Nutrient availability and plant phenological stage influence the substrate microbiome in container-grown Impatiens walleriana 'Xtreme Red'

BACKGROUND

The microbiome plays a fundamental role in plant health and performance. Soil serves as a reservoir of microbial diversity where plants attract microorganisms via root exudates. The soil has an important impact on the composition of the rhizosphere microbiome, but greenhouse ornamental plants are commonly grown in soilless substrates. While soil microbiomes have been extensively studied in traditional agriculture to improve plant performance, health, and sustainability, information about the microbiomes of soilless substrates is still limited. Thus, we conducted an experiment to explore the microbiome of a peat-based substrate used in container production of Impatiens walleriana, a popular greenhouse ornamental plant. We investigated the effects of plant phenological stage and fertilization level on the substrate microbiome.

RESULTS

Impatiens plants grown under low fertilization rates were smaller and produced more flowers than plants grown under optimum and high fertilization. The top five bacterial phyla present in the substrate were Proteobacteria, Actinobacteria, Bacteriodota, Verrucomicrobiota, and Planctomycetota. We found a total of 2,535 amplicon sequence variants (ASV) grouped into 299 genera. The substrate core microbiome was represented by only 1.8% (48) of the identified ASV. The microbiome community composition was influenced by plant phenological stage and fertilizer levels. Phenological stage exhibited a stronger influence on microbiome composition than fertilizer levels. Differential abundance analysis using DESeq2 identified more ASVs significantly affected (enriched or depleted) in the high fertilizer levels at flowering. As observed for community composition, the effect of plant phenological stage on microbial community function was stronger than fertilizer level. Phenological stage and fertilizer treatments did not affect alpha-diversity in the substrate.

CONCLUSIONS

In container-grown ornamental plants, the substrate serves as the main microbial reservoir for the plant, and the plant and agricultural inputs (fertilization) modulate the microbial community structure and function of the substrate. The differences observed in substrate microbiome composition across plant phenological stage were explained by pH, total organic carbon (TOC) and fluoride, and across fertilizer levels by pH and phosphate (PO4). Our project provides an initial diversity profile of the bacteria occurring in soilless substrates, an underexplored source of microbial diversity.

Phylogenomics and molecular marker-based analyses of the order Nevskiales: Proposal for the creation of Steroidobacterales ord. nov. and Peristeroidobacter gen. nov

The order Nevskiales, class Gammaproteobacteria, encompasses four families Algiphilaceae, Salinisphaeraceae, Nevskiaceae, and Steroidobacteraceae. The taxonomy of this order is structured from the inferences derived from the 16S rRNA gene and genome-based phylogenetic tree analyses. However, previous taxonomic studies of the order failed to incorporate most of the representatives from other established orders within the class Gammaproteobacteria. Other divergent members within the class Gammaproteobacteria were therefore overlooked. In this study, the taxonomy of the order Nevskiales was revisited using genome-based analyses with an expanded scope of outgroups representing the vast majority of the diversity within the class Gammaproteobacteria. Results from the phylogenetic analyses strongly supported the exclusion of the family Steroidobacteraceae from the order Nevskiales and further implied the assignment of the family into a novel order. In addition, the analyses also supported the reclassification of Steroidobacter gossypii, Steroidobacter soli, Steroidobacter agariperforans, and Steroidobacter agaridevorans into a novel genus. The identified conserved signature indels in 33 protein sequences further reinforced the new taxonomic assignments. Furthermore, the results of the average nucleotide identity and average amino acid identity analyses, together with the phenotypic and genomic characteristics among the members of the genus Steroidobacter also provided evidence supporting the reclassification of the four Steroidobacter species. Based on these results, the family Steroidobacteraceae is proposed to be assigned into a novel order Steroidobacterales ord. nov., and the species S. gossypii, S. soli, S. agariperforans, and S. agaridevorans are proposed to be moved into a novel genus Peristeroidobacter gen. nov. within the family Steroidobacteraceae.

Flagellatimonas centrodinii gen. nov., sp. nov., a novel member of the family Nevskiaceae isolated from toxin-producing dinoflagellate Centrodinium punctatum

A Gram-stain-negative, aerobic, rod-shaped strain (R2A-3^T) was isolated from the toxin-producing dinoflagellate Centrodinium punctatum and identified as a novel genus and new species based on a polyphasic taxonomic approach. The optimum conditions for growth of the strain were at 25 °C, pH 8.0 and in the presence of 3 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA genes and 92 core genes sets revealed that strain R2A-3^T belongs to the family Nevskiaceae in the class Gammaproteobacteria and represented an independent taxon separated from other genera. The 16S rRNA gene of strain R2A-3^T showed the highest sequence similarity to Polycyclovorans algicola TG408^T (95.2%), Fontimonas thermophila HA-01^T (94.1%) and Sinimarinibacterium flocculans NH6-24^T (93.2%), and less than 92.8 % similarity to other genera in the family Nevskiaceae. The genome length of strain R2A-3^T was 3608892 bp with 65.2 mol% G+C content. Summed feature 8 (comprising C_18 : 1  ω7c and/or C_18 : 1  ω6c) was the major fatty acid (>10 %). Diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine were detected as the major polar lipids. The major respiratory quinone was ubiquinone-8. According to its phylogenetic, phenotypic, chemotaxonomic and genomic features, strain R2A-3^T represents a new species in the new genus of the family Nevskiaceae. It is recommended to name it Flagellatimonas centrodinii gen. nov., sp. nov. The type strain is R2A-3^T (=KCTC 82469^T=GDMCC 1.2523^T).

Solimonas marina sp. nov., isolated from deep seawater of the Pacific Ocean

A taxonomic study was carried out on strain C16B3^T, which was isolated from deep seawater of the Pacific Ocean. The bacterium was Gram-stain-negative, oxidase- and catalase- positive and rod-shaped. Growth was observed at salinities of 0-8.0 % and at temperatures of 10-45 °C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain C16B3^T belonged to the genus Solimonas, with the highest sequence similarity to Solimonas terrae KIS83-12^T (97.2 %), followed by Solimonas variicoloris MN28^T (97.0 %) and the other four species of the genus Solimonas (94.5 -96.8 %). The average nucleotide identity and estimated DNA-DNA hybridization values between strain C16B3^T and the type strains of the genus Solimonas were 74.05-79.48 % and 19.5-22.5 %, respectively. The principal fatty acids (>5 %) were summed feature 8 (C_18 : 1  ω7c/C_18 : 1  ω6c; 20.9 %), iso-C_16 : 0 (14.6 %), C_16 : 1  ω5c (9.4 %), iso-C_12 : 0 (8.4 %), summed feature 2 (C_14 : 0 3-OH/iso I-C_16 : 1 and C_12 : 0 aldehyde; 6.8 %) and C_16 : 0 (5.5 %). The G+C content of the chromosomal DNA was 65.37 mol%. The respiratory quinone was determined to be Q-8 (100 %). The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, four unidentified aminolipids, six unidentified phospholipids and one unidentified polar lipid. The combined genotypic and phenotypic data show that strain C16B3^T represents a novel species within the genus Solimonas, for which the name Solimonas marina sp. nov. is proposed, with the type strain C16B3^T (=MCCC 1A04678^T=KCTC 52314^T).

Microbial community response to environmental changes in a technosol historically contaminated by the burning of chemical ammunitions

The burning of chemical weapons in the 1926-1928 period produced polluted technosols with elevated levels of arsenic, zinc, lead and copper. During an eight-month mesocosm experiment, these soils were submitted to two controlled environmental changes, namely the alternation of dry and water-saturated conditions and the addition of fragmented organic forest litter to the surface soil. We investigated, by sequencing the gene coding 16S rRNA and 18S rRNA, (1) the structure of the prokaryotic and eukaryotic community in this polluted technosol and (2) their response to the simulated environmental changes, in the four distinct layers of the mesocosm. In spite of the high concentrations of toxic elements, microbial diversity was found to be similar to that of non-polluted soils. The bacterial community was dominated by Proteobacteria, Acidobacteria and Bacteroidetes, while the fungal community was dominated by Ascomicota. Amongst the most abundant bacterial Operational Taxonomic Units (OTUs), including Sphingomonas as a major genus, some were common to soil environments in general whereas a few, such as organisms related to Leptospirillum and Acidiferrobacter, seemed to be more specific to the geochemical context. Evolution of the microbial abundance and community structures shed light on modifications induced by water saturation and the addition of forest litter to the soil surface. Co-inertia analysis suggests a relationship between the physico-chemical parameters total organic carbon, Zn, NH₄⁺ and As(III) concentrations and the bacterial community structure. Both these results imply that microbial community dynamics linked to environmental changes should be considered as factors influencing the behavior of toxic elements on former ammunition burning sites.

Stagnimonas aquatica gen. nov., sp. nov., a new member of the family Nevskiaceae isolated from a freshwater mesocosm

A novel bacterial strain, designated THS-13^T, isolated from a freshwater mesocosm in Taiwan, was characterized by taking a polyphasic taxonomic approach. Cells of strain THS-13^T were Gram-stain-negative, aerobic, rod-shaped, motile by means of a single polar flagellum and formed translucent white coloured colonies. Growth occurred at 20-35 °C (optimum, 25 °C), at pH 5-8 (pH 6) and with 0-2 % NaCl (1 %). Phylogenetic analyses based on 16S rRNA gene and coding sequences of 92 protein clusters revealed that the strain belonged to the family Nevskiaceae in the class Gammaproteobacteria and represented an independent taxon separated from other genera. Strain THS-13^T shared low level of 16S rRNA gene sequence similarity (less than 93.0 %) to members of other genera in the family Nevskiaceae and was most closely related to Nevskia aquatilis F2-63^T (92.9 %). Strain THS-13^T showed less than 73.4 % average nucleotide identity and less than 23.8 % digital DNA-DNA hybridization identity compared to the type strains of related genera within the family Nevskiaceae. The predominant fatty acids were C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and iso-C16 : 0. The major isoprenoid quinone was Q-8 and the DNA G+C content was 67.6 mol%. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, an uncharacterized aminophospholipid, an uncharacterized phospholipid and an uncharacterized aminolipid. On the basis of the genotypic and phenotypic data, strain THS-13^T represents a novel species of a new genus in the family Nevskiaceae, for which we propose the name Stagnimonas aquatica gen. nov., sp. nov. The type strain is THS-13^T (=BCRC 81158^T=LMG 30925^T=KCTC 62868^T).

Solimonas fluminis sp. nov., isolated from a freshwater river

A strictly aerobic, catalase-negative and oxidase-positive bacterium (HR-BB^T), isolated from a water sample of the Han River, was taxonomically studied using a polyphasic approach. Cells were Gram-stain-negative motile rods with a polar flagellum. The strain grew at 20-35 °C and pH 7-8 and in the absence of NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain HR-BB^T belonged to the family Nevskiaceae in the phylum Proteobacteria and formed a phylogenic lineage with members of the genus Solimonas. A comparison of the 16S rRNA gene sequences of strain HR-BB^T and the type strains of closely related species of the genus Solimonas showed that it shared highest sequence similarity with Solimonas terrae KIS83-12^T (94.9 %), Solimonas soli DCY12^T (94.8 %), Solimonas variicoloris MN28^T (94.4 %) and Solimonas flava CW-KD 4^T (94.2 %). The fatty acids of the strain consisted of summed features 8 (comprising C18 : 1ω6c and/or C18 : 1ω7c) and 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c), C16 : 0 and C12 : 0 as major components. The polar lipids comprised phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, three unidentified phospholipids and an unidentified lipid. Ubiquinone-8 was detected as the sole respiratory quinone. The DNA G+C content of strain HR-BB^T was 68.5 mol%. Based on the genotypic, chemotaxonomic and phenotypic analyses, strain HR-BB^T represents a novel species of the genus Solimonas, for which the name Solimonas fluminis sp. nov. is proposed. The type strain is HR-BB^T (=KACC 19410^T=JCM 32268^T).

Ahniella affigens gen. nov., sp. nov., a gammaproteobacterium isolated from sandy soil near a stream

A bacterial strain, designated D13^T, was isolated from sandy soil near a stream in Sinan-gun, Republic of Korea. Cells were Gram-stain-negative, aerobic, non-motile and flexible rod-shaped. Growth occurred at 15-35 °C (optimum 30 °C) and pH 6.5-8.0 (pH 7.0). NaCl was not obligatory for growth but could be tolerated at up to 0.5 % (w/v) NaCl. The DNA G+C content of the genomic DNA of strain D13^T was 57.7 mol% and a phylogenetic analysis of the 16S rRNA gene sequence revealed that strain D13^T formed a distinct evolutionary lineage within the family Rhodanobacteraceae of the order Lysobacterales. Strain D13^T showed highest 16S rRNA sequence similarity to Lysobacter hankyongensis KTCe-2^T (92.7 %), followed by Luteimonas cucumeris Y4^T (92.7 %), Dyella japonica XD53^T (92.6 %) and Aquimonas voraii GPTSA 20^T (92.5 %). The major cellular fatty acids (>10 % of the total) were iso-C16 : 0, iso-C15 : 0 and summed feature 9 (iso-C17 : 1ω9с and/or C16 : 0 10-methyl). The respiratory quinone was ubiquinone-8 and the major polar lipids of the isolate consisted of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylmonomethylethanolamine. Based on polyphasic analysis, strain D13^T could be differentiated from other genera in the family Rhodanobacteraceae, which suggests that strain D13^T represents a novel species of a new genus in the family Rhodanobacteraceae, for which the name Ahniella affigens gen. nov., sp. nov. is proposed. The type strain is D13^T (=KACC 19270^T=JCM 31634^T).

Sinimarinibacterium flocculans gen. nov., sp. nov., a gammaproteobacterium from offshore surface seawater

Two aerobic, rod-shaped, non-motile, non-sporulating and Gram-staining-negative bacterial strains, namely NH6-24T and Za3-11, were isolated from the surface seawater of the South China Sea and the estuary of the Yangtze River, respectively. The two isolates grew at 14–44 °C (optimum 37–40 °C) and pH 6.0–8.5 (optimum pH 7.0–7.5). The sea salt ranges for growth were 0.5–10 % (w/v) (optimum 1–2.5 %) for strain NH6-24T and 0–12 % (w/v) (optimum 0.5–4.5 %) for strain Za3-11.Both strains could grow in the absence of NaCl. Results of phylogenetic analysis based on 16S rRNA gene sequences indicated that the two isolates showed closest affinity to the genera Fontimonas (96.0 %) and Solimonas (94.1–95.1 %) and formed a single lineage in the cluster of the family Solimonadaceae. The predominant isoprenoid quinone was ubiquinone-8.The major fatty acids were C18 : 1ω7c, iso-C16 : 0 and C16 : 0.The dominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content was 65 mol%. Based on the polyphasic taxonomic characterization, strains NH6-24T and Za3-11 are considered to represent a novel species of a novel genus, for which the name Sinimarinibacterium flocculans gen. nov., sp. nov. is proposed. The type strain of the type species is NH6-24T ( = CGMCC 1.10815T = JCM 17607T) and an additional strain is Za3-11 ( = CGMCC 1.10816 = JCM 17606).

O leiagrimonas soli gen. nov., sp. nov., a genome-sequenced gammaproteobacterium isolated from an oilfield

A yellow-pigmented strain, designated strain 3.5XT, was isolated from oil-contaminated saline soil in Gudao, Shandong Province, China, and was characterized taxonomically. The results showed that the isolate was a Gram-stain-negative, aerobic, motile, rod-shaped cell with a polar flagellum. Phylogenetic analysis of 16S rRNA gene sequences revealed the strain belonged to the family Xanthomonadaceae in the class Gammaproteobacteria and represented an independent taxon separated from other genera. The closest relative of strain 3.5XT was Fulvimonas soli DSM 14263T (94 % similarity). The genomic DNA G+C content was 67 mol% by thermal denaturation and 66.3 mol% from genome sequences. The cells mainly consisted of branched fatty acids, with iso-C17 : 0, iso-C15 : 0, iso-C17 : 1ω9c and/or C16 : 010-methyl and iso-C11 : 0 as the major fatty acids. The main polar lipids were phosphatidylmonomethylethanolamine, diphosphatidylglycerol and phosphatidylethanolamine. In addition, ubiquinone Q-8 was the major component of the quinone system and the polyamine pattern contained the major compound spermidine plus minor amounts of putrescine and spermine. On the basis of phenotypic, genotypic and phylogenetic distinctiveness, it is proposed that the isolate represents a novel species in a novel genus, namely Oleiagrimonas soli gen. nov., sp. nov. The type strain is 3.5XT ( = NBRC 110685T = KCTC 42351T = CPCC 100614T).

Bacteria of the candidate phylum TM7 are prevalent in acidophilic nitrifying sequencing-batch reactors

Laboratory-scale acidophilic nitrifying sequencing-batch reactors (ANSBRs) were constructed by seeding with sewage-activated sludge and cultivating with ammonium-containing acidic mineral medium (pH 4.0) with or without a trace amount of yeast extract. In every batch cycle, the pH varied between 2.7 and 4.0, and ammonium was completely converted to nitrate. Attempts to detect nitrifying functional genes in the fully acclimated ANSBRs by PCR with previously designed primers mostly gave negative results. 16S rRNA gene-targeted PCR and a subsequent denaturating gradient gel electrophoresis analysis revealed that a marked change occurred in the bacterial community during the overall period of operation, in which members of the candidate phylum TM7 and the class Gammaproteobacteria became predominant at the fully acclimated stage. This result was fully supported by a 16S rRNA gene clone library analysis, as the major phylogenetic groups of clones detected (>5% of the total) were TM7 (33%), Gammaproteobacteria (37%), Actinobacteria (10%), and Alphaproteobacteria (8%). Fluorescence in situ hybridization with specific probes also demonstrated the prevalence of TM7 bacteria and Gammaproteobacteria. These results suggest that previously unknown nitrifying microorganisms may play a major role in ANSBRs; however, the ecophysiological significance of the TM7 bacteria predominating in this process remains unclear.

Effects of different compost amendments on the abundance and composition of alkB harboring bacterial communities in a soil under industrial use contaminated with hydrocarbons

Alkane degrading microorganisms play an important role for the bioremediation of petrogenic contaminated environments. In this study, we investigated the effects of compost addition on the abundance and diversity of bacteria harboring the alkane monooxygenase gene (alkB) in an oil-contaminated soil originated from an industrial zone in Celje, Slovenia (Technosol). Soil without any amendments (control soil) and soil amended with two composts differing in their maturation stage and nutrient availability, were incubated under controlled conditions in a microcosm experiment and sampled after 0, 6, 12, and 36 weeks of incubation. As expected the addition of compost stimulated the degradation of alkanes in the investigated soil shortly after the addition. By using quantitative real-time PCR higher number of alkB genes were detected in soil samples amended with compost compared to the control soils. To get an insight into the composition of alkB harboring microbial communities, we performed next generation sequencing of amplicons of alkB gene fragment. Richness and diversity of alkB gene harboring prokaryotes was higher in soil mixed with compost compared to control soils with stronger effects of the less maturated, nutrient poor compost. The phylogenetic analysis of communities suggested that the addition of compost stimulated the abundance of alkB harboring Actinobacteria during the experiment independent from the maturation stage of the compost. AlkB harboring γ-proteobacteria like Shewanella or Hydrocarboniphaga as well as α-proteobacteria of the genus Agrobacterium responded also positively to the addition of compost to soil. The amendment of the less maturated, nutrient poor compost resulted in addition in a large increase of alkB harboring bacteria of the Cytophaga group (Microscilla) mainly at the early sampling time points. Our data indicates that compost amendments significantly change abundance and diversity pattern of alkB harboring microbes in Technosol and might be a useful agent to stimulate bioremediation of hydrocarbons in contaminated soils.

The growth of Steroidobacter agariperforans sp. nov., a novel agar-degrading bacterium isolated from soil, is enhanced by the diffusible metabolites produced by bacteria belonging to Rhizobiales

An agar-degrading bacterium was isolated from soil collected in a vegetable cropping field. The growth of this isolate was enhanced by supplying culture supernatants of bacteria belonging to the order Rhizobiales. Phylogenetic analysis based on 16S rRNA gene sequences indicated the novel bacterium, strain KA5-B(T), belonged to the genus Steroidobacter in Gammaproteobacteria, but differed from its closest relative, Steroidobacter denitrificans FS(T), at the species level with 96.5% similarity. Strain KA5-B(T) was strictly aerobic, Gram-negative, non-motile, non-spore forming, and had a straight to slightly curved rod shape. Cytochrome oxidase and catalase activities were positive. The strain grew on media containing culture supernatants in a temperature range of 15-37°C and between pH 4.5 and 9.0, with optimal growth occurring at 30°C and pH 6.0-8.0. No growth occurred at 10 or 42°C or at NaCl concentrations more than 3% (w/v). The main cellular fatty acids were iso-C15:0, C16:1ω7c, and iso-C17:1ω9c. The main quinone was ubiquinone-8 and DNA G+C content was 62.9 mol%. In contrast, strain FS(T) was motile, did not grow on the agar plate, and its dominant cellular fatty acids were C15:0 and C17:1ω8c. Based on its phylogenetic and phenotypic properties, strain KA5-B(T) (JCM 18477(T) = KCTC 32107(T)) represents a novel species in genus Steroidobacter, for which the name Steroidobacter agariperforans sp. nov. is proposed.

Solimonas terrae sp. nov., isolated from soil

A Gram-stain-negative, aerobic, motile, rod-shaped bacterium, designated strain KIS83-12(T), was isolated from soil of Gaui island in the Taean region of South Korea. The strain grew at 15-33 °C (optimum, 28 °C), at pH 5.0-8.0 (optimum, pH 7.0). Growth did not occur in the presence of NaCl. The strain was catalase-negative and oxidase-positive. Phylogenetic analysis based on 16S rRNA gene sequences showed that KIS83-12(T) was most closely related to Solimonas soli DCY12(T) (96.9 %), Solimonas variicoloris MN28(T) (96.5 %), Solimonas flava CW-KD 4(T) (96.5 %) and Solimonas aquatica NAA16(T) (96.0 %), and formed a robust phyletic lineage with members of the genus Solimonas. The main isoprenoid quinone was Q-8. Major polar lipids included phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Fatty acids present in large and moderate amounts (>5.0 %) were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C16 : 0, C16 : 1ω5c, summed feature 2 (iso-C16 : 1 I and/or C14 : 0 3-OH) and C12 : 0. The DNA G+C content was 67.9 mol%. On the basis of the taxonomic data obtained in this study, KIS83-12(T) represents a novel species of the genus Solimonas, for which the name Solimonas terrae sp. nov. is proposed, with KIS83-12(T) ( = KACC 16967(T) = DSM 27281(T)) as the type strain.

The family name Solimonadaceae Losey et al. 2013 is illegitimate, proposals to create the names ‘Sinobacter soli’ comb. nov. and ‘Sinobacter variicoloris’ contravene the Code, the family name Xanthomonadaceae Saddler and Bradbury 2005 and the order name Xanthomonadales Saddler and Bradbury 2005 are illegitimate and notes on the application of the family names Solibacteraceae Zhou et al. 2008, Nevskiaceae Henrici and Johnson 1935 (Approved Lists 1980) and Lysobacteraceae Christensen and Cook 1978 (Approved Lists 1980) and order name Lysobacteriales Christensen and Cook 1978 (Approved Lists 1980) with respect to the classification of the corresponding type genera Solibacter Zhou et al. 2008, Nevskia Famintzin 1892 (Approved Lists 1980) and Lysobacter Christensen and Cook 1978 (Approved Lists 1980) and importance of accurately expressing the link between a taxonomic name, its authors and the corresponding description/circumscription/emendation

In a recent publication the name Solimonadaceae Losey et al. 2013 has been proposed as a replacement name for the family name Sinobacteraceae Zhou et al. 2008. This course of action contravenes the current Code governing the nomenclature of prokaryotes, making Solimonadaceae Losey et al. 2013 an illegitimate name that neither has claim to priority nor can be used as a correct name. Closer examination of publications dealing with the taxonomy of members of the genera Solimonas and Sinobacter and the placement of these taxa at the rank of family and order reveal problems associated with the application of the family names Sinobacteraceae Zhou et al. 2008, Nevskiaceae Henrici and Johnson 1935 (Approved Lists 1980) and Lysobacteraceae Christensen and Cook 1978 (Approved Lists 1980) and the order names Lysobacterales Christensen and Cook 1978 (Approved Lists 1980) and Xanthomonadales Saddler and Bradbury 2005.

Fontimonas thermophila gen. nov., sp. nov., a moderately thermophilic bacterium isolated from a freshwater hot spring, and proposal of Solimonadaceae fam. nov. to replace Sinobacteraceae Zhou et al. 2008

A novel bacterial strain designated HA-01T was isolated from a freshwater terrestrial hot spring located at Hot Springs National Park, Arkansas, USA. Cells were Gram-negative-staining, rod-shaped, aerobic, chemo-organotrophic, oxidase- and catalase-positive, non-spore-forming and motile by means of a single polar flagellum. Growth occurred at 37–60 °C, with an optimum between 45 and 50 °C, and at pH 6.5–8.5, with an optimum between pH 6.5 and 7.0. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the closest relatives of strain HA-01T were Solimonas aquatica NAA-16T (93.8 %), Solimonas flava CW-KD 4T (94.1 %), Solimonas soli DCY12T (93.1 %), Solimonas variicoloris MN28T (94.0 %), Nevskia ramosa Soe1T (91.2 %) and Hydrocarboniphaga effusa AP103T (91.1 %). Major fatty acids consisted of C16 : 0, iso-C16 : 0, C16 : 1ω5c and summed feature 8 (C18 : 1ω9c, C18 : 1ω7c and C18 : 1ω6c). Polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, and the major isoprenoid quinone was Q-8. The DNA G+C content was 64.4 mol%. Based on phylogenetic, phenotypic and chemotaxonomic evidence, it is proposed that strain HA-01T represents a novel species in a new genus for which the name Fontimonas thermophila gen. nov., sp. nov. is proposed. The type strain of the type species is HA-01T ( = DSM 23609T = CCUG 59713T). A new family, Solimonadaceae fam. nov., is also proposed to replace Sinobacteriaceae Zhou et al. 2008.

Algiphilus aromaticivorans gen. nov., sp. nov., an aromatic hydrocarbon-degrading bacterium isolated from a culture of the marine dinoflagellate Lingulodinium polyedrum, and proposal of Algiphilaceae fam. nov

A strictly aerobic, halotolerant, Gram-stain-negative, rod-shaped bacterium, designated strain DG1253T, was isolated from a laboratory culture of the marine dinoflagellate Lingulodinium polyedrum (CCAP 1121/2). The strain was able to degrade two- and three-ring polycyclic aromatic hydrocarbons. It exhibited a narrow nutritional spectrum, preferring to utilize aliphatic and aromatic hydrocarbon compounds and small organic acids. Cells produced surface blebs and contained a single polar flagellum. The predominant isoprenoid quinone of strain DG1253T was Q-8. The fatty acid profile was dominated by C18 : 1ω7c. The mean DNA G+C content of strain DG1253T was 63.6±0.25 mol%. 16S rRNA gene sequence analysis placed this organism within the order Xanthomonadales of the class Gammaproteobacteria . Its closest relatives included representatives of the Hydrocarboniphaga – Nevskia – Sinobacter clade (≤89.9 % 16S rRNA gene sequence similarity) in the family Sinobacteraceae . On the basis of distinct phenotypic and genotypic characteristics, strain DG1253T is considered to represent a novel species of a new genus in the class Gammaproteobacteria , for which the name Algiphilus aromaticivorans gen. nov., sp. nov. is proposed. The type strain of the type species, Algiphilus aromaticivorans, is DG1253T ( = ATCC BAA-2243T = DSM 24793T). In addition, a new family, Algiphilaceae fam. nov., is proposed to accommodate the genus Algiphilus.

Polycyclovorans algicola gen. nov., sp. nov., an aromatic-hydrocarbon-degrading marine bacterium found associated with laboratory cultures of marine phytoplankton

A strictly aerobic, halotolerant, rod-shaped bacterium, designated strain TG408, was isolated from a laboratory culture of the marine diatom Skeletonema costatum (CCAP1077/1C) by enrichment with polycyclic aromatic hydrocarbons (PAHs) as the sole carbon source. 16S rRNA gene sequence analysis placed this organism within the order Xanthomonadales of the class Gammaproteobacteria. Its closest relatives included representatives of the Hydrocarboniphaga-Nevskia-Sinobacter clade (<92% sequence similarity) in the family Sinobacteraceae. The strain exhibited a narrow nutritional spectrum, preferring to utilize aliphatic and aromatic hydrocarbon compounds and small organic acids. Notably, it displayed versatility in degrading two- and three-ring PAHs. Moreover, catechol 2,3-dioxygenase activity was detected in lysates, indicating that this strain utilizes the meta-cleavage pathway for aromatic compound degradation. Cells produced surface blebs and contained a single polar flagellum. The predominant isoprenoid quinone of strain TG408 was Q-8, and the dominant fatty acids were C(16:0), C(16:1) ω7c, and C(18:1) ω7c. The G+C content of the isolate's DNA was 64.3 mol% ± 0.34 mol%. On the basis of distinct phenotypic and genotypic characteristics, strain TG408 represents a novel genus and species in the class Gammaproteobacteria for which the name Polycyclovorans algicola gen. nov., sp. nov., is proposed. Quantitative PCR primers targeting the 16S rRNA gene of this strain were developed and used to show that this organism is found associated with other species of marine phytoplankton. Phytoplankton may be a natural biotope in the ocean where new species of hydrocarbon-degrading bacteria await discovery and which contribute significantly to natural remediation processes.

Proposal of Solimonas aquatica sp. nov., reclassification of Sinobacter flavus Zhou et al. 2008 as Solimonas flava comb. nov. and Singularimonas variicoloris Friedrich and Lipski 2008 as Solimonas variicoloris comb. nov. and emended descriptions of the genus Solimonas and its type species Solimonas soli

A bacterial strain designated NAA16(T) was isolated from a freshwater spring in Taiwan and was characterized using a polyphasic taxonomic approach. Strain NAA16(T) was aerobic, Gram-staining-negative, rod-shaped, non-spore-forming and motile by means of a single polar flagellum. Growth occurred at 20-40 °C (optimum, 25 °C), at pH 7.0-8.0 (optimum, pH 7.5) and with up to 1 % NaCl (optimum, 0.5 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that the closest relatives of strain NAA16(T) were Singularimonas variicoloris MN28(T), Sinobacter flavus CW-KD 4(T) and Solimonas soli DCY12(T), with respective sequence similarities of 96.7, 96.6 and 96.2 %. Phylogenetic trees reconstructed from 16S rRNA gene or rpoB sequences (encoding the β-subunit of the RNA polymerase) revealed that the novel strain NAA16(T) and these three closest relatives formed an independent phylogenetic clade within the Gammaproteobacteria. Strain NAA16(T) contained C₁₆:₀, C₁₈:₁ω7c and summed feature 3 (C₁₆:₁ω7c and/or C₁₆:₁ω6c) as predominant fatty acids and possessed phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an uncharacterized aminophospholipid as dominant polar lipids. The major isoprenoid quinone was Q-8. The DNA G+C content of strain NAA16(T) was 66.2 mol%. The taxonomic relationship of strain NAA16(T), Singularimonas variicoloris DSM 15731(T), Sinobacter flavus DSM 18980(T) and Solimonas soli LMG 24014(T) was clarified by means of a direct experimental comparison. Based on phenotypic, chemotaxonomic and phylogenetic data, the descriptions of the genus Solimonas and its type species Solimonas soli are emended. Members of the genus are Gram-negative, oxidase- and catalase-positive, aerobic or facultatively anaerobic and chemo-organotrophic. Chemotaxonomically, members of the genus Solimonas possess Q-8 as the major respiratory quinone, C₁₆:₀ and C₁₈:₁ω7c as predominant fatty acids and phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an uncharacterized aminophospholipid as dominant polar lipids; the DNA G+C content is 64.9-68.4 mol%. Phylogenetic evidence, supported by chemotaxonomic and phenotypic data, allowed us to assign strain NAA16(T) to the genus Solimonas within the novel species Solimonas aquatica sp. nov. (type strain NAA16(T)  = BCRC 17835(T)  = LMG 24500(T)). The reclassification of Sinobacter flavus as Solimonas flava comb. nov. (type strain CW-KD 4(T)  = DSM 18980(T)  = KCTC 12881(T)  = CCTCC AB 206145(T)) and Singularimonas variicoloris as Solimonas variicoloris comb. nov. (type strain MN28(T)  = DSM 15731(T)  = LMG 22844(T)) is also proposed.

Characterisation of hexane-degrading microorganisms in a biofilter by stable isotope-based fatty acid analysis, FISH and cultivation

The hexane-degrading bacterial community of a biofilter was characterised by a combination of stable isotope-based phospholipid fatty acid analyses, fluorescence in situ hybridisation and cultivation. About 70 bacterial strains were isolated from a full-scale biofilter used for treatment of hexane containing waste gas of an oil mill. The isolation approach led to 16 bacterial groups, which were identified as members of the Alpha-, Beta- and Gammaproteobacteria, Actinobacteria and Firmicutes. Three groups showed good growth on hexane as the sole source of carbon. These groups were allocated to the genera Gordonia and Sphingomonas and to the Nevskia-branch of the Gammaproteobacteria. Actively degrading populations in the filter material were characterised by incubation of filter material samples with deuterated hexane and subsequent phospholipid fatty acid analysis. Significant labelling of the fatty acids 16:1 cis10, 18:1 cis9 and 18:0 10methyl affiliated the hexane-degrading activity of the biofilter with the isolates of the genus Gordonia. In vitro growth on hexane and in situ labelling of characteristic fatty acids confirmed the central role of these organisms in the hexane degradation within the full-scale biofilter.