bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogenetic Analysis of Nonthermophilic Members of the Kingdom
Crenarchaeota
and Their Diversity and Abundance in Soils
Authors: Buckley Daniel H. , Graber Joseph R. , Schmidt Thomas M. 
Published: December 2019

ABSTRACT

Within the last several years, molecular techniques have uncovered numerous 16S rRNA gene (rDNA) sequences which represent a unique and globally distributed lineage of the kingdom
Crenarchaeota
that is phylogenetically distinct from currently characterized crenarchaeotal species. rDNA sequences of members of this novel crenarchaeotal group have been recovered from low- to moderate-temperature environments (−1.5 to 32°C), in contrast to the high-temperature environments (temperature, >80°C) required for growth of the currently recognized crenarchaeotal species. We determined the diversity and abundance of the nonthermophilic members of the
Crenarchaeota
in soil samples taken from cultivated and uncultivated fields located at the Kellogg Biological Station’s Long-Term Ecological Research site (Hickory Corners, Mich.). Clones were generated from 16S rDNA that was amplified by using broad-specificity archaeal PCR primers. Twelve crenarchaeotal sequences were identified, and the phylogenetic relationships between these sequences and previously described crenarchaeotal 16S rDNA sequences were determined. Phylogenetic analyses included nonthermophilic crenarchaeotal sequences found in public databases and revealed that the nonthermophilic
Crenarchaeota
group is composed of at least four distinct phylogenetic clusters. A 16S rRNA-targeted oligonucleotide probe specific for all known nonthermophilic crenarchaeotal sequences was designed and used to determine their abundance in soil samples. The nonthermophilic
Crenarchaeota
accounted for as much as 1.42% ± 0.42% of the 16S rRNA in the soils analyzed.
Whole-Cell Kinetics of Trichloroethylene Degradation by Phenol Hydroxylase in a
Ralstonia eutropha
JMP134 Derivative
Authors: Ayoubi Patricia J. , Harker Alan R. 
Published: December 2019

ABSTRACT

The rate, progress, and limits of trichloroethylene (TCE) degradation by
Ralstonia eutropha
AEK301/pYK3021 whole cells were examined in the absence of aromatic induction. At TCE concentrations up to 800 μM, degradation rates were sustained until TCE was no longer detectable. The

K
s

and
V
max
for TCE degradation by AEK301/pYK3021 whole cells were determined to be 630 μM and 22.6 nmol/min/mg of total protein, respectively. The sustained linear rates of TCE degradation by AEK301/pYK3021 up to a concentration of 800 μM TCE suggest that solvent effects are limited during the degradation of TCE and that this construct is little affected by the formation of toxic intermediates at the TCE levels and assay duration tested. TCE degradation by this strain is subject to carbon catabolite repression.
Ammonium Removal by the Oxygen-Limited Autotrophic Nitrification-Denitrification System
Authors: Kuai Linping , Verstraete Willy 
Published: December 2019

ABSTRACT

The present lab-scale research reveals the potential of implementation of an oxygen-limited autotrophic nitrification-denitrification (OLAND) system with normal nitrifying sludge as the biocatalyst for the removal of nitrogen from nitrogen-rich wastewater in one step. In a sequential batch reactor, synthetic wastewater containing 1 g of NH
4
+
-N liter
−1
and minerals was treated. Oxygen supply to the reactor was double-controlled with a pH controller and a timer. At a volumetric loading rate (

B
v

) of 0.13 g of NH
4
+
-N liter
−1
day
−1
, about 22% of the fed NH
4
+
-N was converted to NO
2
−
-N or NO
3
−
-N, 38% remained as NH
4
+
-N, and the other 40% was removed mainly as N
2
. The specific removal rate of nitrogen was on the order of 50 mg of N liter
−1
day
−1
, corresponding to 16 mg of N g of volatile suspended solids
−1
day
−1
. The microorganisms which catalyzed the OLAND process are assumed to be normal nitrifiers dominated by ammonium oxidizers. The loss of nitrogen in the OLAND system is presumed to occur via the oxidation of NH
4
+
to N
2
with NO
2
−
as the electron acceptor. Hydroxylamine stimulated the removal of NH
4
+
and NO
2
−
. Hydroxylamine oxidoreductase (HAO) or an HAO-related enzyme might be responsible for the loss of nitrogen.
Humic Acid Reduction by
Propionibacterium freudenreichii
and Other Fermenting Bacteria
Authors: Benz Marcus , Schink Bernhard , Brune Andreas 
Published: December 2019

ABSTRACT

Iron-reducing bacteria have been reported to reduce humic acids and low-molecular-weight quinones with electrons from acetate or hydrogen oxidation. Due to the rapid chemical reaction of amorphous ferric iron with the reduced reaction products, humic acids and low-molecular-weight redox mediators may play an important role in biological iron reduction. Since many anaerobic bacteria that are not able to reduce amorphous ferric iron directly are known to transfer electrons to other external acceptors, such as ferricyanide, 2,6-anthraquinone disulfonate (AQDS), or molecular oxygen, we tested several physiologically different species of fermenting bacteria to determine their abilities to reduce humic acids.
Propionibacterium freudenreichii
,
Lactococcus lactis
, and
Enterococcus cecorum
all shifted their fermentation patterns towards more oxidized products when humic acids were present;
P. freudenreichii
even oxidized propionate to acetate under these conditions. When amorphous ferric iron was added to reoxidize the electron acceptor, humic acids were found to be equally effective when they were added in substoichiometric amounts. These findings indicate that in addition to iron-reducing bacteria, fermenting bacteria are also capable of channeling electrons from anaerobic oxidations via humic acids towards iron reduction. This information needs to be considered in future studies of electron flow in soils and sediments.
Methanotrophs and Methanogens in Masonry
Authors: Kussmaul Martin , Wilimzig Markus , Bock Eberhard 
Published: December 2019

ABSTRACT

Methanotrophs were present in 48 of 225 stone samples which were removed from 19 historical buildings in Germany and Italy. The average cell number of methanotrophs was 20 CFU per g of stone, and their activities ranged between 11 and 42 pmol of CH
4
g of stone
−1
day
−1
. Twelve strains of methane-oxidizing bacteria were isolated. They belonged to the type II methanotrophs of the genera
Methylocystis
,
Methylosinus
, and
Methylobacterium
. In masonry, growth substrates like methane or methanol are available in very low concentrations. To determine if methane could be produced by the stone at rates sufficient to support growth of methanotrophs, methane production by stone samples under nonoxic conditions was examined. Methane production of 0.07 to 215 nmol of CH
4
g of stone
−1
day
−1
was detected in 23 of 47 stone samples examined. This indicated the presence of the so-called “mini-methane”-producing bacteria and/or methanogenic archaea. Methanotrophs occurred in nearly all samples which showed methane production. This finding indicated that methanotrophs depend on biogenic methane production in or on stone surfaces of historical buildings.
Antagonistic Activity against
Helicobacter
Infection In Vitro and In Vivo by the Human
Lactobacillus acidophilus
Strain LB
Authors: Coconnier Marie-Helene , Lievin Vanessa , Hemery Elisabeth , Servin Alain L. 
Published: December 2019

ABSTRACT

The purpose of the present study was to examine the activity of the human
Lactobacillus acidophilus
strain LB, which secretes an antibacterial substance(s) against
Helicobacter pylori
in vitro and in vivo. The spent culture supernatant (SCS) of the strain LB (LB-SCS) dramatically decreased the viability of
H. pylori
in vitro independent of pH and lactic acid levels. Adhesion of
H. pylori
to the cultured human mucosecreting HT29-MTX cells decreased in parallel with the viability of
H. pylori
. In conventional mice, oral treatment with the LB-SCS protected against infection with
Helicobacter felis
. Indeed, at both 8 and 49 days post-LB-SCS treatment (29 and 70 days postinfection), inhibition of stomach colonization by
H. felis
was observed, and no evidence of gastric histopathological lesions was found. LB-SCS treatment inhibits the
H. pylori
urease activity in vitro and in
H. pylori
that remained associated with the cultured human mucosecreting HT29-MTX cells. Moreover, a decrease in urease activity was detected in the stomach of the mice infected with
H. felis
and treated with LB-SCS.
A Novel Screening Method for Isolating Exopolysaccharide-Deficient Mutants
Authors: Liu Minghsun , González Juan E. , Willis Laura B. , Walker Graham C. 
Published: December 2019

ABSTRACT

A screening method based on differential staining of the wild type and exopolysaccharide-deficient mutants of
Rhizobium
(
Sinorhizobium
)
meliloti
by the lipophilic dye Sudan Black B is described. Mutants defective in the production of either succinoglycan or EPS II (galactoglucan) were isolated by using this method, which might also prove useful for isolating exopolysaccharide-defective derivatives of other bacteria.
Enzymatic Recovery of Elemental Palladium by Using Sulfate-Reducing Bacteria
Authors: Lloyd Jon R. , Yong Ping , Macaskie Lynne E. 
Published: December 2019

ABSTRACT

Worldwide usage of platinum group metals is increasing, prompting new recovery technologies. Resting cells of
Desulfovibrio desulfuricans
reduced soluble Pd
2+
to elemental, cell-bound Pd
0
supported by pyruvate, formate, or H
2
as the electron donor without biochemical cofactors. Pd reduction was O
2
insensitive, opening the way for recycling and recovery of Pd under oxic conditions.
Bacterial Oxidation of Dibromomethane and Methyl Bromide in Natural Waters and Enrichment Cultures
Authors: Goodwin K. D. , Schaefer J. K. , Oremland R. S. 
Published: December 2019

ABSTRACTBacterial oxidation of14CH2Br2and14CH3Br was measured in freshwater, estuarine, seawater, and hypersaline-alkaline samples. In general, bacteria from the various sites oxidized similar amounts of14CH2Br2and comparatively less14CH3Br. Bacterial oxidation of14CH3Br was rapid in freshwater samples compared to bacterial oxidation of14CH3Br in more saline waters. Freshwater was also the only site in which methyl fluoride-sensitive bacteria (e.g., methanotrophs or nitrifiers) governed brominated methane oxidation. Half-life calculations indicated that bacterial oxidation of CH2Br2was potentially significant in all of the waters tested. In contrast, only in freshwater was bacterial oxidation of CH3Br as fast as chemical removal. The values calculated for more saline sites suggested that bacterial oxidation of CH3Br was relatively slow compared to chemical and physical loss mechanisms. However, enrichment cultures demonstrated that bacteria in seawater can rapidly oxidize brominated methanes. Two distinct cultures of nonmethanotrophic methylotrophs were recovered; one of these cultures was able to utilize CH2Br2as a sole carbon source, and the other was able to utilize CH3Br as a sole carbon source.
Pathway of Glucose Catabolism by Strain VeGlc2, an Anaerobe Belonging to the
Verrucomicrobiales
Lineage of Bacterial Descent
Authors: Janssen Peter H. 
Published: December 2019

ABSTRACT

Strain VeGlc2, an anaerobic ultramicrobacterium belonging to the
Verrucomicrobiales
lineage of bacterial descent, fermented glucose to acetate, propionate, succinate, and CO
2
. The distribution of radiolabel in the fermentation end products produced from position-labelled glucose and in vitro measurements of enzyme activities in crude cell extracts prepared from glucose-grown cells showed that glucose was metabolized via the Embden-Meyerhof-Parnas pathway. The 6-phosphofructokinase (EC
2.7.1.90
) activity required pyrophosphate as the phosphoryl donor, and ATP could not replace pyrophosphate. The other enzyme activities were those of a classical Embden-Meyerhof-Parnas pathway.
14
CO
2
was incorporated into propionate and succinate, suggesting that a carboxylation reaction rather than a transcarboxylation reaction was involved in the reductive pathway leading to succinate and propionate. Difference spectra showed that a type
b
cytochrome was present, which could be involved in electron transport in the reductive pathway.
Characterization of the Critical Amino Acids of an
Aspergillus parasiticus
Cytochrome P-450 Monooxygenase Encoded by
ordA
That Is Involved in the Biosynthesis of Aflatoxins B
1
, G
1
, B
2
, and G
2
Authors: Yu Jiujiang , Chang Perng-Kuang , Ehrlich Kenneth C. , Cary Jeffrey W. , Montalbano Beverly , Dyer John M. , Bhatnagar Deepak , Cleveland Thomas E. 
Published: December 2019

ABSTRACT

The conversion of
O
-methylsterigmatocystin (OMST) and dihydro-
O
-methylsterigmatocystin to aflatoxins B
1
, G
1
, B
2
, and G
2
requires a cytochrome P-450 type of oxidoreductase activity.
ordA
, a gene adjacent to the
omtA
gene, was identified in the aflatoxin-biosynthetic pathway gene cluster by chromosomal walking in
Aspergillus parasiticus
. The
ordA
gene was a homolog of the
Aspergillus flavus ord1
gene, which is involved in the conversion of OMST to aflatoxin B
1
. Complementation of
A. parasiticus
SRRC 2043, an OMST-accumulating strain, with the
ordA
gene restored the ability to produce aflatoxins B
1
, G
1
, B
2
, and G
2
. The
ordA
gene placed under the control of the
GAL1
promoter converted exogenously supplied OMST to aflatoxin B
1
in
Saccharomyces cerevisiae
. In contrast, the
ordA
gene homolog in
A. parasiticus
SRRC 2043,
ordA1
, was not able to carry out the same conversion in the yeast system. Sequence analysis revealed that the
ordA1
gene had three point mutations which resulted in three amino acid changes (His-400→Leu-400, Ala-143→Ser-143, and Ile-528→Tyr-528). Site-directed mutagenesis studies showed that the change of His-400 to Leu-400 resulted in a loss of the monooxygenase activity and that Ala-143 played a significant role in the catalytic conversion. In contrast, Ile-528 was not associated with the enzymatic activity. The involvement of the
ordA
gene in the synthesis of aflatoxins G
1
, and G
2
in
A. parasiticus
suggests that enzymes required for the formation of aflatoxins G
1
and G
2
are not present in
A. flavus
. The results showed that in addition to the conserved heme-binding and redox reaction domains encoded by
ordA
, other seemingly domain-unrelated amino acid residues are critical for cytochrome P-450 catalytic activity. The
ordA
gene has been assigned to a new cytochrome P-450 gene family named CYP64 by The Cytochrome P450 Nomenclature Committee.
A New Approach To Utilize PCR–Single-Strand-Conformation Polymorphism for 16S rRNA Gene-Based Microbial Community Analysis
Authors: Schwieger Frank , Tebbe Christoph C. 
Published: December 2019

ABSTRACT
Single-strand-conformation polymorphism (SSCP) of DNA, a method widely used in mutation analysis, was adapted to the analysis and differentiation of cultivated pure-culture soil microorganisms and noncultivated rhizosphere microbial communities. A fragment (approximately 400 bp) of the bacterial 16S rRNA gene (V-4 and V-5 regions) was amplified by PCR with universal primers, with one primer phosphorylated at the 5′ end. The phosphorylated strands of the PCR products were selectively digested with lambda exonuclease, and the remaining strands were separated by electrophoresis with an MDE polyacrylamide gel, a matrix specifically optimized for SSCP purposes. By this means, reannealing and heteroduplex formation of DNA strands during electrophoresis could be excluded, and the number of bands per organism was reduced. PCR products from 10 of 11 different bacterial type strains tested could be differentiated from each other. With template mixtures consisting of pure-culture DNAs from 5 and 10 bacterial strains, most of the single strains could be detected from such model communities after PCR and SSCP analyses. Purified bands amplified from pure cultures and model communities extracted from gels could be reamplified by PCR, but by this process, additional products were also generated, as detected by further SSCP analysis. Profiles generated with DNAs of rhizosphere bacterial communities, directly extracted from two different plant species grown in the same field site, could be clearly distinguished. This study demonstrates the potential of the selected PCR–single-stranded DNA approach for microbial community analysis.
Genetic Diversity and Phylogeny of Rhizobia That Nodulate
Acacia
spp. in Morocco Assessed by Analysis of rRNA Genes
Authors: Khbaya Bouchaib , Neyra Marc , Normand Philippe , Zerhari Karim , Filali-Maltouf Abdelkarim 
Published: December 2019

ABSTRACT

Forty rhizobia nodulating four
Acacia
species (
A. gummifera
,
A. raddiana
,
A. cyanophylla
, and
A. horrida
) were isolated from different sites in Morocco. These rhizobia were compared by analyzing both the 16S rRNA gene (rDNA) and the 16S-23S rRNA spacer by PCR with restriction fragment length polymorphism (RFLP) analysis. Analysis of the length of 16S-23S spacer showed a considerable diversity within these microsymbionts, but RFLP analysis of the amplified spacer revealed no additional heterogeneity. Three clusters were identified when 16S rDNA analysis was carried out. Two of these clusters include some isolates which nodulate, nonspecifically, the four
Acacia
species. These clusters, A and B, fit within the
Sinorhizobium
lineage and are closely related to
S. meliloti
and
S. fredii
, respectively. The third cluster appeared to belong to the
Agrobacterium-Rhizobium galegae
phylum and is more closely related to the
Agrobacterium tumefaciens
species. These relations were confirmed by sequencing a representative strain from each cluster.
Analysis of the Dynamics of Bacterial Communities in the Rhizosphere of the Chrysanthemum via Denaturing Gradient Gel Electrophoresis and Substrate Utilization Patterns
Authors: Duineveld Bernadette M. , Rosado Alexandre S. , van Elsas Jan Dirk , van Veen Johannes A. 
Published: December 2019

ABSTRACT
In order to gain a better understanding of the spatial and temporal dynamics of bacterial communities of the rhizosphere of the chrysanthemum, two complementary methods were used: a molecular bacterial community profiling method, i.e., 16S rRNA gene-based PCR followed by denaturing gradient gel electrophoresis (DGGE), and an agar plate method in which 11 sole-carbon-source utilization tests were used. The DGGE patterns showed that the bacterial communities as determined from direct rhizosphere DNA extracts were largely stable along developing roots of the chrysanthemum, with very little change over time or between root parts of different ages. The patterns were also similar to those produced with DNA extracts obtained from bulk soil samples. The DGGE patterns obtained by using microbial colonies from dilution plates as the source of target DNA were different from those found with the direct DNA extracts. Moreover, these patterns showed differences among plant replicates but also among replicate plates. Results obtained with the sole-carbon-source utilization tests indicated that the metabolic profile of the bacterial communities in the rhizosphere of the root tip did not change substantially during plant growth. This suggests selective development of specific bacterial populations by the presence of a root tip. On the other hand, the metabolic profile of bacterial communities in the rhizosphere of the root base changed during plant growth. With eight sole-carbon-source utilization tests, a significant effect of the development stage of the plant on the number of bacteria which were able to grow on these carbon sources was observed.
Indole-3-Acetic Acid Biosynthesis in
Colletotrichum gloeosporioides
f. sp.
aeschynomene
Authors: Robinson M. , Riov J. , Sharon A. 
Published: December 2019

ABSTRACT

We characterized the biosynthesis of indole-3-acetic acid by the mycoherbicide
Colletotrichum gloeosporioides
f. sp.
aeschynomene
. Auxin production was tryptophan dependent. Compounds from the indole-3-acetamide and indole-3-pyruvic acid pathways were detected in culture filtrates. Feeding experiments and in vitro assay confirmed the presence of both pathways. Indole-3-acetamide was the major pathway utilized by the fungus to produce indole-3-acetic acid in culture.
Induction of the
tod
Operon by Trichloroethylene in
Pseudomonas putida
TVA8
Authors: Shingleton Justin T. , Applegate Bruce M. , Nagel Aaron C. , Bienkowski Paul R. , Sayler Gary S. 
Published: December 2019

ABSTRACT

Bioluminescence, mRNA levels, and toluene degradation rates in
Pseudomonas putida
TVA8 were measured as a function of various concentrations of toluene and trichloroethylene (TCE). TVA8 showed an increasing bioluminescence response to increasing TCE and toluene concentrations. Compared to uninduced TVA8 cultures,
todC1
mRNA levels increased 11-fold for TCE-treated cultures and 13-fold for toluene-treated cultures. Compared to uninduced
P. putida
F1 cultures,
todC1
mRNA levels increased 4.4-fold for TCE-induced cultures and 4.9-fold for toluene-induced cultures. Initial toluene degradation rates were linearly correlated with specific bioluminescence in TVA8 cultures.
Cloning and Targeted Disruption of
MLG1
, a Gene Encoding Two of Three Extracellular Mixed-Linked Glucanases of
Cochliobolus carbonum
Authors: Görlach Jenifer M. , Van Der Knaap Esther , Walton Jonathan D. 
Published: December 2019

ABSTRACT

Mixed-linked glucanases (MLGases), which are extracellular enzymes able to hydrolyze β1,3-1,4-glucans (also known as mixed-linked glucans or cereal β-glucans), were identified in culture filtrates of the plant-pathogenic fungus
Cochliobolus carbonum
. Three peaks of MLGase activity, designated Mlg1a, Mlg1b, and Mlg2, were resolved by cation-exchange and hydrophobic-interaction high-performance liquid chromatography (HPLC). Mlg1a and Mlg1b also hydrolyze β1,3-glucan (laminarin), whereas Mlg2 does not degrade β1,3-glucan but does degrade β1,4-glucan to a slight extent. Mlg1a, Mlg1b, and Mlg2 have monomer molecular masses of 33.5, 31, and 29.5 kDa, respectively. The N-terminal amino acid sequences of Mlg1a and Mlg1b are identical (AAYNLI). Mlg1a is glycosylated, whereas Mlg1b is not. The gene encoding Mlg1b,
MLG1
, was isolated by using PCR primers based on amino acid sequences of Mlg1b. The product of
MLG1
has no close similarity to any known protein but does contain a motif (EIDI) that occurs at the active site of MLGases from several prokaryotes. An internal fragment of
MLG1
was used to create
mlg1
mutants by transformation-mediated gene disruption. The total MLGase and β1,3-glucanase activities in culture filtrates of the mutants were reduced by approximately 50 and 40%, respectively. When analyzed by cation-exchange HPLC, the mutants were missing the two peaks of MLGase activity corresponding to Mlg1a and Mlg1b. Together, the data indicate that Mlg1a and Mlg1b are products of the same gene,
MLG1
. The growth of
mlg1
mutants in culture medium supplemented with macerated maize cell walls or maize bran and the disease symptoms on maize were identical to the growth and disease symptoms of the wild type.