Methylophaga alcalica sp. nov., a novel alkaliphilic and moderately halophilic, obligately methylotrophic bacterium from an East Mongolian saline soda lake

Microbial alchemists: unveiling the hidden potentials of halophilic organisms for soil restoration

Salinity, resulting from various contaminants, is a major concern to global crop cultivation. Soil salinity results in increased osmotic stress, oxidative stress, specific ion toxicity, nutrient deficiency in plants, groundwater contamination, and negative impacts on biogeochemical cycles. Leaching, the prevailing remediation method, is expensive, energy-intensive, demands more fresh water, and also causes nutrient loss which leads to infertile cropland and eutrophication of water bodies. Moreover, in soils co-contaminated with persistent organic pollutants, heavy metals, and textile dyes, leaching techniques may not be effective. It promotes the adoption of microbial remediation as an effective and eco-friendly method. Common microbes such as Pseudomonas, Trichoderma, and Bacillus often struggle to survive in high-saline conditions due to osmotic stress, ion imbalance, and protein denaturation. Halophiles, capable of withstanding high-saline conditions, exhibit a remarkable ability to utilize a broad spectrum of organic pollutants as carbon sources and restore the polluted environment. Furthermore, halophiles can enhance plant growth under stress conditions and produce vital bio-enzymes. Halophilic microorganisms can contribute to increasing soil microbial diversity, pollutant degradation, stabilizing soil structure, participating in nutrient dynamics, bio-geochemical cycles, enhancing soil fertility, and crop growth. This review provides an in-depth analysis of pollutant degradation, salt-tolerating mechanisms, and plant-soil-microbe interaction and offers a holistic perspective on their potential for soil restoration.

Identification of groundwater microbes that decrease the concentration of the conservative tracer uranine

Fluorescent dyes are commonly used as conservative groundwater tracers to track the migration of water. Over- or underestimation of important parameters such as the water flow rate can occur if the concentration of a dye is changed by unexpected reactions. Because such errors may seriously affect the results of experiments, the reactions and processes that change fluorescent dye concentrations need to be understood. In this study, we focused on the widely used fluorescent dye uranine (UR) and aimed to identify microbes contributing to decreases in UR concentrations in groundwater. First, we identified the conditions (water temperature, pH, and salinity) under which significant decreases in UR concentrations occurred to show that the decrease in UR concentrations were caused by the effects of microbes in the groundwater. Next, we obtained information about the metabolism of organic matter by potential contributing microbes. These results were used to narrow down possible microbes that could decrease the UR concentration. Analysis of the microbial community in groundwater using 16S rRNA gene sequencing was then used to further identify contributing microbes. Finally, a verification experiment was conducted using a strain of one of the identified microbes (Parapontixanthobacter aurantiacus). Our results showed that conservation of the concentration of fluorescent dye solutions prepared with on-site groundwater was affected by several microbes with different metabolic characteristics, including P. aurantiacus. When fluorescent dye solutions prepared with on-site groundwater are used in field investigations or tracer tests, the pros and cons of using fluorescent dyes should be carefully evaluated because of the potential effects of microbes in the groundwater.

Methylophaga pinxianii sp. nov., isolated from the Mariana Trench

Two strains, TMB456T and TMB1265, were isolated from different locations in the Mariana Trench. Analysis of the 16S rRNA gene and genomic rRNA sequences indicated that they were from the same novel species and were affiliated with the genus Methylophaga of the class Gammaproteobacteria . Phylogenetic analysis based on 16S rRNA gene sequences indicated that the most closely related validly published species were Methylophaga muralis Kr3T (98.1 % similarity) and Methylophaga nitratireducenticrescens JAM1T (97.3 % similarity). Digital DNA–DNA hybridization values of TMB456T with M. muralis Kr3T and M. nitratireducenticrescens JAM1T were <25 %. The average nucleotide identity value between strain TMB456T and M. muralis Kr3T was 80.9 %. The genomic DNA G+C contents of strains TMB456T and TMB1265 were both 44.9 mol %. Strains TMB456T and TMB1265 could grow at 4–37 °C (optimum at 20–28 °C), at pH 3–10 (optimum at pH 7–9) and in the presence of 0–10 % (w/v) NaCl (optimum at 0–1 %). Cells of strains TMB456T and TMB1265 were Gram-negative rods (0.3–0.6 µm×0.7–1.3 µm). Chemotaxonomic analysis showed that ubiquinone 8 was the sole quinone produced by strain TMB456T and that the major cellular fatty acids were iso-C16 : 0, summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c) and summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c). The polar lipid profile of this strain included phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphoglycolipids and two unidentified polar lipids. Based on the phenotypic, chemotaxonomic and molecular features, strains TMB456T and TMB1265 belong to a novel species within the genus Methylophaga , for which the name Methylophaga pinxianii sp. nov. is proposed. The type strain is TMB456T (=KCTC 82622T= MCCC 1K05898T).

Elucidating the key environmental parameters during the production of ectoines from biogas by mixed methanotrophic consortia

Anaerobic digestion (AD) is a robust biotechnology for the valorisation of organic waste into biogas. However, the rapid decrease in renewable electricity prices requires alternative uses of biogas. In this context, the engineering of innovative platforms for the bio-production of chemicals from CH₄ has recently emerged. The extremolyte and osmoprotectant ectoine, with a market price of ~1000€/Kg, is the industrial flagship of CH₄-based bio-chemicals. This work aimed at optimizing the accumulation of ectoines using mixed microbial consortia enriched from saline environments (a salt lagoon and a salt river) and activated sludge, and biogas as feedstock. The influence of NaCl (0, 3, 6, 9 and 12 %) and Na₂WO₄ (0, 35 and 70 μg L^-1) concentrations and incubation temperature (15, 25 and 35 °C) on the stoichiometry and kinetics of the methanotrophic consortia was investigated. Consortia enriched from activated sludge at 15 °C accumulated the highest yields of ectoine and hydroxyectoine at 6 % NaCl (105.0 ± 27.2 and 24.2 ± 5.4 mg_extremolyte g_biomass^-1, respectively). The consortia enriched from the salt lagoon accumulated the highest yield of ectoine and hydroxyectoine at 9 % NaCl (56.6 ± 2.5 and 51.0 ± 2.0 mg_extremolyte g_biomass^-1, respectively) at 25 °C. The supplementation of tungsten to the cultivation medium did not impact on the accumulation of ectoines in any of the consortia. A molecular characterization of the enrichments revealed a relative abundance of ectoine-accumulating methanotrophs of 7-16 %, with Methylomicrobium buryatense and Methylomicrobium japanense as the main players in the bioconversion of methane into ectoine.

Shift of bacterial community and denitrification functional genes in biofilm electrode reactor in response to high salinity

High salinity suppresses denitrification by inhibiting microorganism activities. The shift of microbial community and denitrification functional genes under salinity gradient was systematically investigated in a biofilm electrode reactor (BER) and biofilm reactor (BR) systems. Denitrification efficiency of both BER and BR was not significantly inhibited during the period of low salinity (0-2.0%). As the salinity increased to 2.5%, BER could overcome the impact of high salinity and maintained a relatively stable denitrification performance, and the effluent NO₃^--N was lower than 1.5 mg/L. High salinity (>2.5%) impoverished microbial diversity and altered the microbial community in both BER and BR. However, two genera Methylophaga and Methyloexplanations were enriched in BER due to electrochemical stimulation, which can tolerate high salinity (>3.0%). The relative abundance of Methylophaga in BER was almost 10 times as much as in BR. Paracoccus is a hydrogen autotrophic denitrifier, which was obviously inhibited with 1.0% NaCl. The hetertrophic denitrifiers were primarily responsible for the nitrate removal in the BER compared to the autotrophic denitrifiers. The abundance and proportion of denitrifying functional genes confirmed that main denitrifiers shift to salt-tolerant species (nirK-type denitrifiers) to reduce the toxic effects. The napA (2.2 × 10⁸ to 6.5 × 10⁸ copies/g biofilm) and nosZ (2.2 × 10⁷ to 4.4 × 10⁷ copies/g biofilm) genes were more abundant in BER compared to BR's, which was attributed to the enrichment of Methylophaga alcalica and Methyloversatilis universalis FAM5 in the BER. The results proved that BER had greater denitrification potential under high salinity (>2.0%) stress at the molecular level.

Evaluation of the taxonomic and functional variation of freshwater plankton communities induced by trace amounts of the antibiotic ciprofloxacin

Ciprofloxacin (CIP), one of the most frequently detected antibiotics in water systems, has become an aquatic contaminant because of improper disposal and excretion by humans and animals. It is still unknown how trace amounts of CIP affect the aquatic microbial community diversity and function. We therefore investigated the effects of CIP on the structure and function of freshwater microbial communities via 16S/18S rRNA gene sequencing and metatranscriptomic analyses. CIP treatment (7 μg/L) did not significantly alter the physical and chemical condition of the water body as well as the composition of the main species in the community, but slightly increased the relative abundance of cyanobacteria and decreased the relative abundance of eukaryotes. Metatranscriptomic results showed that bacteria enhanced their phosphorus transport and photosynthesis after CIP exposure. The replication, transcription, translation and cell proliferation were all suppressed in eukaryotes, while the bacteria were not affected in any of these aspects. This interesting phenomenon was the exact opposite to both the antibacterial property of CIP and its safety for eukaryotes. We hypothesize that reciprocal and antagonistic interactions in the microcosm both contribute to this result: cyanobacteria may enhance their tolerance to CIP through benefiting from cross-feeding and some secreted substances that withstand bacterial CIP stress would also affect eukaryotic growth. The present study thus indicates that a detailed assessment of the aquatic ecotoxicity of CIP is essential, as the effects of CIP are much more complicated in microbial communities than in monocultures. CIP will continue to be an environmental contaminant due to its wide usage and production and more attention should be given to the negative effects of antibiotics as well as other bioactive pollutants on aquatic environments.

Whole genome shotgun sequence of Bacillus amyloliquefaciens TF28, a biocontrol entophytic bacterium

Bacillus amyloliquefaciens TF28 is a biocontrol endophytic bacterium that is capable of inhibition of a broad range of plant pathogenic fungi. The strain has the potential to be developed into a biocontrol agent for use in agriculture. Here we report the whole-genome shotgun sequence of the strain. The genome size of B. amyloliquefaciens TF28 is 3,987,635 bp which consists of 3754 protein-coding genes, 65 tandem repeat sequences, 47 minisatellite DNA, 2 microsatellite DNA, 63 tRNA, 7rRNA, 6 sRNA, 3 prophage and CRISPR domains.

Halophiles: biology, adaptation, and their role in decontamination of hypersaline environments

The unique cellular enzymatic machinery of halophilic microbes allows them to thrive in extreme saline environments. That these microorganisms can prosper in hypersaline environments has been correlated with the elevated acidic amino acid content in their proteins, which increase the negative protein surface potential. Because these microorganisms effectively use hydrocarbons as their sole carbon and energy sources, they may prove to be valuable bioremediation agents for the treatment of saline effluents and hypersaline waters contaminated with toxic compounds that are resistant to degradation. This review highlights the various strategies adopted by halophiles to compensate for their saline surroundings and includes descriptions of recent studies that have used these microorganisms for bioremediation of environments contaminated by petroleum hydrocarbons. The known halotolerant dehalogenase-producing microbes, their dehalogenation mechanisms, and how their proteins are stabilized is also reviewed. In view of their robustness in saline environments, efforts to document their full potential regarding remediation of contaminated hypersaline ecosystems merits further exploration.

Diversity of bacteria in ships ballast water as revealed by next generation DNA sequencing

The bacterial diversity in ballast water from five general cargo ships calling at the Port of Houston was determined with ion semiconductor DNA sequencing (Ion Torrent PGM) of PCR amplified 16S rRNA genes. Phylogenetic analysis revealed that the composition of bacteria in ballast water did not resemble that of typical marine habitats or even open ocean waters where BWEs occur. The predominant group of bacteria in ships conducting BWEs was the Roseobacter clade within the Alphaproteobacteria. In contrast, Gammaproteobacteria were predominant in the ship that did not conduct a BWE. All the ships contained human, fish, and terrestrial plant pathogens as well as bacteria indicative of fecal or activated sludge contamination. Most of the 60 pathogens had not been detected in ballast water previously. Among these were the human pathogens Corynebacterium diptheriae and several Legionella species and the fish pathogens Francisella piscicida and Piscirickettsia salmonis.

Sucrose metabolism in halotolerant methanotroph Methylomicrobium alcaliphilum 20Z

Sucrose accumulation has been observed in some methylotrophic bacteria utilizing methane, methanol, or methylated amines as a carbon and energy source. In this work, we have investigated the biochemical pathways for sucrose metabolism in the model halotolerant methanotroph Methylomicrobium alcaliphilum 20Z. The genes encoding sucrose-phosphate synthase (Sps), sucrose-phosphate phosphatase (Spp), fructokinase (FruK), and amylosucrase (Ams) were co-transcribed and displayed similar expression levels. Functional Spp and Ams were purified after heterologous expression in Escherichia coli. Recombinant Spp exhibited high affinity for sucrose-6-phosphate and stayed active at very high levels of sucrose (K i  = 1.0 ± 0.6 M). The recombinant amylosucrase obeyed the classical Michaelis-Menten kinetics in the reactions of sucrose hydrolysis and transglycosylation. As a result, the complete metabolic network for sucrose biosynthesis and re-utilization in the non-phototrophic organism was reconstructed for the first time. Comparative genomic studies revealed analogous gene clusters in various Proteobacteria, thus indicating that the ability to produce and metabolize sucrose is widespread among prokaryotes.

How could haloalkaliphilic microorganisms contribute to biotechnology?

Haloalkaliphiles are microorganisms requiring Na+concentrations of at least 0.5 mol·L–1and an alkaline pH of 9 for optimal growth. Their unique features enable them to make significant contributions to a wide array of biotechnological applications. Organic compatible solutes produced by haloalkaliphiles, such as ectoine and glycine betaine, are correlated with osmoadaptation and may serve as stabilizers of intracellular proteins, salt antagonists, osmoprotectants, and dermatological moisturizers. Haloalkaliphiles are an important source of secondary metabolites like rhodopsin, polyhydroxyalkanoates, and exopolysaccharides that play essential roles in biogeocycling organic compounds. These microorganisms also can secrete unique exoenzymes, including proteases, amylases, and cellulases, that are highly active and stable in extreme haloalkaline conditions and can be used for the production of laundry detergent. Furthermore, the unique metabolic pathways of haloalkaliphiles can be applied in the biodegradation and (or) biotransformation of a broad range of toxic industrial pollutants and heavy metals, in wastewater treatment, and in the biofuel industry.

Microbial diversity and biogeochemical cycling in soda lakes

Soda lakes contain high concentrations of sodium carbonates resulting in a stable elevated pH, which provide a unique habitat to a rich diversity of haloalkaliphilic bacteria and archaea. Both cultivation-dependent and -independent methods have aided the identification of key processes and genes in the microbially mediated carbon, nitrogen, and sulfur biogeochemical cycles in soda lakes. In order to survive in this extreme environment, haloalkaliphiles have developed various bioenergetic and structural adaptations to maintain pH homeostasis and intracellular osmotic pressure. The cultivation of a handful of strains has led to the isolation of a number of extremozymes, which allow the cell to perform enzymatic reactions at these extreme conditions. These enzymes potentially contribute to biotechnological applications. In addition, microbial species active in the sulfur cycle can be used for sulfur remediation purposes. Future research should combine both innovative culture methods and state-of-the-art 'meta-omic' techniques to gain a comprehensive understanding of the microbes that flourish in these extreme environments and the processes they mediate. Coupling the biogeochemical C, N, and S cycles and identifying where each process takes place on a spatial and temporal scale could unravel the interspecies relationships and thereby reveal more about the ecosystem dynamics of these enigmatic extreme environments.

Bifunctional sucrose phosphate synthase/phosphatase is involved in the sucrose biosynthesis by Methylobacillus flagellatus KT

The aerobic obligate methylotroph Methylobacillus flagellatus KT was shown to synthesize sucrose in the presence of 0.5-2% NaCl in the growth medium. In the genome of this bacterium, an open reading frame (ORF) encoding a predicted 84-kD polypeptide homologous to the plant and cyanobacterial sucrose phosphate synthases (SPSs) was found. Using heterologous expression of the putative sps gene in Escherichia coli, followed by affinity chromatography, pure recombinant protein SPS-His6 was obtained. The enzyme catalyzed two reactions: conversion of fructose 6-phosphate and UDP-glucose into sucrose 6-phosphate and hydrolysis of sucrose 6-phosphate to sucrose. The bifunctional sucrose phosphate synthase/phosphatase (SPS/SPP) was a 340 kDa homotetrameric Mg(2+) -dependent enzyme activated by fructose 1,6-phosphate2 and ATP but inhibited by glucose 6-phosphate, fructose 1-phosphate, AMP and inorganic phosphate. The amino acid sequence of the protein had a C-terminal domain homologous to SPPs. This correlated with the absence of the spp gene in the M. flagellatus chromosome. The ORFs homologous to the M. flagellatus SPS were found in the genomes of another obligate methylotroph Methylovorus glucosetrophus as well as the lithoautotrophic bacteria Acidithiobacillus ferrooxidans, Nitrosomonas europaea and Nitrosospira multiformis whose genomes lacked the spp genes. Thus, data extending the knowledge of biochemical properties of bacterial SPSs have been obtained.

Microbiology of Lonar Lake and other soda lakes

Soda lakes are saline and alkaline ecosystems that are believed to have existed throughout the geological record of Earth. They are widely distributed across the globe, but are highly abundant in terrestrial biomes such as deserts and steppes and in geologically interesting regions such as the East African Rift valley. The unusual geochemistry of these lakes supports the growth of an impressive array of microorganisms that are of ecological and economic importance. Haloalkaliphilic Bacteria and Archaea belonging to all major trophic groups have been described from many soda lakes, including lakes with exceptionally high levels of heavy metals. Lonar Lake is a soda lake that is centered at an unusual meteorite impact structure in the Deccan basalts in India and its key physicochemical and microbiological characteristics are highlighted in this article. The occurrence of diverse functional groups of microbes, such as methanogens, methanotrophs, phototrophs, denitrifiers, sulfur oxidizers, sulfate reducers and syntrophs in soda lakes, suggests that these habitats harbor complex microbial food webs that (a) interconnect various biological cycles via redox coupling and (b) impact on the production and consumption of greenhouse gases. Soda lake microorganisms harbor several biotechnologically relevant enzymes and biomolecules (for example, cellulases, amylases, ectoine) and there is the need to augment bioprospecting efforts in soda lake environments with new integrated approaches. Importantly, some saline and alkaline lake ecosystems around the world need to be protected from anthropogenic pressures that threaten their long-term existence.

Methyloligella halotolerans gen. nov., sp. nov. and Methyloligella solikamskensis sp. nov., two non-pigmented halotolerant obligately methylotrophic bacteria isolated from the Ural saline environments

Two newly isolated halotolerant obligately methylotrophic bacteria (strains C2(T) and SK12(T)) with the serine pathway of C1 assimilation are described. The isolates are strictly aerobic, Gram negative, asporogenous, non-motile rods, forming rosettes, multiplying by binary fission. Mesophilic and neutrophilic, accumulate intracellularly compatible solute ectoine and poly-β-hydroxybutyrate. The novel strains are able to grow at 0 up to 16% NaCl (w/v), optimally at 3-5% NaCl. The major cellular fatty acids are C18:1ω7c and C19:0cyc and the prevailing quinone is Q-10. The predominant phospholipids are phosphatidylcholine, phosphatidylglycerol, phosphatidyldimethylethanolamine and phosphatidylethanolamine. Assimilate NH4(+) by glutamate dehydrogenase and via the glutamate cycle (glutamine synthetase and glutamate synthase). The DNA G+C contents of strains C2(T) and SK12(T) are 60.9 and 60.5 mol% (Tm), respectively. 16S rRNA gene sequence similarity between the two new isolates are 99% but below 94% with other members of the Alphaproteobacteria thus indicating that they can be assigned to a novel genus Methyloligella. Rather low level of DNA-DNA relatedness (53%) between the strains C2(T) and SK12(T) indicates that they represent two separate species of the new genus, for which the names Methyloligella halotolerans gen. nov., sp. nov. and Methyloligella solikamskensis sp. nov. are proposed. The type strain of Methyloligella halotolerans is C2(T) (=VKM B-2706(T)=CCUG 61687(T)=DSM 25045(T)) and the type strain of Methyloligella solikamskensis is SK12(T) (=VKM B-2707(T)=CCUG 61697(T)=DSM 25212(T)).

Methylophaga nitratireducenticrescens sp. nov. and Methylophaga frappieri sp. nov., isolated from the biofilm of the methanol-fed denitrification system treating the seawater at the Montreal Biodome

Two bacterial strains, designated JAM1(T) and JAM7(T), were isolated from a methanol-fed denitrification system treating seawater at the Montreal Biodome, Canada. They were affiliated within the genus Methylophaga of the Gammaproteobacteria by analysis of the 16S rRNA gene sequences. Strain JAM1(T) had the capacity to grow under denitrifying conditions by reducing nitrate into nitrite which is unique among the species of the genus Methylophaga. Major fatty acids were C16:1ω7c or ω6c, C16:0 and C18:1ω7c or ω6c. The major ubiquinone was Q8. Both strains required vitamin B12 and Na(+) ions for growth. The genomes of strains JAM1(T) and JAM7(T) have been completely sequenced and showed a DNA G+C content of 44.7 mol% and 47.8 mol%, respectively. Growth occurred at pH 6-11 and at 0.5-8% NaCl. Both genomes contained predicted ORFs encoding the key enzymes of the ribulose monophosphate pathway. Also, operons encoding two nitrate reductases (Nar), two nitric oxide reductases (Nor), one nitrous oxide reductase (Nos) and one truncated nitrite reductase (NirK) were clustered in a 67 kb chromosomal region in strain JAM1(T). No such operons were found in strain JAM7(T). These results supported the affiliation of the two strains as novel species within the genus Methylophaga. The names Methylophaga nitratireducenticrescens sp. nov. for type strain JAM1(T) (=DSM 25689(T)=ATCC BAA-2433(T)) and Methylophaga frappieri sp. nov. for type strain JAM7(T) (=DSM 25690(T)=ATCC BAA-2434(T)) are proposed.

Complete genome sequences of Methylophaga sp. strain JAM1 and Methylophaga sp. strain JAM7

Methylophaga sp. strains JAM1 and JAM7 have been isolated from a denitrification system. Strain JAM1 was the first Methylophaga strain reported to be able to grow under denitrifying conditions. Here, we report the complete genome sequences of the two strains, which allowed prediction of gene clusters involved in denitrification in strain JAM1.

Emended description of the genus Methylophaga Janvier et al. 1985

The genus Methylophaga Janvier et al. 1985 comprises eight species with validly published names at the time of writing. The original description of the genus was published over 26 years ago and was based on only two species, namely Methylophaga marina and Methylophaga thalassica – as such, the description of the genus requires updating to take into account the other six known species. Based on literature concerning the eight species of Methylophaga published over the last 26 years, an emended description of the genus is presented, taking into account properties of all members of the species with validly published names.

Methylophaga lonarensis sp. nov., a moderately haloalkaliphilic methylotroph isolated from the soda lake sediments of a meteorite impact crater

A moderately haloalkaliphilic methylotrophic bacterium possessing the ribulose monophosphate pathway for carbon assimilation, designated MPLT, was isolated from Lonar Lake sediment microcosms that were oxidizing methane for two weeks. The isolate utilized methanol and was an aerobic, Gram-negative, asporogenous, motile, short rod that multiplied by binary fission. The isolate required NaHCO3 or NaCl for growth and, although not auxotrophic for vitamin B12, had enhanced growth with vitamin B12. Optimal growth occurred with 0.5–2 % (w/v) NaCl, at 28–30 °C and at pH 9.0–10.0. The cellular fatty acid profile consisted primarily of straight-chain saturated C16 : 0 and unsaturated C16 : 1ω7c and C18 : 1ω7c. The major ubiquinone was Q-8. The dominant phospholipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Cells accumulated ectoine as the main compatible solute. The DNA G+C content was 50.0 mol%. The isolate exhibited 94.0–95.4 % 16S rRNA gene sequence similarity with the type strains of methylotrophs belonging to the genus Methylophaga and 31 % DNA–DNA relatedness with the reference strain, Methylophaga alcalica VKM B-2251T. It is proposed that strain MPLT represents a novel species, Methylophaga lonarensis sp. nov. (type strain MPLT = VKM B-2684T = MCC 1002T).

Methylophilus glucosoxydans sp. nov., a restricted facultative methylotroph from rice rhizosphere

Two restricted facultatively methylotrophic strains, designed BT and P, were isolated from rice roots. The isolates were strictly aerobic, Gram-negative, asporogenous, mesophilic, neutrophilic, motile rods that multiplied by binary fission and were able to synthesize indole-3-acetate. The cellular fatty acid profiles of the two strains were dominated by C16 : 0, C16 : 1ω7c and C16 : 0 2-OH. The major ubiquinone was Q-8. The predominant phospholipids were phosphatidylethanolamine and phosphatidylglycerol. Cardiolipin (diphosphatidylglycerol) was absent. The two strains assimilated methanol carbon at the level of formaldehyde via the ribulose monophosphate cycle (2-keto-3-deoxy-6-phosphogluconate variant). They lacked α-ketoglutarate dehydrogenase and glutamate dehydrogenase. They assimilated ammonium via the glutamate cycle enzymes glutamine synthetase and glutamate synthase. The DNA G+C contents of strains BT and P were 52.5 and 51.5 mol% (T m), respectively. The level of DNA–DNA reassociation between these strains was 78 %, indicating that they belong to one species. Phylogenetic analysis of strain BT based on 16S rRNA and methanol dehydrogenase (mxaF) gene sequences showed a high level of similarity to members of the genus Methylophilus. As the two isolates were clearly distinct from all recognized members of the genus Methylophilus based on phenotypic data and levels of DNA–DNA relatedness (30–46 %), they are considered to represent a novel species, for which the name Methylophilus glucosoxydans sp. nov. is proposed; the type strain is BT ( = VKM B-1607T = CCUG 59685T = DSM 5898T).

Diversity and phylogeny of the ectoine biosynthesis genes in aerobic, moderately halophilic methylotrophic bacteria

The genes of ectoine biosynthesis pathway were identified in six species of aerobic, slightly halophilic bacteria utilizing methane, methanol or methylamine. Two types of ectoine gene cluster organization were revealed in the methylotrophs. The gene cluster ectABC coding for diaminobutyric acid (DABA) acetyltransferase (EctA), DABA aminotransferase (EctB) and ectoine synthase (EctC) was found in methanotrophs Methylobacter marinus 7C and Methylomicrobium kenyense AMO1(T). In methanotroph Methylomicrobium alcaliphilum ML1, methanol-utilizers Methylophaga thalassica 33146(T) , Methylophaga alcalica M8 and methylamine-utilizer Methylarcula marina h1(T), the genes forming the ectABC-ask operon are preceded by ectR, encoding a putative transcriptional regulatory protein EctR. Phylogenetic relationships of the Ect proteins do not correlate with phylogenetic affiliation of the strains, thus implying that the ability of methylotrophs to produce ectoine is most likely the result of a horizontal transfer event.

Draft genome sequence of the chemolithoheterotrophic, halophilic methylotroph Methylophaga thiooxydans DMS010

Methylophaga thiooxydans is a mesophilic, obligately halophilic bacterium that is capable of methylotrophic growth on a range of one-carbon compounds as well as chemolithoheterotrophic growth at the expense of thiosulfate. Here we present the draft genome sequence of Methylophaga thiooxydans DMS010 (DSM 22068(T), VKM B2586(T)), the type strain of the species, which has allowed prediction of the genes involved in one-carbon metabolism, nitrogen metabolism, and other aspects of central metabolism.

Genes and enzymes of ectoine biosynthesis in halotolerant methanotrophs

Ectoine (1,4,5,6-tetrahydro-2-methyl-4-pyrimidine carboxylic acid) is a widely distributed compatible solute accumulated by halophilic and halotolerant microorganisms to prevent osmotic stress in highly saline environments. Ectoine as a highly water keeping compound stabilizing biomolecules and whole cells can be used in scientific work, cosmetics, and medicine. Detailed understanding of the organization/regulation of the ectoine biosynthetic pathway in various producers is an active area of research. Here we review current knowledge on some genetic and enzymatic aspects of ectoine biosynthesis in halophilic and halotolerant methanotrophs. By using PCR methodology, the genes coding for the specific enzymes of ectoine biosynthesis, diaminobutyric acid (DABA) aminotransferase (EctB), DABA acetyltransferase (EctA), and ectoine synthase (EctC), were identified in several methanotrophic species. Organization of these genes in either ectABC or ectABC-ask operons, the latter additionally encoding aspartate kinase isozyme (Ask), correlated well with methanotroph halotolerance and intracellular ectoine level. A new gene, ectR1 encoding the MarR-like transcriptional regulatory protein EctR1, negatively controlling transcription of ectoine biosynthetic genes was found upstream of ectABC-ask operon in Methylomicrobium alcaliphilum 20Z. The ectR-like genes were also found in halotolerant methanol utilizers Methylophaga alcalica and Methylophaga thalassica as well as in several genomes of nonmethylotrophic species. The His(6)-tagged DABA acetyltransferases from Mm. alcaliphilum, M. alcalica, and M. thalassica were purified and the enzyme properties were found to correlate with the ecophysiologies of these bacteria. All these discoveries should be very helpful for better understanding the biosynthetic mechanism of this important natural compound, and for the targeted metabolic engineering of its producers.

Indibacter alkaliphilus gen. nov., sp. nov., an alkaliphilic bacterium isolated from a haloalkaline lake

A novel Gram-stain-negative, rod-shaped, non-motile bacterium, strain LW1T, was isolated from a water sample collected at a depth of 3.5 m from Lonar Lake, Buldhana district, Maharashtra, India. The cell suspension was reddish-orange due to the presence of carotenoids. Strain LW1T was positive for catalase, oxidase, ornithine decarboxylase and lysine decarboxylase and negative for gelatinase, urease and lipase. Fatty acids were dominated by branched-chain fatty acids (>76 %), with a high abundance of iso-C15 : 0 (48 %), anteiso-C15 : 0 (7 %) and iso-C17 : 0 3-OH (11 %). Strain LW1T contained MK-4 and MK-7 as the major respiratory quinones and phosphatidylglycerol, phosphatidylcholine and phosphatidylethanolamine as the major phospholipids. A blast sequence similarity search based on 16S rRNA gene sequences indicated that members of the genera Belliella and Aquiflexum were the nearest phylogenetic neighbours with similarities of 91.8–92.3 %. Phylogenetic analyses indicated that strain LW1T formed a deep-rooted lineage distinct from the clades represented by the genera Belliella, Aquiflexum, Cyclobacterium, Echinicola and Algoriphagus. Based on the above-mentioned phenotypic and phylogenetic characteristics, it is proposed that strain LW1T represents a novel species in a new genus, Indibacter alkaliphilus gen. nov., sp. nov. (type strain LW1T=KCTC 22604T=CCUG 57479T). The genomic DNA G+C content of strain LW1T is 42.7±1 mol%.

Methylophilus flavus sp. nov. and Methylophilus luteus sp. nov., aerobic, methylotrophic bacteria associated with plants

Novel yellow, obligately methylotrophic and restricted facultatively methylotrophic bacteria, respectively designated strains Ship(T) and Mim(T), with the ribulose monophosphate pathway of C(1) assimilation are described. Cells were strictly aerobic, Gram-negative, asporogenous, non-motile rods that multiply by binary fission, were mesophilic and neutrophilic and synthesized indole-3-acetic acid and exopolysaccharide. The predominant cellular fatty acids were C(16 : 0) and C(16 : 1). The major ubiquinone was Q-8. The predominant phospholipids were phosphatidylethanolamine and phosphatidylglycerol; diphosphatidylglycerol was absent. The two strains lacked α-ketoglutarate dehydrogenase and glutamate dehydrogenase. They assimilated ammonium via the glutamate cycle enzymes glutamine synthetase and glutamate synthase. The DNA G+C contents of strains Ship(T) and Mim(T) were 50.7 and 54.5 mol% (T(m)), respectively. The level of 16S rRNA gene sequence similarity between these strains was very high (99.8 %) but they shared a low level of DNA-DNA relatedness (44 %). Based on 16S rRNA gene sequence analysis and low levels of DNA-DNA relatedness with the type strains of recognized species of the genus Methylophilus (31-36 %), strains Ship(T) and Mim(T) are considered to represent novel species of the genus Methylophilus, for which the names Methylophilus flavus sp. nov. (type strain Ship(T) =DSM 23073(T) =VKM B-2547(T) =CCUG 58411(T)) and Methylophilus luteus sp. nov. (type strain Mim(T) =DSM 22949(T) =VKM B-2548(T) =CCUG 58412(T)) are proposed.

Chelativorans multitrophicus gen. nov., sp. nov. and Chelativorans oligotrophicus sp. nov., aerobic EDTA-degrading bacteria

Two previously isolated strains (DSM 9103(T) and LPM-4(T)) able to grow with EDTA (facultatively and obligately, respectively) as the source of carbon, nitrogen and energy were investigated in order to clarify their taxonomic positions. The strains were strictly aerobic, Gram-negative, asporogenous and non-motile rods that required biotin for growth. Reproduction occurred by binary fission. The strains were mesophilic and neutrophilic. Their major fatty acids were summed feature 7 (consisting of C(18 : 1)omega7c, C(18 : 1)omega9t and/or C(18 : 1)omega12t) and C(19 : 0) cyclo omega8c. The polyamine pattern revealed homospermidine as a major polyamine. Predominant polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, phosphatidyldimethylethanolamine, phosphatidylmonomethylethanolamine and diphosphatidylglycerol. Mesorhizobium-specific ornithine lipid was absent. The predominant isoprenoid quinone was Q-10. The DNA G+C values were 60.8 and 63.1 mol% (T(m)) for strains LPM-4(T) and DSM 9103(T), respectively. The level of 16S rRNA gene sequence similarity between these EDTA-utilizers was 99.3 % while the DNA-DNA hybridization value was only 37 %. Both strains were phylogenetically related to members of the genera Aminobacter and Mesorhizobium (95-97 % sequence similarity). However, DNA-DNA hybridization values between the novel EDTA-degrading strains and Aminobacter aminovorans DSM 7048(T) and Mesorhizobium loti DSM 2626(T) were low (10-11 %). Based on their genomic and phenotypic properties, the new alphaproteobacterial strains are assigned to a novel genus, Chelativorans gen. nov., with the names Chelativorans multitrophicus sp. nov. (type strain DSM 9103(T)=VKM B-2394(T)) and Chelativorans oligotrophicus sp. nov. (type strain LPM-4(T)=VKM B-2395(T)=DSM 19276(T)).

Characterization of the recombinant diaminobutyric acid acetyltransferase from Methylophaga thalassica and Methylophaga alcalica

Diaminobutyric acid acetyltransferase (EctA) catalyzes the acetylation of diaminobutyric acid to gamma-N-acetyl-alpha,gamma-diaminobutyrate with acetyl coenzyme A. This is the second reaction in the ectoine biosynthetic pathway. The recombinant EctA proteins were purified from two moderately halophilic methylotrophic bacteria: Methylophaga thalassica ATCC 33146T and Methylophaga alcalica ATCC 35842T. EctA found in both methylotrophs is a homodimer with a subunit molecular mass of c. 20 kDa and had similar properties with respect to the optimum temperature for activity (30 degrees C), Km for diaminobutyrate (370 or 375 microM) and the absence of requirements for divalent metal ions. The enzyme from M. thalassica exhibited a lower pH optimum and was inhibited both by sodium carbonates and by high ionic strength but to a lesser extent by copper ions.

Methylohalomonas lacus gen. nov., sp. nov. and Methylonatrum kenyense gen. nov., sp. nov., methylotrophic gammaproteobacteria from hypersaline lakes

Aerobic enrichment at 4 M NaCl, pH 7.5, with methanol as carbon and energy source from sediments of hypersaline chloride–sulfate lakes in Kulunda Steppe (Altai, Russia) resulted in the isolation of a moderately halophilic and obligately methylotrophic bacterium, strain HMT 1T. The bacterium grew with methanol and methylamine within a pH range of 6.8–8.2 with an optimum at pH 7.5 and at NaCl concentrations of 0.5–4 M with an optimum at 2 M. In addition to methanol and methylamine, it can oxidize ethanol, formate, formaldehyde and dimethylamine. Carbon is assimilated via the serine pathway. The main compatible solute is glycine betaine. 16S rRNA gene sequence analysis placed the isolate as a new lineage in the familyEctothiorhodospiraceae(Gammaproteobacteria). It is proposed, therefore, to accommodate this bacterium within a novel genus and species,Methylohalomonas lacusgen. nov., sp. nov., with HMT 1T(=DSM 15733T=NCCB 100208T=UNIQEM U237T) as the type strain. Two strains were obtained in pure culture from sediments of soda lake Magadi in Kenya and the Kulunda Steppe (Russia) on a mineral medium at pH 10 containing 0.6 M total Na+using methanol as a substrate. Strain AMT 1Twas enriched with methanol, while strain AMT 3 originated from an enrichment culture with CO. The isolates are restricted facultative methylotrophs, capable of growth with methanol, formate and acetate as carbon and energy sources. With methanol, the strains grew within a broad salinity range from 0.3 to 3.5–4 M total Na+, with an optimum at 0.5–1 M. The pH range for growth was between 8.3 and 10.5, with an optimum at pH 9.5, which characterized the soda lake isolates as obligate haloalkaliphiles. Carbon is assimilated autotrophically via the Calvin–Benson cycle. Sequence analysis of the gene coding for the key enzyme RuBisCO demonstrated that strain AMT 1Tpossessed a singlecbbLgene of the ‘green’ form I, clustering with members of the familyEctothiorhodospiraceae. Analysis of the 16S rRNA gene sequence showed that strains AMT 1Tand AMT 3 belong to a single species that forms a separate lineage within the familyEctothiorhodospiraceae. On the basis of phenotypic and genetic data, the novel haloalkaliphilic methylotrophs are described as representing a novel genus and species,Methylonatrum kenyensegen. nov., sp. nov. (type strain AMT 1T=DSM 15732T=NCCB 100209T=UNIQEM U238T).

Methylophaga aminisulfidivorans sp. nov., a restricted facultatively methylotrophic marine bacterium

A novel restricted facultatively methylotrophic marine strain, MP(T), possessing the ribulose monophosphate pathway of C(1)-carbon compound assimilation was isolated from a seawater sample obtained from Mokpo, South Korea. The novel isolate is aerobic, Gram-negative, asporogenous and a non-motile short rod. It grows well on methanol, methylated amines, dimethylsulfide and DMSO. Optimal growth occurs with 3 % NaCl at 30 degrees C and pH 7.0. Fructose is utilized as a multicarbon source. Growth factors are not required and vitamin B(12) does not stimulate growth. The cellular fatty acid profile of the novel strain consists primarily of straight-chain saturated C(16 : 0) and unsaturated C(16 : 1) acids. The major ubiquinone is Q-8. The dominant phospholipids are phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content is 44.9 mol% (T(m)). Based on 16S rRNA gene sequence analysis and DNA-DNA relatedness (25-41 %) with the type strains of marine methylotrophs belonging to the genus Methylophaga, it is suggested that isolate MP(T) represents a novel species, Methylophaga aminisulfidivorans sp. nov. (type strain MP(T)=KCTC 12909(T)=VKM B-2441(T)=JCM 14647(T)).

Hansschlegelia plantiphila gen. nov. sp. nov., a new aerobic restricted facultative methylotrophic bacterium associated with plants

A new genus, Hansschlegelia, and a new species, Hansschlegelia plantiphila, are proposed for three strains of methanol-utilizing bacteria isolated from lilac buds (strain S(1)(T)), linden buds (strain S(2)) and blue spruce needles (strain S(4)), which were selected in winter at -17 degrees C. These bacteria are aerobic, Gram-negative, colorless, non-motile short rods that multiply by binary fission and employ the ribulose bisphosphate (RuBP) and the serine pathways for C(1) assimilation. The strains have a limited number of growth substrates and use methanol, methylamine, formate, CO(2)/H(2) and glycerol as carbon and energy sources. Only strain S(1)(T) grows with ethanol and inulin. The strains are neutrophilic and mesophilic, and synthesize phytohormones (auxins and cytokinins) and vitamin B(12). Their major cellular fatty acids are saturated C(16:0), straight-chain, unsaturated C(18:1)(omega)(7) and cyclopropane C(19 cyc) acids. The main ubiquinone is ubiquinone-10 (Q-10). The dominant phospholipids are phosphatidylethanolamine, phosphatidylcholine and diphosphatidylglycerol (cardiolipin). The DNA G+C content is 68.5+/-0.2 mol%. The strains share almost identical 16S rRNA gene sequences, a high DNA-DNA hybridization value (72-86%) and represent a novel lineage of autotrophic methanol-utilizing bacteria within the Alphaproteobacteria. Collectively, these strains comprise a new genus and species H. plantiphila gen. nov., sp. nov., with strain S(1)(T) (VKM B-2347(T), NCIMB 14035(T)) as the type strain.

Stable-isotope probing implicates Methylophaga spp and novel Gammaproteobacteria in marine methanol and methylamine metabolism

The metabolism of one-carbon (C(1)) compounds in the marine environment affects global warming, seawater ecology and atmospheric chemistry. Despite their global significance, marine microorganisms that consume C(1) compounds in situ remain poorly characterized. Stable-isotope probing (SIP) is an ideal tool for linking the function and phylogeny of methylotrophic organisms by the metabolism and incorporation of stable-isotope-labelled substrates into nucleic acids. By combining DNA-SIP and time-series sampling, we characterized the organisms involved in the assimilation of methanol and methylamine in coastal sea water (Plymouth, UK). Labelled nucleic acids were analysed by denaturing gradient gel electrophoresis (DGGE) and clone libraries of 16S rRNA genes. In addition, we characterized the functional gene complement of labelled nucleic acids with an improved primer set targeting methanol dehydrogenase (mxaF) and newly designed primers for methylamine dehydrogenase (mauA). Predominant DGGE phylotypes, 16S rRNA, methanol and methylamine dehydrogenase gene sequences, and cultured isolates all implicated Methylophaga spp, moderately halophilic marine methylotrophs, in the consumption of both methanol and methylamine. Additionally, an mxaF sequence obtained from DNA extracted from sea water clustered with those detected in (13)C-DNA, suggesting a predominance of Methylophaga spp among marine methylotrophs. Unexpectedly, most predominant 16S rRNA and functional gene sequences from (13)C-DNA were clustered in distinct substrate-specific clades, with 16S rRNA genes clustering with sequences from the Gammaproteobacteria. These clades have no cultured representatives and reveal an ecological adaptation of particular uncultured methylotrophs to specific C(1) compounds in the coastal marine environment.

Microbiological community structure of the biofilm of a methanol-fed, marine denitrification system, and identification of the methanol-utilizing microorganisms

We demonstrated in a previous study that the biofilm of the methanol-fed fluidized marine denitrification reactor at the Montreal Biodome was composed of at least 15 bacterial phylotypes. Among those were 16S ribosomal RNA (rDNA) gene sequences affiliated to Hyphomicrobium spp., and Methylophaga spp.; the latter made up 70% of a clone library. By using fluorescent in situ hybridization (FISH), we investigated the structure of the biofilm during the colonization process in the denitrification reactor by targeting most of the bacterial families that the 16S rDNA gene library suggested would occur in the biofilm. Our results revealed that gamma-Proteobacteria (mostly Methylophaga spp.) accounted for up to 79% of the bacterial population, confirming the abundance of Methylophaga spp. within the biofilm. alpha-Proteobacteria represented 27-57% of the population, which included Hyphomicrobium spp. that appeared after 20 days of colonization and represented 7-8% of the population. We noticed a great abundance and diversity of eukaryotic cells, which made up 20% of the biomass at the beginning of the colonization but decreased to 3-5% in the mature biofilm. We then used FISH combined with microautoradiography (MAR-FISH) to identify the methylotrophs in the biofilm. The results showed that alpha-Proteobacteria used (14)C methanol in the presence of nitrate, suggesting their involvement in denitrification. Despite their abundance, Methylophaga spp. did not assimilate methanol under those conditions.

Isolation of Methylophaga spp. from marine dimethylsulfide-degrading enrichment cultures and identification of polypeptides induced during growth on dimethylsulfide

Dimethylsulfide (DMS)-degrading enrichment cultures were established from samples of coastal seawater, nonaxenic Emiliania huxleyi cultures, and mixed marine methyl halide-degrading enrichment cultures. Bacterial populations from a broad phylogenetic range were identified in the mixed DMS-degrading enrichment cultures by denaturing gradient gel electrophoresis (DGGE). Sequences of dominant DGGE bands were similar to those of members of the genera Methylophaga and Alcanivorax. Several closely related Methylophaga strains were obtained that were able to grow on DMS as the carbon and energy source. Roseobacter-related populations were detected in some of the enrichment cultures; however, none of the Roseobacter group isolates that were tested were able to grow on DMS. Oxidation of DMS by Methylophaga sp. strain DMS010 was not affected by addition of the inhibitor chloroform or methyl tert-butyl ether, suggesting that DMS metabolism may occur by a route different from those described for Thiobacillus species and other unidentified marine isolates. Addition of DMS and methanethiol to whole-cell suspensions of strain DMS010 induced oxygen uptake when strain DMS010 was grown on DMS but not in cells grown on methanol. The apparent K(m)s of strain DMS010 for DMS and for methanethiol were 2.1 and 4.6 microM, respectively, when grown on DMS. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the biomass of strain DMS010 and analysis of peptide bands by mass spectrometry techniques and N-terminal sequencing provided the first insight into the identity of polypeptides induced during growth on DMS. These included XoxF, a homolog of the large subunit of methanol dehydrogenase for which a biological role has not been identified previously.