Family Phyllobacteriaceae Research Articles

Phyllobacteriaceae: a family of ecologically and metabolically diverse bacteria with the potential for different applications.

The family Phyllobacteriaceae is a heterogeneous assemblage of more than 146 species of bacteria assigned to its existing 18 genera. Phylogenetic analyses have shown great phylogenetic diversity and also suggested about incorrect classification of several species that need to be reassessed for their proper phylogenetic classification. However, almost 50% of the family members belong to the genus Mesorhizobium only, of which the majority are symbiotic nitrogen fixers associated with different legumes. Other major genera are Phyllobacterium, Nitratireductor, Aquamicrobium, and Aminobacter. Nitrogen-fixing, legume nodulating members are present in Aminobacter and Phyllobacterium as well. Aquamicrobium spp. can degrade environmental pollutants, like 2,4-dichlorophenol, 4-chloro-2-methylphenol, and 4-chlorophenol. Chelativorans, Pseudaminobacter, Aquibium, and Oricola are the other genera that contain multiple species having diverse metabolic capacities, the rest being single-membered genera isolated from varied environments. In addition, heavy metal and antibiotic resistance, chemolithoautotrophy, poly-β-hydroxybutyrate storage, cellulase production, etc., are the other notable characteristics of some of the family members. In this report, we have comprehensively reviewed each of the species of the family Phyllobacteriaceae in their eco-physiological aspects and found that the family is rich with ecologically and metabolically highly diverse bacteria having great potential for human welfare and environmental clean-up.

Genetic diversity of rhizobial strains isolated from the relict legumes <em>Gueldenstaedtia monophylla</em> and <em>G. verna</em> growing in the republics of Altai and Buryatia (Russia)

For the first time, bacteria were isolated and identified from the root nodules of relict legumes Gueldenstaedtia monophylla Fisch. and G. verna (Georgi) Boriss. growing in the republics of Altai and Buryatia. The taxonomic position of the 29 obtained isolates was determined by sequencing the 16S rRNA gene (rrs). Showing a significant biodiversity, the isolates from G. monophylla and G. verna belonged to five genera of the order Rhizobiales: Mesorhizobium and Phyllobacterium (family Phyllobacteriaceae), Rhizobium (family Rhizobiaceae), Bosea (family Boseaceae), Bradyrhizobium (family Bradyrhizobiaceae). Three isolates which belonged to the species Bradyrhizobium valentinum and Rhizobium alamii showed 100 % of rrs-similarity with the type strains B. valentinum LmjM3T and R. alamii GBV016T, respectively. Six isolates of the genera Bosea and Rhizobium had a low level of rrs-similarity with the closest type strains (less than 99.5 %), which indicates that they may be assigned to new species. The data obtained can be used to itemise taxonomy within the order Rhizobiales, as well as to reveal the mechanisms of the formation of specific plant-microbial relationships during the evolution of symbiosis by studying the intermediate link between the extinct and modern rhizobia-legume symbiotic systems.

Oryzicola mucosus gen. nov., sp. nov., a novel slime producing bacterium belonging to the family Phyllobacteriaceae isolated from the rhizosphere of rice plants.

A novel Gram-stain negative, asporogenous, slimy, rod-shaped, non-motile bacterium ROOL2T was isolated from the root samples collected from a rice field located in Ilsan, South Korea. Phylogenetic analysis of the 16S rRNA sequence showed 96.5% similarity to Tianweitania sediminis Z8T followed by species of genera Mesorhizobium (96.4-95.6%), Aquabacterium (95.9-95.7%), Rhizobium (95.8%) and Ochrobactrum (95.6%). Strain ROOL2T grew optimally at 30°C in the presence of 1-6% (w/v) NaCl and at pH 7.5. The major respiratory quinone was ubiquinone-10 and the major cellular fatty acids were C18:1ω7c, summed feature 4 (comprising iso-C17:1 I and/or anteiso-C17:1 B) and summed feature 8 (comprising C18:1ω6c and/or C18:1ω7c). The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylmethylethanolamine, phosphatidylglycerol, one unidentified aminolipid and two unidentified lipids. The assembled draft genome of strain ROOL2T had 28 contigs with N50 value of 656,326 nt, total length of 4,894,583bp and a DNA G + C content of 61.5%. The average amino acid identity (AAI) values of strain ROOL2T against the genomes of related members belonging to the same family were below 68% and the ANI and dDDH values between the strain ROOL2T and the type strains of phylogenetically related species were 61.8-76.3% and 19.4-21.1%, respectively. Strain ROOL2T only produces carotenoid-type pigment when grown on LB agar and slime on R2A agar. In the presence of tryptophan, strain ROOL2T produced indole acetic acid (IAA), a phytohormone in plant growth and development. Gene clusters for indole-3-glycerol phosphatase and tryptophan synthase were found in the genome of strain ROOL2T. The genotypic and phenotypic characteristics indicated that strain ROOL2T represents a novel genus belonging the family Phyllobacteriaceae, for which the name Oryzicola mucosusgen. nov., sp. nov. is proposed. The type strain is ROOL2T (KCTC 82711T = NBRC 114717T).

Mesorhizobium microcysteis sp. nov., isolated from a culture of Microcystis aeruginosa.

Strain MaA-C15T, a Gram-stain-negative, non-spore-forming and strictly aerobic bacterium, was isolated from a xenic culture of Microcystis aeruginosa in the Republic of Korea. Cells were motile rods showing positive reactions in catalase and oxidase tests. Growth was observed between 15 and 37 °C (optimum, 30 °C), between pH 6.0 and pH 11.0 (optimum, pH 7.5) and in the presence of 0-2.0 % (w/v) NaCl (optimum, 0 %). Strain MaA-C15T contained C16 : 0, 11-methyl-C18 : 1 ω7c, cyclo-C19 : 0 ω8c and summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c) as the major cellular fatty acids and ubiquinone-10 as the sole respiratory quinone. Phosphatidylethanolamine, phosphatidylmonomethylethanolamine, an unidentified aminophospholipid, an unidentified glycolipid and three unidentified phospholipids were detected as the major polar lipids. The G+C content of the genomic DNA was 64.1 mol%. Phylogenetic and phylogenomic analyses based on 16S rRNA gene and genome sequences revealed that strain MaA-C15T formed a phyletic lineage with Mesorhizobium sediminum YIM M12096T within the family Phyllobacteriaceae. Strain MaA-C15T was most closely related to Mesorhizobium albiziae DSM 21822T with a 98.2 % 16S rRNA sequence similarity. Average nucleotide identity and in silico DNA-DNA hybridization values between strain MaA-C15T and M. albiziae DSM 21822T were 75.4 and 20.1 %, respectively. Based on the results of phenotypic, chemotaxonomic and molecular analyses, strain MaA-C15T represents a novel species of the genus Mesorhizobium, for which the name Mesorhizobium microcysteis sp. nov. is proposed. The type strain is MaA-C15T (=KACC 21226T=JCM 33503T).

Phylogenomic analysis and characterization of carbon monoxide utilization genes in the family Phyllobacteriaceae with reclassification of Aminobacter carboxidus (Meyer et al. 1993, Hördt et al. 2020) as Aminobacter lissarensis comb. nov. (McDonald et al. 2005)

The monotypic carboxydophilic genus Carbophilus has recently been transferred to the genus Aminobacter within the family Phyllobacteriaceae, and Carbophilus carboxidus was renamed Aminobacter carboxidus (comb. nov.) [Hördt et al. 2020]. Due to the poor resolution of the 16S rRNA gene-based phylogeny, an extensive phylogenomic analysis of the family Phyllobacteriaceae was conducted, with particular focus on the genus Aminobacter. Whole genome-based analyses of Phyllobacteriaceae type strains provided evidenced that the genus Aminobacter forms a monophyletic cluster, clearly demarcated from all other members of the family. Close relatedness between A. carboxidus DSM 1086T and A. lissarensis DSM 17454T was inferred from core proteome phylogeny, shared gene content, and multilocus sequence analyses. ANI and GGDC provided genetic similarity values above the species demarcating threshold for these two type strains. Metabolic profiling and cell morphology analysis corroborated the phenotypic identity between A. carboxidus DSM 1086T and A. lissarensis DSM 17454T. Search for the presence of carbon monoxide dehydrogenase (CODH) genes in Phyllobacteriaceae genomes revealed that the form II CODH is widespread in the family, whereas form I CODH was detected in few Mesorhizobium type strains, and in both A. carboxidus DSM 1086T and A. lissarensis DSM 17454T. Results of phylogenomic, chemotaxonomic, and morphological investigations, combined with the presence of similarly arranged CODH genes, indicate that A. carboxidus DSM 1086T and A. lissarensis DSM 17454T are distinct strains of the same species. Hence A. carboxidus is a later subjective heterotypic synonym of A. lissarensis.

Salaquimonas pukyongi gen. nov., sp. nov., a novel bacterium within the family Phyllobacteriaceae.

A novel aerobic, Gram-negative bacterial strain, RR3-28T, was isolated from a seawater recirculating aquaculture system in Busan, Republic of Korea. Cells were rod-shaped, non-motile, oxidase-positive, catalase-negative and grew optimally at 25-30 °C, pH 8.5 and 3 % (w/v) NaCl. Based on the results of phylogenetic analysis, strain RR3-28T was most closely related to Zhengella mangrovi X9-2-2T within the family Phyllobacteriaceae with 95.97 % 16S rRNA gene sequence similarity. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c, 71.1 %) and 11-methyl C18 : 1ω7c (14.4 %). The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine and unidentified aminolipids. The predominant quinone was ubiquinone Q-10 and the DNA G+C content was 58.6 mol%. On the basis of its phenotypic and genotypic characteristics, strain RR3-28T represents a novel genus and species belonging to the family Phyllobacteriaceae, for which the name Salaquimonas pukyongi gen. nov., sp. nov. is proposed. The type strain of the species is RR3-28T (=KCTC 52649T=DSM 107947T).

Oceaniradius stylonematis gen. nov., sp. nov., isolated from a red alga, Stylonema cornu-cervi

A Gram-stain-negative, strictly aerobic bacterium, designated StC1T, was isolated from a marine alga, Stylonema cornu-cervi, in the Republic of Korea. Cells were oxidase- and catalase-positive rods that were motile by a single lateral flagellum. Growth of strain StC1T was observed at 30-45 °C(optimum, 37 °C), pH 6.0-11.0 (pH 7.0) and in the presence of 1.0-8.0 % (w/v) NaCl (2 %). Strain StC1T contained summed feature 8 (comprising C18 : 1ω7c/C18 : 1 ω6c) and 11-methyl-C18 : 1ω7c as the major fatty acids. Sulfoquinovosyl diacylglycerol, phosphatidylethanolamine and phosphatidylglycerol and ubiquinone-10 were identified as the major polar lipids and the sole isoprenoid quinone, respectively. The G+C content of the genomic DNA was 64.7 mol%. Strain StC1T was most closely related to Oricola cellulosilytica CC-AMH-OT, Nitratireductor basaltis J3T, Aquamicrobiumahrensii 905/1T and Mesorhizobium tamadayense Ala-3T with 97.3 , 96.9 , 96.8 and 96.6 % 16S rRNA gene sequence similarities, respectively, but it formed a distinct phylogenic lineage within the family Phyllobacteriaceae. On the basis of phenotypic, chemotaxonomic and molecular properties, strain StC1T represents a novel genus of the family Phyllobacteriaceae, for which the name Oceaniradius stylonematis gen. nov., sp. nov. is proposed. The type strain is StC1T (=KACC 19231T=JCM 32050T).

The genetic diversity of microsymbionts from Thermopsis lanceolata growing in Mongolia

For the first time, bacteria were isolated and identified from the root nodules of a wild-growing medicinal legume plant Thermopsis lanceolata, originated from Mongolia. The taxonomic position of 14 isolates obtained was determined using of sequencing of the 16S rRNA (rrs) and atpD genes. It was shown a significant biodiversity of the isolates from T. lanceolata, which belonged to three genera of the order Rhizobiales: Phyllobacterium (family Phyllobacteriaceae), Rhizobium (family Rhizobiaceae) and Bosea (family Bradyrhizobiaceae). Six isolates belonged to the species Phyllobacterium zundukense and Phyllobacterium trifolii (100 и 99,9% rrs similarity with the type strains P. zundukense Tri-48T and P. trifolii PETP02T, respectivelly), three isolates were identified as Rhizobium anhuiense (99,8% rrs similarity with the type strain R. anhuiense CCBAU 23252T). Two slow-growing isolates of the genus Bosea Tla-534 and Tla-545 may potentially belong to new species, since their rrs-similarity to the closest type strains B. massiliensis LMG 26221T, B. lathyri LMG 26379T and B. vaviloviae Vaf18T was 98,5-99,0%. Non-rhizobial strains were not isolated. The isolation and future investigation of the rhizobial microsymbionts of the valuable medicinal legume Thermopsis lanceolata is one of the necessary prerequisites for its industrial cultivation.

Pseudaminobacter arsenicus sp. nov., an arsenic-resistant bacterium isolated from arsenic-rich aquifers.

An arsenic-resistant strain, CB3T, was isolated from arsenic-rich aquifers at the Jianghan Plain in Hubei, China. Phylogenetic and biochemical analysis suggested that it should represent a new species of the genus Pseudaminobacter in the family Phyllobacteriaceae. The 16S rRNA gene of CB3T shared the highest sequence similarities to those of the type strains Pseudaminobacter defluvii THI 051T (97.8 % identity) and Pseudaminobacter salicylatoxidans BN12T (97.4 %). The DNA-DNA relatedness values of CB3T with respect to strains belonging to the genus Pseudaminobacter were less than 70 %. The fatty acid profile of CB3T consisted of C16 : 0, cyclo-C19 : 0ω8c and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) as major components. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidyldimethylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylethanolamine and diphosphatidylglycerol. The DNA G+C content was 61.4 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain CB3T was distinct from previously described Pseudaminobacter species. Therefore, we propose that strain CB3T represents a novel species of the genus Pseudaminobacter, Pseudaminobacterarsenicus sp. nov., strain CB3T (=CCTCC AB2016116T=KCTC 52625T) is designated as the type strain.

Mesorhizobium ephedrae sp. nov. isolated from the roots of Ephedra przewalskii in Kumtag desert.

Strain 6GN-30T, a Gram-stain-negative, aerobic, non-spore-forming, rod-shaped, motile bacterium was isolated from Ephedra sinica roots in the Kumtag Desert. On the basis of the 16S rRNA gene sequence, the isolate represented a member of the genus Mesorhizobium of the family Phyllobacteriaceae. The results of a phylogenetic analysis indicated that 6GN-30T was phylogenetically related to Mesorhizobium soliNHI-8T. Strain 6GN-30T grew at a salinity of 0-1.0 % (w/v) NaCl (with optimum growth in the absence of NaCl), pH 6.0-9.0 (optimum 7.0-8.0) and 15-45 °C. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c/C18 : 1ω6c), C19 : 0cyclo ω8c, iso-C17 : 0, C18 : 0, and C16 : 0. The draft genome of 6GN-30T was 6.11 Mb long, with a DNA G+C content of 66.4 mol%. The average nucleotide identity to M. soliNHI-8T was 84.32 %. The strain contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine,aminophospholipids and phospholipids. The chemotaxonomic, phylogenetic and phenotypic data indicate that 6GN-30T represents a novel species of the genus Mesorhizobiumfor which the name Mesorhizobiumephedrae sp. nov. is proposed. The type strain is 6GN-30T (=ACCC 60073T=KCTC 62410T).

Zhengella mangrovi gen. nov., sp. nov., a novel member of family Phyllobacteriaceae isolated from mangrove sediment

A Gram-negative strain, designed X9-2-2T, was isolated from mangrove sediment in Yunxiao Mangrove National Nature Reserve, China. Strain X9-2-2T showed less than 96.2 % 16S rRNA gene sequence similarity to type strains of species with validly published names. Phylogenetic analysis based on 16S rRNA gene sequences and rpoB protein sequences revealed that strain X9-2-2T formed a distinct monophyletic clade within the family Phyllobacteriaceae and clustered distantly with the genera Aliihoeflea, Phyllobacterium and Hoeflea. Cells of X9-2-2T were rod-shaped, motile with subpolar or lateral flagella and facultative anaerobic. Optimal growth occurred at 30-37 °C, at pH 7 and in the presence of 2 % NaCl. The DNA G+C content of strain X9-2-2T was 64.9 mol%. The major fatty acids were summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c 56.0 %), iso -C17 : 0 (9.1 %) and C12 : 0 (6.6 %). The predominant respiratory quinone was ubiquinone-10 and the major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmonomethylethanolamine, an unidentified aminolipid and two unidentified polar lipids. According to its morphology, physiology, fatty acid composition and 16S rRNA gene signature nucleotide patterns, strain X9-2-2T represents a novel species of a novel genus in the family Phyllobacteriaceae, for which the name Zhengella mangrovi gen. nov., sp. nov. is proposed. The type strain is X9-2-2T (=MCCC 1K03307T=JCM 32107T).

Profiling 5-tolyltriazole biodegrading sludge communities using next-generation sequencing and denaturing gradient gel electrophoresis

Efficient biodegradation of 5-tolyltriazole (5-TTri) in wastewater treatment would minimize its potential detrimental effects on aquatic systems. Therefore, in order to profile 5-TTri biodegrading activated sludge communities (ASC) by DGGE and NGS, acclimation experiments with (i) easily degradable substrates, and (ii) various complex substrates mimicking wastewater conditions were performed. DGGE revealed four genera: Aminobacter (family Phyllobacteriaceae), Flavobacterium (family Flavobacteriaceae), Pseudomonas (family Pseudomonaceae), and Hydrogenophaga (family Comamonadaceae). Metagenomics (DNA) revealed the dominant families Alcaligenaceae, Pseudomonadaceae and Comamonadaceae that also represented the most active families at the RNA level (metatranscriptomics), which might indicate their importance for 5-TTri biodegradation. ASC acclimation and the composition of the substrate significantly affected 5-TTri biodegradation and the development of biodegrading communities. Using acetate only, a moderate 5-TTri degrading community was detected with a very low biodiversity and Pseudomonas spp. as dominant organisms. In contrast, setups fed ‘sludge supernatant’ (a complex substrate) efficiently biodegraded 5-TTri and formed a more diverse microbial community but with Hydrogenophaga spp. as the dominant group. Finally, a hypothetical 5-TTri biodegradation pathway was constructed based exclusively on the detected, biodegradation-related, Hydrogenophaga spp. genes.

Does the Miocene-Pliocene relict legume Oxytropis triphylla form nitrogen-fixing nodules with a combination of bacterial strains?

Four pairs of strains were isolated from four individual root nodules collected from different plants of the Miocene-Pliocene relict legume Oxytropis triphylla growing in the Baikal region (one nodule – one pair of strains). Identification of these strains by the 16S rRNA gene sequencing showed that one strain of each pair was fast-growing and phylogenetically closest to the type strains Phyllobacterium endophyticum PEPV15T (98.8–99.5% 16S rDNA similarity) and Phyllobacterium bourgognense STM 201T (98.8–99.3% 16S rDNA similarity). The other strain was slow-growing and closely related to the type strains Bosea vestrisii 34635T and Bosea eneae 34614T (99.5–99.8% 16S rDNA similarity). Results of the atpD gene sequencing suggested that Phyllobacterium-related isolates most probably belong to a new species of Phyllobacterium. It is known that none of the currently described strains of P. endophyticum, P. bourgognense (family Phyllobacteriaceae), B. vestrisii and B. eneae (family Bradyrhizobiaceae) can induce root nodules, but several symbiotic genes were found in the representatives of these two genera. Thus we hypothesize that the pairs of strains isolated from O. triphylla root nodules can be co-microsymbionts having complementary sets of symbiotic genes and their simultaneous presence in roots is required for efficient nodulation of the host plant. The whole genome sequencing of the studied strains is in progress to find and compare symbiotic genes.

Pseudaminobacter granuli sp. nov., isolated from granules used in a wastewater treatment plant.

A Gram negative, aerobic, non-motile and rod-shaped bacterial strain designated as Gr-2T was isolated from granules used in a wastewater treatment plant in Korea, and its taxonomic position was investigated using a polyphasic approach. Strain Gr-2T grew at 18-37°C (optimum temperature, 30°C) and a pH of 6.0-8.0 (optimum pH, 7.0) on R2A agar medium. Based on 16S rRNA gene phylogeny, the novel strain showed a new branch within the genus Pseudaminobacter of the family Phyllobacteriaceae, and formed clusters with Pseudaminobacter defluvii THI 051T (98.9%) and Pseudaminobacter salicylatoxidans BN12T (98.7%). The G+C content of the genomic DNA was 63.6%. The predominant respiratory quinone was ubiquinone-10 (Q-10) and the major fatty acids were cyclo-C19:0 ω8c, C18:1 ω7c, and iso-C17:0. The overall polar lipid patterns of Gr-2T were similar to those determined for the other Pseudaminobacter species. DNA-DNA relatedness values between strain Gr-2T and its closest phylogenetically neighbors were below 18%. Strain Gr-2T could be differentiated genotypically and phenotypically from the recognized species of the genus Pseudaminobacter. The isolate therefore represents a novel species, for which the name Pseudaminobacter granuli sp. nov. is proposed with the type strain Gr-2T (=KACC 18877T =LMG 29567T).

Nitratireductor aestuarii sp. nov., a marine alphaproteobacterium isolated from an estuary

Two bacterial strains, 2-2-12-1T and 2-2-12-2, were isolated from the estuary of the Jiulong River, south-east China. Cells were Gram-stain-negative, non-motile, short rods without flagella. Growth occurred at 25-45 °C, at pH 5.0-9.0 and with 0.5-2 % (w/v) NaCl. The bacteria were unable to reduce nitrate. The predominant fatty acids were C19 : 0 cyclo ω9c and C18 : 1ω7c. Phylogenetic analysis based on 16S rRNA gene sequences showed that both strains belong to the genus Nitratireductor, family Phyllobacteriaceae, class Alphaproteobacteria. Their closest neighbours were 'Nitratireductor lucknowense' DSM 24322 (96.3 and 96.5 % similarity, respectively) and Nitratireductor pacificus MCCC 1A01024T (96.2 and 96.3 % similarity, respectively). The DNA G+C contents of the two strains were 56.7 mol%. DNA-DNA hybridization between strain 2-2-12-1T and the two most closely related type strains revealed 57.3 and 52.3 % relatedness, respectively. Evidence from genotypic, chemotaxonomic and phenotypic data indicated that strains 2-2-12-1T and 2-2-12-2 represent a novel species of the genus Nitratireductor, for which the name Nitratireductor aestuarii sp. nov. is proposed. The type strain is 2-2-12-1T (=LMG 29090T=CGMCC 1.15320T).

Integrated metabolism in sponge-microbe symbiosis revealed by genome-centered metatranscriptomics.

Despite an increased understanding of functions in sponge microbiomes, the interactions among the symbionts and between symbionts and host are not well characterized. Here we reconstructed the metabolic interactions within the sponge Cymbastela concentrica microbiome in the context of functional features of symbiotic diatoms and the host. Three genome bins (CcPhy, CcNi and CcThau) were recovered from metagenomic data of C. concentrica, belonging to the proteobacterial family Phyllobacteriaceae, the Nitrospira genus and the thaumarchaeal order Nitrosopumilales. Gene expression was estimated by mapping C. concentrica metatranscriptomic reads. Our analyses indicated that CcPhy is heterotrophic, while CcNi and CcThau are chemolithoautotrophs. CcPhy expressed many transporters for the acquisition of dissolved organic compounds, likely available through the sponge's filtration activity and symbiotic carbon fixation. Coupled nitrification by CcThau and CcNi was reconstructed, supported by the observed close proximity of the cells in fluorescence in situ hybridization. CcPhy facultative anaerobic respiration and assimilation by diatoms may consume the resulting nitrate. Transcriptional analysis of diatom and sponge functions indicated that these organisms are likely sources of organic compounds, for example, creatine/creatinine and dissolved organic carbon, for other members of the symbiosis. Our results suggest that organic nitrogen compounds, for example, creatine, creatinine, urea and cyanate, fuel the nitrogen cycle within the sponge. This study provides an unprecedented view of the metabolic interactions within sponge-microbe symbiosis, bridging the gap between cell- and community-level knowledge.

Roseitalea porphyridii gen. nov., sp. nov., isolated from a red alga, and reclassification of Hoeflea suaedae Chung et al. 2013 as Pseudohoeflea suaedae gen. nov., comb. nov.

A Gram-staining-negative, strictly aerobic bacterial strain, designated MA7-20T, was isolated from a marine alga, Porphyridium marinum, in Korea. Cells showing oxidase-positive and catalase-positive activities were motile rods with bipolar flagella. Growth of strain MA7-20T was observed at 15-45 °C (optimum, 30-37 °C), at pH 6.0-10.5 (optimum, pH 7.0-8.0) and in the presence of 0-7 % (w/v) NaCl (optimum, 2-3 %). Strain MA7-20T contained summed feature 8 (comprising C18 : 1ω7c/C18 : 1ω6c), 11-methyl C18 : 1ω7c and C18 : 0 as the major fatty acids and ubiquinone-10 as the sole isoprenoid quinone. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidyl-N-methylethanolamine. The G+C content of the genomic DNA was 61.5 mol%. Strain MA7-20T was most closely related to Hoeflea suaedae YC6898T, Oricola cellulosilytica CC-AMH-0T and Nitratireductor basaltis J3T with 96.0, 95.8 and 95.8 % 16S rRNA gene sequence similarities, respectively, but the strain formed a distinct phylogenetic lineage from them within the family Phyllobacteriaceae with a low bootstrap value. H. suaedae also formed a clearly distinct phylogenetic lineage from other members of the genus Hoeflea and closely related genera. On the basis of phenotypic, chemotaxonomic and molecular properties, strain MA7-20T represents a novel species of a new genus of the family Phyllobacteriaceae, for which the name Roseitalea porphyridii gen. nov., sp. nov. is proposed. The type strain is MA7-20T (=KACC 18807T=JCM 31538T). In addition, H. suaedae is also reclassified as Pseudohoeflea suaedae gen. nov., comb. nov. (type strain YC6898T=KACC 14911T=NBRC 107700T).

Corticibacteriumpopuli gen. nov., sp. nov., a member of the family Phyllobacteriaceae, isolated from bark of Populus×euramericana.

Two Gram-staining-negative, aerobic, motile, slimy, glossy bacterial strains were isolated from bark tissue of Populus×euramericana. The bacteria grew at 10-37 °C, pH 5-10, with optimal growth at 28-30 °C, pH 6.0-8.0. Both strains grew with 0-3 % (w/v) NaCl. In the maximum-likelihood phylogenetic tree, the two isolates formed a distinct branch within the family Phyllobacteriaceae, and they were not closely related to any of the genera within the family Phyllobacteriaceae. The two novel isolates werepositive for oxidase andcatalase activity. The polar lipids profile revealed diphosphatidylglycerol, phosphatidylcholine, phospholipid, phosphatidylethanolamine, phosphatidylglycerol and five unknown lipids. The major fatty acids were C18 : 1ω7c and C16 : 0. The DNA G+C content was 56.4 mol%. On the basis of phylogenetic, chemotaxonomic and phenotypic data, the two strains represent a novel species belonging to a novel genus of the family Phyllobacteriaceae, for which the name Corticibacterium populi gen. nov., sp. nov. is proposed. The type strain of the type species is 16B10-2-7T (=CFCC 12884T=KCTC 42249T).

Surface modification of an organic hessian substrate leads to shifts in bacterial biofilm community composition and abundance

Antifouling strategies to limit biofilms on submerged surfaces in the marine environment are of particular interest due to the economic and environmental impacts in industries such as shipping and aquaculture. Here, we investigate the influence of chemically modified hessian bag surfaces on the bacterial abundance and community composition of biofilm formation using flow cytometry and 16S rRNA pyrosequencing. Hessian bags were coated with 5% and 10% Propyl(trimethoxy)silane (PTMS) and half of the bags had their lignin and hemicellulose removed via NaOH mercerisation. Significantly lower bacterial abundance was observed on mercerised bags treated with 5% PTMS (p<0.01). Significant shifts in bacterial taxa were also observed (p=0.0004), whereby unmercerised bags exhibited higher relative abundances of the anaerobic family Desulfovibrionaceae (4.5±1.7%), while mercerised bags displayed higher relative abundances of the aerobic family Phyllobacteriaceae (3.6±1.7%). This suggests that the mercerisation process may lower colonization rates and subsequently produce a thinner biofilm. This hypothesis is strengthened by the lower abundance of bacteria on mercerised bags, particularly on the 5% PTMS coating. Our results show that modifying a hessian surface via non-toxic coating and mercerisation reduces biofilm formation and also shifts the dominant taxa, increasing our understanding of antifouling strategies in the marine environment.

Ahrensia marina sp. nov., a dimethylsulfoniopropionate-cleaving bacterium isolated from seawater, and emended descriptions of the genus Ahrensia and Ahrensia kielensis.

A Gram-stain-negative, strictly aerobic, light-beige, rod-shaped, motile bacterium with peritrichous flagella that cleaves dimethylsulfoniopropionate (DMSP), designated strain LZD062T, was isolated from bottom seawater of the East China Sea. The isolate required sea salts for growth and grew optimally at pH 8.0 and 28 °C and in the presence of 2 % (w/v) NaCl. The major fatty acid (>10 %) was summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and the major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, one unidentified aminolipid and one unidentified glycolipid. Ubiquinone Q-10 was the only quinone detected. Phylogenetic analyses based on 16S rRNA and atpD gene sequences placed LZD062T within the genus Ahrensia of the family Phyllobacteriaceae in the class Alphaproteobacteria. The most closely related type strain was, in both cases, Ahrensia kielensis JCM 20689T ( = IAM 12618T = DSM 5890T), which gave sequence similarities of 97.7 % in the 16S rRNA gene and 90.4 % in the atpD gene. Genome relatedness between strain LZD062T and A. kielensis JCM 20689T was computed using both genome-to-genome distance analysis and average nucleotide identity, giving values of 22.10 ± 2.35 and 79.55 %, respectively. The genomic DNA G+C content calculated from the genome sequence was 50.1 mol%. On the basis of our polyphasic analyses, strain LZD062T is considered to represent a novel species of the genus Ahrensia, for which the name Ahrensia marina sp. nov. is proposed. The type strain is LZD062T ( = MCCC 1K00254T = JCM 30117T = DSM 28886T). Emended descriptions of the genus Ahrensia and Ahrensia kielensis are also proposed.