bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of pH on Isolation and Distribution of Members of Subdivision 1 of the Phylum
Acidobacteria
Occurring in Soil
Authors: Sait Michelle , Davis Kathryn E. R. , Janssen Peter H. 
Published: March 2006

ABSTRACT

The pH strongly influenced the development of colonies by members of subdivision 1 of the phylum
Acidobacteria
on solid laboratory media. Significantly more colonies of this group formed at pH 5.5 than at pH 7.0. At pH 5.5, 7 to 8% of colonies that formed on plates that were incubated for 4 months were formed by subdivision 1 acidobacteria. These colonies were formed by bacteria that spanned almost the entire phylogenetic breadth of the subdivision, and there was considerable congruence between the diversity of this group as determined by the cultivation-based method and by surveying 16S rRNA genes in the same soil. Members of subdivision 1 acidobacteria therefore appear to be readily culturable. An analysis of published libraries of 16S rRNAs or 16S rRNA genes showed a very strong correlation between the abundance of subdivision 1 acidobacteria in soil bacterial communities and the soil pH. Subdivision 1 acidobacteria were most abundant in libraries from soils with pHs of <6, but rare or absent in libraries from soils with pHs of >6.5. This, together with the selective cultivation of members of the group on lower-pH media, indicates that growth of many members of subdivision 1 acidobacteria is favored by slightly to moderately acidic growth conditions.
Composition and Dynamics of Bacterial Communities of a Drinking Water Supply System as Assessed by RNA- and DNA-Based 16S rRNA Gene Fingerprinting
Authors: Eichler Stefan , Christen Richard , Höltje Claudia , Westphal Petra , Bötel Julia , Brettar Ingrid , Mehling Arndt , Höfle Manfred G. 
Published: March 2006

ABSTRACT

Bacterial community dynamics of a whole drinking water supply system (DWSS) were studied from source to tap. Raw water for this DWSS is provided by two reservoirs with different water characteristics in the Harz mountains of Northern Germany. Samples were taken after different steps of treatment of raw water (i.e., flocculation, sand filtration, and chlorination) and at different points along the supply system to the tap. RNA and DNA were extracted from the sampled water. The 16S rRNA or its genes were partially amplified by reverse transcription-PCR or PCR and analyzed by single-strand conformation polymorphism community fingerprints. The bacterial community structures of the raw water samples from the two reservoirs were very different, but no major changes of these structures occurred after flocculation and sand filtration. Chlorination of the processed raw water strongly affected bacterial community structure, as reflected by the RNA-based fingerprints. This effect was less pronounced for the DNA-based fingerprints. After chlorination, the bacterial community remained rather constant from the storage containers to the tap. Furthermore, the community structure of the tap water did not change substantially for several months. Community composition was assessed by sequencing of abundant bands and phylogenetic analysis of the sequences obtained. The taxonomic compositions of the bacterial communities from both reservoirs were very different at the species level due to their different limnologies. On the other hand, major taxonomic groups, well known to occur in freshwater, such as
Alphaproteobacteria
,
Betaproteobacteria
, and
Bacteroidetes
, were found in both reservoirs. Significant differences in the detection of the major groups were observed between DNA-based and RNA-based fingerprints irrespective of the reservoir. Chlorination of the drinking water seemed to promote growth of nitrifying bacteria. Detailed analysis of the community dynamics of the whole DWSS revealed a significant influence of both source waters on the overall composition of the drinking water microflora and demonstrated the relevance of the raw water microflora for the drinking water microflora provided to the end user.
In Vivo
Himar1
-Based Transposon Mutagenesis of
Francisella tularensis
Authors: Maier Tamara M. , Pechous Roger , Casey Monika , Zahrt Thomas C. , Frank D. W. 
Published: March 2006

ABSTRACT

Francisella tularensis
is the intracellular pathogen that causes human tularemia. It is recognized as a potential agent of bioterrorism due to its low infectious dose and multiple routes of entry. We report the development of a
Himar1
-based random mutagenesis system for
F. tularensis
(
HimarFT
). In vivo mutagenesis of
F. tularensis
live vaccine strain (LVS) with
HimarFT
occurs at high efficiency. Approximately 12 to 15% of cells transformed with the delivery plasmid result in transposon insertion into the genome. Results from Southern blot analysis of 33 random isolates suggest that single insertions occurred, accompanied by the loss of the plasmid vehicle in most cases. Nucleotide sequence analysis of rescued genomic DNA with
HimarFT
indicates that the orientation of integration was unbiased and that insertions occurred in open reading frames and intergenic and repetitive regions of the chromosome. To determine the utility of the system, transposon mutagenesis was performed, followed by a screen for growth on Chamberlain's chemically defined medium (CDM) to isolate auxotrophic mutants. Several mutants were isolated that grew on complex but not on the CDM. We genetically complemented two of the mutants for growth on CDM with a newly constructed plasmid containing a nourseothricin resistance marker. In addition, uracil or aromatic amino acid supplementation of CDM supported growth of isolates with insertions in
pyrD
,
carA
, or
aroE1
supporting the functional assignment of genes within each biosynthetic pathway. A mutant containing an insertion in
aroE1
demonstrated delayed replication in macrophages and was restored to the parental growth phenotype when provided with the appropriate plasmid in
trans
. Our results suggest that a comprehensive library of mutants can be generated in
F. tularensis
LVS, providing an additional genetic tool to identify virulence determinants required for survival within the host.
Chromosomal Dynamism in Progeny of Outbreak-Related Sorbitol-Fermenting EnterohemorrhagicEscherichia coliO157:NM
Authors: Bielaszewska Martina , Prager Rita , Zhang Wenlan , Friedrich Alexander W. , Mellmann Alexander , Tschäpe Helmut , Karch Helge 
Published: March 2006

ABSTRACTSorbitol-fermenting (SF) enterohemorrhagicEscherichia coli(EHEC) O157:NM (nonmotile) is a unique clone that causes outbreaks of hemorrhagic colitis and hemolytic-uremic syndrome. In well-defined clusters of cases, we have observed significant variability in pulsed-field gel electrophoresis (PFGE) patterns which could indicate coinfection by different strains. An analysis of randomly selected progeny colonies of an outbreak strain after subcultivation demonstrated that they displayed either the cognate PFGE outbreak pattern or one of four additional patterns and were <89% similar. These profound alterations were associated with changes in the genomic position of one of two Shiga toxin 2-encoding genes (stx2) in the outbreak strain or with the loss of this gene. The twostx2alleles in the outbreak strain were identical but were flanked with phage-related sequences with only 77% sequence identity. Neither of these phages produced plaques, but one lysogenizedE. coliK-12 and integrated inyecEin the lysogens and the wild-type strain. The presence of twostx2genes which correlated with increased production of Stx2 in vitro but not with the clinical outcome of infection was also found in 14 (21%) of 67 SF EHEC O157:NM isolates from sporadic cases of human disease. The variability of PFGE patterns for the progeny of a single colony must be considered when interpreting PFGE patterns in SF EHEC O157-associated outbreaks.
Conservation of the Pho regulon in
Pseudomonas fluorescens
Pf0-1
Authors: Monds Russell D. , Newell Peter D. , Schwartzman Julia A. , O'Toole George A. 
Published: March 2006

ABSTRACT

The Pho regulon integrates the sensing of environmental inorganic phosphate (P
i
) availability with coregulation of gene expression, mediating an adaptive response to P
i
limitation. Many aspects of the Pho regulon have been addressed in studies of
Escherichia coli
; however, it is unclear how transferable this knowledge is to other bacterial systems. Here, we report work to discern the conservation of the Pho regulon in
Pseudomonas fluorescens
Pf0-1. We demonstrate by mutational studies that PhoB/PhoR and the Pst system have conserved functions in the regulation of P
i
-induced phosphatase activities, as well as expression of other P
i
-regulated genes. A genetic screen was carried out to isolate factors that affect Pho-regulated phosphatase activity. We identified the Pho-regulated phosphatases PhoX and PhoD and present evidence that these enzymes are exported via the Tat system. The
phoX
and
phoD
genes were shown to be members of the Pho regulon by reverse transcription-PCR, as well as by functional assessment of putative PhoB binding sites (Pho boxes). Our data also suggested that at least one other non-Tat-secreted Pho-regulated phosphatase exists. From the genetic screen, numerous siderophore mutants that displayed severe defects in Pho-activated phosphatase activity were isolated. Subsequently, iron was shown to be important for modulating the activity of Pho-regulated phosphatases, but it does not regulate this activity at the level of transcription. We also identify and demonstrate a novel role in siderophore production and Pho-regulated phosphatase activity for ApaH, the hydrolase for the nucleotide-signaling molecule AppppA. Finally, numerous mutations in multiple cellular pathways were recovered that may be required for maximal induction of the Pho regulon under P
i
-limiting conditions.
Genome-Based Metabolic Engineering of
Mannheimia succiniciproducens
for Succinic Acid Production
Authors: Lee Sang Jun , Song Hyohak , Lee Sang Yup 
Published: March 2006

ABSTRACT

Succinic acid is a four-carbon dicarboxylic acid produced as one of the fermentation products of anaerobic metabolism. Based on the complete genome sequence of a capnophilic succinic acid-producing rumen bacterium,
Mannheimia succiniciproducens
, gene knockout studies were carried out to understand its anaerobic fermentative metabolism and consequently to develop a metabolically engineered strain capable of producing succinic acid without by-product formation. Among three different CO
2
-fixing metabolic reactions catalyzed by phosphoenolpyruvate (PEP) carboxykinase, PEP carboxylase, and malic enzyme, PEP carboxykinase was the most important for the anaerobic growth of
M. succiniciproducens
and succinic acid production. Oxaloacetate formed by carboxylation of PEP was found to be converted to succinic acid by three sequential reactions catalyzed by malate dehydrogenase, fumarase, and fumarate reductase. Major metabolic pathways leading to by-product formation were successfully removed by disrupting the
ldhA
,
pflB
,
pta
, and
ackA
genes. This metabolically engineered LPK7 strain was able to produce 13.4 g/liter of succinic acid from 20 g/liter glucose with little or no formation of acetic, formic, and lactic acids, resulting in a succinic acid yield of 0.97 mol succinic acid per mol glucose. Fed-batch culture of
M. succiniciproducens
LPK7 with intermittent glucose feeding allowed the production of 52.4 g/liter of succinic acid, with a succinic acid yield of 1.16 mol succinic acid per mol glucose and a succinic acid productivity of 1.8 g/liter/h, which should be useful for industrial production of succinic acid.
Metabolic Engineering of
Corynebacterium glutamicum
for Trehalose Overproduction: Role of the TreYZ Trehalose Biosynthetic Pathway
Authors: Carpinelli Jorge , Krämer Reinhard , Agosin Eduardo 
Published: March 2006

ABSTRACT

Trehalose has many potential applications in biotechnology and the food industry due to its protective effect against environmental stress. Our work explores microbiological production methods based on the capacity of
Corynebacterium glutamicum
to excrete trehalose. We address here raising trehalose productivity through homologous overexpression of maltooligosyltrehalose synthase and the maltooligosyltrehalose trehalohydrolase genes. In addition, heterologous expression of the UDP-glucose pyrophosphorylase gene from
Escherichia coli
improved the supply of glycogen. Gene expression effects were tested on enzymatic activities and intracellular glycogen content, as well as on accumulated and excreted trehalose. Overexpression of the
treY
gene and the
treY/treZ
synthetic operon significantly increased maltooligosyltrehalose synthase activity, the rate-limiting step, and improved the specific productivity and the final titer of trehalose. Furthermore, a strong decrease was noted in glycogen accumulation. Expression of
galU/treY
and
galU/treYZ
synthetic operons showed a partial recovery in the intracellular glycogen levels and a significant improvement in both intra- and extracellular trehalose content.
Unexpected Diversity of Bacteria Capable of Carbon Monoxide Oxidation in a Coastal Marine Environment, and Contribution of the
Roseobacter
-Associated Clade to Total CO Oxidation
Authors: Tolli J. D. , Sievert S. M. , Taylor C. D. 
Published: March 2006

ABSTRACT

The species diversity, phylogenetic affiliations, and physiological activity rates of carbon monoxide-oxidizing microorganisms were investigated, using new isolates from surface waters collected from the coast of New England and type strains from established collections. A direct isolation method allowed the simultaneous recovery of organisms with different growth rates and nutritional requirements and the identification of marine microorganisms that oxidize CO at an environmentally relevant concentration (42 nM CO). Isolates that oxidized CO at environmentally relevant rates (>4.5 × 10
−11
nmol CO oxidized cell
−1
h
−1
) were taxonomically diverse, with representatives in the alpha and gamma subclasses of the
Proteobacteria
and the phylum
Bacteroidetes
, and represent a hitherto unreported metabolic function for several diverse microbial types. Isolates and type strains having the greatest specific rates of CO metabolism (1.1 × 10
−10
to 2.3 × 10
−10
nmol CO oxidized cell
−1
h
−1
) belonged to the
Roseobacter
-associated clade (RAC) of the alpha subclass of the
Proteobacteria
. By using triple-labeled slide preparations, differential counts of active CO-oxidizing RAC cells, total RAC cells, and total bacterial cell counts in environmental samples were obtained. RAC organisms were a major component of total cell numbers (36%). Based on the density of active CO-oxidizing RAC cells in natural samples and RAC-specific metabolic activities determined for pure cultures, active CO-oxidizing RAC cells may contribute up to 15% of the total CO oxidation occurring in coastal waters.
Bacteriophage Migration via Nematode Vectors: Host-Parasite-Consumer Interactions in Laboratory Microcosms
Authors: Dennehy John J. , Friedenberg Nicholas A. , Yang Yul W. , Turner Paul E. 
Published: March 2006

ABSTRACT
Pathogens vectored by nematodes pose serious agricultural, economic, and health threats; however, little is known of the ecological and evolutionary aspects of pathogen transmission by nematodes. Here we describe a novel model system with two trophic levels, bacteriophages and nematodes, each of which competes for bacteria. We demonstrate for the first time that nematodes are capable of transmitting phages between spatially distinct patches of bacteria. This model system has considerable advantages, including the ease of maintenance and manipulation at the laboratory bench, the ability to observe many generations in short periods, and the capacity to freeze evolved strains for later comparison to their ancestors. More generally, experimental studies of complex multispecies interactions, host-pathogen coevolution, disease dynamics, and the evolution of virulence may benefit from this model system because current models (e.g., chickens, mosquitoes, and malaria parasites) are costly to maintain, are difficult to manipulate, and require considerable space. Our initial explorations centered on independently assessing the impacts of nematode, bacterium, and phage population densities on virus migration between host patches. Our results indicated that virus transmission increases with worm density and host bacterial abundance; however, transmission decreases with initial phage abundance, perhaps because viruses eliminate available hosts before migration can occur. We discuss the microbial growth dynamics that underlie these results, suggest mechanistic explanations for nematode transmission of phages, and propose intriguing possibilities for future research.
“CandidatusThiobios zoothamnicoli,” an Ectosymbiotic Bacterium Covering the Giant Marine CiliateZoothamnium niveum
Authors: Rinke Christian , Schmitz-Esser Stephan , Stoecker Kilian , Nussbaumer Andrea D. , Molnár Dávid A. , Vanura Katrina , Wagner Michael , Horn Matthias , Ott Jörg A. , Bright Monika 
Published: March 2006

ABSTRACTZoothamnium niveumis a giant, colonial marine ciliate from sulfide-rich habitats obligatorily covered with chemoautotrophic, sulfide-oxidizing bacteria which appear as coccoid rods and rods with a series of intermediate shapes. Comparative 16S rRNA gene sequence analysis and fluorescence in situ hybridization showed that the ectosymbiont ofZ. niveumbelongs to only one pleomorphic phylotype. TheZ. niveumectosymbiont is only moderately related to previously identified groups of thiotrophic symbionts within theGammaproteobacteria, and shows highest 16S rRNA sequence similarity with the free-living sulfur-oxidizing bacterial strain ODIII6 from shallow-water hydrothermal vents of the Mediterranean Sea (94.5%) and an endosymbiont from a deep-sea hydrothermal vent gastropod of the Indian Ocean Ridge (93.1%). A replacement of this specific ectosymbiont by a variety of other bacteria was observed only for senescent basal parts of the host colonies. The taxonomic status “CandidatusThiobios zoothamnicoli” is proposed for the ectosymbiont ofZ. niveumbased on its ultrastructure, its 16S rRNA gene, the intergenic spacer region, and its partial 23S rRNA gene sequence.
Sulfide Oxidation Coupled to Arsenate Reduction by a Diverse Microbial Community in a Soda Lake
Authors: Hollibaugh James T. , Budinoff Charles , Hollibaugh Ryan A. , Ransom Briana , Bano Nasreen 
Published: March 2006

ABSTRACT

We characterized the arsenate-reducing, sulfide-oxidizing population of Mono Lake, California, by analyzing the distribution and diversity of
rrnA
,
cbbL
, and dissimilatory arsenate reductase (
arrA
) genes in environmental DNA, arsenate-plus sulfide-amended lake water, mixed cultures, and isolates. The arsenate-reducing community was diverse. An organism represented by an
rrnA
sequence previously retrieved from Mono Lake and affiliated with the
Desulfobulbaceae
(
Deltaproteobacteria
) appears to be an important member of the arsenate-reducing, sulfide-oxidizing community. Sulfide oxidation coupled with arsenate reduction appears to proceed via a two-electron transfer, resulting in the production of arsenite and an intermediate S compound that is subsequently disproportionated. A realgar-like As/S mineral was formed in some experiments.
Genome Sequence of the Chemolithoautotrophic Nitrite-Oxidizing Bacterium
Nitrobacter winogradskyi
Nb-255
Authors: Starkenburg Shawn R. , Chain Patrick S. G. , Sayavedra-Soto Luis A. , Hauser Loren , Land Miriam L. , Larimer Frank W. , Malfatti Stephanie A. , Klotz Martin G. , Bottomley Peter J. , Arp Daniel J. , Hickey William J. 
Published: March 2006

ABSTRACT

The alphaproteobacterium
Nitrobacter winogradskyi
(ATCC 25391) is a gram-negative facultative chemolithoautotroph capable of extracting energy from the oxidation of nitrite to nitrate. Sequencing and analysis of its genome revealed a single circular chromosome of 3,402,093 bp encoding 3,143 predicted proteins. There were extensive similarities to genes in two alphaproteobacteria,
Bradyrhizobium japonicum
USDA110 (1,300 genes) and
Rhodopseudomonas palustris
CGA009 CG (815 genes). Genes encoding pathways for known modes of chemolithotrophic and chemoorganotrophic growth were identified. Genes encoding multiple enzymes involved in anapleurotic reactions centered on C
2
to C
4
metabolism, including a glyoxylate bypass, were annotated. The inability of
N. winogradskyi
to grow on C
6
molecules is consistent with the genome sequence, which lacks genes for complete Embden-Meyerhof and Entner-Doudoroff pathways, and active uptake of sugars. Two gene copies of the nitrite oxidoreductase, type I ribulose-1,5-bisphosphate carboxylase/oxygenase, cytochrome
c
oxidase, and gene homologs encoding an aerobic-type carbon monoxide dehydrogenase were present. Similarity of nitrite oxidoreductases to respiratory nitrate reductases was confirmed. Approximately 10% of the
N. winogradskyi
genome codes for genes involved in transport and secretion, including the presence of transporters for various organic-nitrogen molecules. The
N. winogradskyi
genome provides new insight into the phylogenetic identity and physiological capabilities of nitrite-oxidizing bacteria. The genome will serve as a model to study the cellular and molecular processes that control nitrite oxidation and its interaction with other nitrogen-cycling processes.
Denitrifier Community Composition along a Nitrate and Salinity Gradient in a Coastal Aquifer
Authors: Santoro Alyson E. , Boehm Alexandria B. , Francis Christopher A. 
Published: March 2006

ABSTRACTNitrogen flux into the coastal environment via submarine groundwater discharge may be modulated by microbial processes such as denitrification, but the spatial scales at which microbial communities act and vary are not well understood. In this study, we examined the denitrifying community within the beach aquifer at Huntington Beach, California, where high-nitrate groundwater is a persistent feature. Nitrite reductase-encoding gene fragments (nirKandnirS), responsible for the key step in the denitrification pathway, were PCR amplified, cloned, and sequenced from DNAs extracted from aquifer sediments collected along a cross-shore transect, where groundwater ranged in salinity from 8 to 34 practical salinity units and in nitrate concentration from 0.5 to 330 μM. We found taxonomically rich and novel communities, with allnirKclones exhibiting <85% identity andnirSclones exhibiting <92% identity at the amino acid level to those of cultivated denitrifiers and other environmental clones in the database. Unique communities were found at each site, despite being located within 40 m of each other, suggesting that the spatial scale at which denitrifier diversity and community composition vary is small. Statistical analyses ofnirsequences using the Monte Carlo-based program ∫-Libshuff confirmed that some populations were indeed distinct, although further sequencing would be required to fully characterize the highly diverse denitrifying communities at this site.