Synthesis of osmoprotectants by halophilic and alkaliphilic methanotrophs

The¹H-NMR analysis of methanol extracts of halophilic and halotolerant alkaliphilic methanotrophs isolated from the soda lakes of Southern Transbaikal and Tuva showed that bacterial cells grown at an optimum salinity accumulated mainly sucrose and 5-oxo-1-proline, whereas cells adapted to 0.5–1.0 M NaCl additionally synthesized ectoine. A more detailed study showed that nitrogen deficiency in the growth medium ofMethylobacter alcaliphilus 20Z decreased the synthesis of nitrogen-contaihing osmoprotectants, ectoine and 5-oxo-1-proline.M. alcaliphilus 20Z cells exhibited activities of UDP-glucose pyrophosphorylase and sucrose-phosphate synthase involved in sucrose synthesis. Glutamine synthetase in vitro did not require NH ₄ ⁺ ions, which implies that this enzyme is involved in 5-oxo-1-proline synthesis. Cells grown at high salinity exhibited elevated levels of aspartate kinase, aspartate-semialdehyde dehydrogenase, and ectoine synthase. This suggests that ectoine is synthesized via aspartate and aspartate-semialdehyde, i.e., via the route earlier established for extremely halophilic bacteria.     

Osmoadaptation in halophilic and alkaliphilic methanotrophs

By using ¹H- and ¹³C-NMR spectroscopy, an accumulation of sucrose and two cyclic amino acids [ectoine (1,4,5,6-tetrahydro-2-methyl-4-pyrimidine carboxylic acid) and 5-oxoproline (pyrrolidone carboxylic acid)] was detected in the halotolerant methanotrophs Methylobacter alcaliphilus 20Z and Methylobacter modestohalophilus 10S. The organic solute pool was found to increase upon raising the NaCl concentration. In M. alcaliphilus 20Z, the intracellular level of the total solutes was shown to be sufficient to balance the osmotic pressure of the medium, whereas in M. modestohalophilus 10S their content was several times lower. Additionally, phosphatidylglycerol and phosphatidylcholine were predominant cell phospholipids in salt-adapted M. alcaliphilus 20Z. However, no phosphatidylcholine was found in M. modestohalophilus 10S, and the portion of phosphatidylglycerol increased while phosphatidylethanolamine decreased upon elevated external NaCl concentrations. Regularly arranged glycoprotein surface layers (S-layers) of hexagonal and linear (p2) symmetry were observed on the outer cell walls of M. alcaliphilus 20Z and M. modestohalophilus 10S. The S-layer in M alcaliphilus 20Z consisting of tightly packed, cup-shaped subunits was lost during growth at pH 7.2 (the lowest possible pH) in the absence of NaCl. Hence, osmoadaptation in the methanotrophs studied involves structure/function alterations of cell envelopes and changes in the chemical composition of membranes as well as de novo synthesis of compatible solutes. Revision received: 16 July 1999 / Accepted: 2 August 1999     

甲烷生物利用及嗜甲烷菌的工程改造

作为来源广泛、储量丰富的有机碳一气体,甲烷被认为是下一代工业生物技术中最具潜力的碳原料之一.嗜甲烷菌能够利用其体内的甲烷单加氧化酶,将甲烷作为唯一的碳源和能源进行生长和代谢,这为温室气体减排及其开发利用提供了新的策略.目前,嗜甲烷菌生物催化体系的相关研究已开展多年,随着系统生物学和合成生物学的快速发展,利用代谢工程合理...     

Growth yields of methanotrophs

Summary The growth yield ofMethylococcus capsulatus (Bath) on methane was dependent on the availability of copper in the growth medium. In nitrate mineral salts medium the carbon conversion efficiency increased by 38%, concomitant with the transition from soluble to particulate methane monooxygenase, after transfer from low to high copper medium. An increase in growth efficiency was also observed with ammonia as nitrogen source but not when methanol replaced methane as carbon source. The high growth efficiency is attributed to a reduced NADH requirement for methane oxidation. This could only arise if methanol dehydrogenase was capable of electron transfer, either directly or indirectly to the particulate methane monooxygenase (MMO). The carbon conversion efficiency from methanol with nitrate as nitrogen source was as high as theoretically predicted. It is suggested that the previously low yields of methanotrophs grown on methanol resulted from the use, as nitrogen source, of ammonia which was oxidised by the MMO still present under these growth conditions. The term ‘methanotroph’ is used throughout to distinguish those organisms capable of growth on methane from ‘methylotrophs’ capable of growth on reduced C, compounds other than methane     

Thermophilic and thermotolerant aerobic methanotrophs

The review generalizes the modern data on the taxonomic, structural, and functional diversity of aerobic methanotrophs growing at 25–50°C (Methylococcus capsulatus), 30–62°C (Methylocaldum szegediense, Methylocaldum gracile, and Methylocaldum tepidum), and 50–65°C (Methylothermus thermalis), which belong mainly to the Gammaproteobacteria. The specific features of adaptation of these methanotrophs to the temperature influences are considered on the metabolic and genetic levels. The recent sensational reports on the discovery and primary characterization of thermoacidophilic methanotrophs of the phylum Verrucomicrobia surviving at extreme pH (1–2) and temperature (65°C) values, corresponding to extremely low levels of CH₄ and O₂ solubility, are analyzed. The possibilities of implementation of the biotechnological potential of thermophilic and thermotolerant methanotrophs are discussed.     

Isolation and characterization of marine methanotrophs

Four new methane-oxidizing bacteria have been isolated from marine samples taken at the Hyperion sewage outfall, near Los Angeles, CA. These bacteria require NaCl for growth. All exhibit characteristics typical of Type I methanotrophs, except they contain enzyme activities of both the ribulose monophosphate pathway and the serine cycle. All four strains are characterized by rapid growth in liquid culture and on agar plates, and all have temperature optima above 35° C. One strain, chosen for further study, has been shown to maintain broadhost range cloning vectors and is currently being used for genetic studies.     

Bioenergetics of alkalophilic bacteria

Summary The central problem for organisms which grow optimally, and in some cases obligately, at pH values of 10 to 11, is the maintenance of a relatively acidified cytoplasm. A key component of the pH homeostatic mechanism is an electrogenic Na⁺/H⁺ antiporter which—by virtue of kinetic properties and/or its concentration in the membrane—catalyzes net proton uptake while the organisms extrude protons during respiration. The antiporter is also capable of maintaining a constant pH_in during profound elevations in pH_out as long as Na⁺ entry is facilitated by the presence of solutes which are taken up with Na⁺. Secondary to the problem of acidifying the interior is the adverse effect of the large pH gradient, acid in, on the total pmf of alkalophile cells. For the purposes of solute uptake and motility, the organisms appear to largely bypass the problem of a low pmf by utilizing a sodium motive force for energization. However, ATP synthesis appears not to resolve the energetics problem by using Na⁺ or by incorporating the proton-translocating ATPase into intracellular organelles. The current data suggest that effective proton pumping carried out by the alkalophile respiratory chain at high pH may deliver at least some portion of the protons to the proton-utilizing catalysts, i. e., theF ₁ F ₀-ATPase and the Na⁺/H⁺ antiporter, by some localized pathway.     

Denitrification by extremely halophilic bacteria

Abstract Extremely halophilic bacteria were isolated from widely separated sites by anaerobic enrichment in the presence of nitrate. The anaerobic growth of several of these isolates was accompanied by the production of nitrite, nitrous oxide, and dinitrogen. These results are a direct confirmation of the existence of extremely halophilic denitrifying bacteria, and suggest that such bacteria may be common inhabitants of hypersaline environments.     

Genetics and molecular biology of methanotrophs

Abstract Over the last 20 years or so, the obligate methane-oxidizing bacteria (methanotrophs) have attracted considerable interest. As they grow on a relatively cheap and abundant carbon source, they appeared ideal organisms for the production of bulk chemicals, single-cell protein and for use in biotransformations. More recently their cooxidation properties have been investigated for bioremediation, including the removal of chlorinated compounds such as trichloroethylene from polluted groundwaters. These studies have resulted in a great deal of information on the physiology and biochemistry of methanotrophs but sadly the molecular biology and genetic studies of these organisms have lagged behind. This has been in part due to the obligate nature of the methanotrophs and the refractory nature of such organisms to conventional genetic analysis. However, the more recent availability of broad-host range plasmids coupled with improvements in molecular biology methods have allowed the development of molecular genetic techniques for methanotrophs. The purpose of this review is to summarize what is known about the genetics and molecular biology of methanotrophs and how this information can be used to complement previous and current biochemical studies on the unique property of these bacteria, i.e. the ability to oxidize methane to methanol. Recent developments in molecular ecology techniques that may be applied to these apparently ubiquitous organism are also considered.     

Biology of extremophilic and extremotolerant methanotrophs

This review summarizes recent findings on the biology of obligate methanotrophic bacteria living in various extreme environments. By using molecular ecology techniques, it has become clear that obligate methanotrophs are ubiquitous in nature and well adapted to high or low temperature, pH and salinity. The isolation and characterization of pure cultures has led to the discovery of several new genera and species of extremophilic/tolerant methanotrophs. Their major physiological role is participation in the methane cycle and supplying C(1) intermediates and various metabolites to other members of microbial communities in extreme ecosystems. To survive under extreme conditions, methanotrophs have developed diverse structure-function adaptive mechanisms including cell-surface layer formation, changes in cellular phospholipid composition and de novo synthesis of organic osmolytes such as ectoine, 5-oxoproline and sucrose. However, despite the above advances, basic knowledge of other stress protectants, as well as bioenergetic and genetic aspects of methanotroph adaptation, is still lacking. This information is necessary for better understanding the molecular mechanisms underlying the versatility of methanotrophs and for the development of novel biotechnological processes.     

Degumming of ramie fibers by alkalophilic bacteria and their polysaccharide-degrading enzymes

Three strains of alkalophilic bacteria, Bacillus sp. NT-39, NT-53 and NT-76, were selected for the degumming of ramie fibers and production of polysaccharide-degrading enzymes. After 48 h of incubation with the strains, the loss of the gum might amount to 5.0% or more of the fibers and a number of polysaccharide-degrading enzymes were secreted to the culture supernatants. The residual gum of the fibers decreased to 9.4% after 5 h of enzymatic degumming. Analysis of gum contents and enzyme activities revealed that pectate lyase and xylanase played an important role in the degradation of residual gum. Enzymatic degumming resulted in an increment of 5.4 ISO units in fiber brightness, whereas the reduction in bundle breaking tenacity of the fibers was less than 5.%. The results confirmed that degumming of ramie fibers by alkalophilic bacteria and their enzymes had substantial advantages.     

专一营养与兼性甲烷氧化菌降解氯代烃的研究现状、动力学分析及展望

生物修复技术被认为是氯代烃类污染物处理处置的最有效途径之一,而甲烷氧化菌在该领域表现出较大的应用潜力。近期研究发现,突破了仅能利用单碳化合物的局限,兼性甲烷氧化菌能够利用多种底物降解氯代烃,这一独特的新陈代谢特性,使其在污染物生物处置领域逐渐受到关注。结合本课题组研究成果,对甲烷氧化菌降解氯代烃进行了全面总结,主要包括:分析了不同菌株(纯菌株和混合菌株)对不同氯代烃的降解效果;比较了不同类型甲烷单加氧酶在不同底物体系中的活性表达和催化特性;总结了模型菌株甲基弯菌Methylosinus trichosporium OB3b降解氯代烃的动力学特性;概述了兼性甲烷氧化菌株降解氯代烃的特性及其应用潜力;最后讨论了甲烷氧化菌降解氯代烃存在的问题及未来发展方向。     

Halomonas alkaliantarctica sp. nov., isolated from saline lake Cape Russell in Antarctica, an alkalophilic moderately halophilic, exopolysaccharide-producing bacterium

The taxomony of strain CRSS (DSM 15686(T)=ATCC BAA-848(T)) isolated from Cape Russell in Antarctica (Ross Sea, 74 52.35 S 163 53.03 E) was investigated in a polyphasic approach. The morphological, physiological and genetic characteristics were compared with that of related species of the genus Halomonas. The isolate grew optimally at pH 9.0, 10% NaCl at 30 degrees C. The cells were Gram-negative aerobic rods able to produce exopolysaccharide. They accumulated glycine-betaine, as a major osmolyte, with minor components ectoine and glutamate. The strain CRSS biosynthetised alpha-glucosidase. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol as major components. Ubiquinone with nine repetitive unities (Q9) was the only quinone found and the fatty acid composition was dominated by C18:1 (53%). The G+C content of DNA was 55.0mol% and its phylogenetic position was established by 16S rRNA gene sequencing as a member of the genus Halomonas. For physiological, chemotaxonomic and genetic features (DNA-DNA hybridisation) it is proposed to classify the isolate as a new species for which we propose the name Halomonas alkaliantarctica sp. nov.     

Biogeography of wetland rice methanotrophs

We focused on the functional guild of methane oxidizing bacteria (MOB) as model organisms to get deeper insights into microbial biogeography. The pmoA gene was used as a functional and phylogenetic marker for MOB in two approaches: (i) a pmoA database (> 4000 sequences) was evaluated to obtain insights into MOB diversity in Italian rice paddies, and paddy fields worldwide. The results show a wide geographical distribution of pmoA genotypes that seem to be specifically adapted to paddy fields (e.g. Rice Paddy Cluster 1 and Rice Paddy Cluster 2). (ii) On the smaller geographical scale, we designed a factorial experiment including three different locations, two rice varieties and two habitats (soil and roots) within each of three rice fields. Multivariate analysis of terminal restriction fragment analysis profiles revealed different community patterns at the three field sites, located 10–20 km apart. Root samples were characterized by high abundance of type I MOB whereas the rice variety had no effect. With the agronomical practice being nearly identical, historical contingencies might be responsible for the field site differences. Considering a large reservoir of viable yet inactive MOB cells acting as a microbial seed bank, environmental conditions might have selected and activated a different subset at a time thereby shaping the community.     

Effect of mineral media on trichloroethylene oxidation by aquifer methanotrophs

The effect of growth in different mineral media on subsequent oxidation of trichloroethylene (TCE) by type I and type II aquifer methanotrophs was evaluated. Mixed culture MM1, containing a type II methanotroph, and a type I pure culture tentatively identified as aMethylomonas sp., were enriched and isolated from an uncontaminated groundwater aquifer. The second-order rate coefficients (k/K_s) for TCE oxidation by these cultures varied by more than an order of magnitude when the cultures were grown in different mineral media. The presence of a chelator (NaEDTA) in one of these media, termed Whittenbury, significantly enhanced rates of TCE oxidation by all the cultures tested. When pregrown in this mineral medium, the resting cells of the pure cultureMethylomonas sp. MM2 exhibited second-order TCE oxidation rates as great as 0.78 liter/mg·day, whereas when pregrown in Whittenbury lacking the chelator, the rates did not exceed 0.018 liter/mg·day. The rate of TCE oxidation byMethylomonas sp. MM2 pregrown in another mineral medium formulation, devoid of chelators (termed Fogel), was intermediate in value (0.26 liter/mg·day), and adding EDTA to this medium did not affect the rate. Adding 1.6 μM copper to both Whittenbury and Fogel mineral media reduced the TCE oxidation rates about an order of magnitude; subsequent addition of 84 μM EDTA partially alleviated this effect. The maximal rate coefficients (k) for TCE oxidation byMethylomonas sp. MM2 were significantly higher, and the half saturation coefficients (K_s) for TCE significantly lower, following growth in the presence of EDTA. Stationary phase TCE oxidation rates as great as 2.3 liter/mg·day were achieved whenMethylomonas sp. MM2, grown in Whittenbury medium was provided formate as a source of reducing power. Omitting EDTA from Whittenbury medium also significantly reduced the methane oxidation rate and the growth yield. Copper addition did not significantly affect the methane oxidation rate or growth yield. The internal membrane structures ofMethylomonas sp. MM2 evaluated by transmission electron microscopy showed the presence of internal membranes, the ultrastructure of which was the same regardless of growth medium or TCE oxidation rate. The methane monooxygenase responsible for TCE oxidation inMethylomonas sp. MM2 under the conditions of this study appears to be associated with the particulate fraction.     

嗜碱微生物多样性及其应用

碱性环境最适生长的微生物称为嗜碱微生物,这些微生物主要分布在天然碱湖、碱性沙漠和土壤中。除细菌外已分离到各种各样的微生物,包括藻类、放线菌、真菌、酵母和病毒。为了适应碱性因子它们具有特殊的细胞结构和生理机能。因此,研究适应机理并利用其特殊机能具有重要的理论和实际意义,嗜碱微生物能产生多种碱性酶和其他生物活性物质,有着广阔的应用前景。     

Distribution of methanotrophs in the phyllosphere

Plants have been reported to emit methane as well as methanol originating in their cell-wall constituents. We investigated methanotrophs in the phyllosphere by the enrichment culture method with methane as sole carbon source. We enriched methanotrophs from the leaves, flowers, bark, and roots of various plants. Analysis of the pmoA and mxaF genes retrieved from the enrichment cultures revealed that methanotrophs closely related to the genera Methylomonas, Methylosinus, and Methylocystis inhabit not only the rhizosphere but also the phyllosphere, together with methanol-utilizing bacteria.     

Organic acids and ethanol inhibit the oxidation of methane by mire methanotrophs

Aerobic methane (CH(4) ) oxidation reduces the emission of CH(4) from mires and is regulated by various environmental factors. Organic acids and alcohols are intermediates of the anaerobic degradation of organic matter or are released by plant roots. Methanotrophs isolated from mires utilize these compounds preferentially to CH(4) . Thus, the effect of organic acids and ethanol on CH(4) oxidation by methanotrophs of a mire was evaluated. Slurries of mire soil oxidized supplemental CH(4) down to subatmospheric concentrations. The dominant pmoA and mmoX genotypes were affiliated with sequences from Methylocystis species capable of utilization of acetate and atmospheric CH(4) . Soil slurries supplemented with acetate, propionate or ethanol had reduced CH(4) oxidation rates compared with unsupplemented or glucose-supplemented controls. Expression of Methylocystis-affiliated pmoA decreased when CH(4) consumption decreased in response to acetate and was enhanced after acetate was consumed, at which time the consumption of CH(4) reached control levels. The inhibition of methanotroph activity might have been due to either toxicity of organic compounds or their preferred utilization. CH(4) oxidation was reduced at 5 and 0.5 mM of supplemental organic compounds. Acetate concentrations may exceed 3 mM in the investigated mire. Thus, the oxidation of CH(4) might decrease in microzones where organic acids occur.