bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of Cellular and Biomass Specific Activities of Dominant Bacterioplankton Groups in Stratified Waters of the Celtic Sea
Authors: Zubkov Mikhail V. , Fuchs Bernhard M. , Burkill Peter H. , Amann Rudolf 
Published: July 2002

ABSTRACT

A flow-sorting technique was developed to determine unperturbed metabolic activities of phylogenetically characterized bacterioplankton groups with incorporation rates of [
35
S]methionine tracer. According to fluorescence in situ hybridization with rRNA targeted oligonucleotide probes, a clade of α-proteobacteria, related to
Roseobacter
spp., and a
Cytophaga-Flavobacterium
cluster dominated the different groups. Cytometric characterization revealed both these groups to have high DNA (HNA) content, while the α-proteobacteria exhibited high light scatter (hs) and the
Cytophaga-Flavobacterium
cluster exhibited low light scatter (ls). A third abundant group with low DNA (LNA) content contained cells from a SAR86 cluster of γ-proteobacteria. Cellular specific activities of the HNA-hs group were 4- and 1.7-fold higher than the activities in the HNA-ls and LNA groups, respectively. However, the higher cellular protein synthesis by the HNA-hs could simply be explained by their maintenance of a larger cellular protein biomass. Similar biomass specific activities of the different groups strongly support the main assumption that underlies the determination of bacterial production: different bacteria in a complex community incorporate amino acids at a rate proportional to their protein synthesis. The fact that the highest growth-specific rates were determined for the smallest cells of the LNA group can explain the dominance of this group in nutrient-limited waters. The metabolic activities of the three groups accounted for almost the total bacterioplankton activity, indicating their key biogeochemical role in the planktonic ecosystem of the Celtic Sea.
Diversity of the Ring-Cleaving Dioxygenase Gene
pcaH
in a Salt Marsh Bacterial Community
Authors: Buchan Alison , Neidle Ellen L. , Moran Mary Ann 
Published: July 2002

ABSTRACT

Degradation of lignin-related aromatic compounds is an important ecological process in the highly productive salt marshes of the southeastern United States, yet little is known about the mediating organisms or their catabolic pathways. Here we report the diversity of a gene encoding a key ring-cleaving enzyme of the β-ketoadipate pathway,
pcaH
, amplified from bacterial communities associated with decaying
Spartina alterniflora
, the salt marsh grass that dominates these coastal systems, as well as from enrichment cultures with aromatic substrates (
p
-hydroxybenzoate, anthranilate, vanillate, and dehydroabietate). Sequence analysis of 149
pcaH
clones revealed 85 unique sequences. Thirteen of the 53 amino acid residues compared were invariant in the PcaH proteins, suggesting that these residues have a required catalytic or structural function. Fifty-eight percent of the clones matched sequences amplified from a collection of 36 bacterial isolates obtained from seawater, marine sediments, or senescent
Spartina
. Fifty-two percent of the
pcaH
clones could be assigned to the roseobacter group, a marine lineage of the class α-
Proteobacteria
abundant in coastal ecosystems. Another 6% of the clones matched genes retrieved from isolates belonging to the genera
Acinetobacter, Bacillus
, and
Stappia
, and 42% of the clones could not be assigned to a cultured bacterium based on sequence identity. These results suggest that the diversity of the genes encoding a single step in aromatic compound degradation in the coastal marsh examined is high.
Acyl-Homoserine Lactone Production Is More Common among Plant-Associated
Pseudomonas
spp. than among Soilborne
Pseudomonas
spp
Authors: Elasri Miena , Delorme Sandrine , Lemanceau Philippe , Stewart Gordon , Laue Bridget , Glickmann Eric , Oger Phil M. , Dessaux Yves 
Published: July 2002

ABSTRACT

A total of 137 soilborne and plant-associated bacterial strains belonging to different
Pseudomonas
species were tested for their ability to synthesize
N
-acyl-homoserine lactones (NAHL). Fifty-four strains synthesized NAHL. Interestingly, NAHL production appears to be more common among plant-associated than among soilborne
Pseudomonas
spp. Indeed, 40% of the analyzed
Pseudomonas syringae
strains produced NAHL which were identified most often as the short-chain NAHL,
N
-hexanoyl-
l
-homoserine lactone,
N
-(3-oxo-hexanoyl)-homoserine lactone, and
N
-(3-oxo-octanoyl)-
l
-homoserine lactone (no absolute correlation between genomospecies of
P. syringae
and their ability to produce NAHL could be found). Six strains of fluorescent pseudomonads, belonging to the species
P. chlororaphis
,
P. fluorescens
, and
P. putida
, isolated from the plant rhizosphere produced different types of NAHL. In contrast, none of the strains isolated from soil samples were shown to produce NAHL. The gene encoding the NAHL synthase in
P. syringae
pv. maculicola was isolated by complementation of an NAHL-deficient
Chromobacterium
mutant. Sequence analysis revealed the existence of a
luxI
homologue that we named
psmI
. This gene is sufficient to confer NAHL synthesis upon its bacterial host and has strong homology to
psyI
and
ahlI
, two genes involved in NAHL production in
P. syringae
pv. tabaci and
P. syringae
pv. syringae, respectively. We identified another open reading frame that we termed
psmR
, transcribed convergently in relation to
psmI
and partly overlapping
psmI
; this gene encodes a putative LuxR regulatory protein. This gene organization, with
luxI
and
luxR
homologues facing each other and overlapping, has been found so far only in the enteric bacteria
Erwinia
and
Pantoea
and in the related species
P. syringae
pv. tabaci.
Dual Role of GdmH in Producer Immunity and Secretion of the Staphylococcal Lantibiotics Gallidermin and Epidermin
Authors: Hille Matthias , Kies Stefanie , Götz Friedrich , Peschel Andreas 
Published: July 2002

ABSTRACT

The biosynthetic gene clusters of the staphylococcal lantibiotics epidermin and gallidermin are distinguished by the presence of the unique genes
epiH
and
gdmH
, respectively. They encode accessory factors for the ATP-binding cassette transporters that mediate secretion of the antimicrobial peptides. Here, we show that
gdmH
also contributes to immunity to gallidermin but not to nisin.
gdmH
alone affected susceptibility to gallidermin only moderately, but it led to a multiplication of the immunity level mediated by the
FEG
immunity genes when cloned together with the
gdmT
gene, suggesting a synergistic activity of the H and FEG systems.
gdmH
-related genes were identified in the genomes of several bacteria, indicating an involvement in further cellular functions.
Genomic Relatedness within Five Common Finnish
Campylobacter jejuni
Pulsed-Field Gel Electrophoresis Genotypes Studied by Amplified Fragment Length Polymorphism Analysis, Ribotyping, and Serotyping
Authors: Hänninen Marja-Liisa , Perko-Mäkelä Päivikki , Rautelin Hilpi , Duim Birgitta , Wagenaar Jaap A. 
Published: July 2002

ABSTRACT

Thirty-five Finnish
Campylobacter jejuni
strains with five
Sma
I/
Sac
II pulsed-field gel electrophoresis (PFGE) genotypes selected among human and chicken isolates from 1997 and 1998 were used for comparison of their PFGE patterns, amplified fragment length polymorphism (AFLP) patterns,
Hae
III ribotypes, and heat-stable (HS) serotypes. The discriminatory power of PFGE, AFLP, and ribotyping with
Hae
III were shown to be at the same level for this selected set of strains, and these methods assigned the strains into the same groups. The PFGE and AFLP patterns within a genotype were highly similar, indicating genetic relatedness. The same HS serotypes were distributed among different genotypes, and different serotypes were identified within one genotype. HS serotype 12 was only associated with the combined genotype G1 (PFGE-AFLP-ribotype). These studies using polyphasic genotyping methods suggested that common Finnish
C. jejuni
genotypes form genetic lineages which colonize both humans and chickens.
Effect of Exogenous Siderophores on Iron Uptake Activity of Marine Bacteria under Iron-Limited Conditions
Authors: Guan Le Luo , Kanoh Kaneo , Kamino Kei 
Published: July 2002

ABSTRACT

More than 60% of species examined from a total of 421 strains of heterotrophic marine bacteria which were isolated from marine sponges and seawater were observed to have no detectable siderophore production even when Fe(III) was present in the culture medium at a concentration of 1.0 pM. The growth of one such non-siderophore-producing strain, alpha proteobacterium V0210, was stimulated under iron-limited conditions with the addition of an isolated exogenous siderophore,
N
,
N
′-bis (2,3-dihydroxybenzoyl)-
O
-serylserine from a
Vibrio
sp. Growth was also stimulated by the addition of three exogenous siderophore extracts from siderophore-producing bacteria. Radioisotope studies using
59
Fe showed that the iron uptake ability of V0210 increased only with the addition of exogenous siderophores. Biosynthesis of a hydroxamate siderophore by V0210 was shown by paper electrophoresis and chemical assays for the detection of hydroxamates and catechols. An 85-kDa iron-regulated outer membrane protein was induced only under iron-limited conditions in the presence of exogenous siderophores. This is the first report of bacterial iron uptake through an induced siderophore in response to exogenous siderophores. Our results suggest that siderophores are necessary signaling compounds for growth and for iron uptake by some non-siderophore-producing marine bacteria under iron-limited conditions.
Phylogenetic Diversity of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase Large-Subunit Genes from Deep-Sea Microorganisms
Authors: Elsaied Hosam , Naganuma Takeshi 
Published: July 2002

ABSTRACT

The phylogenetic diversity of the ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO, E.C. 4.1.1.39) large-subunit genes of deep-sea microorganisms was analyzed. Bulk genomic DNA was isolated from seven samples, including samples from the Mid-Atlantic Ridge and various deep-sea habitats around Japan. The kinds of samples were hydrothermal vent water and chimney fragment; reducing sediments from a bathyal seep, a hadal seep, and a presumed seep; and symbiont-bearing tissues of the vent mussel,
Bathymodiolus
sp., and the seep vestimentiferan tubeworm,
Lamellibrachia
sp. The RuBisCO genes that encode both form I and form II large subunits (
cbbL
and
cbbM
) were amplified by PCR from the seven deep-sea sample DNA populations, cloned, and sequenced. From each sample, 50
cbbL
clones and 50
cbbM
clones, if amplified, were recovered and sequenced to group them into operational taxonomic units (OTUs). A total of 29 OTUs were recorded from the 300 total
cbbL
clones, and a total of 24 OTUs were recorded from the 250 total
cbbM
clones. All the current OTUs have the characteristic RuBisCO amino acid motif sequences that exist in other RuBisCOs. The recorded OTUs were related to different RuBisCO groups of proteobacteria, cyanobacteria, and eukarya. The diversity of the RuBisCO genes may be correlated with certain characteristics of the microbial habitats. The RuBisCO sequences from the symbiont-bearing tissues showed a phylogenetic relationship with those from the ambient bacteria. Also, the RuBisCO sequences of known species of thiobacilli and those from widely distributed marine habitats were closely related to each other. This suggests that the
Thiobacillus
-related RuBisCO may be distributed globally and contribute to the primary production in the deep sea.
Exploiting Genotypic Diversity of 2,4-Diacetylphloroglucinol-Producing
Pseudomonas
spp.: Characterization of Superior Root-Colonizing
P. fluorescens
Strain Q8r1-96
Authors: Raaijmakers Jos M. , Weller David M. 
Published: July 2002

ABSTRACT

The genotypic diversity that occurs in natural populations of antagonistic microorganisms provides an enormous resource for improving biological control of plant diseases. In this study, we determined the diversity of indigenous 2,4-diacetylphloroglucinol (DAPG)-producing
Pseudomonas
spp. occurring on roots of wheat grown in a soil naturally suppressive to take-all disease of wheat. Among 101 isolates, 16 different groups were identified by random amplified polymorphic DNA (RAPD) analysis. One RAPD group made up 50% of the total population of DAPG-producing
Pseudomonas
spp. Both short- and long-term studies indicated that this dominant genotype, exemplified by
P. fluorescens
Q8r1-96, is highly adapted to the wheat rhizosphere. Q8r1-96 requires a much lower dose (only 10 to 100 CFU seed
−1
or soil
−1
) to establish high rhizosphere population densities (10
7
CFU g of root
−1
) than Q2-87 and 1M1-96, two genotypically different, DAPG-producing
P. fluorescens
strains. Q8r1-96 maintained a rhizosphere population density of approximately 10
5
CFU g of root
−1
after eight successive growth cycles of wheat in three different, raw virgin soils, whereas populations of Q2-87 and 1M1-96 dropped relatively quickly after five cycles and were not detectable after seven cycles. In short-term studies, strains Q8r1-96, Q2-87, and 1M1-96 did not differ in their ability to suppress take-all. After eight successive growth cycles, however, Q8r1-96 still provided control of take-all to the same level as obtained in the take-all suppressive soil, whereas Q2-87 and 1M1-96 gave no control anymore. Biochemical analyses indicated that the superior rhizosphere competence of Q8r1-96 is not related to in situ DAPG production levels. We postulate that certain rhizobacterial genotypes have evolved a preference for colonization of specific crops. By exploiting diversity of antagonistic rhizobacteria that share a common trait, biological control can be improved significantly.
Strategy for Manipulation of Cheese Flora Using Combinations of Lacticin 3147-Producing and -Resistant Cultures
Authors: Ryan Máire P. , Ross R. Paul , Hill Colin 
Published: July 2002

ABSTRACT

The aim of the present study was to develop adjunct strains which can grow in the presence of bacteriocin produced by lacticin 3147-producing starters in fermented products such as cheese. A
Lactobacillus paracasei
subsp.
paracasei
strain (DPC5336) was isolated from a well-flavored, commercial cheddar cheese and exposed to increasing concentrations (up to 4,100 arbitrary units [AU]/ml) of lantibiotic lacticin 3147. This approach generated a stable, more-resistant variant of the isolate (DPC5337), which was 32 times less sensitive to lacticin 3147 than DPC5336. The performance of DPC5336 was compared to that of DPC5337 as adjunct cultures in two separate trials using either
Lactococcus lactis
DPC3147 (a natural producer) or
L. lactis
DPC4275 (a lacticin 3147-producing transconjugant) as the starter. These lacticin 3147-producing starters were previously shown to control adventitious nonstarter lactic acid bacteria in cheddar cheese. Lacticin 3147 was produced and remained stable during ripening, with levels of either 1,280 or 640 AU/g detected after 6 months of ripening. The more-resistant adjunct culture survived and grew in the presence of the bacteriocin in each trial, reaching levels of 10
7
CFU/g during ripening, in contrast to the sensitive strain, which was present at levels 100- to 1,000-fold lower. Furthermore, randomly amplified polymorphic DNA-PCR was employed to demonstrate that the resistant adjunct strain comprised the dominant microflora in the test cheeses during ripening.
Pathways for Extracellular Fenton Chemistry in the Brown Rot Basidiomycete
Gloeophyllum trabeum
Authors: Jensen Kenneth A. , Houtman Carl J. , Ryan Zachary C. , Hammel Kenneth E. 
Published: July 2002

ABSTRACT

The brown rot fungus
Gloeophyllum trabeum
uses an extracellular hydroquinone-quinone redox cycle to reduce Fe
3+
and produce H
2
O
2
. These reactions generate extracellular Fenton reagent, which enables
G. trabeum
to degrade a wide variety of organic compounds. We found that
G. trabeum
secreted two quinones, 2,5-dimethoxy-1,4-benzoquinone (2,5-DMBQ) and 4,5-dimethoxy-1,2-benzoquinone (4,5-DMBQ), that underwent iron-dependent redox cycling. Experiments that monitored the iron- and quinone-dependent cleavage of polyethylene glycol by
G. trabeum
showed that 2,5-DMBQ was more effective than 4,5-DMBQ in supporting extracellular Fenton chemistry. Two factors contributed to this result. First,
G. trabeum
reduced 2,5-DMBQ to 2,5-dimethoxyhydroquinone (2,5-DMHQ) much more rapidly than it reduced 4,5-DMBQ to 4,5-dimethoxycatechol (4,5-DMC). Second, although both hydroquinones reduced ferric oxalate complexes, the predominant form of Fe
3+
in
G. trabeum
cultures, the 2,5-DMHQ-dependent reaction reduced O
2
more rapidly than the 4,5-DMC-dependent reaction. Nevertheless, both hydroquinones probably contribute to the extracellular Fenton chemistry of
G. trabeum
, because 2,5-DMHQ by itself is an efficient reductant of 4,5-DMBQ.
Bacteria Mediate Methylation of Iodine in Marine and Terrestrial Environments
Authors: Amachi Seigo , Kamagata Yoichi , Kanagawa Takahiro , Muramatsu Yasuyuki 
Published: July 2002

ABSTRACT

Methyl iodide (CH
3
I) plays an important role in the natural iodine cycle and participates in atmospheric ozone destruction. However, the main source of this compound in nature is still unclear. Here we report that a wide variety of bacteria including terrestrial and marine bacteria are capable of methylating the environmental level of iodide (0.1 μM). Of the strains tested,
Rhizobium
sp. strain MRCD 19 was chosen for further analysis, and it was found that the cell extract catalyzed the methylation of iodide with
S
-adenosyl-
l
-methionine as the methyl donor. These results strongly indicate that bacteria contribute to iodine transfer from the terrestrial and marine ecosystems into the atmosphere.
Effects of Rice Seed Surface Sterilization with Hypochlorite on Inoculated
Burkholderia vietnamiensis
Authors: Miché Lucie , Balandreau Jacques 
Published: July 2002

ABSTRACT

When a combination of hydrogen peroxide and hypochlorite was used to surface sterilize rice seeds, a 10
2
- to 10
4
-fold decrease in CFU was observed during the first 15 h after inoculation of the rice rhizosphere organism
Burkholderia vietnamiensis
TVV75. This artifact could not be eliminated simply by rinsing the seeds, even thoroughly, with sterile distilled water. When growth resumed, a significant increase in the frequency of rifampin- and nalidixic acid-resistant mutants in the population was observed compared to the control without seeds. This phenomenon was a specific effect of hypochlorite; it was not observed with hydrogen peroxide alone. It was also not observed when the effect of hypochlorite was counteracted by sodium thiosulfate. We hypothesized that the hypochlorite used for disinfection reacted with the rice seed surface, forming a chlorine cover which was not removed by rinsing and generated mutagenic chloramines. We studied a set of rifampin- and nalidixic acid-resistant mutants obtained after seed surface sterilization. The corresponding
rpoB
and
gyrA
genes were amplified and sequenced to characterize the induced mutations. The mutations in five of seven nalidixic acid-resistant mutants and all of the rifampin-resistant mutants studied were found to correspond to single amino acid substitutions. Hypochlorite surface sterilization can thus be a source of artifacts when the initial bacterial colonization of a plant is studied.
Laboratory Evolution of Toluene Dioxygenase To Accept 4-Picoline as a Substrate
Authors: Sakamoto Takeshi , Joern John M. , Arisawa Akira , Arnold Frances H. 
Published: July 2002

ABSTRACT

We are using directed evolution to extend the range of dioxygenase-catalyzed biotransformations to include substrates that are either poorly accepted or not accepted at all by the naturally occurring enzymes. Here we report on the oxidation of a heterocyclic substrate, 4-picoline, by toluene dioxygenase (TDO) and improvement of the enzyme's activity by laboratory evolution. The biotransformation of 4-picoline proceeds at only ∼4.5% of the rate of the natural reaction on toluene. Random mutagenesis, saturation mutagenesis, and screening directly for product formation using a modified Gibbs assay generated mutant TDO 3-B38, in which the wild-type stop codon was replaced with a codon encoding threonine.
Escherichia coli
-expressed TDO 3-B38 exhibited 5.6 times higher activity toward 4-picoline and ∼20% more activity towards toluene than wild-type TDO. The product of the biotransformation of 4-picoline is 3-hydroxy-4-picoline; no
cis
-diols of 4-picoline were observed.
Ruminococcin A, a New Lantibiotic Produced by a
Ruminococcus gnavu
s Strain Isolated from Human Feces
Authors: Dabard J. , Bridonneau C. , Phillipe C. , Anglade P. , Molle D. , Nardi M. , Ladiré M. , Girardin H. , Marcille F. , Gomez A. , Fons M. 
Published: July 2002

ABSTRACT

When cultivated in the presence of trypsin, the
Ruminococcus gnavus
E1 strain, isolated from a human fecal sample, was able to produce an antibacterial substance that accumulated in the supernatant. This substance, called ruminococcin A, was purified to homogeneity by reverse-phase chromatography. It was shown to be a 2,675-Da bacteriocin harboring a lanthionine structure. The utilization of Edman degradation and tandem mass spectrometry techniques, followed by DNA sequencing of part of the structural gene, allowed the identification of 21 amino acid residues. Similarity to other bacteriocins present in sequence libraries strongly suggested that ruminococcin A belonged to class IIA of the lantibiotics. The purified ruminococcin A was active against various pathogenic clostridia and bacteria phylogenetically related to
R. gnavus
. This is the first report on the characterization of a bacteriocin produced by a strictly anaerobic bacterium from human fecal microbiota.
Comparative Genomic Analysis of Archaeal Genotypic Variants in a Single Population and in Two Different Oceanic Provinces
Authors: Béjà Oded , Koonin Eugene V. , Aravind L. , Taylor Lance T. , Seitz Heidi , Stein Jefferey L. , Bensen Daniel C. , Feldman Robert A. , Swanson Ronald V. , DeLong Edward F. 
Published: July 2002

ABSTRACT
Planktonic crenarchaeotes are present in high abundance in Antarctic winter surface waters, and they also make up a large proportion of total cell numbers throughout deep ocean waters. To better characterize these uncultivated marine crenarchaeotes, we analyzed large genome fragments from individuals recovered from a single Antarctic picoplankton population and compared them to those from a representative obtained from deeper waters of the temperate North Pacific. Sequencing and analysis of the entire DNA insert from one Antarctic marine archaeon (fosmid 74A4) revealed differences in genome structure and content between Antarctic surface water and temperate deepwater archaea. Analysis of the predicted gene products encoded by the 74A4 sequence and those derived from a temperate, deepwater planktonic crenarchaeote (fosmid 4B7) revealed many typical archaeal proteins but also several proteins that so far have not been detected in archaea. The unique fraction of marine archaeal genes included, among others, those for a predicted RNA-binding protein of the bacterial cold shock family and a eukaryote-type Zn finger protein. Comparison of closely related archaea originating from a single population revealed significant genomic divergence that was not evident from 16S rRNA sequence variation. The data suggest that considerable functional diversity may exist within single populations of coexisting microbial strains, even those with identical 16S rRNA sequences. Our results also demonstrate that genomic approaches can provide high-resolution information relevant to microbial population genetics, ecology, and evolution, even for microbes that have not yet been cultivated.