bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evidence of Horizontal Transfer of Symbiotic Genes from a
Bradyrhizobium japonicum
Inoculant Strain to Indigenous Diazotrophs
Sinorhizobium
(
Ensifer
)
fredii
and
Bradyrhizobium elkanii
in a Brazilian Savannah Soil
Authors: Barcellos Fernando Gomes , Menna Pâmela , da Silva Batista Jesiane Stefânia , Hungria Mariangela 
Published: February 2007

ABSTRACT

The importance of horizontal gene transfer (HGT) in the evolution and speciation of bacteria has been emphasized; however, most studies have focused on genes clustered in pathogenesis and very few on symbiosis islands. Both soybean (
Glycine max
[L.] Merrill) and compatible
Bradyrhizobium japonicum
and
Bradyrhizobium elkanii
strains are exotic to Brazil and have been massively introduced in the country since the early 1960s, occupying today about 45% of the cropped land. For the past 10 years, our group has obtained several isolates showing high diversity in morphological, physiological, genetic, and symbiotic properties in relation to the putative parental inoculant strains. In this study, parental strains and putative natural variants isolated from field-grown soybean nodules were genetically characterized in relation to conserved genes (by repetitive extragenic palindromic PCR using REP and BOX A1R primers, PCR-restriction fragment length polymorphism, and sequencing of the 16SrRNA genes), nodulation, and N
2
-fixation genes (PCR-RFLP and sequencing of
nodY-nodA
,
nodC
, and
nifH
genes). Both genetic variability due to adaptation to the stressful environmental conditions of the Brazilian Cerrados and HGT events were confirmed. One strain (S 127) was identified as an indigenous
B. elkanii
strain that acquired a
nodC
gene from the inoculant
B. japonicum
. Another one (CPAC 402) was identified as an indigenous
Sinorhizobium
(
Ensifer
)
fredii
strain that received the whole symbiotic island from the
B. japonicum
inoculant strain and maintained an extra copy of the original
nifH
gene. The results highlight the strategies that bacteria may commonly use to obtain ecological advantages, such as the acquisition of genes to establish effective symbioses with an exotic host legume.
Characterization of the Role of
para-
Aminobenzoic Acid Biosynthesis in Folate Production by
Lactococcus lactis
Authors: Wegkamp Arno , van Oorschot Wietske , de Vos Willem M. , Smid Eddy J. 
Published: February 2007

ABSTRACT

The
pab
genes for
para
-aminobenzoic acid (
p
ABA) biosynthesis in
Lactococcus lactis
were identified and characterized. In
L. lactis
NZ9000, only two of the three genes needed for
p
ABA production were initially found. No gene coding for 4-amino-4-deoxychorismate lyase (
pabC
) was initially annotated, but detailed analysis revealed that
pabC
was fused with the 3′ end of the gene coding for chorismate synthetase component II (
pabB
). Therefore, we hypothesize that all three enzyme activities needed for
p
ABA production are present in
L. lactis
, allowing for the production of
p
ABA. Indeed, the overexpression of the
p
ABA gene cluster in
L. lactis
resulted in elevated
p
ABA pools, demonstrating that the genes are involved in the biosynthesis of
p
ABA. Moreover, a
p
ABA knockout (KO) strain lacking
pabA
and
pabB
C
was constructed and shown to be unable to produce folate when cultivated in the absence of
p
ABA. This KO strain was unable to grow in chemically defined medium lacking glycine, serine, nucleobases/nucleosides, and
p
ABA. The addition of the purine guanine, adenine, xanthine, or inosine restored growth but not the production of folate. This suggests that, in the presence of purines, folate is not essential for the growth of
L. lactis
. It also shows that folate is not strictly required for the pyrimidine biosynthesis pathway.
L. lactis
strain NZ7024, overexpressing both the folate and
p
ABA gene clusters, was found to produce 2.7 mg of folate/liter per optical density unit at 600 nm when the strain was grown on chemically defined medium without
p
ABA. This is in sharp contrast to
L. lactis
strains overexpressing only one of the two gene clusters. Therefore, we conclude that elevated folate levels can be obtained only by the overexpression of folate combined with the overexpression of the
p
ABA biosynthesis gene cluster, suggesting the need for a balanced carbon flux through the folate and
p
ABA biosynthesis pathway in the wild-type strain.
Extractable Organic Components and Nutrients in Wastewater from Dairy Lagoons Influence the Growth and Survival of
Escherichia coli
O157:H7
Authors: Ravva Subbarao V. , Korn Anna 
Published: February 2007

ABSTRACT

The influence of nutrients in wastewater from dairy lagoons on the survival of
Escherichia coli
O157:H7 was monitored. Initially, the survival of
E. coli
O157:H7 in wastewater from which the competing native organisms had been removed by filter sterilization or autoclaving was compared with that in wastewater from which competing organisms had not been removed. Numbers of
E. coli
O157:H7 or
E. coli
ONT (O-nontypeable):H32 cells declined rapidly in filter-sterilized water and exhibited a slower decline in nonsterile water, while the organisms proliferated in autoclaved water. Subsequently, the growth of
E. coli
O157:H7 strains was monitored in 300 μl of Luria-Bertani (LB) broth supplemented with incremental proportions of filter-sterilized wastewater.
E. coli
O157:H7 and
E. coli
ONT:H32 strains failed to grow in filter-sterilized wastewater, and their growth was reduced incrementally with wastewater supplementation of LB broth. Consequently, the influence of organic extracts of wastewater on the growth of
E. coli
O157:H7 and
E. coli
ONT:H32 in reduced-strength LB was monitored, followed by scale-up tests in wastewater. Acidic and basic extracts inhibited growth of both strains, while the neutral aqueous extract improved growth. However, a scale-up with a threefold increase in the acidic components supplementing the wastewater did not result in any additional decline in numbers of
E. coli
O157:H7 cells. When protected inside a 300-kDa dialysis tube and exposed to diffusible components,
E. coli
O157:H7 survived longer, with a decimal reduction time of 18.1 days, compared to 3.5 days when inoculated directly into wastewater. Although wastewater can potentially provide nutrients to naturally occurring human pathogens, the chemical components, protozoa, and coliphages in wastewater can inhibit the growth of freshly introduced pathogens from manure.
Molecular Basis of Fructose Utilization by the Wine YeastSaccharomyces cerevisiae: a MutatedHXT3Allele Enhances Fructose Fermentation
Authors: Guillaume Carole , Delobel Pierre , Sablayrolles Jean-Marie , Blondin Bruno 
Published: February 2007

ABSTRACTFructose utilization by wine yeasts is critically important for the maintenance of a high fermentation rate at the end of alcoholic fermentation. ASaccharomyces cerevisiaewine yeast able to ferment grape must sugars to dryness was found to have a high fructose utilization capacity. We investigated the molecular basis of this enhanced fructose utilization capacity by studying the properties of several hexose transporter (HXT) genes. We found that this wine yeast harbored a mutatedHXT3allele. A functional analysis of this mutated allele was performed by examining expression in an hxt1-7Δ strain. Expression of the mutated allele alone was found to be sufficient for producing an increase in fructose utilization during fermentation similar to that observed in the commercial wine yeast. This work provides the first demonstration that the pattern of fructose utilization during wine fermentation can be altered by expression of a mutated hexose transporter in a wine yeast. We also found that the glycolytic flux could be increased by overexpression of the mutant transporter gene, with no effect on fructose utilization. Our data demonstrate that the Hxt3 hexose transporter plays a key role in determining the glucose/fructose utilization ratio during fermentation.
Genetic Engineering of
Zymobacter palmae
for Production of Ethanol from Xylose
Authors: Yanase Hideshi , Sato Dai , Yamamoto Keiko , Matsuda Saori , Yamamoto Sho , Okamoto Kenji 
Published: February 2007

ABSTRACT

Its metabolic characteristics suggest that
Zymobacter palmae
gen. nov., sp. nov. could serve as a useful new ethanol-fermenting bacterium, but its biotechnological exploitation will require certain genetic modifications. We therefore engineered
Z. palmae
so as to broaden the range of its fermentable sugar substrates to include the pentose sugar xylose. The
Escherichia coli
genes encoding the xylose catabolic enzymes xylose isomerase, xylulokinase, transaldolase, and transketolase were introduced into
Z. palmae
, where their expression was driven by the
Zymomonas mobilis
glyceraldehyde-3-phosphate dehydrogenase promoter. When cultured with 40 g/liter xylose, the recombinant
Z. palmae
strain was able to ferment 16.4 g/liter xylose within 5 days, producing 91% of the theoretical yield of ethanol with no accumulation of organic acids as metabolic by-products. Notably, xylose acclimation enhanced both the expression of xylose catabolic enzymes and the rate of xylose uptake into recombinant
Z. palmae
, which enabled the acclimated organism to completely and simultaneously ferment a mixture of 40 g/liter glucose and 40 g/liter xylose within 8 h, producing 95% of the theoretical yield of ethanol. Thus, efficient fermentation of a mixture of glucose and xylose to ethanol can be accomplished by using
Z. palmae
expressing
E. coli
xylose catabolic enzymes.
Oil Field Souring Control by Nitrate-Reducing
Sulfurospirillum
spp. That Outcompete Sulfate-Reducing Bacteria for Organic Electron Donors
Authors: Hubert Casey , Voordouw Gerrit 
Published: February 2007

ABSTRACT

Nitrate injection into oil reservoirs can prevent and remediate souring, the production of hydrogen sulfide by sulfate-reducing bacteria (SRB). Nitrate stimulates nitrate-reducing, sulfide-oxidizing bacteria (NR-SOB) and heterotrophic nitrate-reducing bacteria (hNRB) that compete with SRB for degradable oil organics. Up-flow, packed-bed bioreactors inoculated with water produced from an oil field and injected with lactate, sulfate, and nitrate served as sources for isolating several NRB, including
Sulfurospirillum
and
Thauera
spp. The former coupled reduction of nitrate to nitrite and ammonia with oxidation of either lactate (hNRB activity) or sulfide (NR-SOB activity). Souring control in a bioreactor receiving 12.5 mM lactate and 6, 2, 0.75, or 0.013 mM sulfate always required injection of 10 mM nitrate, irrespective of the sulfate concentration. Community analysis revealed that at all but the lowest sulfate concentration (0.013 mM), significant SRB were present. At 0.013 mM sulfate, direct hNRB-mediated oxidation of lactate by nitrate appeared to be the dominant mechanism. The absence of significant SRB indicated that sulfur cycling does not occur at such low sulfate concentrations. The metabolically versatile
Sulfurospirillum
spp. were dominant when nitrate was present in the bioreactor. Analysis of cocultures of
Desulfovibrio
sp. strain Lac3, Lac6, or Lac15 and
Sulfurospirillum
sp. strain KW indicated its hNRB activity and ability to produce inhibitory concentrations of nitrite to be key factors for it to successfully outcompete oil field SRB.
Outbreak of an Acute Aflatoxicosis in Kenya in 2004: Identification of the Causal Agent
Authors: Probst Claudia , Njapau Henry , Cotty Peter J. 
Published: February 2007

ABSTRACT

Maize contaminated with aflatoxins has been implicated in deadly epidemics in Kenya three times since 1981, but the fungi contaminating the maize with aflatoxins have not been characterized. Here we associate the S strain of
Aspergillus flavus
with lethal aflatoxicoses that took more than 125 lives in 2004.
Identification of
Lactobacillus sakei
Genes Induced during Meat Fermentation and Their Role in Survival and Growth
Authors: Hüfner Eric , Markieton Tobias , Chaillou Stéphane , Crutz-Le Coq Anne-Marie , Zagorec Monique , Hertel Christian 
Published: February 2007

ABSTRACT

Lactobacillus sakei
is a lactic acid bacterium that is ubiquitous in the food environment and is one of the most important constituents of commercial meat starter cultures. In this study, in vivo expression technology (IVET) was applied to investigate gene expression of
L. sakei
23K during meat fermentation. The IVET vector used (pEH100) contained promoterless and transcriptionally fused reporter genes mediating β-glucuronidase activity and erythromycin resistance. A genomic library of
L. sakei
23K was established, and the clones were subjected to fermentation in a raw-sausage model. Fifteen in carne-induced fusions were identified. Several genes encoded proteins which are likely to contribute to stress-related functions. One of these genes was involved in acquisition of ammonia from amino acids, and the remaining either were part of functionally unrelated pathways or encoded hypothetical proteins. The construction and use of isogenic mutants in the sausage model suggested that four genes have an impact on the performance of
L. sakei
during raw-sausage fermentation. Inactivation of the heat shock regulator gene
ctsR
resulted in increased growth, whereas knockout of the genes
asnA2
, LSA1065, and LSA1194 resulted in attenuated performance compared to the wild-type strain. The results of our study are the first to provide an insight into the transcriptional response of
L. sakei
when growing in the meat environment. In addition, this study establishes a molecular basis which allows investigation of bacterial properties that are likely to contribute to the ecological performance of the organism and to influence the final outcome of sausage fermentation.
Tetracycline Resistance Mediated by
tet
(W),
tet
(M), and
tet
(O) Genes of
Bifidobacterium
Isolates from Humans
Authors: Aires J. , Doucet-Populaire F. , Butel M. J. 
Published: February 2007

ABSTRACT

MICs of tetracyclines were determined for 86 human
Bifidobacterium
isolates and three environmental strains. The
tet
(O) gene was found to be absent in these isolates.
tet
(W) and
tet
(M) were found in 26 and 7%, respectively, of the
Bifidobacterium
isolates, and one isolate contained both genes. Chromosomal DNA hybridization showed that there was one chromosomal copy of
tet
(W) and/or
tet
(M).
Prevalence and Genetic Properties ofSalmonella entericaSerovar Typhimurium Definitive Phage Type 104 Isolated fromRattus norvegicusandRattus rattusHouse Rats in Yokohama City, Japan
Authors: Yokoyama Eiji , Maruyama Soichi , Kabeya Hidenori , Hara Siro , Sata Shin , Kuroki Toshiro , Yamamoto Tomoko 
Published: February 2007

ABSTRACTSalmonella entericaserovar Typhimurium was isolated from the intestinal contents ofRattus rattusandRattus norvegicushouse rats captured at two buildings, designated buildings J and YS, in Yokohama City, Japan. From October 1997 to September 1998, 52 of 339 (15.3%) house rats were found to carrySalmonellaserovar Typhimurium definitive phage type 104 (DT104). In building J, 26 of 161 (16.1%) house rats carried DT104 over the 1-year study period, compared to 26 of 178 (14.6%) rats in building YS. The isolation rates of DT104 fromR. rattusandR. norvegicuswere similar in the two buildings. Most DT104 strains from building J (24 of 26) showed resistance to ampicillin, chloramphenicol, streptomycin, sulfisoxazole, and tetracycline and contained both the 1.0- and 1.2-kbp integrons, carrying genespse1,pasppflo-like,aadA2,sulI, andtet(G). All DT104 strains from building YS were resistant to ampicillin and sulfisoxazole, and had the 1.2-kbp integron carryingpse1andsulI. Cluster analysis of pulsed-field gel electrophoresis patterns of BlnI-digested DT104 DNAs showed that 22 of 26 DT104 strains from building J and 24 of 26 strains from building YS could be grouped into separate clusters each specific for the building origin. These results indicated that DT104 strains were prevalent in house rat colonies in each building and suggest that house rats may play an important role in the epidemiology of DT104.
Novel Tetracycline Resistance Determinant Isolated from an Environmental Strain of
Serratia marcescens
Authors: Thompson Stuart A. , Maani Elizabeth V. , Lindell Angela H. , King Catherine J. , McArthur J. Vaun 
Published: February 2007

ABSTRACT

Resistances to tetracycline and mercury were identified in an environmental strain of
Serratia marcescens
isolated from a stream highly contaminated with heavy metals. As a step toward addressing the mechanisms of coselection of heavy metal and antibiotic resistances, the tetracycline resistance determinant was cloned in
Escherichia coli
. Within the cloned 13-kb segment, the tetracycline resistance locus was localized by deletion analysis and transposon mutagenesis. DNA sequence analysis of an 8.0-kb region revealed a novel gene [
tetA
(41)] that was predicted to encode a tetracycline efflux pump. Phylogenetic analysis showed that the TetA(41) protein was most closely related to the Tet(39) efflux protein of
Acinetobacter
spp. yet had less than 80% amino acid identity with known tetracycline efflux pumps. Adjacent to the
tetA
(41) gene was a divergently transcribed gene [
tetR
(41)] predicted to encode a tetracycline-responsive repressor protein. The
tetA
(41)-
tetR
(41) intergenic region contained putative operators for TetR(41) binding. The
tetA
(41) and
tetR
(41) promoters were analyzed using
lacZ
fusions, which showed that the expression of both the
tetA
(41) and
tetR
(41) genes exhibited TetR(41)-dependent regulation by subinhibitory concentrations of tetracycline. The apparent lack of plasmids in this
S. marcescens
strain, as well as the presence of metabolic genes adjacent to the tetracycline resistance locus, suggested that the genes were located on the
S. marcescens
chromosome and may have been acquired by transduction. The cloned Tet 41 determinant did not confer mercury resistance to
E. coli
, confirming that Tet 41 is a tetracycline-specific efflux pump rather than a multidrug transporter.
Diversity, Activity, and Abundance of Sulfate-Reducing Bacteria in Saline and Hypersaline Soda Lakes
Authors: Foti Mirjam , Sorokin Dimitry Y. , Lomans Bart , Mussman Marc , Zacharova Elena E. , Pimenov Nikolay V. , Kuenen J. Gijs , Muyzer Gerard 
Published: February 2007

ABSTRACT

Soda lakes are naturally occurring highly alkaline and saline environments. Although the sulfur cycle is one of the most active element cycles in these lakes, little is known about the sulfate-reducing bacteria (SRB). In this study we investigated the diversity, activity, and abundance of SRB in sediment samples and enrichment cultures from a range of (hyper)saline soda lakes of the Kulunda Steppe in southeastern Siberia in Russia. For this purpose, a polyphasic approach was used, including denaturing gradient gel electrophoresis of
dsr
gene fragments, sulfate reduction rate measurements, serial dilutions, and quantitative real-time PCR (qPCR). Comparative sequence analysis revealed the presence of several novel clusters of SRB, mostly affiliated with members of the order
Desulfovibrionales
and family
Desulfobacteraceae
. We detected sulfate reducers and observed substantial sulfate reducing rates (between 12 and 423 μmol/dm
3
day
−1
) for most lakes, even at a salinity of 475 g/liter. Enrichments were obtained at salt saturating conditions (4 M Na
+
), using H
2
or volatile fatty acids as electron donors, and an extremely halophilic SRB, strain ASO3-1, was isolated. Furthermore, a high
dsr
gene copy number of 10
8
cells per ml was detected in a hypersaline lake by qPCR. Our results indicate the presence of diverse and active SRB communities in these extreme ecosystems.
Gene Expression and Biochemical Analysis of Cheese-Ripening Yeasts: Focus on Catabolism ofl-Methionine, Lactate, and Lactose
Authors: Cholet Orianne , Hénaut Alain , Casaregola Serge , Bonnarme Pascal 
Published: February 2007

ABSTRACTDNA microarrays of 86 genes from the yeastsDebaryomyces hansenii,Kluyveromyces marxianus, andYarrowia lipolyticawere developed to determine which genes were expressed in a medium mimicking a cheese-ripening environment. These genes were selected for potential involvement in lactose/lactate catabolism and the biosynthesis of sulfur-flavored compounds. Hybridization conditions to follow specifically the expression of homologous genes belonging to different species were set up. The microarray was first validated on pure cultures of each yeast; no interspecies cross-hybridization was observed. Expression patterns of targeted genes were studied in pure cultures of each yeast, as well as in coculture, and compared to biochemical data. As expected, a high expression of theLACgenes ofK. marxianuswas observed. This is a yeast that efficiently degrades lactose. Several lactate dehydrogenase-encoding genes were also expressed essentially inD. hanseniiandK. marxianus, which are two efficient deacidifying yeasts in cheese ripening. A set of genes possibly involved inl-methionine catabolism was also used on the array.Y. lipolytica, which efficiently assimilatesl-methionine, also exhibited a high expression of theSaccharomyces cerevisiaeorthologsBAT2andARO8, which are involved in thel-methionine degradation pathway. Our data provide the first evidence that the use of a multispecies microarray could be a powerful tool to investigate targeted metabolism and possible metabolic interactions between species within microbial cocultures.
Increased Prevalence of Ubiquitous Ascomycetes in an Acropoid Coral (
Acropora formosa
) Exhibiting Symptoms of Brown Band Syndrome and Skeletal Eroding Band Disease
Authors: Yarden Oded , Ainsworth Tracy D. , Roff George , Leggat William , Fine Maoz , Hoegh-Guldberg Ove 
Published: February 2007

ABSTRACT

The prevalence of coral-associated fungi was four times higher in diseased
Acropora formosa
colonies than in healthy colonies. Since taxonomically related fungal species were isolated from diseased and healthy colonies, we suggest that their association with coral may be constitutive but that their abundance is dependent on coral health.
Unusual Codon Bias in Vinyl Chloride Reductase Genes of
Dehalococcoides
Species
Authors: McMurdie Paul J. , Behrens Sebastian F. , Holmes Susan , Spormann Alfred M. 
Published: February 2007

ABSTRACT

Vinyl chloride reductases (VC-RDase) are the key enzymes for complete microbial reductive dehalogenation of chloroethenes, including the groundwater pollutants tetrachloroethene and trichloroethene. Analysis of the codon usage of the VC-RDase genes
vcrA
and
bvcA
showed that these genes are highly unusual and are characterized by a low G+C fraction at the third position. The third position of codons in VC-RDase genes is biased toward the nucleotide T, even though available
Dehalococcoides
genome sequences indicate the absence of any tRNAs matching codons that end in T. The comparatively high level of abnormality in the codon usage of VC-RDase genes suggests an evolutionary history that is different from that of most other
Dehalococcoides
genes.
New Insights into Microbial Oxidation of Antimony and Arsenic
Authors: Lehr Corinne R. , Kashyap Des R. , McDermott Timothy R. 
Published: February 2007

ABSTRACTSb(III) oxidation was documented in anAgrobacterium tumefaciensisolate that can also oxidize As(III). Equivalent Sb(III) oxidation rates were observed in the parental wild-type organism and in two well-characterized mutants that cannot oxidize As(III) for fundamentally different reasons. Therefore, despite the literature suggesting that Sb(III) and As(III) may be biochemical analogs, Sb(III) oxidation is catalyzed by a pathway different than that used for As(III). Sb(III) and As(III) oxidation was also observed for an eukaryotic acidothermophilic alga belonging to the orderCyanidiales, implying that the ability to oxidize metalloids may be phylogenetically widespread.