Evolution of glutamate dehydrogenase genes: evidence for lateral gene transfer within and between prokaryotes and eukaryotes.
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BACKGROUND: Lateral gene transfer can introduce genes with novel functions into genomes or replace genes with functionally similar orthologs or paralogs. Here we present a study of the occurrence of the latter gene replacement phenomenon in the four gene families encoding different classes of glutamate dehydrogenase (GDH), to evaluate and compare the patterns and rates of lateral gene transfer (LGT) in prokaryotes and eukaryotes. RESULTS: We extend the taxon sampling of gdh genes with nine new eukaryotic sequences and examine the phylogenetic distribution pattern of the various GDH classes in combination with maximum likelihood phylogenetic analyses. The distribution pattern analyses indicate that LGT has played a significant role in the evolution of the four gdh gene families. Indeed, a number of gene transfer events are identified by phylogenetic analyses, including numerous prokaryotic intra-domain transfers, some prokaryotic inter-domain transfers and several inter-domain transfers between prokaryotes and microbial eukaryotes (protists). CONCLUSION: LGT has apparently affected eukaryotes and prokaryotes to a similar extent within the gdh gene families. In the absence of indications that the evolution of the gdh gene families is radically different from other families, these results suggest that gene transfer might be an important evolutionary mechanism in microbial eukaryote genome evolution. (+info)
Search for Lawsonia intracellularis and Bilophila wadsworthia in malabsorption-diseased chickens.
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Proliferative enteropathy is an important enteric disease caused by Lawsonia intracellularis. A wide range of host species can be infected by the same bacterium, yet the clinico-pathologic features among these hosts remains almost identical. The disease has been recognized regularly among ratites, but not in other avian families, such as galliforms, even though these suffer uncharacterized enteric conditions. Fresh ileum-colon contents were obtained from 228, 3- to 8-week-old chickens with enteric disease, kept at 14 large commercial farms in the southern USA. DNA was extracted from each sample and subjected to polymerase chain reactions (PCR) with primers specific to eubacterial DNA, L. intracellularis, and Bilophila wadsworthia. All chicken samples were positive for eubacterial DNA, 29 chickens (13%) were positive for B. wadsworthia DNA, and none were positive for L. intracellularis DNA. Given the ubiquitous nature of L. intracellularis, we consider it likely that some avian families do not carry the necessary mechanism for L. intracellularis viability. Bilophila wadsworthia appears to be a consistent member of the colonic flora of some host animals. Neither bacterium appears to be associated with malabsorption syndromes in chickens. (+info)
Reclassification of Desulfobacterium macestii as Desulfomicrobium macestii comb. nov.
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Phylogenetic, chemotaxonomic and metabolic data obtained for Desulfobacterium macestii indicate that this species is not a member of the genus Desulfobacterium, but of the genus Desulfomicrobium. Phylogenetically, it is closely related to Desulfomicrobium baculatum and Desulfomicrobium norvegicum, but it can be differentiated from these species by its metabolic properties. It is therefore proposed to reclassify Desulfobacterium macestii as Desulfomicrobium macestii comb. nov. (+info)
Desulfonatronum thiodismutans sp. nov., a novel alkaliphilic, sulfate-reducing bacterium capable of lithoautotrophic growth.
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A novel alkaliphilic, sulfate-reducing bacterium, strain MLF1(T), was isolated from sediments of soda Mono Lake, California. Gram-negative vibrio-shaped cells were observed, which were 0.6-0.7x1.2-2.7 micro m in size, motile by a single polar flagellum and occurred singly, in pairs or as short spirilla. Growth was observed at 15-48 degrees C (optimum, 37 degrees C), >1-7 % NaCl, w/v (optimum, 3 %) and pH 8.0-10.0 (optimum, 9.5). The novel isolate is strictly alkaliphilic, requires a high concentration of carbonate in the growth medium and is obligately anaerobic and catalase-negative. As electron donors, strain MLF1(T) uses hydrogen, formate and ethanol. Sulfate, sulfite and thiosulfate (but not sulfur or nitrate) can be used as electron acceptors. The novel isolate is a lithoheterotroph and a facultative lithoautotroph that is able to grow on hydrogen without an organic source of carbon. Strain MLF1(T) is resistant to kanamycin and gentamicin, but sensitive to chloramphenicol and tetracycline. The DNA G+C content is 63.0 mol% (HPLC). DNA-DNA hybridization with the most closely related species, Desulfonatronum lacustre Z-7951(T), exhibited 51 % homology. Also, the genome size (1.6x10(9) Da) and T(m) value of the genomic DNA (71+/-2 degrees C) for strain MLF1(T) were significantly different from the genome size (2.1x10(9) Da) and T(m) value (63+/-2 degrees C) for Desulfonatronum lacustre Z-7951(T). On the basis of physiological and molecular properties, the isolate was considered to be a novel species of the genus Desulfonatronum, for which the name Desulfonatronum thiodismutans sp. nov. is proposed (the type strain is MLF1(T)=ATCC BAA-395(T)=DSM 14708(T)). (+info)
Desulfonauticus submarinus gen. nov., sp. nov., a novel sulfate-reducing bacterium isolated from a deep-sea hydrothermal vent.
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A novel moderately thermophilic, hydrogenotrophic, sulfate-reducing bacterium, strain 6N(T) (=DSM 15269(T)=CIP 107713(T)), was isolated from matrixes of Alvinella and Riftia originating from deep-sea hydrothermal-vent samples collected on the 13 degrees N East-Pacific Rise at a depth of approximately 2600 m. It was a Gram-negative, non-sporulating, curved rod, motile with one polar flagellum, that did not possess desulfoviridin. It grew at temperatures ranging from 30 to 60 degrees C, with an optimum at 45 degrees C, in the presence of 0-5 % NaCl (optimum 2 %). Strain 6N(T) utilized only H(2)/CO(2) and formate as electron donors with acetate as carbon source. Sulfate, sulfite, thiosulfate and elemental sulfur were used as terminal electron acceptors during hydrogen oxidation. The G+C content of DNA was 34.4 mol%. Strain 6N(T) grouped with members of the family Desulfohalobiaceae in the delta-subclass of the PROTEOBACTERIA: Its closest phylogenetic relative was Desulfonatronovibrio hydrogenovorans, with only 90 % similarity between the sequences of the genes encoding 16S rRNA. Because of significant phylogenetic differences from all sulfate-reducing bacteria described so far in the domain Bacteria, this novel thermophile is proposed to be assigned to a new genus and species, Desulfonauticus submarinus gen. nov., sp. nov. (+info)
Molecular diversity of sulfate-reducing bacteria from two different continental margin habitats.
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This study examined the natural diversity and distributions of sulfate-reducing bacteria along a natural carbon gradient extending down the shelf-slope transition zone of the eastern Pacific continental margin. Dissimilatory (bi)sulfite reductase gene sequences (dsrAB) were PCR amplified and cloned from five different sampling sites, each at a discrete depth, from two different margin systems, one off the Pacific coast of Mexico and another off the coast of Washington State. A total of 1,762 clones were recovered and evaluated by restriction fragment length polymorphism (RFLP) analysis. The majority of the gene sequences recovered showed site and depth restricted distributions; however, a limited number of gene sequences were widely distributed within and between the margin systems. Cluster analysis identified 175 unique RFLP patterns, and nucleotide sequences were determined for corresponding clones. Several different continental margin DsrA sequences clustered with those from formally characterized taxa belonging to the delta subdivision of the class Proteobacteria (Desulfobulbus propionicus, Desulfosarcina variabilis) and the Bacillus-Clostridium (Desulfotomaculum putei) divisions, although the majority of the recovered sequences were phylogenetically divergent relative to all of the other DsrA sequences available for comparison. This study revealed extensive new genetic diversity among sulfate-reducing bacteria in continental margin sedimentary habitats, which appears to be tightly coupled to slope depth, specifically carbon bioavailability. (+info)
Linked redox precipitation of sulfur and selenium under anaerobic conditions by sulfate-reducing bacterial biofilms.
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A biofilm-forming strain of sulfate-reducing bacteria (SRB), isolated from a naturally occurring mixed biofilm and identified by 16S rDNA analysis as a strain of Desulfomicrobium norvegicum, rapidly removed 200 micro M selenite from solution during growth on lactate and sulfate. Elemental selenium and elemental sulfur were precipitated outside SRB cells. Precipitation occurred by an abiotic reaction with bacterially generated sulfide. This appears to be a generalized ability among SRB, arising from dissimilatory sulfide biogenesis, and can take place under low redox conditions and in the dark. The reaction represents a new means for the deposition of elemental sulfur by SRB under such conditions. A combination of transmission electron microscopy, environmental scanning electron microscopy, and cryostage field emission scanning electron microscopy were used to reveal the hydrated nature of SRB biofilms and to investigate the location of deposited sulfur-selenium in relation to biofilm elements. When pregrown SRB biofilms were exposed to a selenite-containing medium, nanometer-sized selenium-sulfur granules were precipitated within the biofilm matrix. Selenite was therefore shown to pass through the biofilm matrix before reacting with bacterially generated sulfide. This constitutes an efficient method for the removal of toxic concentrations of selenite from solution. Implications for environmental cycling and the fate of sulfur and selenium are discussed, and a general model for the potential action of SRB in selenium transformations is presented. (+info)
Enumeration and characterization of iron(III)-reducing microbial communities from acidic subsurface sediments contaminated with uranium(VI).
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Iron(III)-reducing bacteria have been demonstrated to rapidly catalyze the reduction and immobilization of uranium(VI) from contaminated subsurface sediments. Thus, these organisms may aid in the development of bioremediation strategies for uranium contamination, which is prevalent in acidic subsurface sediments at U.S. government facilities. Iron(III)-reducing enrichment cultures were initiated from pristine and contaminated (high in uranium, nitrate; low pH) subsurface sediments at pH 7 and pH 4 to 5. Enumeration of Fe(III)-reducing bacteria yielded cell counts of up to 240 cells ml(-1) for the contaminated and background sediments at both pHs with a range of different carbon sources (glycerol, acetate, lactate, and glucose). In enrichments where nitrate contamination was removed from the sediment by washing, MPN counts of Fe(III)-reducing bacteria increased substantially. Sediments of lower pH typically yielded lower counts of Fe(III)-reducing bacteria in lactate- and acetate-amended enrichments, but higher counts were observed when glucose was used as an electron donor in acidic enrichments. Phylogenetic analysis of 16S rRNA gene sequences extracted from the highest positive MPN dilutions revealed that the predominant members of Fe(III)-reducing consortia from background sediments were closely related to members of the Geobacteraceae family, whereas a recently characterized Fe(III) reducer (Anaeromyxobacter sp.) and organisms not previously shown to reduce Fe(III) (Paenibacillus and Brevibacillus spp.) predominated in the Fe(III)-reducing consortia of contaminated sediments. Analysis of enrichment cultures by terminal restriction fragment length polymorphism (T-RFLP) strongly supported the cloning and sequencing results. Dominant members of the Fe(III)-reducing consortia were observed to be stable over several enrichment culture transfers by T-RFLP in conjunction with measurements of Fe(III) reduction activity and carbon substrate utilization. Enrichment cultures from contaminated sites were also shown to rapidly reduce millimolar amounts of U(VI) in comparison to killed controls. With DNA extracted directly from subsurface sediments, quantitative analysis of 16S rRNA gene sequences with MPN-PCR indicated that Geobacteraceae sequences were more abundant in pristine compared to contaminated environments,whereas Anaeromyxobacter sequences were more abundant in contaminated sediments. Thus, results from a combination of cultivation-based and cultivation-independent approaches indicate that the abundance/community composition of Fe(III)-reducing consortia in subsurface sediments is dependent upon geochemical parameters (pH, nitrate concentration) and that microorganisms capable of producing spores (gram positive) or spore-like bodies (Anaeromyxobacter) were representative of acidic subsurface environments. (+info)