bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nitrogen Cycling and Community Structure of Proteobacterial β-Subgroup Ammonia-Oxidizing Bacteria within Polluted Marine Fish Farm Sediments
Authors: McCaig Allison E. , Phillips Carol J. , Stephen John R. , Kowalchuk George A. , Harvey S. Martyn , Herbert Rodney A. , Embley T. Martin , Prosser James I. 
Published: December 2019

ABSTRACT

A multidisciplinary approach was used to study the effects of pollution from a marine fish farm on nitrification rates and on the community structure of ammonia-oxidizing bacteria in the underlying sediment. Organic content, ammonium concentrations, nitrification rates, and ammonia oxidizer most-probable-number counts were determined in samples of sediment collected from beneath a fish cage and on a transect at 20 and 40 m from the cage. The data suggest that nitrogen cycling was significantly disrupted directly beneath the fish cage, with inhibition of nitrification and denitrification. Although visual examination indicated some slight changes in sediment appearance at 20 m, all other measurements were similar to those obtained at 40 m, where the sediment was considered pristine. The community structures of proteobacterial β-subgroup ammonia-oxidizing bacteria at the sampling sites were compared by PCR amplification of 16S ribosomal DNA (rDNA), using primers which target this group. PCR products were analyzed by denaturing gradient gel electrophoresis (DGGE) and with oligonucleotide hybridization probes specific for different ammonia oxidizers. A DGGE doublet observed in PCR products from the highly polluted fish cage sediment sample was present at a lower intensity in the 20-m sample but was absent from the pristine 40-m sample station. Band migration, hybridization, and sequencing demonstrated that the doublet corresponded to a marine
Nitrosomonas
group which was originally observed in 16S rDNA clone libraries prepared from the same sediment samples but with different PCR primers. Our data suggest that this novel
Nitrosomonas
subgroup was selected for within polluted fish farm sediments and that the relative abundance of this group was influenced by the extent of pollution.
Phylogenetic Affinity of a Wide, Vacuolate, Nitrate-Accumulating
Beggiatoa
sp. from Monterey Canyon, California, with
Thioploca
spp
Authors: Ahmad Azeem , Barry James P. , Nelson Douglas C. 
Published: December 2019

ABSTRACT

Environmentally dominant members of the genus
Beggiatoa
and
Thioploca
spp. are united by unique morphological and physiological adaptations (S. C. McHatton, J. P. Barry, H. W. Jannasch, and D. C. Nelson, Appl. Environ. Microbiol. 62:954–958, 1996). These adaptations include the presence of very wide filaments (width, 12 to 160 μm), the presence of a central vacuole comprising roughly 80% of the cellular biovolume, and the capacity to internally concentrate nitrate at levels ranging from 150 to 500 mM. Until recently, the genera
Beggiatoa
and
Thioploca
were recognized and differentiated on the basis of morphology alone; they were distinguished by the fact that numerous
Thioploca
filaments are contained within a common polysaccharide sheath, while
Beggiatoa
filaments occur singly. Vacuolate
Beggiatoa
or
Thioploca
spp. can dominate a variety of marine sediments, seeps, and vents, and it has been proposed (H. Fossing, V. A. Gallardo, B. B. Jorgensen, M. Huttel, L. P. Nielsen, H. Schulz, D. E. Canfield, S. Forster, R. N. Glud, J. K. Gundersen, J. Kuver, N. B. Ramsing, A. Teske, B. Thamdrup, and O. Ulloa, Nature [London] 374:713–715, 1995) that members of the genus
Thioploca
are responsible for a significant portion of total marine denitrification. In order to investigate the phylogeny of an environmentally dominant
Beggiatoa
sp., we analyzed complete 16S rRNA gene sequence data obtained from a natural population found in Monterey Canyon cold seeps. Restriction fragment length polymorphism analysis of a clone library revealed a dominant clone, which gave rise to a putative Monterey
Beggiatoa
16S rRNA sequence. Fluorescent in situ hybridization with a sequence-specific probe confirmed that this sequence originated from wide
Beggiatoa
filaments (width, 65 to 85 μm). A phylogenetic tree based on evolutionary distances indicated that the Monterey
Beggiatoa
sp. falls in the gamma subdivision of the class
Proteobacteria
and is most closely related to the genus
Thioploca
. This vacuolate
Beggiatoa—Thioploca
cluster and a more distantly related freshwater
Beggiatoa
species cluster form a distinct phylogenetic group.
Conditions for Vigorous Growth on Sulfide and Reactor-Scale Cultivation Protocols for the Thermophilic Green Sulfur Bacterium
Chlorobium tepidum
Authors: Mukhopadhyay Biswarup , Johnson Eric F. , Ascano Manuel 
Published: December 2019

ABSTRACT

We describe a reactor-scale cultivation protocol for the fastest-growing and only known thermophilic member of the family
Chlorobiaceae
,
Chlorobium tepidum
. We discovered that
C. tepidum
would grow with sulfide as the sole electron source at rates and with final cell yields comparable to those found with thiosulfate only if the sulfide concentration was maintained below 0.1 mM and the culture redox potential was at −300 ± 20 mV. Such was also the requirement for growth in a photobioreactor when thiosulfate (optimum level, 12 mM) was used as the preferred electron source. For cultivation of
C. tepidum
on a 5- to 500-ml scale, we used the system of Balch and Wolfe (Appl. Environ. Microbiol. 32:781–791, 1976) using stopper-sealed serum tubes and bottles as an alternative to the methods commonly used for the cultivation of phototrophic anaerobes and obtained consistent results.
Symbiotic Deficiencies Associated with a
coxWXYZ
Mutant of
Bradyrhizobium japonicum
Authors: Surpin Marci Ann , Maier Robert J. 
Published: December 2019

ABSTRACT

The terminal oxidase complexes encoded by
coxMNOP
and
coxWXYZ
were studied by analysis of mutations in each of the two oxidases. Carbon monoxide difference spectra obtained from membranes of
coxMNOP
mutant bacteroids were like those obtained for the wild type, whereas bacteroid membranes of a
coxWXYZ
mutant were deficient in CO-reactive cytochrome
b
. Experiments involving cyanide inhibition of oxidase activity were consistent with the conclusion that the
coxX
mutant is deficient in a membrane-associated O
2
-binding component. The viable cell number (bacteria that could be recultured from crushed nodules) was 20 to 29% lower for the
coxX
mutant than for the wild-type or the CoxN
−
strain. In three separate greenhouse studies, nodules of a
coxX
mutant had significantly lower (28 to 34% less) acetylene reduction rates than the wild-type nodules did, and plants inoculated with a double mutant (
coxMNOP coxWZYZ
) had rates 30% lower than those of wild-type-inoculated plants.
Characterization of a Facultatively Psychrophilic Bacterium,
Vibrio rumoiensis
sp. nov., That Exhibits High Catalase Activity
Authors: Yumoto Isao , Iwata Hideaki , Sawabe Tomoo , Ueno Keisuke , Ichise Nobutoshi , Matsuyama Hidetoshi , Okuyama Hidetoshi , Kawasaki Kosei 
Published: December 2019

ABSTRACT

A novel facultatively psychrophilic bacterium, strain S-1, which exhibits extraordinarily high catalase activity was isolated from the drain pool of a fish product processing plant that uses H
2
O
2
as a bleaching and microbicidal agent. The catalase activity of the isolate was 1 or 2 orders of magnitude higher than those of
Corynebacterium glutamicum
,
Staphylococcus aureus
,
Pseudomonas fluorescens
, and five other species tested in this study. The strain seemed to possess only one kind of catalase, according to the results of polyacrylamide gel electrophoresis of the cell extract. The optimum temperature for catalase activity was about 30°C, which was about 20°C lower than that for bovine catalase activity. Electron microscopic observation revealed that the surface of the microorganism was covered by blebs. Although the isolate was nonflagellated, its taxonomic position on the basis of physiological and biochemical characteristics and analysis of 16S rRNA sequence and DNA-DNA relatedness data indicated that strain S-1 is a new species belonging to the genus
Vibrio
. Accordingly, we propose the name
Vibrio rumoiensis
. The type strain is S-1 (FERM P-14531).
Cloning and Analysis of the
l
-Lactate Utilization Genes from
Streptococcus iniae
Authors: Gibello A. , Collins M. D. , Domínguez L. , Fernández-Garayzábal J. F. , Richardson P. T. 
Published: December 2019

ABSTRACT

The presence of lactate oxidase was examined in eight
Streptococcus
species and some related species of bacteria. A clone (pGR002) was isolated from a genomic library of
Streptococcus iniae
generated in
Escherichia coli
, containing a DNA fragment spanning two genes designated
lctO
and
lctP
. We show that these genes are likely to be involved in the
l
-lactic acid aerobic metabolism of this organism. This DNA fragment has been sequenced and characterized. A comparison of the deduced amino acid sequence of LctP protein demonstrated that the protein had significant homology with the
l
-lactate permeases of other bacteria. The amino acid sequence of the LctO protein of
S. iniae
also showed a strong homology to
l
-lactate oxidase from
Aerococcus viridans
and some NAD-independent lactate dehydrogenases, all belonging to the family of flavin mononucleotide-dependent α-hydroxyacid-oxidizing enzymes. Biochemical assays of the gene products confirm the identity of the genes from the isolated DNA fragment and reveal a possible role for the lactate oxidase from
S. iniae
. This lactate oxidase is discussed in relation to the growth of the organism in response to carbon source availability.
Identification of
Bacillus thuringiensis
Delta-Endotoxin Cry1C Domain III Amino Acid Residues Involved in Insect Specificity
Authors: de Maagd Ruud A. , Bakker Petra , Staykov Nikola , Dukiandjiev Stefan , Stiekema Willem , Bosch Dirk 
Published: December 2019

ABSTRACT

Cry1C domain III amino acid residues involved in specificity for beet armyworm (
Spodoptera exigua
) were identified. For this purpose, intradomain III hybrids between Cry1E (nontoxic) and Cry1E-Cry1C hybrid G27 (toxic) were made. Crossover points of these hybrids defined six sequence blocks containing between 1 and 19 of the amino acid differences between Cry1E and G27. Blocks B, C, D, and E of G27 were shown to be required for optimal activity against
S. exigua
. Block E was also required for optimal activity against the tobacco hornworm (
Manduca sexta
), whereas block D had a negative effect on toxicity for this insect. The mutagenesis of individual amino acids in block B identified Trp-476 as the only amino acid in this block essential, although not sufficient by itself, for full
S. exigua
activity. In block D, we identified a seven-amino-acid insertion in G27 that was not in Cry1E. The deletion of either one of two groups of four consecutive amino acids in this insertion completely abolished activity against
S. exigua
but resulted in higher activity against
M. sexta
. Alanine substitutions of the first group had little effect on toxicity, whereas alanine substitutions of the second group had the same effect as its deletion. These results identify groups of amino acids as well as some individual residues in Cry1C domain III, which are strongly involved in
S. exigua
-specific activity as well as sometimes involved in
M. sexta
-specific activity.
Population Structure and Phylogenetic Characterization of Marine Benthic Archaea in Deep-Sea Sediments
Authors: Vetriani Costantino , Jannasch Holger W. , MacGregor Barbara J. , Stahl David A. , Reysenbach Anna-Louise 
Published: December 2019

ABSTRACT

During the past few years
Archaea
have been recognized as a widespread and significant component of marine picoplankton assemblages and, more recently, the presence of novel archaeal phylogenetic lineages has been reported in coastal marine benthic environments. We investigated the relative abundance, vertical distribution, phylogenetic composition, and spatial variability of
Archaea
in deep-sea sediments collected from several stations in the Atlantic Ocean. Quantitative oligonucleotide hybridization experiments indicated that the relative abundance of archaeal 16S rRNA in deep-sea sediments (1500 m deep) ranged from about 2.5 to 8% of the total prokaryotic rRNA. Clone libraries of PCR-amplified archaeal rRNA genes (rDNA) were constructed from 10 depth intervals obtained from sediment cores collected at depths of 1,500, 2,600, and 4,500 m. Phylogenetic analysis of rDNA sequences revealed the presence of a complex archaeal population structure, whose members could be grouped into discrete phylogenetic lineages within the two kingdoms,
Crenarchaeota
and
Euryarchaeota
. Comparative denaturing gradient gel electrophoresis profile analysis of archaeal 16S rDNA V3 fragments revealed a significant depth-related variability in the composition of the archaeal population.
Use of the [14C]Leucine Incorporation Technique To Measure Bacterial Production in River Sediments and the Epiphyton
Authors: Fischer Helmut , Pusch Martin 
Published: December 2019

ABSTRACTBacterial production is a key parameter for the understanding of carbon cycling in aquatic ecosystems, yet it remains difficult to measure in many aquatic habitats. We therefore tested the applicability of the [14C]leucine incorporation technique for the measurement of bulk bacterial production in various habitats of a lowland river ecosystem. To evaluate the method, we determined (i) extraction efficiencies of bacterial protein from the sediments, (ii) substrate saturation of leucine in sediments, the biofilms on aquatic plants (epiphyton), and the pelagic zone, (iii) bacterial activities at different leucine concentrations, (iv) specificity of leucine uptake by bacteria, and (v) the effect of the incubation technique (perfused-core incubation versus slurry incubation) on leucine incorporation into protein. Bacterial protein was best extracted from sediments and precipitated by hot trichloroacetic acid treatment following ultrasonication. For epiphyton, an alkaline-extraction procedure was most efficient. Leucine incorporation saturation occurred at 1 μM in epiphyton and 100 nM in the pelagic zone. Saturation curves in sediments were difficult to model but showed the first level of leucine saturation at 50 μM. Increased uptake at higher leucine concentrations could be partly attributed to eukaryotes. Addition of micromolar concentrations of leucine did not enhance bacterial electron transport activity or DNA replication activity. Similar rates of leucine incorporation into protein calculated for whole sediment cores were observed after slurry and perfused-core incubations, but the rates exhibited strong vertical gradients after the core incubation. We conclude that the leucine incorporation method can measure bacterial production in a wide range of aquatic habitats, including fluvial sediments, if substrate saturation and isotope dilution are determined.
Regulation of Peroxidase Transcript Levels in Liquid Cultures of the Ligninolytic Fungus
Pleurotus eryngii
Authors: Ruiz-Dueñas Francisco Javier , Guillén Francisco , Camarero Susana , Pérez-Boada Marta , Martínez María Jesús , Martínez Ángel T. 
Published: December 2019

ABSTRACT

A versatile peroxidase able to oxidize Mn
2+
as well as phenolic and nonphenolic aromatic compounds is produced in peptone-containing liquid cultures of
Pleurotus eryngii
encoded by the gene
mnpl
. The regulation of its transcript levels was investigated by Northern blotting of total RNA. High-peroxidase transcripts and activity were found in cultures grown in glucose-peptone medium, whereas only basal levels were detected in glucose-ammonium medium. The addition of more than 25 μM Mn
2+
to the former medium did not result in detectable peroxidase transcripts or activity. Potential regulators were also added to isolated mycelium. In this way, it was shown that high transcript levels (in peroxidase-expressing mycelium) were maintained on peptone, whereas expression was not induced in short-term incubation experiments. Similar results were obtained with Mn
2+
ions. Strong induction of
mnpl
expression was caused by exogenous H
2
O
2
or by continuous H
2
O
2
generation during redox cycling of menadione. By the use of the latter system in the presence of Fe
3+
, which catalyzes the reduction of H
2
O
2
to hydroxyl radical, it was shown for the first time that the presence of this strong oxidant causes a rapid increase of the transcripts of a ligninolytic peroxidase. In conclusion, peptone and Mn
2+
affect the levels of transcripts of this versatile peroxidase in culture, and reduced oxygen species induce short-term expression in isolated mycelium, probably via a stress response mechanism.
Production and Characterization of Monoclonal Antibodies against the Hemolysin BL Enterotoxin Complex Produced by
Bacillus cereus
Authors: Dietrich R. , Fella C. , Strich S. , Märtlbauer E. 
Published: December 2019

ABSTRACT

A total of five hybridoma cell lines that produced monoclonal antibodies against the components of the hemolysin BL (HBL) enterotoxin complex and sphingomyelinase produced by
Bacillus cereus
were established and characterized. Monoclonal antibody 2A3 was specific for the B component, antibodies 1A12 and 8B12 were specific for the L
2
component, and antibody 1C2 was specific for the L
1
protein of the HBL enterotoxin complex. No cross-reactivity with other proteins produced by different strains of
B. cereus
was observed for monoclonal antibodies 2A3, 1A12, and 8B12, whereas antibody 1C2 cross-reacted with an uncharacterized protein of approximately 93 kDa and with a 39-kDa protein, which possibly represents one component of the nonhemolytic enterotoxin complex. Antibody 2A12 finally showed a distinct reactivity with
B. cereus
sphingomyelinase. The monoclonal antibodies developed in this study were also successfully applied in indirect enzyme immunoassays for the characterization of the enterotoxic activity of
B. cereus
strains. About 50% of the strains tested were capable of producing the HBL enterotoxin complex, and it could be demonstrated that all strains producing HBL were also highly cytotoxic.
Identification and Characterization of ComE and ComF, Two Novel Pilin-Like Competence Factors Involved in Natural Transformation of
Acinetobacter
sp. Strain BD413
Authors: Busch Silke , Rosenplänter Christine , Averhoff Beate 
Published: December 2019

ABSTRACT

Although the high level of competence for natural transformation of
Acinetobacter
sp. strain BD413 has been the subject of numerous studies, only two competence genes,
comC
and
comP
, have been identified to date. By chromosomal walking analysis we found two overlapping open reading frames, designated
comE
and
comF
, starting 61 bp downstream of
comC
.
comE
and
comF
are expressed as stable proteins in
Escherichia coli
, thus proving that they are indeed coding regions, but expression was successful only with 5′-deleted genes. ComE and ComF are similar to pilins and pilin-like components. Both genes were mutated, and the phenotypes of the mutants were analyzed. Natural transformation in
comF
mutants is 1,000-fold reduced, whereas
comE
mutants exhibit 10-fold-reduced transformation frequencies. This is clear evidence that
comE
and
comF
are involved in natural transformation. However, ComE and ComF are specific for DNA translocation, since
comE
and
comF
defects affected neither piliation nor lipase secretion. These results suggest that the type IV pili, the general protein secretion pathway, and the DNA translocation machinery in
Acinetobacter
sp. strain BD413 are evolutionary related but functionally distinct systems.
Green Fluorescent Protein-Marked
Pseudomonas fluorescens
: Localization, Viability, and Activity in the Natural Barley Rhizosphere
Authors: Normander Bo , Hendriksen Niels B. , Nybroe Ole 
Published: December 2019

ABSTRACT

The
gfp
-tagged
Pseudomonas fluorescens
biocontrol strain DR54-BN14 was introduced into the barley rhizosphere. Confocal laser scanning microscopy revealed that the rhizoplane populations of DR54-BN14 on 3- to 14-day-old roots were able to form microcolonies closely associated with the indigenous bacteria and that a majority of DR54-BN14 cells appeared small and almost coccoid. Information on the viability of the inoculant was provided by a microcolony assay, while measurements of cell volume, the intensity of green fluorescent protein fluorescence, and the ratio of dividing cells to total cells were used as indicators of cellular activity. At a soil moisture close to the water-holding capacity of the soil, the activity parameters suggested that the majority of DR54-BN14 cells were starving in the rhizosphere. Nevertheless, approximately 80% of the population was either culturable or viable but nonculturable during the 3-week incubation period. No impact of root decay on viability was observed, and differences in viability or activity among DR54-BN14 cells located in different regions of the root were not apparent. In dry soil, however, the nonviable state of DR54-BN14 was predominant, suggesting that desiccation is an important abiotic regulator of cell viability.
Characteristics of Two Forms of α-Amylases and Structural Implication
Authors: Ohdan Kohji , Kuriki Takashi , Kaneko Hiroki , Shimada Jiro , Takada Toshikazu , Fujimoto Zui , Mizuno Hiroshi , Okada Shigetaka 
Published: December 2019

ABSTRACT

Complete (Ba-L) and truncated (Ba-S) forms of α-amylases from
Bacillus subtilis
X-23 were purified, and the amino- and carboxyl-terminal amino acid sequences of Ba-L and Ba-S were determined. The amino acid sequence deduced from the nucleotide sequence of the α-amylase gene indicated that Ba-S was produced from Ba-L by truncation of the 186 amino acid residues at the carboxyl-terminal region. The results of genomic Southern analysis and Western analysis suggested that the two enzymes originated from the same α-amylase gene and that truncation of Ba-L to Ba-S occurred during the cultivation of
B. subtilis
X-23 cells. Although the primary structure of Ba-S was approximately 28% shorter than that of Ba-L, the two enzyme forms had the same enzymatic characteristics (molar catalytic activity, amylolytic pattern, transglycosylation ability, effect of pH on stability and activity, optimum temperature, and raw starch-binding ability), except that the thermal stability of Ba-S was higher than that of Ba-L. An analysis of the secondary structure as well as the predicted three-dimensional structure of Ba-S showed that Ba-S retained all of the necessary domains (domains A, B, and C) which were most likely to be required for functionality as α-amylase.
Unexpected Population Distribution in a Microbial Mat Community: Sulfate-Reducing Bacteria Localized to the Highly Oxic Chemocline in Contrast to a Eukaryotic Preference for Anoxia
Authors: Minz Dror , Fishbain Susan , Green Stefan J. , Muyzer Gerard , Cohen Yehuda , Rittmann Bruce E. , Stahl David A. 
Published: December 2019

ABSTRACTThe distribution and abundance of sulfate-reducing bacteria (SRB) and eukaryotes within the upper 4 mm of a hypersaline cyanobacterial mat community were characterized at high resolution with group-specific hybridization probes to quantify 16S rRNA extracted from 100-μm depth intervals. This revealed a preferential localization of SRB within the region defined by the oxygen chemocline. Among the different groups of SRB quantified, including members of the provisional families “Desulfovibrionaceae” and “Desulfobacteriaceae,”Desulfonema-like populations dominated and accounted for up to 30% of total rRNA extracted from certain depth intervals of the chemocline. These data suggest that recognized genera of SRB are not necessarily restricted by high levels of oxygen in this mat community and the possibility of significant sulfur cycling within the chemocline. In marked contrast, eukaryotic populations in this community demonstrated a preference for regions of anoxia.