bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global Occurrence of Archaeal
amoA
Genes in Terrestrial Hot Springs
Authors: Zhang Chuanlun L. , Ye Qi , Huang Zhiyong , Li WenJun , Chen Jinquan , Song Zhaoqi , Zhao Weidong , Bagwell Christopher , Inskeep William P. , Ross Christian , Gao Lei , Wiegel Juergen , Romanek Christopher S. , Shock Everett L. , Hedlund Brian P. 
Published: August 2008

ABSTRACT

Despite the ubiquity of ammonium in geothermal environments and the thermodynamic favorability of aerobic ammonia oxidation, thermophilic ammonia-oxidizing microorganisms belonging to the crenarchaeota kingdom have only recently been described. In this study, we analyzed microbial mats and surface sediments from 21 hot spring samples (pH 3.4 to 9.0; temperature, 41 to 86°C) from the United States, China, and Russia and obtained 846 putative archaeal ammonia monooxygenase large-subunit (
amoA
) gene and transcript sequences, representing a total of 41
amoA
operational taxonomic units (OTUs) at 2% identity. The
amoA
gene sequences were highly diverse, yet they clustered within two major clades of archaeal
amoA
sequences known from water columns, sediments, and soils: clusters A and B. Eighty-four percent (711/846) of the sequences belonged to cluster A, which is typically found in water columns and sediments, whereas 16% (135/846) belonged to cluster B, which is typically found in soils and sediments. Although a few
amoA
OTUs were present in several geothermal regions, most were specific to a single region. In addition, cluster A
amoA
genes formed geographic groups, while cluster B sequences did not group geographically. With the exception of only one hot spring, principal-component analysis and UPGMA (unweighted-pair group method using average linkages) based on the UniFrac metric derived from cluster A grouped the springs by location, regardless of temperature or bulk water pH, suggesting that geography may play a role in structuring communities of putative ammonia-oxidizing archaea (AOA). The
amoA
genes were distinct from those of low-temperature environments; in particular, pair-wise comparisons between hot spring
amoA
genes and those from sympatric soils showed less than 85% sequence identity, underscoring the distinctness of hot spring archaeal communities from those of the surrounding soil system. Reverse transcription-PCR showed that
amoA
genes were transcribed in situ in one spring and the transcripts were closely related to the
amoA
genes amplified from the same spring. Our study demonstrates the global occurrence of putative archaeal
amoA
genes in a wide variety of terrestrial hot springs and suggests that geography may play an important role in selecting different assemblages of AOA.
Monitoring Abundance and Expression of “
Dehalococcoides
” Species Chloroethene-Reductive Dehalogenases in a Tetrachloroethene-Dechlorinating Flow Column
Authors: Behrens Sebastian , Azizian Mohammad F. , McMurdie Paul J. , Sabalowsky Andrew , Dolan Mark E. , Semprini Lew , Spormann Alfred M. 
Published: August 2008

ABSTRACT

We investigated the distribution and activity of chloroethene-degrading microorganisms and associated functional genes during reductive dehalogenation of tetrachloroethene to ethene in a laboratory continuous-flow column. Using real-time PCR, we quantified “
Dehalococcoides
” species 16S rRNA and chloroethene-reductive dehalogenase (RDase) genes (
pceA, tceA, vcrA
, and
bvcA
) in nucleic acid extracts from different sections of the column.
Dehalococcoides
16S rRNA gene copies were highest at the inflow port [(3.6 ± 0.6) × 10
6
(mean ± standard deviation) per gram soil] where the electron donor and acceptor were introduced into the column. The highest transcript numbers for
tceA, vcrA
, and
bvcA
were detected 5 to 10 cm from the column inflow.
bvcA
was the most highly expressed of all RDase genes and the only vinyl chloride reductase-encoding transcript detectable close to the column outflow. Interestingly, no expression of
pceA
was detected in the column, despite the presence of the genes in the microbial community throughout the column. By comparing the 16S rRNA gene copy numbers to the sum of all four RDase genes, we found that 50% of the
Dehalococcoides
population in the first part of the column did not contain either one of the known chloroethene RDase genes. Analysis of 16S rRNA gene clone libraries from both ends of the flow column revealed a microbial community dominated by members of
Firmicutes
and
Actinobacteria
. Higher clone sequence diversity was observed near the column outflow. The results presented have implications for our understanding of the ecophysiology of reductively dehalogenating
Dehalococcoides
spp. and their role in bioremediation of chloroethenes.
Attached Bacterial Populations Shared by Four Species of Aquatic Angiosperms
Authors: Crump Byron C. , Koch Evamaria W. 
Published: August 2008

ABSTRACTSymbiotic relationships between microbes and plants are common and well studied in terrestrial ecosystems, but little is known about such relationships in aquatic environments. We compared the phylogenetic diversities of leaf- and root-attached bacteria from four species of aquatic angiosperms using denaturing gradient gel electrophoresis (DGGE) and DNA sequencing of PCR-amplified 16S rRNA genes. Plants were collected from three beds in Chesapeake Bay at sites characterized as freshwater (Vallisneria americana), brackish (Potomogeton perfoliatusandStuckenia pectinata), and marine (Zostera marina). DGGE analyses showed that bacterial communities were very similar for replicate samples of leaves from canopy-forming plantsS. pectinataandP. perfoliatusand less similar for replicate samples of leaves from meadow-forming plantsZ. marinaandV. americanaand of roots of all species. In contrast, bacterial communities differed greatly among plant species and between leaves and roots. DNA sequencing identified 154 bacterial phylotypes, most of which were restricted to single plant species. However, 12 phylotypes were found on more than one plant species, and several of these phylotypes were abundant in clone libraries and represented the darkest bands in DGGE banding patterns. Root-attached phylotypes included relatives of sulfur-oxidizingGammaproteobacteriaand sulfate-reducingDeltaproteobacteria. Leaf-attached phylotypes included relatives of polymer-degradingBacteroidetesand phototrophicAlphaproteobacteria. Also, leaves and roots of three plant species hosted relatives of methylotrophicBetaproteobacteriabelonging to the familyMethylophilaceae. These results suggest that aquatic angiosperms host specialized communities of bacteria on their surfaces, including several broadly distributed and potentially mutualistic bacterial populations.
Antibacterial Activities of Naturally Occurring Compounds against
Mycobacterium avium
subsp.
paratuberculosis
Authors: Wong Stella Y. Y. , Grant Irene R. , Friedman Mendel , Elliott Christopher T. , Situ Chen 
Published: August 2008

ABSTRACT

The antibacterial activities of 18 naturally occurring compounds (including essential oils and some of their isolated constituents, apple and green tea polyphenols, and other plant extracts) against three strains of
Mycobacterium avium
subsp.
paratuberculosis
(a bovine isolate [NCTC 8578], a raw-milk isolate [806R], and a human isolate [ATCC 43015]) were evaluated using a macrobroth susceptibility testing method.
M. avium
subsp.
paratuberculosis
was grown in 4 ml Middlebrook 7H9 broth containing 10% oleic acid-albumin-dextrose-catalase, 0.05% Tween 80 (or 0.2% glycerol), and 2 μg/ml mycobactin J supplemented with five concentrations of each test compound. The changes in the optical densities of the cultures at 600 nm as a measure of CFU were recorded at intervals over an incubation period of 42 days at 37°C. Six of the compounds were found to inhibit the growth of
M. avium
subsp.
paratuberculosis
. The most effective compound was
trans
-cinnamaldehyde, with a MIC of 25.9 μg/ml, followed by cinnamon oil (26.2 μg/ml), oregano oil (68.2 μg/ml), carvacrol (72.2 μg/ml), 2,5-dihydroxybenzaldehyde (74 μg/ml), and 2-hydroxy-5-methoxybenzaldehyde (90.4 μg/ml). With the exception of carvacrol, a phenolic compound, three of the four most active compounds are aldehydes, suggesting that the structure of the phenolic group or the aldehyde group may be important to the antibacterial activity. No difference in compound activity was observed between the three
M. avium
subsp.
paratuberculosis
strains studied. Possible mechanisms of the antimicrobial effects are discussed.
Physiological and Transcriptional Responses to High Concentrations of Lactic Acid in Anaerobic Chemostat Cultures of
Saccharomyces cerevisiae
Authors: Abbott Derek A. , Suir Erwin , van Maris Antonius J. A. , Pronk Jack T. 
Published: August 2008

ABSTRACT

Based on the high acid tolerance and the simple nutritional requirements of
Saccharomyces cerevisiae
, engineered strains of this yeast are considered biocatalysts for industrial production of high-purity undissociated lactic acid. However, high concentrations of lactic acid are toxic to
S. cerevisiae
, thus limiting its growth and product formation. Physiological and transcriptional responses to high concentrations of lactic acid were studied in anaerobic, glucose-limited chemostat cultures grown at different pH values and lactic acid concentrations, resulting in a 50% decrease in the biomass yield. At pH 5, the yield decrease was caused mostly by osmotically induced glycerol production and not by the classic weak-acid action, as was observed at pH 3. Cultures grown at pH 5 with 900 mM lactic acid revealed an upregulation of many genes involved in iron homeostasis, indicating that iron chelation occurred at high concentrations of dissociated lactic acid. Chemostat cultivation at pH 3 with 500 mM lactate, resulting in lower anion concentrations, showed an alleviation of this iron homeostasis response. Six of the 10 known targets of the transcriptional regulator Haa1p were strongly upregulated in lactate-challenged cultures at pH 3 but showed only moderate induction by high lactate concentrations at pH 5. Moreover, the
haa1
Δ mutant exhibited a growth defect at high lactic acid concentrations at pH 3. These results indicate that iron homeostasis plays a major role in the response of
S. cerevisiae
to high lactate concentrations, whereas the Haa1p regulon is involved primarily in the response to high concentrations of undissociated lactic acid.
Optimization of Metabolic Capacity and Flux through Environmental Cues To Maximize Hydrogen Production by the Cyanobacterium “
Arthrospira
(
Spirulina
)
maxima
”
Authors: Ananyev Gennady , Carrieri Damian , Dismukes G. Charles 
Published: August 2008

ABSTRACT

Environmental and nutritional conditions that optimize the yield of hydrogen (H
2
) from water using a two-step photosynthesis/fermentation (P/F) process are reported for the hypercarbonate-requiring cyanobacterium “
Arthrospira maxima
.” Our observations lead to four main conclusions broadly applicable to fermentative H
2
production by bacteria: (i) anaerobic H
2
production in the dark from whole cells catalyzed by a bidirectional [NiFe] hydrogenase is demonstrated to occur in two temporal phases involving two distinct metabolic processes that are linked to prior light-dependent production of NADPH (photosynthetic) and dark/anaerobic production of NADH (fermentative), respectively; (ii) H
2
evolution from these reductants represents a major pathway for energy production (ATP) during fermentation by regenerating NAD
+
essential for glycolysis of glycogen and catabolism of other substrates; (iii) nitrate removal during fermentative H
2
evolution is shown to produce an immediate and large stimulation of H
2
, as nitrate is a competing substrate for consumption of NAD(P)H, which is distinct from its slower effect of stimulating glycogen accumulation; (iv) environmental and nutritional conditions that increase anaerobic ATP production, prior glycogen accumulation (in the light), and the intracellular reduction potential (NADH/NAD
+
ratio) are shown to be the key variables for elevating H
2
evolution. Optimization of these conditions and culture age increases the H
2
yield from a single P/F cycle using concentrated cells to 36 ml of H
2
/g (dry weight) and a maximum 18% H
2
in the headspace. H
2
yield was found to be limited by the hydrogenase-mediated H
2
uptake reaction.
Methanogenesis from Methanol at Low Temperatures by a Novel Psychrophilic Methanogen, “
Methanolobus psychrophilus
” sp. nov., Prevalent in Zoige Wetland of the Tibetan Plateau
Authors: Zhang Guishan , Jiang Na , Liu Xiaoli , Dong Xiuzhu 
Published: August 2008

ABSTRACT

The Zoige wetland of the Tibetan plateau is at permanent low temperatures and is a methane emission heartland of the plateau; however, cold-adaptive methanogens in the soil are poorly understood. In this study, a variety of methanogenic enrichments at 15°C and 30°C were obtained from the wetland soil. It was demonstrated that hydrogenotrophic methanogenesis was the most efficient type at 30°C, while methanol supported the highest methanogenesis rate at 15°C. Moreover, methanol was the only substrate to produce methane more efficiently at 15°C than at 30°C. A novel psychrophilic methanogen, strain R15, was isolated from the methanol enrichment at 15°C. Phylogenetic analysis placed strain R15 within the genus
Methanolobus
, loosely clustered with
Methanolobus taylorii
(96.7% 16S rRNA similarity). R15 produced methane from methanol, trimethylamine, and methyl sulfide and differed from other
Methanolobus
species by growing and producing methane optimally at 18°C (specific growth rate of 0.063 ± 0.001 h
−1
) and even at 0°C. Based on these characteristics, R15 was proposed to be a new species and named “
Methanolobus psychrophilus
” sp. nov. The

K
m

and
V
max
of R15 for methanol conversion were determined to be 87.5 ± 0.4 μM and 0.39 ± 0.04 mM h
−1
at 18°C, respectively, indicating a high affinity and conversion efficiency for methanol. The proportion of R15 in the soil was determined by quantitative PCR, and it accounted for 17.2% ± 2.1% of the total archaea, enumerated as 10
7
per gram of soil; the proportion was increased to 42.4% ± 2.3% in the methanol enrichment at 15°C. This study suggests that the psychrophilic methanogens in the Zoige wetland are likely to be methylotrophic and to play a role in methane emission of the wetland.
A New Huanglongbing Species, “
Candidatus
Liberibacter psyllaurous,” Found To Infect Tomato and Potato, Is Vectored by the Psyllid
Bactericera cockerelli
(Sulc)
Authors: Hansen A. K. , Trumble J. T. , Stouthamer R. , Paine T. D. 
Published: August 2008

ABSTRACT

A new huanglongbing (HLB) “
Candidatus
Liberibacter” species is genetically characterized, and the bacterium is designated “
Candidatus
Liberibacter psyllaurous.” This bacterium infects the psyllid
Bactericera cockerelli
and its solanaceous host plants potato and tomato, potentially resulting in “psyllid yellowing.” Host plant-dependent HLB transmission and variation in psyllid infection frequencies are found.
Enhancement of Recombinant Hemoglobin Production in
Escherichia coli
BL21(DE3) Containing the
Plesiomonas shigelloides
Heme Transport System
Authors: Villarreal D. M. , Phillips C. L. , Kelley A. M. , Villarreal S. , Villaloboz A. , Hernandez P. , Olson J. S. , Henderson D. P. 
Published: August 2008

ABSTRACT

To produce recombinant hemoglobin in
Escherichia coli
, sufficient intracellular heme must be present, or the protein folds improperly and is degraded. In this study, coexpression of human hemoglobin genes and
Plesiomonas shigelloides
heme transport genes enhanced recombinant hemoglobin production in
E. coli
BL21(DE3) grown in medium containing heme.
Molecular Detection of Fungal Communities in the Hawaiian Marine Sponges
Suberites zeteki
and
Mycale armata
Authors: Gao Zheng , Li Binglin , Zheng Chengchao , Wang Guangyi 
Published: August 2008

ABSTRACT

Symbiotic microbes play a variety of fundamental roles in the health and habitat ranges of their hosts. While prokaryotes in marine sponges have been broadly characterized, the diversity of sponge-inhabiting fungi has barely been explored using molecular approaches. Fungi are an important component of many marine and terrestrial ecosystems, and they may be an ecologically significant group in sponge-microbe interactions. This study tested the feasibility of using existing fungal primers for molecular analysis of sponge-associated fungal communities. None of the eight selected primer pairs yielded satisfactory results in fungal rRNA gene or internal transcribed spacer (ITS) clone library constructions. However, 3 of 10 denaturing gradient gel electrophoresis (DGGE) primer sets, which were designed to preferentially amplify fungal rRNA gene or ITS regions from terrestrial environmental samples, were successfully amplified from fungal targets in marine sponges. DGGE analysis indicated that fungal communities differ among different sponge species (
Suberites zeteki
and
Mycale armata
) and also vary between sponges and seawater. Sequence analysis of DGGE bands identified 23 and 21 fungal species from each of the two sponge species
S. zeteki
and
M. armata
, respectively. These species were representatives of 11 taxonomic orders and belonged to the phyla of
Ascomycota
(seven orders) and
Basidiomycota
(four orders). Five of these taxonomic orders (
Malasseziales, Corticiales, Polyporales, Agaricales
, and
Dothideomycetes et Chaetothyriomcetes incertae sedis
) have now been identified for the first time in marine sponges. Seven and six fungal species from
S. zeteki
and
M. armata
, respectively, are potentially new species because of their low sequence identity (≤98%) with their references in GenBank. Phylogenetic analysis indicated sponge-derived sequences were clustered into “marine fungus clades” with those from other marine habitats. This is the first report of molecular analysis of fungal communities in marine sponges, adding depth and dimension to our understanding of sponge-associated microbial communities.
Genetic Diversity of Native Bradyrhizobia Isolated from Soybeans (Glycine maxL.) in Different Agricultural-Ecological-Climatic Regions of India
Authors: Appunu Chinnaswamy , N′Zoue Angèle , Laguerre Gisèle 
Published: August 2008

ABSTRACTFifty isolates from root nodules of soybean plants sampled in five agricultural-ecological-climatic regions of India were analyzed by PCR-restriction fragment length polymorphism analysis of the 16S rRNA gene, the intergenic spacer region between the 16S and 23S rRNA genes (IGS), and thenifHandnodCgenes. Eight haplotypes assigned to theBradyrhizobiumgenus were identified, and the genetic diversity was conserved across regions. Sequence analyses of the IGS and thednaK, glnII, recA, andnifHgenes revealed three groups. One of them (26% of isolates) was assigned toBradyrhizobium liaoningense. A second group (36% of isolates) was identified asB. yuanmingensebut likely forms a new biovar able to nodulate soybean plants. The third lineage (38% of isolates) was different from all describedBradyrhizobiumspecies but showed the same symbiotic genotype asB. liaoningenseandB. japonicumbv.glycinearum.
Characterization of a Serine Proteinase Mediating Encystation of
Acanthamoeba
Authors: Moon Eun-Kyung , Chung Dong-Il , Hong Yeon-Chul , Kong Hyun-Hee 
Published: August 2008

ABSTRACT

Members of the genus
Acanthamoeba
, amphizoic protozoan parasites, are causative agents of granulomatous amoebic encephalitis and amoebic keratitis. Proteinases play a role in various biologic actions in
Acanthamoeba
, including host tissue destruction, pathogenesis, and digestion of phagocytosed food. Interestingly, we found that encystation of
Acanthamoeba
was inhibited by the serine proteinase inhibitor phenylmethanesulfonyl fluoride. In this study, we characterize a serine proteinase that is involved in mediating the encystation of
Acanthamoeba
. This encystation-mediating serine proteinase (EMSP) is shown to be highly expressed during encystation by real-time PCR and Western blot analysis. Chemically synthesized small interfering RNA against EMSP inhibited the expression of EMSP mRNA and significantly reduced the encystation efficiency of
Acanthamoeba
. An EMSP-enhanced green fluorescent protein fusion protein localized to vesicle-like structures within the amoeba. Using LysoTracker analysis, these vesicular structures were confirmed to be lysosomes. After incubation of the transfected amoeba in encystment media, small fluorescent vesicle-like structures gathered and formed ball-like structures, which were identified as colocalizing with the autophagosome. Taken together, these results indicate that EMSP plays an important role in the differentiation of
Acanthamoeba
by promoting autolysis.
Sorting Signals within the
Saccharomyces cerevisiae
Sporulation-Specific Dityrosine Transporter, Dtr1p, C Terminus Promote Golgi-to-Prospore Membrane Transport
Authors: Morishita Masayo , Engebrecht JoAnne 
Published: August 2008

ABSTRACT

During sporulation in
Saccharomyces cerevisiae
, the dityrosine transporter Dtr1p, which is required for formation of the outermost layer of the spore wall, is specifically expressed and transported to the prospore membrane, a novel double-lipid-bilayer membrane. Dtr1p consists of 572 amino acids with predicted N- and C-terminal cytoplasmic extensions and 12 transmembrane domains. Dtr1p missing the largest internal cytoplasmic loop was trapped in the endoplasmic reticulum in both mitotically dividing cells and cells induced to sporulate. Deletion of the carboxyl 15 amino acids, but not the N-terminal extension of Dtr1p, resulted in a protein that failed to localize to the prospore membrane and was instead observed in cytoplasmic puncta. The puncta colocalized with a
cis
-Golgi marker, suggesting that Dtr1p missing the last 15 amino acids was trapped in an early Golgi compartment. Deletion of the C-terminal 10 amino acids resulted in a protein that localized to the prospore membrane with a delay and accumulated in cytoplasmic puncta that partially colocalized with a
trans
-Golgi marker. Both full-length Dtr1p and Dtr1p missing the last 10 amino acids expressed in vegetative cells localized to the plasma membrane and vacuoles, while Dtr1p deleted for the carboxyl-terminal 15 amino acids was observed only at vacuoles, suggesting that transport to the prospore membrane is mediated by distinct signals from those that specify plasma membrane localization. Transfer-of-function experiments revealed that both the carboxyl transmembrane domain and the C-terminal tail are important for Golgi complex-to-prospore membrane transport.
Involvement of Sib Proteins in the Regulation of Cellular Adhesion in
Dictyostelium discoideum
Authors: Cornillon Sophie , Froquet Romain , Cosson Pierre 
Published: August 2008

ABSTRACT

Molecular mechanisms ensuring cellular adhesion have been studied in detail in
Dictyostelium
amoebae, but little is known about the regulation of cellular adhesion in these cells. Here, we show that cellular adhesion is regulated in
Dictyostelium
, notably by the concentration of a cellular secreted factor accumulating in the medium. This constitutes a quorum-sensing mechanism allowing coordinated regulation of cellular adhesion in a
Dictyostelium
population. In order to understand the mechanism underlying this regulation, we analyzed the expression of recently identified
Dictyostelium
adhesion molecules (Sib proteins) that present features also found in mammalian integrins.
sibA
and
sibC
are both expressed in vegetative
Dictyostelium
cells, but the expression of
sibC
is repressed strongly in conditions where cellular adhesion decreases. Analysis of
sibA
and
sibC
mutant cells further suggests that variations in the expression levels of
sibC
account largely for changes in cellular adhesion in response to environmental cues.