bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differential Effects of Nitrogenous Fertilizers on Methane-Consuming Microbes in Rice Field and Forest Soils
Authors: Mohanty Santosh R. , Bodelier Paul L. E. , Floris Virgilio , Conrad Ralf 
Published: February 2006

ABSTRACT

The impact of environmental perturbation (e.g., nitrogenous fertilizers) on the dynamics of methane fluxes from soils and wetland systems is poorly understood. Results of fertilizer studies are often contradictory, even within similar ecosystems. In the present study the hypothesis of whether these contradictory results may be explained by the composition of the methane-consuming microbial community and hence whether methanotrophic diversity affects methane fluxes was investigated. To this end, rice field and forest soils were incubated in microcosms and supplemented with different nitrogenous fertilizers and methane concentrations. By labeling the methane with
13
C, diversity and function could be coupled by analyses of phospholipid-derived fatty acids (PLFA) extracted from the soils at different time points during incubation. In both rice field and forest soils, the activity as well as the growth rate of methane-consuming bacteria was affected differentially. For type I methanotrophs, fertilizer application stimulated the consumption of methane and the subsequent growth, while type II methanotrophs were generally inhibited. Terminal restriction fragment length polymorphism analyses of the
pmoA
gene supported the PLFA results. Multivariate analyses of stable-isotope-probing PLFA profiles indicated that in forest and rice field soils,
Methylocystis
(type II) species were affected by fertilization. The type I methanotrophs active in forest soils (
Methylomicrobium/Methylosarcina
related) differed from the active species in rice field soils (
Methylobacter/Methylomonas
related). Our results provide a case example showing that microbial community structure indeed matters, especially when assessing and predicting the impact of environmental change on biodiversity loss and ecosystem functioning.
Host-Symbiont Relationships in Hydrothermal Vent Gastropods of the Genus
Alviniconcha
from the Southwest Pacific
Authors: Suzuki Yohey , Kojima Shigeaki , Sasaki Takenori , Suzuki Masae , Utsumi Takashi , Watanabe Hiromi , Urakawa Hidetoshi , Tsuchida Shinji , Nunoura Takuro , Hirayama Hisako , Takai Ken , Nealson Kenneth H. , Horikoshi Koki 
Published: February 2006

ABSTRACT

Hydrothermal vent gastropods of the genus
Alviniconcha
are unique among metazoans in their ability to derive their nutrition from chemoautotrophic γ- and ε-proteobacterial endosymbionts. Although host-symbiont relationships in
Alviniconcha
gastropods from the Central Indian Ridge in the Indian Ocean and the Mariana Trough in the Western Pacific have been studied extensively, host-symbiont relationships in
Alviniconcha
gastropods from the Southwest Pacific remain largely unknown. Phylogenetic analysis using mitochondrial cytochrome
c
oxidase subunit I gene sequences of host gastropods from the Manus, North Fiji, and Lau Back-Arc Basins in the Southwest Pacific has revealed a new host lineage in a
Alviniconcha
gastropod from the Lau Basin and the occurrence of the host lineage
Alviniconcha
sp. type 2 in the Manus Basin. Based on 16S rRNA gene sequences of bacterial endosymbionts, two γ-proteobacterial lineages and one ε-proteobacterial lineage were identified in the present study. The carbon isotopic compositions of the biomass and fatty acids of the gastropod tissues suggest that the γ- and ε-proteobacterial endosymbionts mediate the Calvin-Benson cycle and the reductive tricarboxylic acid cycle, respectively, for their chemoautotrophic growth. Coupling of the host and symbiont lineages from the three Southwest Pacific basins revealed that each of the
Alviniconcha
lineages harbors different bacterial endosymbionts belonging to either the γ- or ε-
Proteobacteria
. The host specificity exhibited in symbiont selection provides support for the recognition of each of the host lineages as a distinct species. The results from the present study also suggest the possibility that
Alviniconcha
sp. types 1 and 2 separately inhabit hydrothermal vent sites approximately 120 m apart in the North Fiji Basin and 500 m apart in the Manus Basin.
The Thin Pili of
Acinetobacter
sp. Strain BD413 Mediate Adhesion to Biotic and Abiotic Surfaces
Authors: Gohl Olivia , Friedrich Alexandra , Hoppert Michael , Averhoff Beate 
Published: February 2006

ABSTRACT

Two structurally different appendages, thin and thick pili, are found in members of the genus
Acinetobacter
. The presence of pilus structures correlates with different phenotypes, such as adherence to surfaces, a trait not only observed in pathogenic
Acinetobacter
species, as well as motility. However, their distinct individual roles were unknown. To characterize the role of different pili in the physiology of
Acinetobacter
, we isolated the thin pili from the cell surface of
Acinetobacter
sp. strain BD413 (recently recognized as representative of
Acinetobacter baylyi
), a soil bacterium that rapidly takes up naked DNA from its environment. Electron microcopy revealed that the pilus has an external diameter of 2 to 3 nm for single filaments. The filaments are packed into right-handed bundles. The major protein constituting the pilus was purified, and the encoding gene,
acuA
, was cloned. AcuA was found to be weakly related to the structural subunit of F17 pili of
Escherichia coli
. Analyses of the
acuA
flanking DNA region led to the identification of three closely associated genes,
acuD
,
acuC
, and
acuG
, whose deduced proteins are similar to chaperone, usher, and adhesin of F17-related pili, respectively. Transcriptional analyses revealed that
acuA
expression is maximal in the late-stationary-growth phase. Mutation of
acuA
led to a loss of thin pili and concomitantly loss of adhesion to polystyrene and erythrocytes but not loss of competence. Therefore, thin pili of
Acinetobacter
sp. strain BD413 are suggested to be assembled by the chaperone/usher pathway and are involved in adherence to biotic and abiotic surfaces.
Engineering the Genotype ofAcinetobactersp. Strain ADP1 To Enhance Biosynthesis of Cyanophycin
Authors: Elbahloul Yasser , Steinbüchel Alexander 
Published: February 2006

ABSTRACTTo study the importance of arginine provision and phosphate limitation for synthesis and accumulation of cyanophycin (CGP) inAcinetobactersp. strain ADP1, genes encoding the putative arginine regulatory protein (argR) and the arginine succinyltransferase (astA) were inactivated, and the effects of these mutations on CGP synthesis were analyzed. The inactivation of these genes resulted in a 3.5- or 7-fold increase in CGP content, respectively, when the cells were grown on glutamate. Knockout mutations in both genes led to a better understanding of the effect of the addition of other substrates to arginine on CGP synthesis during growth of the cells ofAcinetobactersp. strain ADP1. Overexpression of ArgF (ornithine carbamoyltransferase), CarA-CarB (small and large subunits of carbamoylphosphate synthetase), and PepC (phosphoenolpyruvate carboxylase) triggered synthesis of CGP if amino acids were used as a carbon source whereas it was not triggered by gluconate or other sugars. Cells ofAcinetobactersp. strain ADP1, which is largely lacking genes for carbohydrate metabolism, showed a significant increase in CGP contents when grown on mineral medium supplemented with glutamate, aspartate, or arginine. TheAcinetobactersp.ΔastA(pYargF) strain is unable to utilize arginine but synthesizes more arginine, resulting in CGP contents as high as 30% and 25% of cell dry matter when grown on protamylasse or Luria-Bertani medium, respectively. This recombinant strain overcame the bottleneck of the costly arginine provision where it produces about 75% of the CGP obtained from the parent cells grown on mineral medium containing pure arginine as the sole source of carbon. Phosphate starvation is the only known trigger for CGP synthesis in this bacterium, which possesses the PhoB/PhoR phosphate regulon system. Overexpression ofphoBcaused an 8.6-fold increase in CGP content in comparison to the parent strain at a nonlimiting phosphate concentration.
First Insights into the Evolution of
Streptococcus uberis
: a Multilocus Sequence Typing Scheme That Enables Investigation of Its Population Biology
Authors: Coffey Tracey J. , Pullinger Gillian D. , Urwin Rachel , Jolley Keith A. , Wilson Stephen M. , Maiden Martin C. , Leigh James A. 
Published: February 2006

ABSTRACT

Intramammary infection with
Streptococcus uberis
is a common cause of bovine mastitis throughout the world. Several procedures to differentiate
S. uberis
isolates have been proposed. However, all are prone to interlaboratory variation, and none is suitable for the description of the population structure. We describe here the development of a multilocus sequence typing (MLST) scheme for
S. uberis
to help address these issues. The sequences of seven housekeeping gene fragments from each of 160 United Kingdom milk isolates of
S. uberis
were determined. Between 5 and 17 alleles were obtained per locus, giving the potential to discriminate between 1.3 × 10
7
sequence types. In this study, 57 sequence types (STs) were identified. Statistical comparisons between the maximum-likelihood trees constructed by using the seven housekeeping gene fragments showed that the congruence was no better than that between each tree and trees of random topology, indicating there had been significant recombination within these loci. The population contained one major lineage (designated the ST-5 complex). This dominated the population, containing 24 STs and representing 112 isolates. The other 33 STs were not assigned to any clonal complex. All of the isolates in the ST-5 lineage carried
hasA
, a gene that is essential for capsule production. There was no clear association between ST or clonal complex and disease. The
S. uberis
MLST system offers researchers a valuable tool that allows further investigation of the population biology of this organism and insights into the epidemiology of this disease on a global scale.
Application of
Streptococcus uberis
Multilocus Sequence Typing: Analysis of the Population Structure Detected among Environmental and Bovine Isolates from New Zealand and the United Kingdom
Authors: Pullinger Gillian D. , López-Benavides Mario , Coffey Tracey J. , Williamson John H. , Cursons Ray T. , Summers Emma , Lacy-Hulbert Jane , Maiden Martin C. , Leigh James A. 
Published: February 2006

ABSTRACT

We recently developed a multilocus sequence typing (MLST) scheme to differentiate
S. uberis
isolates and facilitate an understanding of the population biology of this pathogen. The scheme was initially used to study a collection of 160 bovine milk isolates from the United Kingdom and showed that the majority of isolates were from one clonal complex (designated the ST-5 complex). Here we describe the MLST analysis of a collection of New Zealand isolates. These were obtained from diverse sources, including bovine milk, other bovine anatomical sites, and environmental sources. The complete allelic profiles of 253 isolates were determined. The collection was highly diverse and included 131 different sequence types (STs). The New Zealand and United Kingdom populations were distinct, since none of the 131 STs were represented within the previously studied collection of 160 United Kingdom
S. uberis
isolates. However, seven of the STs were members of the ST-5 clonal complex, the major complex within the United Kingdom collection. Two new clonal complexes were identified: ST-143 and ST-86. All three major complexes were isolated from milk, other bovine sites, and the environment. Carriage of the
hasA
gene, which is necessary for capsule formation, correlated with clonal complex and isolation from clinical cases of mastitis.
In Situ and In Vitro Gene Expression by
Vibrio vulnificus
during Entry into, Persistence within, and Resuscitation from the Viable but Nonculturable State
Authors: Smith Ben , Oliver James D. 
Published: February 2006

ABSTRACT

Isolation of
Vibrio vulnificus
during winter months is difficult due to the entrance of these cells into the viable but nonculturable (VBNC) state. While several studies have investigated in vitro gene expression upon entrance into and persistence within the VBNC state, to our knowledge, no in situ studies have been reported. We incubated clinical and environmental isolates of
V. vulnificus
in estuarine waters during winter months to monitor the expression of several genes during the VBNC state and compared these to results from in vitro studies.
katG
(periplasmic catalase) was down-regulated during the VBNC state in vitro and in situ compared to the constitutively expressed gene
tufA
. Our results indicate that the loss of catalase activity we previously reported is a direct result of
katG
repression, which likely accounts for the VBNC response of this pathogen. While expression of
vvhA
(hemolysin) was detectable in environmental strains during in situ incubation, it ceased in all cases by ca. 1 h. These results suggest that the natural role of hemolysin in
V. vulnificus
may be in osmoprotection and/or the cold shock response. Differences in expression of the capsular genes
wza
and
wzb
were observed in the two recently reported genotypes of this species. Expression of
rpoS
, encoding the stress sigma factor RpoS, was continuous upon entry into the VBNC state during both in situ and in vitro studies. We found the half-life of mRNA to be less than 60 minutes, confirming that mRNA detection in these VBNC cells is a result of de novo RNA synthesis.
Paenibacillus
sp. Strain JDR-2 and XynA
1
: a Novel System for Methylglucuronoxylan Utilization
Authors: StJohn Franz J. , Rice John D. , Preston James F. 
Published: February 2006

ABSTRACT

Environmental and economic factors predicate the need for efficient processing of renewable sources of fuels and chemicals. To fulfill this need, microbial biocatalysts must be developed to efficiently process the hemicellulose fraction of lignocellulosic biomass for fermentation of pentoses. The predominance of methylglucuronoxylan (MeGAX
n
), a β-1,4 xylan in which 10% to 20% of the xylose residues are substituted with α-1,2-4-
O
-methylglucuronate residues, in hemicellulose fractions of hardwood and crop residues has made this a target for processing and fermentation. A
Paenibacillus
sp. (strain JDR-2) has been isolated and characterized for its ability to efficiently utilize MeGAX
n
. A modular xylanase (XynA
1
) of glycosyl hydrolase family 10 (GH 10) was identified through DNA sequence analysis that consists of a triplicate family 22 carbohydrate binding module followed by a GH 10 catalytic domain followed by a single family 9 carbohydrate binding module and concluding with C-terminal triplicate surface layer homology (SLH) domains. Immunodetection of the catalytic domain of XynA
1
(XynA
1
CD) indicates that the enzyme is associated with the cell wall fraction, supporting an anchoring role for the SLH modules. With MeGAX
n
as substrate, XynA
1
CD generated xylobiose and aldotetrauronate (MeGAX
3
) as predominant products. The inability to detect depolymerization products in medium during exponential growth of
Paenibacillus
sp. strain JDR-2 on MeGAX
n
, as well as decreased growth rate and yield with XynA
1
CD-generated xylooligosaccharides and aldouronates as substrates, indicates that XynA
1
catalyzes a depolymerization process coupled to product assimilation. This depolymerization/assimilation system may be utilized for development of biocatalysts to efficiently convert MeGAX
n
to alternative fuels and biobased products.
Use of PMA1 as a Housekeeping Biomarker for Assessment of Toxicant-Induced Stress in
Saccharomyces cerevisiae
Authors: Schmitt Marcel , Schwanewilm Petra , Ludwig Jost , Lichtenberg-Fraté Hella 
Published: February 2006

ABSTRACT

The brewer's yeast
Saccharomyces cerevisiae
has emerged as a versatile and robust model system for laboratory use to study toxic effects of various substances. In this study, toxicant-induced stresses of pure compounds were investigated in
Saccharomyces cerevisiae
utilizing a destabilized version of the green fluorescent protein optimized for expression in yeast (yEGFP3) under control of the promoter of the housekeeping plasma membrane ATPase gene
PMA1
. The responses of the biomarker upon increasing test compound concentrations were monitored by determining the decrease in fluorescence. The reporter assay deployed a simple and robust protocol for the rapid detection of toxic effects within a 96-well microplate format. Fluorescence emissions were normalized to cell growth determined by absorption and were correlated to internal reference standards. The results were expressed as effective concentrations (EC
20
). Dose-response experiments were conducted in which yeast cells were exposed in minimal medium and in the presence of 20% fetal calf serum to sublethal concentrations of an array of heavy metals, salt, and a number of stress-inducing compounds (Diclofenac, Lindane, methyl-
N
-nitro-
N
-nitrosoguanidine [MNNG], hydroxyurea, and caffeine). Long-term exposure (7 h) played a considerable role in the adaptive response to intoxication compared to early responses at 4 h exposure. The data obtained after 4 h of exposure and expressed as EC
20
were compared to 50% inhibitory concentration values derived from cell line and ecotoxicological tests. This study demonstrates the versatility of the novel biomarker to complement existing test batteries to assess contaminant exposure and effects.
Comparative Genomics of DNA Fragments from Six Antarctic Marine Planktonic Bacteria
Authors: Grzymski Joseph J. , Carter Brandon J. , DeLong Edward F. , Feldman Robert A. , Ghadiri Amir , Murray Alison E. 
Published: February 2006

ABSTRACT

Six
environmental fosmid clones from Antarctic coastal water
bacterioplankton were completely sequenced. The genome fragments
harbored small-subunit rRNA genes that were between 85 and 91% similar
to those of their nearest cultivated relatives. The six fragments span
four phyla, including the
Gemmatimonadetes
,
Proteobacteria
(α and γ),
Bacteroidetes
, and high-G+C gram-positive bacteria.
Gene-finding and annotation analyses identified 244 total open reading
frames. Amino acid comparisons of 123 and 113 Antarctic
bacterial amino acid sequences to mesophilic homologs from
G+C-specific and SwissProt/UniProt databases, respectively,
revealed widespread adaptation to the cold. The most significant
changes in these Antarctic bacterial protein sequences included a
reduction in salt-bridge-forming residues such as arginine, glutamic
acid, and aspartic acid, reduced proline contents, and a reduction in
stabilizing hydrophobic clusters. Stretches of disordered amino acids
were significantly longer in the Antarctic sequences than in the
mesophilic sequences. These characteristics were not specific to any
one phylum, COG role category, or G+C content and imply that
underlying genotypic and biochemical adaptations to the cold are
inherent to life in the permanently subzero Antarctic
waters.
Multiple-Locus Sequence Typing Analysis of
Bacillus cereus
and
Bacillus thuringiensis
Reveals Separate Clustering and a Distinct Population Structure of Psychrotrophic Strains
Authors: Sorokin Alexei , Candelon Benjamin , Guilloux Kévin , Galleron Nathalie , Wackerow-Kouzova Natalia , Ehrlich S. Dusko , Bourguet Denis , Sanchis Vincent 
Published: February 2006

ABSTRACT

We
used multilocus sequence typing (MLST) to characterize phylogenetic
relationships for a collection of
Bacillus cereus
group
strains isolated from forest soil in the Paris area during a mild
winter. This collection contains multiple strains isolated from the
same soil sample and strains isolated from samples from different
sites. We characterized 115 strains of this collection and 19 other
strains based on the sequences of the
clpC
,
dinB
,
gdpD
,
panC
,
purF
, and
yhfL
loci.
The number of alleles ranged from 36 to 53, and a total of 93 allelic
profiles or sequence types were distinguished. We identified three
major strain clusters—C, T, and W—based on the
comparison of individual gene sequences or concatenated sequences. Some
less representative clusters and subclusters were also distinguished.
Analysis of the MLST data using the concept of clonal complexes led to
the identification of two, five, and three such groups in clusters C,
T, and W, respectively. Some of the forest isolates were closely
related to independently isolated psychrotrophic strains. Systematic
testing of the strains of this collection showed that almost all the
strains that were able to grow at a low temperature (6°C)
belonged to cluster W. Most of these strains, including three
independently isolated strains, belong to two clonal complexes and are
therefore very closely related genetically. These clonal complexes
represent strains corresponding to the previously identified species
Bacillus weihenstephanensis
. Most of the other strains of our
collection, including some from the W cluster, are not psychrotrophic.
B. weihenstephanensis
(cluster W) strains appear to comprise
an effectively sexual population, whereas
Bacillus
thuringiensis
(cluster T) and
B. cereus
(cluster C) have
clonal population
structures.
Multitiered Approach Using Quantitative PCR To Track Sources of Fecal Pollution Affecting Santa Monica Bay, California
Authors: Noble Rachel T. , Griffith John F. , Blackwood A. Denene , Fuhrman Jed A. , Gregory Jason B. , Hernandez Ximena , Liang Xiaolin , Bera Angie A. , Schiff Kenneth 
Published: February 2006

ABSTRACT

The ubiquity of fecal indicator bacteria such as
Escherichia coli
and
Enterococcus
spp. in urban environments makes tracking of fecal contamination extremely challenging. A multitiered approach was used to assess sources of fecal pollution in Ballona Creek, an urban watershed that drains to the Santa Monica Bay (SMB) near Los Angeles, Calif. A mass-based design at six main-stem sites and four major tributaries over a 6-h period was used (i) to assess the flux of
Enterococcus
spp. and
E. coli
by using culture-based methods (tier 1); (ii) to assess levels of
Enterococcus
spp. by using quantitative PCR and to detect and/or quantify additional markers of human fecal contamination, including a human-specific
Bacteroides
sp. marker and enterovirus, using quantitative reverse transcriptase PCR (tier 2); and (iii) to assess the specific types of enterovirus genomes found via sequence analysis (tier 3). Sources of fecal indicator bacteria were ubiquitous, and concentrations were high, throughout Ballona Creek, with no single tributary dominating fecal inputs. The flux of
Enterococcus
spp. and
E. coli
averaged 10
9
to 10
10
cells h
−1
and was as high at the head of the watershed as at the mouth prior to discharge into the SMB. In addition, a signal for the human-specific
Bacteroides
marker was consistently detected: 86% of the samples taken over the extent during the study period tested positive. Enteroviruses were quantifiable in 14 of 36 samples (39%), with the highest concentrations at the site furthest upstream (Cochran). These results indicated the power of using multiple approaches to assess and quantify fecal contamination in freshwater conduits to high-use, high-priority recreational swimming areas.