bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of Temperature on Structure and Function of the Methanogenic Archaeal Community in an Anoxic Rice Field Soil
Authors: Chin Kuk-Jeong , Lukow Thomas , Conrad Ralf 
Published: December 2019

ABSTRACT

Soil temperatures in Italian rice fields typically range between about 15 and 30°C. A change in the incubation temperature of anoxic methanogenic soil slurry from 30°C to 15°C typically resulted in a decrease in the CH
4
production rate, a decrease in the steady-state H
2
partial pressure, and a transient accumulation of acetate. Previous experiments have shown that these changes were due to an alteration of the carbon and electron flow in the methanogenic degradation pathway of organic matter caused by the temperature shift (K. J. Chin and R. Conrad, FEMS Microbiol. Ecol. 18:85–102, 1995). To investigate how temperature affects the structure of the methanogenic archaeal community, total DNA was extracted from soil slurries incubated at 30 and 15°C. The archaeal small-subunit (SSU) rRNA-encoding genes (rDNA) of these environmental DNA samples were amplified by PCR with an archaeal-specific primer system and used for the generation of clone libraries. Representative rDNA clones (
n
= 90) were characterized by terminal restriction fragment length polymorphism (T-RFLP) and sequence analysis. T-RFLP analysis produced for the clones terminally labeled fragments with a characteristic length of mostly 185, 284, or 392 bp. Sequence analysis allowed determination of the phylogenetic affiliation of the individual clones with their characteristic T-RFLP fragment lengths and showed that the archaeal community of the anoxic rice soil slurry was dominated by members of the families
Methanosarcinaceae
(185 bp) and
Methanosaetaceae
(284 bp), the kingdom
Crenarchaeota
(185 or 284 bp), and a novel, deeply branching lineage of the (probably methanogenic) kingdom
Euryarchaeota
(392 bp) that has recently been detected on rice roots (R. Großkopf, S. Stubner, and W. Liesack, Appl. Environ. Microbiol. 64:4983–4989, 1998). The structure of the archaeal community changed when the temperature was shifted from 30°C to 15°C. Before the temperature shift, the clones (
n
= 30) retrieved from the community were dominated by
Crenarchaeota
(70%), “novel
Euryarchaeota
” (23%), and
Methanosarcinacaeae
(7%). Further incubation at 30°C (
n
= 30 clones) resulted in a relative increase in members of the
Methanosarcinaceae
(77%), whereas further incubation at 15°C (
n
= 30 clones) resulted in a much more diverse community consisting of 33%
Methanosarcinaceae
, 23%
Crenarchaeota
, 20%
Methanosaetaceae
, and 17% novel
Euryarchaeota
. The appearance of
Methanosaetaceae
at 15°C was conspicuous. These results demonstrate that the structure of the archaeal community in anoxic rice field soil changed with time and incubation temperature.
A Morphological and Molecular Perspective of
Trichoderma viride
: Is It One or Two Species?
Authors: Lieckfeldt Elke , Samuels Gary J. , Nirenberg Helgard I. , Petrini Orlando 
Published: December 2019

ABSTRACT

Trichoderma
(
Ascomycetes
,
Hypocreales
) strains that have warted conidia are traditionally identified as
T. viride
, the type species of
Trichoderma
. However, two morphologically distinct types of conidial warts (I and II) have been found. Because each type corresponds to a unique mitochondrial DNA pattern, it has been questioned whether
T. viride
comprises more than one species. Combined molecular data (sequences of the internal transcribed spacer 1 [ITS-1] and ITS-2 regions and of part of the 28S rRNA gene along with results of restriction fragment length polymorphism analysis of the endochitinase gene and PCR fingerprinting), morphology, physiology, and colony characteristics distinguish type I and type II as different species. Type I corresponds to “true”
T. viride
, the anamorph of
Hypocrea rufa
. Type II represents a new species,
T. asperellum
, which is, in terms of molecular characteristics, close to the neotype of
T. hamatum
.
Inhibition of Nitrifiers and Methanotrophs from an Agricultural Humisol by Allylsulfide and Its Implications for Environmental Studies
Authors: Neufeld Josh D. , Knowles Roger 
Published: December 2019

ABSTRACTAllylsulfide, an inhibitor of ammonia monooxygenase, was tested to determine its ability to inhibit nitrification and methane oxidation in pure cultures, in agricultural humisol enrichment cultures, and in humisol slurries. We confirmed that allylsulfide is a differential inhibitor of cultures of nitrifiers and methanotrophs at concentrations of 1 and 200 μM, respectively, which result in 50% inhibition. However, although a nitrifying enrichment culture added to sterilized humisol was inhibited 50% by 4 μM allylsulfide, 500 μM allylsulfide was necessary for 50% inhibition of the endogenous nitrifying activity in nonsterile humisol. We concluded that native nitrifiers were protected, possibly by being in colonial aggregates or sheltered microenvironments.
The Carboxy-Terminal Portion of the Aflatoxin Pathway Regulatory Protein AFLR of
Aspergillus parasiticus
Activates
GAL1
::
lacZ
Gene Expression in
Saccharomyces cerevisiae
Authors: Chang Perng-Kuang , Yu Jiujiang , Bhatnagar Deepak , Cleveland Thomas E. 
Published: December 2019

ABSTRACT

AFLR, a DNA-binding protein of 444 amino acids, transactivates the expression of aflatoxin biosynthesis genes in
Aspergillus parasiticus
and
Aspergillus flavus
, as well as the sterigmatocystin synthesis genes in
Aspergillus nidulans
. We show here by fusion of various
aflR
coding regions to the
GAL4
DNA-binding coding region that the AFLR carboxyl terminus contained a region that activated
GAL1
::
lacZ
gene expression in
Saccharomyces cerevisiae
and that the AFLR internal region was required for the activation activity. Compared to the AFLR carboxy-terminal fusion protein (AFLRC), a mutant AFLRC retained approximately 75% of the activation activity after deletion of three acidic amino acids, Asp365, Glu366, and Glu367, in a previously identified acidic stretch. Removal of the carboxy-terminal amino acid, Glu444, did not affect the activation activity. Substitutions of acidic Glu423, Asp439, or Asp436/Asp439 with basic amino acids, Lys and His, resulted in 10- to 15-fold-lower activation activities. Strikingly, the Asp436His mutation abolished the activation activity. Substitutions of basic His428 and His442 with acidic Asp resulted in 20 and 40% decreases in the activation activities, respectively. Simultaneous substitutions of Arg427, Arg429, and Arg431 with Leu also significantly decreased the activation activity; the decrease was approximately 50-fold. Results suggest that the AFLR carboxy-terminal region is involved in transcription activation and that total acidity in this region is not a major determinant of AFLR’s activation ability in
S. cerevisiae
.
Effects of Larval Mosquitoes (Aedes triseriatus) and Stemflow on Microbial Community Dynamics in Container Habitats
Authors: Kaufman Michael G. , Walker Edward D. , Smith Tracy W. , Merritt Richard W. , Klug Michael J. 
Published: December 2019

ABSTRACTThe dynamics of the microbial food sources forAedes triseriatuslarvae in microcosms were found to be strongly influenced by larval presence. The total abundance of bacteria in water samples generally increased in response to larvae, including populations of cultivable, facultatively anaerobic bacteria. Additionally, a portion of the community shifted fromPseudomonaceaetoEnterobacteriaceae. Bacterial abundance on leaf material was significantly reduced in the presence of actively feeding larvae. Principle-component analysis of whole community fatty acid methyl ester (FAME) profiles showed that larvae changed the microbial community structure in both the water column and the leaf material. Cyclopropyl FAMEs, typically associated with bacteria, were reduced in microcosms containing larvae; however, other bacterial fatty acids showed no consistent response. Long-chain polyunsaturated fatty acids characteristic of microeukaryotes (protozoans and meiofauna) declined in abundance when larvae were present, indicating that larval feeding reduced the densities of these microorganisms. However, presumed fungal lipid markers either increased or were unchanged in response to larvae. Larval presence also affected microbial nitrogen metabolism through modification of the physiochemical conditions or by grazing on populations of bacteria involved in nitrification-denitrification. Stemflow primarily influenced inorganic ion and organic compound concentrations in the microcosms and had less-pronounced effects on microbial community parameters than did larval presence. Stemflow treatments diluted concentrations of all inorganic ions (chloride, sulfate, and ammonium) and organic compounds (total dissolved organic carbon, soluble carbohydrates, and total protein) measured, with the exceptions of nitrite and nitrate. Stemflow addition did not measurably affect larval biomass in the microcosms but did enhance development rates and early emergence patterns of adults.
Molecular Analysis of
Pseudomonas aeruginosa
: Epidemiological Investigation of Mastitis Outbreaks in Irish Dairy Herds
Authors: Daly M. , Power E. , Björkroth J. , Sheehan P. , O’Connell A. , Colgan M. , Korkeala H. , Fanning S. 
Published: December 2019

ABSTRACT

Pseudomonas aeruginosa
is a pathogen in both humans and animals. This bacterium, most often associated with respiratory infections in cystic fibrosis patients, was found to be the causative agent in bovine mastitis outbreaks among 11 Irish dairy herds. Epidemiological findings suggested that the infection was spread to all herds by teat wipes that had been contaminated with this organism. Two molecular-typing strategies were used in an attempt to determine the genomic relationship(s), if any, of the
P. aeruginosa
strains isolated from the various herds and to verify whether the same strain was responsible for each outbreak. Thirty-six isolates from the mastitis outbreaks were tested and compared to fourteen clinical isolates from Cork University Hospital. With one exception, all outbreak-linked strains produced identical patterns when ribotyped with
Cla
I and
Pvu
II enzymes. Eight of the clinical isolates gave the same
Cla
I ribotype pattern as the mastitis-causing strains. However,
Pvu
II proved more discriminatory, with only the outbreak isolates producing identical patterns. Similar results were obtained with RW3A-primed DNA amplification fingerprinting, with all outbreak isolates except one displaying the same fingerprint array. The clinical strains produced several fingerprint patterns, all of which were different from those of the mastitis-causing isolates. Fine-resolution DNA fingerprinting with a fluorescence-labelled RW3A primer also identified a number of low-molecular-weight polymorphisms that would have remained undetected by conventional methods. These data support the view that the same
P. aeruginosa
strain was responsible for the mastitis outbreaks in all 11 herds.
Characterization of the
meta
-Cleavage Compound Hydrolase Gene Involved in Degradation of the Lignin-Related Biphenyl Structure by
Sphingomonas paucimobilis
SYK-6
Authors: Peng Xue , Masai Eiji , Katayama Yoshihiro , Fukuda Masao 
Published: December 2019

ABSTRACT

Sphingomonas paucimobilis
SYK-6 has the ability to transform a lignin-related biphenyl compound, 2,2′-dihydroxy-3,3′-dimethoxy-5,5′-dicarboxybiphenyl (DDVA), to 5-carboxyvanillic acid (5CVA) via 2,2′,3-trihydroxy-3′-methoxy-5,5′-dicarboxybiphenyl (OH-DDVA). In the 4.9-kb
Hin
dIII fragment containing the OH-DDVA
meta
-cleavage dioxygenase gene (
ligZ
), we found a novel hydrolase gene (
ligY
) responsible for the conversion of the
meta
-cleavage compound of OH-DDVA to 5CVA. Incorporation of
18
O from H
2
18
O into 5CVA indicated there was a hydrolytic conversion of the OH-DDVA
meta
-cleavage compound to 5CVA. LigY exhibited hydrolase activity only toward the
meta
-cleavage compound of OH-DDVA, suggesting its restricted substrate specificity.
Changes of Fermentation Pathways of Fecal Microbial Communities Associated with a Drug Treatment That Increases Dietary Starch in the Human Colon
Authors: Wolin Meyer J. , Miller Terry L. , Yerry Susan , Zhang Yongchao , Bank Shelton , Weaver Gary A. 
Published: December 2019

ABSTRACT

Acarbose inhibits starch digestion in the human small intestine. This increases the amount of starch available for microbial fermentation to acetate, propionate, and butyrate in the colon. Relatively large amounts of butyrate are produced from starch by colonic microbes. Colonic epithelial cells use butyrate as an energy source, and butyrate causes the differentiation of colon cancer cells. In this study we investigated whether colonic fermentation pathways changed during treatment with acarbose. We examined fermentations by fecal suspensions obtained from subjects who participated in an acarbose-placebo crossover trial. After incubation with [1-
13
C]glucose and
12
CO
2
or with unlabeled glucose and
13
CO
2
, the distribution of
13
C in product C atoms was determined by nuclear magnetic resonance spectrometry and gas chromatography-mass spectrometry. Regardless of the treatment, acetate, propionate, and butyrate were produced from pyruvate formed by the Embden-Meyerhof-Parnas pathway. Considerable amounts of acetate were also formed by the reduction of CO
2
. Butyrate formation from glucose increased and propionate formation decreased with acarbose treatment. Concomitantly, the amounts of CO
2
reduced to acetate were 30% of the total acetate in untreated subjects and 17% of the total acetate in the treated subjects. The acetate, propionate, and butyrate concentrations were 57, 20, and 23% of the total final concentrations, respectively, for the untreated subjects and 57, 13, and 30% of the total final concentrations, respectively, for the treated subjects.
An Outbreak of Nonflocculating Catabolic Populations Caused the Breakdown of a Phenol-Digesting Activated-Sludge Process
Authors: Watanabe Kazuya , Teramoto Maki , Harayama Shigeaki 
Published: December 2019

ABSTRACT

Activated sludge was fed phenol as the sole carbon source, and the phenol-loading rate was increased stepwise from 0.5 to 1.0 g liter
−1
day
−1
and then to 1.5 g liter
−1
day
−1
. After the loading rate was increased to 1.5 g liter
−1
day
−1
, nonflocculating bacteria outgrew the sludge, and the activated-sludge process broke down within 1 week. The bacterial population structure of the activated sludge was analyzed by temperature gradient gel electrophoresis (TGGE) of PCR-amplified 16S ribosomal DNA (rDNA) fragments. We found that the population diversity decreased as the phenol-loading rate increased and that two populations (designated populations R6 and R10) predominated in the sludge during the last several days before breakdown. The R6 population was present under the low-phenol-loading-rate conditions, while the R10 population was present only after the loading rate was increased to 1.5 g liter
−1
day
−1
. A total of 41 bacterial strains with different repetitive extragenic palindromic sequence PCR patterns were isolated from the activated sludge under different phenol-loading conditions, and the 16S rDNA and
gyrB
fragments of these strains were PCR amplified and sequenced. Some bacterial isolates could be associated with major TGGE bands by comparing the 16S rDNA sequences. All of the bacterial strains affiliated with the R6 population had almost identical 16S rDNA sequences, while the
gyrB
phylogenetic analysis divided these strains into two physiologically divergent groups; both of these groups of strains could grow on phenol, while one group (designated the R6F group) flocculated in laboratory media and the other group (the R6T group) did not. A competitive PCR analysis in which specific
gyrB
sequences were used as the primers showed that a population shift from R6F to R6T occurred following the increase in the phenol-loading rate to 1.5 g liter
−1
day
−1
. The R10 population corresponded to nonflocculating phenol-degrading bacteria. Our results suggest that an outbreak of nonflocculating catabolic populations caused the breakdown of the activated-sludge process. This study also demonstrated the usefulness of
gyrB
-targeted fine population analyses in microbial ecology.
Cell Surface Analysis Techniques: What Do Cell Preparation Protocols Do to Cell Surface Properties?
Authors: Pembrey Richard S. , Marshall Kevin C. , Schneider René P. 
Published: December 2019

ABSTRACT

Cell surface analysis often requires manipulation of cells prior to examination. The most commonly employed procedures are centrifugation at different speeds, changes of media during washing or final resuspension, desiccation (either air drying for contact angle measurements or freeze-drying for sensitive spectroscopic analysis, such as X-ray photoelectron spectroscopy), and contact with hydrocarbon (hydrophobicity assays). The effects of these procedures on electrophoretic mobility, adhesion to solid substrata, affinity to a number of Sepharose columns, structural integrity, and cell viability were systematically investigated for a range of model organisms, including carbon- and nitrogen-limited
Psychrobacter
sp. strain SW8 (glycocalyx-bearing cells),
Escherichia coli
(gram-negative cells without a glycocalyx), and
Staphylococcus epidermidis
(gram-positive cells without a glycocalyx). All of the cell manipulation procedures severely modified the physicochemical properties of cells, but with each procedure some organisms were more susceptible than others. Considerable disruption of cell surfaces occurred when organisms were placed in contact with a hydrocarbon (hexadecane). The majority of cells became nonculturable after air drying and freeze-drying. Centrifugation at a high speed (15,000 ×
g
) modified many cell surface parameters significantly, although cell viability was considerably affected only in
E. coli
. The type of washing or resuspension medium had a strong influence on the values of cell surface parameters, particularly when high-salt solutions were compared with low-salt buffers. The values for parameters obtained with different methods that allegedly measure similar cell surface properties did not correlate for most cells. These results demonstrate that the methods used to prepare cells for cell surface analysis need to be critically investigated for each microorganism so that the final results obtained reflect the nature of the in situ microbial cell surface as closely as possible. There is an urgent need for new, reliable, nondestructive, minimally manipulative cell surface analysis techniques that can be used in situ.
Survival of Low-pH Stress by
Escherichia coli
O157:H7: Correlation between Alterations in the Cell Envelope and Increased Acid Tolerance
Authors: Jordan Kieran N. , Oxford Lynn , O’Byrne Conor P. 
Published: December 2019

ABSTRACT

Survival of a nontoxigenic isolate of
Escherichia coli
O157:H7 at low pH (pH 3.0) was examined over prolonged time periods for each of three population types: exponential-phase cells, stationary-phase cells, and acid-adapted exponential-phase cells. In each population, approximately 5 × 10
4
CFU ml
−1
were detected after a 24-h incubation at pH 3.0. Even after 3 days at pH 3.0, significant numbers of survivors from each of the three populations could be detected. The high level of acid tolerance exhibited by these survivors was found to be quickly lost once they were transferred to conditions which permitted growth to resume, indicating that they were not mutants. Proton flux measurements on the three populations of cells revealed that the initial rates of viability loss at pH 3.0 correlated well with net proton accumulation. Cells showing a high initial rate of viability loss (exponential-phase cells) accumulated protons at the highest rate, whereas resistant populations (adapted or stationary-phase cells) accumulated protons only slowly. Differences in the protein composition of the cell envelope between the three populations were studied by two-dimensional polyacrylamide gel electrophoresis. Complex differences in the pattern of proteins expressed by each population were uncovered. The implications of these findings are discussed in the context of a possible model accounting for acid tolerance in this important food-borne pathogen.
Photosynthetic Bradyrhizobia from
Aeschynomene
spp. Are Specific to Stem-Nodulated Species and Form a Separate 16S Ribosomal DNA Restriction Fragment Length Polymorphism Group
Authors: Molouba Flore , Lorquin Jean , Willems Anne , Hoste Bart , Giraud Eric , Dreyfus Bernard , Gillis Monique , de Lajudie Philippe , Masson-Boivin Catherine 
Published: December 2019

ABSTRACT

We obtained nine bacterial isolates from root or collar nodules of the non-stem-nodulated
Aeschynomene
species
A. elaphroxylon
,
A. uniflora
, or
A. schimperi
and 69 root or stem nodule isolates from the stem-nodulated
Aeschynomene
species
A. afraspera
,
A. ciliata
,
A. indica
,
A. nilotica
,
A. sensitiva
, and
A. tambacoundensis
from various places in Senegal. These isolates, together with 45 previous isolates from various
Aeschynomene
species, were studied for host-specific nodulation within the genus
Aeschynomene
, also revisiting cross-inoculation groups described previously by D. Alazard (Appl. Environ. Microbiol. 50:732–734, 1985). The whole collection of
Aeschynomene
nodule isolates was screened for synthesis of photosynthetic pigments by spectrometry, high-pressure liquid chromatography, and thin-layer chromatography analyses. The presence of
puf
genes in photosynthetic
Aeschynomene
isolates was evidenced both by Southern hybridization with a
Rhodobacter capsulatus
photosynthetic gene probe and by DNA amplification with primers defined from photosynthetic genes. In addition, amplified 16S ribosomal DNA restriction analysis was performed on 45
Aeschynomene
isolates, including strain BTAi1, and 19 reference strains from
Bradyrhizobium japonicum
,
Bradyrhizobium elkanii
, and other
Bradyrhizobium
sp. strains of uncertain taxonomic positions. The 16S rRNA gene sequence of the photosynthetic strain ORS278 (LMG 12187) was determined and compared to sequences from databases. Our main conclusion is that photosynthetic
Aeschynomene
nodule isolates share the ability to nodulate particular stem-nodulated species and form a separate subbranch on the
Bradyrhizobium
rRNA lineage, distinct from
B. japonicum
and
B. elkanii
.
In Situ Analysis of Nitrifying Biofilms as Determined by In Situ Hybridization and the Use of Microelectrodes
Authors: Okabe Satoshi , Satoh Hisashi , Watanabe Yoshimasa 
Published: December 2019

ABSTRACT

We investigated the in situ spatial organization of ammonia-oxidizing and nitrite-oxidizing bacteria in domestic wastewater biofilms and autotrophic nitrifying biofilms by using microsensors and fluorescent in situ hybridization (FISH) performed with 16S rRNA-targeted oligonucleotide probes. The combination of these techniques made it possible to relate in situ microbial activity directly to the occurrence of nitrifying bacterial populations. In situ hybridization revealed that bacteria belonging to the genus
Nitrosomonas
were the numerically dominant ammonia-oxidizing bacteria in both types of biofilms. Bacteria belonging to the genus
Nitrobacter
were not detected; instead,
Nitrospira
-like bacteria were the main nitrite-oxidizing bacteria in both types of biofilms.
Nitrospira
-like cells formed irregularly shaped aggregates consisting of small microcolonies, which clustered around the clusters of ammonia oxidizers. Whereas most of the ammonia-oxidizing bacteria were present throughout the biofilms, the nitrite-oxidizing bacteria were restricted to the active nitrite-oxidizing zones, which were in the inner parts of the biofilms. Microelectrode measurements showed that the active ammonia-oxidizing zone was located in the outer part of a biofilm, whereas the active nitrite-oxidizing zone was located just below the ammonia-oxidizing zone and overlapped the location of nitrite-oxidizing bacteria, as determined by FISH.