Evolutionary relationships of bacterial and archaeal glutamine synthetase genes

Glutamine synthetase (GS), an essential enzyme in ammonia assimilation and glutamine biosynthesis, has three distinctive types: GSI, GSII and GSIII. Genes for GSI have been found only in bacteria (eubacteria) and archaea (archaebacteria), while GSII genes only occur in eukaryotes and a few soil-dwelling bacteria. GSIII genes have been found in only a few bacterial species. Recently, it has been suggested that several lateral gene transfers of archaeal GSI genes to bacteria may have occurred. In order to study the evolution of GS, we cloned and sequenced GSI genes from two divergent archaeal species: the extreme thermophile Pyrococcus furiosus and the extreme halophile Haloferax volcanii. Our phylogenetic analysis, which included most available GS sequences, revealed two significant prokaryotic GSI subdivisions: GSI-a and GSI-. GSIa-genes are found in the thermophilic bacterium, Thermotoga maritima, the low G+C Gram-positive bacteria, and the Euryarchaeota (includes methanogens, halophiles, and some thermophiles). GSI--type genes occur in all other bacteria. GSI-- and GSI--type genes also differ with respect to a specific 25-amino-acid insertion and adenylylation control of GS enzyme activity, both absent in the former but present in the latter. Cyanobacterial genes lack adenylylation regulation of GS and may have secondarily lost it. The GSI gene of Sulfolobus solfataricus, a member of the Crenarchaeota (extreme thermophiles), is exceptional and could not be definitely placed in either subdivision. The S. solfataricus GSI gene has a shorter GSI--type insertion, but like GSI-a-type genes, lacks conserved sequences about the adenylylation site. We suspect that the similarity of GSI- genes from Euryarchaeota and several bacterial species does not reflect a common phylogeny but rather lateral transmission between archaea and bacteria.Correspondence to: J.R. Brown 1073     

Potential for bioremediation of fuel‐contaminated soil in Antarctica

A preliminary investigation was conducted to identify the presence of bacteria in fuel‐contaminated Antarctic soil that could potentially be used to bioremediate the contaminated soil at McMurdo Station and other sites in Antarctica. The ability of soil microorganisms to metabolize fuels under the extreme climatic and oligotrophic conditions of Antarctica was of concern. Bacteria were isolated from fuel‐contaminated soil on site at McMurdo Station. Bacteria from noncontaminated soil near the station were also studied for comparison. The Antarctic soil microorganisms exhibited the ability to endure cold and oligotrophic environments. Experiments also showed that bacteria from the fuel spill site were active in their contaminated environment and that acclimation to xenobiotic compounds was necessary. Application of bioremediation in the extreme environmental conditions found at McMurdo Station, Antarctica, were also considered. The possibility of altering environmental factors necessary to adequately support in situ bioremediation in this extreme climate is discussed.     

Genome deterioration: loss of repeated sequences and accumulation of junk DNA

A global survey of microbial genomes reveals a correlation between genome size, repeat content and lifestyle. Free-living bacteria have large genomes with a high content of repeated sequences and self-propagating DNA, such as transposons and bacteriophages. In contrast, obligate intracellular bacteria have small genomes with a low content of repeated sequences and no or few genetic parasites. In extreme cases, such as in the 650kb-genomes of aphid endosymbionts of the genus Buchnera all repeated sequences above 200bp have been eliminated. We speculate that the initial downsizing of the genomes of obligate symbionts and parasites occurred by homologous recombination at repeated genes, leading to the loss of large blocks of DNA as well as to the consumption of repeated sequences. Further sequence elimination in these small genomes seems primarily to result from the accumulation of short deletions within genic sequences. This process may lead to temporary increases in the genomic content of pseudogenes and junk DNA. We discuss causes and long-term consequences of extreme genome size reductions in obligate intracellular bacteria.     

Aminopeptidase Activity of Haloalkalophilic Bacteria of the Genus <Emphasis Type="Italic">Halomonas</Emphasis> Isolated from the Soda-Saline Lakes in the Badain Jaran Desert

Three strains of haloalkaliphilic bacteria were isolated from microbial mats of soda-saline lakes of the Badain Jaran Desert, Inner Mongolia (China). Based on the data on ribosomal phylogeny, they were identified as members of the genus Halomonas. These bacteria were moderate alkaliphiles and extreme halophiles. The peptidases secreted by these bacteria were shown to have narrow substrate specificity. They hydrolyzed proteins and para-nitroanilide substrates and showed maximal activity in the hydrolysis of L-leucyl-p-nitroanilides (LpNA). The maximum activity of the peptidases occurred at alkaline pH values (8–10) and elevated salinity (50–100 g/L); the enzymes were thermostable (up to 50°С). The results of inhibitor analysis and substrate specificity examination of extracellular enzymes indicated them to belong to the class of aminopeptidase-like metallopeptidases.     

Instructions for authors

Although Helicobacter pylori infects 50% of the total human population, only a small fraction of the infected people suffer from severe diseases like peptic ulcers and gastric adenocarcinoma. H. pylori strains, host genotypes and environmental factors play important role in deciding the extent and severity of the gastroduodenal diseases. The bacteria has developed a unique set of virulence factors to survive in the extreme ecological niche of human stomach. Together these virulence factors make H. pylori one of the most successful human pathogenic bacteria colonizing more than half of the human population. Understanding the mechanism of action of the major H. pylori virulence factors will shed light into the molecular basis of its pathogenicity.     

Hyperphagocytic haemocytes in Manduca sexta

We have discovered a new type of haemocyte in the larval stage of the tobacco hornworm moth Manduca sexta that has extreme phagocytic ability; each cell can engulf up to 500 bacteria. This level of phagocytosis may be unprecedented among animal cells. Although these hyperphagocytic cells (HP) only represent about 1% of the circulating haemocytes, they are responsible for sequestering the majority of the bacteria by circulating haemocytes when non-pathogenic, heat-killed Escherichia coli are injected into the haemolymph. Extreme phagocytosis by HP is not limited to Gram-negative bacteria since heat-killed Staphylococcus aureus as well as positively and negatively charged microspheres are also highly phagocytosed. Evidence is presented to show that phagocytosis by HP is involved in the early stages of nodule formation in infected insects. In addition, HP are also present in non-infected insects, characterised by their distinctive spreading morphology, which becomes impaired following hyperphagocytosis of bacteria. This is the first time that a dedicated "professional" phagocytic class of haemocyte has been reported for an invertebrate. The importance of these specialised cell types in the M. sexta immune response and their role in nodule formation is discussed.     

天山北坡家庭牧场复合系统对极端气候的响应过程

在草原牧区,家庭牧场作为取代游牧制度而产生的新生事物,其对极端气候响应过程的研究尚未见报道.以“极端气候敏感性-影响途径-响应方式”为分析框架,基于问卷调查方法,研究了天山北坡山地草原牧民对极端气候的响应过程.结果表明:1)天山北坡1980-2009年冬季雪灾、秋季旱灾风险趋于增大,家庭牧场草料储备不足、畜种结构经济驱动型增加了对极端气候的敏感性;2)旱灾、雪灾是影响家庭牧场的主要极端气候类型,其作用介质为牲畜和草场;3)自适应与外力适应是牧户响应极端气候的2种主要形式,其中购买草料是最主要的响应策略;4)通过Probit模型估计显示,极端气候认知、家庭特征、资产状况与牧户间适应行为选择有显著的关系.研究认为,家庭牧场对极端气候短期响应的反馈过程主要围绕草、畜2因子展开,基于降水波动的周期性,牧户长期响应形成了家庭牧场生产周期.     

Spatio-Temporal Monitoring and Ecological Significance of Retrievable Pelagic Heterotrophic Bacteria in Kongsfjorden,an Arctic Fjord

Kongsfjorden is a glacial fjord in the Arctic that is influenced by both Atlantic and Arctic water masses. In the present report retrievable heterotrophic bacteria isolated from two distinct zones (outer and inner fjord) of Kongsfjorden was studied during summer to fall of 2012. 16S rRNA gene sequences of the retrievable heterotrophic bacteria corresponded to γ-proteobacteria (13 phylotypes), α-proteobacteria (3 phylotypes), Bacteroidetes (4 phylotypes) and Actinobacteria (2 phylotypes). The heterotrophic bacterial community structure was fundamentally different in different months which could be linked to changes in the water masses and/or phytoplankton bloom dynamics. It is hypothesized that monitoring the retrievable heterotrophic bacterial assemblage in the fjord would give valuable insights into the complex ecological role they play under extreme and dynamic conditions.     

1H, 13C,and 15N backbone and side chain resonance assignments of thermophilic Geobacillus kaustophilus cyclophilin-A

Cyclophilins catalyze the reversible peptidyl-prolyl isomerization of their substrates and are present across all kingdoms of life from humans to bacteria. Although numerous biological roles have now been discovered for cyclophilins, their function was initially ascribed to their chaperone-like activity in protein folding where they catalyze the often rate-limiting step of proline isomerization. This chaperone-like activity may be especially important under extreme conditions where cyclophilins are often over expressed, such as in tumors for human cyclophilins (Lee Archiv Pharm Res 33(2): 181–187, 2010), but also in organisms that thrive under extreme conditions, such as theromophilic bacteria. Moreover, the reversible nature of the peptidyl-prolyl isomerization reaction catalyzed by cyclophilins has allowed these enzymes to serve as model systems for probing the role of conformational changes during catalytic turnover (Eisenmesser et al. Science 295(5559): 1520–1523, 2002; Eisenmesser et al. Nature 438(7064): 117–121, 2005). Thus, we present here the resonance assignments of a thermophilic cyclophilin from Geobacillus kaustophilus derived from deep-sea sediment (Takami et al. Extremophiles 8(5): 351–356, 2004). This thermophilic cyclophilin may now be studied at a variety of temperatures to provide insight into the comparative structure, dynamics, and catalytic mechanism of cyclophilins.     

Diversity of Heterotrophic Halophilic Bacteria Isolated from Coastal Solar Salterns,Bulgaria and Their Ability to Synthesize Bioactive Molecules with Biotechnological Impact

Investigations on the microbial life in several coastal solar salterns have revealed the presence of novel organisms and synthesis of unusual molecules active in extreme conditions which might be useful in different biotechnological industries. Biodiversity of heterotrophic aerobic bacteria isolated from two salterns, Pomorie salterns and Burgas salterns located at Burgas Bay, Black Sea coast, Bulgaria, as well as ability of the isolates to synthesize biotechnologically valuable compounds were investigated. The results revealed high taxonomic and metabolic bacterial diversity—we isolated 20 morphologically different moderately halophilic and two halotolerant strains affiliated with 11 species from eight genera referred to the phyla Proteobacteria, Firmicutes, and Actinobacteria. Gram-negative bacteria belonged to the genera Halomonas, Chromohalobacter, Salinivibrio, Cobetia, and Nesiotobacter, and gram-positive strains were representatives of the genera Virgibacillus, Salinicoccus, and Brevibacterium. All isolates were found to be alkalitolerant, and 41% of them were psychrotolerant. The strains degraded nine of the tested 18 substrates; polygalacturonase, catalase, phytase, and lipase producers were predominant. This is the first reported detection of xanthan lyase, gellan lyase, arabinase, and phytase activities in halophilic bacteria. Nine of the strains belonging to five different genera were found to produce exopolysaccharides (EPS). The highest level of EPS was observed in Chromohalobacter canadensis strain 28. More than a half of the strains displayed antimicrobial activity against one to five test bacteria and yeasts. The present study is the first report on halophilic bacteria isolated from salterns at the Black Sea coast indicating that the investigated area is an untapped resource of halophilic bacteria with biotechnological potential.     

Culturability and Secondary Metabolite Diversity of Extreme Microbes: Expanding Contribution of Deep Sea and Deep-Sea Vent Microbes to Natural Product Discovery

Microbes from extreme environments do not necessarily require extreme culture conditions. Perhaps the most extreme environments known, deep-sea hydrothermal vent sites, support an incredible array of archaea, bacteria, and fungi, many of which have now been cultured. Microbes cultured from extreme environments have not disappointed in the natural products arena; diverse bioactive secondary metabolites have been isolated from cultured extreme-tolerant microbes, extremophiles, and deep-sea microbes. The contribution of vent microbes to our arsenal of natural products will likely grow, given the culturability of vent microbes; their metabolic, physiologic, and phylogenetic diversity; numerous reports of bioactive natural products from microbes inhabiting high acid, high temperature, or high pressure environments; and the recent isolation of new chroman derivatives and siderophores from deep-sea hydrothermal vent bacteria.     

Participation of mobile elements in formation of properties of pathogenic bacteria]

Published reports about structural organization of genes coding for pathogenicity factors are reviewed. Many of such genes are often united into "virulence blocks" or "pathogenicity islands" and are surrounded by mobile genetic elements, promoting their transposition between related bacteria genomes and leading to changes in virulence in the course of evolution. Data on the similarity of nucleotide sequences of virulence genes in different bacteria are presented, despite differences in their localization in the relevant genomes. The role of rRNA genes in dissemination of virulence genes among different bacteria during transduction or conjugation is shown.     

Role of the extracellular polymer matrix in resistance of bacterial biofilms to extreme environmental factors

Biofilms of a number of gram-positive and gram-negative bacteria (both environmental strains from the stratal waters of oil fields and collection strains) were found to exhibit higher resistance to extreme physicochemical factors (unfavorable temperature, pH, and salt concentration) than planktonic cultures. The extracellular polymers forming the structure of the biofilm matrix were shown to contribute significantly to this resistance, since suppression of matrix formation by subbacteriostatic concentrations of azithromycin (for Pseudomonas acephalitica) or mutation in the cvil gene encoding N-hexanoyl homoserine lactone synthetase (for Chromobacterium violaceum CV026) resulted in the resistance of biofilms being decreased almost to the level of planktonic cultures. The role of the biofilm matrix for bacterial survival under extreme conditions is discussed.     

Non-iron metalloporphyrins: potent antibacterial compounds that exploit haem/Hb uptake systems of pathogenic bacteria

A new group of potent antibacterial compounds, non-iron metalloporphyrins (MPs), is described. MPs possess a strong antibacterial activity against Gram-positive bacteria, Gram-negative bacteria and mycobacteria. Anaerobically grown bacteria and microorganisms that do not respire and/or express haem uptake systems were resistant to MPs. Antibacterial activity of MPs was not affected by known antibiotic resistance mechanisms operating in bacteria. The most potent MP against Y. enterocolitica, methicillin-resistant S. aureus and M. smegmatis was gallium protoporphyrin IX (Ga-PPIX). When tested alone, Ga ions and metal-free porphyrins had approximately 100-fold higher minimum inhibitory concentration (MIC) values for these organisms. Ga-PPIX was not degraded by MP-sensitive bacteria, indicating that the whole molecule is responsible for antibacterial activity. MPs are antibacterial 'Trojan horses', as they exploit haem transport systems of Gram-negative bacteria as portals of entry into the cell. Bacterial mutants in superoxide dismutases, catalases and stationary-phase sigma factors were hypersensitive to Ga-PPIX. The extreme sensitivity of sod mutants to MPs and the requirement for active respiration for MP activity suggests that these compounds stimulate the production of reactive oxygen radicals in bacteria. Ga-PPIX was not toxic to primary human fibroblasts, several established cell lines and experimental animals at concentrations > 100-fold higher than the MIC for sensitive bacteria.     

Life at extreme elevations on Atacama volcanoes: the closest thing to Mars on Earth?

Here we describe recent breakthroughs in our understanding of microbial life in dry volcanic tephra (“soil”) that covers much of the surface area of the highest elevation volcanoes on Earth. Dry tephra above 6000 m.a.s.l. is perhaps the best Earth analog for the surface of Mars because these “soils” are acidic, extremely oligotrophic, exposed to a thin atmosphere, high UV fluxes, and extreme temperature fluctuations across the freezing point. The simple microbial communities found in these extreme sites have among the lowest alpha diversity of any known earthly ecosystem and contain bacteria and eukaryotes that are uniquely adapted to these extreme conditions. The most abundant eukaryotic organism across the highest elevation sites is a Naganishia species that is metabolically versatile, can withstand high levels of UV radiation and can grow at sub-zero temperatures, and during extreme diurnal freeze–thaw cycles (e.g. ??10 to +?30 °C). The most abundant bacterial phylotype at the highest dry sites sampled (6330 m.a.s.l. on Volcán Llullaillaco) belongs to the enigmatic B12-WMSP1 clade which is related to the Ktedonobacter/Thermosporothrix clade that includes versatile organisms with the largest known bacterial genomes. Close relatives of B12-WMSP1 are also found in fumarolic soils on Volcán Socompa and in oligotrophic, fumarolic caves on Mt. Erebus in Antarctica. In contrast to the extremely low diversity of dry tephra, fumaroles found at over 6000 m.a.s.l. on Volcán Socompa support very diverse microbial communities with alpha diversity levels rivalling those of low elevation temperate soils. Overall, the high-elevation biome of the Atacama region provides perhaps the best “natural experiment” in which to study microbial life in both its most extreme setting (dry tephra) and in one of its least extreme settings (fumarolic soils).     

Collagen-like sequences encoded by extremophilic and extremotolerant bacteria

Collagens and collagen-like proteins are found in a wide range of organisms. The common feature of these proteins is a triple helix fold, requiring a characteristic pattern of amino acid sequences, composed of Gly-X-Y tripeptide repeats. Collagen-like proteins from bacteria are heterogeneous in terms of length and amino acid composition of their collagenous sequences. However, different bacteria live in different environments, some at extreme temperatures and conditions. This study explores the occurrence of collagen-like sequences in the genomes of different extreme condition-adapted bacteria, and investigates features that could be linked to conditions where they thrive. Our results show that proteins containing collagen-like sequences are encoded by genomes of various extremophiles. Some of these proteins contain conservative domains, characteristic of cell or endospore surface proteins, while most other proteins are unknown. The characteristics of collagenous sequences may depend on both, the phylogenetic relationship and the living conditions of the bacteria.     

Metabolism in bacteria at low temperature: A recent report

The adaptability of bacteria to extreme cold environments has been demonstrated from time to time by various investigators. Metabolic activity of bacteria at subzero temperatures is also evidenced. Recent studies indicate that bacteria continue both catabolic and anabolic activities at subzero temperatures. Implications of these findings are discussed.     

Characteristics of the heterotrophic bacterial populations in hypersaline environments of different salt concentrations

Solar salterns, based on a multi-pond system, give a discontinuous gradient of salt concentrations. The heterotrophic bacterial populations of ponds containing from 10% salt to saturation have been studied. Saltern samples were spread on agar plates containing different media for halophilic bacteria and one medium made with water of the pond plus nutrients. Replica plating was done to determine the salt range for growth of the colonies. We studied 150 strains to determine the salt spectra of growth, the morphology, and nutrient requirements. The following conclusions were reached: (a) In salt concentrations above 10% (total salts), most bacteria are halophilic and few are halotolerant; (b) the two types of halophilic bacteria, moderate and extreme, show different distributions; in these ponds a narrow overlap exists between 25% and 32% salts with moderate halophiles predominating below this interval and extreme halophiles above it; (c) the populations of moderate halophiles are highly heterogeneous, and the salt concentration of their habitat affects their taxonomic composition, salt range for growth, and nutrient requirements. The population composition of extreme halophiles is less affected by the salt concentrations at which these bacteria are found.     

<Emphasis Type="Italic">Micrococcus luteus</Emphasis> - Survival in Amber

A growing body of evidence now supports the isolation of microorganisms from ancient materials. However, questions about the stringency of extraction methods and the genetic relatedness of isolated organisms to their closest living relatives continue to challenge the authenticity of these ancient life forms. Previous studies have successfully isolated a number of spore-forming bacteria from organic and inorganic deposits of considerable age whose survival is explained by their ability to enter suspended animation for extended periods of time. However, despite a number of putative reports, the isolation of non-spore-forming bacteria and an explanation for their survival have remained enigmatic. Here we describe the isolation of non-spore-forming cocci from a 120-million-year-old block of amber, which by genetic, morphological, and biochemical analyses are identified as belonging to the bacterial species Micrococcus luteus. Although comparison of 16S rRNA sequences from the ancient isolates with their modern counterparts is unable to confirm the precise age of these bacteria, we demonstrate, using complementary molecular and cell biological techniques, evidence supporting the view that these (and related modern members of the genus) have numerous adaptations for survival in extreme, nutrient-poor environments, traits that will assist in this bacterias persistence and dispersal in the environment. The bacterias ability to utilize succinic acid and process terpine-related compounds, both major components of natural amber, support its survival in this oligotrophic environment.