Pontibacter harenae sp. nov., isolated from the soil of a Populus euphratica forest

A Gram-negative, rod-shaped, aerobic and light pink-pigmented bacterium, designated XAAS-A31T, was isolated from the soil of a Populus euphratica forest located near Hotan City, Xinjiang, PR China. Polyphasic, taxonomic and phylogenomic analyses were used to determine the taxonomy position of the strain. Phylogenetic analysis based on 16S rRNA gene sequence analysis indicated that XAAS-A31T belongs to the genus Pontibacter, family Hymenobacteraceae, and shows highest sequence similarity to Pontibacter silvestris XAAS-R86T (96.2 %). The digital DNA-DNA hybridization (22.0 %-19.2 %) and orthologous average nucleotide identity (74.1 %-72.7 %) values relative to closest validly published Pontibacter species were lower than the recommended thresholds of 70 and 96 %, respectively. The cells grew at 4-40 °C (optimum, 28-30 °C), at pH 6.5-8.5 (pH 7.0-7.5) and with 0-8% NaCl (0.5-2.0% NaCl). The main respiratory quinone of XAAS-A31T is MK-7, and the principal cellular fatty acids are iso-C15 : 0, iso-C17 : 0 3OH and summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B). The major polar lipids are phosphatidylethanolamine, three unidentified amino-phospholipids, one unidentified glycolipid and eight unidentified lipids. The genome length of strain XAAS-A31T is 5.48 Mbp with a DNA G+C content of 44.2 mol% and 4013 protein-coding genes. Phenotypic and genotypic data suggested that XAAS-A31T represents a novel Pontibacter species, for which we propose the name Pontibacter harenae sp. nov. and type strain XAAS-A31T (=CCTCC AB 2017162T=KCTC 62049T).

Pontibacter kalidii sp. nov., isolated from rhizosphere soil of Kalidium foliatum

A Gram-negative, aerobic, gliding motile, rod-shaped bacterium, designated XAAS-72T, was isolated from the rhizosphere soil of Kalidium foliatum sampled in the Xinjiang Uyghur Autonomous Region, PR China. Cells grew at 4-45 °C, pH 5.0-8.0 and 0-8% NaCl, with optimal growth at 20-30 °C, pH 6.0-7.0 and 1-2 % NaCl. Strain XAAS-72T is closely related to members of the genus Pontibacter, namely Pontibacter korlensis CCTCC AB 206081T (97.6%) and Pontibacter flavimaris ACCC 19859T (97.2 %), and <94.6 % related to other currently described Pontibacter strains. The average nucleotide identity values between XAAS-72T and P. korlensis CCTCC AB 206081T and P. flavimaris ACCC 19859T were 77.9 and 86.9 %, respectively; the corresponding digital DNA-DNA hybridization values were 21.7 and 31.8 %. Menaquinone-7 was the predominant respiratory menaquinone. The polar lipids consisted of phosphatidylethanolamine, two unidentified aminophospholipids, two unidentified glycolipids and five unidentified lipids. The major cellular fatty acids were summed feature 4 (containing iso-C17 : 1 I/anteiso-C17 : 1 B), summed feature 3 (containing C16 : 1  ω7c/C16 : 1  ω6c) and iso-C15 : 0. The genome length of strain XAAS-72T was 5 054 860 bp with a genomic DNA G+C content of 54.5 mol%. The phenotypic and genotypic data suggest that strain XAAS-72T represents a novel species of the genus Pontibacter, for which the name Pontibacter kalidii sp. nov. is proposed. The strain is XAAS-72T (CGMCC 16594T=KCTC 72095T).

Pontibacter liquoris sp. nov. and Pontibacter vulgaris sp. nov., two novel bacteria isolated from the pit mud of Chinese liquor

Two pink-pigmented bacterial strains, designated NBU2971^T and NBU2972^T, were isolated from the pit mud of a Chinese liquor. Phylogenetic analyses based on 16S rRNA gene sequences suggested that strains NBU2971^T and NBU2972^T formed a distinct lineage within the family Hymenobacteraceae and were closely related to members of the genus Pontibacter. 16S rRNA gene sequences revealed that strain NBU2971^T showed highest similarity of 97.9 % to Pontibacter arcticus 2b14^T, and strain NBU2972^T showed the highest similarity of 96.9 % to Pontibacter deserti JC215^T. The 16S rRNA gene sequence similarity, average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the two novel strains were 95.2, 73.8 and 19.6 %, respectively, suggesting that they represent different species. The ANI and dDDH values between two novel strains and related species of genus Pontibacter were well below the threshold limit for prokaryotic species delineation. The genomic DNA G+C contents of strains NBU2971^T and NBU2972^T were 51.3 and 44.5 mol%, respectively. The major cellular fatty acids of the two novel strains were iso-C_15 : 0 and summed feature 4 (iso-C_17 : 1 I and/or anteiso-C_17 : 1 B). The major polar lipid of both novel strains was phosphatidylethanolamine. The only respiratory quinone was MK-7. Combining results of phenotypic, chemotaxonomic and genotypic data, strains NBU2971^T and NBU2972^T are considered to be two representatives in the genus Pontibacter, which the name Pontibacter liquoris sp. nov. and Pontibacter vulgaris sp. nov. are proposed. The type strains of the new species are NBU2971^T (=KCTC 82916^T=MCCC 1K06395^T) and NBU2972^T (=KCTC 82917^T=MCCC 1K06396^T), respectively.

Plant growth stages covered the legacy effect of rotation systems on microbial community structure and function in wheat rhizosphere

Legume-based crop rotation is conducive to improve soil multifunctionality, but how the legacy effect of previous legumes influenced the rhizosphere  microbial community of the following crops along with growth stages remains unclear. Here, the wheat rhizosphere microbial community was assessed at the regreening and filling stages with four previous legumes (mungbean, adzuki bean, soybean, and peanut), as well as cereal maize as a control. The composition and structure of both bacterial and fungal communities varied dramatically between two growth stages. The differences in fungal community structure among rotation systems were observed at both the regreening and filling stages, while the difference in bacterial community structure among rotation systems was observed only at the filling stage. The complexity and centrality of the microbial network decreased along with crop growth stages. The species associations were strengthened in legume-based rotation systems than in cereal-based rotation system at the filling stage. The abundance of KEGG orthologs (KOs) associated with carbon, nitrogen, phosphorus, and sulfur metabolism of bacterial community decreased from the regreening stage to the filling stage. However, there was no difference in the abundance of KOs among rotation systems. Together, our results showed that plant growth stages had a stronger impact than the legacy effect of rotation systems in shaping the wheat rhizosphere microbial community, and the differences among rotation systems were more obvious at the late growth stage. Such compositional, structural, and functional changes may provide predictable consequences of crop growth and soil nutrient cycling.

Pontibacter pamirensis sp. nov., isolated from saline-alkaline soil

A novel bacterium, designated TRT317T, was isolated from saline-alkaline soil collected from the Pamir plateau in northwest China. Cells of this strain were Gram-stain-negative, aerobic rods and red-pink-coloured. Phylogenetic analysis using 16S rRNA gene sequences indicated that strain TRT317T showed the highest sequence similarity to the type strains of Pontibacter diazotrophicus (96.3 %) and Pontibacter yuliensis (96.2 %). Growth was observed at 4–40 °C, pH 6.0–10.0 and in the presence of up to 7 % (w/v) NaCl. The major fatty acids were iso-C15 : 0 and summed feature 4 (iso-C17 : 1 I/anteiso-C17 : 1 B). The polar lipids included phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified phospholipid, four unidentified glycolipids and five unidentified lipids. The whole-cell sugars of strain TRT317T were mannose, rhamnose, glucose, galactose, xylose, arabinose and four unidentified sugars. The sole respiratory quinone was MK-7. The genomic DNA G+C content of strain TRT317T was 47.7 mol%. The average nucleotide identity (ANI) value of strain TRT317T with P. diazotrophicus was 88.3 %, which is below the standard ANI threshold for species identification (95–96 %). Combined results of physiological, genotypic, phylogenetic and chemotaxonomic analyses demonstrated that strain TRT317T represents a novel species within the genus Pontibacter , for which the name Pontibacter pamirensis sp. nov. is proposed. The type strain is TRT317T (=CGMCC1.18690T=KCTC 82818T).

Pontibacter cellulosilyticus sp. nov., a carboxymethyl cellulose-hydrolysing bacterium isolated from coastal water

A Gram-stain-negative, rod-shaped, non-motile, red-pink bacterium designated SD6^T was isolated from coastal marine water at Sadong Beach, Ulleung Island, South Korea. Cells of SD6^T grew at 10-42 °C (optimum, 30 °C), pH 5.0-9.0 (optimum, pH 6.0-7.0) and at 0-8.0 % (w/v) NaCl (optimum, 0-3 %). Moreover, 16S rRNA gene sequence analysis indicated that strain SD6^T was a member of the genus Pontibacter, sharing similarities to Pontibacter aydingkolensis XAAS-1^T (98.0 %), Pontibacter amylolyticus 9-2^T (97.3 %), Pontibacter korlensis X14-1^T (97.2 %) and Pontibacter soli HYL7-26^T (96.8 %). The predominant fatty acids of strain SD6^T were identified as iso-C_15 : 0 and summed feature 4 (comprising anteiso-C_17 : 1 B and/or iso-C_17 : 1 I) and the sole respiratory quinone was identified as MK-7 (menaquinone 7). Major polar lipids included phosphatidylethanolamine, one unidentified phosphoglycolipid, two unidentified glycolipids and one unidentified lipid. The average nucleotide identity and in silico DNA-DNA hybridization values of strain SD6^T with its closely related strains were 72.8-79.8 % and 19.2-22.6 %, respectively. The genomic DNA G+C content was 45.4 mol%. In accordance with the results of phenotypic, chemotaxonomic and phylogenetic data, strain SD6^T represents a novel species of the genus Pontibacter, for which the name Pontibacter cellulosilyticus sp. nov. is proposed. The type strain is SD6^T (=KACC 21543^T=NBRC 114313^T=JCM 31022^T).

Pontibacter flavimaris sp. nov., of the family Hymenobacteraceae, isolated from marine sediment

A Gram-stain-negative, ovoid or rod-shaped, non-flagellated, motile-by-gliding and aerobic bacteria, designated S10-8^T, was isolated from marine sediment of the Yellow Sea. Colonies of strain S10-8^T had a pink-red pigmentation and its cells were approximately 0.5-0.8 μm×1.0-2.5 μm in size. Growth occurred at 10-45 °C (optimally at 33-37 °C), in the presence of 0-12.0 % NaCl (optimally at 2.0-5.0 %, w/v) and at pH 5.0-8.5 (optimally at pH 7.0-7.5). Phylogenetic analysis of the 16S rRNA gene indicated that strain S10-8^T is a member of the genus Pontibacter within the family Hymenobacteraceae, and the 16S rRNA gene sequence similarity of strain S10-8^T to its closest relative Pontibacter actiniarum KCTC 12367^T was 96.9 %. Strain S10-8^T contained MK-7 as the predominant menaquinone and summed feature 4 (iso-C_17:1 I and/or anteiso-C_17:1 B) and iso-C_15:0 as the major fatty acids. The major polar lipids were phosphatidylethanolamine, an unidentified aminophospholipid and an unidentified lipid. The size of the draft genome was 4 623 791 bp and the G+C content was 53.5 mol%. There were low DNA-DNA hybridization values (<48.3±5.2 %) and average nucleotide identity values (<86.5 %) between strain S10-8^T and the most closely related recognized Pontibacter species. Therefore, we propose a novel species in the genus Pontibacter to accommodate the novel isolate: Pontibacter flavimaris sp. nov. (type strain S10-8^T=KCTC 42769^T=ACCC 19859^T).

Denitrifying bio-cathodes developed from constructed wetland sediments exhibit electroactive nitrate reducing biofilms dominated by the genera Azoarcus and Pontibacter

To limit the nitrate contamination of ground and surface water, stimulation of denitrification by electrochemical approach is an innovative way to be explored. Two nitrate reducing bio-cathodes were developed under constant polarization (-0.5 V vs SCE) using sediments and water from a constructed wetland (Rampillon, Seine-et-Marne, France). The bio-cathodes responded to nitrate addition on chronoamperometry through an increase of the reductive current. The denitrification efficiency of the pilots increased by 47% compared to the negative controls without electrodes after polarization. 16S rRNA gene sequencing of the biofilms and sediments evidenced the significant and discriminating presence of the Azoarcus and Pontibacter genera in the biofilms from biocathodes active for nitrate reduction. Our study shows the possibility to promote the development of efficient Azoarcus-dominated biocathodes from freshwater sediment to enhance nitrate removal from surface waters.

Identification of nitrogen-incorporating bacteria in a sequencing batch reactor: A combining cultivation-dependent and cultivation-independent method

Nitrogen-incorporating bacteria in activated sludge play important roles in nitrogen removal in sequencing bactch reactor (SBR), but the active microorganisms and their interactions in the complex community are rarely revealed. Herein, a combining cultivation-dependent and cultivation-independent methods associated with DNA-stable-isotope probing (SIP) was applied to determine the microbes responsible for nitrogen-incorporating in SBR. Results revealed that Cytophagaceae and Sphingobacteriales were identified to be involved in nitrification, and Anaerolineae, Plasticicumulans and Elusimicrobia were responsible for denitrification. Cultivable nitrobacter and denitrifiers were isolated from the activated sludge, but they did not participate in the nitrogen-incorporating based on the SIP results. Additionally, the molecular ecological network analysis indicated that the SIP-identified nitrogen-incorporating bacteria exhibited more links with the intra-community, which might explain the failure of isolating these active bacteria. These findings add understanding of the removal of nitrogenous compounds drived by nitrogen-incorporating bacteria in actual wastewater treatment process.

Complete genome sequence of Paracoccus sp. strain AK26: Insights into multipartite genome architecture and methylotropy

The present study reports the functional annotation of complete genome of methylotrophic bacterium Paracoccus sp. strain AK26. The 3.6 Mb genome with average GC content of 65.7% was distributed across five replicons; including chromosome (2.7 Mb) and four extrachromosomal replicons pAK1 (471Kb), pAK2 (189Kb), pAK3 (129Kb) and pAK4 (84 Kb). Interestingly, nearly 23% of the Cluster of Orthologous Group (COG) of proteins were annotated on extrachromosomal replicons and 185Kb genome content was attributed to segregated 19 genomic island regions. Among the four replicons, pAK4 was identified as essential and integral part of the genome, as supported by codon usage, GC content (66%) and synteny analysis. Comparative genome analysis for methylotrophy showed mechanistic variations in oxidation and assimilation of C1 compounds among closely related Paracoccus spp. Collectively, present study reports the functional characterization and genomic architecture of strain AK26 and provides genetic basis for quinone and isoprenoid based secondary metabolites synthesis using strain AK26.

Pontibacter terrae sp. nov., isolated from soil

A bacterial strain, designated 17SD1-15^T, was isolated from soil. Cells of this strain were Gram-stain-negative and aerobic rods. The major fatty acids of strain 17SD1-15^T were iso-C15 : 0 and summed feature 4 (anteiso-C17 : 1 B and/or iso-C17 : 1 I). The polar lipids were phosphatidylethanolamine, one phospholipid and five unidentified lipids. The G+C content of the genomic DNA of strain 17SD1-15^T was 49.0 mol%. The 16S rRNA gene sequence analysis showed that strain 17SD1-15^T was phylogenetically related to Pontibacter saemangeumensis GCM0142^T, Pontibacter korlensis X14-1^T, Pontibacter yuliensis H9X^T, Pontibacter diazotrophicus H4X^T and Pontibacter humi SWU8^T (98.3, 96.4, 96.4, 96.4 and 96.0 % sequence similarity, respectively). DNA-DNA relatedness between 17SD1-15^T and the most closely related type strain of Pontibacter species was 42.9±0.8 %. The low level of DNA-DNA relatedness identified strain 17SD1-15^T as a member of a novel species in the genus Pontibacter. The results of genotypic and phenotypic data, including chemotaxonomic traits, showed that strain 17SD1-15^T could be distinguished from its phylogenetically related species. Therefore, strain 17SD1-15^T represents a novel species within the genus Pontibacter, for which the name Pontibacter terrae sp. nov. is proposed, with the type strain 17SD1-15^T (=KCTC 52915^T=NBRC 113057^T).