bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative and Qualitative β Diversity Measures Lead to Different Insights into Factors That Structure Microbial Communities
Authors: Lozupone Catherine A. , Hamady Micah , Kelley Scott T. , Knight Rob 
Published: January 2007

ABSTRACT

The assessment of microbial diversity and distribution is a major concern in environmental microbiology. There are two general approaches for measuring community diversity: quantitative measures, which use the abundance of each taxon, and qualitative measures, which use only the presence/absence of data. Quantitative measures are ideally suited to revealing community differences that are due to changes in relative taxon abundance (e.g., when a particular set of taxa flourish because a limiting nutrient source becomes abundant). Qualitative measures are most informative when communities differ primarily by what can live in them (e.g., at high temperatures), in part because abundance information can obscure significant patterns of variation in which taxa are present. We illustrate these principles using two 16S rRNA-based surveys of microbial populations and two phylogenetic measures of community β diversity: unweighted UniFrac, a qualitative measure, and weighted UniFrac, a new quantitative measure, which we have added to the UniFrac website (
http://bmf.colorado.edu/unifrac
). These studies considered the relative influences of mineral chemistry, temperature, and geography on microbial community composition in acidic thermal springs in Yellowstone National Park and the influences of obesity and kinship on microbial community composition in the mouse gut. We show that applying qualitative and quantitative measures to the same data set can lead to dramatically different conclusions about the main factors that structure microbial diversity and can provide insight into the nature of community differences. We also demonstrate that both weighted and unweighted UniFrac measurements are robust to the methods used to build the underlying phylogeny.
Identification of a Sterol Δ7 Reductase Gene Involved in Desmosterol Biosynthesis in
Mortierella alpina
1S-4
Authors: Zhang Shuo , Sakuradani Eiji , Shimizu Sakayu 
Published: January 2007

ABSTRACT

Molecular cloning of the gene encoding sterol Δ7 reductase from the filamentous fungus
Mortierella alpina
1S-4, which accumulates cholesta-5,24-dienol (desmosterol) as the main sterol, revealed that the open reading frame of this gene, designated MoΔ
7SR
, consists of 1,404 bp and codes for 468 amino acids with a molecular weight of 53,965. The predicted amino acid sequence of MoΔ7SR showed highest homology of 51% with that of sterol Δ7 reductase (EC 1.3.1.21) from
Xenopus laevis
(African clawed frog). Heterologous expression of the Mo
Δ7SR
gene in yeast
Saccharomyces cerevisiae
revealed that MoΔ7SR converts ergosta-5,7-dienol to ergosta-5-enol (campesterol) by the activity of Δ7 reductase. In addition, with gene silencing of Mo
Δ7SR
gene by RNA interference, the transformant accumulated cholesta-5,7,24-trienol up to 10% of the total sterols with a decrease in desmosterol. Cholesta-5,7,24-trienol is not detected in the control strain. This indicates that MoΔ7SR is involved in desmosterol biosynthesis in
M. alpina
1S-4. This study is the first report on characterization of sterol Δ7 reductase from a microorganism.
Microbial Diversity within Early-Stage CulturedPanulirus ornatusPhyllosomas
Authors: Payne Matthew S. , Hall Mike R. , Sly Lindsay , Bourne David G. 
Published: January 2007

ABSTRACTA thorough understanding of the microorganisms and pathogens associated with the larval stage of the tropical ornate rock lobster,Panulirus ornatus, is required to overcome disease outbreaks that currently block aquaculture attempts. This study used microscopy in addition to culture and molecularly based microbiological techniques to characterize the bacterial community associated with cultured, developmental stage PI to PIIP. ornatusphyllosomas. Scanning electron microscopy demonstrated colonization of phyllosomas by filamentous, rod-shaped, and coccus-shaped bacteria. A clone library constructed from dead phyllosomas sampled from the larval rearing tank on day 10 was dominated byThiothrix-affiliated sequences (56% of clones). A comparable library from live phyllosomas also containedThiothrix-affiliated sequences, though these only represented 19% of clones within the library. Fluorescent in situ hybridization (FISH) confirmed identification of the filamentous bacteria asThiothrixsp., being present on dead phyllosomas. FISH also identifiedLeucothrixsp. andVibriosp., as well as a range of other rod- and coccus-shaped bacteria, colonizing both live and dead phyllosomas. The development of the microbial community associated with phyllosomas was monitored through a standard larval rearing run using denaturing gradient gel electrophoresis (DGGE).Vibriosp.-affiliated bands dominated the profiles of live animals through the rearing period and dead phyllosomas sampled on selected days. The population ofVibriosp. associated with phyllosomas was monitored with culture-based analysis on selective media and demonstrated to increase significantly on day 7, coinciding with the beginning of the larval molt. An isolatedVibrio harveyistrain demonstrated an identical 16S rRNA sequence with retrieved DGGE and clone library sequences. Colonization of phyllosomas with filamentous bacterial species potentially hinders the ability of the animals to molt and, combined with the added stress of the molt process, likely results in reduced immune function, allowing opportunistic pathogenicVibriosp. to cause larval mortalities.
Redirection of Metabolism for Biological Hydrogen Production
Authors: Rey Federico E. , Heiniger Erin K. , Harwood Caroline S. 
Published: January 2007

ABSTRACT

A major route for hydrogen production by purple photosynthetic bacteria is biological nitrogen fixation. Nitrogenases reduce atmospheric nitrogen to ammonia with the concomitant obligate production of molecular hydrogen. However, hydrogen production in the context of nitrogen fixation is a rather inefficient process because about 75% of the reductant consumed by the nitrogenase is used to generate ammonia. In this study we describe a selection strategy to isolate strains of purple photosynthetic bacteria in which hydrogen production is necessary for growth and independent of nitrogen fixation. We obtained four mutant strains of the photosynthetic bacterium
Rhodopseudomonas palustris
that produce hydrogen constitutively, even in the presence of ammonium, a condition where wild-type cells do not accumulate detectable amounts of hydrogen. Some of these strains produced up to five times more hydrogen than did wild-type cells growing under nitrogen-fixing conditions. Transcriptome analyses of the hydrogen-producing mutant strains revealed that in addition to the nitrogenase genes, 18 other genes are potentially required to produce hydrogen. The mutations that caused constitutive hydrogen production mapped to four different sites in the NifA transcriptional regulator in the four different strains. The strategy presented here can be applied to the large number of diverse species of anoxygenic photosynthetic bacteria that are known to exist in nature to identify strains for which there are fitness incentives to produce hydrogen.
Effects of Abiotic Factors on the Phylogenetic Diversity of Bacterial Communities in Acidic Thermal Springs
Authors: Mathur Jayanti , Bizzoco Richard W. , Ellis Dean G. , Lipson David A. , Poole Alexander W. , Levine Richard , Kelley Scott T. 
Published: January 2007

ABSTRACT

Acidic thermal springs offer ideal environments for studying processes underlying extremophile microbial diversity. We used a carefully designed comparative analysis of acidic thermal springs in Yellowstone National Park to determine how abiotic factors (chemistry and temperature) shape acidophile microbial communities. Small-subunit rRNA gene sequences were PCR amplified, cloned, and sequenced, by using evolutionarily conserved bacterium-specific primers, directly from environmental DNA extracted from Amphitheater Springs and Roaring Mountain sediment samples. Energy-dispersive X-ray spectroscopy, X-ray diffraction, and colorimetric assays were used to analyze sediment chemistry, while an optical emission spectrometer was used to evaluate water chemistry and electronic probes were used to measure the pH, temperature, and E
h
of the spring waters. Phylogenetic-statistical analyses found exceptionally strong correlations between bacterial community composition and sediment mineral chemistry, followed by weaker but significant correlations with temperature gradients. For example, sulfur-rich sediment samples contained a high diversity of uncultured organisms related to
Hydrogenobaculum
spp., while iron-rich sediments were dominated by uncultured organisms related to a diverse array of gram-positive iron oxidizers. A detailed analysis of redox chemistry indicated that the available energy sources and electron acceptors were sufficient to support the metabolic potential of
Hydrogenobaculum
spp. and iron oxidizers, respectively. Principal-component analysis found that two factors explained 95% of the genetic diversity, with most of the variance attributable to mineral chemistry and a smaller fraction attributable to temperature.
Cdc37p Is Required for Stress-Induced High-Osmolarity Glycerol and Protein Kinase C Mitogen-Activated Protein Kinase Pathway Functionality by Interaction with Hog1p and Slt2p (Mpk1p)
Authors: Hawle Patricija , Horst Danielle , Bebelman Jan Paul , Yang Xiao Xian , Siderius Marco , van der Vies Saskia M. 
Published: January 2007

ABSTRACT

The yeast
Saccharomyces cerevisiae
utilizes rapidly responding mitogen-activated protein kinase (MAPK) signaling cascades to adapt efficiently to a changing environment. Here we report that phosphorylation of Cdc37p, an Hsp90 cochaperone, by casein kinase 2 controls the functionality of two MAPK cascades in yeast. These pathways, the high-osmolarity glycerol (HOG) pathway and the cell integrity (protein kinase C) MAPK pathway, mediate adaptive responses to high osmotic and cell wall stresses, respectively. Mutation of the phosphorylation site Ser14 in Cdc37p renders cells sensitive to osmotic stress and cell wall perturbation by calcofluor white. We found that levels of the MAPKs Hog1p and Slt2p (Mpk1p) in cells are reduced in a
cdc37
-S14A mutant, and consequently downstream responses mediated by Hog1p and Slt2p are compromised. Furthermore, we present evidence that Hog1p and Slt2p both interact in a complex with Cdc37p in vivo, something that has not been reported previously. The interaction of Hsp90, Slt2p, and Hog1p with Cdc37p depends on the phosphorylation status of Cdc37p. In fact, our biochemical data show that the osmosensitive phenotype of the
cdc37
-S14A mutant is due to the loss of the interaction between Cdc37p, Hog1p, and Hsp90. Likewise, during cell wall stress, the interaction of Slt2p with Cdc37p and Hsp90 is crucial for Slt2p-dependent downstream responses, such as the activation of the transcription factor Rlm1p. Interestingly, phosphorylated Slt2p, but not phosphorylated Hog1p, has an increased affinity for Cdc37p. Together these observations suggest that Cdc37p acts as a regulator of MAPK signaling.
Yersiniabactin Is a Virulence Factor for
Klebsiella pneumoniae
during Pulmonary Infection
Authors: Lawlor Matthew S. , O'Connor Christopher , Miller Virginia L. 
Published: January 2007

ABSTRACT

Iron acquisition systems are essential for the in vivo growth of bacterial pathogens. Despite the epidemiological importance of
Klebsiella pneumoniae
, few experiments have examined the importance of siderophores in the pathogenesis of this species. A previously reported signature-tagged mutagenesis screen identified an attenuated strain that featured an insertional disruption in
ybtQ
, which encodes a transporter for the siderophore yersiniabactin. We used this finding as a starting point to evaluate the importance of siderophores in the physiology and pathogenesis of
K. pneumoniae
. Isogenic strains carrying in-frame deletions in genes required for the synthesis of either enterobactin or yersiniabactin were constructed, and the growth of these mutants was examined both in vitro and in vivo using an intranasal infection model. The results suggest divergent functions for each siderophore in different environments, with enterobactin being more important for growth in vitro under iron limitation than in vivo and the reverse being true for the yersiniabactin locus. These observations represent the first examination of isogenic mutants in iron acquisition systems for
K. pneumoniae
and may indicate that the acquisition of nonenterobactin siderophores is an important step in the evolution of virulent enterobacterial strains.
Human Immunoglobulin G2 (IgG2) and IgG4, but Not IgG1 or IgG3, Protect Mice againstCryptococcus neoformansInfection
Authors: Beenhouwer David O. , Yoo Esther M. , Lai Chun-Wei , Rocha Miguel A. , Morrison Sherie L. 
Published: January 2007

ABSTRACTThe encapsulated yeastCryptococcus neoformansis a significant cause of meningitis and death in patients with AIDS. Some murine monoclonal antibodies (MAbs) against the glucuronoxylomannan (GXM) component of theC. neoformanscapsular polysaccharide can prolong the lives of infected mice, while others have no effect or can even shorten survival. To date, no one has systematically compared the efficacies of antibodies with the same variable regions and different human constant regions with their unique combination of effector functions in providing protection against murineC. neoformansinfection. In the present study, we examined the efficacies of anti-GXM MAbs of the four human immunoglobulin G (IgG) subclasses, which have identical variable regions but differ in their capacities to bind the three types of Fc receptors for IgG (FcγR), their abilities to activate complement, and their half-lives. IgG2 and IgG4 anti-GXM prolonged the lives of infected BALB/c mice, IgG3 anti-GXM did not affect animal survival, while mice treated with IgG1 anti-GXM died earlier than mice treated with phosphate-buffered saline or irrelevant isotype-matched MAbs. All MAbs decreased serum GXM in infected animals. Effector pathways traditionally believed to be important in defense against microbes, such as opsonophagocytosis and complement binding, negatively correlated with antibody efficacy. It is generally accepted that human IgG1 has the most favorable combination of effector functions for therapeutic use against infections. Therefore, our findings have significant implications for humanization of the mouse IgG1 currently in clinical trials for cryptococcal meningitis and for the design of antibody therapeutics to treat other infectious diseases as well.
Native Microbial Colonization of
Drosophila melanogaster
and Its Use as a Model of
Enterococcus faecalis
Pathogenesis
Authors: Cox Christopher R. , Gilmore Michael S. 
Published: January 2007

ABSTRACT

Enterococci are commensal organisms of the gastrointestinal (GI) tracts of a broad range of mammalian and insect hosts, but they are also leading causes of nosocomial infection. Little is known about the ecological role of enterococci in the GI tract consortia. To develop a tractable model for studying the roles of these organisms as commensals and pathogens, we characterized the
Drosophila melanogaster
microflora and examined the occurrence of enterococci in the gastrointestinal consortium of
Drosophila
. In a survey of laboratory-reared
Drosophila
and wild-captured flies, we found that
Drosophila
was naturally colonized by representatives of five bacterial phyla. Among these organisms were several species of enterococci, including
Enterococcus faecalis
,
Enterococcus faecium
,
Enterococcus gallinaraum
, and
Enterococcus durans
, as well as a previously detected but uncultured
Enterococcus
species.
Drosophila
could be cured of enterococcal carriage by antibiotic treatment and could be reassociated with laboratory strains. High-level colonization by a well-characterized strain expressing the enterococcal cytolysin was found to be detrimental to
Drosophila
compared to the effect of an isogenic, noncytolytic control. The anatomical distribution of enterococci in the
Drosophila
GI tract was determined by immunohistochemical staining of thin sections of naturally colonized and reassociated flies.
Burkholderia cenocepacia
Requires a Periplasmic HtrA Protease for Growth under Thermal and Osmotic Stress and for Survival In Vivo
Authors: Flannagan Ronald S. , Aubert Daniel , Kooi Cora , Sokol Pamela A. , Valvano Miguel A. 
Published: January 2007

ABSTRACT

Burkholderia cenocepacia
, a member of the
B. cepacia
complex, is an opportunistic pathogen that causes serious infections in patients with cystic fibrosis. We identified a six-gene cluster in chromosome 1 encoding a two-component regulatory system (BCAL2831 and BCAL2830) and an HtrA protease (BCAL2829) hypothesized to play a role in the
B. cenocepacia
stress response. Reverse transcriptase PCR analysis of these six genes confirmed they are cotranscribed and comprise an operon. Genes in this operon, including
htrA
, were insertionally inactivated by recombination with a newly created suicide plasmid, pGPΩTp. Genetic analyses and complementation studies revealed that HtrA
BCAL2829
was required for growth of
B. cenocepacia
upon exposure to osmotic stress (NaCl or KCl) and thermal stress (44°C). In addition, replacement of the serine residue in the active site with alanine (S245A) and deletion of the HtrA
BCAL2829
PDZ domains demonstrated that these areas are required for protein function. HtrA
BCAL2829
also localizes to the periplasmic compartment, as shown by Western blot analysis and a colicin V reporter assay. Using the rat agar bead model of chronic lung infection, we also demonstrated that inactivation of the
htrA
gene is associated with a bacterial survival defect in vivo. Together, our data demonstrate that HtrA
BCAL2829
is a virulence factor in
B. cenocepacia
.
Mutagenesis of
hetR
Reveals Amino Acids Necessary for HetR Function in the Heterocystous Cyanobacterium
Anabaena
sp. Strain PCC 7120
Authors: Risser Douglas D. , Callahan Sean M. 
Published: January 2007

ABSTRACT

HetR is the master regulator of heterocyst differentiation in the filamentous cyanobacterium
Anabaena
sp. strain PCC 7120. Genetic selection was used to identify 33 amino acid substitutions in HetR that reduced the proportion of cells undergoing heterocyst differentiation to less than 2%. Conservative substitutions in the wild-type HetR protein revealed three mutations that dramatically reduced the amount of heterocyst differentiation when the mutant allele was present in place of the wild-type allele on a replicating plasmid in a mutant lacking
hetR
on the chromosome. An H69Y substitution resulted in heterocyst formation among less than 0.1% of cells, and D17E and G36A substitutions resulted in a Het
−
phenotype, compared to heterocyst formation among approximately 25% of cells with the wild-type
hetR
under the same conditions. The D17E substitution prevented DNA binding activity exhibited by wild-type HetR in mobility shift assays, whereas G36A and H69Y substitutions had no affect on DNA binding. D17E, G36A, and H69Y substitutions also resulted in higher levels of the corresponding HetR protein than of the wild-type protein when each was expressed from an inducible promoter in a
hetR
deletion strain, suggesting an effect on HetR protein turnover. Surprisingly, C48A and S152A substitutions, which were previously reported to result in a Het
−
phenotype, were found to have no effect on heterocyst differentiation or patterning when the corresponding mutations were introduced into an otherwise wild-type genetic background in
Anabaena
sp. strain PCC 7120. The clustering of mutations that satisfied the positive selection near the amino terminus suggests an important role for this part of the protein in HetR function.
Inferring a Population Structure for
Staphylococcus epidermidis
from Multilocus Sequence Typing Data
Authors: Miragaia M. , Thomas J. C. , Couto I. , Enright M. C. , de Lencastre H. 
Published: January 2007

ABSTRACT

Despite its importance as a human pathogen, information on population structure and global epidemiology of
Staphylococcus epidermidis
is scarce and the relative importance of the mechanisms contributing to clonal diversification is unknown. In this study, we addressed these issues by analyzing a representative collection of
S. epidermidis
isolates from diverse geographic and clinical origins using multilocus sequence typing (MLST). Additionally, we characterized the mobile element (SCC
mec
) carrying the genetic determinant of methicillin resistance. The 217
S. epidermidis
isolates from our collection were split by MLST into 74 types, suggesting a high level of genetic diversity. Analysis of MLST data using the eBURST algorithm revealed the existence of nine epidemic clonal lineages that were disseminated worldwide. One single clonal lineage (clonal complex 2) comprised 74% of the isolates, whereas the remaining isolates were clustered into 8 minor clonal lineages and 13 singletons. According to our evolutionary model, SCC
mec
was acquired at least 56 times by
S. epidermidis
. Although geographic dissemination of
S. epidermidis
strains and the value of the index of association between the alleles, 0.2898 (
P
< 0.05), support the clonality of
S. epidermidis
species, examination of the sequence changes at MLST loci during clonal diversification showed that recombination gives rise to new alleles approximately twice as frequently as point mutations. We suggest that
S. epidermidis
has a population with an epidemic structure, in which nine clones have emerged upon a recombining background and evolved quickly through frequent transfer of genetic mobile elements, including SCC
mec
.
Multiple Roles of Biosurfactants in Structural Biofilm Development by
Pseudomonas aeruginosa
Authors: Pamp Sünje Johanna , Tolker-Nielsen Tim 
Published: January 2007

ABSTRACT

Recent studies have indicated that biosurfactants produced by
Pseudomonas aeruginosa
play a role both in maintaining channels between multicellular structures in biofilms and in dispersal of cells from biofilms. Through the use of flow cell technology and enhanced confocal laser scanning microscopy, we have obtained results which suggest that the biosurfactants produced by
P. aeruginosa
play additional roles in structural biofilm development. We present genetic evidence that during biofilm development by
P. aeruginosa
, biosurfactants promote microcolony formation in the initial phase and facilitate migration-dependent structural development in the later phase.
P. aeruginosa rhlA
mutants, deficient in synthesis of biosurfactants, were not capable of forming microcolonies in the initial phase of biofilm formation. Experiments involving two-color-coded mixed-strain biofilms showed that
P. aeruginosa rhlA
mutants were defective in migration-dependent development of mushroom-shaped multicellular structures in the later phase of biofilm formation. Experiments involving three-color-coded mixed-strain
P. aeruginosa
biofilms demonstrated that the wild-type and
rhlA
and
pilA
mutant strains formed distinct subpopulations on top of each other dependent on their ability to migrate and produce biosurfactants.