Sphingobium cyanobacteriorum sp. nov., isolated from fresh water

A novel Gram-stain-negative, yellow-pigmented, short rod-shaped bacterial strain, HBC34T, was isolated from a freshwater sample collected from Daechung Reservoir, Republic of Korea. The results of 16S rRNA gene sequence analysis indicated that HBC34T was affiliated with the genus Sphingobium and shared the highest sequence similarity to the type strains of Sphingobium vermicomposti (98.01 %), Sphingobium psychrophilum (97.87 %) and Sphingobium rhizovicinum (97.59 %). The average nucleotide identity (ANI) and digital DNA-DNA hybridisation (dDDH) values between HBC34T and species of the genus Sphingobium with validly published names were below 84.01 and 28.1 %, respectively. These values were lower than the accepted species-delineation thresholds, supporting its recognition as representing a novel species of the genus Sphingobium. The major fatty acids (>10 % of the total fatty acids) were identified as summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The main polar lipids were phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, two phospholipids and two unidentified polar lipids. The respiratory quinone was Q-10. The genomic DNA G+C content of HBC34T was 64.04 %. The polyphasic evidence supports the classification of HBC34T as the type strain of a novel species of the genus Sphingobium, for which the name Sphingobium cyanobacteriorum sp. nov is proposed. The type strain is HBC34T (= KCTC 8002T= LMG 33140T).

Complex interactions between diverse mobile genetic elements drive the evolution of metal-resistant bacterial genomes

In this study, we compared the genomes of three metal-resistant bacteria isolated from mercury-contaminated soil. We identified diverse and novel MGEs with evidence of multiple LGT events shaping their genomic structure and heavy metal resistance. Among the three metal-resistant strains, Sphingobium sp SA2 and Sphingopyxis sp SE2 were resistant to multiple metals including mercury, cadmium, copper, zinc and lead. Pseudoxanthomonas sp SE1 showed resistance to mercury only. Whole genome sequencing by Illumina and Oxford Nanopore technologies was undertaken to obtain comprehensive genomic data. The Sphingobium and Sphingopyxis strains contained multiple chromosomes and plasmids, whereas the Pseudoxanthomonas strain contained one circular chromosome. Consistent with their metal resistance profiles, the strains of Sphingobium and Sphingopyxis contained a higher quantity of diverse metal resistance genes across their chromosomes and plasmids compared to the single-metal resistant Pseudoxanthomonas SE1. In all three strains, metal resistance genes were principally associated with various novel MGEs including genomic islands (GIs), integrative conjugative elements (ICEs), transposons, insertion sequences (IS), recombinase in trio (RIT) elements and group II introns, indicating their importance in facilitating metal resistance adaptation in a contaminated environment. In the Pseudoxanthomonas strain, metal resistance regions were largely situated on a GI. The chromosomes of the strains of Sphingobium and Sphingopyxis contained multiple metal resistance regions, which were likely acquired by several GIs, ICEs, numerous IS elements, several Tn3 family transposons and RIT elements. Two of the plasmids of Sphingobium were impacted by Tn3 family transposons and ISs likely integrating metal resistance genes. The two plasmids of Sphingopyxis harboured transposons, IS elements, an RIT element and a group II intron. This study provides a comprehensive annotation of complex genomic regions of metal resistance associated with novel MGEs. It highlights the critical importance of LGT in the evolution of metal resistance of bacteria in contaminated environments.

Spatial and Temporal Constraints on the Composition of Microbial Communities in Subsurface Boreholes of the Edgar Experimental Mine

The deep biosphere hosts uniquely adapted microorganisms overcoming geochemical extremes at significant depths within the crust of the Earth. Attention is required to understand the near subsurface and its continuity with surface systems, where numerous novel microbial members with unique physiological modifications remain to be identified. This surface-subsurface relationship raises key questions about networking of surface hydrology, geochemistry affecting near-subsurface microbial composition, and resiliency of subsurface ecosystems. Here, we apply molecular and geochemical approaches to determine temporal microbial composition and environmental conditions of filtered borehole fluid from the Edgar Experimental Mine (∼150 m below the surface) in Idaho Springs, CO. Samples were collected over a 4-year collection period from expandable packers deployed to accumulate fluid in previously drilled boreholes located centimeters to meters apart, revealing temporal evolution of borehole microbiology. Meteoric groundwater feeding boreholes demonstrated variable recharge rates likely due to a complex and undefined fracture system within the host rock. 16S rRNA gene analysis determined that unique microbial communities occupy the four boreholes examined. Two boreholes yielded sequences revealing the presence of Desulfosporosinus, Candidatus Nitrotoga, and Chelatococcus associated with endemic subsurface communities. Two other boreholes presented sequences related to nonsubsurface-originating microbiota. High concentration of sulfate along with detected sulfur reducing and oxidizing microorganisms suggests that sulfur related metabolic strategies are prominent within these near-subsurface boreholes. Overall, results indicate that microbial community composition in the near-subsurface is highly dynamic at very fine spatial scales (<20 cm) within fluid-rock equilibrated boreholes, which additionally supports the role of a relationship for surface geochemical processes infiltrating and influencing subsurface environments. IMPORTANCE The Edgar Experimental Mine, Idaho Springs, CO, provides inexpensive and open access to borehole investigations for subsurface microbiology studies. Understanding how microbial processes in the near subsurface are connected to surface hydrological influences is lacking. Investigating microbial communities of subsurface mine boreholes provides evidence of how geochemical processes are linked to biogeochemical processes within each borehole and the geochemical connectedness and mobility of surface influences. This study details microbial community composition and fluid geochemistry over spatial and temporal scales from boreholes within the Edgar Mine. These findings are relevant to biogeochemistry of near-surface mines, caves, and other voids across planetary terrestrial systems. In addition, this work can lead to understanding how microbial communities relate to both fluid-rock equilibration, and geochemical influences may enhance our understanding of subsurface molecular biological tools that aid mining economic practices to reflect biological signals for lucrative veins in the near subsurface.

Description of Sphingobium psychrophilum sp. nov., a cold-adapted bacterium isolated from Arctic soil

A yellow-coloured, Gram-stain-negative, non-sporulating, psychrotolerant and motile bacterium, designated AR-3-1^T, was isolated from the Arctic soil of Cambridge Bay, Nunavut, Canada. Strain AR-3-1^T could grow at 4-32 °C and pH 5.0- 11.0. Phylogenetic analysis based on its 16S rRNA gene sequence indicated that strain AR-3-1^T formed a lineage within the family Sphingomonadaceae and clustered as a member of the genus Sphingobium. The closest members within this genus were Sphingobium cupriresistens CU4^T (98.1 % sequence similarity), Sphingobium vermicomposti VC-230^T (97.6 %) and Sphingobium lactosutens DS20^T (97.5 %). The only respiratory quinone was the ubiquinone Q-10. Spermidine was the predominant polyamine. The principal cellular fatty acids were summed feature 8 (C_18 : 1  ω7c and/or C_18 : 1  ω6c), summed feature 3 (iso-C_{15  : 0} 2-OH and/or C_{16  : 1} ω7c), C_16 : 0 and C_14 : 0 2-OH. The major polar lipids were phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, sphingoglycolipid and phosphoglycolipid. The DNA G+C content was 63.1 %. The average nucleotide identity and in silico DNA-DNA hybridization relatedness values between strain AR-3-1^T and its most closely related genus members were ≤89.6 and 39.6 %, respectively. The genome was 5 162 327 bp long, with 83 scaffolds and 4824 protein-coding genes. The genome showed six putative biosynthetic gene clusters responsible for various secondary metabolites. Based on this polyphasic study, strain AR-3-1^T represents a novel species within the genus Sphingobium, for which the name Sphingobium psychrophilum sp. nov. is proposed. The type strain is AR-3-1^T (=KACC 21613^T=NBRC 114604^T).

Profiling multiple heavy metal contamination and bacterial communities surrounding an iron tailing pond in Northwest China

Northwest China is abundant in iron ore reserves and has become one of the important iron ore mining bases in China. However, the contamination and microbial community structure of iron tailing ponds in Northwest China have not been extensively investigated. In the present study, we characterized the main physicochemical properties, the multiple heavy metal contamination, and the bacterial community structure of the soils surrounding an iron tailing pond in Linze County, Zhangye city, Gansu Province. The tailing-associated soils were barren, exhibiting alkaline pH and low organic matter (OM), total nitrogen (TN) and total potassium (TK) compared with the control areas. There was considerable multiple heavy metal pollution in the iron tailing pond, mainly including lead (Pb), manganese (Mn), arsenic (As), cadmium (Cd), zinc (Zn), iron (Fe) and copper (Cu). Among the 303 identified core operational taxonomic units (OTUs), Actinobacteria, Proteobacteria and Deinococcus-Thermus were predominant at the phylum level, and Blastococcus, Arthrobacter, Marmoricola, Kocuria, Truepera, and Sphingomonadaceae were prevalent at a finer taxonomic level. The bacterial richness and diversity of the tailing samples were significantly lower than those of the reference samples. RDA, VPA and Spearman correlation analyses showed that the soil pH, CEC, OM, TP, TK, Cd, Pb, Ni, Zn, As and Mn had significant effects on the bacterial community composition and distribution. This work profiles the basic features of the soil physicochemical properties, the multiple heavy metal contamination and the bacterial community structure in an iron tailing pond in Northwest China, thereby providing a foundation for the future ecological remediation of the iron tailing environment in the area.

The responses of soil enzyme activities, microbial biomass and microbial community structure to nine years of varied zinc application rates

Zinc (Zn) fertilizer application can certainly improve the production and nutritional quality of cereal crops. However, Zn accumulation in the soil may lead to some deleterious environmental impacts in agroecosystems. The effects of long-term Zn application on soil microbial properties remain unclear, but it is imperative to understand such effects. In this study, we collected soil samples from a nine-year field experiment in a wheat-maize system that continuously received Zn applied at various rates (0, 2.3, 5.7, 11.4, 22.7 and 34.1 kg ha^-1) to evaluate the soil enzymes, microbial biomass and microbial community structure. The results showed that Zn application at the rate of 5.7 kg ha^-1 significantly increased the activities of urease, invertase, alkaline phosphatase and catalase in the soil, while the rate of 34.1 kg ha^-1 significantly decreased the evaluated enzyme activities. The microbial biomass carbon (C) and nitrogen (N) were not affected by Zn application rates, although an increase in the microbial biomass C was observed in the 11.4 kg ha^-1 treatment. Moreover, the alpha diversity of the bacterial and fungal communities did not vary among the nil Zn, optimal Zn (5.7 kg ha^-1) and excess Zn (34.1 kg ha^-1) treatments. However, the bacterial communities in the soil receiving the optimal and excess Zn application rates were slightly changed. Compared to the nil Zn treatment, the other Zn application rates increased the relative abundances of the Rhodospirillales, Gaiellales and Frankiales orders and decreased the abundance of the Latescibacteria phylum. The redundancy analysis further indicated that the soil bacterial community composition significantly correlated with the concentrations of soil DTPA-Zn and total Zn. These results highlight the importance of optimal Zn application in achieving high production and high grain quality while concurrently promoting soil microbial activity, improving the bacterial community and further maintaining the sustainability of the agroecological environment.

Sphingobium aromaticivastans sp. nov., a novel aniline- and benzene-degrading, and antimicrobial compound producing bacterium

A strictly aerobic, orange-pigmented strain was isolated and designated as UCM-25^T. This strain is capable of degrading aniline and benzene, while is also producing antimicrobial compounds which inhibit the growth of some common pathogenic microbes. A near full-length 16S rRNA gene sequence revealed similarity to Sphingobium chlorophenolicum NBRC 16172^T (98.6%). The level of DNA-DNA hybridization between the new isolate and the related species suggests UCM-25^T to be a new species belonging to the genus Sphingobium. The bacterial cells contained phosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid, phosphatidylcholine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, three unidentified polar lipids, and an unidentified aminophospholipid. Ubiquinone Q-10 was the major quinone and spermidine was the major polyamine. The G+C content in the DNA of strain UCM-25^T was 62.9 mol%. Cells contained summed feature 8 (C_18:1ω7c and/or C_18:1ω6c), summed feature 3 (C_16:1ω7c and/or C_16:1ω6c), C_16:0, and C_14:0 2-OH as major fatty acids. Based on the comparison of phenotypic, genotypic, and chemotaxonomic characteristics, strain UCM-25^T represents a new member of the genus Sphingobium, for which the name S. aromaticivastans sp. nov. is proposed. The type strain is UCM-25^T (=KACC 19288^T =DSM 105181^T).

The Response of a 16S Ribosomal RNA Gene Fragment Amplified Community to Lead, Zinc, and Copper Pollution in a Shanghai Field Trial

Industrial and agricultural activities have caused extensive metal contamination of land throughout China and across the globe. The pervasive nature of metal pollution can be harmful to human health and can potentially cause substantial negative impact to the biosphere. To investigate the impact of anthropogenic metal pollution found in high concentrations in industrial, agricultural, and urban environments, 16S ribosomal RNA gene amplicon sequencing was used to track change in the amplified microbial community after metal contamination in a large-scale field experiment in Shanghai. A total of 1,566 operational taxonomic units (OTUs) identified from 448,108 sequences gathered from 20 plots treated as controls or with lead, zinc, copper, or all three metals. Constrained Analysis of Principal Coordinates ordination did not separate control and lead treatment but could separate control/lead, zinc, copper, and three metal treatment. DESeq2 was applied to identify 93 significantly differentially abundant OTUs varying in 211 pairwise instances between the treatments. Differentially abundant OTUs representing genera or species belonging to the phyla Chloroflexi, Cyanobacteria, Firmicutes, Latescibacteria, and Planctomycetes were almost universally reduced in abundance due to zinc, copper, or three metal treatment; with three metal treatment abolishing the detection of some OTUs, such as Leptolyngbya, Desmonostoc muscorum, and Microcoleus steenstrupii. The greatest increases due to metal treatment were observed in Bacteroidetes, Actinobacteria, Chlamydiae, Nitrospirae, and Proteobacteria (α, β, δ, and γ); the most (relative) abundant being uncharacterized species within the genera Methylobacillus, Solirubrobacter, and Ohtaekwangia. Three metal treatment alone resulted in identification of 22 OTUs (genera or species) which were not detected in control soil, notably including Yonghaparkia alkaliphila, Pedobacter steynii, Pseudolabrys taiwanensis, Methylophilus methylotrophus, Nitrosospira, and Lysobacter mobilis. The capacity to track alterations of an amplified microbial community at high taxonomic resolution using modern bioinformatic approaches, as well as identifying where that resolution is lost for technical or biological reasons, provides an insight into the complexity of the microbial world resisting anthropogenic pollution. While functional assessment of uncharacterized organisms within environmental samples is technically challenging, an important step is observing those organisms able to tolerate extreme stress and to recognize the extent to which important amplifiable community members still require characterization.

Transcriptomic analysis of nickel exposure in Sphingobium sp. ba1 cells using RNA-seq

Nickel acts as cofactor for a number of enzymes of many bacteria species. Its homeostasis is ensured by proteins working as ion efflux or accumulation systems. These mechanisms are also generally adopted to counteract life-threatening high extra-cellular Ni²⁺ concentrations. Little is known regarding nickel tolerance in the genus Sphingobium. We studied the response of the novel Sphingobium sp. ba1 strain, able to adapt to high Ni²⁺ concentrations. Differential gene expression in cells cultured in 10 mM Ni²⁺, investigated by RNA-seq analysis, identified 118 differentially expressed genes. Among the 90 up-regulated genes, a cluster including genes coding for nickel and other metal ion efflux systems (similar to either cnrCBA, nccCBA or cznABC) and for a NreB-like permease was found. Comparative analyses among thirty genomes of Sphingobium species show that this cluster is conserved only in two cases, while in the other genomes it is partially present or even absent. The differential expression of genes encoding proteins which could also work as Ni²⁺-accumulators (HupE/UreJ-like protein, NreA and components of TonB-associated transport and copper-homeostasis systems) was also detected. The identification of Sphingobium sp. ba1 strain adaptive mechanisms to nickel ions, can foster its possible use for biodegradation of poly-aromatic compounds in metal-rich environments.

Bio-augmentation and nutrient amendment decrease concentration of mercury in contaminated soil

Four mercury (Hg) contaminated soils with different pH (7.6, 8.5, 4.2 and 7.02) and total organic carbon contents (2.1, 2.2, 4 and 0.9%) were subjected to bioremediation utilizing a Hg volatilizing bacterial strain Sphingobium SA2 and nutrient amendment. In a field with ~280mg/kgHg, 60% of Hg was removed by bio-augmentation in 7days, and the removal was improved when nutrients were added. Whereas in artificially spiked soils, with ~100mg/kgHg, removal due to bio-augmentation was 33 to 48% in 14days. In the field contaminated soil, nutrient amendment alone without bio-augmentation removed 50% of Hg in 28days. Nutrient amendment also had an impact on Hg remediation in the spiked soils, but the best results were obtained when the strain and nutrients both were applied. The development of longer root lengths from lettuce and cucumber seeds grown in the remediated soils confirmed that the soil quality improved after bioremediation. This study clearly demonstrates the potential of Hg-reducing bacteria in remediation of Hg-contaminated soils. However, it is desirable to trap the volatilized Hg for enhanced bioremediation.

Mercury remediation potential of a mercury resistant strain Sphingopyxis sp. SE2 isolated from contaminated soil

A mercury resistant bacterial strain SE2 was isolated from contaminated soil. The 16s rRNA gene sequencing confirms the strain as Sphingopyxis belongs to the Sphingomonadaceae family of the α-Proteobacteria group. The isolate showed high resistance to mercury with estimated concentrations of Hg that caused 50% reduction in growth (EC₅₀) of 5.97 and 6.22mg/L and minimum inhibitory concentrations (MICs) of 32.19 and 34.95mg/L in minimal and rich media, respectively. The qualitative detection of volatilized mercury and the presence of mercuric reductase enzyme proved that the strain SE2 can potentially remediate mercury. ICP-QQQ-MS analysis of the remaining mercury in experimental broths indicated that a maximum of 44% mercury was volatilized within 6hr by live SE2 culture. Furthermore a small quantity (23%) of mercury was accumulated in live cell pellets. While no volatilization was caused by dead cells, sorption of mercury was confirmed. The mercuric reductase gene merA was amplified and sequenced. Homology was observed among the amino acid sequences of mercuric reductase enzyme of different organisms from α-Proteobacteria and ascomycota groups.

Sphingobium endophyticus sp. nov., isolated from the root of Hylomecon japonica

A yellow-pigmented bacterium, designated strain GZGR-4(T), was isolated from the root of Hylomecon japonica (Thunb.) Prantl et Kündig collected from Taibai Mountain in Shaanxi Province, north-west China. Cells of strain GZGR-4(T) were Gram-negative, rod-shaped, strictly aerobic, non-endospore-forming and non-motile. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain GZGR-4(T) is a member of the genus Sphingobium, exhibiting the highest sequence similarity to Sphingobium aromaticiconvertens DSM 12677(T) (97.3 %). 16S rRNA gene sequence similarities between strain GZGR-4(T) and the type strains of other Sphingobium species with validly published names ranged from 93.4-96.5 %. The predominant respiratory quinone of strain GZGR-4(T) was ubiquinone-10 (Q-10) and the major cellular fatty acids were summed feature 8 (comprising C18:1 ω7c and/or C18:1 ω6c), summed feature 3 (comprising C16:1 ω7c and/or C16:1 ω6c), C16:0 and C14:0 2-OH. Spermidine was the major polyamine. The polar lipid profile consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, sphingoglycolipid, one unidentified phosphoglycolipid, one unidentified phospholipid, one unidentified aminolipid and one unidentified lipid. The DNA G+C content was 63.6 mol%. DNA-DNA relatedness for strain GZGR-4(T) with respect to its closest phylogenetic relative S. aromaticiconvertens DSM 12677(T) was 22.6 ± 5.3 %. On the basis of the polyphasic taxonomic data presented, strain GZGR-4(T) is considered to represent a novel species of the genus Sphingobium, for which the name Sphingobium endophyticus sp. nov. is proposed. The type strain is GZGR-4(T) (=CCTCC AB 2013305(T) = KCTC 32447(T)).