bluuebunny/crossref_metadata_2025_split huggingface dataset:
Flocculation of Escherichia coli Cells in Association with Enhanced Production of Outer Membrane Vesicles
Authors: Ojima Yoshihiro , Nguyen Minh Hong , Yajima Reiki , Taya Masahito 
Published: June 2015

ABSTRACT

Microbial flocculation is a phenomenon of aggregation of dispersed bacterial cells in the form of flocs or flakes. In this study, the mechanism of spontaneous flocculation of
Escherichia coli
cells by overexpression of the
bcsB
gene was investigated. The flocculation induced by overexpression of
bcsB
was consistent among the various
E. coli
strains examined, including the K-12, B, and O strains, with flocs that resembled paper scraps in structure being about 1 to 2 mm. The distribution of green fluorescent protein-labeled
E. coli
cells within the floc structure was investigated by three-dimensional confocal laser scanning microscopy. Flocs were sensitive to proteinase K, indicating that the main component of the flocs was proteinous. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis and nano-liquid chromatography tandem mass spectrometry analyses of the flocs strongly suggested the involvement of outer membrane vesicles (OMVs) in
E. coli
flocculation. The involvement of OMVs in flocculation was supported by transmission electron microscopy observation of flocs. Furthermore,
bcsB
-induced
E. coli
flocculation was greatly suppressed in strains with hypovesiculation phenotypes (Δ
dsbA
and Δ
dsbB
strains). Thus, our results demonstrate the strong correlation between spontaneous flocculation and enhanced OMV production of
E. coli
cells.
Identification and Heterologous Expression of the Chaxamycin Biosynthesis Gene Cluster from Streptomyces leeuwenhoekii
Authors: Castro Jean Franco , Razmilic Valeria , Gomez-Escribano Juan Pablo , Andrews Barbara , Asenjo Juan A. , Bibb Mervyn J. 
Published: June 2015

ABSTRACT

Streptomyces leeuwenhoekii
, isolated from the hyperarid Atacama Desert, produces the new ansamycin-like compounds chaxamycins A to D, which possess potent antibacterial activity and moderate antiproliferative activity. We report the development of genetic tools to manipulate
S. leeuwenhoekii
and the identification and partial characterization of the 80.2-kb chaxamycin biosynthesis gene cluster, which was achieved by both mutational analysis in the natural producer and heterologous expression in
Streptomyces coelicolor
A3(2) strain M1152. Restoration of chaxamycin production in a nonproducing Δ
cxmK
mutant (
cxmK
encodes 3-amino-5-hydroxybenzoic acid [AHBA] synthase) was achieved by supplementing the growth medium with AHBA, suggesting that mutasynthesis may be a viable approach for the generation of novel chaxamycin derivatives.
Pyrobaculum yellowstonensis Strain WP30 Respires on Elemental Sulfur and/or Arsenate in Circumneutral Sulfidic Geothermal Sediments of Yellowstone National Park
Authors: Jay Z. J. , Beam J. P. , Dohnalkova A. , Lohmayer R. , Bodle B. , Planer-Friedrich B. , Romine M. , Inskeep W. P. 
Published: June 2015

ABSTRACT

Thermoproteales
(phylum
Crenarchaeota
) populations are abundant in high-temperature (>70°C) environments of Yellowstone National Park (YNP) and are important in mediating the biogeochemical cycles of sulfur, arsenic, and carbon. The objectives of this study were to determine the specific physiological attributes of the isolate
Pyrobaculum yellowstonensis
strain WP30, which was obtained from an elemental sulfur sediment (Joseph's Coat Hot Spring [JCHS], 80°C, pH 6.1, 135 μM As) and relate this organism to geochemical processes occurring
in situ
. Strain WP30 is a chemoorganoheterotroph and requires elemental sulfur and/or arsenate as an electron acceptor. Growth in the presence of elemental sulfur and arsenate resulted in the formation of thioarsenates and polysulfides. The complete genome of this organism was sequenced (1.99 Mb, 58% G+C content), revealing numerous metabolic pathways for the degradation of carbohydrates, amino acids, and lipids. Multiple dimethyl sulfoxide-molybdopterin (DMSO-MPT) oxidoreductase genes, which are implicated in the reduction of sulfur and arsenic, were identified. Pathways for the
de novo
synthesis of nearly all required cofactors and metabolites were identified. The comparative genomics of
P. yellowstonensis
and the assembled metagenome sequence from JCHS showed that this organism is highly related (∼95% average nucleotide sequence identity) to
in situ
populations. The physiological attributes and metabolic capabilities of
P. yellowstonensis
provide an important foundation for developing an understanding of the distribution and function of these populations in YNP.
Nitrite-Oxidizing Bacterium Nitrobacter winogradskyi Produces
N
-Acyl-Homoserine Lactone Autoinducers
Authors: Mellbye Brett L. , Bottomley Peter J. , Sayavedra-Soto Luis A. 
Published: June 2015

ABSTRACT

Nitrobacter winogradskyi
is a chemolithotrophic bacterium that plays a role in the nitrogen cycle by oxidizing nitrite to nitrate. Here, we demonstrate a functional
N
-acyl-homoserine lactone (acyl-HSL) synthase in this bacterium. The
N. winogradskyi
genome contains genes encoding a putative acyl-HSL autoinducer synthase (nwi0626,
nwiI
) and a putative acyl-HSL autoinducer receptor (nwi0627,
nwiR
) with amino acid sequences 38 to 78% identical to those in
Rhodopseudomonas palustris
and other
Rhizobiales
. Expression of
nwiI
and
nwiR
correlated with acyl-HSL production during culture.
N. winogradskyi
produces two distinct acyl-HSLs,
N
-decanoyl-
l
-homoserine lactone (C
10
-HSL) and a monounsaturated acyl-HSL (C
10:1
-HSL), in a cell-density- and growth phase-dependent manner, during batch and chemostat culture. The acyl-HSLs were detected by bioassay and identified by ultraperformance liquid chromatography with information-dependent acquisition mass spectrometry (UPLC-IDA-MS). The C=C bond in C
10:1
-HSL was confirmed by conversion into bromohydrin and detection by UPLC-IDA-MS.
The United States Culture Collection Network (USCCN): Enhancing Microbial Genomics Research through Living Microbe Culture Collections
Authors: Boundy-Mills Kyria , Hess Matthias , Bennett A. Rick , Ryan Matthew , Kang Seogchan , Nobles David , Eisen Jonathan A. , Inderbitzin Patrik , Sitepu Irnayuli R. , Torok Tamas , Brown Daniel R. , Cho Juliana , Wertz John E. , Mukherjee Supratim , Cady Sherry L. , McCluskey Kevin 
Published: June 2015

ABSTRACT

The mission of the United States Culture Collection Network (USCCN;
http://usccn.org
) is “to facilitate the safe and responsible utilization of microbial resources for research, education, industry, medicine, and agriculture for the betterment of human kind.” Microbial culture collections are a key component of life science research, biotechnology, and emerging global biobased economies. Representatives and users of several microbial culture collections from the United States and Europe gathered at the University of California, Davis, to discuss how collections of microorganisms can better serve users and stakeholders and to showcase existing resources available in public culture collections.
Identification of a Novel Dye-Decolorizing Peroxidase, EfeB, Translocated by a Twin-Arginine Translocation System in Streptococcus thermophilus CGMCC 7.179
Authors: Zhang Chenchen , Xin Yongping , Wang Yue , Guo Tingting , Lu Shiyi , Kong Jian 
Published: June 2015

ABSTRACT

Streptococcus thermophilus
is a facultative anaerobic bacterium that has the ability to grow and survive in aerobic environments, but the mechanism for this remains unclear. In this study, the
efeB
gene, encoding a dye-decolorizing peroxidase, was identified in the genome of
Streptococcus thermophilus
CGMCC 7.179, and purified EfeB was able to decolorize reactive blue 5. Strikingly, genes encoding two components (TatA and TatC) of the twin-arginine translocation (TAT) system were also found in the same operon with the
efeB
gene. Knocking out
efeB
or
tatC
resulted in decreased growth of the strain under aerobic conditions, and complementation of the
efeB
-deficient strains with the
efeB
gene enhanced the biomass of the hosts only in the presence of the
tatC
gene. Moreover, it was proved for both
S. thermophilus
CGMCC 7.179 and
Escherichia coli
DE3 that EfeB could be translocated by the TAT system of
S. thermophilus
. In addition, the transcriptional levels of
efeB
and
tatC
increased when the strain was cultured under aerobic conditions. Overall, these results provide the first evidence that EfeB plays a role in protecting cells of
S. thermophilus
from oxidative stress, with the assistance of the TAT system.
New Insight into Microbial Iron Oxidation as Revealed by the Proteomic Profile of an Obligate Iron-Oxidizing Chemolithoautotroph
Authors: Barco Roman A. , Emerson David , Sylvan Jason B. , Orcutt Beth N. , Jacobson Meyers Myrna E. , Ramírez Gustavo A. , Zhong John D. , Edwards Katrina J. 
Published: June 2015

ABSTRACT

Microaerophilic, neutrophilic, iron-oxidizing bacteria (FeOB) grow via the oxidation of reduced Fe(II) at or near neutral pH, in the presence of oxygen, making them relevant in numerous environments with elevated Fe(II) concentrations. However, the biochemical mechanisms for Fe(II) oxidation by these neutrophilic FeOB are unknown, and genetic markers for this process are unavailable. In the ocean, microaerophilic microorganisms in the genus
Mariprofundus
of the class
Zetaproteobacteria
are the only organisms known to chemolithoautotrophically oxidize Fe and concurrently biomineralize it in the form of twisted stalks of iron oxyhydroxides. The aim of this study was to identify highly expressed proteins associated with the electron transport chain of microaerophilic, neutrophilic FeOB. To this end,
Mariprofundus ferrooxydans
PV-1 was cultivated, and its proteins were extracted, assayed for redox activity, and analyzed via liquid chromatography-tandem mass spectrometry for identification of peptides. The results indicate that a cytochrome
c
4
,
cbb
3
-type cytochrome oxidase subunits, and an outer membrane cytochrome
c
were among the most highly expressed proteins and suggest an involvement in the process of aerobic, neutrophilic bacterial Fe oxidation. Proteins associated with alternative complex III, phosphate transport, carbon fixation, and biofilm formation were abundant, consistent with the lifestyle of
Mariprofundus
.
Microbial Community Composition, Functions, and Activities in the Gulf of Mexico 1 Year after the Deepwater Horizon Accident
Authors: Yergeau Etienne , Maynard Christine , Sanschagrin Sylvie , Champagne Julie , Juck David , Lee Kenneth , Greer Charles W. 
Published: June 2015

ABSTRACT

Several studies have assessed the effects of the released oil on microbes, either during or immediately after the Deepwater Horizon accident. However, little is known about the potential longer-term persistent effects on microbial communities and their functions. In this study, one water column station near the wellhead (3.78 km southwest of the wellhead), one water column reference station outside the affected area (37.77 km southeast of the wellhead), and deep-sea sediments near the wellhead (3.66 km southeast of the wellhead) were sampled 1 year after the capping of the well. In order to analyze microbial community composition, function, and activity, we used metagenomics, metatranscriptomics, and mineralization assays. Mineralization of hexadecane was significantly higher at the wellhead station at a depth of ∼1,200 m than at the reference station. Community composition based on taxonomical or functional data showed that the samples taken at a depth of ∼1,200 m were significantly more dissimilar between the stations than at other depths (surface, 100 m, 750 m, and >1,500 m). Both
Bacteria
and
Archaea
showed reduced activity at depths of ∼1,200 m when the wellhead station was compared to the reference station, and their activity was significantly higher in surficial sediments than in 10-cm sediments. Surficial sediments also harbored significantly different active genera than did 5- and 10-cm sediments. For the remaining microbial parameters assessed, no significant differences could be observed between the wellhead and reference stations and between surface and 5- to 10-cm-deep sediments.
Ectomycorrhizal Communities on the Roots of Two Beech (Fagus sylvatica) Populations from Contrasting Climates Differ in Nitrogen Acquisition in a Common Environment
Authors: Leberecht Martin , Dannenmann Michael , Gschwendtner Silvia , Bilela Silvija , Meier Rudolf , Simon Judy , Rennenberg Heinz , Schloter Michael , Polle Andrea 
Published: June 2015

ABSTRACT

Beech (
Fagus sylvatica
), a dominant forest species in Central Europe, competes for nitrogen with soil microbes and suffers from N limitation under dry conditions. We hypothesized that ectomycorrhizal communities and the free-living rhizosphere microbes from beech trees from sites with two contrasting climatic conditions exhibit differences in N acquisition that contribute to differences in host N uptake and are related to differences in host belowground carbon allocation. To test these hypotheses, young trees from the natural regeneration of two genetically similar populations, one from dryer conditions (located in an area with a southwest exposure [SW trees]) and the other from a cooler, moist climate (located in an area with a northeast exposure [NE trees]), were transplanted into a homogeneous substrate in the same environment and labeled with
13
CO
2
and
15
NH
4
+
. Free-living rhizosphere microbes were characterized by marker genes for the N cycle, but no differences between the rhizospheres of SW or NE trees were found. Lower
15
N enrichment was found in the ectomycorrhizal communities of the NE tree communities than the SW tree communities, whereas no significant differences in
15
N enrichment were observed for nonmycorrhizal root tips of SW and NE trees. Neither the ectomycorrhizal communities nor the nonmycorrhizal root tips originating from NE and SW trees showed differences in
13
C signatures. Because the level of
15
N accumulation in fine roots and the amount transferred to leaves were lower in NE trees than SW trees, our data support the suggestion that the ectomycorrhizal community influences N transfer to its host and demonstrate that the fungal community from the dry condition was more efficient in N acquisition when environmental constraints were relieved. These findings highlight the importance of adapted ectomycorrhizal communities for forest nutrition in a changing climate.
Methanotrophic and Methanogenic Communities in Swiss Alpine Fens Dominated by Carex rostrata and Eriophorum angustifolium
Authors: Cheema Simrita , Zeyer Josef , Henneberger Ruth 
Published: June 2015

ABSTRACT

Vascular plants play a key role in controlling CH
4
emissions from natural wetlands, because they influence CH
4
production, oxidation, and transport to the atmosphere. Here we investigated differences in the abundance and composition of methanotrophic and methanogenic communities in three Swiss alpine fens dominated by different vascular plant species under natural conditions. The sampling locations either were situated at geographically distinct sites with different physicochemical properties but the same dominant plant species (
Carex rostrata
) or were located within the same site, showing comparable physicochemical pore water properties, but had different plant species (
C. rostrata
or
Eriophorum angustifolium
). All three locations were permanently submerged and showed high levels of CH
4
emissions (80.3 to 184.4 mg CH
4
m
−2
day
−1
). Soil samples were collected from three different depths with different pore water CH
4
and O
2
concentrations and were analyzed for
pmoA
and
mcrA
gene and transcript abundance and community composition, as well as soil structure. The dominant plant species appeared to have a significant influence on the composition of the active methanotrophic communities (transcript level), while the methanogenic communities differed significantly only at the gene level. Yet no plant species-specific microbial taxa were discerned. Moreover, for all communities, differences in composition were more pronounced with the site (i.e., with different physicochemical properties) than with the plant species. Moreover, depth significantly influenced the composition of the active methanotrophic communities. Differences in abundance were generally low, and active methanotrophs and methanogens coexisted at all three locations and depths independently of CH
4
and O
2
concentrations or plant species.
Development and Evaluation of Three Real-Time PCR Assays for Genotyping and Source Tracking Cryptosporidium spp. in Water
Authors: Li Na , Neumann Norman F. , Ruecker Norma , Alderisio Kerri A. , Sturbaum Gregory D. , Villegas Eric N. , Chalmers Rachel , Monis Paul , Feng Yaoyu , Xiao Lihua 
Published: June 2015

ABSTRACT

The occurrence of
Cryptosporidium
oocysts in drinking source water can present a serious public health risk. To rapidly and effectively assess the source and human-infective potential of
Cryptosporidium
oocysts in water, sensitive detection and correct identification of oocysts to the species level (genotyping) are essential. In this study, we developed three real-time PCR genotyping assays, two targeting the small-subunit (SSU) rRNA gene (18S-LC1 and 18S-LC2 assays) and one targeting the 90-kDa heat shock protein (hsp90) gene (hsp90 assay), and evaluated the sensitivity and
Cryptosporidium
species detection range of these assays. Using fluorescence resonance energy transfer probes and melt curve analysis, the 18S-LC1 and hsp90 assays could differentiate common human-pathogenic species (
C. parvum
,
C. hominis
, and
C. meleagridis
), while the 18S-LC2 assay was able to differentiate nonpathogenic species (such as
C. andersoni
) from human-pathogenic ones commonly found in source water. In sensitivity evaluations, the 18S-LC2 and hsp90 genotyping assays could detect as few as 1
Cryptosporidium
oocyst per sample. Thus, the 18S-LC2 and hsp90 genotyping assays might be used in environmental monitoring, whereas the 18S-LC1 genotyping assay could be useful for genotyping
Cryptosporidium
spp. in clinical specimens or wastewater samples.
CO Metabolism in the Acetogen Acetobacterium woodii
Authors: Bertsch Johannes , Müller Volker 
Published: June 2015

ABSTRACT

The Wood-Ljungdahl pathway allows acetogenic bacteria to grow on a number of one-carbon substrates, such as carbon dioxide, formate, methyl groups, or even carbon monoxide. Since carbon monoxide alone or in combination with hydrogen and carbon dioxide (synthesis gas) is an increasingly important feedstock for third-generation biotechnology, we studied CO metabolism in the model acetogen
Acetobacterium woodii
. When cells grew on H
2
-CO
2
, addition of 5 to 15% CO led to higher final optical densities, indicating the utilization of CO as a cosubstrate. However, the growth rate was decreased by the presence of small amounts of CO, which correlated with an inhibition of H
2
consumption. Experiments with resting cells revealed that the degree of inhibition of H
2
consumption was a function of the CO concentration. Since the hydrogen-dependent CO
2
reductase (HDCR) of
A. woodii
is known to be very sensitive to CO, we speculated that cells may be more tolerant toward CO when growing on formate, the product of the HDCR reaction. Indeed, addition of up to 25% CO did not influence growth rates on formate, while the final optical densities and the production of acetate increased. Higher concentrations (75 and 100%) led to a slight inhibition of growth and to decreasing rates of formate and CO consumption. Experiments with resting cells revealed that the HDCR is a site of CO inhibition. In contrast,
A. woodii
was not able to grow on CO as a sole carbon and energy source, and growth on fructose-CO or methanol-CO was not observed.
Secretion of Polypeptide Crystals from Tetrahymena thermophila Secretory Organelles (Mucocysts) Depends on Processing by a Cysteine Cathepsin, Cth4p
Authors: Kumar Santosh , Briguglio Joseph S. , Turkewitz Aaron P. 
Published: June 2015

ABSTRACT

In many organisms, sophisticated mechanisms facilitate release of peptides in response to extracellular stimuli. In the ciliate
Tetrahymena thermophila
, efficient peptide secretion depends on specialized vesicles called mucocysts that contain dense crystalline cores that expand rapidly during exocytosis. Core assembly depends of endoproteolytic cleavage of mucocyst proproteins by an aspartyl protease, cathepsin 3 (
CTH3
). Here, we show that a second enzyme identified by expression profiling, Cth4p, is also required for processing of proGrl proteins and for assembly of functional mucocysts. Cth4p is a cysteine cathepsin that localizes partially to endolysosomal structures and appears to act downstream of, and may be activated by, Cth3p. Disruption of
CTH4
results in cells (Δ
cth4
) that show aberrant trimming of Grl proproteins, as well as grossly aberrant mucocyst exocytosis. Surprisingly, Δ
cth4
cells succeed in assembling crystalline mucocyst cores. However, those cores do not undergo normal directional expansion during exocytosis, and they thus fail to efficiently extrude from the cells. We could phenocopy the Δ
cth4
defects by mutating conserved catalytic residues, indicating that the
in vivo
function of Cth4p is enzymatic. Our results indicate that as for canonical proteins packaged in animal secretory granules, the maturation of mucocyst proproteins involves sequential processing steps. The Δ
cth4
defects uncouple, in an unanticipated way, the assembly of mucocyst cores and their subsequent expansion and thereby reveal a previously unsuspected aspect of polypeptide secretion in ciliates.
Acetylcholine Protects against Candida albicans Infection by Inhibiting Biofilm Formation and Promoting Hemocyte Function in a Galleria mellonella Infection Model
Authors: Rajendran Ranjith , Borghi Elisa , Falleni Monica , Perdoni Federica , Tosi Delfina , Lappin David F. , O'Donnell Lindsay , Greetham Darren , Ramage Gordon , Nile Christopher 
Published: June 2015

ABSTRACT

Both neuronal acetylcholine and nonneuronal acetylcholine have been demonstrated to modulate inflammatory responses. Studies investigating the role of acetylcholine in the pathogenesis of bacterial infections have revealed contradictory findings with regard to disease outcome. At present, the role of acetylcholine in the pathogenesis of fungal infections is unknown. Therefore, the aim of this study was to determine whether acetylcholine plays a role in fungal biofilm formation and the pathogenesis of
Candida albicans
infection. The effect of acetylcholine on
C. albicans
biofilm formation and metabolism
in vitro
was assessed using a crystal violet assay and phenotypic microarray analysis. Its effect on the outcome of a
C. albicans
infection, fungal burden, and biofilm formation were investigated
in vivo
using a
Galleria mellonella
infection model. In addition, its effect on modulation of host immunity to
C. albicans
infection was also determined
in vivo
using hemocyte counts, cytospin analysis, larval histology, lysozyme assays, hemolytic assays, and real-time PCR. Acetylcholine was shown to have the ability to inhibit
C. albicans
biofilm formation
in vitro
and
in vivo
. In addition, acetylcholine protected
G. mellonella
larvae from
C. albicans
infection mortality. The
in vivo
protection occurred through acetylcholine enhancing the function of hemocytes while at the same time inhibiting
C. albicans
biofilm formation. Furthermore, acetylcholine also inhibited inflammation-induced damage to internal organs. This is the first demonstration of a role for acetylcholine in protection against fungal infections, in addition to being the first report that this molecule can inhibit
C. albicans
biofilm formation. Therefore, acetylcholine has the capacity to modulate complex host-fungal interactions and plays a role in dictating the pathogenesis of fungal infections.