bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel Group of Leaderless Multipeptide Bacteriocins from Gram-Positive Bacteria
Authors: Ovchinnikov Kirill V. , Chi Hai , Mehmeti Ibrahim , Holo Helge , Nes Ingolf F. , Diep Dzung B. 
Published: June 2016

ABSTRACT

From raw milk we found 10
Lactococcus garvieae
isolates that produce a new broad-spectrum bacteriocin. Though the isolates were obtained from different farms, they turned out to possess identical inhibitory spectra, fermentation profiles of sugars, and repetitive sequence-based PCR (rep-PCR) DNA patterns, indicating that they produce the same bacteriocin. One of the isolates (
L. garvieae
KS1546) was chosen for further assessment. Purification and peptide sequencing combined with genome sequencing revealed that the antimicrobial activity was due to a bacteriocin unit composed of three similar peptides of 32 to 34 amino acids. The three peptides are produced without leader sequences, and their genes are located next to each other in an operon-like structure, adjacent to the genes normally involved in bacteriocin transport (ABC transporter) and self-immunity. The bacteriocin, termed garvicin KS (GarKS), showed sequence homology to four multipeptide bacteriocins in databases: the known staphylococcal aureocin A70, consisting of four peptides, and three unannotated putative multipeptide bacteriocins produced by
Bacillus cereus
. All these multipeptide bacteriocin loci show conserved genetic organization, including being located adjacent to conserved genetic determinants (Cro/cI and integrase) which are normally associated with mobile genetic elements or genome rearrangements. The antimicrobial activity of all multipeptide bacteriocins was confirmed with synthetic peptides, and all were shown to have broad antimicrobial spectra, with GarKS being the most active of them. The inhibitory spectrum of GarKS includes important pathogens belonging to the genera
Staphylococcus
,
Bacillus
,
Listeria
, and
Enterococcus
.

IMPORTANCE
Bacterial resistance to antibiotics is a very serious global problem. There are no new antibiotics with novel antimicrobial mechanisms in clinical trials. Bacteriocins use antimicrobial mechanisms different from those of antibiotics and can kill antibiotic-resistant bacteria, but the number of bacteriocins with very broad antimicrobial spectra is very small. In this study, we have found and purified a novel three-peptide bacteriocin, garvicin KS. By homology search, we were able to find one known and three novel sequence-related bacteriocins consisting of 3 or 4 peptides. None of the peptides has modified amino acids in its sequence. Thus, the activity of all bacteriocins was confirmed with chemically synthesized peptides. All of them, especially garvicin KS, have very broad antibacterial spectra, thus representing a great potential in antimicrobial applications in the food industry and medicine.
Nonnodulating Bradyrhizobium spp. Modulate the Benefits of Legume-Rhizobium Mutualism
Authors: Gano-Cohen Kelsey A. , Stokes Peter J. , Blanton Mia A. , Wendlandt Camille E. , Hollowell Amanda C. , Regus John U. , Kim Deborah , Patel Seema , Pahua Victor J. , Sachs Joel L. 
Published: June 2016

ABSTRACT

Rhizobia are best known for nodulating legume roots and fixing atmospheric nitrogen for the host in exchange for photosynthates. However, the majority of the diverse strains of rhizobia do not form nodules on legumes, often because they lack key loci that are needed to induce nodulation. Nonnodulating rhizobia are robust heterotrophs that can persist in bulk soil, thrive in the rhizosphere, or colonize roots as endophytes, but their role in the legume-rhizobium mutualism remains unclear. Here, we investigated the effects of nonnodulating strains on the native
Acmispon-Bradyrhizobium
mutualism. To examine the effects on both host performance and symbiont fitness, we performed clonal inoculations of diverse nonnodulating
Bradyrhizobium
strains on
Acmispon strigosus
hosts and also coinoculated hosts with mixtures of sympatric nodulating and nonnodulating strains. In isolation, nonnodulating
Bradyrhizobium
strains did not affect plant performance. In most cases, coinoculation of nodulating and nonnodulating strains reduced host performance compared to that of hosts inoculated with only a symbiotic strain. However, coinoculation increased host performance only under one extreme experimental treatment. Nearly all estimates of nodulating strain fitness were reduced in the presence of nonnodulating strains. We discovered that nonnodulating strains were consistently capable of coinfecting legume nodules in the presence of nodulating strains but that the fitness effects of coinfection for hosts and symbionts were negligible. Our data suggest that nonnodulating strains most often attenuate the
Acmispon-Bradyrhizobium
mutualism and that this occurs via competitive interactions at the root-soil interface as opposed to
in planta
.

IMPORTANCE
Rhizobia are soil bacteria best known for their capacity to form root nodules on legume plants and enhance plant growth through nitrogen fixation. Yet, most rhizobia in soil do not have this capacity, and their effects on this symbiosis are poorly understood. We investigated the effects of diverse nonnodulating rhizobia on a native legume-rhizobium symbiosis. Nonnodulating strains did not affect plant growth in isolation. However, compared to inoculations with symbiotic rhizobia, coinoculations of symbiotic and nonnodulating strains often reduced plant and symbiont fitness. Coinoculation increased host performance only under one extreme treatment. Nonnodulating strains also invaded nodule interiors in the presence of nodulating strains, but this did not affect the fitness of either partner. Our data suggest that nonnodulating strains may be important competitors at the root-soil interface and that their capacity to attenuate this symbiosis should be considered in efforts to use rhizobia as biofertilizers.
Algicidal Activity of Streptomyces eurocidicus JXJ-0089 Metabolites and Their Effects on Microcystis Physiology
Authors: Zhang Bing-Huo , Ding Zhang-Gui , Li Han-Quan , Mou Xiao-Zhen , Zhang Yu-Qin , Yang Jian-Yuan , Zhou En-Min , Li Wen-Jun 
Published: June 2016

ABSTRACT

Copper sulfate (CuSO
4
) has been widely used as an algicide to control harmful cyanobacterial blooms (CyanoHABs) in freshwater lakes. However, there are increasing concerns about this application, due mainly to the general toxicity of CuSO
4
to other aquatic species and its long-term persistence in the environment. This study reported the isolation and characterization of two natural algicidal compounds, i.e., tryptamine and tryptoline, from
Streptomyces
eurocidicus
JXJ-0089. At a concentration of 5 μg/ml, both compounds showed higher algicidal efficiencies than CuSO
4
on
Microcystis
sp. FACHB-905 and some other harmful cyanobacterial strains. Tryptamine and tryptoline treatments induced a degradation of chlorophyll and cell walls of cyanobacteria. These two compounds also significantly increased the intracellular oxidant content, i.e., superoxide anion radical (O
2
−
) and malondialdehyde (MDA), but reduced the activity of intracellular reductants, i.e., superoxide dismutase (SOD), of cyanobacteria. Moreover, tryptamine and tryptoline treatments significantly altered the internal and external contents of microcystin-LR (MC-LR), a common cyanotoxin. Like CuSO
4
, tryptamine and tryptoline led to releases of intracellular MC-LR from
Microcystis
, but with lower rates than CuSO
4
. Tryptamine and tryptoline (5 μg/ml) in cyanobacterial cultures were completely degraded within 8 days, while CuSO
4
persisted for months. Overall, our results suggest that tryptamine and tryptoline could potentially serve as more efficient and environmentally friendly alternative algicides than CuSO
4
in controlling harmful cyanobacterial blooms.

IMPORTANCE
Cyanobacterial harmful algal blooms (CyanoHABs) in aquatic environments have become a worldwide problem. Numerous efforts have been made to seek means to prevent, control, and mitigate CyanoHABs. Copper sulfate (CuSO
4
), was once a common algicide to treat and control CyanoHABs. However, its application has become limited due to concerns about its general toxicity to other aquatic species and its long-term persistence in the environment. There is a great need for algicides with higher specificity and low environmental impacts. This study reports the isolation and characterization of two natural algicidal compounds from a streptomycete strain,
Streptomyces eurocidicus
JXJ-0089. Our results suggest that the identified algicides could potentially serve as more efficient and environmentally friendly alternative algicides than CuSO
4
in controlling harmful cyanobacterial blooms.
Tracking Human Adenovirus Inactivation by Gamma Radiation under Different Environmental Conditions
Authors: Pimenta Andreia I. , Guerreiro Duarte , Madureira Joana , Margaça Fernanda M. A. , Cabo Verde Sandra 
Published: June 2016

ABSTRACT

Adenovirus is the most prevalent enteric virus in waters worldwide due to its environmental stability, which leads to public health concerns. Mitigation strategies are therefore required. The aim of this study was to assess the inactivation of human adenovirus type 5 (HAdV-5) by gamma radiation in aqueous environments. Various substrates with different organic loads, including domestic wastewater, were inoculated with HAdV-5 either individually or in a viral pool (with murine norovirus type 1 [MNV-1]) and were irradiated in a Cobalt-60 irradiator at several gamma radiation doses (0.9 to 10.8 kGy). The infectivity of viral particles, before and after irradiation, was tested by plaque assay using A549 cells. D
10
values (dose required to inactivate 90% of a population or the dose of irradiation needed to produce a 1 log
10
reduction in the population) were estimated for each substrate based on virus infectivity inactivation exponential kinetics. The capability of two detection methods, nested PCR and enzyme-linked immunosorbent assay (ELISA), to track inactivated viral particles was also assessed. After irradiation at 3.5 kGy, a reduction of the HAdV-5 titer of 4 log PFU/ml on substrates with lower organic loads was obtained, but in highly organic matrixes, the virus titer reduction was only 1 log PFU/ml. The D
10
values of HAdV-5 in high organic substrates were significantly higher than in water suspensions. The obtained results point out some discrepancies between nested PCR, ELISA, and plaque assay on the assessments of HAdV-5 inactivation. These results suggest that the inactivation of HAdV-5 by gamma radiation, in aqueous environments, is significantly affected by substrate composition. This study highlights the virucidal potential of gamma radiation that may be used as a disinfection treatment for sustainable water supplies.

IMPORTANCE
Human adenovirus (HAdV) is the most prevalent of the enteric viruses in environmental waters worldwide. The purposes of this study are to provide new insights on the inactivation of enteric virus by gamma irradiation and to introduce new concepts and reinforce the benefits and utility of radiation technologies as disinfection processes. This may be an effective tool to guarantee the reduction of viral pathogens and to contribute to public health and sustainable water supplies.
Cell Surface Glycoside Hydrolases of Streptococcus gordonii Promote Growth in Saliva
Authors: Yang Jinghua , Zhou Yuan , Zhang Luxia , Shah Nehal , Jin Cheng , Palmer Robert J. , Cisar John O. 
Published: June 2016

ABSTRACT

The growth of the oral commensal
Streptococcus gordonii
in saliva may depend on a number of glycoside hydrolases (GHs), including three cell wall-anchored proteins that are homologs of pneumococcal β-galactosidase (BgaA), β-
N
-acetylglucosaminidase (StrH), and endo-β-
N
-acetylglucosaminidase D (EndoD). In the present study, we introduced unmarked in-frame deletions into the corresponding genes of
S. gordonii
DL1, verified the presence (or absence) of the encoded proteins on the resulting mutant strains, and compared these strains with wild-type strain DL1 for growth and glycan foraging in saliva. The overnight growth of wild-type DL1 was reduced 3- to 10-fold by the deletion of any one or two genes and approximately 20-fold by the deletion of all three genes. The only notable change in the salivary proteome associated with this reduction of growth was a downward shift in the apparent molecular masses of basic proline-rich glycoproteins (PRG), which was accompanied by the loss of lectin binding sites for galactose-specific
Erythrina cristagalli
agglutinin (ECA) and mannose-specific
Galanthus nivalis
agglutinin (GNA). The binding of ECA to PRG was also abolished in saliva cultures of mutants that expressed cell surface BgaA alone or together with either StrH or EndoD. However, the subsequent loss of GNA binding was seen only in saliva cocultures of different mutants that together expressed all three cell surface GHs. The findings indicate that the growth of
S. gordonii
DL1 in saliva depends to a significant extent on the sequential actions of first BgaA and then StrH and EndoD on N-linked glycans of PRG.

IMPORTANCE
The ability of oral bacteria to grow on salivary glycoproteins is critical for dental plaque biofilm development. Little is known, however, about how specific salivary components are attacked and utilized by different members of the biofilm community, such as
Streptococcus gordonii. Streptococcus gordonii
DL1 has three cell wall-anchored glycoside hydrolases that are predicted to act on host glycans. In the present study, we introduced unmarked in-frame deletions in the corresponding genes, verified the presence (or absence) of encoded proteins on the resulting mutant strains, and compared these strains with wild-type DL1 for growth and glycan foraging in saliva. The results indicate that the growth of
S. gordonii
DL1 depends to a significant extent on sequential action of these cell surface GHs on N-linked glycans of basic proline-rich salivary glycoproteins, which appears to be an essential first step in salivary glycan foraging.
The Glycoside Hydrolase Family 8 Reducing-End Xylose-Releasing Exo-oligoxylanase Rex8A from Paenibacillus barcinonensis BP-23 Is Active on Branched Xylooligosaccharides
Authors: Valenzuela Susana V. , Lopez Sergi , Biely Peter , Sanz-Aparicio Julia , Pastor F. I. Javier 
Published: June 2016

ABSTRACT

A GH8 family enzyme involved in xylan depolymerization has been characterized. The enzyme, Rex8A, is a reducing-end xylose-releasing exo-oligoxylanase (Rex) that efficiently hydrolyzes xylooligosaccharides and shows minor activity on polymeric xylan. Rex8A hydrolyzes xylooligomers of 3 to 6 xylose units to xylose and xylobiose in long-term incubations. Kinetic constants of Rex8A were determined on xylotriose, showing a

K
m

of 1.64 ± 0.03 mM and a
k
cat
value of 118.8 s
−1
. Besides linear xylooligosaccharides, the enzyme hydrolyzed decorated xylooligomers. The catalytic activity on branched xylooligosaccharides, i.e., the release of xylose from the reducing end, is a newly described trait of xylose-releasing exo-oligoxylanases, as the exo-activity on these substrates has not been reported for the few of these enzymes characterized to date. Modeling of the three-dimensional (3D) structure of Rex8A shows an (α/α)
6
barrel fold where the loops connecting the α-helices contour the active site. These loops, which show high sequence diversity among GH8 enzymes, shape a catalytic cleft with a −2 subsite that can accommodate methyl-glucuronic acid decorations. The hydrolytic ability of Rex8A on branched oligomers can be crucial for the complete depolymerization of highly substituted xylans, which is indispensable to accomplish biomass deconstruction and to generate efficient catalysts.

IMPORTANCE
A GH8 family enzyme involved in xylan depolymerization has been characterized. The Rex8A enzyme from
Paenibacillus barcinonensis
is involved in depolymerization of glucuronoxylan, a major component of the lignocellulosic substrates. The study shows that Rex8A is a reducing-end xylose-releasing exo-oligoxylanase that efficiently hydrolyzes xylose from neutral and acidic xylooligosaccharides generated by the action of other xylanases also secreted by the strain. The activity of a Rex enzyme on branched xylooligosaccharides has not been described to date. This report provides original and useful information on the properties of a new example of the rarely studied Rex enzymes. Depolymerization of highly substituted xylans is crucial for biomass valorization as a platform for generation of biofuels, chemicals, and solvents.
Biodegradative Activities of Selected Environmental Fungi on a Polyester Polyurethane Varnish and Polyether Polyurethane Foams
Authors: Álvarez-Barragán Joyce , Domínguez-Malfavón Lilianha , Vargas-Suárez Martín , González-Hernández Ricardo , Aguilar-Osorio Guillermo , Loza-Tavera Herminia 
Published: June 2016

ABSTRACT

Polyurethane (PU) is widely used in many aspects of modern life because of its versatility and resistance. However, PU waste disposal generates large problems, since it is slowly degraded, there are limited recycling processes, and its destruction may generate toxic compounds. In this work, we isolated fungal strains able to grow in mineral medium with a polyester PU (PS-PU; Impranil DLN) or a polyether PU (PE-PU; Poly Lack) varnish as the only carbon source. Of the eight best Impranil-degrading strains, the six best degraders belonged to the
Cladosporium cladosporioides
complex, including the species
C. pseudocladosporioides
,
C. tenuissimum
,
C. asperulatum
, and
C. montecillanum
, and the two others were identified as
Aspergillus fumigatus
and
Penicillium
chrysogenum
. The best Impranil degrader,
C. pseudocladosporioides
strain T1.PL.1, degraded up to 87% after 14 days of incubation. Fourier transform infrared (FTIR) spectroscopy analysis of Impranil degradation by this strain showed a loss of carbonyl groups (1,729 cm
−1
) and N—H bonds (1,540 and 1,261 cm
−1
), and gas chromatography-mass spectrometry (GC-MS) analysis showed a decrease in ester compounds and increase in alcohols and hexane diisocyanate, indicating the hydrolysis of ester and urethane bonds. Extracellular esterase and low urease, but not protease activities were detected at 7 and 14 days of culture in Impranil. The best eight Impranil-degrading fungi were also able to degrade solid foams of the highly recalcitrant PE-PU type to different extents, with the highest levels generating up to 65% of dry-weight losses not previously reported. Scanning electron microscopy (SEM) analysis of fungus-treated foams showed melted and thinner cell wall structures than the non-fungus-treated ones, demonstrating fungal biodegradative action on PE-PU.

IMPORTANCE
Polyurethane waste disposal has become a serious problem. In this work, fungal strains able to efficiently degrade different types of polyurethanes are reported, and their biodegradative activity was studied by different experimental approaches. Varnish biodegradation analyses showed that fungi were able to break down the polymer in some of their precursors, offering the possibility that they may be recovered and used for new polyurethane synthesis. Also, the levels of degradation of solid polyether polyurethane foams reported in this work have never been observed previously. Isolation of efficient polyurethane-degrading microorganisms and delving into the mechanisms they used to degrade the polymer provide the basis for the development of biotechnological processes for polyurethane biodegradation and recycling.
Effects of High-Pressure Treatment on Spores of Clostridium Species
Authors: Doona Christopher J. , Feeherry Florence E. , Setlow Barbara , Wang Shiwei , Li William , Nichols Frank C. , Talukdar Prabhat K. , Sarker Mahfuzur R. , Li Yong-Qing , Shen Aimee , Setlow Peter 
Published: June 2016

ABSTRACT

This work analyzes the high-pressure (HP) germination of spores of the food-borne pathogen
Clostridium perfringens
(with inner membrane [IM] germinant receptors [GRs]) and the opportunistic pathogen
Clostridium difficile
(with no IM GRs), which has growing implications as an emerging food safety threat. In contrast to those of spores of
Bacillus
species, mechanisms of HP germination of clostridial spores have not been well studied. HP treatments trigger
Bacillus
spore germination through spores' IM GRs at ∼150 MPa or through SpoVA channels for release of spores' dipicolinic acid (DPA) at ≥400 MPa, and DPA-less spores have lower wet heat resistance than dormant spores. We found that
C. difficile
spores exhibited no germination events upon 150-MPa treatment and were not heat sensitized. In contrast, 150-MPa-treated unactivated
C. perfringens
spores released DPA and became heat sensitive, although most spores did not complete germination by fully rehydrating the spore core, but this treatment of heat-activated spores led to almost complete germination and greater heat sensitization. Spores of both clostridial organisms released DPA during 550-MPa treatment, but
C. difficile
spores did not complete germination and remained heat resistant. Heat-activated 550-MPa-HP-treated
C. perfringens
spores germinated almost completely and became heat sensitive. However, unactivated 550-MPa-treated
C. perfringens
spores did not germinate completely and were less heat sensitive than spores that completed germination. Since
C. difficile
and
C. perfringens
spores use different mechanisms for sensing germinants, our results may allow refinement of HP methods for their inactivation in foods and other applications and may guide the development of commercially sterile low-acid foods.

IMPORTANCE
Spores of various clostridial organisms cause human disease, sometimes due to food contamination by spores. Because of these spores' resistance to normal decontamination regimens, there is continued interest in ways to kill spores without compromising food quality. High hydrostatic pressure (HP) under appropriate conditions can inactivate bacterial spores. With growing use of HP for food pasteurization, advancement of HP for commercial production of sterile low-acid foods requires understanding of mechanisms of spores' interactions with HP. While much is known about HP germination and inactivation of spores of
Bacillus
species, how HP germinates and inactivates clostridial spores is less well understood. In this work we have tried to remedy this information deficit by examining germination of spores of
Clostridium difficile
and
Clostridium perfringens
by several HP and temperature levels. The results may give insight that could facilitate more efficient methods for spore eradication in food sterilization or pasteurization, biodecontamination, and health care.