Labrys methylaminiphilus sp. nov., a novel facultatively methylotrophic bacterium from a freshwater lake sediment

Description of Labrys sedimenti sp. nov., isolated from a diclofenac-degrading enrichment culture, and genome-based reclassification of Labrys portucalensis as a later heterotypic synonym of Labrys neptuniae

A Gram-stain-negative strain, designated as Zidic-5T, was isolated from diclofenac-degrading enrichment culture and characterized using a polyphasic approach to determine its taxonomic position. The 16S rRNA gene sequence analysis revealed that strain Zidic-5T belongs to the genus Labrys, with the highest 16S rRNA gene similarity to Labrys neptuniae LMG 23578T (99.13%), followed by Labrys portucalensis F11T (99.06%), Labrys methylaminiphilus JLW10T (98.58%) and Labrys okinawensis DSM 18385T (98.32%). The draft genome sequence of strain Zidic-5T is 7.64 Mb long, and the G+C content of the genome is 63.5 mol%. The orthologous average nucleotide identity and digital DNA-DNA hybridization relatedness values between strain Zidic-5T and its closest relatives were below the threshold values for species demarcation, confirming that strain Zidic-5T is distinctly separated from its closest relatives. Additionally, comparative whole-genome analysis of type strains of L. neptuniae and L. portucalensis indicated that they belong to the same genomic species, suggesting that L. portucalensis is a later heterotypic synonym of L. neptuniae. Cells of strain Zidic-5T were strictly aerobic, coccoid-shaped and non-motile. The predominant fatty acids (>10% of the total) of strain Zidic-5T were C18 : 1 ω7c, C16 : 0 and C19 : 0 cyclo ω7c. The major ubiquinone of strain Zidic-5T was Q-10, while the major polar lipids were phosphatidylcholine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and aminophospholipid. Based on the polyphasic study, it is concluded that strain Zidic-5T represents a novel species of the genus Labrys; thus, the name of Labrys sedimenti sp. nov. is proposed. The type strain of the species is strain Zidic-5T (=LMG 33565T=NCAIM B.02686T).

Removal of Ibuprofen in Water by Bioaugmentation with Labrys neptuniae CSW11 Isolated from Sewage Sludge-Assessment of Biodegradation Pathway Based on Metabolite Formation and Genomic Analysis

Ibuprofen (IBP) is one of the most consumed drugs in the world. It is only partially removed in wastewater treatment plants (WWTPs), being present in effluent wastewater and sewage sludge, causing the widespread introduction of IBP as an emergent xenobiotic in different environmental compartments. This study describes the use of Labrys neptuniae CSW11, recently described as an IBP degrader, through bioaugmentation processes for the removal of IBP from water under different conditions (additional carbon sources, various concentrations of glucose and IBP). L. neptuniae CSW11 showed very good results in a wide range of IBP concentrations, with 100% removal in only 4 days for 1 and 5 mg L-1 IBP and 7 days for 10 mg L-1, and up to 48.4% removal in 28 days for IBP 100 mg L-1 when using glucose 3 g L-1 as an additional carbon source. Three IBP metabolites were identified during the biotransformation process: 1-hydroxyibuprofen (1-OH-IBP), 2-hydroxyibuprofen (2-OH-IBP), and carboxyibuprofen (CBX-IBP), whose concentrations declined drastically in the presence of glucose. IBP metabolites maintained a certain degree of toxicity in solution, even when IBP was completely removed. The results indicate that L. neptuniae CSW11 can be quite effective in degrading IBP in water, but the bioaugmentation method should be improved using CSW11 in consortia with other bacterial strains able to degrade the toxic metabolites produced. A genome-based analysis of L. neptuniae CSW11 revealed different enzymes that could be involved in IBP biodegradation, and a potential metabolic pathway was proposed based on the metabolites observed and genome analysis.

Microscale dynamics of dark zone alterations in anthropized karstic cave shows abrupt microbial community switch

Strong anthropization of karstic caves may result in formation of various wall alterations including dark zones, whose microbial community differs from that of non-altered surfaces nearby. Dark zones grow quickly and without gradual visual changes, leading to the hypothesis of a simple process rather than complex microbial successions, but this is counter-intuitive as underground microbial changes are typically slow and dark zones are microbiologically very distinct from unmarked surfaces. We tested this hypothesis in Paleolithic Lascaux Cave, across two years of microscale sampling. Indeed, Illumina MiSeq metabarcoding evidenced only three community stages for bacteria, fungi and all microeukaryotes together (i.e. unmarked surfaces, newly-formed dark zones and intermediate/old dark zones) and just two stages for archaea (unmarked surfaces vs dark zones), indicating abrupt community changes. The onset of dark zone formation coincided with the development of Ochroconis fungi, Bacteroidota and the bacterial genera Labrys, Nonomuraea and Sphingomonas, in parallel to Pseudomonas counter-selection. Modeling of community assembly processes highlighted that the dynamics of rare taxa in unmarked surfaces adjacent to dark zones and in newly-formed dark zones were governed in part by deterministic processes. This suggests that cooperative relationships between these taxa might be important to promote dark zone formation. Taken together, these findings indicate an abrupt community switch as these new alterations form on Lascaux cave walls.

The core microbiome is responsible for volatile silicon and organic compounds degradation during anoxic lab scale biotrickling filter performance

Volatile silicon compounds present in the biogas of anaerobic digesters can cause severe problems in the energy recovery systems, inducing costly damages. Herein, the microbial community of a lab-scale biotrickling filter (BTF) was studied while testing its biodegradation capacity on octamethylcyclotetrasiloxane (D4) and decamethylcyclopentasiloxane (D5), in the presence of toluene, limonene and hexane. The reactor performance was tested at different empty bed residence times (EBRT) and packing materials. Community structure was analysed by bar-coded amplicon sequencing of the 16S rRNA gene. Microbial diversity and richness were higher in the inoculum and progressively decreased during BTF operation (Simpson's diversity index changing from 0.98-0.90 and Richness from 900 to 200 OTUs). Minimum diversity was found when reactor was operated at relatively low EBRT (7.3 min) using a multicomponent feed. The core community was composed of 36 OTUs (accounting for 55% of total sequences). Packing material played a key role in the community structure. Betaproteobacteriales were dominant in the presence of lava rock and were partially substituted by Corynebacteriales and Rhizobiales when activated carbon was added to the BTF. Despite these changes, a stable and resilient core microbiome was selected defining a set of potentially degrading bacteria for siloxane bioremoval as a complementary alternative to non-regenerative adsorption onto activated carbon.

Definition of Core Bacterial Taxa in Different Root Compartments of Dactylis glomerata, Grown in Soil under Different Levels of Land Use Intensity

Plant-associated bacterial assemblages are critical for plant fitness. Thus, identifying a consistent plant-associated core microbiome is important for predicting community responses to environmental changes. Our target was to identify the core bacterial microbiome of orchard grass Dactylis glomerata L. and to assess the part that is most sensitive to land management. Dactylis glomerata L. samples were collected from grassland sites with contrasting land use intensities but comparable soil properties at three different timepoints. To assess the plant-associated bacterial community structure in the compartments rhizosphere, bulk soil and endosphere, a molecular barcoding approach based on high throughput 16S rRNA amplicon sequencing was used. A distinct composition of plant-associated core bacterial communities independent of land use intensity was identified. Pseudomonas, Rhizobium and Bradyrhizobium were ubiquitously found in the root bacterial core microbiome. In the rhizosphere, the majority of assigned genera were Rhodoplanes, Methylibium, Kaistobacter and Bradyrhizobium. Due to the frequent occurrence of plant-promoting abilities in the genera found in the plant-associated core bacterial communities, our study helps to identify “healthy” plant-associated bacterial core communities. The variable part of the plant-associated microbiome, represented by the fluctuation of taxa at the different sampling timepoints, was increased under low land use intensity. This higher compositional variation in samples from plots with low land use intensity indicates a more selective recruitment of bacteria with traits required at different timepoints of plant development compared to samples from plots with high land use intensity.

Acidotolerant Bacteria and Fungi as a Sink of Methanol-Derived Carbon in a Deciduous Forest Soil

Methanol is an abundant atmospheric volatile organic compound that is released from both living and decaying plant material. In forest and other aerated soils, methanol can be consumed by methanol-utilizing microorganisms that constitute a known terrestrial sink. However, the environmental factors that drive the biodiversity of such methanol-utilizers have been hardly resolved. Soil-derived isolates of methanol-utilizers can also often assimilate multicarbon compounds as alternative substrates. Here, we conducted a comparative DNA stable isotope probing experiment under methylotrophic (only [¹³C₁]-methanol was supplemented) and combined substrate conditions ([¹²C₁]-methanol and alternative multi-carbon [¹³C_u]-substrates were simultaneously supplemented) to (i) identify methanol-utilizing microorganisms of a deciduous forest soil (European beech dominated temperate forest in Germany), (ii) assess their substrate range in the soil environment, and (iii) evaluate their trophic links to other soil microorganisms. The applied multi-carbon substrates represented typical intermediates of organic matter degradation, such as acetate, plant-derived sugars (xylose and glucose), and a lignin-derived aromatic compound (vanillic acid). An experimentally induced pH shift was associated with substantial changes of the diversity of active methanol-utilizers suggesting that soil pH was a niche-defining factor of these microorganisms. The main bacterial methanol-utilizers were members of the Beijerinckiaceae (Bacteria) that played a central role in a detected methanol-based food web. A clear preference for methanol or multi-carbon substrates as carbon source of different Beijerinckiaceae-affiliated phylotypes was observed suggesting a restricted substrate range of the methylotrophic representatives. Apart from Bacteria, we also identified the yeasts Cryptococcus and Trichosporon as methanol-derived carbon-utilizing fungi suggesting that further research is needed to exclude or prove methylotrophy of these fungi.

Labrys soli sp. nov., isolated from the rhizosphere of ginseng

In this study, we describe strain DCY64T that was isolated from the rhizosphere of three-year-old Korean ginseng root. Cells were Gram-reaction negative, oxidase- and catalase-positive, strictly aerobic, capsulated, non-motile, non-sporulating and spherical to short rod-shaped. Multiplicative budding cells were produced. Vesicles covered the surface of cells. Phylogenetic analysis placed strain DCY64T within the genus Labrys with the highest similarity to Labrys monachus VKM B-1479T (97.6 % 16S rRNA gene sequence similarity), followed by Labrys okinawensis MAFF 210191T (97.5 %), Labrys miyagiensis G24103T (97.4) and Labrys portucalensis F11T (97.0 %). The genomic DNA G+C content was 63 mol%. The presences of summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C19 : 1 cyclo ω8c and C16 : 0 as major fatty acids; phosphatidylmonomethylethanolamine, phosphatidylglycerol, phosphatidylcholine and diphosphatidylglycerol as major polar lipids; ubiquinone Q-10 as the predominant quinone and sym-homospermidine as the dominant polyamine were found in strain DCY64T. These chemotaxonomic results were in accordance with those of members of the genus Labrys. However, the absence of C16 : 0 2-OH, C16 : 0 3-OH and C18 : 1 2-OH from the fatty acids profile and differences in minor polar lipids and phenotypic characteristics distinguished strain DCY64T from the closest type strains. The discrimination was also supported by unique enterobacterial repetitive intergenic consensus sequence PCR (ERIC-PCR) fingerprints, as well as DNA-DNA hybridization values ( ≤ 48 %) between strain DCY64T and related type strains. Therefore, we propose that strain DCY64T represents a novel species of the genus Labrys. The name Labrys soli sp. nov. is proposed, with DCY64T ( = KCTC 32173T = JCM 19895T) as the type strain.

Multiphyletic origins of methylotrophy in Alphaproteobacteria, exemplified by comparative genomics of Lake Washington isolates

We sequenced the genomes of 19 methylotrophic isolates from Lake Washington, which belong to nine genera within eight families of the Alphaproteobacteria, two of the families being the newly proposed families. Comparative genomic analysis with a focus on methylotrophy metabolism classifies these strains into heterotrophic and obligately or facultatively autotrophic methylotrophs. The most persistent metabolic modules enabling methylotrophy within this group are the N-methylglutamate pathway, the two types of methanol dehydrogenase (MxaFI and XoxF), the tetrahydromethanopterin pathway for formaldehyde oxidation, the serine cycle and the ethylmalonyl-CoA pathway. At the same time, a great potential for metabolic flexibility within this group is uncovered, with different combinations of these modules present. Phylogenetic analysis of key methylotrophy functions reveals that the serine cycle must have evolved independently in at least four lineages of Alphaproteobacteria and that all methylotrophy modules seem to be prone to lateral transfers as well as deletions.

Differentiation between sediment and hypolimnion methanogen communities in humic lakes

The traditional view of carbon cycling within the pelagic zone of freshwater lakes has consisted of methane production within the anoxic sediment, followed by diffusive flux and ebullition through the water column. Methanogenic archaea have been shown to be present within the water columns of freshwater lakes; however, little is known about whether these methanogenic communities are distinct from those in the sediment or how these communities change over space and time. We used the methanogen-specific phylogenetic marker mcrA to perform a 3-year study focusing on the community structure of methanogens within the sediment and anoxic hypolimnion water layer of five humic lakes in WI, USA. The hypolimnion and sediment communities were distinct in composition, richness and phylogenetic diversity. Hypolimnion communities displayed a temporally stable biogeographical pattern among lakes, which was driven by both lake-specific environmental variables and barriers to dispersal. We conclude that the hypolimnion comprised communities of methanogens that are distinct from those in the sediment, differentiated among lakes, and likely have unique ecological roles and evolutionary trajectories in these anaerobic environments.

Frondihabitans cladoniiphilus sp. nov., an actinobacterium of the family Microbacteriaceae isolated from lichen, and emended description of the genus Frondihabitans

A novel actinobacterium, designated strain CafT13(T), was isolated from the thallus of the reindeer lichen Cladonia arbuscula sampled in the Austrian Alps (Koralpe). The organism was aerobic, with rod- to irregular-shaped cells (often forming dense clusters of cells when grown in liquid medium), Gram-stain-positive, oxidase-negative, catalase-positive and non-motile. It was able to grow at 1 °C and at low to neutral pH, but not above 30 °C or at high pH. The peptidoglycan type was B2β with ornithine as the diagnostic diamino acid. The menaquinones were MK-7 and MK-8. The polar lipid profile comprised diphosphatidylglycerol, phosphatidylglycerol, three unidentified phospholipids, three unidentified glycolipids and one unidentified aminolipid. The predominant fatty acids were C(18:1), C(14:0) 2-OH, C(17:1)ω9c, C(16:0) and anteiso-C(15:0). The mean DNA G+C content of strain CafT13(T) was 69.0±0.17 mol%. 16S rRNA gene sequence analysis showed that strain CafT13(T) belongs to the family Microbacteriaceae, within the genus Frondihabitans. The mean level of DNA-DNA relatedness between strain CafT13(T) and the type strain of Frondihabitans australicus was 35.2±5.23%. The enzyme spectrum of strain CafT13(T) differentiated it from recognized species of the genus Frondihabitans. Based on molecular, chemotaxonomic and physiological data, strain CafT13(T) is considered to represent a novel species of the genus Frondihabitans, for which the name Frondihabitans cladoniiphilus sp. nov. is proposed; the type strain is CafT13(T) (=DSM 23273(T)=LMG 25550(T)).

Synergistic metabolism of a broad range of C1 compounds in the marine methylotrophic bacterium HTCC2181

The 1.3 Mbp genome of HTCC2181, a member of the abundant OM43 clade of coastal bacterioplankton, suggested it is an obligate methylotroph. Preliminary experiments demonstrated that methanol and formaldehyde, but not other common C1 compounds such as methylamine, could support growth. Methanol concentrations in seawater are reportedly < 100 nM, suggesting either that the flux of methanol through plankton pools is very rapid, or that methanol may not be the primary growth substrate for HTCC2181. Therefore, we investigated the apparent extreme substrate range restriction of HTCC2181 in greater detail. Growth rate and maximum cell density of HTCC2181 increased with methanol concentration, yielding a K(s) value of 19 µM. In contrast, no growth was observed in the presence of the methylated (C1) compounds, methyl chloride, trimethylamine-oxide (TMAO) or dimethylsulfoniopropionate (DMSP) when they were the sole substrates. However, growth rate, maximum cell density and cellular ATP content were significantly enhanced when any of these methylated compounds were provided in the presence of a limiting concentration of methanol. These observations fit a model in which the metabolic intermediate formaldehyde is required for net carbon assimilation, allowing C1 substrates that do not produce a formaldehyde intermediate to be oxidized for energy, but not assimilated into biomass. Rates of methanol and TMAO oxidation and assimilation were measured with (14)C-radiolabelled compounds in cultures of HTCC2181 and seawater microbial communities collected off the Oregon coast. The results indicated that in nature as well as in culture, C1 substrates are partitioned between those that are mainly oxidized to produce energy and those that are assimilated. These findings indicate that the combined fluxes of C1 compounds in coastal systems are sufficient to support significant populations of obligate methyltrophs by a metabolic strategy that involves the synergistic metabolism of multiple C1 compounds.

Methylotrophy in a lake: from metagenomics to single-organism physiology

This review provides a brief summary of ongoing studies in Lake Washington (Seattle, WA) directed at an understanding of the content and activities of microbial communities involved in methylotrophy. One of the findings from culture-independent approaches, including functional metagenomics, is the prominent presence of Methylotenera species in the site and their inferred activity in C(1) metabolism, highlighting the local environmental importance of this group. Comparative analyses of individual genomes of Methylophilaceae from Lake Washington provide insights into their genomic divergence and suggest significant metabolic flexibility.

Novel methylotrophic isolates from lake sediment, description of Methylotenera versatilis sp. nov. and emended description of the genus Methylotenera

Phylogenetic positions, and genotypic and phenotypic characteristics of three novel methylotrophic isolates, strains 301(T), 30S and SIP3-4, from sediment of Lake Washington, Seattle, USA, are described. The strains were restricted facultative methylotrophs capable of growth on single carbon compounds (methylamine and methanol) in addition to a limited range of multicarbon compounds. All strains used the N-methylglutamate pathway for methylamine oxidation. Strain SIP3-4 possessed the canonical (MxaFI) methanol dehydrogenase, but strains 301(T) and 30S did not. All three strains used the ribulose monophosphate pathway for C1 assimilation. The major fatty acids in the three strains were C(16:0) and C(16:1)ω7c. The DNA G+C contents of strains 301(T) and SIP3-4 were 42.6 and 54.6 mol%, respectively. Based on 16S rRNA gene sequence phylogeny and the relevant phenotypic characteristics, strain SIP3-4 was assigned to the previously defined species Methylovorus glucosotrophus. Strains 301(T) and 30S were closely related to each other (100% 16S rRNA gene sequence similarity) and shared 96.6% 16S rRNA gene sequence similarity with a previously described isolate, Methylotenera mobilis JLW8(T). Based on significant genomic and phenotypic divergence with the latter, strains 301(T) and 30S represent a novel species within the genus Methylotenera, for which the name Methylotenera versatilis sp. nov. is proposed; the type strain is 301(T) (=VKM B-2679(T)=JCM 17579(T)). An emended description of the genus Methylotenera is provided.

Labrys wisconsinensis sp. nov., a budding bacterium isolated from Lake Michigan water, and emended description of the genus Labrys

Two facultatively anaerobic, budding bacterial strains, designated W1215-PCA4(T) and SRNK-1, were isolated from water from Lake Michigan, USA. The two strains showed identical ERIC-PCR-generated genomic fingerprints and shared 99.9 % 16S rRNA gene sequence similarity. Strain W1215-PCA4(T) showed highest 16S rRNA gene sequence similarities to Labrys monachus VKM B-1479(T) (95.8 %), Labrys methylaminiphilus DSM 16812(T) (95.1 %), Labrys okinawensis MAFF 210191(T) (96.0 %), Labrys miyagiensis G24103(T) (95.4 %), Labrys neptuniae BCRC 17578(T) (95.7 %) and Labrys portucalensis DSM 17916(T) (95.8 %). Data suggested that the two strains were members of a single novel species of the genus Labrys. The major cellular fatty acids of the two isolates were C(18 : 1)omega7c, C(19 : 0) cyclo omega8c and C(16 : 0). Their polar lipid profiles were highly similar to that of Labrys monachus DSM 5896(T). The primary quinone was ubiquinone Q-10, with minor amounts of Q-9 and Q-11. sym-Homospermidine was the predominant polyamine, with putrescine present in moderate amounts. The two strains were identical in terms of their biochemical and physiological traits, but were distinguishable from other species of the genus Labrys. Hence, the description of a novel species in this genus appears to be justified. The name Labrys wisconsinensis sp. nov. is proposed; the type strain is W1215-PCA4(T) (=DSM 19619(T)=NRRL B-51088(T)).

Classification of halo(alkali)philic and halo(alkali)tolerant methanotrophs provisionally assigned to the genera Methylomicrobium and Methylobacter and emended description of the genus Methylomicrobium

The taxonomic positions of four aerobic, obligately halo(alkali)philic/-tolerant, methanotrophic bacteria previously affiliated with the genera Methylobacter ('Methylobacter alcaliphilus' strains 20Z and 5Z) and Methylomicrobium (Methylomicrobium strains AMO1 and NI) were investigated. Phylogenetic analysis of 16S rRNA gene sequences indicated that the strains form a separate branch within the type I methanotrophic bacteria and are closely related to Methylomicrobium pelagicum. DNA-DNA hybridization data revealed relatively low levels of relatedness of Methylomicrobium sp. AMO1 and Methylomicrobium sp. N1 with each other and with previously described species of the genera Methylomicrobium and Methylobacter (<55 %), indicating that they may represent novel species. Based on the results presented here and on previously reported morphological and physiological characteristics, we classify these halotolerant and halophilic methanotrophic strains as representing novel species within the genus Methylomicrobium: Methylomicrobium alcaliphilum sp. nov. (type strain 20Z(T) =VKM B-2133(T) =NCIMB 14124(T); reference strain 5Z =VKM B-2180), Methylomicrobium japanense sp. nov. (type strain NI(T) =VKM B-2462(T) =FERM BP-5633(T) =NBRC 103677(T)) and Methylomicrobium kenyense sp. nov. (type strain AMO1(T) =NCCB 97157(T) =NCIMB 13566(T) =VKM B-2464(T)). The genus Methylomicrobium has been emended in its description.

Real-time detection of actively metabolizing microbes by redox sensing as applied to methylotroph populations in Lake Washington

Redox sensor green (RSG), a novel fluorescent dye from Invitrogen was employed as a tool for real-time detection of microbes metabolically active in situ, in combination with flow cytometry and cell sorting. Lake Washington sediment, an environment known for high rates of methane oxidation, was used as a model, and methylotrophs were targeted as a functional group. We first tested and optimized the performance of the dye with pure methylotroph cultures. Most cells in actively growing cultures were positive for staining, whereas in starved cultures, few cells fluoresced. However, starved cells could be activated by addition of substrate. High numbers of fluorescing cells were observed in a Lake Washington sediment sample, and activation of subpopulations of cells was demonstrated in response to methane, methanol, methylamine and formaldehyde. The fraction of the population activated by methane was investigated in more detail, by phylogenetic profiling. This approach showed that the major responding species were the Methylomonas species, previously isolated from the site, and Methylobacter species that have not yet been cultivated from Lake Washington. In addition, from the methane-stimulated fraction, uncultivated bacterial sequences were obtained that belonged to unclassified Deltaproteobacteria, unclassified Verrucomicrobiles and unclassified Acidobacteria, suggesting that these microbes may also be involved in methane metabolism. The approach was further tested for its utility in facilitating enrichment for functional types that possess specific metabolic activities but resist cultivation. It was demonstrated that in enrichment cultures inoculated with cells that were sorted after stimulation with methane, Methylobacter sequences could be detected, whereas in enrichment cultures inoculated by randomly sorted cells, Methylomonas species quickly outcompeted all other types.

Labrys okinawensis sp. nov. and Labrys miyagiensis sp. nov., budding bacteria isolated from rhizosphere habitats in Japan, and emended descriptions of the genus Labrys and Labrys monachus

Three strains, MAFF 210191T, G24103T and G24116, assumed to be members of two novel species, were isolated from several rhizosphere habitats in different parts of Japan. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolates formed a distinct monophyletic group together with the two known species of the genus Labrys, suggesting that the isolates have a close affiliation with this genus. In this study, a polyphasic approach was used to characterize and compare the three isolates with the two species of the genus Labrys, Labrys monachus and Labrys methylaminiphilus. All three isolates were aerobic, Gram-negative, motile and non-sporulating and they ranged in shape from spherical to short rods. The cells multiplied by budding and utilized a wide variety of monosaccharides, disaccharides and sugar alcohols as sole carbon and energy sources, but they did not utilize C1 compounds, salicin or d-melezitose. The strains were inhibited by dl-α-alanine and glycine (both at 10 mM). The major cellular fatty acids were C19 : 0 cyclo ω8c, C16 : 0, C18 : 0 and C18 : 1 ω7c. The three isolates shared <12 % and <11 % DNA–DNA relatedness with L. monachus DSM 5896T and L. methylaminiphilus DSM 16812T, respectively. The G+C content of the isolates (61–62 mol%) was also significantly lower than those of the two previously characterized species. In spite of many morphological, physiological and chemotaxonomic similarities among the three isolates, strain MAFF 210191T could be differentiated from strains G24103T and G24116 on the basis of 16S rRNA gene sequence divergence, DNA–DNA relatedness (<46 %) and gelatin hydrolysis. Two novel species are therefore proposed, namely Labrys okinawensis sp. nov., with the type strain MAFF 210191T (=DSM 18385T), and Labrys miyagiensis sp. nov., with the type strain G24103T (=NBRC 101365T=NCIMB 14143T) and also including strain G24116 (=NBRC 101366=NCIMB 14144). Emended descriptions of the genus Labrys and Labrys monachus are also presented.

Labrys neptuniae sp. nov., isolated from root nodules of the aquatic legume Neptunia oleracea

A bacterium designated strain Liujia-146T was isolated in the Tainan area of southern Taiwan from root nodules of the aquatic legume Neptunia oleracea. 16S rRNA gene sequence analysis indicated that strain Liujia-146T was highly similar to Labrys monachus VKM B-1479T (97.8 %) and Labrys methylaminiphilus JLW10T (95.5 %) and belonged to the order Rhizobiales in the Alphaproteobacteria. On the basis of phylogenetic analysis, DNA–DNA hybridization data, physiological and biochemical characteristics and fatty acid compositions, the organism was shown to belong to the genus Labrys whilst representing a novel species within this genus. We propose to classify strain Liujia-146T (=BCRC 17578T=LMG 23578T) as the type strain of Labrys neptuniae sp. nov.

Methylotenera mobilis gen. nov., sp. nov., an obligately methylamine-utilizing bacterium within the family Methylophilaceae

A novel obligate methylamine utilizer (strain JLW8(T)), isolated from Lake Washington sediment, was characterized taxonomically. The isolate was an aerobic, Gram-negative bacterium. Cells were rod-shaped and motile by means of a single flagellum. Reproduction was by binary fission and no resting bodies were formed. Growth was observed within a pH range of 5-8.5, with optimum growth at pH 7.5. It utilized methylamine as a single source of energy, carbon and nitrogen. Methylamine was oxidized via methylamine dehydrogenase and formaldehyde was assimilated via the ribulose monophosphate cycle. The cellular fatty acid profile was dominated by C(16 : 0)omega7c and C(16 : 0) and the major phospholipid was phosphatidylethanolamine. The DNA G+C content was 54 mol%. 16S rRNA gene sequence analysis indicated that the new isolate was closely related (97-98 % similarity) to a broad group of sequences from uncultured or uncharacterized Betaproteobacteria, but only distantly related (93-96 % similarity) to known methylotrophs of the family Methylophilaceae. Strain JLW8(T) (=ATCC BAA-1282(T)=DSM 17540(T)) is proposed as the type strain of a novel species in a new genus within the family Methylophilaceae, Methylotenera mobilis gen. nov., sp. nov.

Methyloversatilis universalis gen. nov., sp. nov., a novel taxon within the Betaproteobacteria represented by three methylotrophic isolates

The taxonomic positions and phylogenetic relationships of two new methylotrophic isolates from Lake Washington (USA) sediment, FAM5Tand 500, and the previously described methylotrophic strain EHg5 isolated from contaminated soil in Estarreja (Portugal) were investigated. All three strains were facultative methylotrophs capable of growth on a variety of C1and multicarbon compounds. Optimal growth occurred at pH 7.5–8 and 30–37 °C. The major fatty acids were C16 : 1ω7cand C16 : 0. The major quinone was ubiquinone Q8. Neither methanol dehydrogenase nor methanol oxidase activities were detectable in cells grown on methanol, suggesting an alternative, as-yet unknown, mechanism for methanol oxidation. The isolates assimilated C1units at the level of formaldehyde, via the serine cycle. The DNA G+C content of the strains ranged between 64 and 65 mol%. 16S rRNA gene sequence similarity between the three new isolates was 99.85–100 %, but was below 94 % with other members of theBetaproteobacteria, indicating that the isolates represent a novel taxon. Based on physiological, phenotypic and genomic characteristics of the three isolates, a new genus,Methyloversatilisgen. nov., is proposed within the familyRhodocyclaceae. The type strain ofMethyloversatilis universalisgen. nov., sp. nov. is FAM5T(=CCUG 52030T=JCM 13912T).

Pseudolabrys taiwanensis gen. nov., sp. nov., an alphaproteobacterium isolated from soil

A Gram-negative, short rod-shaped micro-organism (CC-BB4T) was isolated on nutrient agar from soil from Sinshe in Taichung County, Taiwan. Analysis of the 16S rRNA gene sequence demonstrated that this isolate was novel, as it showed <92 % similarity to the sequences of species of the genera Labrys, Beijerinckia and Methylocystis. The micro-organism did not utilize methylamine or methanol as a substrate, but was able to use several organic acids. The fatty acid profile was different from those reported for the genera Labrys, Beijerinckia, Methylocystis, Angulomicrobium, Methylorhabdus and Methyloarcula. On the basis of the 16S rRNA gene sequence analysis, in combination with chemotaxonomic and physiological data, strain CC-BB4T represents a novel genus, for which the name Pseudolabrys gen. nov. is proposed. The type species is Pseudolabrys taiwanensis sp. nov., and the type strain of P. taiwanensis is CC-BB4T (=CCUG 51779T=CIP 108932T).