bluuebunny/crossref_metadata_2025 huggingface dataset:
Fermentation of glycerol by Anaerobium acetethylicum and its potential use in biofuel production
Authors: Patil Yogita , Junghare Madan , Müller Nicolai
Published: December 2016

Growth of biodiesel industries resulted in increased coproduction of crude glycerol which is therefore becoming a waste product instead of a valuable ‘coproduct’. Glycerol can be used for the production of valuable chemicals, e.g. biofuels, to reduce glycerol waste disposal. In this study, a novel bacterial strain is described which converts glycerol mainly to ethanol and hydrogen with very little amounts of acetate, formate and 1,2‐propanediol as coproducts. The bacterium offers certain advantages over previously studied glycerol‐fermenting microorganisms. Anaerobium acetethylicum during growth with glycerol produces very little side products and grows in the presence of maximum glycerol concentrations up to 1500 mM and in the complete absence of complex organic supplements such as yeast extract or tryptone. The highest observed growth rate of 0.116 h−1 is similar to that of other glycerol degraders, and the maximum concentration of ethanol that can be tolerated was found to be about 60 mM (2.8 g l−1) and further growth was likely inhibited due to ethanol toxicity. Proteome analysis as well as enzyme assays performed in cell‐free extracts demonstrated that glycerol is degraded via glyceraldehyde‐3‐phosphate, which is further metabolized through the lower part of glycolysis leading to formation of mainly ethanol and hydrogen. In conclusion, fermentation of glycerol to ethanol and hydrogen by this bacterium represents a remarkable option to add value to the biodiesel industries by utilization of surplus glycerol.
Effect of early allograft dysfunction on outcomes following liver transplantation
Authors: Hudcova Jana , Scopa Caitlin , Rashid Jawad , Waqas Ahsan , Ruthazer Robin , Schumann Roman
Published: December 2016

Early allograft dysfunction (EAD) following liver transplantation (LT) remains a challenge for patients and clinicians. We retrospectively analyzed the effect of pre‐defined EAD on outcomes in a 10‐year cohort of deceased‐donor LT recipients with clearly defined exclusion criteria. EAD was defined by at least one of the following: AST or ALT >2000 IU/L within first‐week post‐LT, total bilirubin ≥10 mg/dL, and/or INR ≥1.6 on post‐operative day 7. Ten patients developed primary graft failure and were analyzed separately. EAD occurred in 86 (36%) recipients in a final cohort of 239 patients. In univariate and multivariate analyses, EAD was significantly associated with mechanical ventilation ≥2 days or death on days 0, 1, PACU/SICU stay >2 days or death on days 0‐2 and renal failure (RF) at time of hospital discharge (all P<.05). EAD was also significantly associated with higher one‐year graft loss in both uni‐ and multivariate Cox hazard analyses (P=.0203 and .0248, respectively). There was no difference in patient mortality between groups in either of the Cox proportional hazard models. In conclusion, we observed significant effects of EAD on short‐term post‐LT outcomes and lower graft survival.
Plant defence induced by PGPR against Spodoptera litura in tomato (Solanum lycopersicum L.)
Authors: Bano A. , Muqarab R.
Published: December 2016

The research conducted including its rationale: Spodoptera litura is the major pest of tomato causing significant reduction in tomato yield. Application of Plant growth promoting rhizobacteria(PGPR) prevent use of chemical fertilizer and synthetic pesticides through enhancement of plant growth and yield and induction of systemic resistance. Present investigation is an attempt to evaluate the role of PGPR, Pseudomonas putida and Rothia sp. on the physiology and yield of tomato fruit infested with the S. litura.

Central methods applied: The surface sterilized seeds of tomato were inoculated with 48 h culture of P. putida and Rothia sp. At 6–7 branching stage of the plant, the larvae of S. litura at 2nd in star was used to infect the tomato plant leaves.

Key results: The S. litura infestation decreased dry weight of shoots and roots by 46% and 22%, and significant reduction was recorded in tomato fruit yield. The P. putida and Rothia sp. inoculations alleviated the adverse effects of insect infestation and resulted in 60% increase in plant biomass and 40% increase in yield over infested plants.

Main conclusions including key points of discussion: PGPR: Defense appears to be mediated via increase in proline production, enhanced activities of antioxidant enzymes, stimulation in the activities of protease and polyphenol oxidases, increased contents of phenolics, protein and chlorophyll. The formulation of biopesticide involving PGPR comprise an environment friendly and sustainable approach to overcome insect infestation.
The iron–sulfur cluster biosynthesis protein SUFB is required for chlorophyll synthesis, but not phytochrome signaling
Authors: Hu Xueyun , Page Mike T. , Sumida Akihiro , Tanaka Ayumi , Terry Matthew J. , Tanaka Ryouichi
Published: December 2016

Proteins that contain iron–sulfur (Fe–S) clusters play pivotal roles in various metabolic processes such as photosynthesis and redox metabolism. Among the proteins involved in the biosynthesis of Fe–S clusters in plants, the SUFB subunit of the SUFBCD complex appears to be unique because SUFB has been reported to be involved in chlorophyll metabolism and phytochrome‐mediated signaling. To gain insights into the function of the SUFB protein, we analyzed the phenotypes of two SUFB mutants, laf6 and hmc1, and RNA interference (RNAi) lines with reduced SUFB expression. When grown in the light, the laf6 and hmc1 mutants and the SUFB RNAi lines accumulated higher levels of the chlorophyll biosynthesis intermediate Mg‐protoporphyrin IX monomethylester (Mg‐proto MME), consistent with the impairment of Mg‐proto MME cyclase activity. Both SUFC‐ and SUFD‐deficient RNAi lines accumulated the same intermediate, suggesting that inhibition of Fe‐S cluster synthesis is the primary cause of this impairment. Dark‐grown laf6 seedlings also showed an increase in protoporphyrin IX (Proto IX), Mg‐proto, Mg‐proto MME and 3,8‐divinyl protochlorophyllide a (DV‐Pchlide) levels, but this was not observed in hmc1 or the SUFB RNAi lines, nor was it complemented by SUFB overexpression. In addition, the long hypocotyl in far‐red light phenotype of the laf6 mutant could not be rescued by SUFB overexpression and segregated from the pale‐green SUFB‐deficient phenotype, indicating it is not caused by mutation at the SUFB locus. These results demonstrate that biosynthesis of Fe–S clusters is important for chlorophyll biosynthesis, but that the laf6 phenotype is not due to a SUFB mutation.
Evolutionary drivers of thermoadaptation in enzyme catalysis
Authors: Nguyen Vy , Wilson Christopher , Hoemberger Marc , Stiller John B. , Agafonov Roman V. , Kutter Steffen , English Justin , Theobald Douglas L. , Kern Dorothee
Published: December 2016

With early life likely to have existed in a hot environment, enzymes had to cope with an inherent drop in catalytic speed caused by lowered temperature. Here we characterize the molecular mechanisms underlying thermoadaptation of enzyme catalysis in adenylate kinase using ancestral sequence reconstruction spanning 3 billion years of evolution. We show that evolution solved the enzyme’s key kinetic obstacle—how to maintain catalytic speed on a cooler Earth—by exploiting transition-state heat capacity. Tracing the evolution of enzyme activity and stability from the hot-start toward modern hyperthermophilic, mesophilic, and psychrophilic organisms illustrates active pressure versus passive drift in evolution on a molecular level, refutes the debated activity/stability trade-off, and suggests that the catalytic speed of adenylate kinase is an evolutionary driver for organismal fitness.
In Vivo
Fitness Adaptations of Colistin-Resistant Acinetobacter baumannii Isolates to Oxidative Stress
Authors: Jones Crystal L. , Singh Shweta S. , Alamneh Yonas , Casella Leila G. , Ernst Robert K. , Lesho Emil P. , Waterman Paige E. , Zurawski Daniel V.
Published: December 2016

The loss of fitness in colistin-resistant (CR)
Acinetobacter baumannii
was investigated using longitudinal isolates from the same patient. Early CR isolates were outcompeted by late CR isolates for growth in broth and survival in the lungs of mice. Fitness loss was associated with an increased susceptibility to oxidative stress since early CR strains had reduced
in vitro
survival in the presence of hydrogen peroxide and decreased catalase activity compared to that of late CR and colistin-susceptible (CS) strains.
Nonnucleoside Reverse Transcriptase Inhibitors Reduce HIV-1 Production from Latently Infected Resting CD4
+
T Cells following Latency Reversal
Authors: Zerbato Jennifer M. , Tachedjian Gilda , Sluis-Cremer Nicolas
Published: December 2016

Therapeutic strategies that target the latent HIV-1 reservoir in resting CD4
+
T cells of infected individuals are always administered in the presence of combination antiretroviral therapy. Using a primary cell of HIV-1 latency, we evaluated whether different antiviral drug classes affected latency reversal (as assessed by extracellular virus production) by anti-CD3/CD28 monoclonal antibodies or bryostatin 1. We found that the nonnucleoside reverse transcriptase inhibitors efavirenz and rilpivirine significantly decreased HIV-1 production, by ≥1 log.
Analysis of Ribonucleotide 5′-Triphosphate Analogs as Potential Inhibitors of Zika Virus RNA-Dependent RNA Polymerase by Using Nonradioactive Polymerase Assays
Authors: Lu Gaofei , Bluemling Gregory R. , Collop Paul , Hager Michael , Kuiper Damien , Gurale Bharat P. , Painter George R. , De La Rosa Abel , Kolykhalov Alexander A.
Published: December 2016

Zika virus (ZIKV) is an emerging human pathogen that is spreading rapidly through the Americas and has been linked to the development of microcephaly and to a dramatically increased number of Guillain-Barré syndrome cases. Currently, no vaccine or therapeutic options for the prevention or treatment of ZIKV infections exist. In the study described in this report, we expressed, purified, and characterized full-length nonstructural protein 5 (NS5) and the NS5 polymerase domain (NS5pol) of ZIKV RNA-dependent RNA polymerase. Using purified NS5, we developed an
in vitro
nonradioactive primer extension assay employing a fluorescently labeled primer-template pair. Both purified NS5 and NS5pol can carry out
in vitro
RNA-dependent RNA synthesis in this assay. Our results show that Mn
2+
is required for enzymatic activity, while Mg
2+
is not. We found that ZIKV NS5 can utilize single-stranded DNA but not double-stranded DNA as a template or a primer to synthesize RNA. The assay was used to compare the efficiency of incorporation of analog 5′-triphosphates by the ZIKV polymerase and to calculate their discrimination versus that of natural ribonucleotide triphosphates (rNTPs). The 50% inhibitory concentrations for analog rNTPs were determined in an alternative nonradioactive coupled-enzyme assay. We determined that, in general, 2′-C-methyl- and 2′-C-ethynyl-substituted analog 5′-triphosphates were efficiently incorporated by the ZIKV polymerase and were also efficient chain terminators. Derivatives of these molecules may serve as potential antiviral compounds to be developed to combat ZIKV infection. This report provides the first characterization of ZIKV polymerase and demonstrates the utility of
in vitro
polymerase assays in the identification of potential ZIKV inhibitors.
In Vitro
Activities of MCB3681 and Eight Comparators against Clostridium difficile Isolates with Known Ribotypes and Diverse Geographical Spread
Authors: Freeman Jane , Pilling Sally , Vernon Jonathan , Wilcox Mark H.
Published: December 2016

Treatments for
Clostridium difficile
infection remain limited, despite the introduction of fidaxomicin, and development of new agents is necessary. We determined the
in vitro
susceptibilities of 199 prevalent or emerging
Clostridium difficile
PCR ribotypes to MCB3681, a novel investigational quinolonyl-oxazolidinone, and 8 comparators (metronidazole, vancomycin, fidaxomicin, moxifloxacin, ciprofloxacin, clindamycin, tigecycline, and linezolid). MCB3681 showed good activity against
C. difficile
with no evidence of MCB3681 resistance in isolates showing either moxifloxacin or linezolid resistance or both moxifloxacin and linezolid resistance.
Real-Time Monitoring of
nfxB
Mutant Occurrence and Dynamics in Pseudomonas aeruginosa Biofilm Exposed to Subinhibitory Concentrations of Ciprofloxacin
Authors: Zaborskyte Greta , Andersen Jens Bo , Kragh Kasper Nørskov , Ciofu Oana
Published: December 2016

Biofilm infections caused by
Pseudomonas aeruginosa
are frequently treated with ciprofloxacin (CIP); however, resistance rapidly develops. One of the primary resistance mechanisms is the overexpression of the MexCD-OprJ pump due to a mutation in
nfxB
, encoding the transcriptional repressor of this pump. The aim of this study was to investigate the effect of subinhibitory concentrations of CIP on the occurrence of
nfxB
mutants in the wild-type PAO1 flow cell biofilm model. For this purpose, we constructed fluorescent reporter strains (PAO1 background) with an
mCherry
tag for constitutive red fluorescence and chromosomal transcriptional fusion between the P

mexCD

promoter and
gfp
leading to green fluorescence upon mutation of
nfxB
. We observed a rapid development of
nfxB
mutants by live confocal laser scanning microscopy (CLSM) imaging of the flow cell biofilm (reaching 80 to 90% of the whole population) when treated with 1/10 minimal biofilm inhibitory concentration of CIP for 24 h and 96 h. Based on the observed developmental stages, we propose that
nfxB
mutants emerged
de novo
in the biofilm during CIP treatment from filamentous cells, which might have arisen due to the stress responses induced by CIP. Identical
nfxB
mutations were found in fluorescent colonies from the same flow cell biofilm, especially in 24-h biofilms, suggesting selection and clonal expansion of the mutants during biofilm growth. Our findings point at the significant role of high-enough antibiotic dosages or appropriate combination therapy to avoid the emergence of resistant mutants in biofilms.
FlrA Represses Transcription of the Biofilm-Associated
bpfA
Operon in Shewanella putrefaciens
Authors: Cheng Yuan-Yuan , Wu Chao , Wu Jia-Yi , Jia Hui-Ling , Wang Ming-Yu , Wang Huan-Yu , Zou Si-Min , Sun Rui-Rui , Jia Rong , Xiao Ya-Zhong
Published: December 2016

Manipulation of biofilm formation in
Shewanella
is beneficial for application to industrial and environmental biotechnology. BpfA is an adhesin largely responsible for biofilm formation in many
Shewanella
species. However, the mechanism underlying BpfA production and the resulting biofilm remains vaguely understood. We previously described the finding that BpfA expression is enhanced by DosD, an oxygen-stimulated diguanylate cyclase, under aerobic growth. In the present work, we identify FlrA as a critical transcription regulator of the
bpfA
operon in
Shewanella putrefaciens
CN32 by transposon mutagenesis. FlrA acted as a repressor of the operon promoter by binding to two boxes overlapping the −10 and −35 sites recognized by σ
70
. DosD regulation of the expression of the
bpfA
operon was mediated by FlrA, and cyclic diguanylic acid (c-di-GMP) abolished FlrA binding to the operon promoter. We also demonstrate that FlhG, an accessory protein for flagellum synthesis, antagonized FlrA repression of the expression of the
bpfA
operon. Collectively, this work demonstrates that FlrA acts as a central mediator in the signaling pathway from c-di-GMP to BpfA-associated biofilm formation in
S. putrefaciens
CN32.

IMPORTANCE
Motility and biofilm are mutually exclusive lifestyles, shifts between which are under the strict regulation of bacteria attempting to adapt to the fluctuation of diverse environmental conditions. The FlrA protein in many bacteria is known to control motility as a master regulator of flagellum synthesis. This work elucidates its effect on biofilm formation by controlling the expression of the adhesin BpfA in
S. putrefaciens
CN32 in response to c-di-GMP. Therefore, FlrA plays a dual role in controlling motility and biofilm formation in
S. putrefaciens
CN32. The cooccurrence of
flrA
,
bpfA
, and the FlrA box in the promoter region of the
bpfA
operon in diverse
Shewanella
strains suggests that
bpfA
is a common mechanism that controls biofilm formation in this bacterial species.
Detection of ESKAPE Bacterial Pathogens at the Point of Care Using Isothermal DNA-Based Assays in a Portable Degas-Actuated Microfluidic Diagnostic Assay Platform
Authors: Renner Lars D. , Zan Jindong , Hu Linda I. , Martinez Manuel , Resto Pedro J. , Siegel Adam C. , Torres Clint , Hall Sara B. , Slezak Tom R. , Nguyen Tuan H. , Weibel Douglas B.
Published: December 2016

An estimated 1.5 billion microbial infections occur globally each year and result in ∼4.6 million deaths. A technology gap associated with commercially available diagnostic tests in remote and underdeveloped regions prevents timely pathogen identification for effective antibiotic chemotherapies for infected patients. The result is a trial-and-error approach that is limited in effectiveness, increases risk for patients while contributing to antimicrobial drug resistance, and reduces the lifetime of antibiotics. This paper addresses this important diagnostic technology gap by describing a low-cost, portable, rapid, and easy-to-use microfluidic cartridge-based system for detecting the ESKAPE (
Enterococcus faecium
,
Staphylococcus aureus
,
Klebsiella pneumoniae
,
Acinetobacter baumannii
,
Pseudomonas aeruginosa
, and
Enterobacter
spp.) bacterial pathogens that are most commonly associated with antibiotic resistance. The point-of-care molecular diagnostic system consists of a vacuum-degassed microfluidic cartridge preloaded with lyophilized recombinase polymerase amplification (RPA) assays and a small portable battery-powered electronic incubator/reader. The isothermal RPA assays detect the targeted ESKAPE pathogens with high sensitivity (e.g., a limit of detection of ∼10 nucleic acid molecules) that is comparable to that of current PCR-based assays, and they offer advantages in power consumption, engineering, and robustness, which are three critical elements required for the point-of-care setting.

IMPORTANCE
This paper describes a portable system for rapidly identifying bacteria in resource-limited environments; we highlight the capabilities of the technology by detecting different pathogens within the ESKAPE collection, which cause nosocomial infections. The system is designed around isothermal DNA-based assays housed within an autonomous plastic cartridge that are designed with the end user in mind, who may have limited technological training. Displaying excellent sensitivity and specificity, the assay systems that we demonstrate may enable future diagnoses of bacterial infection to guide the development of effective chemotherapies and may have a role in areas beyond health where rapid detection is valuable, including in industrial processing and manufacturing, food security, agriculture, and water quality testing.
Novel Cadmium Resistance Determinant in Listeria monocytogenes
Authors: Parsons Cameron , Lee Sangmi , Jayeola Victor , Kathariou Sophia
Published: December 2016

Listeria monocytogenes
is a foodborne pathogen that can cause severe disease (listeriosis) in susceptible individuals. It is ubiquitous in the environment and often exhibits resistance to heavy metals. One of the determinants that enables
Listeria
to tolerate exposure to cadmium is the
cadAC
efflux system, with CadA being a P-type ATPase. Three different
cadA
genes (designated
cadA1
to
cadA3
) were previously characterized in
L. monocytogenes
. A novel putative cadmium resistance gene (
cadA4
) was recently identified through whole-genome sequencing, but experimental confirmation for its involvement in cadmium resistance is lacking. In this study, we characterized
cadA4
in
L. monocytogenes
strain F8027, a cadmium-resistant strain of serotype 4b. By screening a mariner-based transposon library of this strain, we identified a mutant with reduced tolerance to cadmium and that harbored a single transposon insertion in
cadA4
. The tolerance to cadmium was restored by genetic complementation with the cadmium resistance cassette (
cadA4C
), and enhanced cadmium tolerance was conferred to two unrelated cadmium-sensitive strains via heterologous complementation with
cadA4C
. Cadmium exposure induced
cadA4
expression, even at noninhibitory levels. Virulence assessments in the
Galleria mellonella
model suggested that a functional
cadA4
suppressed virulence, potentially promoting commensal colonization of the insect larvae. Biofilm assays suggested that
cadA4
inactivation reduced biofilm formation. These data not only confirm
cadA4
as a novel cadmium resistance determinant in
L. monocytogenes
but also provide evidence for roles in virulence and biofilm formation.

IMPORTANCE
Listeria monocytogenes
is an intracellular foodborne pathogen causing the disease listeriosis, which is responsible for numerous hospitalizations and deaths every year. Among the adaptations that enable the survival of
Listeria
in the environment are the abilities to persist in biofilms, grow in the cold, and tolerate toxic compounds, such as heavy metals. Here, we characterized a novel determinant that was recently identified on a larger mobile genetic island through whole-genome sequencing. This gene (
cadA4
) was found to be responsible for cadmium detoxification and to be a divergent member of the Cad family of cadmium efflux pumps. Virulence assessments in a
Galleria mellonella
model suggested that
cadA4
may suppress virulence. Additionally,
cadA4
may be involved in the ability of
Listeria
to form biofilms. Beyond the role in cadmium detoxification, the involvement of
cadA4
in other cellular functions potentially explains its retention and wide distribution in
L. monocytogenes
.
Whole-Genome Analysis of Antimicrobial-Resistant and Extraintestinal Pathogenic Escherichia coli in River Water
Authors: Gomi Ryota , Matsuda Tomonari , Matsumura Yasufumi , Yamamoto Masaki , Tanaka Michio , Ichiyama Satoshi , Yoneda Minoru
Published: December 2016

Contamination of surface waters by antimicrobial-resistant bacteria and pathogenic bacteria is a great concern. In this study, 531
Escherichia coli
isolates obtained from the Yamato River in Japan were evaluated phenotypically for resistance to 25 antimicrobials. Seventy-six isolates (14.3%) were multidrug resistant (MDR), 66 (12.4%) were nonsusceptible to one or two classes of agents, and 389 (73.3%) were susceptible. We performed whole-genome sequencing of selected strains by using Illumina technology. In total, the genome sequences of 155 strains were analyzed for antibiotic resistance determinants and phylogenetic characteristics. More than 50 different resistance determinants, including acquired resistance genes and chromosomal resistance mutations, were detected. Among the sequenced MDR strains (
n
= 66), sequence type 155 (ST155) complex (
n
= 9), ST10 complex (
n
= 9), and ST69 complex (
n
= 7) were prevalent. Among extraintestinal pathogenic
E. coli
(ExPEC) strains (
n
= 58), clinically important clonal groups, namely, ST95 complex (
n
= 18), ST127 complex (
n
= 8), ST12 complex (
n
= 6), ST14 complex (
n
= 6), and ST131 complex (
n
= 6), were prevalent, demonstrating the clonal distribution of environmental ExPEC strains. Typing of the
fimH
(type 1 fimbrial adhesin) gene revealed that ST131 complex strains carried
fimH22
or
fimH41
, and no strains belonging to the
fimH30
subgroup were detected. Fine-scale phylogenetic analysis and virulence gene content analysis of strains belonging to the ST95 complex (one of the major clonal ExPEC groups causing community-onset infections) revealed no significant differences between environmental and clinical strains. The results indicate contamination of surface waters by
E. coli
strains belonging to clinically important clonal groups.

IMPORTANCE
The prevalence of antimicrobial-resistant and pathogenic
E. coli
strains in surface waters is a concern because surface waters are used as sources for drinking water, irrigation, and recreational purposes. In this study, MDR and ExPEC strains in river water were characterized by genomic sequencing and analysis. We detected more than 50 resistance determinants and identified clonal groups specific to MDR and ExPEC strains. This study showed contamination of surface waters by
E. coli
strains belonging to clinically important clonal groups. Overall, this study advances our understanding of environmental MDR and ExPEC strains.
Unexpected Diversity and High Abundance of Putative Nitric Oxide Dismutase (Nod) Genes in Contaminated Aquifers and Wastewater Treatment Systems
Authors: Zhu Baoli , Bradford Lauren , Huang Sichao , Szalay Anna , Leix Carmen , Weissbach Max , Táncsics András , Drewes Jörg E. , Lueders Tillmann
Published: December 2016

It has recently been suggested that oxygenic dismutation of NO into N
2
and O
2
may occur in the anaerobic methanotrophic “
Candidatus
Methylomirabilis oxyfera” and the alkane-oxidizing gammaproteobacterium HdN1. It may represent a new pathway in microbial nitrogen cycling catalyzed by a putative NO dismutase (Nod). The formed O
2
enables microbes to employ aerobic catabolic pathways in anoxic habitats, suggesting an ecophysiological niche space of substantial appeal for bioremediation and water treatment. However, it is still unknown whether this physiology is limited to “
Ca
. Methylomirabilis oxyfera” and HdN1 and whether it can be coupled to the oxidation of electron donors other than alkanes. Here, we report insights into an unexpected diversity and remarkable abundance of
nod
genes in natural and engineered water systems. Phylogenetically diverse
nod
genes were recovered from a range of contaminated aquifers and N-removing wastewater treatment systems. Together with
nod
genes from “
Ca
. Methylomirabilis oxyfera” and HdN1, the novel environmental
nod
sequences formed no fewer than 6 well-supported phylogenetic clusters, clearly distinct from canonical NO reductase (quinol-dependent NO reductase [qNor] and cytochrome
c
-dependent NO reductase [cNor]) genes. The abundance of
nod
genes in the investigated samples ranged from 1.6 × 10
7
to 5.2 × 10
10
copies · g
−1
(wet weight) of sediment or sludge biomass, accounting for up to 10% of total bacterial 16S rRNA gene counts. In essence, NO dismutation could be a much more widespread physiology than currently perceived. Understanding the controls of this emergent microbial capacity could offer new routes for nitrogen elimination or pollutant remediation in natural and engineered water systems.

IMPORTANCE
NO dismutation into N
2
and O
2
is a novel process catalyzed by putative NO dismutase (Nod). To date, only two bacteria, the anaerobic methane-oxidizing bacterium “
Ca
. Methylomirabilis oxyfera” and the alkane-oxidizing gammaproteobacterium HdN1, are known to harbor
nod
genes. In this study, we report efficient molecular tools that can detect and quantify a wide diversity of
nod
genes in environmental samples. A surprisingly high diversity and abundance of
nod
genes were found in contaminated aquifers as well as wastewater treatment systems. This evidence indicates that NO dismutation may be a much more widespread physiology in natural and man-made environments than currently perceived. The molecular tools presented here will facilitate further studies on these enigmatic microbes in the future.
Insight into the Genome of Brochothrix thermosphacta, a Problematic Meat Spoilage Bacterium
Authors: Stanborough Tamsyn , Fegan Narelle , Powell Shane M. , Tamplin Mark , Chandry P. Scott
Published: December 2016

Brochothrix thermosphactais a dominant but poorly studied meat spoilage organism. It is a close relative of the foodborne pathogenListeria monocytogenes, andBrochothrixconstitutes the second genus in theListeriaceaefamily. Here, the genomes of 12B. thermosphactastrains were sequenced, assembled into draft genomes, characterized, and compared with the genomes ofBrochothrix campestrisandL. monocytogenes. Phenotypic properties including biogenic amine production and antibiotic and heavy metal susceptibilities were tested. Comparative genomic analyses revealed a high degree of similarity among theB. thermosphactastrains, with bacteriophage genes constituting a significant proportion of the accessory genome. Genes for the production of the malodorous compounds acetate, acetoin, butanediol, and fatty acids were found, as were stress response regulatory genes, which likely play important roles in the spoilage process. Amino acid decarboxylases were not identified in the genomes, and phenotypic testing confirmed their absence. Orthologs ofListeriavirulence proteins involved in virulence regulation, intracellular survival, and surface protein anchoring were found; however, key virulence genes were absent. Analysis of antibiotic susceptibility showed that strains were sensitive to the four tested antibiotics, except for one tetracycline-resistant isolate with plasmid-mediated tetracycline resistance genes. Strains tolerated higher levels of copper and cobalt than of cadmium although not at concentrations high enough to categorize the strains as being resistant. This study provides insight into theBrochothrixgenome, links previous phenotypic data and data provided here to the gene inventory, and identifies genes that may contribute to the persistence of this organism in the food chain.

IMPORTANCEDespite increasing knowledge and advances in food preservation techniques, microbial spoilage of foods causes substantial losses, with negative social and economic consequences. To better control the contamination and microbial spoilage of foods, fundamental knowledge of the biology of key spoilage bacteria is crucial. As a common meat spoilage organism,B. thermosphactacontributes substantially to spoilage-associated losses. Nonetheless, this organism and particularly its genome remain largely unstudied. This study contributes to improving our knowledge of theBrochothrixgenus. Spoilage-relevant pathways and genes that may play a role in the survival of this organism in a food processing environment were identified, linking previous phenotypic data and data provided here to the gene inventory ofBrochothrixand establishing parallels to and differences from the closely related foodborne pathogenL. monocytogenes.
Sybr Green- and TaqMan-Based Quantitative PCR Approaches Allow Assessment of the Abundance and Relative Distribution of Frankia Clusters in Soils
Authors: Ben Tekaya Seifeddine , Ganesan Abirama Sundari , Guerra Trina , Dawson Jeffrey O. , Forstner Michael R. J. , Hahn Dittmar
Published: December 2016

The nodule-forming actinobacterial genus
Frankia
can generally be divided into 4 taxonomic clusters, with clusters 1, 2, and 3 representing nitrogen-fixing strains of different host infection groups and cluster 4 representing atypical, generally non-nitrogen-fixing strains. Recently, quantitative PCR (qPCR)-based quantification methods have been developed for frankiae of clusters 1 and 3; however, similar approaches for clusters 2 and 4 were missing. We amended a database of partial 23S rRNA gene sequences of
Frankia
strains belonging to clusters 1 and 3 with sequences of frankiae representing clusters 2 and 4. The alignment allowed us to design primers and probes for the specific detection and quantification of these
Frankia
clusters by either Sybr Green- or TaqMan-based qPCR. Analyses of frankiae in different soils, all obtained from the same region in Illinois, USA, provided similar results, independent of the qPCR method applied, with abundance estimates of 10 × 10
5
to 15 × 10
5
cells (g soil)
−1
depending on the soil. Diversity was higher in prairie soils (native, restored, and cultivated), with frankiae of all 4 clusters detected and those of cluster 4 dominating, while diversity in soils under
Alnus glutinosa
, a host plant for cluster 1 frankiae, or
Betula nigra
, a related nonhost plant, was restricted to cluster 1 and 3 frankiae and generally members of subgroup 1b were dominating. These results indicate that vegetation affects the basic composition of frankiae in soils, with higher diversity in prairie soils compared to much more restricted diversity under some host and nonhost trees.

IMPORTANCE
Root nodule formation by the actinobacterium
Frankia
is host plant specific and largely, but not exclusively, correlates with assignments of strains to specific clusters within the genus. Due to the lack of adequate detection and quantification tools, studies on
Frankia
have been limited to clusters 1 and 3 and generally excluded clusters 2 and 4. We have developed tools for the detection and quantification of clusters 2 and 4, which can now be used in combination with those developed for clusters 1 and 3 to retrieve information on the ecology of all clusters delineated within the genus
Frankia
. Our initial results indicate that vegetation affects the basic composition of frankiae in soils, with higher diversity in prairie soils compared to much more restricted diversity under some host and nonhost trees.
Western Bats as a Reservoir of Novel Streptomyces Species with Antifungal Activity
Authors: Hamm Paris S. , Caimi Nicole A. , Northup Diana E. , Valdez Ernest W. , Buecher Debbie C. , Dunlap Christopher A. , Labeda David P. , Lueschow Shiloh , Porras-Alfaro Andrea
Published: December 2016

At least two-thirds of commercial antibiotics today are derived fromActinobacteria, more specifically from the genusStreptomyces. Antibiotic resistance and new emerging diseases pose great challenges in the field of microbiology. Cave systems, in which actinobacteria are ubiquitous and abundant, represent new opportunities for the discovery of novel bacterial species and the study of their interactions with emergent pathogens. White-nose syndrome is an invasive bat disease caused by the fungusPseudogymnoascus destructans, which has killed more than six million bats in the last 7 years. In this study, we isolated naturally occurring actinobacteria from white-nose syndrome (WNS)-free bats from five cave systems and surface locations in the vicinity in New Mexico and Arizona, USA. We sequenced the 16S rRNA region and tested 632 isolates from 12 different bat species using a bilayer plate method to evaluate antifungal activity. Thirty-six actinobacteria inhibited or stopped the growth ofP. destructans, with 32 (88.9%) actinobacteria belonging to the genusStreptomyces. Isolates in the generaRhodococcus,Streptosporangium,Luteipulveratus, andNocardiopsisalso showed inhibition. Twenty-five of the isolates with antifungal activity againstP. destructansrepresent 15 novelStreptomycesspp. based on multilocus sequence analysis. Our results suggest that bats in western North America caves possess novel bacterial microbiota with the potential to inhibitP. destructans.

IMPORTANCEThis study reports the largest collection of actinobacteria from bats with activity againstPseudogymnoascus destructans, the fungal causative agent of white-nose syndrome. Using multigene analysis, we discovered 15 potential novel species. This research demonstrates that bats and caves may serve as a rich reservoir for novelStreptomycesspecies with antimicrobial bioactive compounds.
Draft Genome Sequence of the Nonpathogenic, Thermotolerant, and Exopolysaccharide-Producing Bacillus anthracis Strain PFAB2 from Panifala Hot Water Spring in West Bengal, India
Authors: Banerjee Aparna , Halder Urmi , Chaudhry Vasvi , Varshney Rajeev K. , Mantri Shrikant , Bandopadhyay Rajib
Published: December 2016

Bacillus anthracis
is the causative agent of fatal anthrax in both animals and humans. It is prevalently pathogenic. Here, we present a
Bacillus anthracis
PFAB2 strain from a relatively unexplored Panifala hot water spring in West Bengal, India. It is nonpathogenic, exopolysaccharide producing, and thermotolerant in nature.
Complete Genome Sequence of
Streptococcus
sp. Strain NPS 308
Authors: Kondo Yoshio , Ogura Yoshitoshi , Sato Keiko , Imamura Keigo , Hoshino Tomonori , Nishiguchi Miyuki , Hasuwa Tomoyuki , Moriuchi Hiroyuki , Hayashi Tetsuya , Fujiwara Taku
Published: December 2016

Streptococcus
sp. strain NPS 308, isolated from an 8-year-old girl diagnosed with infective endocarditis, likely presents a novel species of
Streptococcus
. Here, we present a complete genome sequence of this species, which will contribute to better understanding of the pathogenesis of infective endocarditis.
Genome Sequences of a Novel Vietnamese Bat Bunyavirus
Authors: Oude Munnink Bas B. , Phan My V. T. , van der Hoek Lia , Kellam Paul , Cotten Matthew
Published: December 2016

To document the viral zoonotic risks in Vietnam, fecal samples were systematically collected from a number of mammals in southern Vietnam and subjected to agnostic deep sequencing. We describe here novel Vietnamese bunyavirus sequences detected in bat feces. The complete L and S segments from 14 viruses were determined.
Whole-Genome Sequences of 26 Vibrio cholerae Isolates
Authors: Watve Samit S. , Chande Aroon T. , Rishishwar Lavanya , Mariño-Ramírez Leonardo , Jordan I. King , Hammer Brian K.
Published: December 2016

The human pathogen
Vibrio cholerae
employs several adaptive mechanisms for environmental persistence, including natural transformation and type VI secretion, creating a reservoir for the spread of disease. Here, we report whole-genome sequences of 26 diverse
V. cholerae
isolates, significantly increasing the sequence diversity of publicly available
V. cholerae
genomes.
Genome Sequence of the Soviet/Russian Bacillus anthracis Vaccine Strain 55-VNIIVViM
Authors: Farlow Jason , Kotorashvili Adam
Published: December 2016

Bacillus anthracis
strain 55-VNIIVViM is a live-attenuated nonencapsulated Soviet/Russian veterinary anthrax vaccine strain. We report here the genome of 55-VNIIVViM and confirm its phylogenetic placement in the global population structure of
B. anthracis
.
Complete Genome Sequences of Four Bordetella pertussis Vaccine Reference Strains from Serum Institute of India
Authors: Weigand Michael R. , Peng Yanhui , Loparev Vladimir , Johnson Taccara , Juieng Phalasy , Gairola Sunil , Kumar Rakesh , Shaligram Umesh , Gowrishankar Ramnath , Moura Hercules , Rees Jon , Schieltz David M. , Williamson Yulanda , Woolfitt Adrian , Barr John , Tondella M. Lucia , Williams Margaret M.
Published: December 2016

Serum Institute of India is among the world's largest vaccine producers. Here, we report the complete genome sequences for four
Bordetella pertussis
strains used by Serum Institute of India in the production of whole-cell pertussis vaccines.
Complete Genome Sequence of a Novel Aquareovirus That Infects the Endangered Fountain Darter,
Etheostoma fonticola
Authors: Iwanowicz Luke R. , Iwanowicz Deborah D. , Adams Cynthia R. , Lewis Teresa D. , Brandt Thomas M. , Cornman Robert S. , Sanders Lakyn
Published: December 2016

Here, we report the complete genome of a novel aquareovirus isolated from clinically normal fountain darters,
Etheostoma fonticola
, inhabiting the San Marcos River, Texas, USA. The complete genome consists of 23,958 bp consisting of 11 segments that range from 783 bp (S11) to 3,866 bp (S1).
Complete Genome Sequence of the Industrial Bacterium Ketogulonicigenium vulgare SKV
Authors: Jia Nan , Ding Ming-Zhu , Du Yu-Zhang , Feng Shuai , Gao Feng , Yuan Ying-Jin
Published: December 2016

Ketogulonicigenium vulgare
has been widely used in vitamin C two-step fermentation, which converts
l
-sorbose to 2-keto-
l
-gluonic acid. Here, the complete genome of
K. vulgare
SKV, which performs better fermentation production than
K. vulgare
Hbe602, is deciphered to understand the key differences in metabolism between
K. vulgare
strains SKV and Hbe602.
Complete Genome Sequence of a Mosaic NADC30-Like Porcine Reproductive and Respiratory Syndrome Virus in China
Authors: Wang Lin-jian , Guo Zhenhua , Qiao Songlin , Chen Xin-xin , Zhang Gaiping
Published: December 2016

Here, we report the complete genome of an NADC30-like porcine reproductive and respiratory syndrome virus (PRRSV) strain, HNhx, which was isolated from Henan Province, China, in 2016 and was characterized by recombination with JXA1 strain (an epidemic highly pathogenic PRRSV strain in China) in Nsp4 to Nsp9.
Genome Sequence of the Acetogenic Bacterium Acetobacterium wieringae DSM 1911
T
Authors: Poehlein Anja , Bengelsdorf Frank Robert , Schiel-Bengelsdorf Bettina , Daniel Rolf , Dürre Peter
Published: December 2016

Here, we report the draft genome sequence of
Acetobacterium wieringae
DSM 1911
T
, an anaerobic, autotrophic, acetogenic,
d
,
l
-lactate-utilizing bacterium. The genome consists of a chromosome (3.88 Mb) and 3,620 predicted protein-encoding genes.
Draft Genome Sequence of
Kluyvera
intestini
Strain GT-16 Isolated from the Stomach of a Patient with Gastric Cancer
Authors: Tetz George , Tetz Victor
Published: December 2016

Here, we report the complete genome sequence of the novel, non-spore-forming
Kluyvera intestini
strain GT-16, isolated from the stomach of a patient with gastric cancer. The genome is 5,868,299 bp in length with a G+C content of 53.0%. It possesses 5,350 predicted protein-coding genes encoding virulence factors and antibiotic resistance proteins.
Draft Whole-Genome Sequence of a Catalase-Negative Staphylococcus aureus subsp.
aureus
(Sequence Type 25) Strain Isolated from a Patient with Endocarditis and Septic Arthritis
Authors: Berenger Byron , Chen Justin , Bernier Anne-Marie , Bernard Kathryn
Published: December 2016

Staphylococcus aureus
strains without catalase activity are rare, challenging to identify with conventional biochemical methods, and, despite a supposed decreased pathogenicity, can still cause disease. The first whole-genome sequence of a catalase-negative
S. aureus
isolate causing severe recurrent invasive infection with two novel missense mutations in the
katA
gene is reported here.
Quorum Sensing in a Methane-Oxidizing Bacterium
Authors: Puri Aaron W. , Schaefer Amy L. , Fu Yanfen , Beck David A. C. , Greenberg E. Peter , Lidstrom Mary E.
Published: December 2016

Aerobic methanotrophic bacteria use methane as their sole source of carbon and energy and serve as a major sink for the potent greenhouse gas methane in freshwater ecosystems. Dissecting the molecular details of how these organisms interact in the environment may increase our understanding of how they perform this important ecological role. Many bacterial species use quorum sensing (QS) systems to regulate gene expression in a cell density-dependent manner. We have identified a QS system in the genome of
Methylobacter tundripaludum
, a dominant methane oxidizer in methane enrichments of sediment from Lake Washington (Seattle, WA). We determined that
M. tundripaludum
produces primarily
N
-3-hydroxydecanoyl-
l
-homoserine lactone (3-OH-C
10
-HSL) and that its production is governed by a positive feedback loop. We then further characterized this system by determining which genes are regulated by QS in this methane oxidizer using transcriptome sequencing (RNA-seq) and discovered that this system regulates the expression of a putative nonribosomal peptide synthetase biosynthetic gene cluster. Finally, we detected an extracellular factor that is produced by
M. tundripaludum
in a QS-dependent manner. These results identify and characterize a mode of cellular communication in an aerobic methane-oxidizing bacterium.

IMPORTANCE
Aerobic methanotrophs are critical for sequestering carbon from the potent greenhouse gas methane in the environment, yet the mechanistic details of chemical interactions in methane-oxidizing bacterial communities are not well understood. Understanding these interactions is important in order to maintain, and potentially optimize, the functional potential of the bacteria that perform this vital ecosystem function. In this work, we identify a quorum sensing system in the aerobic methanotroph
Methylobacter tundripaludum
and use both chemical and genetic methods to characterize this system at the molecular level.
Disturbance Regimes Predictably Alter Diversity in an Ecologically Complex Bacterial System
Authors: Gibbons Sean M. , Scholz Monika , Hutchison Alan L. , Dinner Aaron R. , Gilbert Jack A. , Coleman Maureen L.
Published: December 2016

Diversity is often associated with the functional stability of ecological communities from microbes to macroorganisms. Understanding how diversity responds to environmental perturbations and the consequences of this relationship for ecosystem function are thus central challenges in microbial ecology. Unimodal diversity-disturbance relationships, in which maximum diversity occurs at intermediate levels of disturbance, have been predicted for ecosystems where life history tradeoffs separate organisms along a disturbance gradient. However, empirical support for such peaked relationships in macrosystems is mixed, and few studies have explored these relationships in microbial systems. Here we use complex microbial microcosm communities to systematically determine diversity-disturbance relationships over a range of disturbance regimes. We observed a reproducible switch between community states, which gave rise to transient diversity maxima when community states were forced to mix. Communities showed reduced compositional stability when diversity was highest. To further explore these dynamics, we formulated a simple model that reveals specific regimes under which diversity maxima are stable. Together, our results show how both unimodal and non-unimodal diversity-disturbance relationships can be observed as a system switches between two distinct microbial community states; this process likely occurs across a wide range of spatially and temporally heterogeneous microbial ecosystems.

IMPORTANCE
The diversity of microbial communities is linked to the functioning and stability of ecosystems. As humanity continues to impact ecosystems worldwide, and as diet and disease perturb our own commensal microbial communities, the ability to predict how microbial diversity will respond to disturbance is of critical importance. Using microbial microcosm experiments, we find that community diversity responds to different disturbance regimes in a reproducible and predictable way. Maximum diversity occurs when two communities, each suited to different environmental conditions, are mixed due to disturbance. This maximum diversity is transient except under specific regimes. Using a simple mathematical model, we show that transient unimodality is likely a common feature of microbial diversity-disturbance relationships in fluctuating environments.