bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel Bacterial Lineages at the (Sub)Division Level as Detected by Signature Nucleotide-Targeted Recovery of 16S rRNA Genes from Bulk Soil and Rice Roots of Flooded Rice Microcosms
Authors: Derakshani Manigee , Lukow Thomas , Liesack Werner 
Published: July 2002

ABSTRACT

Using a newly developed 16S rRNA gene (rDNA)-targeted PCR assay with proposed group specificity for planctomycetes, we examined anoxic bulk soil of flooded rice microcosms for the presence of novel planctomycete-like diversity. For comparison, oxic rice roots were included as an additional sample in this investigation. The bacterial diversity detectable by this PCR assay was assessed by using a combined approach that included terminal restriction fragment length polymorphism (T-RFLP) analysis and comparative sequence analysis of cloned 16S rDNA. T-RFLP fingerprint patterns generated from rice roots contained 12 distinct terminal restriction fragments (T-RFs). In contrast, the T-RFLP fingerprint patterns obtained from the anoxic bulk soil contained 33 distinct T-RFs, a clearly higher level of complexity. A survey of 176 bulk soil 16S rDNA clone sequences permitted correlation of 20 T-RFs with phylogenetic information. The other 13 T-RFs remained unidentified. The predominant T-RFs obtained from rice roots could be assigned to members of the genus
Pirellula
within the
Planctomycetales
, while most of the T-RFs obtained from the bulk soil corresponded to novel lines of bacterial descent. Using a level of 16S rDNA sequence dissimilarity to cultured microorganisms of approximately 20% as a threshold value, we detected 11 distinct bacterial lineages for which pure-culture representatives are not known. Four of these lineages could be assigned to the order
Planctomycetales
, while one lineage was affiliated with the division
Verrucomicrobia
and one lineage was affiliated with the spirochetes. The other five lineages either could not be assigned to any of the main lines of bacterial descent or clearly expanded the known diversity of division level lineages WS3 and OP3. Our results indicate the presence of bacterial diversity at a subdivision and/or division level that has not been detected previously by the so-called universal 16S rDNA PCR assays.
α- and β-
Proteobacteria
Control the Consumption and Release of Amino Acids on Lake Snow Aggregates
Authors: Schweitzer Bernhard , Huber Ingrid , Amann Rudolf , Ludwig Wolfgang , Simon Meinhard 
Published: July 2002

ABSTRACT

We analyzed the composition of aggregate (lake snow)-associated bacterial communities in Lake Constance from 1994 until 1996 between a depth of 25 m and the sediment surface at 110 m by fluorescent in situ hybridization with rRNA-targeted oligonucleotide probes of various specificity. In addition, we experimentally examined the turnover of dissolved amino acids and carbohydrates together with the microbial colonization of aggregates formed in rolling tanks in the lab. Generally, between 40 and more than 80% of the microbes enumerated by DAPI staining (4′,6′-diamidino-2-phenylindole) were detected as
Bacteria
by the probe EUB338. At a depth of 25 m, 10.5% ± 7.9% and 14.2% ± 10.2% of the DAPI cell counts were detected by probes specific for α- and β-
Proteobacteria
. These proportions increased to 12.0% ± 3.3% and 54.0% ± 5.9% at a depth of 50 m but decreased again at the sediment surface at 110 m to 2.7% ± 1.4% and 41.1% ± 8.4%, indicating a clear dominance of β-
Proteobacteria
at depths of 50 and 110 m, where aggregates have an age of 3 to 5 and 8 to 11 days, respectively. From 50 m to the sediment surface, cells detected by a
Cytophaga/Flavobacteria
-specific probe (CF319a) comprised increasing proportions up to 18% of the DAPI cell counts. γ-
Proteobacteria
always comprised minor proportions of the aggregate-associated bacterial community. Using only two probes highly specific for clusters of bacteria closely related to
Sphingomonas
species and
Brevundimonas diminuta
, we identified between 16 and 60% of the α-
Proteobacteria
. In addition, with three probes highly specific for close relatives of the β-
Proteobacteria Duganella zoogloeoides
(formerly
Zoogloea ramigera
),
Acidovorax facilis
, and
Hydrogenophaga palleroni
, bacteria common in activated sludge, 42 to 70% of the β-
Proteobacteria
were identified. In the early phase (<20 h) of 11 of the 15 experimental incubations of aggregates, dissolved amino acids were consumed by the aggregate-associated bacteria from the surrounding water. This stage was followed by a period of 1 to 3 days during which dissolved amino acids were released into the surrounding water, paralleled by an increasing dominance of β-
Proteobacteria
. Hence, our results show that lake snow aggregates are inhabited by a community dominated by a limited number of α- and β-
Proteobacteria
, which undergo a distinct succession. They successively decompose the amino acids bound in the aggregates and release substantial amounts into the surrounding water during aging and sinking.
Bacterial Diversity and Community Structure in an Aerated Lagoon Revealed by Ribosomal Intergenic Spacer Analyses and 16S Ribosomal DNA Sequencing
Authors: Yu Zhongtang , Mohn William W. 
Published: July 2002

ABSTRACT

We investigated the bacterial community structure in an aerated plug-flow lagoon treating pulp and paper mill effluent. For this investigation, we developed a composite method based on analyses of PCR amplicons containing the ribosomal intergenic spacer (RIS) and its flanking partial 16S rRNA gene. Community percent similarity was determined on the basis of RIS length polymorphism. A community succession was evident in the lagoon, indicated by a progressive community transition through seven sample locations. The most abrupt changes in community structure were associated with a temperature change from 39 to 35°C and with increases in dissolved oxygen. The temporal differences in community structure, based on summer and winter samplings, were greater than the spatial differences during either season. Clone libraries of rDNA-RIS amplicons were constructed from each of three summer samples. Among 90 clones analyzed (30 clones from each sample), 56 phylotypes were distinguished by restriction fragment length polymorphism. Indices of phylotype richness, evenness, and diversity all increased in clone libraries from the beginning to the end of the lagoon. A representative clone of each phylotype was phylogenetically analyzed on the basis of its partial 16S rRNA gene sequence (ca. 450 bp). Phylogenetic analysis confirmed the increase in diversity and further indicated increasing richness of bacterial divisions. Pioneers in the community spatial succession appeared to include thermotolerant, microaerophilic methanol-oxidizing bacteria related to the genus
Methylobacillus
, as well as thermotolerant, microaerophilic nitrogen-fixing bacteria related to the genus
Azospirillum
.
Dual-Bioaugmentation Strategy To Enhance Remediation of Cocontaminated Soil
Authors: Roane T. M. , Josephson K. L. , Pepper I. L. 
Published: July 2002

ABSTRACT

Although metals are thought to inhibit the ability of microorganisms to degrade organic pollutants, several microbial mechanisms of resistance to metal are known to exist. This study examined the potential of cadmium-resistant microorganisms to reduce soluble cadmium levels to enhance degradation of 2,4-dichlorophenoxyacetic acid (2,4-D) under conditions of cocontamination. Four cadmium-resistant soil microorganisms were examined in this study. Resistant up to a cadmium concentration of 275 μg ml
−1
, these isolates represented the common soil genera
Arthrobacter
,
Bacillus,
and
Pseudomonas
. Isolates
Pseudomonas
sp. strain H1 and
Bacillus
sp. strain H9 had a plasmid-dependent intracellular mechanism of cadmium detoxification, reducing soluble cadmium levels by 36%. Isolates
Arthrobacter
strain D9 and
Pseudomonas
strain I1a both produced an extracellular polymer layer that bound and reduced soluble cadmium levels by 22 and 11%, respectively. Although none of the cadmium-resistant isolates could degrade 2,4-D, results of dual-bioaugmentation studies conducted with both pure culture and laboratory soil microcosms showed that each of four cadmium-resistant isolates supported the degradation of 500-μg ml
−1
2,4-D by the cadmium-sensitive 2,4-D degrader
Ralstonia eutropha
JMP134. Degradation occurred in the presence of up to 24 μg of cadmium ml
−1
in pure culture and up to 60 μg of cadmium g
−1
in amended soil microcosms. In a pilot field study conducted with 5-gallon soil bioreactors, the dual-bioaugmentation strategy was again evaluated. Here, the cadmium-resistant isolate
Pseudomonas
strain H1 enhanced degradation of 2,4-D in reactors inoculated with
R. eutropha
JMP134 in the presence of 60 μg of cadmium g
−1
. Overall, dual bioaugmentation appears to be a viable approach in the remediation of cocontaminated soils.
Examination of Recovery In Vitro and In Vivo of Nonculturable
Escherichia coli
O157:H7
Authors: Kolling Glynis L. , Matthews Karl R. 
Published: July 2002

ABSTRACT

Escherichia coli
O157:H7 (strains ATCC 43895 and FO46) became nonculturable in sterile, distilled, deionized water or after exposure to chlorine. Recovery of nonculturable
E. coli
O157:H7 was examined by in vitro and in vivo methods. The decline in culturability of starved
E. coli
O157:H7 was measured by plate count on rich medium. Recovery in vitro of nonculturable cells was conducted with media amended with catalase or sodium pyruvate; however, there was no apparent increase over culturable cell counts on amended versus nonamended media. Although nonculturable
E. coli
O157:H7 did not recover under in vitro conditions, a mouse model was used to determine if in vivo conditions would provide sufficient conditions for recovery of nonculturable
E. coli
O157:H7. In separate studies, mice were orally challenged with starvation-induced nonculturable cells (FO46) or chlorine-induced nonculturable cells (43895 and FO46). Passage through the mouse gastrointestinal tract had no effect on recovery of nonculturable (starvation or chlorine induced)
E. coli
O157:H7 (43895 or FO46), based on analysis of fecal samples. Mouse kidneys were assayed for the presence of Shiga toxin using the Vero cell assay. Differences in cytotoxicity towards Vero cells from kidney samples of mice receiving nonculturable cells and control mice were not significant, suggesting a loss of virulence.
UDP-
N
-Acetylglucosamine 4-Epimerase Activity Indicates the Presence of
N
-Acetylgalactosamine in Exopolysaccharides of
Streptococcus thermophilus
Strains
Authors: Degeest Bart , Vaningelgem Frederik , Laws Andrew P. , De Vuyst Luc 
Published: July 2002

ABSTRACT

The monomer composition of the exopolysaccharides (EPS) produced by
Streptococcus thermophilus
LY03 and
S. thermophilus
Sfi20 were evaluated by high-pressure liquid chromatography with amperometric detection and nuclear magnetic resonance spectroscopy. Both strains produced the same EPS composed of galactose, glucose, and
N
-acetylgalactosamine. Further, it was demonstrated that the activity of the precursor-producing enzyme UDP-
N
-acetylglucosamine 4-epimerase, converting UDP-
N
-acetylglucosamine into UDP-
N
-acetylgalactosamine, is responsible for the presence of
N
-acetylgalactosamine in the EPS repeating units of both strains. The activity of UDP-
N
-acetylglucosamine 4-epimerase was higher in both
S. thermophilus
strains than in a non-EPS-producing control strain. However, the level of this activity was not correlated with EPS yields, a result independent of the carbohydrate source applied in the fermentation process. On the other hand, both the amounts of EPS and the carbohydrate consumption rates were influenced by the type of carbohydrate source used during
S. thermophilus
Sfi20 fermentations. A correlation between activities of the enzymes α-phosphoglucomutase, UDP-glucose pyrophosphorylase, and UDP-galactose 4-epimerase and EPS yields was seen. These experiments confirm earlier observed results for
S. thermophilus
LY03, although
S. thermophilus
Sfi20 preferentially consumed glucose for EPS production instead of lactose in contrast to the former strain.
Bacteriophage Latent-Period Evolution as a Response to Resource Availability
Authors: Abedon Stephen T. , Herschler Troy D. , Stopar David 
Published: July 2002

ABSTRACTBacteriophages (phages) modify microbial communities by lysing hosts, transferring genetic material, and effecting lysogenic conversion. To understand how natural communities are affected it is important to develop predictive models. Here we consider how variation between models—in eclipse period, latent period, adsorption constant, burst size, the handling of differences in host quantity and host quality, and in modeling strategy—can affect predictions. First we compare two published models of phage growth, which differ primarily in terms of how they model the kinetics of phage adsorption; one is a computer simulation and the other is an explicit calculation. At higher host quantities (∼108cells/ml), both models closely predict experimentally determined phage population growth rates. At lower host quantities (107cells/ml), the computer simulation continues to closely predict phage growth rates, but the explicit model does not. Next we concentrate on predictions of latent-period optima. A latent-period optimum is the latent period that maximizes the population growth of a specific phage growing in the presence of a specific quantity and quality of host cells. Both models predict similar latent-period optima at higher host densities (e.g., 17 min at 108cells/ml). At lower host densities, however, the computer simulation predicts latent-period optima that are much shorter than those suggested by explicit calculations (e.g., 90 versus 1,250 min at 105cells/ml). Finally, we consider the impact of host quality on phage latent-period evolution. By taking care to differentiate latent-period phenotypic plasticity from latent-period evolution, we argue that the impact of host quality on phage latent-period evolution may be relatively small.
Phylogenetic Diversity Analysis of Subterranean Hot Springs in Iceland
Authors: Marteinsson Viggó Thór , Hauksdóttir Sigurbjörg , Hobel Cédric F. V. , Kristmannsdóttir Hrefna , Hreggvidsson Gudmundur Oli , Kristjánsson Jakob K. 
Published: July 2002

ABSTRACT

Geothermal energy has been harnessed and used for domestic heating in Iceland. In wells that are typically drilled to a depth of 1,500 to 2,000 m, the temperature of the source water is 50 to 130°C. The bottoms of the boreholes can therefore be regarded as subterranean hot springs and provide a unique opportunity to study the subterranean biosphere. Large volumes of geothermal fluid from five wells and a mixture of geothermal water from 50 geothermal wells (hot tap water) were sampled and concentrated through a 0.2-μm-pore-size filter. Cells were observed in wells RG-39 (91.4°C) and MG-18 (71.8°C) and in hot tap water (76°C), but no cells were detected in wells SN-4, SN-5 (95 to 117°C), and RV-5 (130°C).
Archaea
and
Bacteria
were detected by whole-cell fluorescent in situ hybridization. DNAs were extracted from the biomass, and small-subunit rRNA genes (16S rDNAs) were amplified by PCR using primers specific for the
Archaea
and
Bacteria
domains. The PCR products were cloned and sequenced. The sequence analysis showed 11 new operational taxonomic units (OTUs) out of 14, 3 of which were affiliated with known surface OTUs. Samples from RG-39 and hot tap water were inoculated into enrichment media and incubated at 65 and 85°C. Growth was observed only in media based on geothermal water. 16S rDNA analysis showed enrichments dominated with
Desulfurococcales
relatives. Two strains belonging to
Desulfurococcus mobilis
and to the
Thermus
/
Deinococcus
group were isolated from borehole RG-39. The results indicate that subsurface volcanic zones are an environment that provides a rich subsurface for novel thermophiles.
Electrotransformation of
Lactobacillus delbrueckii
subsp.
bulgaricus
and
L. delbrueckii
subsp.
lactis
with Various Plasmids
Authors: Serror Pascale , Sasaki Takashi , Ehrlich S. Dusko , Maguin Emmanuelle 
Published: July 2002

ABSTRACT

We describe, for the first time, a detailed electroporation procedure for
Lactobacillus delbrueckii
. Three
L. delbrueckii
strains were successfully transformed. Under optimal conditions, the transformation efficiency was 10
4
transformants per μg of DNA. Using this procedure, we identified several plasmids able to replicate in
L. delbrueckii
and integrated an integrative vector based on phage integrative elements into the
L. delbrueckii
subsp.
bulgaricus
chromosome. These vectors provide a good basis for developing molecular tools for
L. delbrueckii
and open the field of genetic studies in
L. delbrueckii
.
Hindgut Fermentation in Three Species of Marine Herbivorous Fish
Authors: Mountfort Douglas O. , Campbell Jane , Clements Kendall D. 
Published: July 2002

ABSTRACT

Symbioses with gut microorganisms provides a means by which terrestrial herbivores are able to obtain energy. These microorganisms ferment cell wall materials of plants to short-chain fatty acids (SCFA), which are then absorbed and used by the host animal. Many marine herbivorous fishes contain SCFA (predominantly acetate) in their hindgut, indicative of gut microbial activity, but rates of SCFA production have not been measured. Such information is an important prerequisite to understanding the contribution that gut microorganisms make in satisfying the energy needs of the fish. We have estimated the rates of acetate production in the gut of three species of temperate marine herbivorous fish from northeastern New Zealand:
Kyphosus sydneyanus
(family Kyphosidae),
Odax pullus
(family Odacidae), and
Aplodactylus arctidens
(family Aplodactylidae). Ex vivo preparations of freshly caught fish were maintained with their respiratory and circulatory systems intact, radiolabeled acetate was injected into ligated hindgut sections, and gut fluid was sampled at 20-min intervals for 2 h. Ranges for acetate turnover in the hindguts of the studied species were determined from the slope of plots as the log of the specific radioactivity of acetate versus time and pool size, expressed on a nanomole per milliliter per minute basis. Values were 450 to 570 (
K. sydneyanus
), 373 to 551 (
O. pullus
), and 130 to 312 (
A. arctidens
). These rates are comparable to those found in the guts of herbivorous reptiles and mammals. To determine the contribution of metabolic pathways to the fate of acetate, rates of sulfate reduction and methanogenesis were measured in the fore-, mid-, and hindgut sections of the three fish species. Both rates increased from the distal to proximal end of the hindgut, where sulfate reduction accounted for only a small proportion (<5%) of acetate methyl group transformed to CO
2
, and exceeded methanogenesis from acetate by >50-fold. When gut size was taken into account, acetate uptake from the hindgut of the fish species, determined on a millimole per day per kilogram of body weight basis, was 70 (
K. sydneyanus
), 18 (
O. pullus
), and 10 (
A. arctidens
).
Activity and Diversity of Sulfate-Reducing Bacteria in a Petroleum Hydrocarbon-Contaminated Aquifer
Authors: Kleikemper Jutta , Schroth Martin H. , Sigler William V. , Schmucki Martina , Bernasconi Stefano M. , Zeyer Josef 
Published: July 2002

ABSTRACT

Microbial sulfate reduction is an important metabolic activity in petroleum hydrocarbon (PHC)-contaminated aquifers. We quantified carbon source-enhanced microbial SO
4
2−
reduction in a PHC-contaminated aquifer by using single-well push-pull tests and related the consumption of sulfate and added carbon sources to the presence of certain genera of sulfate-reducing bacteria (SRB). We also used molecular methods to assess suspended SRB diversity. In four consecutive tests, we injected anoxic test solutions (1,000 liters) containing bromide as a conservative tracer, sulfate, and either propionate, butyrate, lactate, or acetate as reactants into an existing monitoring well. After an initial incubation period, 1,000 liters of test solution-groundwater mixture was extracted from the same well. Average total test duration was 71 h. We measured concentrations of bromide, sulfate, and carbon sources in native groundwater as well as in injection and extraction phase samples and characterized the SRB population by using fluorescence in situ hybridization (FISH) and denaturing gradient gel electrophoresis (DGGE). Enhanced sulfate reduction concomitant with carbon source degradation was observed in all tests. Computed first-order rate coefficients ranged from 0.19 to 0.32 day
−1
for sulfate reduction and from 0.13 to 0.60 day
−1
for carbon source degradation. Sulfur isotope fractionation in unconsumed sulfate indicated that sulfate reduction was microbially mediated. Enhancement of sulfate reduction due to carbon source additions in all tests and variability of rate coefficients suggested the presence of specific SRB genera and a high diversity of SRB. We confirmed this by using FISH and DGGE. A large fraction of suspended bacteria hybridized with SRB-targeting probes SRB385 plus SRB385-Db (11 to 24% of total cells). FISH results showed that the activity of these bacteria was enhanced by addition of sulfate and carbon sources during push-pull tests. However, DGGE profiles indicated that the bacterial community structure of the dominant species did not change during the tests. Thus, the combination of push-pull tests with molecular methods provided valuable insights into microbial processes, activities, and diversity in the sulfate-reducing zone of a PHC-contaminated aquifer.
EglC, a New Endoglucanase from
Aspergillus niger
with Major Activity towards Xyloglucan
Authors: Hasper Alinda A. , Dekkers Ester , van Mil Marc , van de Vondervoort Peter J. I. , de Graaff Leo H. 
Published: July 2002

ABSTRACT

A novel gene,
eglC
, encoding an endoglucanase, was cloned from
Aspergillus niger
. Transcription of
eglC
is regulated by XlnR, a transcriptional activator that controls the degradation of polysaccharides in plant cell walls. EglC is an 858-amino-acid protein and contains a conserved C-terminal cellulose-binding domain. EglC can be classified in glycoside hydrolase family 74. No homology to any of the endoglucanases from
Trichoderma reesei
was found. In the plant cell wall xyloglucan is closely linked to cellulose fibrils. We hypothesize that the EglC cellulose-binding domain anchors the enzyme to the cellulose chains while it is cleaving the xyloglucan backbone. By this action it may contribute to the degradation of the plant cell wall structure together with other enzymes, including hemicellulases and cellulases. EglC is most active towards xyloglucan and therefore is functionally different from the other two endoglucanases from
A. niger
, EglA and EglB, which exhibit the greatest activity towards β-glucan. Although the mode of action of EglC is not known, this enzyme represents a new enzyme function involved in plant cell wall polysaccharide degradation by
A. niger
.