bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distinct Responses in Ammonia-Oxidizing Archaea and Bacteria after Addition of Biosolids to an Agricultural Soil
Authors: Kelly John J. , Policht Katherine , Grancharova Tanya , Hundal Lakhwinder S. 
Published: July 2011

ABSTRACT

The recently discovered ammonia-oxidizing archaea (AOA) have been suggested as contributors to the first step of nitrification in terrestrial ecosystems, a role that was previously assigned exclusively to ammonia-oxidizing bacteria (AOB). The current study assessed the effects of agricultural management, specifically amendment of soil with biosolids or synthetic fertilizer, on nitrification rates and copy numbers of archaeal and bacterial ammonia monooxygenase (
amoA
) genes. Anaerobically digested biosolids or synthetic fertilizer was applied annually for three consecutive years to field plots used for corn production. Biosolids were applied at two loading rates, a typical agronomic rate (27 Mg hectare
−1
year
−1
) and double the agronomic rate (54 Mg hectare
−1
year
−1
), while synthetic fertilizer was applied at an agronomic rate typical for the region (291 kg N hectare
−1
year
−1
). Both biosolids amendments and synthetic fertilizer increased soil N and corn yield, but only the biosolids amendments resulted in significant increases in nitrification rates and increases in the copy numbers of archaeal and bacterial
amoA
genes. In addition, only archaeal
amoA
gene copy numbers increased in response to biosolids applied at the typical agronomic rate and showed a significant correlation with nitrification rates. Finally, copy numbers of archaeal
amoA
genes were significantly higher than copy numbers of bacterial
amoA
genes for all treatments. These results implicate AOA as being primarily responsible for the increased nitrification observed in an agricultural soil amended with biosolids. These results also support the hypothesis that physiological differences between AOA and AOB may enable them to occupy distinct ecological niches.
Effects of Animal Diet, Manure Application Rate, and Tillage on Transport of Microorganisms from Manure-Amended Fields
Authors: Durso Lisa M. , Gilley John E. , Marx David B. , Woodbury Bryan L. 
Published: July 2011

ABSTRACT
Manure from cattle fed distillers' grain or corn diets was applied to fields, and the fields were subjected to rainfall simulation tests. Manure was added at three rates on till and no-till plots. Correlations between microbial transport and runoff characteristics were identified. Results indicate that diet affects phage but not bacterial transport from manure-amended fields.
Effect of Dietary Supplementation with a Saccharomyces cerevisiae Mannan Oligosaccharide on the Bacterial Community Structure of Broiler Cecal Contents
Authors: Corrigan A. , Horgan K. , Clipson N. , Murphy R. A. 
Published: July 2011

ABSTRACT

This study investigated the effects of dietary supplementation with a prebiotic mannan oligosaccharide (MOS) on broiler performance, bacterial community structure, and phylogenetic populations of cecal contents. Bird performance data were collected, and cecal samples were extracted from randomly caught poults from each treatment group every 7 days from hatching to the age of 42 days. Weight gain, feed consumption, and feed efficiency ratios did not differ significantly between groups. Automated ribosomal intergenic spacer analysis (ARISA) of the bacterial communities in birds receiving MOS-supplemented diets indicated that dietary supplementation with MOS at either of 2 levels significantly altered the bacterial community structure from that of the control group on all sample days. The phylogenetic identities of bacteria contained within the cecum were determined by constructing a 16S rRNA gene clone library. A total of 594 partial 16S rRNA gene sequences from the cecal contents were analyzed and compared for the three dietary treatments. The dominant bacteria of the cecum belonged to three phyla,
Firmicutes
,
Bacteroidetes
, and
Proteobacteria
; of these,
Firmicutes
were the most dominant in all treatment groups. Statistical analysis of the bacterial 16S rRNA gene clone libraries showed that the compositions of the clone libraries from broilers receiving MOS-supplemented diets were, in most cases, significantly different from that of the control group. It can be concluded that in this trial MOS supplementation significantly altered the cecal bacterial community structure.
Robust Linuron Degradation in On-Farm Biopurification Systems Exposed to Sequential Environmental Changes
Authors: Sniegowski Kristel , Bers Karolien , Ryckeboer Jaak , Jaeken Peter , Spanoghe Pieter , Springael Dirk 
Published: July 2011

ABSTRACT

On-farm biopurification systems (BPS) treat pesticide-contaminated wastewater of farms through biodegradation. Adding pesticide-primed soil has been shown to be beneficial for the establishment of pesticide-degrading populations in BPS. However, no data exist on the response of pesticide-degrading microbiota, either endogenous or introduced with pesticide-primed soil, when BPS are exposed to expected less favorable environmental conditions like cold periods, drought periods, and periods without a pesticide supply. Therefore, the response of microbiota mineralizing the herbicide linuron in BPS microcosm setups inoculated either with a linuron-primed soil or a nonprimed soil to a sequence of such less favorable conditions was examined. A period without linuron supply or a drought period reduced the size of the linuron-mineralizing community in both setups. The most severe effect was recorded for the setup containing nonprimed soil, in which stopping the linuron supply decreased the linuron degradation capacity to nondetectable levels. In both systems, linuron mineralization rapidly reestablished after conventional operation conditions were restored. A cold period and feeding with a pesticide mixture did not affect linuron mineralization. The changes in the linuron-mineralizing capacity in microcosms containing primed soil were associated with the dynamics of a particular
Variovorax
phylotype that previously had been associated with linuron mineralization. This study suggests that the pesticide-mineralizing community in BPS is robust in stress situations imposed by changes in environmental conditions expected to occur on farms. Moreover, it suggests that, in cases where effects do occur, recovery is rapid after restoring conventional operation conditions.
Identification of New Single Nucleotide Polymorphism-Based Markers for Inter- and Intraspecies Discrimination of Obligate Bacterial Parasites (Pasteuria spp.) of Invertebrates
Authors: Mauchline Tim H. , Knox Rachel , Mohan Sharad , Powers Stephen J. , Kerry Brian R. , Davies Keith G. , Hirsch Penny R. 
Published: July 2011

ABSTRACTProtein-encoding and 16S rRNA genes ofPasteuria penetranspopulations from a wide range of geographic locations were examined. Most interpopulation single nucleotide polymorphisms (SNPs) were detected in the 16S rRNA gene. However, in order to fully resolve all populations, these were supplemented with SNPs from protein-encoding genes in a multilocus SNP typing approach. Examination of individual 16S rRNA gene sequences revealed the occurrence of “cryptic” SNPs which were not present in the consensus sequences of anyP. penetranspopulation. Additionally, hierarchical cluster analysis separatedP. penetrans16S rRNA gene clones into four groups, and one of which contained sequences from the most highly passaged population, demonstrating that it is possible to manipulate the population structure of this fastidious bacterium. The other groups were made from representatives of the other populations in various proportions. Comparison of sequences among threePasteuriaspecies, namely,P. penetrans,P. hartismeri, andP. ramosa, showed that the protein-encoding genes provided greater discrimination than the 16S rRNA gene. From these findings, we have developed a toolbox for the discrimination ofPasteuriaat both the inter- and intraspecies levels. We also provide a model to monitor genetic variation in other obligate hyperparasites and difficult-to-culture microorganisms.
Enzymatic Properties and Substrate Specificity of the Trehalose Phosphorylase from Caldanaerobacter subterraneus
Authors: Van der Borght Jef , Chen Chao , Hoflack Lieve , Van Renterghem Lucas , Desmet Tom , Soetaert Wim 
Published: July 2011

ABSTRACTA putative glycoside phosphorylase fromCaldanaerobacter subterraneussubsp.pacificuswas recombinantly expressed inEscherichia coli, after codon optimization and chemical synthesis of the encoding gene. The enzyme was purified by His tag chromatography and was found to be specifically active toward trehalose, with an optimal temperature of 80°C. In addition, no loss of activity could be detected after 1 h of incubation at 65°C, which means that it is the most stable trehalose phosphorylase reported so far. The substrate specificity was investigated in detail by measuring the relative activity on a range of alternative acceptors, applied in the reverse synthetic reaction, and determining the kinetic parameters for the best acceptors. These results were rationalized based on the enzyme-substrate interactions observed in a homology model with a docked ligand. The specificity for the orientation of the acceptor's hydroxyl groups was found to decrease in the following order: C-3 > C-2 > C-4. This results in a particularly high activity on the monosaccharidesd-fucose,d-xylose,l-arabinose, andd-galactose, as well as onl-fucose. However, determination of the kinetic parameters revealed that these acceptors bind less tightly in the active site than the natural acceptord-glucose, resulting in drastically increasedKmvalues. Nevertheless, the enzyme's high thermostability and broad acceptor specificity make it a valuable candidate for industrial disaccharide synthesis.
Role of Glucosyltransferase B in Interactions of Candida albicans with Streptococcus mutans and with an Experimental Pellicle on Hydroxyapatite Surfaces
Authors: Gregoire S. , Xiao J. , Silva B. B. , Gonzalez I. , Agidi P. S. , Klein M. I. , Ambatipudi K. S. , Rosalen P. L. , Bauserman R. , Waugh R. E. , Koo H. 
Published: July 2011

ABSTRACT

Candida albicans
and mutans streptococci are frequently detected in dental plaque biofilms from toddlers afflicted with early childhood caries. Glucosyltransferases (Gtfs) secreted by
Streptococcus mutans
bind to saliva-coated apatite (sHA) and to bacterial surfaces, synthesizing exopolymers
in situ
, which promote cell clustering and adherence to tooth enamel. We investigated the potential role Gtfs may play in mediating the interactions between
C. albicans
SC5314 and
S. mutans
UA159, both with each other and with the sHA surface. GtfB adhered effectively to the
C. albicans
yeast cell surface in an enzymatically active form, as determined by scintillation spectroscopy and fluorescence imaging. The glucans formed on the yeast cell surface were more susceptible to dextranase than those synthesized in solution or on sHA and bacterial cell surfaces (
P
< 0.05), indicating an elevated α-1,6-linked glucose content. Fluorescence imaging revealed that larger numbers of
S. mutans
cells bound to
C. albicans
cells with glucans present on their surface than to yeast cells without surface glucans (uncoated). The glucans formed
in situ
also enhanced
C. albicans
interactions with sHA, as determined by a novel single-cell micromechanical method. Furthermore, the presence of glucan-coated yeast cells significantly increased the accumulation of
S. mutans
on the sHA surface (versus
S. mutans
incubated alone or mixed with uncoated
C. albicans
;
P
< 0.05). These data reveal a novel cross-kingdom interaction that is mediated by bacterial GtfB, which readily attaches to the yeast cell surface. Surface-bound GtfB promotes the formation of a glucan-rich matrix
in situ
and may enhance the accumulation of
S. mutans
on the tooth enamel surface, thereby modulating the development of virulent biofilms.
Self-Inducible Bacillus subtilis Expression System for Reliable and Inexpensive Protein Production by High-Cell-Density Fermentation
Authors: Wenzel Marian , Müller Alexander , Siemann-Herzberg Martin , Altenbuchner Josef 
Published: July 2011

ABSTRACT

A novel technically compliant expression system was developed for heterologous protein production in
Bacillus subtilis
with the aim of increasing product yields at the same time as decreasing production costs. Standard systems involve the positively regulated
manP
promoter of the mannose operon, which led to relatively high product yields of 5.3% (5.3 g enhanced green fluorescent protein [eGFP] per 100 g cell dry weight [CDW]) but required large quantities of mannose to induce the reactions, thus rendering the system's technical application rather expensive. To improve this situation, mutant
B. subtilis
strains were used: the Δ
manA
(mannose metabolism) strain TQ281 and the Δ
manP
(mannose uptake) strain TQ356. The total amount of inducer could be reduced with TQ281, which, however, displayed sensitivity to mannose. An inducer-independent self-induction system was developed with TQ356 to further improve the cost efficiency and product yield of the system, in which glucose prevents induction by carbon catabolite repression. To create optimal self-induction conditions, a glucose-limited process strategy, namely, a fed-batch process, was utilized as follows. The initiation of self-induction at the beginning of the glucose-restricted transition phase between the batch and fed-batch phase of fermentation and its maintenance throughout the glucose-limiting fed-batch phase led to a nearly 3-fold increase of product yield, to 14.6%. The novel
B. subtilis
self-induction system thus makes a considerable contribution to improving product yield and reducing the costs associated with its technical application.
Use of Acid Treatment and a Selective Medium To Enhance the Recovery of Francisella tularensis from Water
Authors: Humrighouse B. W. , Adcock N. J. , Rice E. W. 
Published: July 2011

ABSTRACT

Francisella tularensis
has been associated with naturally occurring waterborne outbreaks and is also of interest as a potential biological weapon. Recovery of this pathogen from water using cultural methods is challenging due to the organism's fastidious growth requirements and interference by indigenous bacteria. A 15-min acid treatment procedure prior to culture on a selective agar was evaluated for recovery of
F. tularensis
from seeded water samples. Mean levels of reduction of virulent strains of
F. tularensis
subsp
. holarctica
and subsp.
tularensis
were less than 20% following acid treatment. The attenuated live vaccine strain (LVS) was less resistant to acid exposure. The acid treatment procedure coupled with plating on cystine heart agar with rabbit blood and antibiotics (CHARBab) allowed the isolation of
F. tularensis
seeded into five natural water samples.
Coproduction of Acetaldehyde and Hydrogen during Glucose Fermentation by Escherichia coli
Authors: Zhu Huilin , Gonzalez Ramon , Bobik Thomas A. 
Published: July 2011

ABSTRACT

Escherichia coli
K-12 strain MG1655 was engineered to coproduce acetaldehyde and hydrogen during glucose fermentation by the use of exogenous acetyl-coenzyme A (acetyl-CoA) reductase (for the conversion of acetyl-CoA to acetaldehyde) and the native formate hydrogen lyase. A putative acetaldehyde dehydrogenase/acetyl-CoA reductase from
Salmonella enterica
(SeEutE) was cloned, produced at high levels, and purified by nickel affinity chromatography.
In vitro
assays showed that this enzyme had both acetaldehyde dehydrogenase activity (68.07 ± 1.63 μmol min
−1
mg
−1
) and the desired acetyl-CoA reductase activity (49.23 ± 2.88 μmol min
−1
mg
−1
). The
eutE
gene was engineered into an
E. coli
mutant lacking native glucose fermentation pathways (Δ
adhE
, Δ
ackA
-
pta
, Δ
ldhA
, and Δ
frdC
). The engineered strain (ZH88) produced 4.91 ± 0.29 mM acetaldehyde while consuming 11.05 mM glucose but also produced 6.44 ± 0.26 mM ethanol. Studies showed that ethanol was produced by an unknown alcohol dehydrogenase(s) that converted the acetaldehyde produced by SeEutE to ethanol. Allyl alcohol was used to select for mutants with reduced alcohol dehydrogenase activity. Three allyl alcohol-resistant mutants were isolated; all produced more acetaldehyde and less ethanol than ZH88. It was also found that modifying the growth medium by adding 1 g of yeast extract/liter and lowering the pH to 6.0 further increased the coproduction of acetaldehyde and hydrogen. Under optimal conditions, strain ZH136 converted glucose to acetaldehyde and hydrogen in a 1:1 ratio with a specific acetaldehyde production rate of 0.68 ± 0.20 g h
−1
g
−1
dry cell weight and at 86% of the maximum theoretical yield. This specific production rate is the highest reported thus far and is promising for industrial application. The possibility of a more efficient “no-distill” ethanol fermentation procedure based on the coproduction of acetaldehyde and hydrogen is discussed.
Lachnospiraceae and Bacteroidales Alternative Fecal Indicators Reveal Chronic Human Sewage Contamination in an Urban Harbor
Authors: Newton Ryan J. , VandeWalle Jessica L. , Borchardt Mark A. , Gorelick Marc H. , McLellan Sandra L. 
Published: July 2011

ABSTRACT

The complexity of fecal microbial communities and overlap among human and other animal sources have made it difficult to identify source-specific fecal indicator bacteria. However, the advent of next-generation sequencing technologies now provides increased sequencing power to resolve microbial community composition within and among environments. These data can be mined for information on source-specific phylotypes and/or assemblages of phylotypes (i.e., microbial signatures). We report the development of a new genetic marker for human fecal contamination identified through microbial pyrotag sequence analysis of the V6 region of the 16S rRNA gene. Sequence analysis of 37 sewage samples and comparison with database sequences revealed a human-associated phylotype within the
Lachnospiraceae
family, which was closely related to the genus
Blautia
. This phylotype, termed Lachno2, was on average the second most abundant fecal bacterial phylotype in sewage influent samples from Milwaukee, WI. We developed a quantitative PCR (qPCR) assay for Lachno2 and used it along with the qPCR-based assays for human
Bacteroidales
(based on the HF183 genetic marker), total
Bacteroidales
spp., and enterococci and the conventional
Escherichia coli
and enterococci plate count assays to examine the prevalence of fecal and human fecal pollution in Milwaukee's harbor. Both the conventional fecal indicators and the human-associated indicators revealed chronic fecal pollution in the harbor, with significant increases following heavy rain events and combined sewer overflows. The two human-associated genetic marker abundances were tightly correlated in the harbor, a strong indication they target the same source (i.e., human sewage). Human adenoviruses were routinely detected under all conditions in the harbor, and the probability of their occurrence increased by 154% for every 10-fold increase in the human indicator concentration. Both Lachno2 and human
Bacteroidales
increased specificity to detect sewage compared to general indicators, and the relationship to a human pathogen group suggests that the use of these alternative indicators will improve assessments for human health risks in urban waters.
Biocontrol of Listeria monocytogenes and Escherichia coli O157:H7 in Meat by Using Phages Immobilized on Modified Cellulose Membranes
Authors: Anany H. , Chen W. , Pelton R. , Griffiths M. W. 
Published: July 2011

ABSTRACT

The ability of phages to specifically interact with and lyse their host bacteria makes them ideal antibacterial agents. The range of applications of bacteriophage can be extended by their immobilization on inert surfaces. A novel method for the oriented immobilization of bacteriophage has been developed. The method was based on charge differences between the bacteriophage head, which exhibits an overall net negative charge, and the tail fibers, which possess an overall net positive charge. Hence, the head would be more likely to attach to positively charged surfaces, leaving the tails free to capture and lyse bacteria. Cellulose membranes modified so that they had a positive surface charge were used as the support for phage immobilization. It was established that the number of infective phages immobilized on the positively charged cellulose membranes was significantly higher than that on unmodified membranes. Cocktails of phages active against
Listeria
or
Escherichia coli
immobilized on these membranes were shown to effectively control the growth of
L. monocytogenes
and
E. coli
O157:H7 in ready-to-eat and raw meat, respectively, under different storage temperatures and packaging conditions. The phage storage stability was investigated to further extend their industrial applications. It was shown that lyophilization can be used as a phage-drying method to maintain their infectivity on the newly developed bioactive materials. In conclusion, utilizing the charge difference between phage heads and tails provided a simple technique for oriented immobilization applicable to a wide range of phages and allowed the retention of infectivity.
Sources of Bacteria in Outdoor Air across Cities in the Midwestern United States
Authors: Bowers Robert M. , Sullivan Amy P. , Costello Elizabeth K. , Collett Jeff L. , Knight Rob , Fierer Noah 
Published: July 2011

ABSTRACT
Bacteria are abundant in the atmosphere, where they often represent a major portion of the organic aerosols. Potential pathogens of plants and livestock are commonly dispersed through the atmosphere, and airborne bacteria can have important effects on human health as pathogens or triggers of allergic asthma and seasonal allergies. Despite their importance, the diversity and biogeography of airborne microorganisms remain poorly understood. We used high-throughput pyrosequencing to analyze bacterial communities present in the aerosol fraction containing fine particulate matter of ≤2.5 μm from 96 near-surface atmospheric samples collected from cities throughout the midwestern United States and found that the communities are surprisingly diverse and strongly affected by the season. We also directly compared the airborne communities to those found in hundreds of samples representing potential source environments. We show that, in addition to the more predictable sources (soils and leaf surfaces), fecal material, most likely dog feces, often represents an unexpected source of bacteria in the atmosphere at more urbanized locations during the winter. Airborne bacteria are clearly an important, but understudied, component of air quality that needs to be better integrated into efforts to measure and model pollutants in the atmosphere.