bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assimilation of Polysaccharides and Glucose by Major Bacterial Groups in the Delaware Estuary
Authors: Elifantz Hila , Malmstrom Rex R. , Cottrell Matthew T. , Kirchman David L. 
Published: December 2005

ABSTRACT

The contribution of major bacterial groups to the assimilation of extracellular polymeric substances (EPS) and glucose in the Delaware Estuary was assessed using microautoradiography and fluorescence in situ hybridization. Bacterial groups contributed to EPS and glucose assimilation in part according to their distribution in the estuary. Abundance of the phylogenetic groups explained 35% and 55% of the variation in EPS and glucose assimilation, respectively.
Actinobacteria
contributed 70% to glucose assimilation in freshwater, while
Alphaproteobacteria
assimilated 60% of this compound in saline water. In contrast, various bacterial groups dominated the assimilation of EPS.
Actinobacteria
and
Betaproteobacteria
contributed the most in the freshwater section, whereas
Cytophaga
-like bacteria and
Alpha
- and
Gammaproteobacteria
participated in EPS assimilation in the lower part of the estuary. In addition, we examined the fraction of bacteria in each group that assimilated glucose or EPS. Overall, the fraction of bacteria in all groups that assimilated glucose was higher than the fraction that assimilated EPS (15 to 30% versus 5 to 20%, respectively). We found no correlation between the relative abundance of a group in the estuary and the fraction of bacteria actively assimilating glucose or EPS; the more active groups were often less abundant. Our results imply that the bacterial community in the Delaware Estuary is not controlled solely by “bottom-up” factors such as dissolved organic matter.
Detection and Isolation of Ultrasmall Microorganisms from a 120,000-Year-Old Greenland Glacier Ice Core
Authors: Miteva Vanya I. , Brenchley Jean E. 
Published: December 2005

ABSTRACT

The abundant microbial population in a 3,043-m-deep Greenland glacier ice core was dominated by ultrasmall cells (<0.1 μm
3
) that may represent intrinsically small organisms or starved, minute forms of normal-sized microbes. In order to examine their diversity and obtain isolates, we enriched for ultrasmall psychrophiles by filtering melted ice through filters with different pore sizes, inoculating anaerobic low-nutrient liquid media, and performing successive rounds of filtrations and recultivations at 5°C. Melted ice filtrates, cultures, and isolates were analyzed by scanning electron microscopy, flow cytometry, cultivation, and molecular methods. The results confirmed that numerous cells passed through 0.4-μm, 0.2-μm, and even 0.1-μm filters. Interestingly, filtration increased cell culturability from the melted ice, yielding many isolates related to high-G+C gram-positive bacteria. Comparisons between parallel filtered and nonfiltered cultures showed that (i) the proportion of 0.2-μm-filterable cells was higher in the filtered cultures after short incubations but this difference diminished after several months, (ii) more isolates were obtained from filtered (1,290 isolates) than from nonfiltered (447 isolates) cultures, and (iii) the filtration and liquid medium cultivation increased isolate diversity (
Proteobacteria
;
Cytophaga-Flavobacteria-Bacteroides
; high-G+C gram-positive; and spore-forming, low-G+C gram-positive bacteria). Many isolates maintained their small cell sizes after recultivation and were phylogenetically novel or related to other ultramicrobacteria. Our filtration-cultivation procedure, combined with long incubations, enriched for novel ultrasmall-cell isolates, which is useful for studies of their metabolic properties and mechanisms for long-term survival under extreme conditions.
Microbial Diversity in Coastal Subsurface Sediments: a Cultivation Approach Using Various Electron Acceptors and Substrate Gradients
Authors: Köpke Beate , Wilms Reinhard , Engelen Bert , Cypionka Heribert , Sass Henrik 
Published: December 2005

ABSTRACT

Microbial communities in coastal subsurface sediments are scarcely investigated and have escaped attention so far. But since they are likely to play an important role in biogeochemical cycles, knowledge of their composition and ecological adaptations is important. Microbial communities in tidal sediments were investigated along the geochemical gradients from the surface down to a depth of 5.5 m. Most-probable-number (MPN) series were prepared with a variety of different carbon substrates, each at a low concentration, in combination with different electron acceptors such as iron and manganese oxides. These achieved remarkably high cultivation efficiencies (up to 23% of the total cell counts) along the upper 200 cm. In the deeper sediment layers, MPN counts dropped significantly. Parallel to the liquid enrichment cultures in the MPN series, gradient cultures with embedded sediment subcores were prepared as an additional enrichment approach. In total, 112 pure cultures were isolated; they could be grouped into 53 different operational taxonomic units (OTU). The isolates belonged to the
Proteobacteria
, “
Bacteroidetes
,” “
Fusobacteria
,”
Actinobacteria
, and “
Firmicutes
.” Each cultivation approach yielded a specific set of isolates that in general were restricted to this single isolation procedure. Analysis of the enrichment cultures by PCR and denaturing gradient gel electrophoresis revealed an even higher diversity in the primary enrichments that was only partially reflected by the culture collection. The majority of the isolates grew well under anoxic conditions, by fermentation, or by anaerobic respiration with nitrate, sulfate, ferrihydrite, or manganese oxides as electron acceptors.
Characterization and Functional Analysis of the
MAL
and
MPH
Loci for Maltose Utilization in Some Ale and Lager Yeast Strains
Authors: Vidgren Virve , Ruohonen Laura , Londesborough John 
Published: December 2005

ABSTRACT

Maltose and maltotriose are the major sugars in brewer's wort. Brewer's yeasts contain multiple genes for maltose transporters. It is not known which of these express functional transporters. We correlated maltose transport kinetics with the genotypes of some ale and lager yeasts. Maltose transport by two ale strains was strongly inhibited by other α-glucosides, suggesting the use of broad substrate specificity transporters, such as Agt1p. Maltose transport by three lager strains was weakly inhibited by other α-glucosides, suggesting the use of narrow substrate specificity transporters. Hybridization studies showed that all five strains contained complete
MAL1
,
MAL2
,
MAL3
, and
MAL4
loci, except for one ale strain, which lacked a
MAL2
locus. All five strains also contained both
AGT1
(coding a broad specificity α-glucoside transporter) and
MAL11
alleles.
MPH
genes (maltose permease homologues) were present in the lager but not in the ale strains. During growth on maltose, the lager strains expressed
AGT1
at low levels and
MALx1
genes at high levels, whereas the ale strains expressed
AGT1
at high levels and
MALx1
genes at low levels.
MPHx
expression was negligible in all strains. The
AGT1
sequences from the ale strains encoded full-length (616 amino acid) polypeptides, but those from both sequenced lager strains encoded truncated (394 amino acid) polypeptides that are unlikely to be functional transporters. Thus, despite the apparently similar genotypes of these ale and lager strains revealed by hybridization, maltose is predominantly carried by
AGT1
-encoded transporters in the ale strains and by
MALx1
-encoded transporters in the lager strains.
Microbiological Study of Lactic Acid Fermentation of Caper Berries by Molecular and Culture-Dependent Methods
Authors: Pérez Pulido Rubén , Ben Omar Nabil , Abriouel Hikmate , Lucas López Rosario , Martínez Cañamero Magdalena , Gálvez Antonio 
Published: December 2005

ABSTRACT

Fermentation of capers (the fruits of
Capparis
sp.) was studied by molecular and culture-independent methods. A lactic acid fermentation occurred following immersion of caper berries in water, resulting in fast acidification and development of the organoleptic properties typical of this fermented food. A collection of 133 isolates obtained at different times of fermentation was reduced to 75 after randomly amplified polymorphic DNA (RAPD)-PCR analysis. Isolates were identified by PCR or 16S rRNA gene sequencing as
Lactobacillus plantarum
(37 isolates),
Lactobacillus paraplantarum
(1 isolate),
Lactobacillus pentosus
(5 isolates),
Lactobacillus brevis
(9 isolates),
Lactobacillus fermentum
(6 isolates),
Pediococcus pentosaceus
(14 isolates),
Pediococcus acidilactici
(1 isolate), and
Enterococcus faecium
(2 isolates). Cluster analysis of RAPD-PCR patterns revealed a high degree of diversity among lactobacilli (with four major groups and five subgroups), while pediococci clustered in two closely related groups. A culture-independent analysis of fermentation samples by temporal temperature gradient electrophoresis (TTGE) also indicated that
L. plantarum
is the predominant species in this fermentation, in agreement with culture-dependent results. The distribution of
L. brevis
and
L. fermentum
in samples was also determined by TTGE, but identification of
Pediococcus
at the species level was not possible. TTGE also allowed a more precise estimation of the distribution of
E. faecium
, and the detection of
Enterococcus casseliflavus
(which was not revealed by the culture-dependent analysis). Results from this study indicate that complementary data from molecular and culture-dependent analysis provide a more accurate determination of the microbial community dynamics during caper fermentation.
Characterization of a Thermoacidophilic
l
-Arabinose Isomerase from
Alicyclobacillus acidocaldarius
: Role of Lys-269 in pH Optimum
Authors: Lee Sang-Jae , Lee Dong-Woo , Choe Eun-Ah , Hong Young-Ho , Kim Seong-Bo , Kim Byoung-Chan , Pyun Yu-Ryang 
Published: December 2005

ABSTRACT

The
araA
gene encoding
l
-arabinose isomerase (AI) from the thermoacidophilic bacterium
Alicyclobacillus acidocaldarius
was cloned, sequenced, and expressed in
Escherichia coli
. Analysis of the sequence revealed that the open reading frame of the
araA
gene consists of 1,491 bp that encodes a protein of 497 amino acid residues with a calculated molecular mass of 56,043 Da. Comparison of the deduced amino acid sequence of
A. acidocaldarius
AI (AAAI) with other AIs demonstrated that AAAI has 97% and 66% identities (99% and 83% similarities) to
Geobacillus stearothermophilus
AI (GSAI) and
Bacillus halodurans
AI (BHAI), respectively. The recombinant AAAI was purified to homogeneity by heat treatment, ion-exchange chromatography, and gel filtration. The purified enzyme showed maximal activity at pH 6.0 to 6.5 and 65°C under the assay conditions used, and it required divalent cations such as Mn
2+
, Co
2+
, and Mg
2+
for its activity. The isoelectric point (pI) of the enzyme was about 5.0 (calculated pI of 5.5). The apparent

K
m

values of the recombinant AAAI for
l
-arabinose and
d
-galactose were 48.0 mM (
V
max
, 35.5 U/mg) and 129 mM (
V
max
, 7.5 U/mg), respectively, at pH 6 and 65°C. Interestingly, although the biochemical properties of AAAI are quite similar to those of GSAI and BHAI, the three AIs from
A. acidocaldarius
(pH 6),
G. stearothermophilus
(pH 7), and
B. halodurans
(pH 8) exhibited different pH activity profiles. Based on alignment of the amino acid sequences of these homologous AIs, we propose that the Lys-269 residue of AAAI may be responsible for the ability of the enzyme to act at low pH. To verify the role of Lys-269, we prepared the mutants AAAI-K269E and BHAI-E268K by site-directed mutagenesis and compared their kinetic parameters with those of wild-type AIs at various pHs. The pH optima of both AAAI-K269E and BHAI-E268K were rendered by 1.0 units (pH 6 to 7 and 8 to 7, respectively) compared to the wild-type enzymes. In addition, the catalytic efficiency (
k
cat
/

K
m

) of each mutant at different pHs was significantly affected by an increase or decrease in
V
max
. From these results, we propose that the position corresponding to the Lys-269 residue of AAAI could play an important role in the determination of the pH optima of homologous AIs.
Chitinase Genes in Lake Sediments of Ardley Island, Antarctica
Authors: Xiao Xiang , Yin Xuebin , Lin Jian , Sun Liguang , You Ziyong , Wang Peng , Wang Fengping 
Published: December 2005

ABSTRACT

A sediment core spanning approximately 1,600 years was collected from a lake on Ardley Island, Antarctica. The sediment core had been greatly influenced by penguin guano. Using molecular methods, the chitinolytic bacterial community along the sediment core was studied over its entire length. Primers targeting conserved sequences of the catalytic domains of family 18 subgroup A chitinases detected group A chitinases from a wide taxonomic range of bacteria. Using quantitative competitive PCR (QC-PCR), chitinase gene copies in each 1-cm section of the whole sediment column were quantified. QC-PCR determination of the chitinase gene copies indicated significant correlation with phosphorus and total organic carbon concentration, suggesting a historical connection between chitinase gene copies and the amount of penguin guano input into the lake sediment. Most of the chitinase genes cloned from the historic sediment core were novel. Analysis of the chitinase gene diversity in selected sediment layers and in the fresh penguin deposits indicated frequent shifts in the chitinolytic bacterial community over time. Sequence analysis of the 16S rRNA genes of chitinolytic bacteria isolated from the lake sediment revealed that the isolates belonged to
Janthinobacterium
species,
Stenotrophomonas
species of γ-
Proteobacteria
,
Cytophaga
species of the
Cytophaga
-
Flexibacter
-
Bacteroides
group, and
Streptomyces
and
Norcardiopsis
species of
Actinobacteria
. Chitinase gene fragments were cloned and sequenced from these cultivated chitinolytic bacteria. The phylogeny of the chitinase genes obtained from the isolates did not correspond well to that of the isolates, suggesting acquisition via horizontal gene transfer.
Class 1 Integrons and Tetracycline Resistance Genes in
Alcaligenes
,
Arthrobacter
, and
Pseudomonas
spp. Isolated from Pigsties and Manured Soil
Authors: Agersø Yvonne , Sandvang Dorthe 
Published: December 2005

ABSTRACT

The presence of tetracycline resistance (Tc
r
) genes and class I integrons (in-1), and their ability to cotransfer were investigated in Tc
r
gram-negative (185 strains) and gram-positive (72 strains) bacteria from Danish farmland and pigsties. The isolates belonged to the groups or species
Escherichia coli
,
Enterobacter
spp.,
Arthrobacter
spp.,
Alcaligenes
spp.,
Pseudomonas
spp., and
Corynebacterium glutamicum.
The 257 isolates were screened for in-1. Eighty-one of the gram-negative isolates were also screened for the Tc
r
genes
tet
(A),
tet
(B), and
tet
(C), and all (
n
= 72) gram-positive isolates were screened for
tet
(33). Fourteen (7%) of the soil isolates and eleven (25%) of the pigsty isolates contained in-1. All isolates that contained
tet
genes also contained in-1, except one gram-negative isolate from a pigsty that contained
tet
(B). All gram-positive isolates with in-1 also contained
tet
(33). No isolates contained more than one
tet
gene. The in-1-positive isolates were tested for resistance to selected antimicrobial agents and showed resistance to three to nine drugs. Filter-mating experiments showed cotransfer of Tc
r
and class I integrons from soil isolates to
Escherichia coli
and/or
Pseudomonas putida
. We conclude that soil bacteria in close contact to manure or pigsty environment may thus have an important role in horizontal spread of resistance. Use of tetracyclines in food animal production may increase not only Tc
r
but also multidrug resistance (caused by the presence
tet
genes and in-1) in bacteria.
Determination of the Viability of
Aeromonas hydrophila
in Different Types of Water by Flow Cytometry, and Comparison with Classical Methods
Authors: Pianetti Anna , Falcioni Tania , Bruscolini Francesca , Sabatini Luigia , Sisti Elivio , Papa Stefano 
Published: December 2005

ABSTRACT

The presence of
Aeromonas
spp. in water can represent a risk for human health. Therefore, it is important to know the physiological status of these bacteria and their survival in the environment. We studied the behavior of a strain of
Aeromonas hydrophila
in river water, spring water, brackish water, mineral water, and chlorinated drinking water, which had different physical and chemical characteristics. The bacterial content was evaluated by spectrophotometric and plate count techniques. Flow cytometric determination of viability was carried out using a dual-staining technique that enabled us to distinguish viable bacteria from damaged and membrane-compromised bacteria. The traditional methods showed that the bacterial content was variable and dependent on the type of water. The results obtained from the plate count analysis correlated with the absorbance data. In contrast, the flow cytometric analysis results did not correlate with the results obtained by traditional methods; in fact, this technique showed that there were viable cells even when the optical density was low or no longer detectable and there was no plate count value. According to our results, flow cytometry is a suitable method for assessing the viability of bacteria in water samples. Furthermore, it permits fast detection of bacteria that are in a viable but nonculturable state, which are not detectable by conventional methods.
Effects of Common Forage Phenolic Acids on
Escherichia coli
O157:H7 Viability in Bovine Feces
Authors: Wells J. E. , Berry E. D. , Varel V. H. 
Published: December 2005

ABSTRACT

Ruminant animals are carriers of
Escherichia coli
O157:H7, and the transmission of
E. coli
O157:H7 from cattle to the environment and to humans is a concern. It is unclear if diet can influence the survivability of
E. coli
O157:H7 in the gastrointestinal system or in feces in the environment. Feces from cattle fed bromegrass hay or corn silage diets were inoculated with
E. coli
O157:H7, and the survival of this pathogen was analyzed. When animals consumed bromegrass hay for <1 month, viable
E. coli
O157:H7 was not recovered after 28 days postinoculation, but when animals consumed the diet for >1 month,
E. coli
O157:H7 cells were recovered for >120 days. Viable
E. coli
O157:H7 cells in feces from animals fed corn silage were detected until day 45 and differed little with the time on the diet. To determine if forage phenolic acids affected the viability of
E. coli
O157:H7, feces from animals fed corn silage or cracked corn were amended with common forage phenolic acids. When 0.5%
trans
-cinnamic acid or 0.5%
para
-coumaric acid was added to feces from silage-fed animals, the
E. coli
O157:H7 death rate was increased significantly (17-fold and 23-fold, respectively) compared to that with no addition. In feces from animals fed cracked corn,
E. coli
O157:H7 death rates were increased significantly with the addition of 0.1% and 0.5%
trans
-cinnamic acid (7- and 13-fold), 0.1% and 0.5%
p
-coumaric acid (3- and 8-fold), and 0.5% ferulic acid (3-fold). These data suggest that phenolic acids common to forage plants can decrease viable counts of
E. coli
O157:H7 shed in feces.
Cometabolism of Trihalomethanes by
Nitrosomonas europaea
Authors: Wahman David G. , Katz Lynn E. , Speitel Gerald E. 
Published: December 2005

ABSTRACT

The ammonia-oxidizing bacterium
Nitrosomonas europaea
(ATCC 19718) was shown to degrade low concentrations (50 to 800 μg/liter) of the four trihalomethanes (trichloromethane [TCM], or chloroform; bromodichloromethane [BDCM]; dibromochloromethane [DBCM]; and tribromomethane [TBM], or bromoform) commonly found in treated drinking water. Individual trihalomethane (THM) rate constants (

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) increased with increasing THM bromine substitution, with TBM > DBCM > BDCM > TCM (0.23, 0.20, 0.15, and 0.10 liters/mg/day, respectively). Degradation kinetics were best described by a reductant model that accounted for two limiting reactants, THMs and ammonia-nitrogen (NH
3
-N). A decrease in the temperature resulted in a decrease in both ammonia and THM degradation rates with ammonia rates affected to a greater extent than THM degradation rates. Similarly to the THM degradation rates, product toxicity, measured by transformation capacity (

T
c

), increased with increasing THM bromine substitution. Because both the rate constants and product toxicities increase with increasing THM bromine substitution, a water's THM speciation will be an important consideration for process implementation during drinking water treatment. Even though a given water sample may be kinetically favored based on THM speciation, the resulting THM product toxicity may not allow stable treatment process performance.
Horizontal Transfer of Bacterial Symbionts: Heritability and Fitness Effects in a Novel Aphid Host
Authors: Russell Jacob A. , Moran Nancy A. 
Published: December 2005

ABSTRACT

Members of several bacterial lineages are known only as symbionts of insects and move among hosts through maternal transmission. Such vertical transfer promotes strong fidelity within these associations, favoring the evolution of microbially mediated effects that improve host fitness. However, phylogenetic evidence indicates occasional horizontal transfer among different insect species, suggesting that some microbial symbionts retain a generalized ability to infect multiple hosts. Here we examine the abilities of three vertically transmitted bacteria from the
Gammaproteobacteria
to infect and spread within a novel host species, the pea aphid,
Acyrthosiphon pisum
. Using microinjection, we transferred symbionts from three species of natural aphid hosts into a common host background, comparing transmission efficiencies between novel symbionts and those naturally infecting
A. pisum
. We also examined the fitness effects of two novel symbionts to determine whether they should persist under natural selection acting at the host level. Our results reveal that these heritable bacteria vary in their capacities to utilize
A. pisum
as a host. One of three novel symbionts failed to undergo efficient maternal transmission in
A. pisum
, and one of the two efficiently transmitted bacteria depressed aphid growth rates. Although these findings reveal that negative fitness effects and low transmission efficiency can prevent the establishment of a new infection following horizontal transmission, they also indicate that some symbionts can overcome these obstacles, accounting for their widespread distributions across aphids and related insects.