bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid Redox Signal Transmission by “Cable Bacteria” beneath a Photosynthetic Biofilm
Authors: Malkin S. Y. , Meysman F. J. R. 
Published: November 2014

ABSTRACT

Recently, long filamentous bacteria, belonging to the family
Desulfobulbaceae
, were shown to induce electrical currents over long distances in the surface layer of marine sediments. These “cable bacteria” are capable of harvesting electrons from free sulfide in deeper sediment horizons and transferring these electrons along their longitudinal axes to oxygen present near the sediment-water interface. In the present work, we investigated the relationship between cable bacteria and a photosynthetic algal biofilm. In a first experiment, we investigated sediment that hosted both cable bacteria and a photosynthetic biofilm and tested the effect of an imposed diel light-dark cycle by continuously monitoring sulfide at depth. Changes in photosynthesis at the sediment surface had an immediate and repeatable effect on sulfide concentrations at depth, indicating that cable bacteria can rapidly transmit a geochemical effect to centimeters of depth in response to changing conditions at the sediment surface. We also observed a secondary response of the free sulfide at depth manifest on the time scale of hours, suggesting that cable bacteria adjust to a moving oxygen front with a regulatory or a behavioral response, such as motility. Finally, we show that on the time scale of days, the presence of an oxygenic biofilm results in a deeper and more acidic suboxic zone, indicating that a greater oxygen supply can enable cable bacteria to harvest a greater quantity of electrons from marine sediments. Rapid acclimation strategies and highly efficient electron harvesting are likely key advantages of cable bacteria, enabling their success in high sulfide generating coastal sediments.
Temporal and Vertical Distributions of Bacterioplankton at the Gray's Reef National Marine Sanctuary
Authors: Lu Xinxin , Sun Shulei , Zhang Yu-Qin , Hollibaugh James T. , Mou Xiaozhen 
Published: November 2014

ABSTRACT

Large spatial scales and long-term shifts of bacterial community composition (BCC) in the open ocean can often be reliably predicted based on the dynamics of physical-chemical variables. The power of abiotic factors in shaping BCC on shorter time scales in shallow estuarine mixing zones is less clear. We examined the diurnal variation in BCC at different water depths in the spring and fall of 2011 at a station in the Gray's Reef National Marine Sanctuary (GRNMS). This site is located in the transition zone between the estuarine plume and continental shelf waters of the South Atlantic Bight. A total of 234,516 pyrotag sequences of bacterial 16S rRNA genes were recovered; they were taxonomically affiliated with >200 families of 23 bacterial phyla. Nonmetric multidimensional scaling analysis revealed significant differences in BCC between spring and fall samples, likely due to seasonality in the concentrations of dissolved organic carbon and nitrate plus nitrite. Within each diurnal sampling, BCC differed significantly by depth only in the spring and differed significantly between day and night only in the fall. The former variation largely tracked changes in light availability, while the latter was most correlated with concentrations of polyamines and chlorophyll
a
. Our results suggest that at the GRNMS, a coastal mixing zone, diurnal variation in BCC is attributable to the mixing of local and imported bacterioplankton rather than to bacterial growth in response to environmental changes. Our results also indicate that, like members of the
Roseobacter
clade, SAR11 bacteria may play an important role in processing dissolved organic material in coastal oceans.
Population Genetic Analysis of Streptomyces albidoflavus Reveals Habitat Barriers to Homologous Recombination in the Diversification of Streptomycetes
Authors: Cheng Kun , Rong Xiaoying , Pinto-Tomás Adrián A. , Fernández-Villalobos Marcela , Murillo-Cruz Catalina , Huang Ying 
Published: November 2014

ABSTRACT

Examining the population structure and the influence of recombination and ecology on microbial populations makes great sense for understanding microbial evolution and speciation. Streptomycetes are a diverse group of bacteria that are widely distributed in nature and a rich source of useful bioactive compounds; however, they are rarely subjected to population genetic investigations. In this study, we applied a five-gene-based multilocus sequence analysis (MLSA) scheme to 41 strains of
Streptomyces albidoflavus
derived from diverse sources, mainly insects, sea, and soil. Frequent recombination was detected in
S. albidoflavus
, supported by multiple lines of evidence from the pairwise homoplasy index (Φ

w

) test, phylogenetic discordance, the Shimodaira-Hasegawa (SH) test, and network analysis, underpinning the predominance of homologous recombination within
Streptomyces
species. A strong habitat signal was also observed in both phylogenetic and Structure 2.3.3 analyses, indicating the importance of ecological difference in shaping the population structure. Moreover, all three habitat-associated groups, particularly the entomic group, demonstrated significantly reduced levels of gene flow with one another, generally revealing habitat barriers to recombination. Therefore, a combined effect of homologous recombination and ecology is inferred for
S. albidoflavus
, where dynamic evolution is at least partly balanced by the extent that differential distributions of strains among habitats limit genetic exchange. Our study stresses the significance of ecology in microbial speciation and reveals the coexistence of homologous recombination and ecological divergence in the evolution of streptomycetes.
Novel Variant Serotype of Streptococcus suis Isolated from Piglets with Meningitis
Authors: Pan Zihao , Ma Jiale , Dong Wenyang , Song Wenchao , Wang Kaicheng , Lu Chengping , Yao Huochun 
Published: November 2014

ABSTRACTStreptococcus suisis an emerging zoonotic pathogen causing severe infections in pigs and humans. In previous studies, 33 serotypes ofS. suishave been identified using serum agglutination. Here, we describe a novelS. suisstrain, CZ130302, isolated from an outbreak of acute piglet meningitis in eastern China. Strong pathogenicity of meningitis caused by strain CZ130302 was reproduced in the BALB/c mouse model. The strain showed a high fatality rate (8/10), higher than those for known virulent serotype 2 strains P1/7 (1/10) and 9801 (2/10). Cell adhesion assay results with bEnd.3 and HEp2 cells showed that CZ130302 was significantly close to P1/7 and 9801. Both the agglutination test and its complementary test showed that strain CZ130302 had no strong cross-reaction with the other 33S. suisserotypes. The multiplex PCR assays revealed no specified bands for all four sets used to detect the other 33 serotypes. In addition, genetic analysis of the wholecpsgene clusters of all serotypes was performed in this study. The results of comparative genomics showed that thecpsgene cluster of CZ130302, which was not previously reported, showed no homology to the gene sequences of the other strains. Especially, thewzy,wzx, and acetyltransferase genes of strain CZ130302 are phylogenetically distinct from strains of the other 33 serotypes. Therefore, this study suggested that strain CZ130302 represents a novel variant serotype ofS. suis(designated serotype Chz) which has a high potential to be virulent and associated with meningitis in animals.
De Novo
Amino Acid Biosynthesis Contributes to Salmonella enterica Growth in Alfalfa Seedling Exudates
Authors: Kwan Grace , Pisithkul Tippapha , Amador-Noguez Daniel , Barak Jeri 
Published: November 2014

ABSTRACT

Salmonella enterica
is a member of the plant microbiome. Growth of
S. enterica
in sprouting-seed exudates is rapid; however, the active metabolic networks essential in this environment are unknown. To examine the metabolic requirements of
S. enterica
during growth in sprouting-seed exudates, we inoculated alfalfa seeds and identified 305
S. enterica
proteins extracted 24 h postinoculation from planktonic cells. Over half the proteins had known metabolic functions, and they are involved in over one-quarter of the known metabolic reactions. Ion and metabolite transport accounted for the majority of detected reactions. Proteins involved in amino acid transport and metabolism were highly represented, suggesting that amino acid metabolic networks may be important for
S. enterica
growth in association with roots. Amino acid auxotroph growth phenotypes agreed with the proteomic data; auxotrophs in amino acid-biosynthetic pathways that were detected in our screen developed growth defects by 48 h. When the perceived sufficiency of each amino acid was expressed as a ratio of the calculated biomass requirement to the available concentration and compared to growth of each amino acid auxotroph, a correlation between nutrient availability and bacterial growth was found. Furthermore, glutamate transport acted as a fitness factor during
S. enterica
growth in association with roots. Collectively, these data suggest that
S. enterica
metabolism is robust in the germinating-alfalfa environment; that single-amino-acid metabolic pathways are important but not essential; and that targeting central metabolic networks, rather than dedicated pathways, may be necessary to achieve dramatic impacts on bacterial growth.
Few Highly Abundant Operational Taxonomic Units Dominate within Rumen Methanogenic Archaeal Species in New Zealand Sheep and Cattle
Authors: Seedorf Henning , Kittelmann Sandra , Janssen Peter H. 
Published: November 2014

ABSTRACT

Sequencing and analyses of 16S rRNA gene amplicons were performed to estimate the composition of the rumen methanogen community in 252 samples from eight cohorts of sheep and cattle, separated into 16 different sample groups by diet, and to determine which methanogens are most prominent in the rumens of farmed New Zealand ruminants.
Methanobacteriales
(relative abundance ± standard deviation, 89.6% ± 9.8%) and
Methanomassiliicoccales
(10.4% ± 9.8%) were the two major orders and contributed 99.98% (±0.1%) to the rumen methanogen communities in the samples. Sequences from
Methanobacteriales
were almost entirely from only four different species (or clades of very closely related species). Each was detectable in at least 89% of the samples. These four species or clades were the
Methanobrevibacter gottschalkii
clade and
Methanobrevibacter ruminantium
clade with a mean abundance of 42.4% (±19.5% standard deviation) and 32.9% (±18.8%), respectively, and
Methanosphaera
sp. ISO3-F5 (8.2% ± 6.7%) and
Methanosphaera
sp. group5 (5.6% ± 5.7%). These four species or clades appeared to be primarily represented by only one or, in one case, two dominant sequence types per species or clade when the sequences were grouped into operational taxonomic units (OTUs) at 99% sequence identity. The mean relative abundance of
Methanomassiliicoccales
in the samples was relatively low but exceeded 40% in some of the treatment groups. Animal feed affected the apparent methanogen community structure of both orders, as evident from differences in relative abundances of the major OTUs in animals under different feeding regimens.
A Regulatory Feedback Loop between RpoS and SpoT Supports the Survival of Legionella pneumophila in Water
Authors: Trigui Hana , Dudyk Paulina , Oh Jinrok , Hong Jong-In , Faucher Sebastien P. 
Published: November 2014

ABSTRACT

Legionella pneumophila
is a waterborne pathogen, and survival in the aquatic environment is central to its transmission to humans. Therefore, identifying genes required for its survival in water could help prevent Legionnaires' disease outbreaks. In the present study, we investigate the role of the sigma factor RpoS in promoting survival in water, where
L. pneumophila
experiences severe nutrient deprivation. The
rpoS
mutant showed a strong survival defect compared to the wild-type strain in defined water medium. The transcriptome of the
rpoS
mutant during exposure to water revealed that RpoS represses genes associated with replication, translation, and transcription, suggesting that the mutant fails to shut down major metabolic programs. In addition, the
rpoS
mutant is transcriptionally more active than the wild-type strain after water exposure. This could be explained by a misregulation of the stringent response in the
rpoS
mutant. Indeed, the
rpoS
mutant shows an increased expression of
spoT
and a corresponding decrease in the level of (p)ppGpp, which is due to the presence of a negative feedback loop between RpoS and SpoT. Therefore, the lack of RpoS causes an aberrant regulation of the stringent response, which prevents the induction of a successful response to starvation.
Lipopolysaccharide O-Chain Core Region Required for Cellular Cohesion and Compaction of
In Vitro
and Root Biofilms Developed by Rhizobium leguminosarum
Authors: Russo Daniela M. , Abdian Patricia L. , Posadas Diana M. , Williams Alan , Vozza Nicolás , Giordano Walter , Kannenberg Elmar , Downie J. Allan , Zorreguieta Angeles 
Published: November 2014

ABSTRACT

The formation of biofilms is an important survival strategy allowing rhizobia to live on soil particles and plant roots. Within the microcolonies of the biofilm developed by
Rhizobium leguminosarum
, rhizobial cells interact tightly through lateral and polar connections, forming organized and compact cell aggregates. These microcolonies are embedded in a biofilm matrix, whose main component is the acidic exopolysaccharide (EPS). Our work shows that the O-chain core region of the
R. leguminosarum
lipopolysaccharide (LPS) (which stretches out of the cell surface) strongly influences bacterial adhesive properties and cell-cell cohesion. Mutants defective in the O chain or O-chain core moiety developed premature microcolonies in which lateral bacterial contacts were greatly reduced. Furthermore, cell-cell interactions within the microcolonies of the LPS mutants were mediated mostly through their poles, resulting in a biofilm with an altered three-dimensional structure and increased thickness. In addition, on the root epidermis and on root hairs, O-antigen core-defective strains showed altered biofilm patterns with the typical microcolony compaction impaired. Taken together, these results indicate that the surface-exposed moiety of the LPS is crucial for proper cell-to-cell interactions and for the formation of robust biofilms on different surfaces.
MS2 Virus Inactivation by Atmospheric-Pressure Cold Plasma Using Different Gas Carriers and Power Levels
Authors: Wu Yan , Liang Yongdong , Wei Kai , Li Wei , Yao Maosheng , Zhang Jue , Grinshpun Sergey A. 
Published: November 2014

ABSTRACT

In this study, airborne MS2 bacteriophages were exposed for subsecond time intervals to atmospheric-pressure cold plasma (APCP) produced using different power levels (20, 24, and 28 W) and gas carriers (ambient air, Ar-O
2
[2%, vol/vol], and He-O
2
[2%, vol/vol]). In addition, waterborne MS2 viruses were directly subjected to the APCP treatment for up to 3 min. MS2 viruses with and without the APCP exposure were examined by scanning electron microscopy (SEM), reverse transcription-PCR (RT-PCR), and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Viral inactivation was shown to exhibit linear relationships with the APCP generation power and exposure time (
R
2
> 0.95 for all energy levels tested) up to 95% inactivation (1.3-log reduction) after a subsecond airborne exposure at 28 W; about the same inactivation level was achieved for waterborne viruses with an exposure time of less than 1 min. A larger amount of reactive oxygen species (ROS), such as atomic oxygen, in APCP was detected for a higher generation power with Ar-O
2
and He-O
2
gas carriers. SEM images, SDS-PAGE, and agarose gel analysis of exposed waterborne viruses showed various levels of damage to both surface proteins and their related RNA genes after the APCP exposure, thus leading to the loss of their viability and infectivity.
Induction of Humoral and Cell-Mediated Immune Responses by Hepatitis B Virus Epitope Displayed on the Virus-Like Particles of Prawn Nodavirus
Authors: Yong Chean Yeah , Yeap Swee Keong , Goh Zee Hong , Ho Kok Lian , Omar Abdul Rahman , Tan Wen Siang 
Published: November 2014

ABSTRACTHepatitis B virus (HBV) is a deadly pathogen that has killed countless people worldwide.Saccharomyces cerevisiae-derived HBV vaccines based upon hepatitis B surface antigen (HBsAg) is highly effective. However, the emergence of vaccine escape mutants due to mutations on the HBsAg and polymerase genes has produced a continuous need for the development of new HBV vaccines. In this study, the “a” determinant within HBsAg was displayed on the recombinant capsid protein ofMacrobrachium rosenbergiinodavirus (MrNV), which can be purified easily in a single step through immobilized metal affinity chromatography (IMAC). The purified protein self-assembled into virus-like particles (VLPs) when observed under a transmission electron microscope (TEM). Immunization of BALB/c mice with this chimeric protein induced specific antibodies against the “a” determinant. In addition, it induced significantly more natural killer and cytotoxic T cells, as well as an increase in interferon gamma (IFN-γ) secretion, which are vital for virus clearance. Collectively, these findings demonstrated that the MrNV capsid protein is a potential carrier for the HBV “a” determinant, which can be further extended to display other foreign epitopes. This paper is the first to report the application of MrNV VLPs as a novel platform to display foreign epitopes.
Ctk1 Function Is Necessary for Full Translation Initiation Activity in Saccharomyces cerevisiae
Authors: Coordes Britta , Brünger Katharina M. , Burger Kaspar , Soufi Boumediene , Horenk Juliane , Eick Dirk , Olsen Jesper V. , Sträßer Katja 
Published: November 2014

ABSTRACT

Translation is a fundamental and highly regulated cellular process. Previously, we reported that the kinase and transcription elongation factor Ctk1 increases fidelity during translation elongation in
Saccharomyces cerevisiae
. Here, we show that loss of Ctk1 function also affects the initiation step of translation. Translation active extracts from Ctk1-depleted cells show impaired translation activity of capped mRNA, but not mRNA reporters containing the cricket paralysis virus (CrPV) internal ribosome entry site (IRES). Furthermore, the formation of 80S initiation complexes is decreased, which is probably due to reduced subunit joining. In addition, we determined the changes in the phosphorylation pattern of a ribosome enriched fraction after depletion of Ctk1. Thus, we provide a catalogue of phosphoproteomic changes dependent on Ctk1. Taken together, our data suggest a stimulatory function of Ctk1 in 80S formation during translation initiation.
In Vitro
Alterations Do Not Reflect a Requirement for Host Cell Cycle Progression during Plasmodium Liver Stage Infection
Authors: Hanson Kirsten K. , March Sandra , Ng Shengyong , Bhatia Sangeeta N. , Mota Maria M. 
Published: November 2014

ABSTRACT

Prior to invading nonreplicative erythrocytes,
Plasmodium
parasites undergo their first obligate step in the mammalian host inside hepatocytes, where each sporozoite replicates to generate thousands of merozoites. While normally quiescent, hepatocytes retain proliferative capacity and can readily reenter the cell cycle in response to diverse stimuli. Many intracellular pathogens, including protozoan parasites, manipulate the cell cycle progression of their host cells for their own benefit, but it is not known whether the hepatocyte cell cycle plays a role during
Plasmodium
liver stage infection. Here, we show that
Plasmodium
parasites can be observed in mitotic hepatoma cells throughout liver stage development, where they initially reduce the likelihood of mitosis and ultimately lead to significant acquisition of a binucleate phenotype. However, hepatoma cells pharmacologically arrested in S phase still support robust and complete
Plasmodium
liver stage development, which thus does not require cell cycle progression in the infected cell
in vitro
. Furthermore, murine hepatocytes remain quiescent throughout
in vivo
infection with either
Plasmodium berghei
or
Plasmodium yoelii
, as do
Plasmodium falciparum
-infected primary human hepatocytes, demonstrating that the rapid and prodigious growth of liver stage parasites is accomplished independent of host hepatocyte cell cycle progression during natural infection.
The Krebs Cycle Enzyme α-Ketoglutarate Decarboxylase Is an Essential Glycosomal Protein in Bloodstream African Trypanosomes
Authors: Sykes Steven , Szempruch Anthony , Hajduk Stephen 
Published: November 2014

ABSTRACT

α-Ketoglutarate decarboxylase (α-KDE1) is a Krebs cycle enzyme found in the mitochondrion of the procyclic form (PF) of
Trypanosoma brucei
. The bloodstream form (BF) of
T. brucei
lacks a functional Krebs cycle and relies exclusively on glycolysis for ATP production. Despite the lack of a functional Krebs cycle, α-KDE1 was expressed in BF
T. brucei
and RNA interference knockdown of α-KDE1 mRNA resulted in rapid growth arrest and killing. Cell death was preceded by progressive swelling of the flagellar pocket as a consequence of recruitment of both flagellar and plasma membranes into the pocket. BF
T. brucei
expressing an epitope-tagged copy of α-KDE1 showed localization to glycosomes and not the mitochondrion. We used a cell line transfected with a reporter construct containing the N-terminal sequence of α-KDE1 fused to green fluorescent protein to examine the requirements for glycosome targeting. We found that the N-terminal 18 amino acids of α-KDE1 contain overlapping mitochondrion- and peroxisome-targeting sequences and are sufficient to direct localization to the glycosome in BF
T. brucei
. These results suggest that α-KDE1 has a novel moonlighting function outside the mitochondrion in BF
T. brucei
.
Insect Stage-Specific Adenylate Cyclases Regulate Social Motility in African Trypanosomes
Authors: Lopez Miguel A. , Saada Edwin A. , Hill Kent L. 
Published: November 2014

ABSTRACT

Sophisticated systems for cell-cell communication enable unicellular microbes to act as multicellular entities capable of group-level behaviors that are not evident in individuals. These group behaviors influence microbe physiology, and the underlying signaling pathways are considered potential drug targets in microbial pathogens.
Trypanosoma brucei
is a protozoan parasite that causes substantial human suffering and economic hardship in some of the most impoverished regions of the world.
T. brucei
lives on host tissue surfaces during transmission through its tsetse fly vector, and cultivation on surfaces causes the parasites to assemble into multicellular communities in which individual cells coordinate their movements in response to external signals. This behavior is termed “social motility,” based on its similarities with surface-induced social motility in bacteria, and it demonstrates that trypanosomes are capable of group-level behavior. Mechanisms governing
T. brucei
social motility are unknown. Here we report that a subset of receptor-type adenylate cyclases (ACs) in the trypanosome flagellum regulate social motility. RNA interference-mediated knockdown of adenylate cyclase 6 (AC6), or dual knockdown of AC1 and AC2, causes a hypersocial phenotype but has no discernible effect on individual cells in suspension culture. Mutation of the AC6 catalytic domain phenocopies AC6 knockdown, demonstrating that loss of adenylate cyclase activity is responsible for the phenotype. Notably, knockdown of other ACs did not affect social motility, indicating segregation of AC functions. These studies reveal interesting parallels in systems that control social behavior in trypanosomes and bacteria and provide insight into a feature of parasite biology that may be exploited for novel intervention strategies.