Novosphingobium profundi sp. nov. isolated from a deep-sea seamount

Diversity links to functionality: Unraveling the impact of pressure disruption and culture medium on crude oil-enriched microbial communities from the deep Eastern Mediterranean Sea

Mesopelagic water from the deep Eastern Mediterranean Sea (EMS) was collected under disrupted (REPRESS) or undisturbed (HP) pressure conditions and was acclimated to oil (OIL) or dispersed-oil (DISPOIL) under in situ pressure and temperature (10 MPa, 14 °C). Decompression resulted in oil-acclimatised microbial communities of lower diversity despite the restoration of in situ pressure conditions during the 1-week incubation. Further biodiversity loss was observed when oil-acclimatised communities were transferred to ONR7 medium to facilitate the isolation of oil-degrading bacteria. Microbial diversity loss impacted the degradation of recalcitrant oil compounds, especially PAHs, as low-abundance taxa, linked with PAH degradation, were outcompeted in the enrichment process. Thalassomonas, Pseudoalteromonas, Halomonas and Alcanivorax were enriched in ONR7 under all experimental conditions. No effect of dispersant application on the microbial community structure was identified. A. venustensis was isolated under all tested conditions suggesting a potential key role of this species in hydrocarbons removal in the deep EMS.

Novosphingobium album sp. nov., Novosphingobium organovorum sp. nov. and Novosphingobium mangrovi sp. nov. with the organophosphorus pesticides degrading ability isolated from mangrove sediments

Members of the genus Novosphingobium were frequently isolated from polluted environments and possess great bioremediation potential. Here, three species, designated B2637^T, B2580^T and B1949^T, were isolated from mangrove sediments and might represent novel species in the genus Novosphingobium based on a polyphasic taxonomy study. Phylogenomic analysis revealed that strains B2580^T, B1949^T and B2637^T clustered with Novosphingobium naphthalenivorans NBRC 102051^T, 'N. profundi' F72 and N. decolorationis 502str22^T, respectively. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between isolates and their closely related species were less than 94 and 54 %, respectively, all below the threshold of species discrimination. The sizes of the genomes of isolates B2580^T, B2637^T and B1949^T ranged from 4.4 to 4.6 Mb, containing 63.3-66.4 % G+C content. Analysis of their genomic sequences identified genes related to pesticide degradation, heavy-metal resistance, nitrogen fixation, antibiotic resistance and sulphur metabolism, revealing the biotechnology potential of these isolates. Except for B2637^T, B1949^T and B2580^T were able to grow in the presence of quinalphos. Results from these polyphasic taxonomic analyses support the affiliation of these strains to three novel species within the genus Novosphingobium, for which we propose the name Novosphingobium album sp. nov. B2580^T (=KCTC 72967^T=MCCC 1K04555^T), Novosphingobium organovorum sp. nov. B1949^T (=KCTC 92158^T=MCCC 1K03763^T) and Novosphingobium mangrovi sp. nov. B2637^T (KCTC 72969^T=MCCC 1K04460^T).

Changes in microbial community diversity, composition, and functions upon nitrate and Cr(VI) contaminated groundwater

With the increasing occurrences of nitrate and Cr(VI) pollution globally, microbially driven pollutant reduction and its interaction effects were of growing interest. Despite the increasing number of experimental reports on the simultaneous reduction of nitrate and Cr(VI), a broad picture of the keystone species and metabolic differences in this process remained elusive. This study explored the changing of microorganisms with the introduction of Cr(VI)/NO₃^- through analyzing 242 samples from the NCBI database. The correlation between microbial abundance and environmental factors showed that, the types of energy substances and pollutants species in the environment had an impact on the diversity of microorganisms and community structure. The genus of Zoogloea, Candidatus Accumulibacter, and Candidatus Kapabacteria sp. 59-99 had the ability of denitrification, while genus of Alcaligenes, Kerstersia, Petrimonas, and Leucobacter showed effectively Cr(VI) resistance and reducing ability. Azoarcus, Pseudomonas, and Thauera were recognized as important candidates in the simultaneous reduction of nitrate and Cr(VI). Metagenomic predictions of these microorganisms using PICRUSt2 further highlighted the enrichment of Cr(VI)and nitrate reduction-related genes (such as chrA and norC). Special attention should therefore be paid to these bacteria in subsequent studies to evaluate their performance and mechanisms involved in simultaneous denitrification and chromium removal. The microbial co-occurrence network analysis conducted on this basis emphasized a strong association between community collaboration and pollution removal. Collectively, either site surveys or laboratory experiments, subsequent studies should focus on these microbial populations and the interspecific collaborations as they strongly influence the occurrence of simultaneous nitrate and Cr(VI) reduction.

Novosphingobium decolorationis sp. nov., an aniline blue-decolourizing bacterium isolated from East Pacific sediment

Aniline blue-decolourizing bacterial strain 502str22^T, isolated from sediment collected in the East Pacific, was subjected to characterization by a polyphasic taxonomic approach. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain 502str22^T belongs to the genus Novosphingobium, with closely related type strains 'Novosphingobium profundi' F72^T (97.6%), N. mathurense SM117^T (97.1%) and N. arvoryzae Jyi-02^T (97.0%). Digital DNA-DNA hybridization and average nucleotide identity values between strain 502str22^T and closely related type strains were 20.3-24.8% and 74.1-81.9%, respectively. The major cellular fatty acid (>10%) was C_18:1 ω7c. The polar lipid profile consisted of a mixture of phosphatidylcholine, one sphingoglycolipid, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylmonomethylethanolamine. The DNA G+C content of strain 502str22^T was 65.5 mol%. The polyphasic taxonomic results indicated that strain 502str22^T represents a novel species of the genus Novosphingobium, for which the name Novosphingobium decolorationis sp. nov is proposed. The type strain is 502str22^T (=KCTC 82134^T= MCCC 1K04799 ^T).

Pelagihabitans pacificus gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from a deep-sea seamount

The Gram-stain-negative, orange-pigmented, non-spore-forming, non-motile, strictly aerobic, rod-shaped bacterial strain, designated TP-CH-4^T, was isolated from a seamount near the Yap Trench in the tropical western Pacific. The optimal growth conditions were determined to be at pH 7-8, 25-30 °C and in the presence of 2 % (w/v) NaCl. The major respiratory quinone was MK-6. The polar lipid profile contained phosphatidylethanolamine, two unidentified aminolipids, two unidentified phospholipids and three unidentified polar lipids. The predominant cellular fatty acids were iso-C_15 : 0 and summed feature 1 (composed of C_13 : 03-OH and/or iso-C_15 : 1H). Phylogenetic analysis of 16S rRNA gene sequences revealed that strain TP-CH-4^T was a member of the family Flavobacteriaceae and formed a distinct lineage. Strain TP-CH-4^T displayed highest sequence similarities to Pseudozobellia thermophila KMM 3531^T (95.1 %) and Flagellimonas flava A11^T (93.9 %). Genome sequencing revealed the strain TP-CH-4^T has a genome size of 4.5 Mbp and a G+C content of 44.5 mol%. Collectively, based on phenotypic, chemotaxonomic, phylogenetic and genomic evidence, strain TP-CH-4^T represents a novel species of a novel genus of the family Flavobacteriaceae, for which the name Pelagihabitans pacificus gen. nov., sp. nov. is proposed. The type strain of Pelagihabitans pacificus is TP-CH-4^T (=CGMCC 1.17120^T=KCTC 72434^T).

Flavobacterium profundi sp. nov., isolated from a deep-sea seamount

The Gram-stain-negative, rod-shaped, facultative anaerobic, motile bacterial strain, designated TP390^T, was isolated from a seamount near the Yap Trench in the tropical western Pacific. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain TP390^T was related to the genus Flavobacterium and had highest 16S rRNA gene sequence identity with the type strain of Flavobacterium jejuense EC11^T (97.8 %). Sequence similarities to all other type strains of current species of the genus Flavobacterium were below 97 %. The predominant cellular fatty acids were iso-C_15 : 0 and iso-C_15 : 1G. The quinone system for strain TP390^T comprised predominantly menaquinone MK-6 and the polar lipid profile contained phosphatidylethanolamine, four unknown aminolipids, one glycolipid and six unknown polar lipids. The genomic DNA G+C content of strain TP390^T was 31.2 mol%. In addition, the maximum values of in silico DNA-DNA hybridization (isDDH) and average nucleotide identity (ANI) between strain TP390^T with F. jejuense KCTC 42149^T were 22.60 and 80.01% respectively. Combined data from phenotypic, phylogenetic, isDDH and ANI data demonstrated that the strain TP390^T is representative of a novel species of the genus Flavobacterium, for which we propose the name Flavobacterium profundi sp. nov. (type strain TP390^T=KACC 18559^T=CGMCC 1.15398^T).

Algibacter pacificus sp. nov., isolated from a deep-sea seamount

The Gram-stain-negative, rod-shaped, yellow-pigmented and facultative anaerobic bacterial strain, designated H164T, was isolated from seawater collected from the Caroline Seamounts in the Pacific Ocean. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain H164T was related to the genus Algibacter and had highest 16S rRNA gene sequence similarity to Algibacter wandonensis WS-MY22T (97.4 %). The major cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C15 : 1 G, iso-C15 : 0 3-OH and iso-C17 : 0 3-OH. The predominant menaquinone was MK-6. The polar lipid profile contained phosphatidylethanolamine, one unidentified aminolipid and two unidentified lipids. The genomic DNA G+C content of strain H164T was 33.2 mol%. The values of in silico DNA–DNA hybridization (isDDH) and average nucleotide identity (ANI) between strain H164T and A. wandonensis KCTC 32381T were 26.10 and 81.88 %. The isDDH and ANI values between strain H164T and Algibacter lectus DSM 15365T were 25.40 and 81.79 %. Combined data from phenotypic, phylogenetic, isDDH and ANI analyses demonstrated that strain H164T represents a novel species of the genus Algibacter , for which we propose the name Algibacter pacificus sp. nov. (type strain H164T=KCTC 72432T=CGMCC 1.17117T).

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.

Mesoflavibacter profundi sp. nov. Isolated from a Deep-Sea Seamount

The Gram-stain-negative, rod-shaped, aerobic strain, designated YC1039^T, was isolated from a seamount northern Mariana Trench in the tropical western Pacific. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain YC1039^T was related to the genus Mesoflavibacter and had highest 16S rRNA gene sequence similarities to Mesoflavibacter sabulilitoris GJMS-9^T (98.3%) and Mesoflavibacter zeaxanthinifaciens TD-ZX30^T (98.2%). The predominant cellular fatty acids were iso-C_15:1 G and iso-C_15:0. The polar lipid profile contained phosphatidylethanolamine, two unidentified phospholipids, and 13 unidentified lipids. The respiratory quinone was MK-6. The genomic DNA G+C content of strain YC1039^T was 29.8 mol%. On the basis of the evidence presented in this study, strain YC1039^T represents a novel species of the genus Mesoflavibacter, for which we propose the name Mesoflavibacter profundi sp. nov. (type strain YC1039^T = KACC 19026^T = CGMCC 1.16329^T).

Ponticaulis profundi sp. nov. isolated from a deep-sea seamount

A Gram-stain negative, rod-shaped, strictly aerobic, motile bacterial strain, designated YC239^T, was isolated from a seamount near the Yap Trench in the tropical western Pacific. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain YC239^T is related to the genus Ponticaulis and has high 16S rRNA gene sequence similarity with the type strain of Ponticaulis koreensis GSW-23^T (97.9%). The predominant cellular fatty acids were C_18:1ω7c, C_16:0, C_17:0 and C_17:1ω6c. Strain YC239^T had Q-10 as the predominant ubiquinone. The polar lipid profile contained phosphatidylglycerol, two unidentified aminolipids and six unidentified polar lipids. The genomic DNA G+C content of strain YC239^T was 52.8 mol%. Strain YC239^T shared DNA relatedness of 38% with Ponticaulis koreensis KCTC 22146^T. On the basis of the evidence presented in this study, strain YC239^T represents a novel species of the genus Ponticaulis, for which we propose the name Ponticaulis profundi sp. nov. (type strain YC239^T = KACC 19027^T = CGMCC 1.15741^T).

Rheinheimera marina sp. nov., isolated from a deep-sea seamount

A bacterial strain designated TP462^T, isolated from a seamount near the Yap Trench in the tropical western Pacific, was characterized using a polyphasic taxonomic approach. Strain TP462^T was found to be Gram-stain-negative, aerobic, rod-shaped and motile by means of a single polar flagellum. Growth occurred at 4-37 °C (optimum, 25-30 °C) and with 0-4.0 % NaCl (optimum, 2-3 %). Phylogenetic analysis based on 16S rRNA gene sequence showed that strain TP462^T was related to the genus Rheinheimera and had the highest 16S rRNA gene sequence similarity with the type strain Rheinheimera tangshanensis JA3-B52^T (96.8 %). The predominant cellular fatty acids were C17 : 1ω8c, summed feature 3 (composed of iso-C15 : 0 2-OH and/or C16 : 1ω7c) and C16 : 0. The polar lipid profile contained phosphatidylglycerol, phosphatidylethanolamine and two unidentified lipids. The genomic DNA G+C content of strain TP462^T was 48.7 mol%. On the basis of the evidence presented in this study, strain TP462^T represents a novel species of the genus Rheinheimera, for which we propose the name Rheinheimera marina sp. nov. (type strain TP462^T=KACC 18560^T=CGMCC 1.15399^T).

Maribacter marinus sp. nov. isolated from a deep-sea seamount

A Gram-stain negative, rod-shaped, aerobic strain, designated YC973^T, was isolated from a seamount near the Yap Trench in the tropical western Pacific. Phylogenetic analysis based on its 16S rRNA gene sequence showed that strain YC973^T is related to the genus Maribacter and has high 16S rRNA gene sequence similarity to Maribacter orientalis KMM 3947^T (97.6%). The predominant cellular fatty acids were iso-C_15:0, iso-C_15:1 G and an unidentified fatty acid of equivalent chain-length 13.565. The polar lipid profile contained phosphatidylethanolamine and five unidentified lipids. The genomic DNA G+C content of strain YC973^T was 36.1 mol%. On the basis of the evidence presented in this study, strain YC973^T represents a novel species of the genus Maribacter, for which we propose the name Maribacter marinus sp. nov. (type strain YC973^T = KACC 19025^T = CGMCC 1.16328^T).

Thalassotaleaprofundi sp. nov. isolated from a deep-sea seamount

The Gram-stain-negative, rod-shaped, strictly aerobic, motile bacterial strain, designated YM155^T, was isolated from a seamount near the Yap Trench in the tropical western Pacific. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain YM155^T was related to the genus Thalassotalea and had highest 16S rRNA gene sequence similarities with the type strains of Thalassotalea piscium T202^T (97.2 %) and Thalassotalea agariperforans M-M1^T (97.2 %). The predominant cellular fatty acids were C17 : 1ω8c, summed feature 3 (composed of iso-C15 : 0 2-OH and/or C16 : 1ω7c) and iso-C16 : 0. Ubiquinone 8 (Q-8) was the respiratory quinone. The polar lipid profile contained phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids and one unidentified lipid. The genomic DNA G+C content of strain YM155^T was 36.1 mol%. On the basis of the evidence presented in this study, strain YM155^T represents a novel species of the genus Thalassotalea, for which we propose the name Thalassotalea profundi sp. nov. (type strain YM155^T=KACC 18563^T=CGMCC 1.15922^T).

Influence of bicarbonate on the abundance of microbial communities capable of reducing U(vi) in groundwater

7 experiments amended with 0, 5, 10, 15, 20, 25 and 30 mM initial concentrations of bicarbonate were conducted to investigate the influence of different concentrations of bicarbonate on the abundance of microbial communities capable of reducing U(vi) in groundwater.