Novosphingobium humi sp. nov., isolated from soil of a military shooting range

Phosphate (Bio)mineralization Remediation of 90Sr-Contaminated Groundwaters

Historical operations at nuclear mega-facilities such as Hanford, USA, and Sellafield, UK have led to a legacy of radioactivity-contaminated land. Calcium phosphate phases (e.g., hydroxyapatite) can adsorb and/or incorporate radionuclides, including 90Sr. Past work has shown that aqueous injection of Ca-phosphate-generating solutions into the contaminated ground on both laboratory and field scales can reduce the amount of aqueous 90Sr in the systems. Here, two microbially mediated phosphate amendment techniques which precipitated Ca-phosphate, (i) Ca-citrate/Na-phosphate and (ii) glycerol phosphate, were tested in batch experiments alongside an abiotic treatment ((iii) polyphosphate), using stable Sr and site relevant groundwaters and sediments. All three amendments led to enhanced Sr removal from the solution compared to the sediment-only control. The Ca-citrate/Na-phosphate treatment removed 97%, glycerol phosphate 60%, and polyphosphate 55% of the initial Sr. At experimental end points, scanning electron microscopy showed that Sr-containing, Ca-phosphate phases were deposited on sediment grains, and XAS analyses of the sediments amended with Ca-citrate/Na-phosphate and glycerol phosphate confirmed Sr incorporation into Ca-phosphates occurred. Overall, Ca-phosphate-generating treatments have the potential to be applied in a range of nuclear sites and are a key option within the toolkit for 90Sr groundwater remediation.

Using custom-built primers and nanopore sequencing to evaluate CO-utilizer bacterial and archaeal populations linked to bioH2 production

The microbial community composition of five distinct thermophilic hot springs was effectively described in this work, using broad-coverage nanopore sequencing (ONT MinION sequencer). By examining environmental samples from the same source, but from locations with different temperatures, bioinformatic analysis revealed dramatic changes in microbial diversity and archaeal abundance. More specifically, no archaeal presence was reported with universal bacterial primers, whereas a significant archaea presence and also a wider variety of bacterial species were reported. These results revealed the significance of primer preference for microbiomes in extreme environments. Bioinformatic analysis was performed by aligning the reads to 16S microbial databases for identification using three different alignment methods, Epi2Me (Fastq 16S workflow), Kraken, and an in-house BLAST tool, including comparison at the genus and species levels. As a result, this approach to data analysis had a significant impact on the genera identified, and thus, it is recommended that use of multiple analysis tools to support findings on taxonomic identification using the 16S region until more precise bioinformatics tools become available. This study presents the first compilation of the ONT-based inventory of the hydrogen producers in the designated hot springs in Türkiye.

Novosphingobium aureum sp. nov., a marine bacterium isolated from salt flat sediment

A Gram-stain-negative, aerobic, pale yellow-coloured, rod-shaped marine bacterium designated strain YJ-S2-02^T was isolated from salt flat sediment sampled in Yongyu-do, Republic of Korea. Strain YJ-S2-02^T grew at pH 6.0-9.0 (optimum, pH 7.0), 10-40 °C (optimum, 30 °C) and with optimum 1 % (w/v) NaCl. The 16S rRNA gene sequence analysis indicated that strain YJ-S2-02^T was closely related to Novosphingobium naphthalenivorans NBRC 102051^T (97.8 %) followed by Novosphingobium mathurense SM117^T (97.5 %), Novosphingobium indicum H25^T (97.3 %), Novosphingobium pentaromativorans US6-1^T (96.8 %), Novosphingobium fontis STM-14^T (96.6 %), Novosphingobium endophyticum EGI60015^T (96.5 %), Novosphingobium naphthae D39^T (96.5 %) and Novosphingobium malaysiense MUSC 273^T (95.9 %). The average nucleotide identity and estimated DNA-DNA hybridization values between YJ-S2-02^T and related type strains were 77.0-77.9 % and 19.1-24.0 %. Strain YJ-S2-02^T was characterized as having Q-10 as the predominant respiratory quinone and the principal fatty acids (>10 %) were summed feature 8 (C_18 : 1  ω6c/ω7c, 20.7 %), C_18 : 3  ω6c (16.3 %) and C_17 : 1  ω6c (11.8 %). The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, sphingolipids and two unidentified lipids. The DNA G+C content of strain YJ-S2-02^T was 65.6 mol%. On the basis of the polyphasic taxonomic evidence presented in this study, YJ-S2-02^T should be classified as representing a novel species within the genus Novosphingobium, for which name Novosphingobium aureum is proposed, with the type strain YJ-S2-02^T (=KACC 21677^T =KCTC 72891^T=JCM 33996^T).

Novosphingobium umbonatum sp. nov., isolated from a freshwater mesocosm

A bacterial strain designated FSY-9^T was isolated from a freshwater mesocosm in Taiwan and characterized to determine its taxonomic affiliation. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain FSY-9^T formed a phylogenetic lineage in the genus Novosphingobium. Strain FSY-9^T was most closely related to Novosphingobium humi R1-4^T with a 97.2 % 16S rRNA gene sequence similarity. Strain FSY-9^T showed 71.3-72.6 % average nucleotide identity and 17.7-23.0 % digital DNA-DNA hybridization identity with the strains of other Novosphingobium species. Cells of strain FSY-9^T were facultatively anaerobic, Gram-negative, rod-shaped, non-motile and formed light yellow coloured colonies. Growth occurred at 15-37 °C and pH 5.5-7, and in the presence of 0-0.5 % NaCl. The major fatty acids (>10 %) of strain FSY-9^T were summed feature 3 (C_16 : 1ω7c and/or C_16 : 1ω6c), C_18 : 1ω7c and C_16 : 0. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphatidyldimethylethanolamine, sphingoglycolipid, an uncharacterized aminophospholipid, an uncharacterized glycolipid and an uncharacterized lipid. The major polyamine was spermidine. The major isoprenoid quinone was Q-10. The DNA G+C content was 61.5 mol%. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain FSY-9^T should be classified as a novel species of the genus Novosphingobium, for which the name Novosphingobium umbonatum sp. nov. is proposed. The type strain is FSY-9^T (=BCRC 81052^T=LMG 30054^T=KCTC 52813^T).

Comparative Genomics of Degradative Novosphingobium Strains With Special Reference to Microcystin-Degrading Novosphingobium sp. THN1

Bacteria in genus Novosphingobium associated with biodegradation of substrates are prevalent in environments such as lakes, soil, sea, wood and sediments. To better understand the characteristics linked to their wide distribution and metabolic versatility, we report the whole genome sequence of Novosphingobium sp. THN1, a microcystin-degrading strain previously isolated by Jiang et al. (2011) from cyanobacteria-blooming water samples from Lake Taihu, China. We performed a genomic comparison analysis of Novosphingobium sp. THN1 with 21 other degradative Novosphingobium strains downloaded from GenBank. Phylogenetic trees were constructed using 16S rRNA genes, core genes, protein-coding sequences, and average nucleotide identity of whole genomes. Orthologous protein analysis showed that the 22 genomes contained 674 core genes and each strain contained a high proportion of distributed genes that are shared by a subset of strains. Inspection of their genomic plasticity revealed a high number of insertion sequence elements and genomic islands that were distributed on both chromosomes and plasmids. We also compared the predicted functional profiles of the Novosphingobium protein-coding genes. The flexible genes and all protein-coding genes produced the same heatmap clusters. The COG annotations were used to generate a dendrogram correlated with the compounds degraded. Furthermore, the metabolic profiles predicted from KEGG pathways showed that the majority of genes involved in central carbon metabolism, nitrogen, phosphate, sulfate metabolism, energy metabolism and cell mobility (above 62.5%) are located on chromosomes. Whereas, a great many of genes involved in degradation pathways (21-50%) are located on plasmids. The abundance and distribution of aromatics-degradative mono- and dioxygenases varied among 22 Novosphingoibum strains. Comparative analysis of the microcystin-degrading mlr gene cluster provided evidence for horizontal acquisition of this cluster. The Novosphingobium sp. THN1 genome sequence contained all the functional genes crucial for microcystin degradation and the mlr gene cluster shared high sequence similarity (≥85%) with the sequences of other microcystin-degrading genera isolated from cyanobacteria-blooming water. Our results indicate that Novosphingobium species have high genomic and functional plasticity, rearranging their genomes according to environment variations and shaping their metabolic profiles by the substrates they are exposed to, to better adapt to their environments.