bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative Analysis of Small-Subunit rRNA Genes in Mixed Microbial Populations via 5′-Nuclease Assays
Authors: Suzuki Marcelino T. , Taylor Lance T. , DeLong Edward F. 
Published: July 2002

ABSTRACT

Few techniques are currently available for quantifying specific prokaryotic taxa in environmental samples. Quantification of specific genotypes has relied mainly on oligonucleotide hybridization to extracted rRNA or intact rRNA in whole cells. However, low abundance and cellular rRNA content limit the application of these techniques in aquatic environments. In this study, we applied a newly developed quantitative PCR assay (5′-nuclease assay, also known as TaqMan) to quantify specific small-subunit (SSU) rRNA genes (rDNAs) from uncultivated planktonic prokaryotes in Monterey Bay. Primer and probe combinations for quantification of SSU rDNAs at the domain and group levels were developed and tested for specificity and quantitative reliability. We examined the spatial and temporal variations of SSU rDNAs from
Synechococcus
plus
Prochlorococcus
and marine
Archaea
and compared the results of the quantitative PCR assays to those obtained by alternative methods. The 5′-nuclease assays reliably quantified rDNAs over at least 4 orders of magnitude and accurately measured the proportions of genes in artificial mixtures. The spatial and temporal distributions of planktonic microbial groups measured by the 5′-nuclease assays were similar to the distributions estimated by quantitative oligonucleotide probe hybridization, whole-cell hybridization assays, and flow cytometry.
Heavy Metal Coprecipitation with Hydrozincite [Zn
5
(CO
3
)
2
(OH)
6
] from Mine Waters Caused by Photosynthetic Microorganisms
Authors: Podda Francesca , Zuddas Paola , Minacci Andrea , Pepi Milva , Baldi Franco 
Published: July 2002

ABSTRACT

An iron-poor stream of nearly neutral pH polluted by mine tailings has been investigated for a natural phenomenon responsible for the polishing of heavy metals in mine wastewaters. A white mineralized mat, which was determined to be hydrozincite [Zn
5
(CO
3
)
2
(OH)
6
] by X-ray diffraction analysis, was observed in the stream sediments mainly in spring. The precipitate shows a total organic matter residue of 10% dry weight and contains high concentrations of Pb, Cd, Ni, Cu, and other metals. Scanning electron microscopy analysis suggests that hydrozincite is mainly of biological origin. Dormant photosynthetic microorganisms have been retrieved from 1-year-old dry hydrozincite. The autofluorescent microorganisms were imaged by a scanning confocal laser microscope. A photosynthetic filamentous bacterium, classified as
Scytonema
sp. strain ING-1, was found associated with microalga
Chlorella
sp. strain SA1. This microbial community is responsible for the natural polishing of heavy metals in the water stream by coprecipitation with hydrozincite.
Community Composition of Marine Bacterioplankton Determined by 16S rRNA Gene Clone Libraries and Fluorescence In Situ Hybridization
Authors: Cottrell Matthew T. , Kirchman David L. 
Published: July 2002

ABSTRACT

We determined the compositions of bacterioplankton communities in surface waters of coastal California using clone libraries of 16S rRNA genes and fluorescence in situ hybridization (FISH) in order to compare the community structures inferred from these two culture-independent approaches. The compositions of two clone libraries were quite similar to those of clone libraries of marine bacterioplankton examined by previous studies. Clones from γ-proteobacteria comprised ca. 28% of the libraries, while approximately 55% of the clones came from α-proteobacteria, which dominated the clone libraries. The
Cytophaga-Flavobacter
group and three others each comprised 10% or fewer of the clone libraries. The community composition determined by FISH differed substantially from the composition implied by the clone libraries. The
Cytophaga-Flavobacter
group dominated 8 of the 11 communities assayed by FISH, including the two communities assayed using clone libraries. On average only 10% of DAPI (4′,6′-diamidino-2-phenylindole)-stained bacteria were detected by FISH with a probe for α-proteobacteria, but 30% of DAPI-stained bacteria appeared to be in the
Cytophaga-Flavobacter
group as determined by FISH. α-Proteobacteria were greatly overrepresented in clone libraries compared to their relative abundance determined by FISH, while the
Cytophaga-Flavobacter
group was underrepresented in clone libraries. Our data show that the
Cytophaga-Flavobacter
group can be a numerically dominant component of coastal marine bacterioplankton communities.
Biological Role of Xanthomonadin Pigments in
Xanthomonas campestris
pv. Campestris
Authors: Poplawsky A. R. , Urban S. C. , Chun W. 
Published: July 2002

ABSTRACT

Previous studies have indicated that the yellow pigments (xanthomonadins) produced by phytopathogenic
Xanthomonas
bacteria are unimportant during pathogenesis but may be important for protection against photobiological damage. We used a
Xanthomonas campestris
pv. campestris parent strain, single-site transposon insertion mutant strains, and chromosomally restored mutant strains to define the biological role of xanthomonadins. Although xanthomonadin mutant strains were comparable to the parent strain for survival when exposed to UV light; after their exposure to the photosensitizer toluidine blue and visible light, survival was greatly reduced. Chromosomally restored mutant strains were completely restored for survival in these conditions. Likewise, epiphytic survival of a xanthomonadin mutant strain was greatly reduced in conditions of high light intensity, whereas a chromosomally restored mutant strain was comparable to the parent strain for epiphytic survival. These results are discussed with respect to previous results, and a model for epiphytic survival of
X. campestris
pv. campestris is presented.
Naphthalene Degradation and Incorporation of Naphthalene-Derived Carbon into Biomass by the Thermophile
Bacillus thermoleovorans
Authors: Annweiler E. , Richnow H. H. , Antranikian G. , Hebenbrock S. , Garms C. , Franke S. , Francke W. , Michaelis W. 
Published: July 2002

ABSTRACT

The thermophilic aerobic bacterium
Bacillus thermoleovorans
Hamburg 2 grows at 60°C on naphthalene as the sole source of carbon and energy. In batch cultures, an effective substrate degradation was observed. The carbon balance, including naphthalene, metabolites, biomass, and CO
2
, was determined by the application of [1-
13
C]naphthalene. The incorporation of naphthalene-derived carbon into the bulk biomass as well as into specified biomass fractions such as fatty acids and amino acids was confirmed by coupled gas chromatography-mass spectrometry (GC-MS) and isotope analyses. Metabolites were characterized by GC-MS; the established structures allow tracing the degradation pathway under thermophilic conditions. Apart from typical metabolites of naphthalene degradation known from mesophiles, intermediates such as 2,3-dihydroxynaphthalene, 2-carboxycinnamic acid, and phthalic and benzoic acid were identified for the pathway of this bacterium. These compounds indicate that naphthalene degradation by the thermophilic
B. thermoleovorans
differs from the known pathways found for mesophilic bacteria.
Culture-Dependent and Culture-Independent Characterization of Microbial Assemblages Associated with High-Temperature Petroleum Reservoirs
Authors: Orphan V. J. , Taylor L. T. , Hafenbradl D. , Delong E. F. 
Published: July 2002

ABSTRACT

Recent investigations of oil reservoirs in a variety of locales have indicated that these habitats may harbor active thermophilic prokaryotic assemblages. In this study, we used both molecular and culture-based methods to characterize prokaryotic consortia associated with high-temperature, sulfur-rich oil reservoirs in California. Enrichment cultures designed for anaerobic thermophiles, both autotrophic and heterotrophic, were successful at temperatures ranging from 60 to 90°C. Heterotrophic enrichments from all sites yielded sheathed rods (
Thermotogales
), pleomorphic rods resembling
Thermoanaerobacter
, and
Thermococcus
-like isolates. The predominant autotrophic microorganisms recovered from inorganic enrichments using H
2
, acetate, and CO
2
as energy and carbon sources were methanogens, including isolates closely related to
Methanobacterium
,
Methanococcus
, and
Methanoculleus
species. Two 16S rRNA gene (rDNA) libraries were generated from total community DNA collected from production wellheads, using either archaeal or universal oligonucleotide primer sets. Sequence analysis of the universal library indicated that a large percentage of clones were highly similar to known bacterial and archaeal isolates recovered from similar habitats. Represented genera in rDNA clone libraries included
Thermoanaerobacter
,
Thermococcus
,
Desulfothiovibrio
,
Aminobacterium
,
Acidaminococcus
,
Pseudomonas
,
Halomonas
,
Acinetobacter
,
Sphingomonas
,
Methylobacterium
, and
Desulfomicrobium
. The archaeal library was dominated by methanogen-like rDNAs, with a lower percentage of clones belonging to the
Thermococcales
. Our results strongly support the hypothesis that sulfur-utilizing and methane-producing thermophilic microorganisms have a widespread distribution in oil reservoirs and the potential to actively participate in the biogeochemical transformation of carbon, hydrogen, and sulfur in situ.
Quantification of
phnAc
and
nahAc
in Contaminated New Zealand Soils by Competitive PCR
Authors: Laurie Andrew D. , Lloyd-Jones Gareth 
Published: July 2002

ABSTRACT

Unculturable polycyclic aromatic hydrocarbon (PAH)-degrading bacteria are a significant reservoir of the microbial potential to catabolize low-molecular-weight PAHs. The population of these bacteria is larger than the population of
nah
-like bacteria that are the dominant organisms in culture-based studies. We used the recently described
phn
genes of
Burkholderia
sp. strain RP007, which feature only rarely in culture-based studies, as an alternative genotype for naphthalene and phenanthrene degradation and compared this genotype with the genotypically distinct but ubiquitous
nah
-like class in different soils. Competitive PCR quantification of
phnAc
and
nahAc
, which encode the iron sulfur protein large (α) subunits of PAH dioxygenases in
nah
-like and
phn
catabolic operons, revealed that the
phn
genotype can have a greater ecological significance than the
nah
-like genotype.
Production of Volatile Derivatives of Metal(loid)s by Microflora Involved in Anaerobic Digestion of Sewage Sludge
Authors: Michalke K. , Wickenheiser E. B. , Mehring M. , Hirner A. V. , Hensel R. 
Published: July 2002

ABSTRACT

Gases released from anaerobic wastewater treatment facilities contain considerable amounts of volatile methyl and hydride derivatives of metals and metalloids, such as arsine (AsH
3
), monomethylarsine, dimethylarsine, trimethylarsine, trimethylbismuth (TMBi), elemental mercury (Hg
0
), trimethylstibine, dimethyltellurium, and tetramethyltin. Most of these compounds could be shown to be produced by pure cultures of microorganisms which are representatives of the anaerobic sewage sludge microflora, i.e., methanogenic archaea (
Methanobacterium formicicum
,
Methanosarcina barkeri
,
Methanobacterium thermoautotrophicum
), sulfate-reducing bacteria (
Desulfovibrio vulgaris
,
D. gigas
), and a peptolytic bacterium (
Clostridium collagenovorans
). Additionally, dimethylselenium and dimethyldiselenium could be detected in the headspace of most of the pure cultures. This is the first report of the production of TMBi, stibine, monomethylstibine, and dimethylstibine by a pure culture of
M. formicicum
.
Intracellular Accumulation of Polyphosphate by the Yeast
Candida humicola
G-1 in Response to Acid pH
Authors: McGrath John W. , Quinn John P. 
Published: July 2002

ABSTRACT

Cells of a newly isolated environmental strain of
Candida humicola
accumulated 10-fold more polyphosphate (polyP), during active growth, when grown in complete glucose-mineral salts medium at pH 5.5 than when grown at pH 7.5. Neither phosphate starvation, nutrient limitation, nor anaerobiosis was required to induce polyP formation. An increase in intracellular polyP was accompanied by a 4.5-fold increase in phosphate uptake from the medium and sixfold-higher levels of cellular polyphosphate kinase activity. This novel accumulation of polyP by
C. humicola
G-1 in response to acid pH provides further evidence as to the importance of polyP in the physiological adaptation of microbial cells during growth and development and in their response to environmental stresses.
Factors Influencing Numbers of
Mycobacterium avium
,
Mycobacterium intracellulare
, and Other Mycobacteria in Drinking Water Distribution Systems
Authors: Falkinham Joseph O. , Norton Cheryl D. , LeChevallier Mark W. 
Published: July 2002

ABSTRACT

Eight water distribution systems were sampled over an 18-month period (528 water and 55 biofilm samples) to measure the frequency of recovery and number of mycobacteria, particularly
Mycobacterium avium
and
Mycobacterium intracellulare
, in raw source waters before and after treatment and within the distribution system. The systems were chosen to assess the influence of source water, treatment, and assimilable organic carbon levels on mycobacterial numbers. Overall, mycobacterial recovery from the systems was low (15% of samples). Numbers of mycobacteria ranged from 10 to 700,000 CFU liter
−1
. The number of
M. avium
in raw waters was correlated with turbidity. Water treatment substantially reduced the number of mycobacteria in raw waters by 2 to 4 log units. Mycobacterial numbers were substantially higher in the distribution system samples (average, 25,000-fold) than in those collected immediately downstream from the treatment facilities, indicating that mycobacteria grow in the distribution system. The increase in mycobacterial numbers was correlated with assimilable organic carbon and biodegradable organic carbon levels (
r
2
= 0.65,
P
= 0.03). Although
M. intracellulare
was seldom recovered from water samples, it was frequently recovered (six of eight systems) in high numbers from biofilms (average, 600 CFU/cm
2
). Evidently, the ecological niches of
M. avium
and
M. intracellulare
are distinct.
Degradation of Phenanthrene and Anthracene by Cell Suspensions ofMycobacteriumsp. Strain PYR-1
Authors: Moody Joanna D. , Freeman James P. , Doerge Daniel R. , Cerniglia Carl E. 
Published: July 2002

ABSTRACTCultures ofMycobacteriumsp. strain PYR-1 were dosed with anthracene or phenanthrene and after 14 days of incubation had degraded 92 and 90% of the added anthracene and phenanthrene, respectively. The metabolites were extracted and identified by UV-visible light absorption, high-pressure liquid chromatography retention times, mass spectrometry,1H and13C nuclear magnetic resonance spectrometry, and comparison to authentic compounds and literature data. Neutral-pH ethyl acetate extracts from anthracene-incubated cells showed four metabolites, identified ascis-1,2-dihydroxy-1,2-dihydroanthracene, 6,7-benzocoumarin, 1-methoxy-2-hydroxyanthracene, and 9,10-anthraquinone. A novel anthracene ring fission product was isolated from acidified culture media and was identified as 3-(2-carboxyvinyl)naphthalene-2-carboxylic acid. 6,7-Benzocoumarin was also found in that extract. WhenMycobacteriumsp. strain PYR-1 was grown in the presence of phenanthrene, three neutral metabolites were identified ascis- andtrans-9,10-dihydroxy-9,10-dihydrophenanthrene andcis-3,4-dihydroxy-3,4-dihydrophenanthrene. Phenanthrene ring fission products, isolated from acid extracts, were identified as 2,2′-diphenic acid, 1-hydroxynaphthoic acid, and phthalic acid. The data point to the existence, next to already known routes for both gram-negative and gram-positive bacteria, of alternative pathways that might be due to the presence of different dioxygenases or to a relaxed specificity of the same dioxygenase for initial attack on polycyclic aromatic hydrocarbons.
Natural Communities of Novel Archaea and Bacteria Growing in Cold Sulfurous Springs with a String-of-Pearls-Like Morphology
Authors: Rudolph Christian , Wanner Gerhard , Huber Robert 
Published: July 2002

ABSTRACT

We report the identification of novel archaea living in close association with bacteria in the cold (approximately 10°C) sulfurous marsh water of the Sippenauer Moor near Regensburg, Bavaria, Germany. These microorganisms form a characteristic, macroscopically visible structure, morphologically comparable to a string of pearls. Tiny, whitish globules (the pearls; diameter, about 0.5 to 3.0 mm) are connected to each other by thin, white-colored threads. Fluorescent in situ hybridization (FISH) studies have revealed that the outer part of the pearls is mainly composed of bacteria, with a filamentous bacterium predominating. Internally, archaeal cocci are the predominant microorganisms, with up to 10
7
cells estimated to be present in a single pearl. The archaea appear to be embedded in a polymer of unknown chemical composition. According to FISH and 16S rRNA gene sequence analysis, the archaea are affiliated with the euryarchaeal kingdom. The new euryarchaeal sequence represents a deep phylogenetic branch within the 16S rRNA tree and does not show extensive similarity to any cultivated archaea or to 16S rRNA gene sequences from environmental samples.
Purification and Characterization of Pyranose Oxidase from the White Rot Fungus
Trametes multicolor
Authors: Leitner Christian , Volc Jindrich , Haltrich Dietmar 
Published: July 2002

ABSTRACT

We purified an intracellular pyranose oxidase from mycelial extracts of the white rot fungus
Trametes multicolor
by using ammonium sulfate fractionation, hydrophobic interaction, ion-exchange chromatography, and gel filtration. The native enzyme has a molecular mass of 270 kDa as determined by equilibrium ultracentrifugation and is composed of four identical 68-kDa subunits as determined by matrix-assisted laser desorption ionization mass spectrometry. Each subunit contains one covalently bound flavin adenine dinucleotide as its prosthetic group. The enzyme oxidizes several aldopyranoses specifically at position C-2, and its preferred electron donor substrates are
d
-glucose,
d-
xylose, and
l-
sorbose. During this oxidation reaction electrons are transferred to oxygen, yielding hydrogen peroxide. In addition, the enzyme catalyzes the two-electron reduction of 1,4-benzoquinone, several substituted benzoquinones, and 2,6-dichloroindophenol, as well as the one-electron reduction of the ABTS [2,2′-azinobis(3-ethylbenzthiazolinesulfonic acid)] cation radical. As judged by the catalytic efficiencies (
k
cat
/

K
m

), some of these quinone electron acceptors are much better substrates for pyranose oxidase than oxygen. The optimum pH of the pyranose oxidase-catalyzed reaction depends strongly on the electron acceptor employed and varies from 4 to 8. It has been proposed that the main metabolic function of pyranose oxidase is as a constituent of the ligninolytic system of white rot fungi that provides peroxidases with H
2
O
2
. An additional function could be reduction of quinones, key intermediates that are formed during mineralization of lignin.
Detection of Methanotroph Diversity on Roots of Submerged Rice Plants by Molecular Retrieval of
pmoA
,
mmoX
,
mxaF
, and 16S rRNA and Ribosomal DNA, Including
pmoA
-
Based Terminal Restriction Fragment Length Polymorphism Profiling
Authors: Horz Hans-Peter , Yimga Merlin Tchawa , Liesack Werner 
Published: July 2002

ABSTRACT

The diversity of methanotrophic bacteria associated with roots of submerged rice plants was assessed using cultivation-independent techniques. The research focused mainly on the retrieval of
pmoA
, which encodes the α subunit of the particulate methane monooxygenase. A novel methanotroph-specific community-profiling method was established using the terminal restriction fragment length polymorphism (T-RFLP) technique. The T-RFLP profiles clearly revealed a more complex root-associated methanotrophic community than did banding patterns obtained by
pmoA
-based denaturing gradient gel electrophoresis. The comparison of
pmoA
-based T-RFLP profiles obtained from rice roots and bulk soil of flooded rice microcosms suggested that there was a substantially higher abundance of type I methanotrophs on rice roots than in the bulk soil. These were affiliated to the genera
Methylomonas
,
Methylobacter
,
Methylococcus
, and to a novel type I methanotroph sublineage. By contrast, type II methanotrophs of the
Methylocystis
-
Methylosinus
group could be detected with high relative signal intensity in both soil and root compartments. Phylogenetic treeing analyses and a set of substrate-diagnostic amino acid residues provided evidence that a novel
pmoA
lineage was detected. This branched distinctly from all currently known methanotrophs. To examine whether the retrieval of
pmoA
provided a complete view of root-associated methanotroph diversity, we also assessed the diversity detectable by recovery of genes coding for subunits of soluble methane monooxygenase (
mmoX
) and methanol dehydrogenase (
mxaF
). In addition, both 16S rRNA and 16S ribosomal DNA (rDNA) were retrieved using a PCR primer set specific to type I methanotrophs. The overall methanotroph diversity detected by recovery of
mmoX
,
mxaF
, and 16S rRNA and 16S rDNA corresponded well to the diversity detectable by retrieval of
pmoA
.
Isolation and Characterization of
Novosphingobium
sp. Strain MT1, a Dominant Polychlorophenol-Degrading Strain in a Groundwater Bioremediation System
Authors: Tiirola Marja A. , Männistö Minna K. , Puhakka Jaakko A. , Kulomaa Markku S. 
Published: July 2002

ABSTRACT

A high-rate fluidized-bed bioreactor has been treating polychlorophenol-contaminated groundwater in southern Finland at 5 to 8°C for over 6 years. We examined the microbial diversity of the bioreactor using three 16S ribosomal DNA (rDNA)-based methods: denaturing gradient gel electrophoresis, length heterogeneity-PCR analysis, and restriction fragment length polymorphism analysis. The molecular study revealed that the process was dependent on a stable bacterial community with low species diversity. The dominant organism,
Novosphingobium
sp. strain MT1, was isolated and characterized.
Novosphingobium
sp. strain MT1 degraded the main contaminants of the groundwater, 2,4,6-trichlorophenol, 2,3,4,6-tetrachlorophenol, and pentachlorophenol, at 8°C. The strain carried a homolog of the
pcpB
gene, coding for the pentachlorophenol-4-monooxygenase in
Sphingobium chlorophenolicum
. Spontaneous deletion of the
pcpB
gene homolog resulted in the loss of degradation ability. Phenotypic dimorphism (planktonic and sessile phenotypes), low growth rate (0.14 to 0.15 h
−1
), and low-copy-number 16S rDNA genes (single copy) were characteristic of strain MT1 and other MT1-like organisms isolated from the bioreactor.