BS), root adhering soil (RAS), and root tissue (RT) of Vicia faba when exposed to 100 μg L-1 MCs in a greenhouse pot experiment. Under MC exposure, the structure, co-occurrence network, and assembly processes of the bacterial microbiota were modulated with the greatest impact on RT-inhabiting bacteria, followed by BS and, to a lesser extent, RAS. The analyses revealed a significant decrease in the abundances of several Actinobacteriota-related taxa within the RT microbiota, including the most abundant and known genus of Streptomyces. Furthermore, MCs significantly increased the abundance of methylotrophic bacteria (Methylobacillus, Methylotenera) and other Proteobacteria-affiliated genera (e.g., Paucibacter), which are supposed to degrade MCs. The co-occurrence network of the bacterial community in the presence of MCs was less complex than the control network. In MC-exposed RT, the turnover in community composition was more strongly driven by deterministic processes, as proven by the beta-nearest taxon index. Whereas in MC-treated BS and RAS, both deterministic and stochastic processes can influence community assembly to some extent, with a relative dominance of deterministic processes. Altogether, these results suggest that MCs may reshape the structure of the microbiota in the soil-plant system by reducing bacterial taxa with potential phytobeneficial traits and increasing other taxa with the potential capacity to degrade MCs.

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.

Genomic Insights into Paucibacter aquatile DH15, a Cyanobactericidal Bacterium, and Comparative Genomics of the Genus Paucibacter

Microcystis blooms threaten ecosystem function and cause substantial economic losses. Microorganism-based methods, mainly using cyanobactericidal bacteria, are considered one of the most ecologically sound methods to control Microcystis blooms. This study focused on gaining genomic insights into Paucibacter aquatile DH15 that exhibited excellent cyanobactericidal effects against Microcystis. Additionally, a pan-genome analysis of the genus Paucibacter was conducted to enhance our understanding of the ecophysiological significance of this genus. Based on phylogenomic analyses, strain DH15 was classified as a member of the species Paucibacter aquatile. The genome analysis supported that strain DH15 can effectively destroy Microcystis, possibly due to the specific genes involved in the flagellar synthesis, cell wall degradation, and the production of cyanobactericidal compounds. The pan-genome analysis revealed the diversity and adaptability of the genus Paucibacter, highlighting its potential to absorb external genetic elements. Paucibacter species were anticipated to play a vital role in the ecosystem by potentially providing essential nutrients, such as vitamins B7, B12, and heme, to auxotrophic microbial groups. Overall, our findings contribute to understanding the molecular mechanisms underlying the action of cyanobactericidal bacteria against Microcystis and shed light on the ecological significance of the genus Paucibacter.

Metagenomic analysis reveals diverse microbial community and potential functional roles in Baner rivulet, India

BACKGROUND

The health index of any population is directly correlated with the water quality, which in turn depends upon physicochemical characteristics and the microbiome of that aquatic source. For maintaining the water quality, knowledge of microbial diversity is a must. The present investigation attempts to evaluate the microflora of Baner. Metagenomics has been proven to be the technique for examining the genetic diversity of unculturable microbiota without using traditional culturing techniques. The microbial profile of Baner is analyzed using metagenomics for the first time to the best of our knowledge.

RESULTS

To explore the microbial diversity of Baner, metagenomics analysis from 3 different sites was done. Data analysis identified 29 phyla, 62 classes, 131 orders, 268 families, and 741 genera. Proteobacteria was found to be the most abundant phylum in all the sampling sites, with the highest abundance at S3 sampling site (94%). Bacteroidetes phylum was found to be second abundant in S1 and S2 site, whereas Actinobacteria was second dominant in sampling site S3. Enterobacteriaceae family was dominant in site S1, whereas Comamonadaceae and Pseudomonadaceae was abundant in sites S2 and S3 respectively. The Baner possesses an abundant bacterial profile that holds great promise for developing bioremediation tactics against a variety of harmful substances.

CONCLUSION

Baner river's metagenomic analysis offers the first insight into the microbial profile of this hilly stream. Proteobacteria was found to be the most abundant phylum in all the sampling sites indicating anthropogenic interference and sewage contamination. The highest abundance of proteobacteria at S3 reveals it to be the most polluted site, as it is the last sampling site downstream of the area under investigation, and falls after crossing the main city, so more human intervention and pollution were observed. Despite some pathogens, a rich profile of bacteria involved in bioremediation, xenobiotic degradation, and beneficial fish probiotics was observed, reflecting their potential applications for improving water quality and establishing a healthy aquaculture and fishery section.

Roseateles amylovorans sp. nov., isolated from freshwater

A Gram-stain-negative, rod-shaped, amylolytic bacterial strain, designated as bsSlp3-1T, was isolated from the Slepian water system, a freshwater reservoir. Strain bsSlp3-1T was found to be aerobic, oxidase-positive and catalase-negative, grew at 5-37 °C (optimum, 28 °C), pH 5.0-9.5 (optimum, pH 7.0) and low NaCl concentration (up to 1.0 %). Comparative analysis of 16S rRNA gene sequence similarity revealed that strain bsSlp3-1T clustered with Roseateles species and is closely related to Roseateles depolymerans KCTC 42856T (98.7 %) and Roseateles terrae CCUG 52222T (98.6 %). Whole-genome comparisons using average nucleotide identity and digital DNA-DNA hybridization values suggested that strain bsSlp3-1T represents a novel species within the genus Roseateles and is most closely related to Roseateles aquatilis CCUG 48205T (81.2 and 25.6 %, respectively). The genome of strain bsSlp3-1T consisted of a single circular chromosome with size 6 289 366 bp and DNA G+C content of 66.8 mol%. The predominant cellular fatty acids of bsSlp3-1T were cis-9-hexadecanoic and hexadecenoic acids. According to the data obtained in this work, strain bsSlp3-1T represents a novel Roseateles species for which the name Roseateles amylovorans sp. nov. is proposed. The type strain is bsSlp3-1T (=BIM B-1768T=NBIMCC 9098T=VKM B-3671T).

Roseateles albus sp. nov., Roseateles koreensis sp. nov. and Janthinobacterium fluminis sp. nov., isolated from freshwater at Jucheon River, and emended description of Roseateles aquaticus comb. nov

Three Gram-stain-negative, facultatively anaerobic, rod-shaped, catalase-positive, oxidase-negative bacterial strains were designated as hw1T, hw8T and hw3T. Strains hw1T, hw8T and hw3T grew at 15-28 °C (optimum, 25 °C), 15-35 °C (optimum, 30 °C) and 4-28 °C (optimum, 20 °C), respectively, and at pH 7.0-12.0 (optimum, pH 9.0), pH 6.0-11.0 (optimum, pH 9.0) and 5.0-12.0 (optimum, pH 7.0), respectively. Additionally, strains hw1T and hw8T only grew when the NaCl concentration was 0 %, while strain hw3T grew at between 0 and 0.5 % (w/v; optimum, 0 %). The average nucleotide identity (ANI) values between strains hw1T, hw8T and the Roseateles type strains ranged from 73.8 to 84.2 %, while the digital DNA-DNA hybridization (dDDH) values ranged from 19.7 to 27.5 %. The ANI values between strain hw3T and the Janthinobacterium type strains ranged from 78.7 to 80.7 %, while dDDH values ranged from 22.3 to 23.0 %. The draft genomes of strains hw1T, hw8T and hw3T consisted of 5.5, 4.4 and 5.9 Mbp, with DNA G+C contents of 61.7, 61.8 and 66.0 mol%, respectively. The results of the dDDH, ANI, phylogenetic, biochemical and physiological analyses indicated that the novel strains were distinct from other members of their genera. Thus, we proposed the names Roseateles albus sp. nov. (type strain hw1T= KACC 22887T= TBRC 16613T), Roseateles koreensis sp. nov. (type strain hw8T= KACC 22885T= TBRC 16614T) and Janthinobacterium fluminis sp. nov. (type strain hw3T= KACC 22886T= TBRC 16615T).

Neotropical Frog Foam Nest’s Microbiomes

Amphibian foam nests are unique microenvironments that play a crucial role in the development of tadpoles. They contain high levels of proteins and carbohydrates, yet little is known about the impact of their microbiomes on tadpole health. This study provides a first characterization of the microbiome of foam nests from three species of Leptodactylids (Adenomera hylaedactyla, Leptodactylus vastus, and Physalaemus cuvieri) by investigating the DNA extracted from foam nests, adult tissues, soil, and water samples, analyzed via 16S rRNA gene amplicon sequencing to gain insight into the factors driving its composition. The results showed that the dominant phyla were proteobacteria, bacteroidetes, and firmicutes, with the most abundant genera being Pseudomonas, Sphingobacterium, and Paenibacillus. The foam nest microbiomes of A. hylaedactyla and P. cuvieri were more similar to each other than to that of L. vastus, despite their phylogenetic distance. The foam nests demonstrated a distinct microbiome that clustered together and separated from the microbiomes of the environment and adult tissue samples. This suggests that the peculiar foam nest composition shapes its microbiome, rather than vertical or horizontal transference forces. We expanded this knowledge into amphibian foam nest microbiomes, highlighting the importance of preserving healthy foam nests for amphibian conservation.

Diversity, distribution and organic substrates preferences of microbial communities of a low anthropic activity cave in North-Western Romania

Introduction

Karst caves are characterized by relatively constant temperature, lack of light, high humidity, and low nutrients availability. The diversity and functionality of the microorganisms dwelling in caves micro-habitats are yet underexplored. Therefore, in-depth investigations of these ecosystems aid in enlarging our understanding of the microbial interactions and microbially driven biogeochemical cycles. Here, we aimed at evaluating the diversity, abundance, distribution, and organic substrate preferences of microbial communities from Peștera cu Apă din Valea Leșului (Leșu Cave) located in the Apuseni Mountains (North-Western Romania).

Materials and Methods

To achieve this goal, we employed 16S rRNA gene amplicon sequencing and community-level physiological profiling (CLPP) paralleled by the assessment of environmental parameters of cave sediments and water.

Results and Discussion

Pseudomonadota (synonym Proteobacteria) was the most prevalent phylum detected across all samples whereas the abundance detected at order level varied among sites and between water and sediment samples. Despite the general similarity at the phylum-level in Leșu Cave across the sampled area, the results obtained in this study suggest that specific sites drive bacterial community at the order-level, perhaps sustaining the enrichment of unique bacterial populations due to microenvironmental conditions. For most of the dominant orders the distribution pattern showed a positive correlation with C-sources such as putrescine, γ-amino butyric acid, and D-malic acid, while particular cases were positively correlated with polymers (Tween 40, Tween 80 and α-cyclodextrin), carbohydrates (α-D-lactose, i-erythritol, D-mannitol) and most of the carboxylic and ketonic acids. Physicochemical analysis reveals that sediments are geochemically distinct, with increased concentration of Ca, Fe, Al, Mg, Na and K, whereas water showed low nitrate concentration. Our PCA indicated the clustering of different dominant orders with Mg, As, P, Fe, and Cr. This information serves as a starting point for further studies in elucidating the links between the taxonomic and functional diversity of subterranean microbial communities.

Review: Current understanding on biological filtration for the removal of microcystins

Harmful algal blooms (HABs) have become a global problem not only in aquatic habitats but also in public health and safety due to the production of cyanotoxins as their secondary metabolites. Among the various identified cyanotoxin groups, microcystins (MCs) are one of the most prevalent cyanotoxin detected during HABs. Different strategies including advanced physical and chemical treatment processes have been developed to mitigate the threat of cyanotoxins in water utilities, but these have revealed certain limitations in terms of high operational costs, low removal efficacy, and harmful by-products formation. Recently, biological filtration systems (BFS) have gained attention for safe drinking water production as they can treat various natural organic matter (NOM) and emerging contaminants through a highly efficient and environmentally sustainable process. However, limited attention has been given to understand the current research progress, research challenges, and knowledge gaps for the successful implementation of BFS for MC removal. Therefore, in this review, currently identified MC biodegradation pathways and MC-degrading microorganisms with their degradation rates are summarized, which may be pivotal for studying bioaugmented BFS to enhance the MC removal during HABs. Moreover, both laboratory and field studies on BFS for MC removal are reviewed, followed by a discussion of current challenges and future research needs for the practical application of BFS.

Functional modulation of chemical mediators in microbial communities

Interactions between microorganisms are often mediated by specialized metabolites. Although the structures and biosynthesis of these compounds may have been elucidated, microbes exist within complex microbiomes and chemical signals can thus also be subject to community-dependent modifications. Increasingly powerful chemical and biological tools allow to shed light on this poorly understood aspect of chemical ecology. We provide an overview of loss-of-function and gain-of-function chemical mediator (CM) modifications within microbial multipartner relationships. Although loss-of-function modifications are abundant in the literature, few gain-of-function modifications have been described despite their important role in microbial interactions. Research in this field holds great potential for our understanding of microbial interactions and may also provide novel tools for targeted interference with microbial signaling.

The cyanobactericidal bacterium Paucibacter aquatile DH15 caused the decline of Microcystis and aquatic microbial community succession: A mesocosm study

Microcystis blooms pose a major threat to the quality of drinking water. Cyanobactericidal bacteria have attracted much attention in the research community as a vehicle for controlling Microcystis blooms because of their ecological safety. Nonetheless, most studies on cyanobactericidal bacteria have been conducted on a laboratory scale but have not been scaled-up as field experiments. Thus, our understanding of the microbial response to cyanobactericidal bacteria in natural ecosystems remains elusive. Herein, we applied Paucibacter aquatile DH15 to control Microcystis blooms in a 1000 L mesocosm experiment and demonstrated its potential with the following results: (1) DH15 reduced Microcystis cell density by 90.7% within two days; (2) microcystins released by Microcystis death decreased to the control level in four days; (3) during the cyanobactericidal processes, the physicochemical parameters of water quality remained safe for other aquatic organisms; and (4) the cyanobactericidal processes promoted the growth of eukaryotic microalgae, replacing cyanobacteria. The cyanobactericidal processes accelerated turnover rates, decreased stability, and altered the functional profile of the microbial community. Network analysis demonstrated that this process resulted in more complex interactions between microbes. Overall, our findings suggest that strain DH15 could be considered a promising candidate for controlling Microcystis blooms in an eco-friendly manner.

Algicide capacity of Paucibacter aquatile DH15 on Microcystis aeruginosa by attachment and non-attachment effects

The excessive proliferation of Microcystis aeruginosa can lead to ecological damage, economic losses, and threaten animal and human health. For controlling Microcystis blooms, microorganism-based methods have attracted much attention from researchers because of their eco-friendliness and species-specificity. Herein, we first found that a Paucibacter strain exhibits algicidal activity against M. aeruginosa and microcystin degradation capability. The algicidal activity of DH15 (2.1 × 10⁴ CFU/ml) against M. aeruginosa (2 × 10⁶ cells/ml) was 94.9% within 36 h of exposure. DH15 also degraded microcystin (1.6 mg/L) up to 62.5% after 72 h. We demonstrated that the algicidal activity of DH15 against M. aeruginosa can be mediated by physical attachment and indirect attack: (1) Both washed cells and cell-free supernatant could kill M. aeruginosa efficiently; (2) Treatment with DH15 cell-free supernatants caused oxidative stress, altered the fatty acid profile, and damaged photosynthetic system, carbohydrate, and protein metabolism in M. aeruginosa. The combination of direct and indirect attacks supported that strain DH15 exerts high algicidal activity against M. aeruginosa. The expression of most key genes responsible for photosynthesis, antioxidant activity, microcystin synthesis, and other metabolic pathways in M. aeruginosa was downregulated. Strain DH15, with its microcystin degradation capacity, can overcome the trade-off between controlling Microcystis blooms and increasing microcystin concentration. Our findings suggest that strain DH15 possesses great potential to control outbreaks of Microcystis blooms.

Genomic Analysis of Sphingopyxis sp. USTB-05 for Biodegrading Cyanobacterial Hepatotoxins

Sphingopyxis sp. USTB-05, which we previously identified and examined, is a well-known bacterial strain for biodegrading cyanobacterial hepatotoxins of both nodularins (NODs) and microcystins (MCs). Although the pathways for biodegrading the different types of [D-Asp¹] NOD, MC-YR, MC-LR and MC-RR by Sphingopyxis sp. USTB-05 were suggested, and several biodegradation genes were successfully cloned and expressed, the comprehensive genomic analysis of Sphingopyxis sp. USTB-05 was not reported. Here, based on second and third generation sequencing technology, we analyzed the whole genome of Sphingopyxis sp. USTB-05, which is 4,679,489 bp and contains 4,312 protein coding genes. There are 88 protein-coding genes related to the NODs and MCs biodegradation, of which 16 genes (bioA, hmgL, hypdh, speE, nspC, phy, spuC, murD, glsA, ansA, ocd, crnA, ald, gdhA, murC and murI) are unique. These genes for the transformation of phenylacetic acid CoA (PA-CoA) to CO₂ were also found in Sphingopyxis sp. USTB-05. This study expands the understanding of the pathway for complete biodegradation of cyanobacterial hepatotoxins by Sphingopyxis sp. USTB-05.

Widespread Distribution and Adaptive Degradation of Microcystin Degrader (mlr-Genotype) in Lake Taihu, China

Microbial degradation is an important route for removing environmental microcystins (MCs). Here, we investigated the ecological distribution of microcystin degraders (mlr-genotype), and the relationship between the substrate specificity of the microcystin degrader and the profile of microcystin congener production in the habitat. We showed that microcystin degraders were widely distributed and closely associated with Microcystis abundance in Lake Taihu, China. We characterized an indigenous degrader, Sphingopyxis N5 in the northern Lake Taihu, and it metabolized six microcystin congeners in increasing order (RR > LR > YR > LA > LF and LW). Such a substrate-specificity pattern was congruent to the order of the dominance levels of these congeners in northern Lake Taihu. Furthermore, a meta-analysis on global microcystin degraders revealed that the substrate-specificity patterns varied geographically, but generally matched the profiles of microcystin congener production in the degrader habitats, and the indigenous degrader typically metabolized well the dominant MC congeners, but not the rare congeners in the habitat. This highlighted the phenotypic congruence between microcystin production and degradation in natural environments. We theorize that such congruence resulted from the metabolic adaptation of the indigenous degrader to the local microcystin congeners. Under the nutrient microcystin selection, the degraders might have evolved to better exploit the locally dominant congeners. This study provided the novel insight into the ecological distribution and adaptive degradation of microcystin degraders.

Biodegradation of Nodularin by a Microcystin-Degrading Bacterium: Performance, Degradation Pathway, and Potential Application

Currently, studies worldwide have comprehensively recognized the importance of Sphingomonadaceae bacteria and the mlrCABD gene cluster in microcystin (MC) degradation. However, knowledge about their degradation of nodularin (NOD) is still unclear. In this study, the degradation mechanism of NOD by Sphingopyxis sp. m6, an efficient MC degrader isolated from Lake Taihu, was investigated in several aspects, including degradation ability, degradation products, and potential application. The strain degraded NOD of 0.50 mg/L with a zero-order rate constant of 0.1656 mg/L/d and a half-life of 36 h. The average degradation rate of NOD was significantly influenced by the temperature, pH, and initial toxin concentrations. Moreover, four different biodegradation products, linear NOD, tetrapeptide H-Glu-Mdhb-MeAsp-Arg-OH, tripeptide H-Mdhb-MeAsp-Arg-OH, and dipeptide H-MeAsp-Arg-OH, were identified, of which the latter two are the first reported. Furthermore, the four mlr genes were upregulated during NOD degradation. The microcystinase MlrA encoded by the mlrA gene hydrolyzes the Arg-Adda bond to generate linear NOD as the first step of NOD biodegradation. Notably, recombinant MlrA showed higher degradation activity and stronger environmental adaptability than the wild strain, suggesting future applications in NOD pollution remediation. This research proposes a relatively complete NOD microbial degradation pathway, which lays a foundation for exploring the mechanisms of NOD degradation by MC-degrading bacteria.

Association of the alga Cladogonium sp. with a multifactorial disease outbreak in dwarf shrimp (Neocaridina davidi)

This study outlines a multifactorial disease outbreak in a population of the freshwater shrimp Neocaridina davidi, with the focus on a rarely described parasitic alga. Within this multifactorial disease outbreak, low but consistent mortality was observed. During microscopic examination, an infection of the shrimp with bacterial and fungal-like agents was diagnosed. Furthermore, the green alga Cladogonium sp. was found in pleopodal regions. The alga compromised the body surface of the shrimp, and its rhizoids penetrated the chitin shell and reached into the subcutaneous tissue. This might be a first indication of a parasitic lifestyle. In addition to a morphological description, sequencing data are presented which allow the taxonomic classification of the organism within the order Trentepohliales.

Role of Rhizospheric Microbiota as a Bioremediation Tool for the Protection of Soil-Plant Systems from Microcystins Phytotoxicity and Mitigating Toxin-Related Health Risk

Frequent toxic cyanoblooms in eutrophic freshwaters produce various cyanotoxins such as the monocyclic heptapeptides microcystins (MCs), known as deleterious compounds to plant growth and human health. Recently, MCs are a recurrent worldwide sanitary problem in irrigation waters and farmland soils due to their transfer and accumulation in the edible tissues of vegetable produce. In such cases, studies about the persistence and removal of MCs in soil are scarce and not fully investigated. In this study, we carried out a greenhouse trial on two crop species: faba bean (Vicia faba var. Alfia 321) and common wheat (Triticum aestivum var. Achtar) that were grown in sterile (microorganism-free soil) and non-sterile (microorganism-rich soil) soils and subjected to MC-induced stress at 100 µg equivalent MC-LR L⁻¹. The experimentation aimed to assess the prominent role of native rhizospheric microbiota in mitigating the phytotoxic impact of MCs on plant growth and reducing their accumulation in both soils and plant tissues. Moreover, we attempted to evaluate the health risk related to the consumption of MC-polluted plants for humans and cattle by determining the estimated daily intake (EDI) and health risk quotient (RQ) of MCs in these plants. Biodegradation was liable to be the main removal pathway of the toxin in the soil; and therefore, bulk soil (unplanted soil), as well as rhizospheric soil (planted soil), were used in this experiment to evaluate the accumulation of MCs in the presence and absence of microorganisms (sterile and non-sterile soils). The data obtained in this study showed that MCs had no significant effects on growth indicators of faba bean and common wheat plants in non-sterile soil as compared to the control group. In contrast, plants grown in sterile soil showed a significant decrease in growth parameters as compared to the control. These results suggest that MCs were highly bioavailable to the plants, resulting in severe growth impairments in the absence of native rhizospheric microbiota. Likewise, MCs were more accumulated in sterile soil and more bioconcentrated in root and shoot tissues of plants grown within when compared to non-sterile soil. Thereby, the EDI of MCs in plants grown in sterile soil was more beyond the tolerable daily intake recommended for both humans and cattle. The risk level was more pronounced in plants from the sterile soil than those from the non-sterile one. These findings suggest that microbial activity, eventually MC-biodegradation, is a crucial bioremediation tool to remove and prevent MCs from entering the agricultural food chain.

Genomic insight for algicidal activity in Rhizobium strain AQ_MP

Occurrence of Harmful Algal Blooms (HABs) creates a threat to aquatic ecosystem affecting the existing flora and fauna. Hence, the mitigation of HABs through an eco-friendly approach remains a challenge for environmentalists. The present study provides the genomic insights of Rhizobium strain AQ_MP, an environmental isolate that showed the capability of degrading Microcystis aeruginosa (Cyanobacteria) through lytic mechanisms. Genome sequence analysis of Rhizobium strain AQ_MP unraveled the algal lytic features and toxin degradative pathways in it. Functional genes of CAZymes such as glycosyltransferases (GT), glycoside hydrolases (GH), polysaccharide lyases (PL) which supports algal polysaccharide degradation (lysis) were present in Rhizobium strain AQ_MP. Genome analysis also clarified the presence of the glutathione metabolic pathway, which is the biological detoxification pathway responsible for toxin degradation. The conserved region mlrC, a microcystin toxin-degrading gene was also annotated in the genome. The study illustrated that Rhizobium strain AQ_MP harbored a wide range of mechanisms for the lysis of Microcystis aeruginosa cells and its toxin degradation. In future, this study finds promiscuity for employing Rhizobium strain AQ_MP species for bioremediation, based on its physiological and genomic analysis.

Degradation of Multiple Peptides by Microcystin-Degrader Paucibacter toxinivorans (2C20)

Since conventional drinking water treatments applied in different countries are inefficient at eliminating potentially toxic cyanobacterial peptides, a number of bacteria have been studied as an alternative to biological filters for the removal of microcystins (MCs). Here, we evaluated the degradation of not only MCs variants (-LR/DM-LR/-RR/-LF/-YR), but also non-MCs peptides (anabaenopeptins A/B, aerucyclamides A/D) by Paucibactertoxinivorans over 7 days. We also evaluated the degradation rate of MC-LR in a peptide mix, with all peptides tested, and in the presence of M. aeruginosa crude extract. Furthermore, biodegradation was assessed for non-cyanobacterial peptides with different chemical structures, such as cyclosporin A, (Glu1)-fibrinopeptide-B, leucine-enkephalin, and oxytocin. When cyanopeptides were individually added, P. toxinivorans degraded them (99%) over 7 days, except for MC-LR and -RR, which decreased by about 85 and 90%, respectively. The degradation rate of MC-LR decreased in the peptide mix compared to an individual compound, however, in the presence of the Microcystis extract, it was degraded considerably faster (3 days). It was noted that biodegradation rates decreased in the mix for all MCs while non-MCs peptides were immediately degraded. UPLC-QTOF-MS/MS allowed us to identify two linear biodegradation products for MC-LR and MC-YR, and one for MC-LF. Furthermore, P. toxinivorans demonstrated complete degradation of non-cyanobacterial peptides, with the exception of oxytocin, where around 50% remained after 7 days. Thus, although P. toxinivorans was previously identified as a MC-degrader, it also degrades a wide range of peptides under a range of conditions, which could be optimized as a potential biological tool for water treatment.

Comprehensive insights into the occurrence and toxicological issues of nodularins

The occurrence of cyanobacterial toxins is being increasingly reported. Nodularins (NODs) are one of the cyanotoxins group mainly produced by Nodularia spumigena throughout the world. NODs may exert adverse effects on animal and human health, and NOD-R variant is the most widely investigated. However, research focused on them is still limited. In order to understand the realistic risk well, the aim of this review is to compile the available information in the scientific literature regarding NODs, including their sources, distribution, structural characteristics, physicochemical properties, biosynthesis and degradation, adverse effects in vitro and vivo, and toxicokinetics. More data is urgently needed to integrate the cumulative or synergistic effects of NODs on different species and various cells to better understand, anticipate and aggressively manage their potential toxicity after both short- and long-term exposure in ecosystem, and to minimize or prevent the adverse effects on human health, environment and the economy.

Exploring microcystin-degrading bacteria thriving on recycled membranes during a cyanobacterial bloom

Microcystins (MC) are highly toxic secondary metabolites produced by cyanobacterial blooms in many freshwater ecosystems used for recreational and drinking water purposes. So far, biological processes remain to be optimized for an efficient cyanotoxin removal, and new approaches are necessary to compete with physical-chemical treatments. In previous studies we provided a new concept of membrane biofilm reactor made of recycled material, in which a single MC-degrading bacterial strain was inoculated. The present study evaluates the capacity of bacterial consortia associated with freshwater cyanobacterial blooms to form biofilms on recycled membranes and remove MC. Three different discarded reverse osmosis (RO) membranes, previously used in desalination plants after treating brackish water (BWd), seawater (SWd) and brackish water but transformed into nanofiltration (BWt-NF), were exposed to a cyanobacterial bloom in San Juan reservoir (central Spain). Results showed that the three recycled membranes developed a bacterial community with MC removal capacity. Little differences in bacterial coverage and MC removal efficiency between membranes were observed after their exposure in the reservoir. High-throughput sequencing of 16S rRNA gene analysis showed similar bacterial community composition at the phylum level but dissimilar at the order level between the three membranes. This suggests possible surface selectivity on the attached bacterial community. The mlr^- candidates such as Burkholderiales and Methylophilales were highly abundant in BWt-NF and BWd, respectively, while mlr⁺ candidates (e.g. Sphingomonadales) were low abundant in all membranes. Analysis of mlrA and mlrB genes used as markers for MC degradation following mlr-pathway confirmed the presence of this pathway in all membranes. These results suggest the co-existence of both genotypes in membrane-attached native biofilms. Therefore, this study confirms that recycled membranes are suitable support for many MC-degrading bacteria, thus giving value to discarded membranes for eco-friendly and low-cost biological filters.

Taxonomic and Genotypical Heterogeneity of Microcystin degrading Bacterioplankton in Western Lake Erie

Microcystins (MCs) are among the predominant cyanotoxins that are primarily degraded by heterotrophic bacteria in various freshwater environments, including Lake Erie, a Laurentian Great Lake. However, despite the prevalence of MCs in Lake Erie basins, our knowledge about the taxonomic diversity of local MC-degrading bacteria is largely limited. The current study obtained thirty-four MC-degrading bacterial pure isolates from Lake Erie surface water and characterized their taxonomical and phenotypic identities as well as their MC-degradation rates under different pH, temperature, availability of organic substrates and with other MC-degrading isolates. Obtained MC-degrading isolates included both Gram-positive (18 isolates of Actinobacteria and Firmicutes) and Gram-negative bacteria (16 isolates of Gamma-proteobacteria); and 7 of these isolates were motile, and 13 had the capacity to form biofilms. In general, MC-degradation rates of the isolates were impacted by temperature and pH but insensitive to the presence of cyanobacterial exudates. At the optimal temperature (30-35°C) and pH (7-8), individual isolates degraded MC-LR, the most abundant MC isomer, at an average of 0.20 µg/mL/hr. With additions of cyanobacterial exudates, only Pseudomonas sp. LEw-2029, a non-motile biofilm maker, showed increased MC degradation (0.25 µg/mL/hr). Five out of nine tested dual culture mixtures showed rises in MC degradation rates than their corresponding monocultures; the highest rate reached 0.40 µg/mL/hr for the pair LEw-(1132 + 2029). PCR amplification of mlrA genes yielded negative results for all isolates; subsequent enzyme assay-Mass Spectrum analysis identified no product associated with the mlr gene-based MC degradation pathway. Collectively, our results demonstrated that a diversity of indigenous Lake Erie bacteria can degrade MCs via a novel mlr-independent pathway. Obtained MC degraders, especially Pseudomonas sp. LEw-2029, may serve as candidates for the development of biological filters to remove cyanotoxins in water treatment systems.

A complete route for biodegradation of potentially carcinogenic cyanotoxin microcystin-LR in a novel indigenous bacterium

Microcystin-leucine-arginine (MC-LR), a cyclic potentially carcinogenic hepatotoxin, occurs frequently in aquatic habitats worldwide and seriously threatens ecosystem and public health. Limited effectiveness of physicochemical treatments to remove MC-LR from drinking water has led to a search for alternative cost-effective and environment friendly biodegradation strategies. Obtaining MC-degrading bacteria and understanding their MC-degrading mechanisms are outstanding challenges. Here, a novel indigenous bacterium named Sphingopyxis sp. YF1 with a high efficient capacity for MC-degradation was successfully isolated from eutrophic Lake Taihu. Through integrating mass spectrometer and multi-omics analyses accompanied by functional verification of certain genes and proteins, a complete MC-degradation pathway was firstly identified, in which MC-LR was sequentially degraded into linearized MC-LR, tetrapeptide, Adda, phenylacetic acid, and finally potential product CO₂. Some specific proteins such as microcystinase, linearized-microcystinase, tetrapeptidease and PAAase responsible for this pathway were identified. This study pioneeringly demonstrated that MC-LR can be completely degraded through natural remediation processes and revealed a significant potential for MC-LR biodegradation in both natural environment and engineered systems.

A Mini Review on Microcystins and Bacterial Degradation

Microcystins (MCs) classified as hepatotoxic and carcinogenic are the most commonly reported cyanobacterial toxins found in the environment. Microcystis sp. possessing a series of MC synthesis genes (mcyA-mcyJ) are well documented for their excessive abundance, numerous bloom occurrences and MC producing capacity. About 246 variants of MC which exert severe animal and human health hazards through the inhibition of protein phosphatases (PP1 and PP2A) have been characterized. To minimize and prevent MC health consequences, the World Health Organization proposed 1 µg/L MC guidelines for safe drinking water quality. Further the utilization of bacteria that represent a promising biological treatment approach to degrade and remove MC from water bodies without harming the environment has gained global attention. Thus the present review described toxic effects and bacterial degradation of MCs.

Network analysis reveals succession of Microcystis genotypes accompanying distinctive microbial modules with recurrent patterns

Every member of the ecological community is connected via a network of vital and complex relationships, called the web of life. To elucidate the ecological network and interactions among producers, consumers, and decomposers in the Daechung Reservoir, Korea, during cyanobacterial harmful algal blooms (cyanoHAB), especially those involving Microcystis, we investigated the diversity and compositions of the cyanobacterial (16S rRNA gene), including the genotypes of Microcystis (cpcBA-IGS gene), non-cyanobacterial (16S), and eukaryotic (18S) communities through high-throughput sequencing. Microcystis blooms were divided into the Summer Major Bloom and Autumn Minor Bloom with different dominant genotypes of Microcystis. Network analysis demonstrated that the modules involved in the different phases of the Microcystis blooms were categorized into the Pre-Bloom, Bloom, Post-Bloom, and Non-Bloom Groups at all sampling stations. In addition, the non-cyanobacterial components of each Group were classified, while the same Group showed similarity across all stations, suggesting that Microcystis and other microbes were highly interdependent and organized into cyanoHAB-related module units. Importantly, the Microcystis genotype-based sub-network uncovered that Pirellula, Pseudanabaena, and Vampirovibrionales preferred to interact with specific Microcystis genotypes in the Summer Major Bloom than with other genotypes in the Autumn Minor Bloom, while the copepod Skistodiaptomus exhibited the opposite pattern. In conclusion, the transition patterns of cyanoHAB-related modules and their key components could be crucial in the succession of Microcystis genotypes and to enhance the understanding of microbial ecology in an aquatic environment.

Priming of microcystin degradation in carbon-amended membrane biofilm communities is promoted by oxygen-limited conditions

Microbial biofilms are an important element of gravity-driven membrane (GDM) filtration systems for decentralized drinking water production. Mature biofilms fed with biomass from the toxic cyanobacterium Microcystis aeruginosa efficiently remove the cyanotoxin microcystin (MC). MC degradation can be ‘primed’ by prior addition of biomass from a non-toxic M. aeruginosa strain. Increased proportions of bacteria with an anaerobic metabolism in M. aeruginosa-fed biofilms suggest that this ‘priming’ could be due to higher productivity and the resulting changes in habitat conditions. We, therefore, investigated GDM systems amended with the biomass of toxic (WT) or non-toxic (MUT) M. aeruginosa strains, of diatoms (DT), or with starch solution (ST). After 25 days, these treatments were changed to receiving toxic cyanobacterial biomass. MC degradation established significantly more rapidly in MUT and ST than in DT. Oxygen measurements suggested that this was due to oxygen-limited conditions in MUT and ST already prevailing before addition of MC-containing biomass. Moreover, the microbial communities in the initial ST biofilms featured high proportions of facultative anaerobic taxa, whereas aerobes dominated in DT biofilms. Thus, the ‘priming’ of MC degradation in mature GDM biofilms seems to be related to the prior establishment of oxygen-limited conditions mediated by higher productivity.

Cloning and Expression of Genes for Biodegrading Nodularin by Sphingopyxis sp. USTB-05

Biodegradation is efficient for removing cyanobacterial toxins, such as microcystins (MCs) and nodularin (NOD). However, not all the microbial strains with the microcystin-biodegrading enzymes MlrA and MlrC could biodegrade NOD. Studies on genes and enzymes for biodegrading NOD can reveal the function and the biodegradation pathway of NOD. Based on successful cloning and expression of the USTB-05-A and USTB-05-C genes from Sphingopyxis sp. USTB-05, which are responsible for the biodegradation of MCs, the pathway for biodegrading NOD by these two enzymes was investigated in this study. The findings showed that the enzyme USTB-05-A converted cyclic NOD (m/z 825.4516) into its linear type as the first product by hydrolyzing the arginine and Adda peptide bond, and that USTB-05-C cut off the Adda and glutamic acid peptide bond of linearized NOD (m/z 843.4616) and produced dimeric Adda (m/z 663.4377) as the second product. Further, based on the homology modeling of enzyme USTB-05-A, site-directed mutants of USTB-05-A were constructed and seven crucial sites for enzyme USTB-05-A activity were found. A complete enzymatic mechanism for NOD biodegradation by USTB-05-A in the first step was proposed: glutamic acid 172 and histidine 205 activate a water molecule facilitating a nucleophilic attack on the arginine and Adda peptide bond of NOD; tryptophan 176 and tryptophan 201 contact the carboxylate side chain of glutamic acid 172 and accelerate the reaction rates; and histidine 260 and asparagine 264 function as an oxyanion hole to stabilize the transition states.

Stable-isotope probing of bacterial community for dissolved inorganic carbon utilization in Microcystis aeruginosa-dominated eutrophic water

Dissolved inorganic carbon (DIC) is an important source of carbon in aquatic ecosystems, especially under conditions of increased frequency of cyanobacterial bloom. However, the importance of bacteria in direct or indirect utilization of DIC has been widely overlooked in eutrophic freshwater. To identify the functional bacteria that can actively utilize DIC in eutrophic freshwater during cyanobacterial bloom, stable-isotope probing (SIP) experiments were conducted on eutrophic river water with or without inoculation with cyanobacteria (Microcystis aeruginosa). Our 16S rRNA sequencing results revealed the significance of Betaproteobacteria, with similar relative abundance as Alphaproteobacteria, in the active assimilation of H¹³CO₃^- into their DNA directly or indirectly, which include autotrophic genera Betaproteobacterial ammonia-oxidizing bacteria. Other bacterial groups containing autotrophic members, e.g. Planctomycetes and Nitrospira, also presented higher abundance among free-living bacteria in water without cyanobacteria. Microcystis aggregates showed a preference for some specific bacterial members that may utilize H¹³CO₃^- metabolized by Microcystis as organic matter, e.g. Bacteroidetes (Cytophagales, Sphingobacteriales), and microcystin-degrading bacteria Betaproteobacteria (Paucibacter/Burkholderiaceae). This study provides some valuable information regarding the functional bacteria that can actively utilize DIC in eutrophic freshwater.

Source Community and Assembly Processes Affect the Efficiency of Microbial Microcystin Degradation on Drinking Water Filtration Membranes

Microbial biofilms in gravity-driven membrane (GDM) filtration systems can efficiently degrade the cyanotoxin microcystin (MC), but it is unclear if this function depends on the presence of MC-producing cyanobacteria in the source water habitat. We assessed the removal of MC from added Microcystis aeruginosa biomass in GDMs fed with water from a lake with regular blooms of toxic cyanobacteria (ExpL) or from a stream without such background (ExpS). While initial MC removal was exclusively due to abiotic processes, significantly higher biological MC removal was observed in ExpL. By contrast, there was no difference in MC degradation capacity between lake and stream bacteria in separately conducted liquid enrichments on pure MC. Co-occurrence network analysis revealed a pronounced modularity of the biofilm communities, with a clear hierarchic distinction according to feed water origin and treatment type. Genotypes in the network modules associated with ExpS had significantly more links to each other, indicating that these biofilms had assembled from a more coherent source community. In turn, signals for stochastic community assembly were stronger in ExpL biofilms. We propose that the less "tightly knit" ExpL biofilm assemblages allowed for the better establishment of facultatively MC degrading bacteria, and thus for higher overall functional efficiency.

Importance of bacterial biodegradation and detoxification processes of microcystins for environmental health

Microcystins (MC) the most frequently reported cyanobacterial harmful algal bloom toxins primarily found in some species of freshwater genera pose a serious threat to human and animal health. To reduce health risks associated with MC exposure it is important to remove these toxins found in drinking and recreational waterbodies. Since the physical and chemical water treatment methods are inefficient in completely degrading MC, alternative approaches to effectively detoxify MC have become the focus of global research. The aim of this review was to provide the current approach to cost-effective biological treatment methods which utilize bacteria to degrade MC without generation of harmful by-products. In addition, the catabolic pathways involved in MC-degradation involving proteins encoded mlr gene cluster, intermediate products and efficiencies of bacteria strain/bacteria community are presented and compared.

Draft Genome Sequence of Paucibacter aquatile CR182T, a Strain with Antimicrobial Activity Isolated from Freshwater of Nakdong River in South Korea

This report details a draft genome sequence of Paucibacter aquatile CR182^T, isolated from river water, which contains 5,523,543 bp, has a G+C content of 66.3%, and harbors 4,544 protein-coding genes in 4 contigs. These genome data provide insights into the genetic basis of this strain’s antibacterial activity and adaptive mechanisms.

Paucibacter aquatile sp. nov. isolated from freshwater of the Nakdong River, Republic of Korea

A Gram-negative, aerobic, motile, and rod-shaped bacterial strain designated CR182^T was isolated from freshwater of the Nakdong River, Republic of Korea. Optimal growth conditions for this novel strain were found to be: 25-30 °C, pH 6.5-8.5, and 3% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence indicates that the strain CR182^T belongs to type strains of genus Paucibacter. Strain CR182^T showed 98.0% 16S rRNA gene sequence similarity with Paucibacter oligotrophus CHU3^T and formed a robust phylogenetic clade with this species. The average nucleotide identity value between strain CR182^T and P. oligotrophus CHU3^T was 78.4% and the genome-to-genome distance was 22.2% on average. The genomic DNA G+C content calculated from the genome sequence was 66.3 mol%. Predominant cellular fatty acids of strain CR182^T were summed feature 3 (C_16:1 ω7c and/or C_16:1 ω6c) (31.2%) and C_16:0 (16.0%). Its major respiratory quinine was ubiquinone Q-8. Its polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, and two unidentified phospholipids. Its genomic DNA G+C content was 66.3%. Based on data obtained from this polyphasic taxonomic study, strain CR182^T represents a novel species belonging to genus Paucibacter, for which a name of P. aquatile sp. nov. is proposed. The type strain is CR182^T (= KCCM 90284^T = NBRC 113032^T).

Assessment of the influence of key abiotic factors on the alternative microcystin degradation pathway(s) (mlr-): A detailed comparison with the mlr route (mlr+)

Cyanobacterial proliferation and toxin production in water bodies around the world have led to global concern about the control of these issues. Indigenous bacteria have been shown to degrade the cyanotoxin microcystin (MC) in natural environments. The mlr cluster has been widely used as a marker for microcystin biodegradation; however, recent studies have shown that alternative pathway(s) also contribute to the natural removal of MCs in the ecosystem. The main objective of this study is to provide initial insights concerning how key abiotic factors affect the rate of MC biodegradation via alternative pathway(s) and to provide a detailed comparison with the mlr⁺ pathway. Our results show that nutrient inputs and previous exposure to MCs trigger changes in the rate of MC degradation via alternative pathway(s), while temperature does not produce any significant change. Our results further indicate that the alternative pathway(s) may be less efficient at degrading MCs than the mlr⁺ pathway, suggesting the importance of microbial diversity in determining the half-life of MCs in the water column.

Diversity and temporal shifts of the bacterial community associated with a toxic cyanobacterial bloom: An interplay between microcystin producers and degraders

The biodegradation of microcystins (MCs) by bacteria constitutes an important process in freshwater ecosystems to prevent the accumulation of toxins. However, little is known about the diversity and the seasonal dynamics of the bacterial community composition (BCC) involved in the degradation of MCs in nature. To explore these BCC shifts, high-throughput sequencing was used to analyse the 16S rRNA, mcyE and mlrA genes during a year in a freshwater reservoir with a toxic cyanobacterial bloom episode. The analysis of the mcyE and mlrA genes from water samples revealed the coexistence of different MC-producing and MC-degrading genotypes, respectively. The patchy temporal distribution of the mlrA genotypes (from the families Sphingomonadaceae and Xanthomonadaceae) suggests their dissimilar response to environmental conditions and the influence of other factors besides the MCs that may control their presence and relative abundance. During the maximum toxic cyanobacterial biomass and cell lysis, other bacterial taxa that lack mlr genes increased their relative abundance. Among these bacteria, those with a recognized role in the degradation of xenobiotic and other complex organic compounds (e.g., orders Myxococcales, Ellin6067, Spirobacillales and Cytophagales) were the most representative and suggest their possible involvement in the removal of MCs in the environment.

The biodegradation of microcystins in temperate freshwater bodies with previous cyanobacterial history

Cyanobacterial blooms and cyanotoxins occur in freshwater lakes and reservoirs all over the world. Bacterial degradation of microcystins (MC), hepatotoxins produced by several cyanobacterial species, has also been broadly documented. However, information regarding MC biodegradation in European water bodies is very limited. In this paper, the occurrence and identification of MC biodegradation products was documented for 21 European lakes and reservoirs, many of which have well-documented cyanobacterial bloom histories. Varying cyanobacterial abundance and taxonomical composition were documented and MC producers were found in all the analysed samples. Planktothrix agardhii was the most common cyanobacterial species and it formed mass occurrences in four lakes. MC biodegradation was observed in 86% of the samples (18 out of 21), and four products of dmMC-LR decomposition were detected by HPLC and LC-MS methods. The two main products were cyclic dmMC-LR with modifications in the Arg-Asp-Leu region; additionally one product was recognized as the tetrapeptide Adda-Glu-Mdha-Ala. The composition of the detected products suggested a new biochemical pathway of MC degradation. The results confirmed the hypothesis that microcystin biodegradation is a common phenomenon in central European waters and that it may occur by a mechanism which is different from the one previously reported. Such a finding implies the necessity to develop a more accurate methodology for screening bacteria with MC biodegradation ability. Furthermore, it warrants new basic and applied studies on the characterization and utilization of new MC-degrading strains and biodegradation pathways.

Current research scenario for microcystins biodegradation - A review on fundamental knowledge, application prospects and challenges

Microcystins (MCs) are common cyanotoxins produced by harmful cyanobacterial blooms (HCBs) and severely threaten human and ecosystems health. Biodegradation is an efficient and sustainable biological strategy for MCs removal. Many novel findings in fundamental knowledge and application potential of MC-biodegradation have been documented. Little effort has devoted to summarize and comment recent research progress on MC-biodegradation, and discuss the research problems and gaps. This review deals with current research scenario in aerobic and anaerobic biodegradation for MCs. Diverse organisms capable of degrading MCs are encapsulated. Enzymatic mechanisms and influence factors regulating aerobic and anaerobic MC-biodegradation are summarized and discussed, which are essential for assessing and reducing MC-risks during HCBs episodes. Also, we propose some ideas to solve the challenges and bottleneck problems in practical application of MC-biodegradation, and discuss research gaps and promising research methods which deserve special attention. This review may provide new insights on future direction of MC-biodegradation research, in order to further broaden its application prospects for bioremediation.

Watershed Urbanization Linked to Differences in Stream Bacterial Community Composition

Urbanization strongly influences headwater stream chemistry and hydrology, but little is known about how these conditions impact bacterial community composition. We predicted that urbanization would impact bacterial community composition, but that stream water column bacterial communities would be most strongly linked to urbanization at a watershed-scale, as measured by impervious cover, while sediment bacterial communities would correlate with environmental conditions at the scale of stream reaches. To test this hypothesis, we determined bacterial community composition in the water column and sediment of headwater streams located across a gradient of watershed impervious cover using high-throughput 16S rRNA gene amplicon sequencing. Alpha diversity metrics did not show a strong response to catchment urbanization, but beta diversity was significantly related to watershed impervious cover with significant differences also found between water column and sediment samples. Samples grouped primarily according to habitat—water column vs. sediment—with a significant response to watershed impervious cover nested within each habitat type. Compositional shifts for communities in urbanized streams indicated an increase in taxa associated with human activity including bacteria from the genus Polynucleobacter, which is widespread, but has been associated with eutrophic conditions in larger water bodies. Another indicator of communities in urbanized streams was an OTU from the genus Gallionella, which is linked to corrosion of water distribution systems. To identify changes in bacterial community interactions, bacterial co-occurrence networks were generated from urban and forested samples. The urbanized co-occurrence network was much smaller and had fewer co-occurrence events per taxon than forested equivalents, indicating a loss of keystone taxa with urbanization. Our results suggest that urbanization has significant impacts on the community composition of headwater streams, and suggest that processes driving these changes in urbanized water column vs. sediment environments are distinct.

Paucibacter oligotrophus sp. nov., isolated from fresh water, and emended description of the genus Paucibacter

A Gram-stain-negative, rod-shaped, non-spore forming, motile and strictly oxidative bacterium, strain CHU3T, was isolated from fresh water in the Daecheong Reservoir, South Korea. A comparison of the 16S rRNA gene sequence showed that the novel bacterium is closely related to Paucibacter toxinivorans 2C20T (=KCTC 42569T) with a sequence similarity value of 97.8 %, Pelomonas saccharophila DSM 654T (=KCTC 52256T) with 97.4 % similarity and Pelomonas aquatica CCUG 52575T (=KCTC 42961T) with 97.3 % similarity, respectively. The major fatty acids (>10 %) of the isolate were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. Ubiquinone-8 was detected as the respiratory quinone. The polar lipids contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylserine and an unidentified aminolipid. The DNA G+C content was 62.5 mol%. DNA-DNA hybridization experiments with PaucibactertoxinivoransKCTC 42569T (=2C20T), PelomonassaccharophilaKCTC 52256T (=DSM 654T) and PelomonasaquaticaKCTC 42961T (=CCUG 52575T) resulted in relatedness values of 20 % (reciprocal 11 %), 16 % (reciprocal 17 %) and 15 % (reciprocal 19 %), respectively. The phylogenetic analysis, DNA-DNA hybridization value, polar lipids, fatty acid composition and other physiological characteristics confirmed that strain CHU3T represents a novel species in the genus Paucibacter for which the name Paucibacter oligotrophus sp. nov. is proposed. The type strain is CHU3T (=KCTC 42519T=CICC 24092T). An emended description of the genus Paucibacter is also proposed on the basis of new data obtained in this study.

Grazing of Nuclearia thermophila and Nuclearia delicatula (Nucleariidae, Opisthokonta) on the toxic cyanobacterium Planktothrix rubescens

During the last decades, the planktonic cyanobacterium Planktothrix rubescens became a dominant primary producer in many deep pre-alpine lakes. While altered physiochemical conditions due to lake warming seem to favour this cyanobacterial species, its dominance is partly attributed to factors conferring grazing resistance. The rigid structure of the cyanobacterial filaments and toxic secondary metabolites (e.g. microcystins) protect against diverse grazers. Nonetheless, species of the protistan genus Nuclearia (Nucleariidae, Opisthokonta) are able to overcome this grazing protection. Time lapse video documentation served as tool to record slow feeding processes of N. thermophila and N. delicatula. Three different feeding strategies could be distinguished: (i) Phagocytosis of small fragments, (ii) serial break-ups of cyanobacterial cells and (iii) bending and breaking of filaments. While observations revealed mechanical manipulation to be important for the efficient breakdown of P. rubescens filaments, the toxin microcystin had no pronounced negative effects on nucleariid cells. Growth experiments with N. thermophila/N. delicatula and different accompanying bacterial assemblages pointed to a pivotal role of distinct prokaryotic species for toxin degradation and for the growth success of the protists. Thus, the synergistic effect of nucleariids and specific bacteria favours an efficient degradation of P. rubescens along with its toxin.

Characterization of bacterial community associated with phytoplankton bloom in a eutrophic lake in South Norway using 16S rRNA gene amplicon sequence analysis

Interactions between different phytoplankton taxa and heterotrophic bacterial communities within aquatic environments can differentially support growth of various heterotrophic bacterial species. In this study, phytoplankton diversity was studied using traditional microscopic techniques and the bacterial communities associated with phytoplankton bloom were studied using High Throughput Sequencing (HTS) analysis of 16S rRNA gene amplicons from the V1-V3 and V3-V4 hypervariable regions. Samples were collected from Lake Akersvannet, a eutrophic lake in South Norway, during the growth season from June to August 2013. Microscopic examination revealed that the phytoplankton community was mostly represented by Cyanobacteria and the dinoflagellate Ceratium hirundinella. The HTS results revealed that Proteobacteria (Alpha, Beta, and Gamma), Bacteriodetes, Cyanobacteria, Actinobacteria and Verrucomicrobia dominated the bacterial community, with varying relative abundances throughout the sampling season. Species level identification of Cyanobacteria showed a mixed population of Aphanizomenon flos-aquae, Microcystis aeruginosa and Woronichinia naegeliana. A significant proportion of the microbial community was composed of unclassified taxa which might represent locally adapted freshwater bacterial groups. Comparison of cyanobacterial species composition from HTS and microscopy revealed quantitative discrepancies, indicating a need for cross validation of results. To our knowledge, this is the first study that uses HTS methods for studying the bacterial community associated with phytoplankton blooms in a Norwegian lake. The study demonstrates the value of considering results from multiple methods when studying bacterial communities.

Cyanobacterial Toxins in Freshwater and Food: Important Sources of Exposure to Humans

A recent ecological study demonstrated a significant association between an increased risk of nonalcoholic liver disease mortality and freshwater cyanobacterial blooms. Moreover, previous epidemiology studies highlighted a relationship between cyanotoxins in drinking water with liver cancer and damage and colorectal cancer. These associations identified cyanobacterial blooms as a global public health and environmental problem, affecting freshwater bodies that are important sources for drinking water, agriculture, and aquafarms. Furthermore, as a result of climate change, it is expected that our freshwater environments will become more favorable for producing harmful blooms that produce various cyanotoxins. Food is an important source of cyanotoxin exposure to humans, but it has been less addressed. This paper synthesizes information from the studies that have investigated cyanotoxins in freshwater and food on a global scale. We also review and summarize the health effects and exposure routes of cyanotoxins and candidates for cyanotoxin treatment methods that can be applied to food.

Cyanotoxin degradation activity and mlr gene expression profiles of a Sphingopyxis sp. isolated from Lake Champlain, Canada

A bacterium capable of degrading five microcystin (MC) variants, microcystin-LR, YR, LY, LW and LF at an initial total concentration of 50 μg l^-1 in less than 16 hours was isolated from Missisquoi Bay, in the south of Quebec, Canada. Phylogenetic analysis of the 16S rRNA gene sequence identified the bacterium as Sphingopyxis sp., designated strain MB-E. It was shown that microcystin biodegradation activity was reduced at acidic and basic pH values. Even though no biodegradation occurred at pH values of 5.05 and 10.23, strain MB-E was able to degrade MCLR and MCYR at pH 9.12 and all five MCs variants tested at pH 6.1. Genomic sequencing revealed that strain MB-E contained the microcystin degrading gene cluster, including the mlrA, mlrB, mlrC and mlrD genes, and transcriptomic analysis demonstrated that all of these genes were induced during the degradation of MCLR alone or in the mixture of all five MCs. This novel transcriptomic analysis showed that the expression of the mlr gene cluster was similar for MCLR alone, or the mixture of MCs, and appeared to be related to the total concentration of substrate. The results suggested that the bacterium used the same pathway for the degradation of all MC variants.

Presence or Absence of mlr Genes and Nutrient Concentrations Co-Determine the Microcystin Biodegradation Efficiency of a Natural Bacterial Community

The microcystin biodegradation potential of a natural bacterial community coexisting with a toxic cyanobacterial bloom was investigated in a water reservoir from central Spain. The biodegradation capacity was confirmed in all samples during the bloom and an increase of mlrA gene copies was found with increasing microcystin concentrations. Among the 24 microcystin degrading strains isolated from the bacterial community, only 28% showed presence of mlrA gene, strongly supporting the existence and abundance of alternative microcystin degradation pathways in nature. In vitro degradation assays with both mlr⁺ and mlr⁻ bacterial genotypes (with presence and absence of the complete mlr gene cluster, respectively) were performed with four isolated strains (Sphingopyxis sp. IM-1, IM-2 and IM-3; Paucibacter toxinivorans IM-4) and two bacterial degraders from the culture collection (Sphingosinicella microcystinivorans Y2; Paucibacter toxinivorans 2C20). Differences in microcystin degradation efficiencies between genotypes were found under different total organic carbon and total nitrogen concentrations. While mlr⁺ strains significantly improved microcystin degradation rates when exposed to other carbon and nitrogen sources, mlr⁻ strains showed lower degradation efficiencies. This suggests that the presence of alternative carbon and nitrogen sources possibly competes with microcystins and impairs putative non-mlr microcystin degradation pathways. Considering the abundance of the mlr⁻ bacterial population and the increasing frequency of eutrophic conditions in aquatic systems, further research on the diversity of this population and the characterization and conditions affecting non-mlr degradation pathways deserves special attention.

Using H2O2 treatments for the degradation of cyanobacteria and microcystins in a shallow hypertrophic reservoir

Toxins produced by cyanobacteria in freshwater ecosystems constitute a serious health risk worldwide for humans that may use the affected water bodies for recreation, drinking water, and/or irrigation. Cyanotoxins have also been deemed responsible for loss of animal life in many places around the world. This paper explores the effect of H₂O₂ treatments on cyanobacteria and microcystins in natural samples from a hypertrophic reservoir in microcosm experiments. According to the results, cyanobacteria were more easily affected by H₂O₂ than by other phytoplanktonic groups. This was shown by the increase in the fractions of chlorophyll-a (a proxy for phytoplankton) and chlorophyll-b (a proxy for green algae) over total phytoplankton pigments and the decrease in the fraction of phycocyanin (a proxy for cyanobacteria) over total phytoplankton pigments. Thus, while an overall increase in phytoplankton occurred, a preferential decrease in cyanobacteria was observed with H₂O₂ treatments over a few hours. Moreover, significant degradation of total microcystins was observed under H₂O₂ treatments, while more microcystins were degraded when UV radiation was used in combination with H₂O₂. The combination of H₂O₂ and ultraviolet (UV) treatment in natural samples resulted in total microcystin concentrations that were below the World Health Organization limit for safe consumption of drinking water of 1 μg/L. Although further investigation into the effects of H₂O₂ addition on ecosystem function must be performed, our results show that the application of H₂O₂ could be a promising method for the degradation of microcystins in reservoirs and the reduction of public health risks related to the occurrence of harmful algal blooms.

Discerning biodegradation and adsorption of microcystin-LR in a shallow semi-enclosed bay and bacterial community shifts in response to associated process

Hepatotoxic microcystins (MCs) produced by cyanobacteria pose serious risks to aquatic ecosystems and human health, to understand elimination pathways and mechanisms for MCs, especially in a shallow and semi-enclosed eutrophic area, is of great significance. This study succeed in discerning biodegradation and adsorption of microcystin-LR (MCLR) mediated by water and/or sediment in northern part of Meiliang Bay in Lake Taihu, China, and among the first to reveal the shifts of indigenous bacterial community composition in response to MCLR-biodegradation in sediment by Illumina high-throughput sequencing (HTS). Results confirmed that biodegradation predominantly governed MCLR elimination as compared to adsorption in study area. Through faster biodegradation with a rate of 49.21μgL(-1)d(-1), lake water contributed more to overall MCLR removal than sediment. Sediment also played indispensable role in MCLR removal via primarily biodegradation by indigenous community (a rate of 17.27μgL(-1)d(-1)) and secondarily adsorption (<20% of initial concentration). HTS analysis showed that indigenous community composition shifted with decreased phylogenetic diversity in response to sediment-mediated MCLR-biodegradation. Proteobacteria became predominant (39.34-86.78%) in overall composition after biodegradation, which was mostly contributed by sharp proliferation of β-proteobacteria (22.76-74.80%), and might closely link to MCLR-biodegradation in sediment. Moreover, the members of several genera belonging to α-proteobacteria, β-proteobacteria and γ-proteobacteria seemed to be key degraders because of their dominance or increasing population as MCLR degraded. This study expands understanding on natural elimination mechanism for MCs, and provides guidance to reduce MCs' biological risks and guarantee ecosystem safety in aquatic habitats.

Piscinibacterium candidicorallinum gen. nov., sp. nov., a member of the order Burkholderiales isolated from a fish pond

A bacterial strain designated LYH-15T was isolated from a freshwater fish pond in Taiwan and characterized using a polyphasic taxonomy approach. Cells of LYH-15T were Gram-staining-negative, aerobic, motile by means of a single polar flagellum, poly-β-hydroxybutyrate-containing, non-spore forming, straight rods and formed light-coral-colored colonies. Growth occurred at 15-40 °C (optimum, 30 °C), at pH 5.0-9.0 (optimum, pH 7.0) and with 0-0.5 % NaCl (optimum, 0 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that LYH-15T forms a distinct phyletic line within the order Burkholderiales, with less than 94 % sequence similarity to its closest relatives with validly published names. The predominant fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c. The major isoprenoid quinone was Q-8 and the DNA G+C content was 63.8 mol%. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several uncharacterized lipids. The major polyamines were 2-hydroxyputrescine and putrescine. On the basis of the genotypic and phenotypic data, LYH-15T represents a novel species of a new genus in the order Burkholderiales, for which the name Piscinibacterium candidicorallinum gen. nov., sp. nov. is proposed. The type strain is LYH-15T (=BCRC 80969T=LMG 29480T=KCTC 52168T).