Runella limosa sp. nov., isolated from activated sludge

Silver nanomaterials released from commercial textiles have minimal impacts on soil microbial communities at environmentally relevant concentrations

Silver nanomaterials (Ag NMs) have been used in a variety of commercial products to take advantage of their antimicrobial properties. However, there are concerns that these AgNMs can be released during/after use and enter wastewater streams, potentially impacting aquatic systems or accumulating in wastewater biosolids. Biosolids, which are a residual of wastewater treatment processes, have been found to contain AgNMs and are frequently used as agricultural fertilizer. Since the function of soil microbial communities is imperative to nutrient cycling and agricultural productivity, it is important to characterize and assess the effects that silver nanomaterials could have in agricultural soils. In this study agricultural soil was amended with pristine engineered (PVP-coated or uncoated AgNMs), aged silver (sulphidized or released from textiles) nanomaterials, and ionic silver to determine the fate and toxicity over the course of three months. Exposures were carried out at various environmentally relevant concentrations (1 and 10 mg Ag/kg soil) representing between 30 to over 800 years of equivalent biosolid loadings. Over thirteen different methodologies and measures were used throughout this study to assess for potential effects of the silver nanomaterials on soil, including microbial community composition, average well colour development (AWCD) and enzymatic activity. Overall, the AgNM exposures did not exhibit significant toxic effects to the soil microbial communities in terms of density, activity, function and diversity. However, the positive ionic silver treatment (100 mg Ag/kg soil) resulted in suppression to microbial activity while also resulting in significantly higher populations of Frankia alni (nitrogen-fixer) and Arenimonas malthae (phytopathogen) as compared to the negative control (p < 0.05, Tukey HSD) which warrants further investigation.

Runella aurantiaca sp. nov., isolated from sludge of a manganese mine

A Gram-stain-negative, filamentous rod-shaped, aerobic and non-motile strain, YX9^T, was isolated from sludge of a manganese mine. Analysis of the 16S rRNA gene sequence revealed that strain YX9^T formed the same branch within the members of the genus Runella and showed high relatedness to Runella slithyformis DSM 19594^T (98.1 %), Runella palustris HMF3829^T (96.0 %) and Runella zeae NS12^T (95.4 %). The genome length of strain YX9^T was 7.21 Mb, had 5985 coding sequences and a DNA G+C content of 44.8 mol%. The average nucleotide identity value of the draft genomes between strain YX9^T and R. slithyformis DSM 19594^T was 80.7 %. The major fatty acids of strain YX9^T were iso-C_15 : 0, C_16:1 ω5c and summed feature 3 (C_16:1 ω7c and/or C_16:1 ω6c). The predominant respiratory quinone was menaquinone 7. The polar lipids of strain YX9^T were phosphatidylethanolamine, four unidentified lipids, two aminolipids, a phospholipid and a glycolipid. Based on the results of genotypic and phenotypic studies, strain YX9^T represents a novel species within the genus Runella, for which the name Runellaaurantiaca sp. nov. is proposed (=KCTC 62875^T=CCTCC AB 2018214^T).

Arundinibacter roseus gen. nov., sp. nov., a new member of the family Cytophagaceae

Three Gram-stain-negative, aerobic, non-motile, oxidase- and catalase positive, rod-shaped, pink-coloured bacterial strains, DMA-K-7a^T, DMA-K-1 and DMG-N-1, were isolated from water sampled at Lake Fertő/Neusiedler See (Hungary). Phylogenetic analysis based on the 16S rRNA gene sequences revealed that the strains form a distinct linage within the family Cytophagaceae of the phylum Bacteroidetes, and their closest relatives are Rhabdobacter roseus R49^T (95.66 %) and Dyadobacter sediminis Z12^T (95.38 %). The assembled genome of strain DMA-K-7a^T had a total length of 5.8 Mb and a DNA G+C content of 45.7 mol%. The major isoprenoid quinone was menaquinone-7 (MK-7). The major cellular fatty acids were C16 : 1 ω7c, iso-C15 : 0, C16 : 1 ω5c, C16 : 0 and iso-C17 : 0 3-OH. The polar lipid profile contained phosphatidylethanolamine, phosphatidylserine, an unknown aminolipid, an unknown glycolipid and five unknown lipids. Flexirubin-type pigments were absent. Strain DMA-K-7a^T (=DSM 106737^T=NCAIM B.02641^T) is proposed as the type strain of a new genus and species in the family Cytophagaceae, for which the name Arundinibacter roseus gen. nov., sp. nov. is proposed.

Aquifer recharge with stormwater runoff in urban areas: Influence of vadose zone thickness on nutrient and bacterial transfers from the surface of infiltration basins to groundwater

Stormwater infiltration systems (SIS) have been built in urban areas to reduce the environmental impacts of stormwater runoff. Infiltration basins allow the transfer of stormwater runoff to aquifers but their abilities to retain contaminants depend on vadose zone properties. This study assessed the influence of vadose zone thickness (VZT) on the transfer of inorganic nutrients (PO₄^3-, NO₃^-, NH₄⁺), dissolved organic carbon (total -DOC- and biodegradable -BDOC-) and bacteria. A field experiment was conducted on three SIS with a thin vadose zone (<3 m) and three SIS with a thick vadose zone (>10 m). Water samples were collected at three times during a rainy period of 10 days in each infiltration basin (stormwater runoff), in the aquifer impacted by infiltration (impacted groundwater) and in the same aquifer but upstream of the infiltration area (non-impacted groundwater). Inorganic nutrients, organic matter, and dissolved oxygen (DO) were measured on all water samples. Bacterial community structures were investigated on water samples through a next-generation sequencing (NGS) scheme of 16S rRNA gene amplicons (V5-V6). The concentrations of DO and phosphate measured in SIS-impacted groundwaters were significantly influenced by VZT due to distinct biogeochemical processes occurring in the vadose zone. DOC and BDOC were efficiently retained in the vadose zone, regardless of its thickness. Bacterial transfers to the aquifer were overall low, but data obtained on day 10 indicated a significant bacterial transfer in SIS with a thin vadose zone. Water transit time and water saturation of the vadose zone were found important parameters for bacterial transfers. Most bacterial taxa (>60%) from impacted groundwaters were not detected in stormwater runoff and in non-impacted groundwaters, indicating that groundwater bacterial communities were significantly modified by processes associated with infiltration (remobilization of bacteria from vadose zone and/or species sorting).

Chronic toxicity of graphene and graphene oxide in sequencing batch bioreactors: A comparative investigation

The present study investigates the chronic toxicity of graphene (G) and graphene oxide (GO) in activated sludge. Sequencing batch bioreactors were fed with influents containing 0, 1 and 5mgL^-1 of GO or G (12h cycles) for ten days. Reduction in performance of the bioreactors in relation to chemical oxygen demand, ammonia and phosphate removals was observed after three days in the bioreactors fed with 5mgL^-1 of nanomaterials. After about eight days, these reactors reached a steady state nutrient removal, which corresponded to recovery of certain groups of ammonia oxidizing bacteria and phosphate accumulating bacteria despite the increasing accumulation of nanomaterials in the sludge. These results suggested that biological treatment can be affected transiently by initial exposure to the nanomaterials, but certain groups of microorganisms, less sensitive to these nanomaterials, can potentially strive in the presence of these nanomaterials. Results of 16S rRNA gene deep sequencing showed that G and GO affected differently the microbial communities in the activated sludge. Between the two nanomaterials investigated, GO presented the highest impact in nutrient removal, gene abundance and changes in microbial population structures.

Genome-Based Taxonomic Classification of Bacteroidetes

The bacterial phylum Bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes from Bacteroidetes and closely related phyla for assessing their taxonomy based on the principles of phylogenetic classification and trees inferred from genome-scale data. No significant conflict between 16S rRNA gene and whole-genome phylogenetic analysis is found, whereas many but not all of the involved taxa are supported as monophyletic groups, particularly in the genome-scale trees. Phenotypic and phylogenomic features support the separation of Balneolaceae as new phylum Balneolaeota from Rhodothermaeota and of Saprospiraceae as new class Saprospiria from Chitinophagia. Epilithonimonas is nested within the older genus Chryseobacterium and without significant phenotypic differences; thus merging the two genera is proposed. Similarly, Vitellibacter is proposed to be included in Aequorivita. Flexibacter is confirmed as being heterogeneous and dissected, yielding six distinct genera. Hallella seregens is a later heterotypic synonym of Prevotella dentalis. Compared to values directly calculated from genome sequences, the G+C content mentioned in many species descriptions is too imprecise; moreover, corrected G+C content values have a significantly better fit to the phylogeny. Corresponding emendations of species descriptions are provided where necessary. Whereas most observed conflict with the current classification of Bacteroidetes is already visible in 16S rRNA gene trees, as expected whole-genome phylogenies are much better resolved.

Runella palustris sp. nov., isolated from wetland freshwater

A novel, Gram-stain-negative, aerobic, non-motile and filamentous bacterial strain, designated HMF3829T, was isolated from wetland freshwater in Gyeong-an wetland, Republic of Korea. A phylogenetic tree based on 16S rRNA gene sequences showed that strain HMF3829T formed a lineage within the genus Runella. Strain HMF3829T was closely related to Runella slithyformis DSM 19594T (95.2 % 16S rRNA gene sequence similarity), Runellalimosa DSM 17973T (94.9 %), Runellazeae NS12T (94.2 %) and Runella defluvii EMB13T (94.0 %). The major fatty acids of strain HMF3829T were iso-C15 : 0, summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 1ω5c and iso-C17 : 0 3-OH. The predominant isoprenoid quinone was menaquinone 7 (MK-7). The polar lipids of strain HMF3829T consisted of phosphatidylethanolamine, three unidentified aminolipids, one unidentified phospholipid, three unidentified aminophospholipids and 12 unidentified lipids. The DNA G+C content of strain HMF3829T was 46.2 mol%. On the basis of the evidence presented in this study, strain HMF3829T represents a novel species of the genus Runella, for which the name Runella palustris sp. nov. is proposed. The type strain is HMF3829T (=KCTC 42850T=CECT 8978T).

Aliiglaciecola aliphaticivorans sp. nov., an aliphatic hydrocarbon-degrading bacterium, isolated from a sea-tidal flat and emended description of the genus Aliiglaciecola Jean et al. 2013

A Gram-stain-negative heterotrophic bacterium, designated GSD6T, capable of growth on aliphatic hydrocarbons as a sole carbon and energy source, was isolated from sea-tidal flat sediment of the Yellow Sea, South Korea. Cells were facultatively aerobic, catalase- and oxidase-positive, motile rods with a single polar flagellum. Growth of strain GSD6T was observed at 4–37 °C (optimum 30 °C), at pH 5.5–9.0 (optimum pH 6.5–7.5) and in the presence of 1–9 % (w/v) NaCl (optimum 2 %). Strain GSD6T contained ubiquinone-8 (Q-8) as the sole isoprenoid quinone and summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0, C18 : 1ω7c, C17 : 0 10-methyl and C17 : 1ω8c as the major fatty acids. Phosphatidylethanolamine and phosphatidylglycerol were identified as the major polar lipids. The G+C content of the genomic DNA was 44.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain GSD6T formed a phylogenetic lineage with members of the genus Aliiglaciecola . Strain GSD6T was most closely related to Aliiglaciecola lipolytica E3T with a 16S rRNA gene sequence similarity of 97.4 %, but their DNA–DNA hybridization value was 39.1±7.1 %. On the basis of phenotypic, chemotaxonomic and molecular features, strain GSD6T represents a novel species of the genus Aliiglaciecola , for which the name Aliiglaciecola aliphaticivorans sp. nov. is proposed. The type strain is GSD6T ( = KACC 18129T = JCM 30133T). An emended description of the genus Aliiglaciecola is also proposed.

Fluviimonas pallidilutea gen. nov., sp. nov., a new member of the family Cytophagaceae isolated from a freshwater river

A bacterial strain designated TQQ6T was isolated from a freshwater river in Taiwan and characterized using a polyphasic taxonomy approach. Cells of strain TQQ6T were strictly aerobic, Gram-staining-negative, poly-β-hydroxybutyrate-containing, non-motile, non-spore-forming, long rods surrounded by a thick capsule and forming pale orange colonies. Growth occurred at 20–40 °C (optimum, 25 °C), at pH 7.0–9.0 (optimum, pH 8.0) and with 0–0.5 % NaCl (optimum, 0 %). The predominant fatty acids were iso-C15 : 0, summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c), iso-C17 : 0 3-OH, C16 : 1ω5c and C16 : 0. The major isoprenoid quinone was MK-7 and the DNA G+C content was 42.2 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine, two uncharacterized aminophospholipids and three uncharacterized phospholipids. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain TQQ6T represents a distinct phyletic line that reflects a novel generic status within the family Cytophagaceae with relatively low sequence similarities (less than 90 %) to members of other genera with validly published names. On the basis of the genotypic and phenotypic data, strain TQQ6T represents a new genus and novel species of the family Cytophagaceae , for which the name Fluviimonas pallidilutea gen. nov., sp. nov. is proposed. The type strain is TQQ6T ( = BCRC 80447T = LMG 27056T = KCTC 32035T).

Characterization of aerobic granular sludge treating high strength agro-based wastewater at different volumetric loadings

Understanding the relationship between microbial community and mechanism of aerobic granulation could enable wider applications of granules for high-strength wastewater treatment. The majority of granulation studies principally determine the engineering aspects of granules formation with little emphasis on the microbial diversity. In this study, three identical reactors namely R1, R2 and R3 were operated using POME at volumetric loadings of 1.5, 2.5 and 3.5 kg COD m(-3) d(-1), respectively. Aeration was provided at a volumetric flow rate of 2.5 cms(-1). Aerobic granules were successfully developed in R2 and R3 while bioflocs dominated R1 until the end of experiments. Fractal dimension (D(f)) averaged at 1.90 suggesting good compactness of granules. The PCR-DGGE results indicated microbial evolutionary shift throughout granulation despite different operating OLRs based on decreased Raup and Crick similarity indices upon mature granule formation. The characteristics of aerobic granules treating high strength agro-based wastewater are determined at different volumetric loadings.

Complete genome sequence of the aquatic bacterium Runella slithyformis type strain (LSU 4(T))

Runella slithyformis Larkin and Williams 1978 is the type species of the genus Runella, which belongs to the Cytophagaceae, a family that was only recently classified to the order Cytophagales in the class Cytophagia. The species is of interest because it is able to grow at temperatures as low as 4°C. This is the first completed genome sequence of a member of the genus Runella and the sixth sequence from the family Cytophagaceae. The 6,919,729 bp long genome consists of a 6.6 Mbp circular genome and five circular plasmids of 38.8 to 107.0 kbp length, harboring a total of 5,974 protein-coding and 51 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Runella defluvii sp. nov., isolated from a domestic wastewater treatment plant

A long, Gram-negative, rod-shaped bacterium, designated strain EMB13T, was isolated from a wastewater treatment plant in Korea. The isolate was strictly aerobic and non-motile. The strain grew optimally at 30–35 °C and pH 7.5–8.0, and the predominant fatty acids were iso-C15 : 0, summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH), C16 : 1 ω5c and iso-C17 : 0 3-OH. The strain contained a large amount of phosphatidylethanolamine and small amounts of phosphatidylcholine and an unknown phospholipid as the polar lipids. The G+C content of the genomic DNA was 40.1 mol% and the major isoprenoid quinone was menaquinone-7. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain EMB13T belonged to the genus Runella and was most closely related to Runella limosa EMB111T, with a 16S rRNA gene sequence similarity of 97.1 %. DNA–DNA relatedness between strain EMB13T and R. limosa EMB111T was approximately 25 %. On the basis of phenotypic, chemotaxonomic and molecular data, it is clear that strain EMB13T represents a novel species within the genus Runella, for which the name Runella defluvii sp. nov. is proposed. The type strain is EMB13T (=KCTC 12614T =DSM 17976T).