bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular Analysis of Diazotroph Diversity in the Rhizosphere of the Smooth Cordgrass,
Spartina alterniflora
Authors: Lovell Charles R. , Piceno Yvette M. , Quattro Joseph M. , Bagwell Christopher E. 
Published: July 2002

ABSTRACT

N
2
fixation by diazotrophic bacteria associated with the roots of the smooth cordgrass,
Spartina alterniflora
, is an important source of new nitrogen in many salt marsh ecosystems. However, the diversity and phylogenetic affiliations of these rhizosphere diazotrophs are unknown. Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified
nifH
sequence segments was used in previous studies to examine the stability and dynamics of the
Spartina
rhizosphere diazotroph assemblages in the North Inlet salt marsh, near Georgetown, S.C. In this study, plugs were taken from gel bands from representative DGGE gels, the
nifH
amplimers were recovered and cloned, and their sequences were determined. A total of 59 sequences were recovered, and the amino acid sequences predicted from them were aligned with sequences from known and unknown diazotrophs in order to determine the types of organisms present in the
Spartina
rhizosphere. We recovered numerous sequences from diazotrophs in the γ subdivision of the division
Proteobacteria
(γ-
Proteobacteria
) and from various anaerobic diazotrophs. Diazotrophs in the α-
Proteobacteria
were poorly represented. None of the
Spartina
rhizosphere DGGE band sequences were identical to any known or previously recovered environmental
nifH
sequences. The
Spartina
rhizosphere diazotroph assemblage is very diverse and apparently consists mainly of unknown organisms.
The Group I Strain of
Streptococcus mutans
, UA140, Produces Both the Lantibiotic Mutacin I and a Nonlantibiotic Bacteriocin, Mutacin IV
Authors: Qi Fengxia , Chen Ping , Caufield Page W. 
Published: July 2002

ABSTRACT

Strains of
Streptococcus mutans
produce at least three mutacins, I, II, and III. Mutacin II is a member of subgroup AII in the lantibiotic family of bacteriocins, and mutacins I and III belong to subgroup AI in the lantibiotic family. In this report, we characterize two mutacins produced by UA140, a group I strain of
S. mutans
. One is identical to the lantibiotic mutacin I produced by strain CH43 (F. Qi et al., Appl. Environ. Microbiol. 66:3221–3229, 2000); the other is a nonlantibiotic bacteriocin, which we named mutacin IV. Mutacin IV belongs to the two-peptide, nonlantibiotic family of bacteriocins produced by gram-positive bacteria. Peptide A, encoded by gene
nlmA
, is 44 amino acids (aa) in size and has a molecular mass of 4,169 Da; peptide B, encoded by
nlmB
, is 49 aa in size and has a molecular mass of 4,826 Da. Both peptides derive from prepeptides with glycines at positions −2 and −1 relative to the processing site. Production of mutacins I and IV by UA140 appears to be regulated by different mechanisms under different physiological conditions. The significance of producing two mutacins by one strain under different conditions and the implication of this property in terms of the ecology of
S. mutans
in the oral cavity are discussed.
Genetic and Molecular Organization of the Alkylbenzene Catabolism Operon in the Psychrotrophic Strain
Pseudomonas putida
01G3
Authors: Chablain P. A. , Zgoda A. L. , Sarde C.-O. , Truffaut N. 
Published: July 2002

ABSTRACT

The 11-kb sequence encompassing the alkylbenzene upper pathway in
Pseudomonas putida
01G3, a psychrotrophic strain able to degrade alkylbenzenes at low temperatures, was characterized. Together with a potential regulator (EbdR), six putative enzymes (EbdAaAbAcAdBC) were identified, and they exhibited highly significant similarities with enzymes implicated in the equivalent pathway in
P. putida
RE204.
ebd
genes appeared to be preferentially induced by ethylbenzene. Multiple-alignment data and growth rate measurements led us to classify 01G3 and closely related strains in two groups with distinct substrate specificities. Close to identified genes, remnants of IS
5
-like elements provided insight into the evolution of catabolic sequences through rearrangements from a less complex ancestral cluster.
Group-Specific Monitoring of Phenol Hydroxylase Genes for a Functional Assessment of Phenol-Stimulated Trichloroethylene Bioremediation
Authors: Futamata Hiroyuki , Harayama Shigeaki , Watanabe Kazuya 
Published: July 2002

ABSTRACT

The sequences of the largest subunit of bacterial multicomponent phenol hydroxylases (LmPHs) were compared. It was found that LmPHs formed three phylogenetic groups, I, II, and III, corresponding to three previously reported kinetic groups, low-
K

s

(the half-saturation constant in Haldane's equation for trichloroethylene [TCE]), moderate-
K

s

, and high-
K

s

groups. Consensus sequences and specific amino acid residues for each group of LmPH were found, which facilitated the design of universal and group-specific PCR primers. PCR-mediated approaches using these primers were applied to analyze phenol/TCE-degrading populations in TCE-contaminated aquifer soil. It was found that the aquifer soil harbored diverse genotypes of LmPH, and the group-specific primers successfully amplified LmPH fragments affiliated with each of the three groups. Analyses of phenol-degrading bacteria isolated from the aquifer soil confirmed the correlation between genotype and phenotype. Competitive PCR assays were used to quantify LmPHs belonging to each group during the enrichment of phenol/TCE-degrading bacteria from the aquifer soil. We found that an enrichment culture established by batch phenol feeding expressed low TCE-degrading activity at a TCE concentration relevant to the contaminated aquifer (e.g., 0.5 mg liter
−1
); group II and III LmPHs were predominant in this batch enrichment. In contrast, group I LmPHs overgrew an enrichment culture when phenol was fed continuously. This enrichment expressed unexpectedly high TCE-degrading activity that was comparable to the activity expressed by a pure culture of
Methylosinus trichosporium
OB3b. These results demonstrate the utility of the group-specific monitoring of LmPH genes in phenol-stimulated TCE bioremediation. It is also suggested that phenol biostimulation could become a powerful TCE bioremediation strategy when bacteria possessing group I LmPHs are selectively stimulated.
Fungal Growth, Production, and Sporulation during Leaf Decomposition in Two Streams
Authors: Suberkropp Keller 
Published: July 2002

ABSTRACT

I examined the activity of fungi associated with yellow poplar (
Liriodendron tulipifera
) and white oak (
Quercus alba
) leaves in two streams that differed in pH and alkalinity (a hardwater stream [pH 8.0] and a softwater stream [pH 6.7]) and contained low concentrations of dissolved nitrogen (<35 μg liter
−1
) and phosphorus (<3 μg liter
−1
). The leaves of each species decomposed faster in the hardwater stream (decomposition rates, 0.010 and 0.007 day
−1
for yellow poplar and oak, respectively) than in the softwater stream (decomposition rates, 0.005 and 0.004 day
−1
for yellow poplar and oak, respectively). However, within each stream, the rates of decomposition of the leaves of the two species were not significantly different. During the decomposition of leaves, the fungal biomasses determined from ergosterol concentrations, the production rates determined from rates of incorporation of [
14
C]acetate into ergosterol, and the sporulation rates associated with leaves were dynamic, typically increasing to maxima and then declining. The maximum rates of fungal production and sporulation associated with yellow poplar leaves were greater than the corresponding rates associated with white oak leaves in the hardwater stream but not in the softwater stream. The maximum rates of fungal production associated with the leaves of the two species were higher in the hardwater stream (5.8 mg g
−1
day
−1
on yellow poplar leaves and 3.1 mg g
−1
day
−1
on oak leaves) than in the softwater stream (1.6 mg g
−1
day
−1
on yellow poplar leaves and 0.9 mg g
−1
day
−1
on oak leaves), suggesting that effects of water chemistry other than the N and P concentrations, such as pH or alkalinity, may be important in regulating fungal activity in streams. In contrast, the amount of fungal biomass (as determined from ergosterol concentrations) on yellow poplar leaves was greater in the softwater stream (12.8% of detrital mass) than in the hardwater stream (9.6% of detrital mass). This appeared to be due to the decreased amount of fungal biomass that was converted to conidia and released from the leaf detritus in the softwater stream.
Direct Detection by In Situ PCR of the
amoA
Gene in Biofilm Resulting from a Nitrogen Removal Process
Authors: Hoshino Tatsuhiko , Noda Naohiro , Tsuneda Satoshi , Hirata Akira , Inamori Yuhei 
Published: July 2002

ABSTRACT

Ammonia oxidation is a rate-limiting step in the biological removal of nitrogen from wastewater. Analysis of microbial communities possessing the
amoA
gene, which is a small subunit of the gene encoding ammonia monooxygenase, is important for controlling nitrogen removal. In this study, the
amoA
gene present in
Nitrosomonas europaea
cells in a pure culture and biofilms in a nitrifying reactor was amplified by in situ PCR. In this procedure, fixed cells were permeabilized with lysozyme and subjected to seminested PCR with a digoxigenin-labeled primer. Then, the amplicon was detected with an alkaline phosphatase-labeled antidigoxigenin antibody and HNPP (2-hydroxy-3-naphthoic acid-2′-phenylanilide phosphate), which was combined with Fast Red TR, and with an Alexa Fluor 488-labeled antidigoxigenin antibody. The
amoA
gene in the biofilms was detected with an unavoidable nonspecific signal when the former method was used for detection. On the other hand, the
amoA
gene in the biofilms was detected without a nonspecific signal, and the cells possessing the
amoA
gene were clearly observed near the surface of the biofilm when Alexa Fluor 488-labeled antidigoxigenin antibody was used for detection. Although functional gene expression was not detected in this study, detection of cells in a biofilm based on their function was demonstrated.
Cultivation-Independent, Semiautomatic Determination of Absolute Bacterial Cell Numbers in Environmental Samples by Fluorescence In Situ Hybridization
Authors: Daims Holger , Ramsing Niels B. , Schleifer Karl-Heinz , Wagner Michael 
Published: July 2002

ABSTRACT

Fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes has found widespread application for analyzing the composition of microbial communities in complex environmental samples. Although bacteria can quickly be detected by FISH, a reliable method to determine absolute numbers of FISH-stained cells in aggregates or biofilms has, to our knowledge, never been published. In this study we developed a semiautomated protocol to measure the concentration of bacteria (in cells per volume) in environmental samples by a combination of FISH, confocal laser scanning microscopy, and digital image analysis. The quantification is based on an internal standard, which is introduced by spiking the samples with known amounts of
Escherichia coli
cells. This method was initially tested with artificial mixtures of bacterial cultures and subsequently used to determine the concentration of ammonia-oxidizing bacteria in a municipal nitrifying activated sludge. The total number of ammonia oxidizers was found to be 9.8 × 10
7
± 1.9 × 10
7
cells ml
−1
. Based on this value, the average in situ activity was calculated to be 2.3 fmol of ammonia converted to nitrite per ammonia oxidizer cell per h. This activity is within the previously determined range of activities measured with ammonia oxidizer pure cultures, demonstrating the utility of this quantification method for enumerating bacteria in samples in which cells are not homogeneously distributed.
Molecular Characterization of the Iron-Hydroxamate Uptake System in
Staphylococcus aureus
Authors: Cabrera Guillermo , Xiong Anming , Uebel Michelle , Singh Vineet K. , Jayaswal Radheshyam K. 
Published: July 2002

ABSTRACT

To investigate iron uptake, a chromosomal locus containing three consecutive open reading frames, designated
fhuC
,
fhuB
, and
fhuD
, was identified in
Staphylococcus aureus
. Whereas the
fhuC
gene encodes an ATP-binding protein,
fhuB
and
fhuD
code for ferrichrome permeases and thus resemble an ATP-binding cassette transporter. A
fhuB
knockout mutant showed impaired uptake of iron bound to the siderophores but not of ferric chloride, suggesting that this operon is specific for siderophore-mediated iron uptake.
Binding Analyses of
Bacillus thuringiensis
Cry δ-Endotoxins Using Brush Border Membrane Vesicles of
Ostrinia nubilalis
Authors: Hua Gang , Masson Luke , Jurat-Fuentes Juan Luis , Schwab George , Adang Michael J. 
Published: July 2002

ABSTRACT

Transgenic corn expressing the
Bacillus thuringiensis
Cry1Ab gene is highly insecticidal to
Ostrinia nubilalis
(European corn borer) larvae. We ascertained whether Cry1F, Cry9C, or Cry9E recognizes the Cry1Ab binding site on the
O. nubilalis
brush border by three approaches. An optical biosensor technology based on surface plasmon resonance measured binding of brush border membrane vesicles (BBMV) injected over a surface of immobilized Cry toxin. Preincubation with Cry1Ab reduced BBMV binding to immobilized Cry1Ab, whereas preincubation with Cry1F, Cry9C, or Cry9E did not inhibit BBMV binding. BBMV binding to a Cry1F-coated surface was reduced when vesicles were preincubated in Cry1F or Cry1Ab but not Cry9C or Cry9E. A radioligand approach measured
125
I-Cry1Ab toxin binding to BBMV in the presence of homologous (Cry1Ab) and heterologous (Cry1Ac, Cry1F, Cry9C, or Cry9E) toxins. Unlabeled Cry1Ac effectively competed for
125
I-Cry1Ab binding in a manner comparable to Cry1Ab itself. Unlabeled Cry9C and Cry9E toxins did not inhibit
125
I-Cry1Ab binding to BBMV. Cry1F inhibited
125
I-Cry1Ab binding at concentrations greater than 500 nM. Cry1F had low-level affinity for the Cry1Ab binding site. Ligand blot analysis identified Cry1Ab, Cry1Ac, and Cry1F binding proteins in BBMV. The major Cry1Ab signals on ligand blots were at 145 kDa and 154 kDa, but a strong signal was present at 220 kDa and a weak signal was present at 167 kDa. Cry1Ac and Cry1F binding proteins were detected at 220 and 154 kDa. Anti-
Manduca sexta
aminopeptidase serum recognized proteins of 145, 154, and 167 kDa, and anti-cadherin serum recognized the 220 kDa protein. We speculate that isoforms of aminopeptidase and cadherin in the brush border membrane serve as Cry1Ab, Cry1Ac, and Cry1F binding proteins.
Archaeal Diversity in Waters from Deep South African Gold Mines
Authors: Takai Ken , Moser Duane P. , DeFlaun Mary , Onstott Tullis C. , Fredrickson James K. 
Published: July 2002

ABSTRACT

A culture-independent molecular analysis of archaeal communities in waters collected from deep South African gold mines was performed by performing a PCR-mediated terminal restriction fragment length polymorphism (T-RFLP) analysis of rRNA genes (rDNA) in conjunction with a sequencing analysis of archaeal rDNA clone libraries. The water samples used represented various environments, including deep fissure water, mine service water, and water from an overlying dolomite aquifer. T-RFLP analysis revealed that the ribotype distribution of archaea varied with the source of water. The archaeal communities in the deep gold mine environments exhibited great phylogenetic diversity; the majority of the members were most closely related to uncultivated species. Some archaeal rDNA clones obtained from mine service water and dolomite aquifer water samples were most closely related to environmental rDNA clones from surface soil (soil clones) and marine environments (marine group I [MGI]). Other clones exhibited intermediate phylogenetic affiliation between soil clones and MGI in the
Crenarchaeota
. Fissure water samples, derived from active or dormant geothermal environments, yielded archaeal sequences that exhibited novel phylogeny, including a novel lineage of
Euryarchaeota
. These results suggest that deep South African gold mines harbor novel archaeal communities distinct from those observed in other environments. Based on the phylogenetic analysis of archaeal strains and rDNA clones, including the newly discovered archaeal rDNA clones, the evolutionary relationship and the phylogenetic organization of the domain
Archaea
are reevaluated.
Microbial Populations Involved in Cycling of Dimethyl Sulfide and Methanethiol in Freshwater Sediments
Authors: Lomans Bart P. , Luderer Rianne , Steenbakkers Peter , Pol Arjan , van der Drift Chris , Vogels Godfried D. , Op den Camp Huub J. M. 
Published: July 2002

ABSTRACTAlthough several microorganisms that produce and degrade methanethiol (MT) and dimethyl sulfide (DMS) have been isolated from various habitats, little is known about the numbers of these microorganisms in situ. This study reports on the identification and quantification of microorganisms involved in the cycling of MT and DMS in freshwater sediments. Sediment incubation studies revealed that the formation of MT and DMS is well balanced with their degradation. MT formation depends on the concentrations of both sulfide and methyl group-donating compounds. A most-probable number (MPN) dilution series with syringate as the growth substrate showed that methylation of sulfide with methyl groups derived from syringate is a commonly occurring process in situ. MT appeared to be primarily degraded by obligately methylotrophic methanogens, which were found in the highest positive dilutions on DMS and mixed substrates (methanol, trimethylamine [TMA], and DMS). Amplified ribosomal DNA restriction analysis (ARDRA) and 16S rRNA gene sequence analysis of the total DNA isolated from the sediments and of the DNA isolated from the highest positive dilutions of the MPN series (mixed substrates) revealed that the methanogens that are responsible for the degradation of MT, DMS, methanol, and TMA in situ are all phylogenetically closely related toMethanomethylovorans hollandica. This was confirmed by sequence analysis of the product obtained from a nested PCR developed for the selective amplification of the 16S rRNA gene fromM. hollandica. The data from sediment incubation experiments, MPN series, and molecular-genetics detection correlated well and provide convincing evidence for the suggested mechanisms for MT and DMS cycling and the common presence of the DMS-degrading methanogenM. hollandicain freshwater sediments.
Emulsifying Activities of Purified Alasan Proteins from
Acinetobacter radioresistens
KA53
Authors: Toren Amir , Navon-Venezia Shiri , Ron Eliora Z. , Rosenberg Eugene 
Published: July 2002

ABSTRACT

The bioemulsifier of
Acinetobacter radioresistens
KA53, referred to as alasan, is a high-molecular-weight complex of polysaccharide and protein. The emulsifying activity of the purified polysaccharide (apo-alasan) is very low. Three of the alasan proteins were purified by preparative sodium dodecyl sulfate-polyacrylamide gel electrophoresis and had apparent molecular masses of 16, 31, and 45 kDa. Emulsification assays using the isolated alasan proteins demonstrated that the active components of the alasan complex are the proteins. The 45-kDa protein had the highest specific emulsifying activity, 11% higher than the intact alasan complex. The 16- and 31-kDa proteins gave relatively low emulsifying activities, but they were significantly higher than that of apo-alasan. The addition of the purified 16- and 31-kDa proteins to the 45-kDa protein resulted in a 1.8-fold increase in the specific emulsifying activity and increased stability of the oil-in-water emulsion. Fast-performance liquid chromatography analysis indicated that the 45-kDa protein forms a dimer in nondenaturing conditions and interacts with the 16- and 31-kDa proteins to form a high-molecular-mass complex. The 45-kDa protein and the three-protein complex had substrate specificities for emulsification and a range of pH activities similar to that of alasan. The fact that the purified proteins are active emulsifiers should simplify structure-function studies and advance our understanding of their biological roles.
Cryptosporidium parvum
Infection Involving Novel Genotypes in Wildlife from Lower New York State
Authors: Perz Joseph F. , Le Blancq Sylvie M. 
Published: July 2002

ABSTRACT

Cryptosporidium
, an enteric parasite of humans and a wide range of other mammals, presents numerous challenges to the supply of safe drinking water. We performed a wildlife survey, focusing on white-tailed deer and small mammals, to assess whether they may serve as environmental sources of
Cryptosporidium
. A PCR-based approach that permitted genetic characterization via sequence analysis was applied to wildlife fecal samples (
n
= 111) collected from September 1996 to July 1998 from three areas in lower New York State. Southern analysis revealed 22 fecal samples containing
Cryptosporidium
small-subunit (SSU) ribosomal DNA; these included 10 of 91 white-tailed deer (
Odocoileus virginianus
) samples, 3 of 5 chipmunk (
Tamias striatus
) samples, 1 of 2 white-footed mouse (
Peromyscus leucopus
) samples, 1 of 2 striped skunk (
Mephitis mephitis
) samples, 1 of 5 racoon (
Procyon lotor
) samples, and 6 of 6 muskrat (
Ondatra zibethicus
) samples. All of the 15 SSU PCR products sequenced were characterized as
Cryptosporidium parvum
; two were identical to genotype 2 (bovine), whereas the remainder belonged to two novel SSU sequence groups, designated genotypes 3 and 4. Genotype 3 comprised four deer-derived sequences, whereas genotype 4 included nine sequences from deer, mouse, chipmunk, and muskrat samples. PCR analysis was performed on the SSU-positive fecal samples for three other
Cryptosporidium
loci (dihydrofolate reductase, polythreonine-rich protein, and beta-tubulin), and 8 of 10 cloned PCR products were consistent with
C. parvum
genotype 2. These data provide evidence that there is sylvatic transmission of
C. parvum
involving deer and other small mammals. This study affirmed the importance of wildlife as potential sources of
Cryptosporidium
in the catchments of public water supplies.
Spiroplasma
Symbiont of the Pea Aphid,
Acyrthosiphon pisum
(Insecta: Homoptera)
Authors: Fukatsu Takema , Tsuchida Tsutomu , Nikoh Naruo , Koga Ryuichi 
Published: July 2002

ABSTRACT

From a laboratory strain of the pea aphid,
Acyrthosiphon pisum,
we discovered a previously unknown facultative endosymbiotic bacterium. Molecular phylogenetic analysis based on 16S ribosomal DNA revealed that the bacterium is a member of the genus
Spiroplasma
. The
Spiroplasma
organism showed stable vertical transmission through successive generations of the host. Injection of hemolymph from infected insects into uninfected insects established a stable infection in the recipients. The
Spiroplasma
symbiont exhibited negative effects on growth, reproduction, and longevity of the host, particularly in older adults. Of 58 clonal strains of
A. pisum
established from natural populations in central Japan, 4 strains possessed the
Spiroplasma
organism.
Determination of Virus Abundance in Marine Sediments
Authors: Danovaro R. , Dell'Anno A. , Trucco A. , Serresi M. , Vanucci S. 
Published: July 2002

ABSTRACT
In this study, we optimized procedures to enumerate viruses from marine sediments by epifluorescence microscopy using SYBR Green I as a stain. The highest virus yields from the bulk of the sediments were obtained by utilizing pyrophosphate and 3 min of sonication. The efficiency of extraction benthic viruses by pyrophosphate-ultrasound treatment was about 60% of the extractable virus particles. Samples treated with nucleases had increased virus counts, suggesting a masking effect of extracellular DNA. No significant differences were observed between virus counts obtained by epifluorescence microscopy and transmission electron microscopy. Both formaldehyde and glutaraldehyde gave significant reductions of virus counts after only 24 h of sediment storage, but no further loss occurred after 7 days.