bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative Assessment of Ammonia-Oxidizing Bacterial Communities in the Epiphyton of Submerged Macrophytes in Shallow Lakes
Authors: Coci M. , Nicol G. W. , Pilloni G. N. , Schmid M. , Kamst-van Agterveld M. P. , Bodelier P. L. E. , Laanbroek H. J. 
Published: January 2010

ABSTRACT

In addition to the benthic and pelagic habitats, the epiphytic compartment of submerged macrophytes in shallow freshwater lakes offers a niche to bacterial ammonia-oxidizing communities. However, the diversity, numbers, and activity of epiphytic ammonia-oxidizing bacteria have long been overlooked. In the present study, we analyzed quantitatively the epiphytic communities of three shallow lakes by a potential nitrification assay and by quantitative PCR of 16S rRNA genes. On the basis of the m
2
of the lake surface, the gene copy numbers of epiphytic ammonia oxidizers were not significantly different from those in the benthic and pelagic compartments. The potential ammonia-oxidizing activities measured in the epiphytic compartment were also not significantly different from the activities determined in the benthic compartment. No potential ammonia-oxidizing activities were observed in the pelagic compartment. No activity was detected in the epiphyton of
Chara aspera
, the dominant submerged macrophyte in Lake Nuldernauw in The Netherlands. The presence of ammonia-oxidizing bacterial cells in the epiphyton of
Potamogeton pectinatus
was also demonstrated by fluorescent
in situ
hybridization microscopy images. By comparing the community composition as assessed by the 16S rRNA gene PCR-denaturing gradient gel electrophoresis approach, it was concluded that the epiphytic ammonia-oxidizing communities consisted of cells that were also present in the benthic and pelagic compartments. Of the environmental parameters examined, only the water retention time, the Kjeldahl nitrogen content, and the total phosphorus content correlated with potential ammonia-oxidizing activities. None of these parameters correlated with the numbers of gene copies related to ammonia-oxidizing betaproteobacteria.
Inhibition of the Early Stage of
Salmonella enterica
Serovar Enteritidis Biofilm Development on Stainless Steel by Cell-Free Supernatant of a
Hafnia alvei
Culture
Authors: Chorianopoulos Nikos G. , Giaouris Efstathios D. , Kourkoutas Yiannis , Nychas George-John E. 
Published: January 2010

ABSTRACT

Compounds present in
Hafnia alvei
cell-free culture supernatant cumulatively negatively influence the early stage of biofilm development by
Salmonella enterica
serovar Enteritidis on stainless steel while they also reduce the overall metabolic activity of
S
. Enteritidis planktonic cells. Although acylhomoserine lactones (AHLs) were detected among these compounds, the use of several synthetic AHLs was not able to affect the initial stage of biofilm formation by this pathogen.
Bacterial Symbionts of the Brown Planthopper,Nilaparvata lugens(Homoptera: Delphacidae)
Authors: Tang Ming , Lv Lu , Jing Shengli , Zhu Lili , He Guangcun 
Published: January 2010

ABSTRACTThe brown planthopper (Nilaparvata lugensStål), the most destructive pest of rice, has been identified, including biotypes with high virulence towards previously resistant rice varieties. There have also been many reports of a yeast-like symbiont ofN. lugens, but little is known about the bacterial microbes. In this study, we examined the bacterial microbes inN. lugensand identified a total of 18 operational taxonomic units (OTUs) representing four phyla (Proteobacteria,Firmicutes,Actinobacteria, andBacteroidetes) by sequencing and analyzing 16S rRNA gene libraries obtained from three populations ofN. lugens, which were maintained on the rice varieties TN1, Mudgo, and ASD7. Several of the OTUs were similar to previously reported secondary symbionts of other insects, including an endosymbiont of the psyllidGlycapsis brimblecombei, anAsaiasp. found in the mosquitoAnopheles stephensi, andWolbachia, found in the miteMetaseiulus occidentalis. However, the species and numbers of the detected OTUs differed substantially among theN. lugenspopulations. Further,in situhybridization analysis using digoxigenin-labeled probes indicated that OTU 1 was located in hypogastrium tissues near the ovipositor and ovary in biotype 1 insects, while OTU 2 was located in the front of the ovipositor sheath in biotype 2 insects. In addition, masses of bacterium-like organisms were observed in the tubes of salivary sheaths in rice plant tissues that the insects had fed upon. The results provide indications of the diversity of the bacterial microbes harbored by the brown planthopper and of possible associations between specific bacterial microbes and biotypes ofN. lugens.
Significance of Wall Structure, Macromolecular Composition, and Surface Polymers to the Survival and Transport of
Cryptosporidium parvum
Oocysts
Authors: Jenkins Michael B. , Eaglesham Barbara S. , Anthony Larry C. , Kachlany Scott C. , Bowman Dwight D. , Ghiorse William C. 
Published: January 2010

ABSTRACT

The structure and composition of the oocyst wall are primary factors determining the survival and hydrologic transport of
Cryptosporidium parvum
oocysts outside the host. Microscopic and biochemical analyses of whole oocysts and purified oocyst walls were undertaken to better understand the inactivation kinetics and hydrologic transport of oocysts in terrestrial and aquatic environments. Results of microscopy showed an outer electron-dense layer, a translucent middle layer, two inner electron-dense layers, and a suture structure embedded in the inner electron-dense layers. Freeze-substitution showed an expanded glycocalyx layer external to the outer bilayer, and Alcian Blue staining confirmed its presence on some but not all oocysts. Biochemical analyses of purified oocyst walls revealed carbohydrate components, medium- and long-chain fatty acids, and aliphatic hydrocarbons. Purified walls contained 7.5% total protein (by the Lowry assay), with five major bands in SDS-PAGE gels. Staining of purified oocyst walls with magnesium anilinonaphthalene-8-sulfonic acid indicated the presence of hydrophobic proteins. These structural and biochemical analyses support a model of the oocyst wall that is variably impermeable and resistant to many environmental pressures. The strength and flexibility of oocyst walls appear to depend on an inner layer of glycoprotein. The temperature-dependent permeability of oocyst walls may be associated with waxy hydrocarbons in the electron-translucent layer. The complex chemistry of these layers may explain the known acid-fast staining properties of oocysts, as well as some of the survival characteristics of oocysts in terrestrial and aquatic environments. The outer glycocalyx surface layer provides immunogenicity and attachment possibilities, and its ephemeral nature may explain the variable surface properties noted in oocyst hydrologic transport studies.
Effects of Trp- and Arg-Containing Antimicrobial-Peptide Structure on Inhibition of
Escherichia coli
Planktonic Growth and Biofilm Formation
Authors: Hou Shuyu , Liu Zhigang , Young Anne W. , Mark Sheron L. , Kallenbach Neville R. , Ren Dacheng 
Published: January 2010

ABSTRACT

Biofilms are sessile microbial communities that cause serious chronic infections with high morbidity and mortality. In order to develop more effective approaches for biofilm control, a series of linear cationic antimicrobial peptides (AMPs) with various arginine (Arg or R) and tryptophan (Trp or W) repeats [(RW)

n

-NH
2
, where
n
= 2, 3, or 4] were rigorously compared to correlate their structures with antimicrobial activities affecting the planktonic growth and biofilm formation of
Escherichia coli
. The chain length of AMPs appears to be important for inhibition of bacterial planktonic growth, since the hexameric and octameric peptides significantly inhibited
E. coli
growth, while tetrameric peptide did not cause noticeable inhibition. In addition, all AMPs except the tetrameric peptide significantly reduced
E. coli
biofilm surface coverage and the viability of biofilm cells, when added at inoculation. In addition to inhibition of biofilm formation, significant killing of biofilm cells was observed after a 3-hour treatment of preformed biofilms with hexameric peptide. Interestingly, treatment with the octameric peptide caused significant biofilm dispersion without apparent killing of biofilm cells that remained on the surface; e.g., the surface coverage was reduced by 91.5 ± 3.5% by 200 μM octameric peptide. The detached biofilm cells, however, were effectively killed by this peptide. Overall, these results suggest that hexameric and octameric peptides are potent inhibitors of both bacterial planktonic growth and biofilm formation, while the octameric peptide can also disperse existing biofilms and kill the detached cells. These results are helpful for designing novel biofilm inhibitors and developing more effective therapeutic methods.
Anaerobic Digestion of Renewable Biomass: Thermophilic Temperature Governs Methanogen Population Dynamics
Authors: Krakat Niclas , Westphal A. , Schmidt S. , Scherer P. 
Published: January 2010

ABSTRACT

Beet silage and beet juice were digested continuously as representative energy crops in a thermophilic biogas fermentor for more than 7 years. Fluorescence microscopy of 15 samples covering a period of 650 days revealed that a decrease in temperature from 60°C to 55°C converted a morphologically uniform archaeal population (rods) into a population of methanogens exhibiting different cellular morphologies (rods and coccoid cells). A subsequent temperature increase back to 60°C reestablished the uniform morphology of methanogens observed in the previous 60°C period. In order to verify these observations, representative samples were investigated by amplified rRNA gene restriction analysis (ARDRA) and fluorescence in situ hybridization (FISH). Both methods confirmed the temperature-dependent population shift observed by fluorescence microscopy. Moreover, all samples investigated demonstrated that hydrogenotrophic
Methanobacteriales
dominated in the fermentor, as 29 of 34 identified operational taxonomic units (OTUs) were assigned to this order. This apparent discrimination of acetoclastic methanogens contradicts common models for anaerobic digestion processes, such as anaerobic digestion model 1 (ADM1), which describes the acetotrophic
Euryarchaeota
as predominant organisms.
Microbial Community Analysis of Anodes from Sediment Microbial Fuel Cells Powered by Rhizodeposits of Living Rice Plants
Authors: De Schamphelaire Liesje , Cabezas Angela , Marzorati Massimo , Friedrich Michael W. , Boon Nico , Verstraete Willy 
Published: January 2010

ABSTRACT

By placing the anode of a sediment microbial fuel cell (SMFC) in the rhizosphere of a rice plant, root-excreted rhizodeposits can be microbially oxidized with concomitant current generation. Here, various molecular techniques were used to characterize the composition of bacterial and archaeal communities on such anodes, as influenced by electrical circuitry, sediment matrix, and the presence of plants. Closed-circuit anodes in potting soil were enriched with
Desulfobulbus
-like species, members of the family
Geobacteraceae
, and as yet uncultured representatives of the domain
Archaea
.
The Carnivorous Pale Pitcher Plant Harbors Diverse, Distinct, and Time-Dependent Bacterial Communities
Authors: Koopman Margaret M. , Fuselier Danielle M. , Hird Sarah , Carstens Bryan C. 
Published: January 2010

ABSTRACT

The ability of American carnivorous pitcher plants (
Sarracenia
) to digest insect prey is facilitated by microbial associations. Knowledge of the details surrounding this interaction has been limited by our capability to characterize bacterial diversity in this system. To describe microbial diversity within and between pitchers of one species,
Sarracenia alata
, and to explore how these communities change over time as pitchers accumulate and digest insect prey, we collected and analyzed environmental sequence tag (454 pyrosequencing) and genomic fingerprint (automated ribosomal intergenic spacer analysis and terminal restriction fragment length polymorphism) data. Microbial richness associated with pitcher plant fluid is high; more than 1,000 unique phylogroups were identified across at least seven phyla and 50 families. We documented an increase in bacterial diversity and abundance with time and observed repeated changes in bacterial community composition. Pitchers from different plants harbored significantly more similar bacterial communities at a given time point than communities coming from the same genetic host over time. The microbial communities in pitcher plant fluid also differ significantly from those present in the surrounding soil. These findings indicate that the bacteria associated with pitcher plant leaves are far from random assemblages and represent an important step toward understanding this unique plant-microbe interaction.
Use of Fatty Acid Methyl Ester Profiles for Discrimination ofBacillus cereusT-Strain Spores Grown on Different Media
Authors: Ehrhardt Christopher J. , Chu Vivian , Brown TeeCie , Simmons Terrie L. , Swan Brandon K. , Bannan Jason , Robertson James M. 
Published: January 2010

ABSTRACTThe goal of this study was to determine if cellular fatty acid methyl ester (FAME) profiling could be used to distinguish among spore samples from a single species (Bacillus cereusT strain) that were prepared on 10 different medium formulations. To analyze profile differences and identify FAME biomarkers diagnostic for the chemical constituents in each sporulation medium, a variety of statistical techniques were used, including nonmetric multidimensional scaling (nMDS), analysis of similarities (ANOSIM), and discriminant function analysis (DFA). The results showed that one FAME biomarker, oleic acid (18:1 ω9c), was exclusively associated with spores grown on Columbia agar supplemented with sheep blood and was indicative of blood supplements that were present in the sporulation medium. For spores grown in other formulations, multivariate comparisons across several FAME biomarkers were required to discern profile differences. Clustering patterns in nMDS plots andRvalues from ANOSIM revealed that dissimilarities among FAME profiles were most pronounced when spores grown with disparate sources of complex additives or protein supplements were compared (R> 0.8), although other factors also contributed to FAME differences. DFA indicated that differentiation could be maximized with a targeted subset of FAME variables, and the relative contributions of branched FAME biomarkers to group dissimilarities changed when different media were compared. When taken together, these analyses indicate thatB. cereusspore samples grown in different media can be resolved with FAME profiling and that this may be a useful technique for providing intelligence about the production methods ofBacillusorganisms in a forensic investigation.
Rapid Assessment of the Viability of
Mycobacterium avium
subsp.
paratuberculosis
Cells after Heat Treatment, Using an Optimized Phage Amplification Assay
Authors: Foddai Antonio , Elliott Christopher T. , Grant Irene R. 
Published: January 2010

ABSTRACT

Thermal inactivation experiments were carried out to assess the utility of a recently optimized phage amplification assay to accurately enumerate viable
Mycobacterium avium
subsp.
paratuberculosis
cells in milk. Ultra-heat-treated (UHT) whole milk was spiked with large numbers of
M. avium
subsp.
paratuberculosis
organisms (10
6
to 10
7
CFU/ml) and dispensed in 100-μl aliquots in thin-walled 200-μl PCR tubes. A Primus 96 advanced thermal cycler (Peqlab, Erlangen, Germany) was used to achieve the following time and temperature treatments: (i) 63°C for 3, 6, and 9 min; (ii) 68°C for 20, 40, and 60 s; and (iii) 72°C for 5, 10, 15, and 25 s. After thermal stress, the number of surviving
M. avium
subsp.
paratuberculosis
cells was assessed by both phage amplification assay and culture on Herrold's egg yolk medium (HEYM). A high correlation between PFU/ml and CFU/ml counts was observed for both unheated (
r
2
= 0.943) and heated (
r
2
= 0.971)
M. avium
subsp.
paratuberculosis
cells.
D
and
z
values obtained using the two types of counts were not significantly different (
P
> 0.05). The
D
68°C
, mean
D
63°C
, and
D
72°C
for four
M. avium
subsp.
paratuberculosis
strains were 81.8, 9.8, and 4.2 s, respectively, yielding a mean
z
value of 6.9°C. Complete inactivation of 10
6
to 10
7
CFU of
M. avium
subsp.
paratuberculosis
/ml milk was not observed for any of the time-temperature combinations studied; 5.2- to 6.6-log
10
reductions in numbers were achieved depending on the temperature and time. Nonlinear thermal inactivation kinetics were consistently observed for this bacterium. This study confirms that the optimized phage assay can be employed in place of conventional culture on HEYM to speed up the acquisition of results (48 h instead of a minimum of 6 weeks) for inactivation experiments involving
M. avium
subsp.
paratuberculosis
-spiked samples.
Development and Application of a PCR-Targeted Gene Disruption Method for Studying CelR Function in
Thermobifida fusca
Authors: Deng Yu , Fong Stephen S. 
Published: January 2010

ABSTRACT

Thermobifida fusca
is a high-G+C-content, thermophilic, Gram-positive soil actinobacterium with high cellulolytic activity. In
T. fusca
, CelR is thought to act as the primary regulator of cellulase gene expression by binding to a 14-bp inverted repeat [5′-(T)GGGAGCGCTCCC(A)] that is upstream of many known cellulase genes. Previously, the ability to study the roles and regulation of cellulase genes in
T. fusca
has been limited largely by a lack of established genetic engineering methods for
T. fusca
. In this study, we developed an efficient procedure for creating precise chromosomal gene disruptions and demonstrated this procedure by generating a
celR
deletion strain. The
celR
deletion strain was then characterized using measurements for growth behavior, cellulase activity, and gene expression. The
celR
deletion strain of
T. fusca
exhibited a severely crippled growth phenotype with a prolonged lag phase and decreased cell yields for growth on both glucose and cellobiose. While the maximum endoglucanase activity and cellulase activity were not significantly changed, the endoglucanase activity and cellulase activity per cell were highly elevated. Measurements of mRNA transcript levels in both the
celR
deletion strain and the wild-type strain indicated that the CelR protein potentially acts as a repressor for some genes and as an activator for other genes. Overall, we established and demonstrated a method for manipulating chromosomal DNA in
T. fusca
that can be used to study the cellulolytic capabilities of this organism. Components of this method may be useful in developing genetic engineering methods for other currently intractable organisms.
Improved Strains and Plasmid Vectors for Conditional Overexpression of His-Tagged Proteins in
Haloferax volcanii
Authors: Allers Thorsten , Barak Shahar , Liddell Susan , Wardell Kayleigh , Mevarech Moshe 
Published: January 2010

ABSTRACT

Research into archaea will not achieve its full potential until systems are in place to carry out genetics and biochemistry in the same species.
Haloferax volcanii
is widely regarded as the best-equipped organism for archaeal genetics, but the development of tools for the expression and purification of
H. volcanii
proteins has been neglected. We have developed a series of plasmid vectors and host strains for conditional overexpression of halophilic proteins in
H. volcanii
. The plasmids feature the tryptophan-inducible p.
tnaA
promoter and a 6×His tag for protein purification by metal affinity chromatography. Purification is facilitated by host strains, where
pitA
is replaced by the ortholog from
Natronomonas pharaonis
. The latter lacks the histidine-rich linker region found in
H. volcanii
PitA and does not copurify with His-tagged recombinant proteins. We also deleted the
mrr
restriction endonuclease gene, thereby allowing direct transformation without the need to passage DNA through an
Escherichia coli dam
mutant.
Dependence of Continuous-Flow Biofilm Formation by
Listeria monocytogenes
EGD-e on SOS Response Factor YneA
Authors: van der Veen Stijn , Abee Tjakko 
Published: January 2010

ABSTRACT

Listeria monocytogenes
was previously shown to form biofilms composed of a network of knitted chains under continuous-flow conditions. Here we show that the SOS response is activated under these conditions and that deletion of its regulon member
yneA
results in diminished biofilm formation under continuous-flow conditions.
d
-Xylose as a Repressor or Inducer of Xylanase Expression in
Hypocrea jecorina
(
Trichoderma reesei
)
Authors: Mach-Aigner Astrid R. , Pucher Marion E. , Mach Robert L. 
Published: January 2010

ABSTRACT

For
Hypocrea jecorina
(anamorph
Trichoderma reesei
), a filamentous fungus used for hydrolase production in different industries, it has been a long-term practice to use
d
-xylose as an inducing substance. We demonstrate in this study that the degree of xylanase-encoding gene induction strictly depends on the concentration of
d
-xylose, which was found to be optimal from 0.5 to 1 mM for 3 h of cultivation. At higher concentrations of
d
-xylose, a reduced level of xylanase gene expression was observed. In the present study, we also provide evidence that the
d
-xylose concentration-dependent induction is antagonized by carbon catabolite repressor 1. This repressor mediates its influence on
d
-xylose indirectly, by reducing the expression of xylanase regulator 1, the main activator of most hydrolase-encoding genes. Additionally, a direct influence of the repressor on xylanase 1 expression in the presence of
d
-xylose was found. Furthermore, we show that
d
-xylose reductase 1 is needed to metabolize
d
-xylose to achieve full induction of xylanase expression. Finally, a strain which expresses xylanase regulator 1 at a constant level was used to partially overcome the negative influence exerted by carbon catabolite repressor 1 on
d
-xylose.
Molecular Characterization of Sewage-Borne Pathogens and Detection of Sewage Markers in an Urban Stream in Caracas, Venezuela
Authors: Betancourt W. Q. , Querales L. , Sulbaran Y. F. , Rodriguez-Diaz J. , Caraballo L. , Pujol F. H. 
Published: January 2010

ABSTRACT

Molecular characterization of two sewage-borne pathogens identified hepatitis A virus (HAV) subgenotype IA and
Giardia duodenalis
assemblages A and B as predominant genotypes circulating in an urban area of Venezuela. This study reveals epidemiological features of human pathogens of worldwide distribution and the efficacy of molecular methods for accurate assessment of sewage pollution.