| acpi, a novel isoschizomer of asuii from acidiphilium cryptum 25h, recognizes the sequence 5'tt decreases cgaa3'. | | 1991 | 1956800 |
| phylogenetic analysis of the genera thiobacillus and thiomicrospira by 5s rrna sequences. | 5s rrna nucleotide sequences from thiobacillus neapolitanus, thiobacillus ferrooxidans, thiobacillus thiooxidans, thiobacillus intermedius, thiobacillus perometabolis, thiobacillus thioparus, thiobacillus versutus, thiobacillus novellus, thiobacillus acidophilus, thiomicrospira pelophila, thiomicrospira sp. strain l-12, and acidiphilium cryptum were determined. a phylogenetic tree, based upon comparison of these and other related 5s rrna sequences, is presented. the results place the thiobacilli ... | 1985 | 3924899 |
| cultural and phylogenetic analysis of mixed microbial populations found in natural and commercial bioleaching environments. | a range of autotrophic and heterotrophic enrichment cultures were established to determine the cultural bacterial diversity present in samples obtained from the acidic runoff of a chalcocite overburden heap and from laboratory-scale (1- to 4-liter) batch and continuous bioreactors which were being used for the commercial assessment of the bioleachability of zinc sulfide ore concentrates. strains identified as thiobacillus ferrooxidans, thiobacillus thiooxidans, "leptospirillum ferrooxidans," and ... | 1994 | 7517131 |
| transfer and expression of degradative and antibiotic resistance plasmids in acidophilic bacteria. | the genetic accessibility of selected acidophilic bacteria was investigated to evaluate their applicability to degrading pollutants in acidic environments. the incp1 antibiotic resistance plasmids rp4 and pvk101 and the phenol degradation-encoding plasmid ppgh11 were transferred from neutrophilic bacteria into the extreme acidophilic eubacterium acidiphilium cryptum at frequencies of 1.8 x 10(-2) to 9.8 x 10(-4) transconjugants per recipient cell. the incq antibiotic resistance plasmid psup106 w ... | 1994 | 8161188 |
| biodegradation of aromatic hydrocarbons in an extremely acidic environment | the potential for biodegradation of aromatic hydrocarbons was evaluated in soil samples recovered along gradients of both contaminant levels and ph values existing downstream of a long-term coal pile storage basin. ph values for areas greatly impacted by runoff from the storage basin were 2.0. even at such a reduced ph, the indigenous microbial community was metabolically active, showing the ability to oxidize more than 40% of the parent hydrocarbons, naphthalene and toluene, to carbon dioxide a ... | 1998 | 9797263 |
| leaching of pyrite by acidophilic heterotrophic iron-oxidizing bacteria in pure and mixed cultures. | seven strains of heterotrophic iron-oxidizing acidophilic bacteria were examined to determine their abilities to promote oxidative dissolution of pyrite (fes2) when they were grown in pure cultures and in mixed cultures with sulfur-oxidizing thiobacillus spp. only one of the isolates (strain t-24) oxidized pyrite when it was grown in pyrite-basal salts medium. however, when pyrite-containing cultures were supplemented with 0.02% (wt/vol) yeast extract, most of the isolates oxidized pyrite, and o ... | 1999 | 9925586 |
| microbial reduction of fe(iii) in acidic sediments: isolation of acidiphilium cryptum jf-5 capable of coupling the reduction of fe(iii) to the oxidation of glucose. | to evaluate the microbial populations involved in the reduction of fe(iii) in an acidic, iron-rich sediment, the anaerobic flow of supplemental carbon and reductant was evaluated in sediment microcosms at the in situ temperature of 12 degrees c. supplemental glucose and cellobiose stimulated the formation of fe(ii); 42 and 21% of the reducing equivalents that were theoretically obtained from glucose and cellobiose, respectively, were recovered in fe(ii). likewise, supplemental h(2) was consumed ... | 1999 | 10427060 |
| bacterial primary colonization and early succession on surfaces in marine waters as determined by amplified rrna gene restriction analysis and sequence analysis of 16s rrna genes. | the nearly universal colonization of surfaces in marine waters by bacteria and the formation of biofilms and biofouling communities have important implications for ecological function and industrial processes. however, the dynamics of surface attachment and colonization in situ, particularly during the early stages of biofilm establishment, are not well understood. experimental surfaces that differed in their degrees of hydrophilicity or hydrophobicity were incubated in a salt marsh estuary tida ... | 2000 | 10653705 |
| evaluation of a fluorescent lectin-based staining technique for some acidophilic mining bacteria. | a fluorescence-labeled wheat germ agglutinin staining technique (r. k. sizemore et al., appl. environ. microbiol. 56:2245-2247, 1990) was modified and found to be effective for staining gram-positive, acidophilic mining bacteria. bacteria identified by others as being gram positive through 16s rrna sequence analyses, yet clustering near the divergence of that group, stained weakly. gram-negative bacteria did not stain. background staining of environmental samples was negligible, and pyrite and s ... | 2000 | 10788401 |
| development and application of small-subunit rrna probes for assessment of selected thiobacillus species and members of the genus acidiphilium. | culture-dependent studies have implicated sulfur-oxidizing bacteria as the causative agents of acid mine drainage and concrete corrosion in sewers. thiobacillus species are considered the major representatives of the acid-producing bacteria in these environments. small-subunit rrna genes from all of the thiobacillus and acidiphilium species catalogued by the ribosomal database project were identified and used to design oligonucleotide dna probes. two oligonucleotide probes were synthesized to co ... | 2000 | 10877807 |
| enzymatic manganese(ii) oxidation by a marine alpha-proteobacterium. | a yellow-pigmented marine bacterium, designated strain sd-21, was isolated from surface sediments of san diego bay, san diego, calif., based on its ability to oxidize soluble mn(ii) to insoluble mn(iii, iv) oxides. 16s rrna analysis revealed that this organism was most closely related to members of the genus erythrobacter, aerobic anoxygenic phototrophic bacteria within the alpha-4 subgroup of the proteobacteria (alpha-4 proteobacteria). sd-21, however, has a number of distinguishing phenotypic ... | 2001 | 11526000 |
| microbial ecology of an extreme acidic environment, the tinto river. | the tinto river (huelva, southwestern spain) is an extreme environment with a rather constant acidic ph along the entire river and a high concentration of heavy metals. the extreme conditions of the tinto ecosystem are generated by the metabolic activity of chemolithotrophic microorganisms thriving in the rich complex sulfides of the iberian pyrite belt. molecular ecology techniques were used to analyze the diversity of this microbial community. the community's composition was studied by denatur ... | 2003 | 12902280 |
| novel primers reveal wider diversity among marine aerobic anoxygenic phototrophs. | aerobic anoxygenic phototrophic bacteria (aanps) were previously proposed to account for up to 11% of marine bacterioplankton and to potentially have great ecological importance in the world's oceans. our data show that previously used primers based on the m subunit of anoxygenic photosynthetic reaction center genes (pufm) do not comprehensively identify the diversity of aanps in the ocean. we have designed and tested a new set of pufm-specific primers and revealed several new aanp variants in e ... | 2005 | 16332899 |
| glucose catabolism in strains of acidophilic, heterotrophic bacteria. | pathways of glucose catabolism, potentially operational in six strains of obligately aerobic, acidophilic bacteria, including acidiphilium cryptum strain lhet2, were investigated by short-term radiorespirometry and enzyme assays. short-term radiorespirometry was conducted at ph 3.0 with specifically labeled [c]glucose. the high rate and yield of c-1 oxidized to co(2) indicated that the entner-doudoroff, pentose phosphate, or both pathways were operational in all strains. apparent nonequivalent y ... | 1985 | 16346876 |
| macroscopic streamer growths in acidic, metal-rich mine waters in north wales consist of novel and remarkably simple bacterial communities. | the microbial composition of acid streamers (macroscopic biofilms) in acidic, metal-rich waters in two locations (an abandoned copper mine and a chalybeate spa) in north wales was studied using cultivation-based and biomolecular techniques. known chemolithotrophic and heterotrophic acidophiles were readily isolated from disrupted streamers, but they accounted for only <1 to 7% of the total microorganisms present. fluorescent in situ hybridization (fish) revealed that 80 to 90% of the microbes in ... | 2006 | 16517651 |
| x-ray crystallographic analysis of the sulfur carrier protein soxy from chlorobium limicola f. thiosulfatophilum reveals a tetrameric structure. | dissimilatory oxidation of thiosulfate in the green sulfur bacterium chlorobium limicola f. thiosulfatophilum is carried out by the ubiquitous sulfur-oxidizing (sox) multi-enzyme system. in this system, soxy plays a key role, functioning as the sulfur substrate-binding protein that offers its sulfur substrate, which is covalently bound to a conserved c-terminal cysteine, to another oxidizing sox enzyme. here, we report the crystal structures of a stand-alone soxy protein of c. limicola f. thiosu ... | 2007 | 17327392 |
| heterologous expression and identification of the genes involved in anaerobic degradation of 1,3-dihydroxybenzene (resorcinol) in azoarcus anaerobius. | azoarcus anaerobius, a strictly anaerobic, gram-negative bacterium, utilizes resorcinol as a sole carbon and energy source with nitrate as an electron acceptor. previously, we showed that resorcinol degradation by this bacterium is initiated by two oxidative steps, both catalyzed by membrane-associated enzymes that lead to the formation of hydroxyhydroquinone (hhq; 1,2,4-benzenetriol) and 2-hydroxy-1,4-benzoquinone (hbq). this study presents evidence for the further degradation of hbq in cell ex ... | 2007 | 17369298 |
| phylogenomics and signature proteins for the alpha proteobacteria and its main groups. | alpha proteobacteria are one of the largest and most extensively studied groups within bacteria. however, for these bacteria as a whole and for all of its major subgroups (viz. rhizobiales, rhodobacterales, rhodospirillales, rickettsiales, sphingomonadales and caulobacterales), very few or no distinctive molecular or biochemical characteristics are known. | 2007 | 18045498 |
| ph gradient-induced heterogeneity of fe(iii)-reducing microorganisms in coal mining-associated lake sediments. | lakes formed because of coal mining are characterized by low ph and high concentrations of fe(ii) and sulfate. the anoxic sediment is often separated into an upper acidic zone (ph 3; zone i) with large amounts of reactive iron and a deeper slightly acidic zone (ph 5.5; zone iii) with smaller amounts of iron. in this study, the impact of ph on the fe(iii)-reducing activities in both of these sediment zones was investigated, and molecular analyses that elucidated the sediment microbial diversity w ... | 2008 | 18083864 |
| ph gradient-induced heterogeneity of fe(iii)-reducing microorganisms in coal mining-associated lake sediments. | lakes formed because of coal mining are characterized by low ph and high concentrations of fe(ii) and sulfate. the anoxic sediment is often separated into an upper acidic zone (ph 3; zone i) with large amounts of reactive iron and a deeper slightly acidic zone (ph 5.5; zone iii) with smaller amounts of iron. in this study, the impact of ph on the fe(iii)-reducing activities in both of these sediment zones was investigated, and molecular analyses that elucidated the sediment microbial diversity w ... | 2008 | 18083864 |
| a new iron-oxidizing/o2-reducing supercomplex spanning both inner and outer membranes, isolated from the extreme acidophile acidithiobacillus ferrooxidans. | the iron respiratory chain of the acidophilic bacterium acidithiobacillus ferrooxidans involves various metalloenzymes. here we demonstrate that the oxygen reduction pathway from ferrous iron (named downhill pathway) is organized as a supercomplex constituted of proteins located in the outer and inner membranes as well as in the periplasm. for the first time, the outer membrane-bound cytochrome c cyc2 was purified, and we showed that it is responsible for iron oxidation and determined that its r ... | 2008 | 18632666 |
| microbial iron management mechanisms in extremely acidic environments: comparative genomics evidence for diversity and versatility. | iron is an essential nutrient but can be toxic at high intracellular concentrations and organisms have evolved tightly regulated mechanisms for iron uptake and homeostasis. information on iron management mechanisms is available for organisms living at circumneutral ph. however, very little is known about how acidophilic bacteria, especially those used for industrial copper bioleaching, cope with environmental iron loads that can be 1018 times the concentration found in ph neutral environments. t ... | 2008 | 19025650 |
| improved prediction of malaria degradomes by supervised learning with svm and profile kernel. | the spread of drug resistance through malaria parasite populations calls for the development of new therapeutic strategies. however, the seemingly promising genomics-driven target identification paradigm is hampered by the weak annotation coverage. to identify potentially important yet uncharacterized proteins, we apply support vector machines using profile kernels, a supervised discriminative machine learning technique for remote homology detection, as a complement to the traditional alignment ... | 2009 | 19057851 |
| improved prediction of malaria degradomes by supervised learning with svm and profile kernel. | the spread of drug resistance through malaria parasite populations calls for the development of new therapeutic strategies. however, the seemingly promising genomics-driven target identification paradigm is hampered by the weak annotation coverage. to identify potentially important yet uncharacterized proteins, we apply support vector machines using profile kernels, a supervised discriminative machine learning technique for remote homology detection, as a complement to the traditional alignment ... | 2009 | 19057851 |
| functional mapping of brucella abortus cyclic beta-1,2-glucan synthase: identification of the protein domain required for cyclization. | cyclic beta-1,2-glucans (cbetag) are periplasmic homopolysaccharides that have been shown to play an important role in several symbiotic and pathogenic relationships. cyclic beta-1,2-glucan synthase (cgs), the enzyme responsible for the synthesis of cbetag, is an integral membrane polyfunctional protein that catalyzes the four enzymatic activities (initiation, elongation, phosphorolysis, and cyclization) required for the synthesis of cbetag. recently, we have identified the glycosyltransferase a ... | 2009 | 19074375 |
| functional mapping of brucella abortus cyclic beta-1,2-glucan synthase: identification of the protein domain required for cyclization. | cyclic beta-1,2-glucans (cbetag) are periplasmic homopolysaccharides that have been shown to play an important role in several symbiotic and pathogenic relationships. cyclic beta-1,2-glucan synthase (cgs), the enzyme responsible for the synthesis of cbetag, is an integral membrane polyfunctional protein that catalyzes the four enzymatic activities (initiation, elongation, phosphorolysis, and cyclization) required for the synthesis of cbetag. recently, we have identified the glycosyltransferase a ... | 2009 | 19074375 |
| conservation and variability of west nile virus proteins. | west nile virus (wnv) has emerged globally as an increasingly important pathogen for humans and domestic animals. studies of the evolutionary diversity of the virus over its known history will help to elucidate conserved sites, and characterize their correspondence to other pathogens and their relevance to the immune system. we describe a large-scale analysis of the entire wnv proteome, aimed at identifying and characterizing evolutionarily conserved amino acid sequences. this study, which used ... | 2009 | 19401763 |
| whole-genome analyses reveal genetic instability of acetobacter pasteurianus. | acetobacter species have been used for brewing traditional vinegar and are known to have genetic instability. to clarify the mutability, acetobacter pasteurianus nbrc 3283, which forms a multi-phenotype cell complex, was subjected to genome dna sequencing. the genome analysis revealed that there are more than 280 transposons and five genes with hyper-mutable tandem repeats as common features in the genome consisting of a 2.9-mb chromosome and six plasmids. there were three single nucleotide muta ... | 2009 | 19638423 |
| identification of functional lsrb-like autoinducer-2 receptors. | although a variety of bacterial species have been reported to use the interspecies communication signal autoinducer-2 (ai-2) to regulate multiple behaviors, the molecular mechanisms of ai-2 recognition and signal transduction remain poorly understood. to date, two types of ai-2 receptors have been identified: luxp, present in vibrio spp., and lsrb, first identified in salmonella enterica serovar typhimurium. in s. typhimurium, lsrb is the ligand binding protein of a transport system that enables ... | 2009 | 19749048 |
| complete genome sequence of the sugarcane nitrogen-fixing endophyte gluconacetobacter diazotrophicus pal5. | gluconacetobacter diazotrophicus pal5 is an endophytic diazotrophic bacterium that lives in association with sugarcane plants. it has important biotechnological features such as nitrogen fixation, plant growth promotion, sugar metabolism pathways, secretion of organic acids, synthesis of auxin and the occurrence of bacteriocins. | 2009 | 19775431 |
| are algal genes in nonphotosynthetic protists evidence of historical plastid endosymbioses? | how photosynthetic organelles, or plastids, were acquired by diverse eukaryotes is among the most hotly debated topics in broad scale eukaryotic evolution. the history of plastid endosymbioses commonly is interpreted under the "chromalveolate" hypothesis, which requires numerous plastid losses from certain heterotrophic groups that now are entirely aplastidic. in this context, discoveries of putatively algal genes in plastid-lacking protists have been cited as evidence of gene transfer from a ph ... | 2009 | 19843329 |
| a type vi secretion system effector protein, vgrg1, from aeromonas hydrophila that induces host cell toxicity by adp ribosylation of actin. | we recently delineated the importance of a type vi secretion system (t6ss) gene cluster in the virulence of diarrheal isolate ssu of aeromonas hydrophila and showed that vash, a sigma(54) activator and t6ss component, was involved in the production of its associated effectors, e.g., hemolysin-coregulated protein. to identify additional t6ss effectors and/or secreted proteins, we subjected culture supernatants from deletion mutants of a. hydrophila, namely, a delta act mutant (a t2ss-associated c ... | 2010 | 19880608 |
| a type vi secretion system effector protein, vgrg1, from aeromonas hydrophila that induces host cell toxicity by adp ribosylation of actin. | we recently delineated the importance of a type vi secretion system (t6ss) gene cluster in the virulence of diarrheal isolate ssu of aeromonas hydrophila and showed that vash, a sigma(54) activator and t6ss component, was involved in the production of its associated effectors, e.g., hemolysin-coregulated protein. to identify additional t6ss effectors and/or secreted proteins, we subjected culture supernatants from deletion mutants of a. hydrophila, namely, a delta act mutant (a t2ss-associated c ... | 2010 | 19880608 |
| cohesion group approach for evolutionary analysis of aspartokinase, an enzyme that feeds a branched network of many biochemical pathways. | aspartokinase (ask) exists within a variable network that supports the synthesis of 9 amino acids and a number of other important metabolites. lysine, isoleucine, aromatic amino acids, and dipicolinate may arise from the ask network or from alternative pathways. ask proteins were subjected to cohesion group analysis, a methodology that sorts a given protein assemblage into groups in which evolutionary continuity is assured. two subhomology divisions, ask(alpha) and ask(beta), have been recognize ... | 2009 | 19946135 |
| magnetospirillum bellicus sp. nov., a novel dissimilatory perchlorate-reducing alphaproteobacterium isolated from a bioelectrical reactor. | previously isolated dissimilatory perchlorate-reducing bacteria (dprb) have been primarily affiliated with the betaproteobacteria. enrichments from the cathodic chamber of a bioelectrical reactor (ber) inoculated from creek water in berkeley, ca, yielded a novel organism most closely related to a previously described strain, wd (99% 16s rrna gene identity). strain vdy(t) has 96% 16s rrna gene identity to both magnetospirillum gryphiswaldense and magnetospirillum magnetotacticum, and along with s ... | 2010 | 20495050 |
| ecophysiology of fe-cycling bacteria in acidic sediments. | using a combination of cultivation-dependent and -independent methods, this study aimed to elucidate the diversity of microorganisms involved in iron cycling and to resolve their in situ functional links in sediments of an acidic lignite mine lake. using six different media with ph values ranging from 2.5 to 4.3, 117 isolates were obtained that grouped into 38 different strains, including 27 putative new species with respect to the closest characterized strains. among the isolated strains, 22 st ... | 2010 | 20971876 |
| novel pan-genomic analysis approach in target selection for multiplex pcr identification and detection of burkholderia pseudomallei, burkholderia thailandensis, and burkholderia cepacia complex species: a proof-of-concept study. | burkholderia pseudomallei, burkholderia thailandensis, and the burkholderia cepacia complex differ greatly in pathogenicity and epidemiology. yet, they are occasionally misidentified by biochemical profiling, and even 16s rrna gene sequencing may not offer adequate discrimination between certain species groups. using the 23 b. pseudomallei, four b. thailandensis, and 16 b. cepacia complex genome sequences available, we identified gene targets specific to each of them (a tat domain protein, a 70- ... | 2010 | 21177905 |
| cellular tropism, population dynamics, host range and taxonomic status of an aphid secondary symbiont, smls (sitobion miscanthi l type symbiont). | smls (sitobion miscanthi l type symbiont) is a newly reported aphid secondary symbiont. phylogenetic evidence from molecular markers indicates that smls belongs to the rickettsiaceae and has a sibling relationship with orientia tsutsugamushi. a comparative analysis of coxa nucleotide sequences further supports recognition of smls as a new genus in the rickettsiaceae. in situ hybridization reveals that smls is housed in both sheath cells and secondary bacteriocytes and it is also detected in aphi ... | 2011 | 21789197 |
| microbial diversity in anaerobic sediments at rio tinto, a naturally acidic environment with a high heavy metal content. | the tinto river is an extreme environment located at the core of the iberian pyritic belt (ipb). it is an unusual ecosystem due to its size (100 km long), constant acidic ph (mean ph, 2.3), and high concentration of heavy metals, iron, and sulfate in its waters, characteristics that make the tinto river basin comparable to acidic mine drainage (amd) systems. in this paper we present an extensive survey of the tinto river sediment microbiota using two culture-independent approaches: denaturing gr ... | 2011 | 21724883 |
| sequence of the hyperplastic genome of the naturally competent thermus scotoductus sa-01. | many strains of thermus have been isolated from hot environments around the world. thermus scotoductus sa-01 was isolated from fissure water collected 3.2 km below surface in a south african gold mine. the isolate is capable of dissimilatory iron reduction, growth with oxygen and nitrate as terminal electron acceptors and the ability to reduce a variety of metal ions, including gold, chromate and uranium, was demonstrated. the genomes from two different thermus thermophilus strains have been com ... | 2011 | 22115438 |
| the rhizome of reclinomonas americana, homo sapiens, pediculus humanus and saccharomyces cerevisiae mitochondria. | mitochondria are thought to have evolved from eubacteria-like endosymbionts; however, the origin of the mitochondrion remains a subject of debate. in this study, we investigated the phenomenon of chimerism in mitochondria to shed light on the origin of these organelles by determining which species played a role in their formation. we used the mitochondria of four distinct organisms, reclinomonas americana, homo sapiens, saccharomyces cerevisiae and multichromosome pediculus humanus, and attempte ... | 2011 | 22014084 |
| Is the sequence-specific binding of aminoacyl-tRNAs by EF-Tu universal among bacteria? | Three base pairs in the T-stem are primarily responsible for the sequence-specific interaction of tRNA with Escherichia coli and Thermus thermophilus EF-Tu. While the amino acids on the surface of EF-Tu that contact aminoacyl-tRNA (aa-tRNA) are highly conserved among bacteria, the T-stem sequences of individual tRNA are variable, making it unclear whether or not this protein-nucleic acid interaction is also sequence specific in other bacteria. We propose and validate a thermodynamic model that p ... | 2011 | 21893586 |
| biotechnology of polyketides: new breath of life for the novel antibiotic genetic pathways discovery through metagenomics. | the discovery of secondary metabolites produced by microorganisms (e.g., penicillin in 1928) and the beginning of their industrial application (1940) opened new doors to what has been the main medication source for the treatment of infectious diseases and tumors. in fact, approximately 80 years after the discovery of the first antibiotic compound, and despite all of the warnings about the failure of the "goose that laid the golden egg," the potential of this wealth is still inexorable: simply ad ... | 2014 | 24688489 |
| biotechnology of polyketides: new breath of life for the novel antibiotic genetic pathways discovery through metagenomics. | the discovery of secondary metabolites produced by microorganisms (e.g., penicillin in 1928) and the beginning of their industrial application (1940) opened new doors to what has been the main medication source for the treatment of infectious diseases and tumors. in fact, approximately 80 years after the discovery of the first antibiotic compound, and despite all of the warnings about the failure of the "goose that laid the golden egg," the potential of this wealth is still inexorable: simply ad ... | 2014 | 24688489 |
| nickel-resistance determinants in acidiphilium sp. pm identified by genome-wide functional screening. | acidiphilium spp. are conspicuous dwellers of acidic, metal-rich environments. indeed, they are among the most metal-resistant organisms; yet little is known about the mechanisms behind the metal tolerance in this genus. acidiphilium sp. pm is an environmental isolate from rio tinto, an acidic, metal-laden river located in southwestern spain. the characterization of its metal resistance revealed a remarkable ability to tolerate high ni concentrations. here we report the screening of a genomic li ... | 2014 | 24740277 |
| evolution of mitochondria reconstructed from the energy metabolism of living bacteria. | the ancestors of mitochondria, or proto-mitochondria, played a crucial role in the evolution of eukaryotic cells and derived from symbiotic α-proteobacteria which merged with other microorganisms - the basis of the widely accepted endosymbiotic theory. however, the identity and relatives of proto-mitochondria remain elusive. here we show that methylotrophic α-proteobacteria could be the closest living models for mitochondrial ancestors. we reached this conclusion after reconstructing the possibl ... | 2014 | 24804722 |
| unexpected diversity of signal peptides in prokaryotes. | signal peptides are a cornerstone mechanism for cellular protein localization, yet until now experimental determination of signal peptides has come from only a narrow taxonomic sampling. as a result, the dominant view is that sec-cleaved signal peptides in prokaryotes are defined by a canonical axa motif. although other residues are permitted in the motif, alanine is by far the most common. here we broadly examine proteomics data to reveal the signal peptide sequences for 32 bacterial and archae ... | 2012 | 23169999 |
| methods of combinatorial optimization to reveal factors affecting gene length. | in this paper we present a novel method for genome ranking according to gene lengths. the main outcomes described in this paper are the following: the formulation of the genome ranking problem, presentation of relevant approaches to solve it, and the demonstration of preliminary results from prokaryotic genomes ordering. using a subset of prokaryotic genomes, we attempted to uncover factors affecting gene length. we have demonstrated that hyperthermophilic species have shorter genes as compared ... | 2012 | 23300345 |
| lengths of orthologous prokaryotic proteins are affected by evolutionary factors. | proteins of the same functional family (for example, kinases) may have significantly different lengths. it is an open question whether such variation in length is random or it appears as a response to some unknown evolutionary driving factors. the main purpose of this paper is to demonstrate existence of factors affecting prokaryotic gene lengths. we believe that the ranking of genomes according to lengths of their genes, followed by the calculation of coefficients of association between genome ... | 2015 | 26114113 |
| on the molecular mechanism of gc content variation among eubacterial genomes. | as a key parameter of genome sequence variation, the gc content of bacterial genomes has been investigated for over half a century, and many hypotheses have been put forward to explain this gc content variation and its relationship to other fundamental processes. previously, we classified eubacteria into dnae-based groups (the dimeric combination of dna polymerase iii alpha subunits), according to a hypothesis where gc content variation is essentially governed by genome replication and dna repai ... | 2012 | 22230424 |
| cohesion group approach for evolutionary analysis of tyra, a protein family with wide-ranging substrate specificities. | many enzymes and other proteins are difficult subjects for bioinformatic analysis because they exhibit variant catalytic, structural, regulatory, and fusion mode features within a protein family whose sequences are not highly conserved. however, such features reflect dynamic and interesting scenarios of evolutionary importance. the value of experimental data obtained from individual organisms is instantly magnified to the extent that given features of the experimental organism can be projected u ... | 2008 | 18322033 |
| characteristics and adaptability of iron- and sulfur-oxidizing microorganisms used for the recovery of metals from minerals and their concentrates. | microorganisms are used in large-scale heap or tank aeration processes for the commercial extraction of a variety of metals from their ores or concentrates. these include copper, cobalt, gold and, in the past, uranium. the metal solubilization processes are considered to be largely chemical with the microorganisms providing the chemicals and the space (exopolysaccharide layer) where the mineral dissolution reactions occur. temperatures at which these processes are carried out can vary from ambie ... | 2005 | 15877814 |
| bioleaching genomics. | | 2009 | 21261924 |
| distribution of genes encoding nucleoid-associated protein homologs in plasmids. | bacterial nucleoid-associated proteins (naps) form nucleoprotein complexes and influence the expression of genes. recent studies have shown that some plasmids carry genes encoding nap homologs, which play important roles in transcriptional regulation networks between plasmids and host chromosomes. in this study, we determined the distributions of the well-known naps fis, h-ns, hu, ihf, and lrp and the newly found naps mvat and ndpa among the whole-sequenced 1382 plasmids found in gram-negative b ... | 2011 | 21350637 |
| bacterial cellulose biosynthesis: diversity of operons, subunits, products, and functions. | recent studies of bacterial cellulose biosynthesis, including structural characterization of a functional cellulose synthase complex, provided the first mechanistic insight into this fascinating process. in most studied bacteria, just two subunits, bcsa and bcsb, are necessary and sufficient for the formation of the polysaccharide chain in vitro. other subunits - which differ among various taxa - affect the enzymatic activity and product yield in vivo by modulating (i) the expression of the bios ... | 2015 | 26077867 |
| phylogenomic analysis and predicted physiological role of the proton-translocating nadh:quinone oxidoreductase (complex i) across bacteria. | the proton-translocating nadh:quinone oxidoreductase (complex i) is a multisubunit integral membrane enzyme found in the respiratory chains of both bacteria and eukaryotic organelles. although much research has focused on the enzyme's central role in the mitochondrial respiratory chain, comparatively little is known about its role in the diverse energetic lifestyles of different bacteria. here, we used a phylogenomic approach to better understand the distribution of complex i across bacteria, th ... | 2015 | 25873378 |
| genomics against flatulence. | | 2007 | 17635535 |
| a comparison of the caulobacter na1000 and k31 genomes reveals extensive genome rearrangements and differences in metabolic potential. | the genus caulobacter is found in a variety of habitats and is known for its ability to thrive in low-nutrient conditions. k31 is a novel caulobacter isolate that has the ability to tolerate copper and chlorophenols, and can grow at 4 ° c with a doubling time of 40 h. k31 contains a 5.5 mb chromosome that codes for more than 5500 proteins and two large plasmids (234 and 178 kb) that code for 438 additional proteins. a comparison of the k31 and the caulobacter crescentus na1000 genomes revealed e ... | 2014 | 25274120 |
| an evolutionary network of genes present in the eukaryote common ancestor polls genomes on eukaryotic and mitochondrial origin. | to test the predictions of competing and mutually exclusive hypotheses for the origin of eukaryotes, we identified from a sample of 27 sequenced eukaryotic and 994 sequenced prokaryotic genomes 571 genes that were present in the eukaryote common ancestor and that have homologues among eubacterial and archaebacterial genomes. maximum-likelihood trees identified the prokaryotic genomes that most frequently contained genes branching as the sister to the eukaryotic nuclear homologues. among the arch ... | 2012 | 22355196 |
| evolutionary diversification and characterization of the eubacterial gene family encoding dxr type ii, an alternative isoprenoid biosynthetic enzyme. | isoprenoids constitute a vast family of natural compounds performing diverse and essential functions in all domains of life. in most eubacteria, isoprenoids are synthesized through the methylerythritol 4-phosphate (mep) pathway. the production of mep is usually catalyzed by deoxyxylulose 5-phosphate reductoisomerase (dxr-i) but a few organisms use an alternative dxr-like enzyme (dxr-ii). | 2013 | 24004839 |
| origin of an alternative genetic code in the extremely small and gc-rich genome of a bacterial symbiont. | the genetic code relates nucleotide sequence to amino acid sequence and is shared across all organisms, with the rare exceptions of lineages in which one or a few codons have acquired novel assignments. recoding of uga from stop to tryptophan has evolved independently in certain reduced bacterial genomes, including those of the mycoplasmas and some mitochondria. small genomes typically exhibit low guanine plus cytosine (gc) content, and this bias in base composition has been proposed to drive ug ... | 2009 | 19609354 |
| structural and functional insights from the metagenome of an acidic hot spring microbial planktonic community in the colombian andes. | a taxonomic and annotated functional description of microbial life was deduced from 53 mb of metagenomic sequence retrieved from a planktonic fraction of the neotropical high andean (3,973 meters above sea level) acidic hot spring el coquito (ec). a classification of unassembled metagenomic reads using different databases showed a high proportion of gammaproteobacteria and alphaproteobacteria (in total read affiliation), and through taxonomic affiliation of 16s rrna gene fragments we observed th ... | 2012 | 23251687 |
| analysis of the ctra pathway in magnetospirillum reveals an ancestral role in motility in alphaproteobacteria. | developmental events across the prokaryotic life cycle are highly regulated at the transcriptional and posttranslational levels. key elements of a few regulatory networks are conserved among phylogenetic groups of bacteria, although the features controlled by these conserved systems are as diverse as the organisms encoding them. in this work, we probed the role of the ctra regulatory network, conserved throughout the alphaproteobacteria, in the magnetotactic bacterium magnetospirillum magneticum ... | 2012 | 22467786 |
| the twin-arginine translocation pathway in α-proteobacteria is functionally preserved irrespective of genomic and regulatory divergence. | the twin-arginine translocation (tat) pathway exports fully folded proteins out of the cytoplasm of gram-negative and gram-positive bacteria. although much progress has been made in unraveling the molecular mechanism and biochemical characterization of the tat system, little is known concerning its functionality and biological role to confer adaptive skills, symbiosis or pathogenesis in the α-proteobacteria class. a comparative genomic analysis in the α-proteobacteria class confirmed the presenc ... | 2012 | 22438962 |
| phylogenetic analysis of erythritol catabolic loci within the rhizobiales and proteobacteria. | the ability to use erythritol as a sole carbon source is not universal among the rhizobiaceae. based on the relatedness to the catabolic genes in brucella it has been suggested that the eryabcd operon may have been horizontally transferred into rhizobium. during work characterizing a locus necessary for the transport and catabolism of erythritol, adonitol and l-arabitol in sinorhizobium meliloti, we became interested in the differences between the erythritol loci of s. meliloti and r. leguminosa ... | 2013 | 23432981 |
| gene identification and protein classification in microbial metagenomic sequence data via incremental clustering. | the identification and study of proteins from metagenomic datasets can shed light on the roles and interactions of the source organisms in their communities. however, metagenomic datasets are characterized by the presence of organisms with varying gc composition, codon usage biases etc., and consequently gene identification is challenging. the vast amount of sequence data also requires faster protein family classification tools. | 2008 | 18402669 |
| insights into the evolution of sorbitol metabolism: phylogenetic analysis of sdr196c family. | short chain dehydrogenases/reductases (sdr) are nad(p)(h)-dependent oxidoreductases with a highly conserved 3d structure and of an early origin, which has allowed them to diverge into several families and enzymatic activities. the sdr196c family (http://www.sdr-enzymes.org) groups bacterial sorbitol dehydrogenases (sdh), which are of great industrial interest. in this study, we examine the phylogenetic relationship between the members of this family, and based on the findings and some sequence c ... | 2012 | 22899811 |
| proteomic properties reveal phyloecological clusters of archaea. | in this study, we propose a novel way to describe the variety of environmental adaptations of archaea. we have clustered 57 archaea by using a non-redundant set of proteomic features, and verified that the clusters correspond to environmental adaptations to the archaeal habitats. the first cluster consists dominantly of hyperthermophiles and hyperthermoacidophilic aerobes. the second cluster joins together halophilic and extremely halophilic archaea, while the third cluster contains mesophilic ( ... | 2012 | 23133575 |
| the genes and enzymes of phosphonate metabolism by bacteria, and their distribution in the marine environment. | phosphonates are compounds that contain the chemically stable carbon-phosphorus (c-p) bond. they are widely distributed amongst more primitive life forms including many marine invertebrates and constitute a significant component of the dissolved organic phosphorus reservoir in the oceans. virtually all biogenic c-p compounds are synthesized by a pathway in which the key step is the intramolecular rearrangement of phosphoenolpyruvate to phosphonopyruvate. however c-p bond cleavage by degradative ... | 2012 | 22303297 |
| crystal structure of the ectoine hydroxylase, a snapshot of the active site. | ectoine and its derivative 5-hydroxyectoine are compatible solutes that are widely synthesized by bacteria to cope physiologically with osmotic stress. they also serve as chemical chaperones and maintain the functionality of macromolecules. 5-hydroxyectoine is produced from ectoine through a stereo-specific hydroxylation, an enzymatic reaction catalyzed by the ectoine hydroxylase (ectd). the ectd protein is a member of the non-heme-containing iron(ii) and 2-oxoglutarate-dependent dioxygenase sup ... | 2014 | 25172507 |
| complete genome sequence and comparative analysis of acetobacter pasteurianus 386b, a strain well-adapted to the cocoa bean fermentation ecosystem. | acetobacter pasteurianus 386b, an acetic acid bacterium originating from a spontaneous cocoa bean heap fermentation, proved to be an ideal functional starter culture for coca bean fermentations. it is able to dominate the fermentation process, thereby resisting high acetic acid concentrations and temperatures. however, the molecular mechanisms underlying its metabolic capabilities and niche adaptations are unknown. in this study, whole-genome sequencing and comparative genome analysis was used t ... | 2013 | 23902333 |
| ecological roles of dominant and rare prokaryotes in acid mine drainage revealed by metagenomics and metatranscriptomics. | high-throughput sequencing is expanding our knowledge of microbial diversity in the environment. still, understanding the metabolic potentials and ecological roles of rare and uncultured microbes in natural communities remains a major challenge. to this end, we applied a 'divide and conquer' strategy that partitioned a massive metagenomic data set (>100 gbp) into subsets based on k-mer frequency in sequence assembly to a low-diversity acid mine drainage (amd) microbial community and, by integrat ... | 2014 | 25361395 |
| ecological roles of dominant and rare prokaryotes in acid mine drainage revealed by metagenomics and metatranscriptomics. | high-throughput sequencing is expanding our knowledge of microbial diversity in the environment. still, understanding the metabolic potentials and ecological roles of rare and uncultured microbes in natural communities remains a major challenge. to this end, we applied a 'divide and conquer' strategy that partitioned a massive metagenomic data set (>100 gbp) into subsets based on k-mer frequency in sequence assembly to a low-diversity acid mine drainage (amd) microbial community and, by integrat ... | 2014 | 25361395 |
| discovery of a novel (r)-selective bacterial hydroxynitrile lyase from acidobacterium capsulatum. | hydroxynitrile lyases (hnls) are powerful carbon-carbon bond forming enzymes. the reverse of their natural reaction - the stereoselective addition of hydrogen cyanide (hcn) to carbonyls - yields chiral cyanohydrins, versatile building blocks for the pharmaceutical and chemical industry. recently, bacterial hnls have been discovered, which represent a completely new type: hnls with a cupin fold. due to various benefits of cupins (e.g. high yield recombinant expression in escherichia coli), the cl ... | 2014 | 25210600 |
| plasmids of carotenoid-producing paracoccus spp. (alphaproteobacteria) - structure, diversity and evolution. | plasmids are components of many bacterial genomes. they enable the spread of a large pool of genetic information via lateral gene transfer. many bacterial strains contain mega-sized replicons and these are particularly common in alphaproteobacteria. considerably less is known about smaller alphaproteobacterial plasmids. we analyzed the genomes of 14 such plasmids residing in 4 multireplicon carotenoid-producing strains of the genus paracoccus (alphaproteobacteria): p. aestuarii dsm 19484, p. hae ... | 2013 | 24260361 |
| biochemical properties of ectoine hydroxylases from extremophiles and their wider taxonomic distribution among microorganisms. | ectoine and hydroxyectoine are well-recognized members of the compatible solutes and are widely employed by microorganisms as osmostress protectants. the ectabc enzymes catalyze the synthesis of ectoine from the precursor l-aspartate-β-semialdehyde. a subgroup of the ectoine producers can convert ectoine into 5-hydroxyectoine through a region-selective and stereospecific hydroxylation reaction. this compatible solute possesses stress-protective and function-preserving properties different from t ... | 2014 | 24714029 |
| gene loss and horizontal gene transfer contributed to the genome evolution of the extreme acidophile "ferrovum". | acid mine drainage (amd), associated with active and abandoned mining sites, is a habitat for acidophilic microorganisms that gain energy from the oxidation of reduced sulfur compounds and ferrous iron and that thrive at ph below 4. members of the recently proposed genus "ferrovum" are the first acidophilic iron oxidizers to be described within the betaproteobacteria. although they have been detected as typical community members in amd habitats worldwide, knowledge of their phylogenetic and meta ... | 2016 | 27303384 |
| omics on bioleaching: current and future impacts. | bioleaching corresponds to the microbial-catalyzed process of conversion of insoluble metals into soluble forms. as an applied biotechnology globally used, it represents an extremely interesting field of research where omics techniques can be applied in terms of knowledge development, but moreover in terms of process design, control, and optimization. in this mini-review, the current state of genomics, proteomics, and metabolomics of bioleaching and the major impacts of these analytical methods ... | 2015 | 26278538 |
| uncovering a microbial enigma: isolation and characterization of the streamer-generating, iron-oxidizing, acidophilic bacterium "ferrovum myxofaciens". | a betaproteobacterium, shown by molecular techniques to have widespread global distribution in extremely acidic (ph 2 to 4) ferruginous mine waters and also to be a major component of "acid streamer" growths in mine-impacted water bodies, has proven to be recalcitrant to enrichment and isolation. a modified "overlay" solid medium was devised and used to isolate this bacterium from a number of mine water samples. the physiological and phylogenetic characteristics of a pure culture of an isolate f ... | 2014 | 24242243 |
| contemporary environmental variation determines microbial diversity patterns in acid mine drainage. | a wide array of microorganisms survive and thrive in extreme environments. however, we know little about the patterns of, and controls over, their large-scale ecological distribution. to this end, we have applied a bar-coded 16s rrna pyrosequencing technology to explore the phylogenetic differentiation among 59 microbial communities from physically and geochemically diverse acid mine drainage (amd) sites across southeast china, revealing for the first time environmental variation as the major fa ... | 2012 | 23178673 |
| contemporary environmental variation determines microbial diversity patterns in acid mine drainage. | a wide array of microorganisms survive and thrive in extreme environments. however, we know little about the patterns of, and controls over, their large-scale ecological distribution. to this end, we have applied a bar-coded 16s rrna pyrosequencing technology to explore the phylogenetic differentiation among 59 microbial communities from physically and geochemically diverse acid mine drainage (amd) sites across southeast china, revealing for the first time environmental variation as the major fa ... | 2012 | 23178673 |
| draft genome sequence of the electricigen acidiphilium sp. strain pm (dsm 24941). | acidiphilium sp. strain pm (dsm 24941) was isolated from rio tinto's acidic, heavy metal-rich waters. voltammetry experiments revealed that this strain is capable of electricity production even under aerobic conditions. here we report the draft genome sequence of acidiphilium sp. pm and a preliminary genome analysis that reveals a versatile respiratory metabolism. | 2011 | 21914891 |
| complete genome sequence of the extremely acidophilic methanotroph isolate v4, methylacidiphilum infernorum, a representative of the bacterial phylum verrucomicrobia. | the phylum verrucomicrobia is a widespread but poorly characterized bacterial clade. although cultivation-independent approaches detect representatives of this phylum in a wide range of environments, including soils, seawater, hot springs and human gastrointestinal tract, only few have been isolated in pure culture. we have recently reported cultivation and initial characterization of an extremely acidophilic methanotrophic member of the verrucomicrobia, strain v4, isolated from the hell's gate ... | 2008 | 18593465 |
| a specialized citric acid cycle requiring succinyl-coenzyme a (coa):acetate coa-transferase (aarc) confers acetic acid resistance on the acidophile acetobacter aceti. | microbes tailor macromolecules and metabolism to overcome specific environmental challenges. acetic acid bacteria perform the aerobic oxidation of ethanol to acetic acid and are generally resistant to high levels of these two membrane-permeable poisons. the citric acid cycle (cac) is linked to acetic acid resistance in acetobacter aceti by several observations, among them the oxidation of acetate to co2 by highly resistant acetic acid bacteria and the previously unexplained role of a. aceti citr ... | 2008 | 18502856 |
| preferential use of an anode as an electron acceptor by an acidophilic bacterium in the presence of oxygen. | several anaerobic metal-reducing bacteria have been shown to be able to donate electrons directly to an electrode. this property is of great interest for microbial fuel cell development. to date, microbial fuel cell design requires avoiding o(2) diffusion from the cathodic compartment to the sensitive anodic compartment. here, we show that acidiphilium sp. strain 3.2 sup 5 cells that were isolated from an extreme acidic environment are able to colonize graphite felt electrodes. these bacterial e ... | 2008 | 18487393 |
| an ompa family protein, a target of the gini/ginr quorum-sensing system in gluconacetobacter intermedius, controls acetic acid fermentation. | via n-acylhomoserine lactones, the gini/ginr quorum-sensing system in gluconacetobacter intermedius nci1051, a gram-negative acetic acid bacterium, represses acetic acid and gluconic acid fermentation. two-dimensional polyacrylamide gel electrophoretic analysis of protein profiles of strain nci1051 and gini and ginr mutants identified a protein that was produced in response to the gini/ginr regulatory system. cloning and nucleotide sequencing of the gene encoding this protein revealed that it en ... | 2008 | 18487322 |
| phenotypic properties and microbial diversity of methanogenic granules from a full-scale upflow anaerobic sludge bed reactor treating brewery wastewater. | methanogenic granules from an anaerobic bioreactor that treated wastewater of a beer brewery consisted of different morphological types of granules. in this study, the microbial compositions of the different granules were analyzed by molecular microbiological techniques: cloning, denaturing gradient gel electrophoresis and fluorescent in situ hybridization (fish), and scanning and transmission electron microscopy. we propose here that the different types of granules reflect the different stages ... | 2006 | 16820491 |
| analysis of the microbiome: advantages of whole genome shotgun versus 16s amplicon sequencing. | the human microbiome has emerged as a major player in regulating human health and disease. translational studies of the microbiome have the potential to indicate clinical applications such as fecal transplants and probiotics. however, one major issue is accurate identification of microbes constituting the microbiota. studies of the microbiome have frequently utilized sequencing of the conserved 16s ribosomal rna (rrna) gene. we present a comparative study of an alternative approach using whole g ... | 2015 | 26718401 |
| analysis of the microbiome: advantages of whole genome shotgun versus 16s amplicon sequencing. | the human microbiome has emerged as a major player in regulating human health and disease. translational studies of the microbiome have the potential to indicate clinical applications such as fecal transplants and probiotics. however, one major issue is accurate identification of microbes constituting the microbiota. studies of the microbiome have frequently utilized sequencing of the conserved 16s ribosomal rna (rrna) gene. we present a comparative study of an alternative approach using whole g ... | 2015 | 26718401 |
| insights into the structure and metabolic function of microbes that shape pelagic iron-rich aggregates ("iron snow"). | microbial ferrous iron [fe(ii)] oxidation leads to the formation of iron-rich macroscopic aggregates ("iron snow") at the redoxcline in a stratified lignite mine lake in east-central germany. we aimed to identify the abundant fe-oxidizing and fe-reducing microorganisms likely to be involved in the formation and transformation of iron snow present in the redoxcline in two basins of the lake that differ in their ph values. nucleic acid- and lipid-stained microbial cells of various morphologies det ... | 2013 | 23645202 |
| bioleaching of arsenic-rich gold concentrates by bacterial flora before and after mutation. | in order to improve the bioleaching efficiency of arsenic-rich gold concentrates, a mixed bacterial flora had been developed, and the mutation breeding method was adopted to conduct the research. the original mixed bacterial flora had been enrichedin acid mine drainage of dexing copper mine, jiangxi province, china. it was induced by uv (ultraviolet), ultrasonic, and microwave, and their combination mutation. the most efficient bacterial flora after mutation was collected for further bioleaching ... | 2013 | 24381948 |
| metagenome analyses of corroded concrete wastewater pipe biofilms reveal a complex microbial system. | concrete corrosion of wastewater collection systems is a significant cause of deterioration and premature collapse. failure to adequately address the deteriorating infrastructure networks threatens our environment, public health, and safety. analysis of whole-metagenome pyrosequencing data and 16s rrna gene clone libraries was used to determine microbial composition and functional genes associated with biomass harvested from crown (top) and invert (bottom) sections of a corroded wastewater pipe. | 2012 | 22727216 |
| novel bacterial community associated with 500-year-old unpreserved archaeological wood from king henry viii's tudor warship the mary rose. | a 500-year-old unpreserved mary rose sample, historically containing an iron bolt, was analyzed using enrichment cultures and 16s sequencing. the novel community of bacteria present demonstrates a biological pathway of fe and s oxidation and a range of acid-generating metabolisms, with implications for preservation and biogeochemical cycling. | 2012 | 23023757 |
| pyrosequencing of mytilus galloprovincialis cdnas: tissue-specific expression patterns. | mytilus species are important in marine ecology and in environmental quality assessment, yet their molecular biology is poorly understood. molecular aspects of their reproduction, hybridisation between species, mitochondrial inheritance, skewed sex ratios of offspring and adaptation to climatic and pollution factors are priority areas. | 2010 | 20111607 |
| diversity of aerobic anoxygenic phototrophic bacteria in paddy soil and their response to elevated atmospheric co₂. | aerobic anoxygenic phototrophic bacteria (aanpb) are recognized as an important group driving the global carbon cycling. however, the diversity of aanpb in terrestrial environment remains largely unknown as well as their responses to the elevated atmospheric co2. by using culture-independent techniques, the diversity of aanpb in paddy soil and the changes in response to the rising atmospheric co₂ were investigated within china face (free-air co₂ enrichment) platform. there was a phylogenetically ... | 2010 | 21255374 |
| diversity of aerobic anoxygenic phototrophic bacteria in paddy soil and their response to elevated atmospheric co₂. | aerobic anoxygenic phototrophic bacteria (aanpb) are recognized as an important group driving the global carbon cycling. however, the diversity of aanpb in terrestrial environment remains largely unknown as well as their responses to the elevated atmospheric co2. by using culture-independent techniques, the diversity of aanpb in paddy soil and the changes in response to the rising atmospheric co₂ were investigated within china face (free-air co₂ enrichment) platform. there was a phylogenetically ... | 2010 | 21255374 |
| permanent draft genome sequence of acidiphilium sp. ja12-a1. | the tenacious association between strains of the heterotrophic alphaproteobacterial genus acidiphilium and chemolithotrophic iron oxidizing bacteria has long been known. in this context the genome of the heterotroph acidiphilium sp. ja12-a1, an isolate from an iron oxidizing mixed culture derived from a pilot plant for bioremediation of acid mine drainage, was determined with the aim to reveal metabolic properties that are fundamental for the syntrophic interaction between acidiphilium sp. ja12- ... | 2015 | 26380040 |
| genomic analysis unravels reduced inorganic sulfur compound oxidation of heterotrophic acidophilic acidicaldus sp. strain dx-1. | although reduced inorganic sulfur compound (risc) oxidation in many chemolithoautotrophic sulfur oxidizers has been investigated in recent years, there is little information about risc oxidation in heterotrophic acidophiles. in this study, acidicaldus sp. strain dx-1, a heterotrophic sulfur-oxidizing acidophile, was isolated. its genome was sequenced and then used for comparative genomics. furthermore, real-time quantitative pcr was performed to identify the expression of genes involved in the r ... | 2016 | 27239474 |
| distribution and origin of oxygen-dependent and oxygen-independent forms of mg-protoporphyrin monomethylester cyclase among phototrophic proteobacteria. | magnesium-protoporphyrin ix monomethylester cyclase is one of the key enzymes of the bacteriochlorophyll biosynthesis pathway. there exist two fundamentally different forms of this enzyme. the oxygen-dependent form, encoded by the gene acsf, catalyzes the formation of the bacteriochlorophyll fifth ring using oxygen, whereas the oxygen-independent form encoded by the gene bche utilizes an oxygen atom extracted from water. the presence of acsf and bche genes was surveyed in various phototrophic pr ... | 2013 | 23396335 |
| putative bacterial interactions from metagenomic knowledge with an integrative systems ecology approach. | following the trend of studies that investigate microbial ecosystems using different metagenomic techniques, we propose a new integrative systems ecology approach that aims to decipher functional roles within a consortium through the integration of genomic and metabolic knowledge at genome scale. for the sake of application, using public genomes of five bacterial strains involved in copper bioleaching: acidiphilium cryptum, acidithiobacillus ferrooxidans, acidithiobacillus thiooxidans, leptospir ... | 2015 | 26677108 |