bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of the Levels of Bacterial Diversity in Freshwater, Intertidal Wetland, and Marine Sediments by Using Millions of Illumina Tags
Authors: Wang Yu , Sheng Hua-Fang , He Yan , Wu Jin-Ya , Jiang Yun-Xia , Tam Nora Fung-Yee , Zhou Hong-Wei 
Published: September 2012

ABSTRACT

Sediment, a special realm in aquatic environments, has high microbial diversity. While there are numerous reports about the microbial community in marine sediment, freshwater and intertidal sediment communities have been overlooked. The present study determined millions of Illumina reads for a comparison of bacterial communities in freshwater, intertidal wetland, and marine sediments along Pearl River, China, using a technically consistent approach. Our results show that both taxon richness and evenness were the highest in freshwater sediment, medium in intertidal sediment, and lowest in marine sediment. The high number of sequences allowed the determination of a wide variety of bacterial lineages in all sediments for reliable statistical analyses. Principal component analysis showed that the three types of communities could be well separated from phylum to operational taxonomy unit (OTU) levels, and the OTUs from abundant to rare showed satisfactory resolutions. Statistical analysis (LEfSe) demonstrated that the freshwater sediment was enriched with
Acidobacteria
,
Nitrospira
,
Verrucomicrobia
,
Alphaproteobacteria
, and
Betaproteobacteria
. The intertidal sediment had a unique community with diverse primary producers (such as
Chloroflexi
,
Bacillariophyta
,
Gammaproteobacteria
, and
Epsilonproteobacteria
) as well as saprophytic microbes (such as
Actinomycetales
,
Bacteroidetes
, and
Firmicutes
). The marine sediment had a higher abundance of
Gammaproteobacteria
and
Deltaproteobacteria
, which were mainly involved in sulfate reduction in anaerobic conditions. These results are helpful for a systematic understanding of bacterial communities in natural sediment environments.
Genetic Barcodes for Improved Environmental Tracking of an Anthrax Simulant
Authors: Buckley Patricia , Rivers Bryan , Katoski Sarah , Kim Michael H. , Kragl F. Joseph , Broomall Stacey , Krepps Michael , Skowronski Evan W. , Rosenzweig C. Nicole , Paikoff Sari , Emanuel Peter , Gibbons Henry S. 
Published: September 2012

ABSTRACT

The development of realistic risk models that predict the dissemination, dispersion and persistence of potential biothreat agents have utilized nonpathogenic surrogate organisms such as
Bacillus atrophaeus
subsp.
globigii
or commercial products such as
Bacillus thuringiensis
subsp.
kurstaki
. Comparison of results from outdoor tests under different conditions requires the use of genetically identical strains; however, the requirement for isogenic strains limits the ability to compare other desirable properties, such as the behavior in the environment of the same strain prepared using different methods. Finally, current methods do not allow long-term studies of persistence or reaerosolization in test sites where simulants are heavily used or in areas where
B. thuringiensis
subsp.
kurstaki
is applied as a biopesticide. To create a set of genetically heterogeneous yet phenotypically indistinguishable strains so that variables intrinsic to simulations (e.g., sample preparation) can be varied and the strains can be tested under otherwise identical conditions, we have developed a strategy of introducing small genetic signatures (“barcodes”) into neutral regions of the genome. The barcodes are stable over 300 generations and do not impact
in vitro
growth or sporulation. Each barcode contains common and specific tags that allow differentiation of marked strains from wild-type strains and from each other. Each tag is paired with specific real-time PCR assays that facilitate discrimination of barcoded strains from wild-type strains and from each other. These uniquely barcoded strains will be valuable tools for research into the environmental fate of released organisms by providing specific artificial detection signatures.
Effects of Iron and Nitrogen Limitation on Sulfur Isotope Fractionation during Microbial Sulfate Reduction
Authors: Sim Min Sub , Ono Shuhei , Bosak Tanja 
Published: September 2012

ABSTRACT

Sulfate-reducing microbes utilize sulfate as an electron acceptor and produce sulfide that is depleted in heavy isotopes of sulfur relative to sulfate. Thus, the distribution of sulfur isotopes in sediments can trace microbial sulfate reduction (MSR), and it also has the potential to reflect the physiology of sulfate-reducing microbes. This study investigates the relationship between the availability of iron and reduced nitrogen and the magnitude of S-isotope fractionation during MSR by a marine sulfate-reducing bacterium, DMSS-1, a
Desulfovibrio
species, isolated from salt marsh in Cape Cod, MA. Submicromolar levels of iron increase sulfur isotope fractionation by about 50% relative to iron-replete cultures of DMSS-1. Iron-limited cultures also exhibit decreased cytochrome
c
-to-total protein ratios and cell-specific sulfate reduction rates (csSRR), implying changes in the electron transport chain that couples carbon and sulfur metabolisms. When DMSS-1 fixes nitrogen in ammonium-deficient medium, it also produces larger fractionation, but it occurs at faster csSRRs than in the ammonium-replete control cultures. The energy and reducing power required for nitrogen fixation may be responsible for the reverse trend between S-isotope fractionation and csSRR in this case. Iron deficiency and nitrogen fixation by sulfate-reducing microbes may lead to the large observed S-isotope effects in some euxinic basins and various anoxic sediments.
Heterotrophic Archaea Contribute to Carbon Cycling in Low-pH, Suboxic Biofilm Communities
Authors: Justice Nicholas B. , Pan Chongle , Mueller Ryan , Spaulding Susan E. , Shah Vega , Sun Christine L. , Yelton Alexis P. , Miller Christopher S. , Thomas Brian C. , Shah Manesh , VerBerkmoes Nathan , Hettich Robert , Banfield Jillian F. 
Published: September 2012

ABSTRACT

Archaea are widely distributed and yet are most often not the most abundant members of microbial communities. Here, we document a transition from
Bacteria
- to
Archaea
-dominated communities in microbial biofilms sampled from the Richmond Mine acid mine drainage (AMD) system (∼pH 1.0, ∼38°C) and in laboratory-cultivated biofilms. This transition occurs when chemoautotrophic microbial communities that develop at the air-solution interface sink to the sediment-solution interface and degrade under microaerobic and anaerobic conditions. The archaea identified in these sunken biofilms are from the class
Thermoplasmata
, and in some cases, the highly divergent ARMAN nanoarchaeal lineage. In several of the sunken biofilms, nanoarchaea comprise 10 to 25% of the community, based on fluorescent
in situ
hybridization and metagenomic analyses. Comparative community proteomic analyses show a persistence of bacterial proteins in sunken biofilms, but there is clear evidence for amino acid modifications due to acid hydrolysis. Given the low representation of bacterial cells in sunken biofilms based on microscopy, we infer that hydrolysis reflects proteins derived from lysed cells. For archaea, we detected ∼2,400 distinct proteins, including a subset involved in proteolysis and peptide uptake. Laboratory cultivation experiments using complex carbon substrates demonstrated anaerobic enrichment of
Ferroplasma
and Aplasma coupled to the reduction of ferric iron. These findings indicate dominance of acidophilic archaea in degrading biofilms and suggest that they play roles in anaerobic nutrient cycling at low pH.
Choline and
N
,
N
-Dimethylethanolamine as Direct Substrates for Methanogens
Authors: Watkins Andrew J. , Roussel Erwan G. , Webster Gordon , Parkes R. John , Sass Henrik 
Published: September 2012

ABSTRACT

Choline (
N
,
N
,
N
-trimethylethanolamine), which is widely distributed in membrane lipids and is a component of sediment biota, has been shown to be utilized anaerobically by mixed prokaryote cultures to produce methane but not by pure cultures of methanogens. Here, we show that five recently isolated
Methanococcoides
strains from a range of sediments (Aarhus Bay, Denmark; Severn Estuary mudflats at Portishead, United Kingdom; Darwin Mud Volcano, Gulf of Cadiz; Napoli mud volcano, eastern Mediterranean) can directly utilize choline for methanogenesis producing ethanolamine, which is not further metabolized. Di- and monomethylethanolamine are metabolic intermediates that temporarily accumulate. Consistent with this, dimethylethanolamine was shown to be another new growth substrate, but monomethylethanolamine was not. The specific methanogen inhibitor 2-bromoethanesulfonate (BES) inhibited methane production from choline. When choline and trimethylamine are provided together, diauxic growth occurs, with trimethylamine being utilized first, and then after a lag (∼7 days) choline is metabolized. Three type strains of
Methanococcoides
(
M. methylutens
,
M. burtonii
, and
M. alaskense
), in contrast, did not utilize choline. However, two of them (
M. methylutens
and
M. burtonii
) did metabolize dimethylethanolamine. These results extend the known substrates that can be directly utilized by some methanogens, giving them the advantage that they would not be reliant on bacterial syntrophs for their substrate supply.
Prevalence and Diversity of Viruses in the Entomopathogenic Fungus Beauveria bassiana
Authors: Herrero Noemí , Dueñas Encarna , Quesada-Moraga Enrique , Zabalgogeazcoa Iñigo 
Published: September 2012

ABSTRACT

Viruses have been discovered in numerous fungal species, but unlike most known animal or plant viruses, they are rarely associated with deleterious effects on their hosts. The knowledge about viruses among entomopathogenic fungi is very limited, although their existence is suspected because of the presence of virus-like double-stranded RNA (dsRNA) in isolates of several species.
Beauveria bassiana
is one of the most-studied species of entomopathogenic fungi; it has a cosmopolitan distribution and is used as a biological control agent against invertebrates in agriculture. We analyzed a collection of 73 isolates obtained at different locations and from different habitats in Spain and Portugal, searching for dsRNA elements indicative of viral infections. The results revealed that the prevalence of viral infections is high; 54.8% of the isolates contained dsRNA elements with viral characteristics. The dsRNA electropherotypes of infected isolates indicated that virus diversity was high in the collection analyzed and that mixed virus infections occurred in fungal isolates. However, a hybridization experiment indicated that dsRNA bands that are similar in size do not always have similar sequences. Particular virus species or dsRNA profiles were not associated with locations or types of habitats, probably because of the ubiquity and efficient dispersion of this fungus as an airborne species. The sequence of one of the most common dsRNA elements corresponded to the 5.2-kbp genome of a previously undescribed member of the
Totiviridae
family, termed
B. bassiana
RNA virus 1 (BbRV1).
Biosynthesis of
cis
,
cis
-Muconic Acid and Its Aromatic Precursors, Catechol and Protocatechuic Acid, from Renewable Feedstocks by Saccharomyces cerevisiae
Authors: Weber Christian , Brückner Christine , Weinreb Sheila , Lehr Claudia , Essl Christine , Boles Eckhard 
Published: September 2012

ABSTRACT

Adipic acid is a high-value compound used primarily as a precursor for the synthesis of nylon, coatings, and plastics. Today it is produced mainly in chemical processes from petrochemicals like benzene. Because of the strong environmental impact of the production processes and the dependence on fossil resources, biotechnological production processes would provide an interesting alternative. Here we describe the first engineered
Saccharomyces cerevisiae
strain expressing a heterologous biosynthetic pathway converting the intermediate 3-dehydroshikimate of the aromatic amino acid biosynthesis pathway via protocatechuic acid and catechol into
cis
,
cis
-muconic acid, which can be chemically dehydrogenated to adipic acid. The pathway consists of three heterologous microbial enzymes, 3-dehydroshikimate dehydratase, protocatechuic acid decarboxylase composed of three different subunits, and catechol 1,2-dioxygenase. For each heterologous reaction step, we analyzed several potential candidates for their expression and activity in yeast to compose a functional
cis
,
cis
-muconic acid synthesis pathway. Carbon flow into the heterologous pathway was optimized by increasing the flux through selected steps of the common aromatic amino acid biosynthesis pathway and by blocking the conversion of 3-dehydroshikimate into shikimate. The recombinant yeast cells finally produced about 1.56 mg/liter
cis
,
cis
-muconic acid.
Detection and Tracking of a Novel Genetically Tagged Biological Simulant in the Environment
Authors: Emanuel Peter A. , Buckley Patricia E. , Sutton Tiffany A. , Edmonds Jason M. , Bailey Andrew M. , Rivers Bryan A. , Kim Michael H. , Ginley William J. , Keiser Christopher C. , Doherty Robert W. , Kragl F. Joseph , Narayanan Fiona E. , Katoski Sarah E. , Paikoff Sari , Leppert Samuel P. , Strawbridge John B. , VanReenen Daniel R. , Biberos Sally S. , Moore Douglas , Phillips Douglas W. , Mingioni Lisa R. , Melles Ogba , Ondercin Daniel G. , Hirsh Beth , Bieschke Kendall M. , Harris Crystal L. , Omberg Kristin M. , Rastogi Vipin K. , Van Cuyk Sheila , Gibbons Henry S. 
Published: September 2012

ABSTRACT

A variant of
Bacillus thuringiensis
subsp.
kurstaki
containing a single, stable copy of a uniquely amplifiable DNA oligomer integrated into the genome for tracking the fate of biological agents in the environment was developed. The use of genetically tagged spores overcomes the ambiguity of discerning the test material from pre-existing environmental microflora or from previously released background material. In this study, we demonstrate the utility of the genetically “barcoded” simulant in a controlled indoor setting and in an outdoor release. In an ambient breeze tunnel test, spores deposited on tiles were reaerosolized and detected by real-time PCR at distances of 30 m from the point of deposition. Real-time PCR signals were inversely correlated with distance from the seeded tiles. An outdoor release of powdered spore simulant at Aberdeen Proving Ground, Edgewood, MD, was monitored from a distance by a light detection and ranging (LIDAR) laser. Over a 2-week period, an array of air sampling units collected samples were analyzed for the presence of viable spores and using barcode-specific real-time PCR assays. Barcoded
B. thuringiensis
subsp.
kurstaki
spores were unambiguously identified on the day of the release, and viable material was recovered in a pattern consistent with the cloud track predicted by prevailing winds and by data tracks provided by the LIDAR system. Finally, the real-time PCR assays successfully differentiated barcoded
B. thuringiensis
subsp.
kurstaki
spores from wild-type spores under field conditions.
Inactivation of Salmonella enterica by UV-C Light Alone and in Combination with Mild Temperatures
Authors: Gayán E. , Serrano M. J. , Raso J. , Álvarez I. , Condón S. 
Published: September 2012

ABSTRACT

The aim of this investigation was to study the efficacy of the combined processes of UV light and mild temperatures for the inactivation of
Salmonella enterica
subsp.
enterica
and to explore the mechanism of inactivation. The doses to inactivate the 99.99% (4D) of the initial population ranged from 18.03 (
Salmonella enterica
serovar Typhimurium STCC 878) to 12.75 J ml
−1
(
Salmonella enterica
serovar Enteritidis ATCC 13076). The pH and water activity of the treatment medium did not change the UV tolerance, but it decreased exponentially by increasing the absorption coefficient. An inactivating synergistic effect was observed by applying simultaneous UV light and heat treatment (UV-H). A less synergistic effect was observed by applying UV light first and heat subsequently. UV did not damage cell envelopes, but the number of injured cells was higher after a UV-H treatment than after heating. The synergistic effect observed by combining simultaneous UV and heat treatment opens the possibility to design combined treatments for pasteurization of liquid food with high UV absorptivity, such as fruit juices.
Seasonal Variations of Indoor Microbial Exposures and Their Relation to Temperature, Relative Humidity, and Air Exchange Rate
Authors: Frankel Mika , Bekö Gabriel , Timm Michael , Gustavsen Sine , Hansen Erik Wind , Madsen Anne Mette 
Published: September 2012

ABSTRACT

Indoor microbial exposure has been related to adverse pulmonary health effects. Exposure assessment is not standardized, and various factors may affect the measured exposure. The aim of this study was to investigate the seasonal variation of selected microbial exposures and their associations with temperature, relative humidity, and air exchange rates in Danish homes. Airborne inhalable dust was sampled in five Danish homes throughout the four seasons of 1 year (indoors,
n
= 127; outdoors,
n
= 37). Measurements included culturable fungi and bacteria, endotoxin,
N
-acetyl-beta-
d
-glucosaminidase, total inflammatory potential, particles (0.75 to 15 μm), temperature, relative humidity, and air exchange rates. Significant seasonal variation was found for all indoor microbial exposures, excluding endotoxin. Indoor fungi peaked in summer (median, 235 CFU/m
3
) and were lowest in winter (median, 26 CFU/m
3
). Indoor bacteria peaked in spring (median, 2,165 CFU/m
3
) and were lowest in summer (median, 240 CFU/m
3
). Concentrations of fungi were predominately higher outdoors than indoors, whereas bacteria, endotoxin, and inhalable dust concentrations were highest indoors. Bacteria and endotoxin correlated with the mass of inhalable dust and number of particles. Temperature and air exchange rates were positively associated with fungi and
N
-acetyl-beta-
d
-glucosaminidase and negatively with bacteria and the total inflammatory potential. Although temperature, relative humidity, and air exchange rates were significantly associated with several indoor microbial exposures, they could not fully explain the observed seasonal variations when tested in a mixed statistical model. In conclusion, the season significantly affects indoor microbial exposures, which are influenced by temperature, relative humidity, and air exchange rates.
Fate of Bacillus thuringiensis subsp. israelensis in the Field: Evidence for Spore Recycling and Differential Persistence of Toxins in Leaf Litter
Authors: Tetreau Guillaume , Alessi Mattia , Veyrenc Sylvie , Périgon Sophie , David Jean-Philippe , Reynaud Stéphane , Després Laurence 
Published: September 2012

ABSTRACT

Bacillus thuringiensis
subsp.
israelensis
is a bioinsecticide increasingly used worldwide for mosquito control. Despite its apparent low level of persistence in the field due to the rapid loss of its insecticidal activity, an increasing number of studies suggested that the recycling of
B. thuringiensis
subsp.
israelensis
can occur under specific, unknown conditions. Decaying leaf litters sampled in mosquito breeding sites in the French Rhône-Alpes region several months after a treatment were shown to exhibit a high level of larval toxicity and contained large amounts of spores. In the present article, we show that the high concentration of toxins found in these litters is consistent with spore recycling in the field, which gave rise to the production of new crystal toxins. Furthermore, in these toxic leaf litter samples, Cry4Aa and Cry4Ba toxins became the major toxins instead of Cyt1Aa in the commercial mixture. In a microcosm experiment performed in the laboratory, we also demonstrated that the toxins, when added in their crystal form to nontoxic leaf litter, exhibited patterns of differential persistence consistent with the proportions of toxins observed in the field-collected toxic leaf litter samples (Cry4 > Cry11 > Cyt). These results give strong evidence that
B. thuringiensis
subsp.
israelensis
recycled in specific breeding sites containing leaf litters, and one would be justified in asking whether mosquitoes can become resistant when exposed to field-persistent
B. thuringiensis
subsp.
israelensis
for several generations.
Homologous Alkalophilic and Acidophilic
l
-Arabinose Isomerases Reveal Region-Specific Contributions to the pH Dependence of Activity and Stability
Authors: Lee Sang-Jae , Lee Sang Jun , Lee Yong-Jik , Kim Seong-Bo , Kim Sung-Kun , Lee Dong-Woo 
Published: September 2012

ABSTRACT

To study the pH dependence of
l
-arabinose isomerase (AI) activity and stability, we compared homologous AIs with their chimeras. This study demonstrated that an ionizable amino acid near the catalytic site determines the optimal pH (pH
opt
) for activity, whereas the N-terminal surface R residues play an important role in determining the pH
opt
for stability.
Quantitative Analysis of the Modes of Growth Inhibition by Weak Organic Acids in Saccharomyces cerevisiae
Authors: Ullah Azmat , Orij Rick , Brul Stanley , Smits Gertien J. 
Published: September 2012

ABSTRACT

Weak organic acids are naturally occurring compounds that are commercially used as preservatives in the food and beverage industries. They extend the shelf life of food products by inhibiting microbial growth. There are a number of theories that explain the antifungal properties of these weak acids, but the exact mechanism is still unknown. We set out to quantitatively determine the contributions of various mechanisms of antifungal activity of these weak acids, as well as the mechanisms that yeast uses to counteract their effects. We analyzed the effects of four weak organic acids differing in lipophilicity (sorbic, benzoic, propionic, and acetic acids) on growth and intracellular pH (pH
i
) in
Saccharomyces cerevisiae
. Although lipophilicity of the acids correlated with the rate of acidification of the cytosol, our data confirmed that not initial acidification, but rather the cell's ability to restore pH
i
, was a determinant for growth inhibition. This pH
i
recovery in turn depended on the nature of the organic anion. We identified long-term acidification as the major cause of growth inhibition under acetic acid stress. Restoration of pH
i
, and consequently growth rate, in the presence of this weak acid required the full activity of the plasma membrane ATPase Pma1p. Surprisingly, the proposed anion export pump Pdr12p was shown to play an important role in the ability of yeast cells to restore the pH
i
upon lipophilic (sorbic and benzoic) acid stress, probably through a charge interaction of anion and proton transport.