bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale
Authors: Lauber Christian L. , Hamady Micah , Knight Rob , Fierer Noah 
Published: June 2009

ABSTRACT

Soils harbor enormously diverse bacterial populations, and soil bacterial communities can vary greatly in composition across space. However, our understanding of the specific changes in soil bacterial community structure that occur across larger spatial scales is limited because most previous work has focused on either surveying a relatively small number of soils in detail or analyzing a larger number of soils with techniques that provide little detail about the phylogenetic structure of the bacterial communities. Here we used a bar-coded pyrosequencing technique to characterize bacterial communities in 88 soils from across North and South America, obtaining an average of 1,501 sequences per soil. We found that overall bacterial community composition, as measured by pairwise UniFrac distances, was significantly correlated with differences in soil pH (
r
= 0.79), largely driven by changes in the relative abundances of
Acidobacteria
,
Actinobacteria
, and
Bacteroidetes
across the range of soil pHs. In addition, soil pH explains a significant portion of the variability associated with observed changes in the phylogenetic structure within each dominant lineage. The overall phylogenetic diversity of the bacterial communities was also correlated with soil pH (

R
2

= 0.50), with peak diversity in soils with near-neutral pHs. Together, these results suggest that the structure of soil bacterial communities is predictable, to some degree, across larger spatial scales, and the effect of soil pH on bacterial community composition is evident at even relatively coarse levels of taxonomic resolution.
Characterization of Airborne Microbial Communities at a High-Elevation Site and Their Potential To Act as Atmospheric Ice Nuclei
Authors: Bowers Robert M. , Lauber Christian L. , Wiedinmyer Christine , Hamady Micah , Hallar Anna G. , Fall Ray , Knight Rob , Fierer Noah 
Published: June 2009

ABSTRACT

Bacteria and fungi are ubiquitous in the atmosphere. The diversity and abundance of airborne microbes may be strongly influenced by atmospheric conditions or even influence atmospheric conditions themselves by acting as ice nucleators. However, few comprehensive studies have described the diversity and dynamics of airborne bacteria and fungi based on culture-independent techniques. We document atmospheric microbial abundance, community composition, and ice nucleation at a high-elevation site in northwestern Colorado. We used a standard small-subunit rRNA gene Sanger sequencing approach for total microbial community analysis and a bacteria-specific 16S rRNA bar-coded pyrosequencing approach (4,864 sequences total). During the 2-week collection period, total microbial abundances were relatively constant, ranging from 9.6 × 10
5
to 6.6 × 10
6
cells m
−3
of air, and the diversity and composition of the airborne microbial communities were also relatively static. Bacteria and fungi were nearly equivalent, and members of the proteobacterial groups
Burkholderiales
and
Moraxellaceae
(particularly the genus
Psychrobacter
) were dominant. These taxa were not always the most abundant in freshly fallen snow samples collected at this site. Although there was minimal variability in microbial abundances and composition within the atmosphere, the number of biological ice nuclei increased significantly during periods of high relative humidity. However, these changes in ice nuclei numbers were not associated with changes in the relative abundances of the most commonly studied ice-nucleating bacteria.
Homo-
d
-Lactic Acid Fermentation from Arabinose by Redirection of the Phosphoketolase Pathway to the Pentose Phosphate Pathway in
l
-Lactate Dehydrogenase Gene-Deficient
Lactobacillus plantarum
Authors: Okano Kenji , Yoshida Shogo , Tanaka Tsutomu , Ogino Chiaki , Fukuda Hideki , Kondo Akihiko 
Published: June 2009

ABSTRACT

Optically pure
d
-lactic acid fermentation from arabinose was achieved by using the
Lactobacillus plantarum
NCIMB 8826 strain whose
l
-lactate dehydrogenase gene was deficient and whose phosphoketolase gene was substituted with a heterologous transketolase gene. After 27 h of fermentation, 38.6 g/liter of
d
-lactic acid was produced from 50 g/liter of arabinose.
Structure-Based Rational Design of a Phosphotriesterase
Authors: Jackson Colin J. , Weir Kahli , Herlt Anthony , Khurana Jeevan , Sutherland Tara D. , Horne Irene , Easton Christopher , Russell Robyn J. , Scott Colin , Oakeshott John G. 
Published: June 2009

ABSTRACT

In silico substrate docking of both stereoisomers of the pesticide chlorfenvinphos (CVP) in the phosphotriesterase from
Agrobacterium radiobacter
identified two residues (F131 and W132) that prevent productive substrate binding and cause stereospecificity. A variant (W131H/F132A) was designed that exhibited ca. 480-fold and 8-fold increases in the rate of
Z
-CVP and
E
-CVP hydrolysis, respectively, eliminating stereospecificity.
Molecular Biological Detection and Quantification of Novel
Fibrobacter
Populations in Freshwater Lakes
Authors: McDonald James E. , de Menezes Alexandre B. , Allison Heather E. , McCarthy Alan J. 
Published: June 2009

ABSTRACT

PCR and quantitative PCR (qPCR) primers targeting the 16S rRNA gene were used to detect and quantify members of the genus
Fibrobacter
in lake water, sediment and colonized cotton taken from two freshwater lakes. Phylogenetic analysis identified two groups of sequences; those clustered with
Fibrobacter succinogenes
, the type species, and a defined cluster of clones loosely associated with several
Fibrobacter
sequences observed previously in clone libraries from freshwater environments. 16S rRNA gene sequences recovered in the same way from soil samples and ovine feces in the surrounding land were all
F. succinogenes
and did not include any from this group of the “freshwater”
Fibrobacteres
. In all cases, nested PCR was required to detect
Fibrobacter
16S rRNA genes, and qPCR analysis of reverse transcribed bacterial community RNA confirmed their very low relative abundance on colonized cotton baits in the water column (at 0, 3, 7, 11, and 13 m) and on the sediment surface (<0.02% of total bacterial rRNA). However, in Esthwaite Water sediment itself, the relative abundance of fibrobacters was 2 orders of magnitude higher (ca. 1% of total bacterial rRNA). The presence of fibrobacters, including the cellulolytic rumen species
F. succinogenes
, on colonized cellulose samples and in lake sediment suggests that these organisms may contribute to the primary degradation of plant and algal biomass in freshwater lake ecosystems.
Aerobic Vanillate Degradation and C
1
Compound Metabolism in
Bradyrhizobium japonicum
Authors: Sudtachat Nirinya , Ito Naofumi , Itakura Manabu , Masuda Sachiko , Eda Shima , Mitsui Hisayuki , Kawaharada Yasuyuki , Minamisawa Kiwamu 
Published: June 2009

ABSTRACT

Bradyrhizobium japonicum
, a symbiotic nitrogen-fixing soil bacterium, has multiple gene copies for aromatic degradation on the genome and is able to use low concentrations of vanillate, a methoxylated lignin monomer, as an energy source. A transcriptome analysis indicated that one set of
vanA1B
,
pcaG1H1
, and genes for C
1
compound catabolism was upregulated in
B. japonicum
USDA110 cells grown in vanillate (N. Ito, M. Itakura, S. Eda, K. Saeki, H. Oomori, T. Yokoyama, T. Kaneko, S. Tabata, T. Ohwada, S. Tajima, T. Uchiumi, E. Masai, M. Tsuda, H. Mitsui, and K. Minamisawa, Microbes Environ.
21:
240-250, 2006). To examine the functions of these genes in vanillate degradation, we tested cell growth and substrate consumption in
vanA1B
,
pcaG1H1
, and
mxaF
mutants of USDA110. The
vanA1B
and
pcaG1H1
mutants were unable to grow in minimal media containing 1 mM vanillate and protocatechuate, respectively, although wild-type USDA110 was able to grow in both media, indicating that the upregulated copies of
vanA1B
and
pcaG1H1
are exclusively responsible for vanillate degradation. Mutating
mxaF
eliminated expression of
gfa
and
flhA
, which contribute to glutathione-dependent C
1
metabolism. The
mxaF
mutant had markedly lower cell growth in medium containing vanillate than the wild-type strain. In the presence of protocatechuate, there was no difference in cell growth between the
mxaF
mutant and the wild-type strain. These results suggest that the C
1
pathway genes are required for efficient vanillate catabolism. In addition, wild-type USDA110 oxidized methanol, whereas the
mxaF
mutant did not, suggesting that the metabolic capability of the C
1
pathway in
B. japonicum
extends to methanol oxidation. The
mxaF
mutant showed normal nodulation and N
2
fixation phenotypes with soybeans, which was not similar to symbiotic phenotypes of methylotrophic rhizobia.
Biochemical Properties of Two Cinnamoyl Esterases Purified from a
Lactobacillus johnsonii
Strain Isolated from Stool Samples of Diabetes-Resistant Rats
Authors: Lai Kin Kwan , Lorca Graciela L. , Gonzalez Claudio F. 
Published: June 2009

ABSTRACT

Cinnamic acids (i.e., ferulic and caffeic acids) that are esterified to the vegetable cell walls should be enzymatically released to be absorbed in a mammal's intestines. A low dosage of ferulic acid in rodent diets stimulates insulin production and alleviates symptoms caused by diabetes (M. Sri Balasubashini, R. Rukkumani, and V. P. Menon, Acta Diabetol. 40:118-122, 2003). Several lactic acid bacteria are able to display ferulic acid esterase (FAE) activity, suggesting that their probiotic activity could be, in part, mediated by the slow release of ferulic acid. In the present work, we describe the isolation of one strain identified as being
Lactobacillus johnsonii
that displayed strong FAE activity in stool samples from diabetes-resistant biobreeding rats. These animals are genetically susceptible to becoming diabetic but do not develop the disease. By using genomic analysis coupled to protein purification and catalytic screening, we were able to purify two proteins with FAE activity. The enzymes displayed 42% sequence identity and a broad range of substrate preferences. High affinities and catalytic efficiencies toward aromatic compounds such as ethyl ferulate (

K
m

= 20 to 60 μM) and chlorogenic acid (

K
m

= 10 to 50 μM) were observed. The strain isolated herein as well as the enzymes studied could be potentially useful for the formulation of probiotics to ameliorate diabetes symptoms.
Quantification of Key Genes Steering the Microbial Nitrogen Cycle in the Rhizosphere of Sorghum Cultivars in Tropical Agroecosystems
Authors: Hai Brigitte , Diallo Ndeye Hélène , Sall Saidou , Haesler Felix , Schauss Kristina , Bonzi Moussa , Assigbetse Komi , Chotte Jean-Luc , Munch Jean Charles , Schloter Michael 
Published: June 2009

ABSTRACT
The effect of agricultural management practices on geochemical cycles in moderate ecosystems is by far better understood than in semiarid regions, where fertilizer availability and climatic conditions are less favorable. We studied the impact of different fertilizer regimens in an agricultural long-term observatory in Burkina Faso at three different plant development stages (early leaf development, flowering, and senescence) of sorghum cultivars. Using real-time PCR, we investigated functional microbial communities involved in key processes of the nitrogen cycle (nitrogen fixation, ammonia oxidation, and denitrification) in the rhizosphere. The results indicate that fertilizer treatments and plant development stages combined with environmental factors affected the abundance of the targeted functional genes in the rhizosphere. While nitrogen-fixing populations dominated the investigated communities when organic fertilizers (manure and straw) were applied, their numbers were comparatively reduced in urea-treated plots. In contrast, ammonia-oxidizing bacteria (AOB) increased not only in absolute numbers but also in relation to the other bacterial groups investigated in the urea-amended plots. Ammonia-oxidizing archaea exhibited higher numbers compared to AOB independent of fertilizer application. Similarly, denitrifiers were also more abundant in the urea-treated plots. Our data imply as well that, more than in moderate regions, water availability might shape microbial communities in the rhizosphere, since low gene abundance data were obtained for all tested genes at the flowering stage, when water availability was very limited.
Differential Activation of Peritoneal Cells by Subcutaneous Treatment of Rats with Cryptococcal Antigens
Authors: Baronetti José L. , Chiapello Laura S. , Garro Ana P. , Masih Diana T. 
Published: June 2009

ABSTRACTPrevious studies in our laboratory have shown that the subcutaneous pretreatment of rats with heat-killed cells (HKC) ofCryptococcus neoformansemulsified in complete Freund adjuvant (CFA) promotes protective immunity against an intraperitoneal challenge withC. neoformans. In contrast, subcutaneous treatment with the capsular polysaccharide (PSC) emulsified in CFA exacerbates the cryptococcal infection. The purpose of this study was to analyze the mechanisms involved in these phenomena. Adherent peritoneal cells from rats treated with HKC-CFA showed upregulated ED2, CD80, and CD86 expression; an increase in the level of production of anticryptococcal metabolites; and the enhanced production of interleukin-12 (IL-12) in comparison with the findings for cells from rats treated with CFA-phosphate-buffered saline (PBS). Adherent peritoneal cells from rats treated with PSC-CFA, however, also presented upregulated ED2, CD80, and CD86 expression compared to the level of expression for peritoneal cells from controls, but these cells showed an increase in arginase activity and decreased levels of production of IL-12 and tumor necrosis factor (TNF) compared with the activity and levels of production by peritoneal cells from CFA-PBS-treated rats. In addition, treatment with HKC-CFA resulted in a rise in the phagocytic and anticryptococcal activities of adherent peritoneal cells compared to those for control rats. However, adherent peritoneal cells from rats treated with PSC-CFA presented a reduction in anticryptococcal activity in comparison with that for cells from animals treated with CFA-PBS. These results show the differential activation between adherent peritoneal cells from HKC-CFA- and PSC-CFA-treated rats, with this differential activation at the primary site of infection possibly being responsible, at least in part, for the phenomena of protection and exacerbation observed in our model.
Characterization of Two Putative Protein Translocation Components in the Apicoplast ofPlasmodium falciparum
Authors: Kalanon Ming , Tonkin Christopher J. , McFadden Geoffrey I. 
Published: June 2009

ABSTRACTProtein trafficking to the stroma of the apicoplast ofPlasmodium falciparumrequires translocation across several membranes. To further elucidate the mechanisms responsible, we investigated two proteins:P. falciparumTic22 (PfTic22), a putative component of the translocon of the inner chloroplast membrane; and PfsDer1-1, one of two homologues of theP. falciparumsymbiont-derived Der1 (sDer1) protein, a putative component of an endoplasmic reticulum-associated degradation (ERAD) complex in the periplastid membrane. We constructed parasites expressing hemagglutinin (HA)-tagged PfTic22 and PfsDer1-1 under the control of their endogenous promoters using the 3′ replacement strategy. We show that both PfTic22-HA and PfsDer1-1-HA are expressed predominantly during the trophozoite stage of the asexual replication cycle, which corresponds to the most dynamic stages of apicoplast activity. Although both proteins localize to the periphery of the apicoplast, PfTic22-HA is a membrane-associated protein while PfsDer1-1-HA is an integral membrane protein. Phylogenetic analysis indicates that PfsDer1-1 is one of two Der1 paralogues predicted to localize to the apicoplast inP. falciparumand that it has orthologues in diatom algae, supporting the chromalveolate hypothesis. These observations are consistent with putative roles for PfTic22 and PfsDer1-1 in protein translocation into the apicoplast ofP. falciparum.
Phosphatidylinositol-4,5-Bisphosphate and Phospholipase D-Generated Phosphatidic Acid Specify SNARE-Mediated Vesicle Fusion for Prospore Membrane Formation
Authors: Mendonsa Rima , Engebrecht JoAnne 
Published: June 2009

ABSTRACT

The soluble
N
-ethylmaleimide sensitive factor attachment protein receptor (SNARE) family of proteins is required for eukaryotic intracellular membrane fusions. Vesicle fusion for formation of the prospore membrane (PSM), a membrane compartment that forms de novo during yeast sporulation, requires SNARE function, phosphatidylinositol-4,5-bisphosphate [PI(4,5)P
2
], and the activity of the phospholipase D (PLD) Spo14p, which generates phosphatidic acid (PA). The SNARE syntaxin Sso1p is essential for PSM production while the functionally redundant homolog in vegetative growth, Sso2p, is not. We demonstrate that Sso1p and Sso2p bind similarly in vitro to PA or phosphoinositide-containing liposomes and that the conserved SNARE (H3) domain largely mediates PA-binding. Both green fluorescent protein-Sso fusion proteins localize to the developing PSM in wild-type cells and to the spindle pole body in
spo14
Δ cells induced to sporulate. However, the autoregulatory region of Sso1p binds PI(4,5)P
2
-containing liposomes in vitro with a greater ability than the equivalent region of Sso2p. Overexpression of the phosphatidylinositol-4-phosphate 5-kinase
MSS4
in
sso1
Δ cells induced to sporulate stimulates PSM production; PLD activity is not increased under these conditions, indicating that PI(4,5)P
2
has roles in addition to stimulating PLD in PSM formation. These data suggest that PLD-generated PA and PI(4,5)P
2
collaborate at multiple levels to promote SNARE-mediated fusion for PSM formation.
An Unusual ERAD-Like Complex Is Targeted to the Apicoplast ofPlasmodium falciparum
Authors: Spork Simone , Hiss Jan A. , Mandel Katharina , Sommer Maik , Kooij Taco W. A. , Chu Trang , Schneider Gisbert , Maier Uwe G. , Przyborski Jude M. 
Published: June 2009

ABSTRACTMany apicomplexan parasites, includingPlasmodium falciparum, harbor a so-called apicoplast, a complex plastid of red algal origin which was gained by a secondary endosymbiotic event. The exact molecular mechanisms directing the transport of nuclear-encoded proteins to the apicoplast ofP. falciparumare not well understood. Recently, in silico analyses revealed a second copy of proteins homologous to components of the endoplasmic reticulum (ER)-associated protein degradation (ERAD) system in organisms with secondary plastids, including the malaria parasiteP. falciparum. These proteins are predicted to be endowed with an apicoplast targeting signal and are suggested to play a role in the transport of nuclear-encoded proteins to the apicoplast. Here, we have studied components of this ERAD-derived putative preprotein translocon complex in malaria parasites. Using transfection technology coupled with fluorescence imaging techniques we can demonstrate that the N terminus of several ERAD-derived components targets green fluorescent protein to the apicoplast. Furthermore, we confirm that full-length PfsDer1-1 and PfsUba1 (homologues of yeast ERAD components) localize to the apicoplast, where PfsDer1-1 tightly associates with membranes. Conversely, PfhDer1-1 (a host-specific copy of the Der1-1 protein) localizes to the ER. Our data suggest that ERAD components have been “rewired” to provide a conduit for protein transport to the apicoplast. Our results are discussed in relation to the nature of the apicoplast protein transport machinery.
The Extent of Migration of the Holliday Junction Is a Crucial Factor for Gene Conversion in
Rhizobium etli
Authors: Castellanos Mildred , Romero David 
Published: June 2009

ABSTRACT

Gene conversion, defined as the nonreciprocal transfer of DNA, is one result of homologous recombination. Three steps in recombination could give rise to gene conversion: (i) DNA synthesis for repair of the degraded segment, (ii) Holliday junction migration, leading to heteroduplex formation, and (iii) repair of mismatches in the heteroduplex. There are at least three proteins (RuvAB, RecG, and RadA) that participate in the second step. Their roles have been studied for homologous recombination, but evidence of their relative role in gene conversion is lacking. In this work, we showed the effect on gene conversion of mutations in
ruvB
,
recG
, and
radA
in
Rhizobium etli
, either alone or in combination, using a cointegration strategy previously developed in our laboratory. The results indicate that the RuvAB system is highly efficient for gene conversion, since its absence provokes smaller gene conversion segments than those in the wild type as well as a shift in the preferred position of conversion tracts. The RecG system possesses a dual role for gene conversion. Inactivation of
recG
leads to longer gene conversion tracts than those in the wild type, indicating that its activity may hinder heteroduplex extension. However, under circumstances where it is the only migration activity present (as in the
ruvB radA
double mutant), conversion segments can still be seen, indicating that RecG can also promote gene conversion. RadA is the least efficient system in
R. etli
but is still needed for the production of detectable gene conversion tracts.
The StkP/PhpP Signaling Couple inStreptococcus pneumoniae: Cellular Organization and Physiological Characterization
Authors: Osaki Makoto , Arcondéguy Tania , Bastide Amandine , Touriol Christian , Prats Hervé , Trombe Marie-Claude 
Published: June 2009

ABSTRACTInStreptococcus pneumoniae,stkPandphpP, encoding the eukaryotic-type serine-threonine kinase and PP2C phosphatase, respectively, form an operon. PhpP has the features of a so-called “soluble” protein, whereas StkP protein is membrane associated. Here we provide the first genetic and physiological evidence that PhpP and StkP, with antagonist enzymatic activities, constitute a signaling couple. The StkP-PhpP couple signals competence upstream of the competence-specific histidine kinase ComD, receptor for the oligopeptide pheromone “competence stimulating peptide.” We show that PhpP activity is essential in astkP+genetic background, suggesting tight control of StkP activity by PhpP. Proteins PhpP and StkP colocalized to the cell membrane subcellular fraction and likely belong to the same complex, as revealed by coimmunoprecipitation in cellular extracts. Specific coimmunoprecipitation of the N-kinase domain of StkP and PhpP recombinant proteins by PhpP-specific antibodies demonstrates direct interaction between these proteins. Consistently, flow cytometry analysis allowed the determination of the cytoplasmic localization of PhpP and of the N-terminal kinase domain of StkP, in contrast to the periplasmic localization of the StkP C-terminal PASTA (penicillin-binding proteinandserine-threonine kinaseassociated) domain. A signaling route involving interplay between serine, threonine, and histidine phosphorylation is thus described for the first time in this human pathogen.