bluuebunny/crossref_metadata_2025_split huggingface dataset:
Leaf-Cutter Ant Fungus Gardens Are Biphasic Mixed Microbial Bioreactors That Convert Plant Biomass to Polyols with Biotechnological Applications
Authors: Somera Alexandre F. , Lima Adriel M. , dos Santos-Neto Álvaro J. , Lanças Fernando M. , Bacci Maurício 
Published: April 2015

ABSTRACT

Leaf-cutter ants use plant matter to culture the obligate mutualistic basidiomycete
Leucoagaricus
gongylophorus
. This fungus mediates ant nutrition on plant resources. Furthermore, other microbes living in the fungus garden might also contribute to plant digestion. The fungus garden comprises a young sector with recently incorporated leaf fragments and an old sector with partially digested plant matter. Here, we show that the young and old sectors of the grass-cutter
Atta
bisphaerica
fungus garden operate as a biphasic solid-state mixed fermenting system. An initial plant digestion phase occurred in the young sector in the fungus garden periphery, with prevailing hemicellulose and starch degradation into arabinose, mannose, xylose, and glucose. These products support fast microbial growth but were mostly converted into four polyols. Three polyols, mannitol, arabitol, and inositol, were secreted by
L
.
gongylophorus
, and a fourth polyol, sorbitol, was likely secreted by another, unidentified, microbe. A second plant digestion phase occurred in the old sector, located in the fungus garden core, comprising stocks of microbial biomass growing slowly on monosaccharides and polyols. This biphasic operation was efficient in mediating symbiotic nutrition on plant matter: the microbes, accounting for 4% of the fungus garden biomass, converted plant matter biomass into monosaccharides and polyols, which were completely consumed by the resident ants and microbes. However, when consumption was inhibited through laboratory manipulation, most of the plant polysaccharides were degraded, products rapidly accumulated, and yields could be preferentially switched between polyols and monosaccharides. This feature might be useful in biotechnology.
Systematic Analysis of White Pox Disease in Acropora palmata of the Florida Keys and Role of Serratia marcescens
Authors: Joyner Jessica L. , Sutherland Kathryn P. , Kemp Dustin W. , Berry Brett , Griffin Ashton , Porter James W. , Amador Molly H. B. , Noren Hunter K. G. , Lipp Erin K. 
Published: April 2015

ABSTRACT

White pox disease (WPD) affects the threatened elkhorn coral,
Acropora palmata
. Owing in part to the lack of a rapid and simple diagnostic test, there have been few systematic assessments of the prevalence of acroporid serratiosis (caused specifically by
Serratia marcescens
) versus general WPD signs. Six reefs in the Florida Keys were surveyed between 2011 and 2013 to determine the disease status of
A. palmata
and the prevalence of
S. marcescens
. WPD was noted at four of the six reefs, with WPD lesions found on 8 to 40% of the colonies surveyed.
S. marcescens
was detected in 26.9% (7/26) of the WPD lesions and in mucus from apparently healthy colonies both during and outside of disease events (9%; 18/201).
S. marcescens
was detected with greater frequency in
A. palmata
than in the overlying water column, regardless of disease status (
P
= 0.0177).
S. marcescens
could not be cultured from
A. palmata
but was isolated from healthy colonies of other coral species and was identified as pathogenic pulsed-field gel electrophoresis type PDR60. WPD lesions were frequently observed on the reef, but unlike in prior outbreaks, no whole-colony death was observed. Pathogenic
S. marcescens
was circulating on the reef but did not appear to be the primary pathogen in these recent WPD episodes, suggesting that other pathogens or stressors may contribute to signs of WPD. Results highlight the critical importance of diagnostics in coral disease investigations, especially given that field manifestation of disease may be similar, regardless of the etiological agent.
Heat Shock-Enhanced Conjugation Efficiency in Standard Campylobacter jejuni Strains
Authors: Zeng Ximin , Ardeshna Devarshi , Lin Jun 
Published: April 2015

ABSTRACT

Campylobacter jejuni
, the leading bacterial cause of human gastroenteritis in the United States, displays significant strain diversity due to horizontal gene transfer. Conjugation is an important horizontal gene transfer mechanism contributing to the evolution of bacterial pathogenesis and antimicrobial resistance. It has been observed that heat shock could increase transformation efficiency in some bacteria. In this study, the effect of heat shock on
C. jejuni
conjugation efficiency and the underlying mechanisms were examined. With a modified
Escherichia coli
donor strain, different
C. jejuni
recipient strains displayed significant variation in conjugation efficiency ranging from 6.2 × 10
−8
to 6.0 × 10
−3
CFU per recipient cell. Despite reduced viability, heat shock of standard
C. jejuni
NCTC 11168 and 81-176 strains (e.g., 48 to 54°C for 30 to 60 min) could dramatically enhance
C. jejuni
conjugation efficiency up to 1,000-fold. The phenotype of the heat shock-enhanced conjugation in
C. jejuni
recipient cells could be sustained for at least 9 h. Filtered supernatant from the heat shock-treated
C. jejuni
cells could not enhance conjugation efficiency, which suggests that the enhanced conjugation efficiency is independent of secreted substances. Mutagenesis analysis indicated that the clustered regularly interspaced short palindromic repeats system and the selected restriction-modification systems (Cj0030/Cj0031, Cj0139/Cj0140, Cj0690c, and HsdR) were dispensable for heat shock-enhanced conjugation in
C. jejuni
. Taking all results together, this study demonstrated a heat shock-enhanced conjugation efficiency in standard
C. jejuni
strains, leading to an optimized conjugation protocol for molecular manipulation of this organism. The findings from this study also represent a significant step toward elucidation of the molecular mechanism of conjugative gene transfer in
C. jejuni
.
Comparative Genotypic and Phenotypic Analysis of Cronobacter Species Cultured from Four Powdered Infant Formula Production Facilities: Indication of Pathoadaptation along the Food Chain
Authors: Yan Qiongqiong , Wang Juan , Gangiredla Jayanthi , Cao Yu , Martins Marta , Gopinath Gopal R. , Stephan Roger , Lampel Keith , Tall Ben D. , Fanning Séamus 
Published: April 2015

ABSTRACT

Cronobacter
species are opportunistic pathogens commonly found in the environment. Among the seven
Cronobacter
species,
Cronobacter sakazakii
sequence type 4 (ST-4) is predominantly associated with recorded cases of infantile meningitis. This study reports on a 26-month powdered infant formula (PIF) surveillance program in four production facilities located in distinct geographic regions. The objective was to identify the ST(s) in PIF production environments and to investigate the phenotypic features that support their survival. Of all 168
Cronobacter
isolates, 133 were recovered from a PIF production environment, 31 were of clinical origin, and 4 were laboratory type strains. Sequence type 1 (
n
= 84 isolates; 63.9%) was the dominant type in PIF production environments. The majority of these isolates clustered with an indistinguishable pulsotype and persisted for at least an 18-month period. Moreover, DNA microarray results identified two phylogenetic lineages among ST-4 strains tested. Thereafter, the ST-1 and -4 isolates were phenotypically compared. Differences were noted based on the phenotypes expressed by these isolates. The ST-1 PIF isolates produced stronger biofilms at both 28°C and 37°C, while the ST-4 clinical isolates exhibited greater swimming activity and increased binding to Congo red dye. Given the fact that PIF is a low-moisture environment and that the clinical environment provides for an interaction between the pathogen and its host, these differences may be consistent with a form of pathoadaptation. These findings help to extend our current understanding of the epidemiology and ecology of
Cronobacter
species in PIF production environments.
Highly Active and Specific Tyrosine Ammonia-Lyases from Diverse Origins Enable Enhanced Production of Aromatic Compounds in Bacteria and Saccharomyces cerevisiae
Authors: Jendresen Christian Bille , Stahlhut Steen Gustav , Li Mingji , Gaspar Paula , Siedler Solvej , Förster Jochen , Maury Jérôme , Borodina Irina , Nielsen Alex Toftgaard 
Published: April 2015

ABSTRACT

Phenylalanine and tyrosine ammonia-lyases form cinnamic acid and
p
-coumaric acid, which are precursors of a wide range of aromatic compounds of biotechnological interest. Lack of highly active and specific tyrosine ammonia-lyases has previously been a limitation in metabolic engineering approaches. We therefore identified 22 sequences
in silico
using synteny information and aiming for sequence divergence. We performed a comparative
in vivo
study, expressing the genes intracellularly in bacteria and yeast. When produced heterologously, some enzymes resulted in significantly higher production of
p
-coumaric acid in several different industrially important production organisms. Three novel enzymes were found to have activity exclusively for phenylalanine, including an enzyme from the low-GC Gram-positive bacterium
Brevibacillus laterosporus
, a bacterial-type enzyme from the amoeba
Dictyostelium discoideum
, and a phenylalanine ammonia-lyase from the moss
Physcomitrella patens
(producing 230 μM cinnamic acid per unit of optical density at 600 nm [OD
600
]) in the medium using
Escherichia coli
as the heterologous host). Novel tyrosine ammonia-lyases having higher reported substrate specificity than previously characterized enzymes were also identified. Enzymes from
Herpetosiphon aurantiacus
and
Flavobacterium johnsoniae
resulted in high production of
p
-coumaric acid in
Escherichia coli
(producing 440 μM
p
-coumaric acid OD
600
unit
−1
in the medium) and in
Lactococcus lactis
. The enzymes were also efficient in
Saccharomyces cerevisiae
, where
p
-coumaric acid accumulation was improved 5-fold over that in strains expressing previously characterized tyrosine ammonia-lyases.
Vibriophages Differentially Influence Biofilm Formation by Vibrio anguillarum Strains
Authors: Tan Demeng , Dahl Amalie , Middelboe Mathias 
Published: April 2015

ABSTRACTVibrio anguillarumis an important pathogen in marine aquaculture, responsible for vibriosis. Bacteriophages can potentially be used to control bacterial pathogens; however, successful application of phages requires a detailed understanding of phage-host interactions under both free-living and surface-associated growth conditions. In this study, we exploredin vitrophage-host interactions in two different strains ofV. anguillarum(BA35 and PF430-3) during growth in microcolonies, biofilms, and free-living cells. Two vibriophages, ΦH20 (Siphoviridae) and KVP40 (Myoviridae), had completely different effects on the biofilm development. Addition of phage ΦH20 to strain BA35 showed efficient control of biofilm formation and density of free-living cells. The interactions between BA35 and ΦH20 were thus characterized by a strong phage control of the phage-sensitive population and subsequent selection for phage-resistant mutants. Addition of phage KVP40 to strain PF430-3 resulted in increased biofilm development, especially during the early stage. Subsequent experiments in liquid cultures showed that addition of phage KVP40 stimulated the aggregation of host cells, which protected the cells against phage infection. By the formation of biofilms, strain PF430-3 created spatial refuges that protected the host from phage infection and allowed coexistence between phage-sensitive cells and lytic phage KVP40. Together, the results demonstrate highly variable phage protection mechanisms in two closely relatedV. anguillarumstrains, thus emphasizing the challenges of using phages to control vibriosis in aquaculture and adding to the complex roles of phages as drivers of prokaryotic diversity and population dynamics.
Extraintestinal Pathogenic and Antimicrobial-Resistant Escherichia coli Contamination of 56 Public Restrooms in the Greater Minneapolis-St. Paul Metropolitan Area
Authors: Mohamed Muhanad , Owens Kris , Gajewski Abby , Clabots Connie , Johnston Brian , Thuras Paul , Kuskowski Michael A. , Johnson James R. 
Published: April 2015

ABSTRACT

How extraintestinal pathogenic
Escherichia coli
(ExPEC) and antimicrobial-resistant
E. coli
disseminate through the population is undefined. We studied public restrooms for contamination with
E. coli
and ExPEC in relation to source and extensively characterized the
E. coli
isolates. For this, we cultured 1,120 environmental samples from 56 public restrooms in 33 establishments (obtained from 10 cities in the greater Minneapolis-St. Paul, MN, metropolitan area in 2003) for
E. coli
and compared ecological data with culture results. Isolates underwent virulence genotyping, phylotyping, clonal typing, pulsed-field gel electrophoresis (PFGE), and disk diffusion antimicrobial susceptibility testing. Overall, 168 samples (15% from 89% of restrooms) fluoresced, indicating presumptive
E. coli
: 25 samples (2.2% from 32% of restrooms) yielded
E. coli
isolates, and 10 samples (0.9% from 16% of restrooms) contained ExPEC. Restroom category and cleanliness level significantly predicted only fluorescence, gender predicted fluorescence and
E. coli
, and feces-like material and toilet-associated sites predicted all three endpoints. Of the 25
E. coli
isolates, 7 (28%) were from phylogenetic group B2(virulence-associated), and 8 (32%) were ExPEC. ExPEC isolates more commonly represented group B2 (50% versus 18%) and had significantly higher virulence gene scores than non-ExPEC isolates. Six isolates (24%) exhibited ≥3-class antibiotic resistance, 10 (40%) represented classic human-associated sequence types, and one closely resembled reference human clinical isolates by pulsed-field gel electrophoresis. Thus,
E. coli
, ExPEC, and antimicrobial-resistant
E. coli
sporadically contaminate public restrooms, in ways corresponding with restroom characteristics and within-restroom sites. Such restroom-source
E. coli
strains likely reflect human fecal contamination, may pose a health threat, and may contribute to population-wide dissemination of such strains.
VirR-Mediated Resistance of Listeria monocytogenes against Food Antimicrobials and Cross-Protection Induced by Exposure to Organic Acid Salts
Authors: Kang Jihun , Wiedmann Martin , Boor Kathryn J. , Bergholz Teresa M. 
Published: April 2015

ABSTRACT

Formulations of ready-to-eat (RTE) foods with antimicrobial compounds constitute an important safety measure against foodborne pathogens such as
Listeria monocytogenes
. While the efficacy of many commercially available antimicrobial compounds has been demonstrated in a variety of foods, the current understanding of the resistance mechanisms employed by
L. monocytogenes
to counteract these stresses is limited. In this study, we screened in-frame deletion mutants of two-component system response regulators associated with the cell envelope stress response for increased sensitivity to commercially available antimicrobial compounds (nisin, lauric arginate, ε-polylysine, and chitosan). A
virR
deletion mutant showed increased sensitivity to all antimicrobials and significantly greater loss of membrane integrity when exposed to nisin, lauric arginate, or ε-polylysine (
P
< 0.05). The VirR-regulated operon,
dltABCD
, was shown to be the key contributor to resistance against these antimicrobial compounds, whereas another VirR-regulated gene,
mprF
, displayed an antimicrobial-specific contribution to resistance. An experiment with a β-glucuronidase (GUS) reporter fusion with the
dlt
promoter indicated that nisin does not specifically induce VirR-dependent upregulation of
dltABCD
. Lastly, prior exposure of
L. monocytogenes
parent strain H7858 and the Δ
virR
mutant to 2% potassium lactate enhanced subsequent resistance against nisin and ε-polylysine (
P
< 0.05). These data demonstrate that VirRS-mediated regulation of
dltABCD
is the major resistance mechanism used by
L. monocytogenes
against cell envelope-damaging food antimicrobials. Further, the potential for cross-protection induced by other food-related stresses (e.g., organic acids) needs to be considered when applying these novel food antimicrobials as a hurdle strategy for RTE foods.
Thermophilic Coenzyme B
12
-Dependent Acyl Coenzyme A (CoA) Mutase from Kyrpidia tusciae DSM 2912 Preferentially Catalyzes Isomerization of (
R
)-3-Hydroxybutyryl-CoA and 2-Hydroxyisobutyryl-CoA
Authors: Weichler Maria-Teresa , Kurteva-Yaneva Nadya , Przybylski Denise , Schuster Judith , Müller Roland H. , Harms Hauke , Rohwerder Thore 
Published: April 2015

ABSTRACT

The recent discovery of a coenzyme B
12
-dependent acyl-coenzyme A (acyl-CoA) mutase isomerizing 3-hydroxybutyryl- and 2-hydroxyisobutyryl-CoA in the mesophilic bacterium
Aquincola tertiaricarbonis
L108 (N. Yaneva, J. Schuster, F. Schäfer, V. Lede, D. Przybylski, T. Paproth, H. Harms, R. H. Müller, and T. Rohwerder, J Biol Chem 287:15502–15511, 2012,
http://dx.doi.org/10.1074/jbc.M111.314690
) could pave the way for a complete biosynthesis route to the building block chemical 2-hydroxyisobutyric acid from renewable carbon. However, the enzyme catalyzes only the conversion of the stereoisomer (
S
)-3-hydroxybutyryl-CoA at reasonable rates, which seriously hampers an efficient combination of mutase and well-established bacterial poly-(
R
)-3-hydroxybutyrate (PHB) overflow metabolism. Here, we characterize a new 2-hydroxyisobutyryl-CoA mutase found in the thermophilic knallgas bacterium
Kyrpidia tusciae
DSM 2912. Reconstituted mutase subunits revealed highest activity at 55°C. Surprisingly, already at 30°C, isomerization of (
R
)-3-hydroxybutyryl-CoA was about 7,000 times more efficient than with the mutase from strain L108. The most striking structural difference between the two mutases, likely determining stereospecificity, is a replacement of active-site residue Asp found in strain L108 at position 117 with Val in the enzyme from strain DSM 2912, resulting in a reversed polarity at this binding site. Overall sequence comparison indicates that both enzymes descended from different prokaryotic thermophilic methylmalonyl-CoA mutases. Concomitant expression of PHB enzymes delivering (
R
)-3-hydroxybutyryl-CoA (beta-ketothiolase PhaA and acetoacetyl-CoA reductase PhaB from
Cupriavidus necator
) with the new mutase in
Escherichia coli
JM109 and BL21 strains incubated on gluconic acid at 37°C led to the production of 2-hydroxyisobutyric acid at maximal titers of 0.7 mM. Measures to improve production in
E. coli
, such as coexpression of the chaperone MeaH and repression of thioesterase II, are discussed.
Efficient Genome Editing in Clostridium cellulolyticum via CRISPR-Cas9 Nickase
Authors: Xu Tao , Li Yongchao , Shi Zhou , Hemme Christopher L. , Li Yuan , Zhu Yonghua , Van Nostrand Joy D. , He Zhili , Zhou Jizhong 
Published: April 2015

ABSTRACT

The CRISPR-Cas9 system is a powerful and revolutionary genome-editing tool for eukaryotic genomes, but its use in bacterial genomes is very limited. Here, we investigated the use of the
Streptococcus pyogenes
CRISPR-Cas9 system in editing the genome of
Clostridium cellulolyticum
, a model microorganism for bioenergy research. Wild-type Cas9-induced double-strand breaks were lethal to
C. cellulolyticum
due to the minimal expression of nonhomologous end joining (NHEJ) components in this strain. To circumvent this lethality, Cas9 nickase was applied to develop a single-nick-triggered homologous recombination strategy, which allows precise one-step editing at intended genomic loci by transforming a single vector. This strategy has a high editing efficiency (>95%) even using short homologous arms (0.2 kb), is able to deliver foreign genes into the genome in a single step without a marker, enables precise editing even at two very similar target sites differing by two bases preceding the seed region, and has a very high target site density (median interval distance of 9 bp and 95.7% gene coverage in
C. cellulolyticum
). Together, these results establish a simple and robust methodology for genome editing in NHEJ-ineffective prokaryotes.
Combining Lactic Acid Spray with Near-Infrared Radiation Heating To Inactivate Salmonella enterica Serovar Enteritidis on Almond and Pine Nut Kernels
Authors: Ha Jae-Won , Kang Dong-Hyun 
Published: April 2015

ABSTRACT

The aim of this study was to investigate the efficacy of near-infrared radiation (NIR) heating combined with lactic acid (LA) sprays for inactivating
Salmonella enterica
serovar Enteritidis on almond and pine nut kernels and to elucidate the mechanisms of the lethal effect of the NIR-LA combined treatment. Also, the effect of the combination treatment on product quality was determined. Separately prepared
S
. Enteritidis phage type (PT) 30 and non-PT 30
S
. Enteritidis cocktails were inoculated onto almond and pine nut kernels, respectively, followed by treatments with NIR or 2% LA spray alone, NIR with distilled water spray (NIR-DW), and NIR with 2% LA spray (NIR-LA). Although surface temperatures of nuts treated with NIR were higher than those subjected to NIR-DW or NIR-LA treatment, more
S
. Enteritidis survived after NIR treatment alone. The effectiveness of NIR-DW and NIR-LA was similar, but significantly more sublethally injured cells were recovered from NIR-DW-treated samples. We confirmed that the enhanced bactericidal effect of the NIR-LA combination may not be attributable to cell membrane damage
per se
. NIR heat treatment might allow
S
. Enteritidis cells to become permeable to applied LA solution. The NIR-LA treatment (5 min) did not significantly (
P
> 0.05) cause changes in the lipid peroxidation parameters, total phenolic contents, color values, moisture contents, and sensory attributes of nut kernels. Given the results of the present study, NIR-LA treatment may be a potential intervention for controlling food-borne pathogens on nut kernel products.
Patterns and Determinants of Halophilic Archaea (Class Halobacteria) Diversity in Tunisian Endorheic Salt Lakes and Sebkhet Systems
Authors: Najjari Afef , Elshahed Mostafa S. , Cherif Ameur , Youssef Noha H. 
Published: April 2015

ABSTRACT

We examined the diversity and community structure of members of the halophilic
Archaea
(class
Halobacteria
) in samples from central and southern Tunisian endorheic salt lakes and sebkhet (also known as sebkha) systems using targeted 16S rRNA gene diversity survey and quantitative PCR (qPCR) approaches. Twenty-three different samples from four distinct locations exhibiting a wide range of salinities (2% to 37%) and physical characteristics (water, salt crust, sediment, and biofilm) were examined. A total of 4,759 operational taxonomic units at the 0.03 (species-level) cutoff (OTU
0.03
s) belonging to 45 currently recognized genera were identified, with 8 to 43 genera (average, 30) identified per sample. In spite of the large number of genera detected per sample, only a limited number (i.e., 2 to 16) usually constituted the majority (≥80%) of encountered sequences.
Halobacteria
diversity showed a strong negative correlation to salinity (Pearson correlation coefficient = −0.92), and community structure analysis identified salinity, rather than the location or physical characteristics of the sample, as the most important factor shaping the
Halobacteria
community structure. The relative abundance of genera capable of biosynthesis of the compatible solute(s) trehalose or 2-sulfotrehalose decreased with increasing salinities (Pearson correlation coefficient = −0.80). Indeed, qPCR analysis demonstrated that the
Halobacteria
otsB
(trehalose-6-phosphatase)/16S rRNA gene ratio decreases with increasing salinities (Pearson correlation coefficient = −0.87). The results highlight patterns and determinants of
Halobacteria
diversity at a previously unexplored ecosystem and indicate that genera lacking trehalose biosynthetic capabilities are more adapted to growth in and colonization of hypersaline (>25% salt) ecosystems than trehalose producers.