bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diversity, Abundance, and Spatial Distribution of Sediment Ammonia-OxidizingBetaproteobacteriain Response to Environmental Gradients and Coastal Eutrophication in Jiaozhou Bay, China
Authors: Dang Hongyue , Li Jing , Chen Ruipeng , Wang Lin , Guo Lizhong , Zhang Zhinan , Klotz Martin G. 
Published: May 2010

ABSTRACTOngoing anthropogenic eutrophication of Jiaozhou Bay offers an opportunity to study the influence of human activity on bacterial communities that drive biogeochemical cycling. Nitrification in coastal waters appears to be a sensitive indicator of environmental change, suggesting that function and structure of the microbial nitrifying community may be associated closely with environmental conditions. In the current study, theamoAgene was used to unravel the relationship between sediment aerobic obligate ammonia-oxidizingBetaproteobacteria(Beta-AOB) and their environment in Jiaozhou Bay. Protein sequences deduced fromamoAgene sequences grouped within four distinct clusters in theNitrosomonaslineage, including a putative new cluster. In addition, AmoA sequences belonging to three newly defined clusters in theNitrosospiralineage were also identified. Multivariate statistical analyses indicated that the studied Beta-AOB community structures correlated with environmental parameters, of which nitrite-N and sediment sand content had significant impact on the composition, structure, and distribution of the Beta-AOB community. BothamoAclone library and quantitative PCR (qPCR) analyses indicated that continental input from the nearby wastewater treatment plants and polluted rivers may have significant impact on the composition and abundance of the sediment Beta-AOB assemblages in Jiaozhou Bay. Our work is the first report of a direct link between a sedimentological parameter and the composition and distribution of the sediment Beta-AOB and indicates the potential for using the Beta-AOB community composition in general and individual isolates or environmental clones in theNitrosomonas oligotrophalineage in particular as bioindicators and biotracers of pollution or freshwater or wastewater input in coastal environments.
Novel Assay To Assess Permissiveness of a Soil Microbial Community toward Receipt of Mobile Genetic Elements
Authors: Musovic Sanin , Dechesne Arnaud , Sørensen Jan , Smets Barth F. 
Published: May 2010

ABSTRACT

There is a wealth of evidence indicating that mobile genetic elements can spread in natural microbial communities. However, little is known regarding the fraction of the community that actually engages in this behavior. Here we report on a new approach to quantify the fraction of a bacterial community that is able to receive and maintain an exogenous conjugal plasmid termed community permissiveness. Conjugal transfer of a broad-host-range plasmid labeled with a zygotically inducible green fluorescent protein (RP4::
gfp
) from a donor strain (
Pseudomonas putida
) to a soil bacterial suspension was examined. The mixture of cells was incubated on membrane filters supported by different solid media. Plasmid transfer was scored by
in situ
visualization of green fluorescent transconjugant microcolonies, and host range was determined by traditional plating or microcolony isolation by using a micromanipulator. Among the conditions tested, the highest plasmid transfer incidence (approximately 1 transfer per 10
4
soil bacteria) was measured after 48 h of incubation on either a 10% soil extract or a 10-fold diluted R2A medium. Stereomicroscopy combined with image analysis allowed easy examination and enumeration of green fluorescent microcolonies. In all experiments, however, stereomicroscopy consistently underestimated the number of conjugation events (approximately 10-fold) in comparison to confocal laser scanning microscopy. The plasmid host range was broad and included bacteria belonging to the
Alphaproteobacteria
,
Betaproteobacteria
, and
Gammaproteobacteria
classes of proteobacteria. The isolation of transconjugant microcolonies by micromanipulation greatly extended the estimated plasmid host range among soil bacteria. The new approach can be applied to examine the permissiveness of various communities toward receipt of different mobile elements.
Improvement of Phosphate Solubilization and
Medicago
Plant Yield by an Indole-3-Acetic Acid-Overproducing Strain of
Sinorhizobium meliloti
Authors: Bianco Carmen , Defez Roberto 
Published: May 2010

ABSTRACT

Nitrogen (N) and phosphorus (P) are the most limiting factors for plant growth. Some microorganisms improve the uptake and availability of N and P, minimizing chemical fertilizer dependence. It has been published that the RD64 strain, a
Sinorhizobium meliloti
1021 strain engineered to overproduce indole-3-acetic acid (IAA), showed improved nitrogen fixation ability compared to the wild-type 1021 strain. Here, we present data showing that RD64 is also highly effective in mobilizing P from insoluble sources, such as phosphate rock (PR). Under P-limiting conditions, the higher level of P-mobilizing activity of RD64 than of the 1021 wild-type strain is connected with the upregulation of genes coding for the high-affinity P transport system, the induction of acid phosphatase activity, and the increased secretion into the growth medium of malic, succinic, and fumaric acids.
Medicago truncatula
plants nodulated by RD64 (
Mt
-RD64), when grown under P-deficient conditions, released larger amounts of another P-solubilizing organic acid, 2-hydroxyglutaric acid, than plants nodulated by the wild-type strain (
Mt
-1021). It has already been shown that
Mt
-RD64 plants exhibited higher levels of dry-weight production than
Mt
-1021 plants. Here, we also report that P-starved
Mt
-RD64 plants show significant increases in both shoot and root fresh weights when compared to P-starved
Mt
-1021 plants. We discuss how, in a
Rhizobium
-legume model system, a balanced interplay of different factors linked to bacterial IAA overproduction rather than IAA production
per se
stimulates plant growth under stressful environmental conditions and, in particular, under P starvation.
Mosaic-Like Sequences Containing Transposon, Phage, and Plasmid Elements among
Listeria monocytogenes
Plasmids
Authors: Canchaya Carlos , Giubellini Vanessa , Ventura Marco , de los Reyes-Gavilán Clara G. , Margolles Abelardo 
Published: May 2010

ABSTRACT

Sequencing of plasmid pLM33 from the food isolate
Listeria monocytogenes
Lm1 revealed a molecule of 32,307 bp with a G+C content of 36.2%. The plasmid displays a mosaic pattern of identities common to several closely related
L. monocytogenes
plasmids isolated from food and clinical sources.
Multigeneration Cross Contamination of Mail with
Bacillus
Species Spores by Tumbling
Authors: Edmonds Jason , Clark Paul , Williams Leslie , Lindquist H. D. Alan , Martinez Kenneth , Gardner Warren , Shadomy Sean , Hornsby-Myers Jennifer 
Published: May 2010

ABSTRACT

In 2001, envelopes loaded with
Bacillus anthracis
spores were mailed to Senators Daschle and Leahy as well as to the New York Post and NBC News buildings. Additional letters may have been mailed to other news agencies because there was confirmed anthrax infection of employees at these locations. These events heightened the awareness of the lack of understanding of the mechanism(s) by which objects contaminated with a biological agent might spread disease. This understanding is crucial for the estimation of the potential for exposure to ensure the appropriate response in the event of future attacks. In this study, equipment to simulate interactions between envelopes and procedures to analyze the spread of spores from a “payload” envelope (i.e., loaded internally with a powdered spore preparation) onto neighboring envelopes were developed. Another process to determine whether an aerosol could be generated by opening contaminated envelopes was developed. Subsequent generations of contaminated envelopes originating from a single payload envelope showed a consistent two-log decrease in the number of spores transferred from one generation to the next. Opening a tertiary contaminated envelope resulted in an aerosol containing 10
3
B. anthracis
spores. We developed a procedure for sampling contaminated letters by a nondestructive method aimed at providing information useful for consequence management while preserving the integrity of objects contaminated during the incident and preserving evidence for law enforcement agencies.
Influence of Forest Trees on the Distribution of Mineral Weathering-Associated Bacterial Communities of the
Scleroderma citrinum
Mycorrhizosphere
Authors: Calvaruso Christophe , Turpault Marie-Pierre , Leclerc Elisabeth , Ranger Jacques , Garbaye Jean , Uroz Stéphane , Frey-Klett Pascale 
Published: May 2010

ABSTRACT

In acidic forest soils, availability of inorganic nutrients is a tree-growth-limiting factor. A hypothesis to explain sustainable forest development proposes that tree roots select soil microbes involved in central biogeochemical processes, such as mineral weathering, that may contribute to nutrient mobilization and tree nutrition. Here we showed, by combining soil analyses with cultivation-dependent analyses of the culturable bacterial communities associated with the widespread mycorrhizal fungus
Scleroderma citrinum
, a significant enrichment of bacterial isolates with efficient mineral weathering potentials around the oak and beech mycorrhizal roots compared to bulk soil. Such a difference did not exist in the rhizosphere of Norway spruce. The mineral weathering ability of the bacterial isolates was assessed using a microplaque assay that measures the pH and the amount of iron released from biotite. Using this microplate assay, we demonstrated that the bacterial isolates harboring the most efficient mineral weathering potential belonged to the
Burkholderia
genus. Notably, previous work revealed that oak and beech harbored very similar pHs in the 5- to 10-cm horizon in both rhizosphere and bulk soil environments. In the spruce rhizosphere, in contrast, the pH was significantly lower than that in bulk soil. Because the production of protons is one of the main mechanisms responsible for mineral weathering, our results suggest that certain tree species have developed indirect strategies for mineral weathering in nutrient-poor soils, which lie in the selection of bacterial communities with efficient mineral weathering potentials.
Unsuitability of Quantitative
Bacteroidales
16S rRNA Gene Assays for Discerning Fecal Contamination of Drinking Water
Authors: van der Wielen Paul W. J. J. , Medema Gertjan 
Published: May 2010

ABSTRACT

Bacteroidales
species were detected in (tap) water samples from treatment plants with three different PCR assays. 16S rRNA gene sequence analysis indicated that the sequences had an environmental rather than fecal origin. We conclude that assays for
Bacteroidales
16S rRNA genes are not specific enough to discern fecal contamination of drinking water in the Netherlands.
Sequence Diversity of Genes Encoding Botulinum Neurotoxin Type F
Authors: Raphael Brian H. , Choudoir Mallory J. , Lúquez Carolina , Fernández Rafael , Maslanka Susan E. 
Published: May 2010

ABSTRACTBotulism due to type F botulinum neurotoxin (BoNT/F) is rare (<1% of cases), and only a limited number of clostridial strains producing this toxin type have been isolated. As a result, analysis of the diversity of genes encoding BoNT/F has been challenging. In this study, the entirebont/Fnucleotide sequences were determined from 33 type F botulinum toxin-producing clostridial strains isolated from environmental sources and botulism outbreak investigations. We examined proteolytic and nonproteolyticClostridium botulinumtype F strains, bivalent strains, including Bf and Af, andClostridium baratiitype F strains. Phylogenetic analysis revealed that thebont/Fgenes examined formed 7 subtypes (F1 to F7) and that the nucleotide sequence identities of these subtypes differed by up to 25%. The genes from proteolytic (group I)C. botulinumstrains formed subtypes F1 through F5, while the genes from nonproteolytic (group II)C. botulinumstrains formed subtype F6. Subtype F7 was composed exclusively ofbont/Fgenes fromC. baratiistrains. The region of thebont/F5gene encoding the neurotoxin light chain was found to be highly divergent compared to the other subtypes. Although thebont/F5nucleotide sequences were found to be identical in strains harboring this gene, the gene located directly upstream (ntnh/F) demonstrated sequence variation among representative strains of this subtype. These results demonstrate that extensive nucleotide diversity exists among genes encoding type F neurotoxins from strains with different phylogenetic backgrounds and from various geographical sources.
The Virulence Regulator PrfA Promotes Biofilm Formation byListeria monocytogenes
Authors: Lemon Katherine P. , Freitag Nancy E. , Kolter Roberto 
Published: May 2010

ABSTRACTListeria monocytogenesis a food-borne facultative intracellular pathogen. It is widespread in the environment and has several distinct life-styles. The key transcriptional activator PrfA positively regulatesL. monocytogenesvirulence genes to mediate the transition from extracellular, flagellum-propelled cell to intracellular pathogen. Here we report the first evidence that PrfA also has a significant positive impact on extracellular biofilm formation. Mutants lackingprfAwere defective in surface-adhered biofilm formation. The ΔprfAmutant exhibited wild-type flagellar motility, and its biofilm defect occurred after initial surface adhesion. We also observed that mutations that led to the constitutive expression of PrfA-dependent virulence genes had a minimal impact on biofilm formation. Furthermore, biofilm development was enhanced in a mutant encoding a PrfA protein variant unable to fully transition from the extracellular form to the virulent, intracellular activity conformation. These results indicate that PrfA positively regulates biofilm formation and suggest that PrfA has a global role in modulating the life-style ofL. monocytogenes. The requirement of PrfA for optimal biofilm formation may provide selective pressure to maintain this critical virulence regulator whenL. monocytogenesis outside host cells in the environment.
Identification of
trans
- and
cis
-Control Elements Involved in Regulation of the Carbon Monoxide Dehydrogenase Genes in
Mycobacterium
sp. Strain JC1 DSM 3803
Authors: Oh Jeong-Il , Park Su-Jeong , Shin Sun-Joo , Ko In-Jeong , Han Seung J. , Park Sae W. , Song Taeksun , Kim Young M. 
Published: May 2010

ABSTRACT

The
cutR
gene was identified 314 bp upstream of the divergently oriented
cutB1C1A1
operon encoding carbon monoxide (CO) dehydrogenase in
Mycobacterium
sp. strain JC1. Its deduced product was composed of 320 amino acid residues with a calculated molecular mass of 34.1 kDa and exhibits a basal sequence similarity to the regulatory proteins belonging to the LysR family. Using a
cutR
deletion mutant, it was demonstrated that CutR is required for the efficient utilization of CO by
Mycobacterium
sp. strain JC1 growing with CO as the sole source of carbon and energy. CutR served as a transcriptional activator for expression of the duplicated
cutBCA
operons (
cutB1C1A1
and
cutB2C2A2
) and was involved in the induction of the
cutBCA
operons by CO. The
cutBCA
operons were also subjected to catabolite repression. An inverted repeat sequence (TGTGA-N
6
-TCACA) with a perfect match with the binding motif of cyclic AMP receptor protein was identified immediately upstream of and overlapping with the translational start codons of
cutB1
and
cutB2
. This palindrome sequence was shown to be involved in catabolite repression of the
cutBCA
operons. The transcription start point of
cutR
was determined to be the nucleotide G located 36 bp upstream of the start codon of
cutR
. Expression of
cutR
was higher in
Mycobacterium
sp. strain JC1 grown with glucose than that grown with CO.
Role of MrkJ, a Phosphodiesterase, in Type 3 Fimbrial Expression and Biofilm Formation in
Klebsiella pneumoniae
Authors: Johnson Jeremiah G. , Clegg Steven 
Published: May 2010

ABSTRACT

Klebsiella pneumoniae
is an opportunistic pathogen that has been shown to adhere to human extracellular matrices using the type 3 fimbriae. Introduction of plasmids carrying genes known to alter intracellular cyclic-di-GMP pools in
Vibrio parahaemolyticus
revealed that these genes also altered type 3 fimbrial surface expression in
K. pneumoniae
. Immediately adjacent to the type 3 fimbrial gene cluster is a gene,
mrkJ
, that is related to a family of bacterial genes encoding phosphodiesterases. We identify here a role for MrkJ, a functional phosphodiesterase exhibiting homology to EAL domain-containing proteins, in controlling type 3 fimbria production and biofilm formation in
K. pneumoniae
. Deletion of
mrkJ
resulted in an increase in type 3 fimbria production and biofilm formation as a result of the accumulation of intracellular cyclic-di-GMP. This gene was shown to encode a functional phosphodiesterase via restoration of motility in a
V. parahaemolyticus
strain previously shown to accumulate cyclic-di-GMP and
in vitro
using phosphodiesterase activity assays. The effect of the
mrkJ
mutation on type 3 fimbrial expression was shown to be at the level of
mrkA
gene transcription by using quantitative reverse transcription-PCR. These results reveal a previously unknown role for cyclic-di-GMP in type 3 fimbrial production.
Replication ofVibrio choleraeChromosome I inEscherichia coli: Dependence on Dam Methylation
Authors: Koch Birgit , Ma Xiaofang , Løbner-Olesen Anders 
Published: May 2010

ABSTRACTWe successfully substitutedEscherichia coli's origin of replicationoriCwith the origin region ofVibrio choleraechromosome I (oriCIVc). Replication fromoriCIVcinitiated at a similar or slightly reduced cell mass compared to that of normalE. coli oriC. With respect to sequestration-dependent synchrony of initiation and stimulation of initiation by the loss of Hda activity, replication initiation fromoriCandoriCIVcwere similar. Since Hda is involved in the conversion of DnaAATP(DnaA bound to ATP) to DnaAADP(DnaA bound to ADP), this indicates that DnaA associated with ATP is limiting forV. choleraechromosome I replication, which similar to what is observed forE. coli. Nohdahomologue has been identified inV. choleraeyet. InV. cholerae,damis essential for viability, whereas inE. coli,dammutants are viable. Replacement ofE. coli oriCwithoriCIVcallowed us to specifically address the role of the Dam methyltransferase and SeqA in replication initiation fromoriCIVc. We show that whenE. coli's origin of replication is substituted byoriCIVc,dam, but notseqA, becomes important for growth, arguing that Dam methylation exerts a critical function at the origin of replication itself. We propose that Dam methylation promotes DnaA-assisted successful duplex opening and replisome assembly atoriCIVcinE. coli. In this model, methylation atoriCIVcwould ease DNA melting. This is supported by the fact that the requirement fordamcan be alleviated by increasing negative supercoiling of the chromosome through oversupply of the DNA gyrase or loss of SeqA activity.
Complete Genome Sequence of Probiotic
Bifidobacterium animalis
subsp.
lactis
Strain V9
Authors: Sun Zhihong , Chen Xia , Wang Jicheng , Gao Pengfei , Zhou Zhemin , Ren Yi , Sun Tiansong , Wang Lei , Meng He , Chen Wei , Zhang Heping 
Published: May 2010

ABSTRACT

Bifidobacterium animalis
subsp.
lactis
strain V9 is a Chinese commercial bifidobacteria with several probiotic functions. It was isolated from a healthy Mongolian child in China. We present here the complete genome sequence of V9 and compare it to 3 other published genome sequences of
B. animalis
subsp.
lactis
strains. The result indicates the lack of polymorphism among strains of this subspecies from different continents.
Nooks and Crannies in Type VI Secretion Regulation
Authors: Bernard Christophe S. , Brunet Yannick R. , Gueguen Erwan , Cascales Eric 
Published: May 2010

ABSTRACTType VI secretion systems (T6SS) are macromolecular, transenvelope machines encoded within the genomes of most Gram-negative bacteria, including plant, animal, and human pathogens, as well as soil and environmental isolates. T6SS are involved in a broad variety of functions: from pathogenesis to biofilm formation and stress sensing. This large array of functions is reflected by a vast diversity of regulatory mechanisms: repression by histone-like proteins and regulation by quorum sensing, transcriptional factors, two-component systems, alternative sigma factors, or small regulatory RNAs. Finally, T6SS may be produced in an inactive state and are turned on through the action of a posttranslational cascade involving phosphorylation and subunit recruitment. The current data reviewed here highlight how T6SS have been integrated into existing regulatory networks and how the expression of the T6SS loci is precisely modulated to adapt T6SS production to the specific needs of individual bacteria.
Revisiting the Assignment of Rv0241c to Fatty Acid Synthase Type II ofMycobacterium tuberculosis
Authors: Sacco Emmanuelle , Slama Nawel , Bäckbro Kristina , Parish Tanya , Laval Françoise , Daffé Mamadou , Eynard Nathalie , Quémard Annaık̈ 
Published: May 2010

ABSTRACTThe fatty acid synthase type II enzymatic complex ofMycobacterium tuberculosis(FAS-IIMt) catalyzes an essential metabolic pathway involved in the biosynthesis of major envelope lipids, mycolic acids. The partner proteins of this singular FAS-II system represent relevant targets for antituberculous drug design. Two heterodimers of the hydratase 2 protein family, HadAB and HadBC, were shown to be involved in the (3R)-hydroxyacyl-ACP dehydration (HAD) step of FAS-IIMtcycles. Recently, an additional member of this family, Rv0241c, was proposed to have the same function, based on the heterologous complementation of a HAD mutant of the yeast mitochondrial FAS-II system. In the present work,Rv0241cwas able to complement a HAD mutant in theEscherichia colimodel but not a dehydratase-isomerase deficient mutant. However, an enzymatic study of the purified protein demonstrated that Rv0241c possesses a broad chain length specificity for the substrate, unlike FAS-IIMtenzymes. Most importantly, Rv0241c exhibited a strict dependence on the coenzyme A (CoA) as opposed to AcpM, the natural acyl carrier protein bearing the chains elongated by FAS-IIMt. The deletion ofRv0241cshowed that this gene is not essential toM. tuberculosissurvivalin vitro. The resulting mutant did not display any change in the mycolic acid profile. This demonstrates that Rv0241c is atrans-2-enoyl-CoA hydratase/3-hydroxyacyl-CoA dehydratase that does not belong to FAS-IIMt. The relevance of a heterologous complementation strategy to identifying proteins of such a system is questioned.