bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ultradian Growth in
Prochlorococcus
spp
Authors: Shalapyonok Alexi , Olson Robert J. , Shalapyonok Ludmila S. 
Published: December 2019

ABSTRACT

Species of the widespread marine prokaryote
Prochlorococcus
exhibited ultradian growth (faster than 1 division per day) both in situ and in culture, even though cell division is strictly phased to the light-dark cycle. Under optimal conditions a second DNA replication and cell division closely followed, but did not overlap with, the first division. The timing of cell cycle events was not affected by light intensity or duration, suggesting control by a light-triggered timer or circadian clock rather than by completion of a light-dependent assimilation phase. This mode of ultradian growth has not been observed previously and poses new questions about the regulation of cellular rhythms in prokaryotes. In addition, it implies that conclusions regarding the lack of nutrient limitation of
Prochlorococcus
in the open ocean, which were based on the appearance that cells were growing at their maximal rate, need to be reconsidered.
Methanol Improves Methane Uptake in Starved Methanotrophic Microorganisms
Authors: Jensen Sigmund , Priemé Anders , Bakken Lars 
Published: December 2019

ABSTRACT
Methanotrophs in enrichment cultures grew and sustained atmospheric methane oxidation when supplied with methanol. If they were not supplied with methanol or formate, their atmospheric methane oxidation came to a halt, but it was restored within hours in response to methanol or formate. Indigenous forest soil methanotrophs were also dependent on a supply of methanol upon reduced methane access but only when exposed to a methane-free atmosphere. Their immediate response to each methanol addition, however, was to shut down the oxidation of atmospheric methane and to reactivate atmospheric methane oxidation as the methanol was depleted.
Lipopolysaccharide Profiles from Nodules as Markers of
Bradyrhizobium
Strains Nodulating Wild Legumes
Authors: Santamaría Mónica , Gutiérrez-Navarro Ángel M. , Corzo Javier 
Published: December 2019

ABSTRACT

To develop the use of electrophoretic lipopolysaccharide profiles for
Bradyrhizobium
strain identification, we studied the feasibility of using electrophoresis of whole legume nodule homogenates to obtain distinctive lipopolysaccharide profiles. The electrophoretic patterns were the same whether we used nodule extracts, bacteroids, or cultured bacteria as samples, and there was no evidence of changes in the ladder-like pattern during the nodulation process. To assess the reliability of using lipopolysaccharide profiling performed with individual nodules for studying the diversity and microdistribution of the rhizobia nodulating wild shrub legumes, we used a population of
Adenocarpus foliolosus
seedlings. We obtained 75 different profiles from the 147 nodules studied. There was no dominant profile in the sample, and a plant with different nodules generally produced different profiles. Electrophoresis of legume root nodules proved to be a fast and discriminating technique for determining the diversity of a bradyrhizobial population, although it did not allow the genetic relationships among the nodulating strains to be studied.
Complete Reductive Dehalogenation of Brominated Biphenyls by Anaerobic Microorganisms in Sediment
Authors: Bedard Donna L. , Van Dort Heidi M. 
Published: December 2019

ABSTRACT

We sought to determine whether microorganisms from the polychlorinated biphenyl (PCB)-contaminated sediment in Woods Pond (Lenox, Mass.) could dehalogenate brominated biphenyls. The PCB dechlorination specificities for the microorganisms in this sediment have been well characterized. This allowed us to compare the dehalogenation specificities for brominated biphenyls and chlorinated biphenyls within a single sediment. Anaerobic sediment microcosms were incubated separately at 25°C with 16 different mono- to tetrabrominated biphenyls (350 μM) and disodium malate (10 mM). Samples were extracted and analyzed by gas chromatography with an electron capture detector and a mass spectrometer detector at various times for up to 54 weeks. All of the tested brominated biphenyls were dehalogenated. For most congeners, including 2,6-dibromobiphenyl (26-BB) and 24-25-BB, the dehalogenation began within 1 to 2 weeks. However, for 246-BB and 2-2-BB, debromination was first observed at 7 and 14 weeks, respectively. Most intermediate products did not persist, but when 2-2-BB was produced as a dehalogenation product, it persisted for at least 15 weeks before it was dehalogenated to 2-BB and then to biphenyl. The dehalogenation specificities for brominated and chlorinated biphenyls were similar:
meta
and
para
substituents were generally removed first, and
ortho
substituents were more recalcitrant. However, the brominated biphenyls were better dehalogenation substrates than the chlorinated biphenyls. All of the tested bromobiphenyls, including those with
ortho
and unflanked
meta
and
para
substituents, were ultimately dehalogenated to biphenyl, whereas their chlorinated counterparts either were not dehalogenation substrates or were only partially dehalogenated. Our data suggest that PCB-dechlorinating microorganisms may be able to dehalogenate brominated biphenyls and may exhibit a relaxed specificity for these substrates.
Distribution of a Population ofRhizobium leguminosarumbv. trifolii among Different Size Classes of Soil Aggregates
Authors: Mendes Ieda C. , Bottomley Peter J. 
Published: December 2019

ABSTRACTA combination of the plant infection-soil dilution technique (most-probable-number [MPN] technique) and immunofluorescence direct count (IFDC) microscopy was used to examine the effects of three winter cover crop treatments on the distribution of a soil population ofRhizobium leguminosarumbv. trifolii across different size classes of soil aggregates (<0.25, 0.25 to 0.5, 0.5 to 1.0, 1.0 to 2.0, and 2.0 to 5.0 mm). The aggregates were prepared from a Willamette silt loam soil immediately after harvest of broccoli (September 1995) and before planting and after harvest of sweet corn (June and September 1996, respectively). The summer crops were grown in soil that had been either fallowed or planted with a cover crop of red clover (legume) or triticale (cereal) from September to April. TheRhizobiumsoil population was heterogeneously distributed across the different size classes of soil aggregates, and the distribution was influenced by cover crop treatment and sampling time. On both September samplings, the smallest size class of aggregates (<0.25 mm) recovered from the red clover plots carried between 30 and 70% of the total nodulatingR. leguminosarumpopulation, as estimated by the MPN procedure, while the same aggregate size class from the June sampling carried only ∼6% of the population. In June, IDFC microscopy revealed that the 1.0- to 2.0-mm size class of aggregates from the red clover treatment carried a significantly greater population density of the successful nodule-occupying serotype, AR18, than did the aggregate size classes of <0.5 mm, and 2 to 5 mm. In September, however, the population profile of AR18 had shifted such that the density was significantly greater in the 0.25- to 0.5-mm size class than in aggregates of <0.25 mm and >1.0 mm. The populations of two otherRhizobiumserotypes (AR6 and AS36) followed the same trends of distribution in the June and September samplings. These data indicate the existence of structural microsites that vary in their suitabilities to support growth and protection of bacteria and that are influenced by the presence and type of plant grown in the soil.
Population Dynamics of Phenol-Degrading Bacteria in Activated Sludge Determined by
gyrB
-Targeted Quantitative PCR
Authors: Watanabe Kazuya , Yamamoto Satoshi , Hino Sanae , Harayama Shigeaki 
Published: December 2019

ABSTRACT

A method for quantifying bacterial populations introduced into an activated-sludge microbial community is described. The method involves extraction of DNA from activated sludge, appropriate dilution of the extracted DNA with DNA extracted from nonintroduced activated sludge, PCR amplification of a
gyrB
gene fragment from the introduced strain with a set of strain-specific primers, and quantification of the electrophoresed PCR product by densitometry. The adequacy of the method was examined by analyzing the population dynamics of two phenol-degrading bacteria,
Pseudomonas putida
BH and
Comamonas
sp. strain E6, that had been introduced into phenol-digesting activated sludge. The density of each of the two populations determined by the PCR method immediately after the introduction was consistent with the density estimated from a plate count of the inoculum. This quantitative PCR method revealed different population dynamics for the two strains in the activated sludge under different phenol-loading conditions. The behavior of both of these strains in the activated sludge reflected the growth kinetics of the strains determined in laboratory axenic cultures.
Characterization of the Dominant and Rare Members of a Young Hawaiian Soil Bacterial Community with Small-Subunit Ribosomal DNA Amplified from DNA Fractionated on the Basis of Its Guanine and Cytosine Composition
Authors: Nüsslein Klaus , Tiedje James M. 
Published: December 2019

ABSTRACTThe small-subunit ribosomal DNA (rDNA) diversity was found to be very high in a Hawaiian soil community that might be expected to have lower diversity than the communities in continental soils because the Hawaiian soil is geographically isolated and only 200 years old, is subjected to a constant climate, and harbors low plant diversity. Since an underlying community structure could not be revealed by analyzing the total eubacterial rDNA, we first fractionated the DNA on the basis of guanine-plus-cytosine (G+C) content by using bis-benzimidazole and equilibrium centrifugation and then analyzed the bacterial rDNA amplified from a fraction with a high biomass (63% G+C fraction) and a fraction with a low biomass (35% G+C fraction). The rDNA clone libraries were screened by amplified rDNA restriction analysis to determine phylotype distribution. The dominant biomass reflected by the 63% G+C fraction contained several dominant phylotypes, while the community members that were less successful (35% G+C fraction) did not show dominance but there was a very high diversity of phylotypes. Nucleotide sequence analysis revealed taxa belonging to the groups expected for the G+C contents used. The dominant phylotypes in the 63% G+C fraction were members of thePseudomonas,Rhizobium-Agrobacterium, andRhodospirillumassemblages, while all of the clones sequenced from the 35% G+C fraction were affiliated with severalClostridiumassemblages. The two-step rDNA analysis used here uncovered more diversity than can be detected by direct rDNA analysis of total community DNA. The G+C separation step is also a way to detect some of the less dominant organisms in a community.
Buffering Capacity and Membrane H
+
Conductance of Neutrophilic and Alkalophilic Gram-Positive Bacteria
Authors: Rius Núria , Lorén José G. 
Published: December 2019

ABSTRACT

Buffering capacity and membrane H
+
conductance were examined in three gram-positive bacteria,
Staphylococcus aureus
,
Bacillus subtilis
, and
Bacillus alcalophilus
. An acid pulse technique was used to measure both parameters. The buffering capacity and membrane H
+
conductance of
B. alcalophilus
are influenced by the pH of the medium and the culture conditions. Suspensions of
B. alcalophilus
cells from both H. A. medium and
l
-malate medium cultures grown at pH 10.5 exhibited higher values for these parameters than cells grown at pH 8.5.
B. alcalophilus
grown aerobically had a lower buffering capacity and a lower membrane conductance for protons than the neutrophilic bacteria
S. aureus
and
B. subtilis
. Fermenting cells exhibited significantly higher values for both variables than respiring cells.
COVASIAM: an Image Analysis Method That Allows Detection of Confluent Microbial Colonies and Colonies of Various Sizes for Automated Counting
Authors: Corkidi G. , Diaz-Uribe R. , Folch-Mallol J. L. , Nieto-Sotelo J. 
Published: December 2019

ABSTRACT

In this work we introduce the confluent and various sizes image analysis method (COVASIAM), an automated colony count technique that uses digital imaging technology for detection and separation of confluent microbial colonies and colonies of various sizes growing on petri dishes. The proposed method takes advantage of the optical properties of the surfaces of most microbial colonies. Colonies in the petri dish are epi-illuminated in order to direct the reflection of concentrated light coming from a halogen lamp towards an image-sensing device. In conjunction, a multilevel threshold algorithm is proposed for colony separation and counting. These procedures improved the quantification of colonies showing confluence or differences in size. We tested COVASIAM with a sample set of microorganisms that form colonies with contrasting physical properties:
Saccharomyces cerevisiae
,
Aspergillus nidulans
,
Escherichia coli
,
Azotobacter vinelandii
,
Pseudomonas aeruginosa
, and
Rhizobium etli
. These physical properties range from smooth to hairy, from bright to opaque, and from high to low convexities. COVASIAM estimated an average of 95.47% (ς = 8.55%) of the manually counted colonies, while an automated method based on a single-threshold segmentation procedure estimated an average of 76% (ς = 16.27) of the manually counted colonies. This method can be easily transposed to almost every image-processing analyzer since the procedures to compile it are generically standard.
Structural and Kinetic Properties of Nonglycosylated RecombinantPenicillium amagasakienseGlucose Oxidase Expressed inEscherichia coli
Authors: Witt Susanne , Singh Mahavir , Kalisz Henryk M. 
Published: December 2019

ABSTRACTThe gene coding forPenicillium amagasakienseglucose oxidase (GOX; β-d-glucose; oxygen 1-oxidoreductase [EC1.1.3.4]) has been cloned by PCR amplification with genomic DNA as template with oligonucleotide probes derived from amino acid sequences of N- and C-terminal peptide fragments of the enzyme. RecombinantEscherichia coliexpression plasmids have been constructed from the heat-induced pCYTEXP1 expression vector containing the mature GOX coding sequence. When transformed intoE. coliTG2, the plasmid directed the synthesis of 0.25 mg of protein in insoluble inclusion bodies per ml ofE. coliculture containing more than 60% inactive GOX. Enzyme activity was reconstituted by treatment with 8 M urea and 30 mM dithiothreitol and subsequent 100-fold dilution to a final protein concentration of 0.05 to 0.1 mg ml−1in a buffer containing reduced glutathione-oxidized glutathione, flavin adenine dinucleotide, and glycerol. Reactivation followed first-order kinetics and was optimal at 10°C. The reactivated recombinant GOX was purified to homogeneity by mild acidification and anion-exchange chromatography. Up to 12 mg of active GOX could be purified from a 1-literE. coliculture. Circular dichroism demonstrated similar conformations for recombinant and nativeP. amagasakienseGOXs. The purified enzyme has a specific activity of 968 U mg−1and exhibits kinetics of glucose oxidation similar to those of, but lower pH and thermal stabilities than, native GOX fromP. amagasakiense. In contrast to the native enzyme, recombinant GOX is nonglycosylated and contains a single isoform of pI 4.5. This is the first reported expression of a fully active, nonglycosylated form of a eukaryotic, glycosylated GOX inE. coli.
Failure To Differentiate
Cryptosporidium parvum
from
C. meleagridis
Based on PCR Amplification of Eight DNA Sequences
Authors: Champliaud Dominique , Gobet Philippe , Naciri Muriel , Vagner Odile , Lopez José , Buisson Jean Christophe , Varga Istvan , Harly Géraldine , Mancassola Roseline , Bonnin Alain 
Published: December 2019

ABSTRACT

In order to determine the specificities of PCR-based assays used for detecting
Cryptosporidium parvum
DNA, eight pairs of previously described PCR primers targeting six distinct regions of the
Cryptosporidium
genome were evaluated for the detection of
C. parvum
, the agent of human cryptosporidiosis, and
C. muris
,
C. baileyi
, and
C. meleagridis
, three
Cryptosporidium
species that infect birds or mammals but are not considered to be human pathogens. The four
Cryptosporidium
species were divided into two groups:
C. parvum
and
C. meleagridis
, which gave the same-sized fragments with all the reactions, and
C. muris
and
C. baileyi
, which gave positive results with primer pairs targeting the 18S rRNA gene only. In addition to being genetically similar at each of the eight loci analyzed by DNA amplification,
C. parvum
and
C. meleagridis
couldn’t be differentiated even after restriction enzyme digestion of the PCR products obtained from three of the target genes. This study indicates that caution should be exercised in the interpretation of data from water sample analysis performed by these methods, since a positive result does not necessarily reflect a contamination by the human pathogen
C. parvum.
Release of Dimethylsulfide from Dimethylsulfoniopropionate by Plant-Associated Salt Marsh Fungi
Authors: Bacic M. K. , Newell S. Y. , Yoch D. C. 
Published: December 2019

ABSTRACT

The range of types of microbes with dimethylsulfoniopropionate (DMSP) lyase capability (enzymatic release of dimethylsulfide [DMS] from DMSP) has recently been expanded from bacteria and eukaryotic algae to include fungi (a species of the genus
Fusarium
[M. K. Bacic and D. C. Yoch, Appl. Environ. Microbiol. 64:106–111, 1998]). Fungi (especially ascomycetes) are the predominant decomposers of shoots of smooth cordgrass, the principal grass of Atlantic salt marshes of the United States. Since the high rates of release of DMS from smooth cordgrass marshes have a temporal peak that coincides with peak shoot death, we hypothesized that cordgrass fungi were involved in this DMS release. We tested seven species of the known smooth cordgrass ascomycetes and discovered that six of them exhibited DMSP lyase activity. We also tested two species of ascomycetes from other DMSP-containing plants, and both were DMSP lyase competent. For comparison, we tested 11 species of ascomycetes and mitosporic fungi from halophytes that do not contain DMSP; of these 11, only 3 were positive for DMSP lyase. A third group tested, marine oomycotes (four species of the genera
Halophytophthora
and
Pythium
, mostly from mangroves), showed no DMSP lyase activity. Two of the strains of fungi found to be positive for DMSP lyase also exhibited uptake of DMS, an apparently rare combination of capabilities. In conclusion, a strong correlation exists between a fungal decomposer’s ability to catabolize DMSP via the DMSP lyase pathway and the host plant’s production of DMSP as a secondary product.
Extremely Barophilic Bacteria Isolated from the Mariana Trench, Challenger Deep, at a Depth of 11,000 Meters
Authors: Kato Chiaki , Li Lina , Nogi Yuichi , Nakamura Yuka , Tamaoka Jin , Horikoshi Koki 
Published: December 2019

ABSTRACT

Two strains of obligately barophilic bacteria were isolated from a sample of the world’s deepest sediment, which was obtained by the unmanned deep-sea submersible
Kaiko
in the Mariana Trench, Challenger Deep, at a depth of 10,898 m. From the results of phylogenetic analysis based on 16S rRNA gene sequences, DNA-DNA relatedness study, and analysis of fatty acid composition, the first strain (DB21MT-2) appears to be most highly similar to
Shewanella benthica
and close relatives, and the second strain (DB21MT-5) appears to be closely related to the genus
Moritella
. The optimal pressure conditions for growth of these isolates were 70 MPa for strain DB21MT-2 and 80 MPa for strain DB21MT-5, and no growth was detected at pressures of less than 50 MPa with either strain. This is the first evidence of the existence of an extreme-barophile bacterium of the genus
Moritella
isolated from the deep-sea environment.
Analysis of Stable Low-Molecular-Weight RNA Profiles of Members of the Family
Rhizobiaceae
Authors: Velázquez Encarna , Cruz-Sánchez JoséMaría , Mateos Pedro F. , Martínez-Molina Eustoquio 
Published: December 2019

ABSTRACT

Staircase electrophoresis in polyacrylamide gels was used to analyze the stable low-molecular-weight (LMW) RNA profiles of 24 type strains belonging to the family
Rhizobiaceae
. This new electrophoretic technique results in good separation of the molecules forming the LMW RNA profiles. Differences in the number and distribution of the RNA bands in these profiles allowed us to identify differences among the 24 strains assayed. Species assignments based on LMW RNAs proved to be consistent with the established taxonomic classification. Analysis of the data obtained and the corresponding dendrograms revealed relationships between genera and species; these relationships were essentially the same as those obtained with other techniques, such as DNA hybridization and 16S rRNA sequencing. Use of the technique described here, with which it is possible to analyze a large number of strains in a short time, permits rapid identification of species belonging to the family
Rhizobiaceae
and should in the future facilitate biodiversity studies and detection of new species.
Influence of Cold Stress on the Preliminary Enrichment Time Needed for Detection of Enterohemorrhagic
Escherichia coli
in Ground Beef by PCR
Authors: Uyttendaele M. , Grangette C. , Rogerie F. , Pasteau S. , Debevere J. , Lange M. 
Published: December 2019

ABSTRACT

The influence of cold stress at 4 and 0°C on the detection time as assessed by impedance technology (Bactometer; Biomérieux, Marcy l’Etoile, France) of different enterohemorrhagic
Escherichia coli
(EHEC) strains was determined. Although there is some variation in susceptibility among EHEC strains, prolonged exposure of EHEC to cold stress, i.e., 4 and 5 days at 4 and 0°C, respectively, in general significantly increased their detection time. This reflects an increase of the lag-phase time caused by cold stress. Two EHEC strains were selected to determine the minimum preliminary enrichment time that would ensure a positive PCR detection of low numbers of verotoxin-producing
E. coli
(VTEC; 2 to 2 × 10
5
CFU/25 g) inoculated into ground beef (25 g) and stored at 4 or −20°C for 8 and 14 days, respectively. Incubation times of 6 and 9 h of 1 to 10 CFU/g and 1 to 10 CFU/25 g, respectively, were sufficient for PCR detection of VTEC in ground beef when analysis was performed immediately after inoculation (no cold stress). When cells are exposed to cold stress (4 or −20°C) a 24-h enrichment period is recommended. Restriction of enrichment time to 9 h under these circumstances decreases the sensitivity of PCR detection to 80 CFU/g. Hence, to obtain maximum sensitivity, PCR detection of VTEC in naturally contaminated ground beef should be performed after 24 h of enrichment.