Phosphorylation of PppA at threonine 253 controls T6SS2 expression and bacterial killing capacity in the marine pathogen Vibrio alginolyticus Microbiol. Res. (IF 3.037) Pub Date : 2018-02-22 Zhen Yang, Xuetong Wang, Wensheng Xu, Mian Zhou, Yuanxing Zhang, Yue Ma, Qiyao Wang
Type VI secretion systems (T6SSs) are multi-protein secretory nano-machines that mediate inter-bacterial competition. Vibrio alginolyticus is an abundant gram-negative marine bacterium that efficiently kills other bacteria with its T6SS2. The V. alginolyticus T6SS2 gene cluster encodes a phosphatase, PppA, and a type II membrane-spanning Hanks-type threonine kinase, PpkA2, which have been implicated in the activation of T6S. Meanwhile, T6SS2 gene expression is under the control of quorum sensing. However, the role of PppA in T6SS2 activity is unclear. Here, our phosphoproteomic screen identified PppA as a novel PpkA2 substrate. Phosphorylation at threonine 253 (T253) of PppA is not conserved in other bacteria, suggesting that PppA may play a unique role in T6SS2 activation in V. alginolyticus. Interestingly, PppA phosphatase activity was modulated by the cognate kinase PpkA2, which implied that a homeostasis is required for optimal T6S activity. PppA and phosphorylation of PppA at T253 are important for T6S activity and T6SS2-mediated bacterial killing. Moreover, PppA and the phosphorylation of PppA are also essential for the expression of LuxR, the master regulator of quorum sensing, thus augmenting T6SS2 expression. Collectively, our data demonstrated that phosphorylation of PppA at T253 controls the activity of T6SS2, thereby enhancing the competitive fitness of V. alginolyticus.
Antidiabetic “gliptins” affect biofilm formation by Streptococcus mutans Microbiol. Res. (IF 3.037) Pub Date : 2018-02-19 Arpan De, Arianna Pompilio, Jenifer Francis, Iain C. Sutcliffe, Gary W. Black, Giulio Lupidi, Dezemona Petrelli, Luca A. Vitali
Streptococcus mutans, a dental caries causing odontopathogen, produces X-prolyl dipeptidyl peptidase (Sm-XPDAP, encoded by pepX), a serine protease known to have a nutritional role. Considering the potential of proteases as therapeutic targets in pathogens, this study was primarily aimed at investigating the role of Sm-XPDAP in contributing to virulence-related traits. Dipeptidyl peptidase (DPP IV), an XPDAP analogous enzyme found in mammalian tissues,is a well known therapeutic target in Type II diabetes. Based on the hypothesis that gliptins, commonly used as anti-human-DPP IV drugs, may affect bacterial growth upon inhibition of Sm-XPDAP, we have determined their ex vivo antimicrobial and anti-biofilm activity towards S. mutans. All three DPP IV drugs tested reduced biofilm formation as determined by crystal violet staining. To link the observed biofilm inhibition to the human-DPP IV analogue present in S. mutans UA159, a pepX isogenic mutant was generated. In addition to reduced biofilm formation, CLSM studies of the biofilm formed by the pepX isogenic mutant showed these were comparable to those formed in the presence of saxagliptin, suggesting a probable role of this enzyme in biofilm formation by S. mutans UA159. The effects of both pepX deletion and DPP IV drugs on the proteome were studied using LC-MS/MS. Overall, this study highlights the potential of Sm-XPDAP as a novel anti-biofilm target and suggests a template molecule to synthesize lead compounds effective against this enzyme.
Heat stress-induced reactive oxygen species participate in the regulation of HSP expression, hyphal branching and ganoderic acid biosynthesis in Ganoderma lucidum Microbiol. Res. (IF 3.037) Pub Date : 2018-02-19 Rui Liu, Xue Zhang, Ang Ren, Deng-Ke Shi, Liang Shi, Jing Zhu, Han-Shou Yu, Ming-Wen Zhao
Heat stress (HS) is an important environmental factor that affects the growth and metabolism of edible fungi, but the molecular mechanism of the heat stress response (HSR) remains unclear. We previously reported that HS treatment increased the length between two hyphal branches and induced the accumulation of ganoderic acid biosynthesis and the gene expression of heat shock proteins (HSPs) in Ganoderma lucidum. In this study, we found that HS induced a significant increase in the cytosolic ROS concentration, and exogenously added ROS scavengers NAC, VC and NADPH oxidase (Nox) inhibitor DPI reduce the cytosolic ROS accumulation in G. lucidum. In addition, the phenomena of the increased gene expression and increased length between the two hyphal branches and the accumulation of GA biosynthesis induced by HS were mitigated. Furthermore, we investigated the effects of HS on Nox-silenced strains (NoxABi-10, NoxABi-11 and NoxRi-4, NoxRi-7) and found that the level of ROS concentration was lower than that in wild-type (WT) strains treated with HS. Additionally, Nox silenced strains reduced the HS-induced increase in HSP expression, the length between two hyphal branches and GA biosynthesis compared with the WT strain. These data indicate that HS-induced ROS participate in the regulation of HSP expression, hyphal branching and ganoderic acid biosynthesis in G. lucidum. In addition, these findings identified potential pathways linking ROS networks to HSR, physiological and metabolic processes in fungi and provide a valuable reference for studying the role of ROS in HSR, mycelium growth and secondary metabolites.
Biocontrol activity of surfactin A purified from Bacillus NH-100 and NH-217 against rice bakanae disease Microbiol. Res. (IF 3.037) Pub Date : 2018-02-15 Ambrin Sarwar, Muhammad Nadeem Hassan, Muhammad Imran, Mazhar Iqbal, Saima Majeed, Günter Brader, Angela Sessitsch, Fauzia Yusuf Hafeez
The potential of the Bacillus genus to antagonize phytopathogens is associated with the production of cyclic lipopeptides. Depending upon the type of lipopeptide, they may serve as biocontrol agents that are eco-friendly alternatives to chemical fertilizers. This study evaluates the biocontrol activity of surfactin-producing Bacillus (SPB) strains NH-100 and NH-217 and purified surfactin A from these strains against rice bakanae disease. Biologically active surfactin fractions were purified by HPLC, and surfactin A variants with chain lengths from C12 to C16 were confirmed by LCMS-ESI. In hemolytic assays, a positive correlation between surfactin A production and halo zone formation was observed. The purified surfactin A had strong antifungal activity against Fusarium oxysporum, F. moniliforme, F. solani, Trichoderma atroviride and T. reesei. Maximum fungal growth suppression (84%) was recorded at 2000 ppm against F. moniliforme. Surfactin A retained antifungal activity at different pH levels (5–9) and temperatures (20, 50 and 121 °C). Hydroponic and pot experiments were conducted to determine the biocontrol activity of SPB strains and the purified surfactin A from these strains on Super Basmati rice. Surfactin production in the rice rhizosphere was detected by LCMS-ESI at early growth stages in hydroponics experiments inoculated with SPB strains. However, the maximum yield was observed with a consortium of SPB strains (T4) and purified surfactin A (T5) treatments in the pot experiment. The outcomes of the present study revealed that surfactin A significantly reduced rice bakanae disease by up to 80%. These findings suggest that purified surfactin A could be an effective biocontrol agent against bakanae disease in rice and should be incorporated into strategies for disease management.
Plant Growth Promoting Bacteria as an Alternative Strategy for Salt Tolerance in Plants: A Review Microbiol. Res. (IF 3.037) Pub Date : 2018-02-13 Muhammad Numan, Samina Bashir, Yasmin Khan, Roqayya Mumtaz, Zabta Khan Shinwari, Abdul Latif Khan, Ajmal Khan, Ahmed AL-Harrasi
Physiologically distinct subpopulations formed in Escherichia coli cultures in response to heat shock Microbiol. Res. (IF 3.037) Pub Date : 2018-02-13 Bożena Bruhn-Olszewska, Paweł Szczepaniak, Ewelina Matuszewska, Dorota Kuczyńska-Wiśnik, Karolina Stojowska-Swędrzyńska, María Moruno Algara, Ewa Laskowska
Bacteria can form heterogeneous populations containing phenotypic variants of genetically identical cells. The heterogeneity of populations can be considered a bet-hedging strategy allowing adaptation to unknown environmental changes – at least some individual subpopulations or cells might be able to withstand future adverse conditions. Using Percoll gradient centrifugation, we demonstrated that in an Escherichia coli culture exposed to heat shock at 50 °C, two physiologically distinct subpopulations were formed. A high-density subpopulation (HD50) demonstrated continued growth immediately after its transfer to LB medium, whereas the growth of a low-density subpopulation (LD50) was considerably postponed. The LD50 subpopulation contained mainly viable but non-culturable bacteria and exhibited higher tolerance to sublethal concentrations of antibiotics or H2O2 than HD50 cells. The levels of aggregated proteins and main molecular chaperones were comparable in both subpopulations; however, a decreased number of ribosomes and a significant increase in protein oxidation were observed in the LD50 subpopulation as compared with the HD50 subpopulation. Interestingly, under anaerobic heat stress, the formation of the HD50 subpopulation was decreased and culturability of the LD50 subpopulation was significantly increased. In both subpopulations the level of protein aggregates formed under anaerobic and aerobic heat stress was comparable. We concluded that the formation of protein aggregates was independent of oxidative damage induced by heat stress, and that oxidative stress and not protein aggregation limited growth and caused loss of LD50 culturability. Our results indicate that heat stress induces the formation of distinct subpopulations differing in their ability to grow under standard and stress conditions.
Transcriptional control of the phenol hydroxylase gene phe of Corynebacterium glutamicum by the AraC-type regulator PheR Microbiol. Res. (IF 3.037) Pub Date : 2018-02-06 Can Chen, Yaoling Zhang, Lei Xu, Kaixiang Zhu, Yanyan Feng, Junfeng Pan, Meiru Si, Lei Zhang, Xihui Shen
Corynebacterium glutamicum can degrade phenol by a meta-cleavage pathway, which depends on ncgl2588 (phe) of the phe operon encoding phenol hydroxylase. An additional gene, ncgl2587 (pheR), is located upstream of phe. The pheR encodes an AraC/XylR-type regulator protein with 377 amino acid residues and is transcribed in the same direction as phe. Disruption of pheR by homologous recombination resulteds in the accumulation of phenol degradation in C. glutamicum. PheR demonstrates a low type of constitutive expression where phenol induces phe expression. PheR shares 75% sequence identity with AraC-type regulator of Corynebacterium lubricantis and 37 conserved residues, characteristic of AraC family, were located. A constructed pK18mobsacB-Pphe:lacZ transcriptional fusion plasmid was transformed into the wild-type, ΔpheR, and ΔpheR+ strains, and the results indicated that PheR activates the expression of phe encoding phenol hydroxylase. Electrophoretic mobility shift assay (EMSA) demonstrated a direct interaction of PheR with the phe promoter region and binding site of PheR on the Pphe was located 109-bp upstream of phe, as indicated by foot printing analysis. Our research provides deep insight into PheR expression and its regulatory function on Phe in C. glutamicum.
Gibberellin biosynthesis and metabolism: a convergent route for plants, fungi and bacteria Microbiol. Res. (IF 3.037) Pub Date : 2018-02-03 Sonia Salazar-Cerezo, Nancy Martínez-Montiel, Jenny García-Sánchez, Rocío Pérez-y-Terrón, Rebeca D. Martínez-Contreras
Gibberellins (GAs) are natural complex biomolecules initially identified as secondary metabolites in the fungus Gibberella fujikuroi with strong implications in plant physiology. GAs have been identified in different fungal and bacterial species, in some cases related to virulence, but the full understanding of the role of these metabolites in the different organisms would need additional investigation. In this review, we summarize the current evidence regarding a common pathway for GA synthesis in fungi, bacteria and plant from the genes depicted as part of the GA production cluster to the enzymes responsible for the catalytic transformations and the biosynthetical routes involved. Moreover, we present the relationship between these observations and the biotechnological applications of GAs in plants, which has shown an enormous commercial impact.
Marine microbial L-asparaginase: biochemistry, molecular approaches and applications in tumor therapy and in food industry Microbiol. Res. (IF 3.037) Pub Date : 2018-02-02 Fatemeh Izadpanah, Ahmad Homaei, Pedro Fernandes, Sedigheh Javadpour
The marine environment is a rich source of biological and chemical diversity. It covers more than 70% of the Earth’s surface and features a wide diversity of habitats, often displaying extreme conditions, where marine organisms thrive, offering a vast pool for microorganisms and enzymes. Given the dissimilarity between marine and terrestrial habitats, enzymes and microorganisms, either novel or with different and appealing features as compared to terrestrial counterparts, may be identified and isolated. L-asparaginase (E.C. 184.108.40.206), is among the relevant enzymes that can be obtained from marine sources. This amidohydrolase acts on L-asparagine and produce L-aspartate and ammonia, accordingly it has an acknowledged chemotherapeutic application, namely in acute lymphoblastic leukemia. Moreover, L-asparaginase is also of interest in the food industry as it prevents acrylamide formation. Terrestrial organisms have been largely tapped for L-asparaginases, but most failed to comply with criteria for practical applications, whereas marine sources have only been marginally screened. This work provides an overview on the relevant features of this enzyme and the framework for its application, with a clear emphasis on the use of L-asparaginase from marine sources. The review envisages to highlight the unique properties of marine L-asparaginases that could make them good candidates for medical applications and industries, especially in food safety.
Identification and characterization of a new Bacillus atrophaeus strain B5 as biocontrol agent of postharvest anthracnose disease in soursop (Annona muricata) and avocado (Persea americana) Microbiol. Res. (IF 3.037) Pub Date : 2018-02-02 Lizeth Guardado Valdivia, Erik Tovar Pérez, Alejandra Chacón López, Ulises López García, Porfirio Gutiérrez Martínez, Selene Aguilera
Anthracnose is a fungal disease caused by Colletotrichum species that is detrimental to numerous fruit, including soursop and avocado. The use of fungicides to maintain the high quality of fruit creates a potential health risk. One alternative to this problem is the biological control, which has been applied successfully during postharvest. The Bacillus species are one of the most studied biological agents against postharvest pathogens because accomplish their biocontrol performance by producing a variety of metabolites. In this study, we evaluated the activity of metabolites contained in the cell free supernatant, obtained from Bacillus strain B5 culture, against micelial growth and spore germination of two virulent strains of C. gloeosporioides isolated from soursop and avocado. On the basis of 16S rDNA gene sequence analysis, this strain was identified as Bacillus atrophaeus. A preventive treatment using cell free supernatant, reduced severity and incidence of anthracnose disease on harvested soursop and avocado fruit. B. atrophaeus strain B5 harbors genes involved in the production of antibiotics such as surfactin, bacillomycin and iturin, which could be contributing to the efficiency of the preventive treatment during postharvest. The antagonistic role of metabolites contained in the cell free supernatant against anthracnose disease, provide a new approach by which to attack this problem and can help reduce the use of chemical pesticides, environmental pollution, leading to the safer fruit preservation.
Microbiome engineering to improve biocontrol and plant growth-promoting mechanisms Microbiol. Res. (IF 3.037) Pub Date : 2018-01-31 Ma del Carmen Orozco-Mosqueda, Ma del Carmen Rocha-Granados, Bernard R. Glick, Gustavo Santoyo
A plant microbiome includes a microbial community that typically interacts extensively with a plant. The plant microbiome can survive either inside or outside of plant tissues, performing various plant beneficial activities including biocontrol of potential phytopathogens and promotion of plant growth. An important part of the plant microbiome includes plant growth-promoting bacteria (PGPB) that commonly reside in the rhizosphere and phyllosphere, and as endophytic bacteria (inside of plant tissues). As new plant microbiome-manipulating strategies have emerged in recent years, we have critically reviewed relevant literature, chiefly from the last decade. We have analysed and compared the rhizosphere, phyllosphere and endosphere as potential ecosystems for manipulation, in order to improve positive interactions with the plant. In addition, many studies on the bioengineering of the endophyte microbiome and its potential impact on the core microbiome were analysed with respect to five different strategies, including host mediated and multi-generation microbiome selection, inoculation into soil and rhizosphere, inoculations into seeds or seedlings, tissue atomisation and direct injection into tissues or wounds. Finally, microbiome engineering presents a feasible strategy to solve multiple agriculture-associated problems in an eco-friendly way.
Microbial volatiles as plant growth inducers Microbiol. Res. (IF 3.037) Pub Date : 2018-01-31 Paola Fincheira, Andrés Quiroz
Agricultural practices require novel products that allow sustainable development and commercial production according to the needs of farmers and consumers. Therefore, in the last decade, eco-friendly alternatives have been studied, so volatile organic compounds (VOCs) emitted by microorganisms have emerged as a cheaper, effective, efficient, and an eco-friendly alternative. VOCs are lipophilic compounds derived from microbial metabolic pathways with low molecular weight (< 300 g mol−1), low boiling point, and high vapor pressure that allow them to act as signal molecules over short and long distances. Main case studies provide evidence that VOCs released from diverse microorganisms (i.e. Bacillus, Pseudomonas, Arthrobacter, Fusarium, and Alternaria) can stimulate growth on a specific “target” seedling, such as Arabidopsis and tobacco. Some identified compounds, such as 3-hydroxy-2-butanone (acetoin), 2,3-butanediol, 2-pentylfuran, or dimethylhexadecylmine have shown their ability to elicit growth at root or leaf level. Few studies indicate that VOCs act in the regulation at phytohormone, metabolic pathways and nutrition levels according to genetic, proteomic, and metabolic analyses; but action mechanisms associated with growth-inducing activity are poorly understood. In this work, we reviewed case studies regarding identified compounds and action mechanisms for a better understanding of the information collected so far. Additionally, a brief description about the effects of VOCs for induction of resistance and tolerance in plants are presented, where compounds such as acetoin, dimethyl disulfide, 3-pentanol and 6-pentyl-α-pyrone have been reported. Furthermore, we summarized the knowledge to direct future studies that propose microbial VOCs as a technological innovation in agriculture and horticulture.
Microbial communities and their potential for degradation of dissolved organic carbon in cryoconite hole environments of Himalaya and Antarctica Microbiol. Res. (IF 3.037) Pub Date : 2018-01-31 Aritri Sanyal, Runa Antony, Gautami Samui, Meloth Thamban
Cryoconite holes (cylindrical melt-holes on the glacier surface) are important hydrological and biological systems within glacial environments that support diverse microbial communities and biogeochemical processes. This study describes retrievable heterotrophic microbes in cryoconite hole water from three geographically distinct sites in Antarctica and a Himalayan glacier, along with their potential to degrade organic compounds found in these environments. Microcosm experiments (22 days) show that 13–60% of the dissolved organic carbon in the water within cryoconite holes is bio-available to resident microbes. Biodegradation tests of organic compounds such as lactate, acetate, formate, propionate and oxalate that are present in cryoconite hole water show that microbes have good potential to metabolize the compounds tested. Substrate utilization tests on Biolog Ecoplate show that microbial communities in the Himalayan samples are able to oxidize a diverse array of organic substrates including carbohydrates, carboxylic acids, amino acids, amines/amides and polymers, while Antarctic communities generally utilized complex polymers. In addition, as determined by the extracellular enzyme activities, majority of the microbes (82%, total of 355) isolated in this study (Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria and Basidiomycota) had ability to degrade a variety of compounds such as proteins, lipids, carbohydrates, cellulose and lignin that are documented to be present within cryoconite holes. Thus, microbial communities have good potential to metabolize organic compounds found in the cryoconite hole environment, thereby influencing the water chemistry in these holes. Moreover, microbes exported downstream during melting and flushing of cryoconite holes may participate in carbon cycling processes in recipient ecosystems.
Antagonistic Bacillus spp. reduce blast incidence on rice and increase grain yield under field conditions—Bio control effects on blast disease suppression on rice crop Microbiol. Res. (IF 3.037) Pub Date : 2018-01-31 Afroz Rais, Muhammad Shakeel, Kamran Malik, Fauzia Yusuf Hafeez, Humaira Yasmin, Saqib Mumtaz, Muhammad Nadeem Hassan
Rice blast is a severe threat for agricultural production. Plant growth promoting rhizobacteria could be suitable biocontrol agents to reduce the disease incidence. In this study, Bacillus spp. KFP-5, KFP-7, KFP-17 significantly reduced disease severity by 40–52% with grain yield of 3.2–3.9 ton ha−1 in two rice varieties i.e., basmati super and basmati 385. Bacillus spp. significantly colonized the rice rhizosphere with a cell population of 2.40E+06–5.6E+07CFU. Rice plants treated with antagonistic bacterial suspension followed by challenge inoculation with P. oryzae were found to have higher activities of antioxidant enzymes such as superoxide dismutase (308–266 Ug−1 FW), peroxidase (change in absorbance (ΔA) = 0.20–0.71 min−1 g−1 FW), polyphenol oxidase (ΔA = 0.29–0.58 min−1 g−1 FW) and phenylalanine ammonia lyase (ΔA = 0.32–0.59 min−1 g−1 FW). A consistency in the performance of strains was observed in the consecutive years 2013–2014. These findings suggest that indigenous Bacillus spp. could be a potential bio-inoculum for rice to control blast diseases and enhance yield.
Isolation, identification, and the growth promoting effects of two antagonistic actinomycete strains from the rhizosphere of Mikania micrantha Kunth Microbiol. Res. (IF 3.037) Pub Date : 2018-01-11 Dandan Han, Lanying Wang, Yanping Luo
Actinomycetes are an important group of gram-positive bacteria that play an essential role in the rhizosphere ecosystem. The confrontation culture and Oxford cup method were used to evaluate the antagonistic activities of strains, which were isolated from the rhizosphere soil of Mikania micrantha. The two isolates were identified using morphological and physiological tests combined with 16S rRNA-based molecular analysis, respectively. The type I polyketone synthase (PKS-I) was amplified. The constituents of fermentation metabolites were analyzed by gas chromatography mass spectrometry. The plant growth promoting effect was determined. Finally, the growth of wheat seedlings was assessed using the Petri dish method. Overall, of the isolated twelve strains, WZS1-1 and WZS2-1 could significantly inhibit target fungi. Isolate WZS1-1 was identified as Streptomyces rochei, and WZS2-1 was identified as Streptomyces sundarbansensis. In particular, Fusarium graminearum (FG) from wheat was inhibited by more than 80%, and the inhibitory bandwidths against FG were 31 ± 0.3 mm and 19 ± 0.5 mm, respectively. The genes PKS-I were successfully amplified, confirming that these strains are capable of producing biosynthetic secondary metabolites. Major component analysis revealed aliphatic ketones, carboxylic acids, and esters, with n-hexadecanoic acid being the most abundant compound. Plant growth promoting test indicated that both strains produced IAA, presented with orange loops on CAS plates, dissolved phosphorus and potassium, fixed nitrogen, but did not generate organic acids; both strains colonized in soil, while only WZS1-1 colonized in wheat roots. Additionally, the fermentation broth significantly promoted the growth of wheat.
Interdependence of bacterial cell division and genome segregation and its potential in drug development Microbiol. Res. (IF 3.037) Pub Date : 2018-01-05 Hari S. Misra, Ganesh K. Maurya, Reema Chaudhary, Chitra S. Misra
Cell division and genome segregation are mutually interdependent processes, which are tightly linked with bacterial multiplication. Mechanisms underlying cell division and the cellular machinery involved are largely conserved across bacteria. Segregation of genome elements on the other hand, follows different pathways depending upon its type and the functional components encoded on these elements. Small molecules, that are known to inhibit cell division and/or resolution of intertwined circular chromosome and maintenace of DNA topology have earlier been tested as antibacterial agents. The utility of such drugs in controlling bacterial infections has witnessed only partial success, possibly due to functional redundancy associated with targeted components. However, in due course, literature has grown with newer information. This review has brought forth some recent findings on bacterial cell division with special emphasis on crosstalk between cell division and genome segregation that could be explored as novel targets in drug development.
Functional analysis of an APSES transcription factor (GlSwi6) involved in fungal growth, fruiting body development and ganoderic-acid biosynthesis in Ganoderma lucidum Microbiol. Res. (IF 3.037) Pub Date : 2018-01-04 Guang Zhang, Ang Ren, Liang Shi, Jing Zhu, Ailiang Jiang, Dengke Shi, Mingwen Zhao
The APSES transcription factors have been identified as key regulators of fungal development and other biological processes in fungi. In the present study, the function of Ganoderma lucidum GlSwi6, a homolog of Saccharomyces cerevisiae Swi6, was characterized. RNAi was used to examine the function of GlSwi6 in G. lucidum. Silencing GlSwi6 resulted in multiple developmental defects, including reduced fungal growth and increased hyphal branching, and the GlSwi6-silenced strains did not exhibit primordium or fruiting body formation. In addition, the H2O2 and ganoderic-acid (GA) levels of the GlSwi6-silenced strains decreased approximately 50% and 25%, respectively, compared with those of the WT strain. Furthermore, the addition of H2O2 led to the recovery of the GA levels of GlSwi6-silenced strains, implying that GlSwi6 might regulate GA biosynthesis by regulating the intracellular ROS levels. Taken together, these results indicate that GlSwi6 is involved in fungal growth, development and GA biosynthesis in G. lucidum.
Diversity and Bioprospecting of Extremely Halophilic Archaea isolated from Algerian Arid and Semi-Arid Wetland Ecosystems for Halophilic-Active Hydrolytic Enzymes Microbiol. Res. (IF 3.037) Pub Date : 2018-01-04 Taha Menasria, Margarita Aguilera, Hacène Hocine, Leyla Benammar, Ammar Ayachi, Abdelkrim Si Bachir, Ahmed Dekak, Mercedes Monteoliva-Sánchez
The diversity of haloarchaea associated with different dry salt lakes in northeastern Algeria was investigated together with their potential of hydrolytic enzyme production. A total of 68 aerobic halophilic archaea were isolated from saline sediments. Based on the 16S rRNA gene sequencing, the isolates were assigned to seven phylotypes within the class Halobacteria sequences, namely Haloarcula, Halococcus, Haloferax, Halogeometricum, Haloterrigena, Natrialba, and Natrinema. The results showed that Haloferax group was found to be dominant in all samples (30 isolates) (44%) with high diversity, followed by Halococcus spp. (13%) (9 isolates). All phylotypes are extreme halophiles and thermotolerant with the ability to grow at temperatures up to 48 °C. In addition, the screening for extracellular halophilic enzymes showed that 89.7% of the isolates were able to produce at least two types of the screened enzymes respectively. The strains producing esterase, gelatinase, inulinase, cellulase and protease activities were the most diverse functional group. These data showed an abundant and diverse haloarchaeal community, detected in Algerian wetland ecosystems, presenting a promising source of molecules with important biotechnological applications.
Volatiles produced by Bacillus mojavensis RRC101 act as plant growth modulators and are strongly culture-dependent Microbiol. Res. (IF 3.037) Pub Date : 2018-01-03 M. Rath, T.R. Mitchell, S.E. Gold
Volatile organic compounds (VOCs) produced by Plant Growth Promoting Rhizobacteria have recently been investigated due to their role in plant growth promotion and defense. Whereas some bacterial VOCs like 3-hydroxy-2-butanone (acetoin) and 2,3-butanediol produced by strains of Bacillus subtilis and Bacillus amyloliquefaciens promote plant growth, others like hydrogen cyanide and 3-phenylpropionic acid are phytotoxic, inhibiting plant growth. Bacillus mojavensis, a close relative of B. subtilis, is an endophytic bacterium of maize that has been shown to have antagonistic activity against the mycotoxigenic phytopathogen Fusarium verticillioides and growth promotion activity on maize seedlings. To investigate the growth promotion activity of B. mojavensis, Arabidopsis thaliana seedlings were grown on 1/2x Murashige & Skoog (MS) medium in divided Petri dishes while bacteria were grown either on 1/2x MS or nutrient agar (NA) medium, so that only microbial volatiles reached the seedlings. Significant plant growth promotion in Arabidopsis seedlings was observed when 1/2x MS medium was used for bacterial growth. In contrast, phytotoxicity was observed with bacterial growth on NA medium. These results indicate that VOCs produced by B. mojavensis may act as plant growth modulators rather than just promoters. Using Solid Phase Microextraction (SPME) coupled with GC–MS, the plant growth promoting compounds acetoin and 2, 3-butanediol were both identified as being produced by B. mojavensis on growth promoting 1/2x MS medium. In contrast, while no phytotoxic VOC was conclusively identified from B. mojavensis on NA medium, detection of relatively high levels of acetone/2-propanone indicates its possible contribution to Arabidopsis phytotoxicity.
Phospholipases play multiple cellular roles including growth, stress tolerance, sexual development, and virulence in fungi Microbiol. Res. (IF 3.037) Pub Date : 2018-01-03 Ananya Barman, Dibakar Gohain, Utpal Bora, Ranjan Tamuli
Phospholipases are ubiquitous enzymes that hydrolyze phospholipids. Based on the cleavage site of the ester linkage in the substrate phospholipids, phospholipases are classified into four major types phospholipase A (PLA), phospholipase B (PLB), phospholipase C (PLC), and phospholipase D (PLD), which are further classified into various subtypes. Phospholipases hydrolyze phospholipids into various signaling products including phosphatidic acid (PA), diacylglycerol (DAG), free fatty acids (FFAs), and lyso-phospholipids (LPLs). These signaling products regulate numerous processes such as cytoskeletal dynamics, growth, homeostasis, membrane remodeling, nutrient acquisition, secretion, signal transduction, stress tolerance, sexual development, and virulence in various organisms including fungi. Due to these key cellular roles, phospholipases are also promising targets in diagnostic and therapeutic applications. In this review, we discuss current knowledge about the cellular roles of different classes of phospholipases in fungi.
Genetic manipulation of Fonsecaea pedrosoi using particles bombardment and Agrobacterium mediated transformation Microbiol. Res. (IF 3.037) Pub Date : 2018-01-02 Camille Silva Florencio, Fabiana Alves Silva Brandão, Marcus de Mello Teixeira, Anamélia Lorenzetti Bocca, Maria Sueli S. Felipe, Vânia Aparecida Vicente, Larissa Fernandes
Fonsecaea pedrosoi, a melanized fungal pathogen that causes Chromoblastomycosis, a human disease with a worldwide distribution. Biolistic is a widely used technique for direct delivery of genetic material into intact cells by particles bombardment. Another well-established transformation method is Agrobacterium-mediated transformation (ATMT), which involves the transfer of a T-DNA from the bacterium to the target cells. In F. pedrosoi there are no reports of established protocols for genetic transformation, which require optimization of physical and biological parameters. In this work, intact conidia of F. pedrosoi were particle bombarded and subjected to ATMT. In addition, we proposed Hygromycin B, Nourseothricin and Neomycin as dominant selective markers for F. pedrosoi and vectors were constructed. We tested two parameters for biolistic: the distance of the particles to the target cells and time of cells recovery in nonselective medium. The biolistic efficiency was 37 transformants/μg of pFpHYG, and 45 transformants/μg of pAN7.1. Transformants expressing GFP were successfully obtained by biolistic. A co-culture ratio of 10: 1 (bacterium: conidia) and co-incubation time of 72 hours yielded the largest number of transformants after ATMT. Southern blot analysis showed the number of foreign DNA insertion into the genome is dependent upon the plasmid used to generate the mutants. This work describes for the first time two efficient methods for genetic modification of Fonsecaea and these results open new avenues to better understand the biology and pathogenicity of the main causal agent of this neglected disease.
Rapid screening of starter cultures for maari based on antifungal properties Microbiol. Res. (IF 3.037) Pub Date : 2017-11-11 Donatien Kaboré, Mérilie Gagnon, Denis Roy, Hagrétou Sawadogo-Lingani, Bréhima Diawara, Gisèle LaPointe
Forty Bacillus isolates obtained from maari (used as condiment in Burkina Faso) including 17 B. subtilis, 4 B. circulans, 7 B. pumilus and 6 B. licheniformis were investigated for use as starter cultures in maari production. The isolates were screened by PCR for the sfp gene responsible for the production of the lipopeptide biosurfactant, surfactin. The sfp gene was detected in all of the seventeen B. subtilis isolates, in 2 out of 7 B. pumilus, in 4 out of 6 B. licheniformis whereas no B. circulans was positive for the sfp gene by PCR screening. Furthermore, all the 40 Bacillus spp. were screened for biosurfactant production and inhibitory activity against Aspergillus flavus, A. niger, A. versicolor and Rhizopus oryzae. Results demonstrated a relationship between the presence of the sfp gene and the antifungal activity and biosurfactant production of Bacillus isolates. In addition, molecular typing of the 17 B. subtilis isolates by Multilocus Sequence Typing (MLST) resulted in 15 Sequence Types, one of them included three strains. Randomly Amplified Polymorphic DNA-PCR (RAPD-PCR), used for B. licheniformis, B. megaterium, B. circulans and B. pumilus revealed that the inhibitory activity and biosurfactant production were strain-dependent. Finally, the detection of chitinase (chi) and β-glucanase (glu) biosynthesis genes was found to be associated with the antifungal activity for 16 B. subtilis isolates. The present work provides a greater understanding of the antifungal activity and biosurfactant production ability within the Bacillus spp. isolated from maari and contributes to the selection of Bacillus isolates to be used as starter cultures for controlled production of maari.
DNA sequence-specific dimeric bisbenzimidazoles DBP(n) and DBPA(n) as inhibitors of H-NS silencing in bacterial cells Microbiol. Res. (IF 3.037) Pub Date : 2017-11-14 Olga E. Melkina, Vasilii S. Koval, Alexander A. Ivanov, Alexei L. Zhuze, Gennadii B. Zavilgelsky
DNA sequence-specific fluorescent dimeric bisbenzimidazoles DBP(n) and DBPA(n), noncovalently interacting with A-T pairs in the minor groove of double-stranded DNA were used for studying and monitoring the expression of histone-like H-NS-dependent promoters. Histone-like H-NS selectively binds to AT-rich segments of DNA and silences a large number of genes in bacterial chromosomes. The H-NS-dependent promoters of Quorum Sensing (QS)-regulated lux operons of the marine bacteria mesophilic Aliivibrio fischeri, psychrophilic Aliivibrio logei were used. Escherichia coli lux biosensors were constructed by cloning fragments bearing QS-regulated promoters into the vector, thereby placing each fragment upstream of the promoterless Photorhabdus luminescens luxCDABE genes. It was shown that the dimeric bisbenzimidazoles DBP(n) and DBPA(n) counteract the H-NS silencing activity. Thus, the presence of DBP(n) or DBPA(n) in the medium leads to an approximately 10–100-fold increase in the level of transcription of QS promoters in E. coli hns+. The largest decrease in the level of H-NS repression was observed using ligands containing a linker with a length of ca. 18 Å, such as DBP(2) and DBPA(2). Ligands containing linkers with n = 1 and 3 are an order of magnitude less active; ligands with n = 4 are inactive. DBPA(2) exhibits activity starting with a concentration of 0.5 μM; the minimum concentration of DBP(2) is 5–7 times higher. It is suggested that A-T pairs located at five nucleotide pair intervals, which correspond to the linker length in highly active ligands with n = 2, play a key role in the structure of H-NS-binding sites in QS-regulated promoters.
Desert actinobacteria as a source of bioactive compounds production with a special emphases on Pyridine-2,5-diacetamide a new pyridine alkaloid produced by Streptomyces sp. DA3-7 Microbiol. Res. (IF 3.037) Pub Date : 2017-11-21 Krishnasamy Nithya, Chinnasamy Muthukumar, Bhaskar Biswas, Naiyf S. Alharbi, Shine Kadaikunnan, Jamal M. Khaled, Dharumadurai Dhanasekaran
In the present study, 134 morphologically distinct actinobacteria isolates were obtained from soil samples from 10 different localities in the Saudi Arabian desert. The preliminary screening revealed that 16 of these isolates possessed antimicrobial activity. One isolate, which was identified as Streptomyces sp. DA3-7, possessed broad-spectrum antimicrobial activity against both gram-positive and gram-negative bacteria, as well as against fungi, and modified nutrient glucose medium was suitable for Streptomyces sp. DA3-7 to produce extracellular metabolites. The ethyl acetate extract of Streptomyces sp. DA3-7 exhibited antimicrobial activity against Enterococcus faecalis and Salmonella typhimurium, with minimum inhibitory concentrations of 78 and 156 μg/mL, respectively, as well as strong cytotoxicity (24 h IC50 85 μg/mL) against MCF-7 human breast adenocarcinoma cells. The active compound was separated, purified, and identified as Pyridine-2,5-diacetamide (C9H11N3O2 + H+, 194.21), which possessed a lowest minimum inhibitory concentration (31.25 μg/mL) against both Escherichia coli and Cryptococcus neoformans. The antimicrobial activities of this novel compound are reported here for the first time.
Multifarious plant growth promotion by an entomopathogenic fungus Lecanicillium psalliotae Microbiol. Res. (IF 3.037) Pub Date : 2017-12-01 C.M. Senthil Kumar, T.K. Jacob, S. Devasahayam, Stephy Thomas, C. Geethu
For the greater good: Programmed cell death in bacterial communities Microbiol. Res. (IF 3.037) Pub Date : 2017-12-01 Stijn H. Peeters, Marien I. de Jonge
Functional characterization of murB-potABCD operon for polyamine uptake and peptidoglycan synthesis in Streptococcus suis Microbiol. Res. (IF 3.037) Pub Date : 2017-11-14 Wanquan Liu, Meifang Tan, Chunyan Zhang, Zhuofei Xu, Lu Li, Rui Zhou
Spermidine (Spd), spermine (Spm), and putrescine (Put), which are the most widely distributed cellular polyamines, are essential for normal growth and multiplication of both eukaryotic and prokaryotic cells. In this study, we identified the only putative polyamine transport system PotABCD in Streptococcus suis, a worldwide zoonotic Gram-positive pathogen causing lethal infections in humans and pigs. It was discovered that S. suis could uptake polyamines preferably Spd and Spm. By constructing a potA deleted mutant, we confirmed that PotABCD was responsible for polyamine uptake, and PotD bound to the protein of polyamines. The four PotABCD genes were co-transcribed with murB, a gene involved in peptidoglycan (PG) synthesis. Furthermore the roles of polyamine transport system in maintaining the PG structure were detected to understand the biological significance of this co-transcription. In contrast to the wild type, the mutant ΔpotA exhibited elongated chain length and abnormal cell division morphology. Phenotypic changes were attributed to be the up-regulation of genes involved in PG synthesis and hydrolysis in ΔpotA. Additionally, polyamines functioned not only as feedback regulators of PotA by inhibiting PotA activity but also as regulators on potABCD and genes involved in PG synthesis. This study reveals the functions of PotABCD in polyamine transport and the regulatory roles of polyamines in PG synthesis. Results provide new insights into the machineries contributing to normal growth and cell division of S. suis.
The opportunistic human fungal pathogen Candida albicans promotes the growth and proliferation of commensal Escherichia coli through an iron-responsive pathway Microbiol. Res. (IF 3.037) Pub Date : 2017-12-20 Shanshan Li, Xiaoyu Yu, Wenjuan Wu, Daniel Z. Chen, Ming Xiao, Xinhua Huang
Candida albicans is a commensal fungal species that commonly colonizes a heterogeneous mixture of human body where it intimately interacts with other microbes in the host environment such as the gastrointestinal (GI) tract. Most studies in fungal-bacterial interactions are about synergistic or antagonistic effects of bacterial functions on fungal physiological activities including pathogenicity. Very few studies have been demonstrated about the role of fungi on bacteria. In this study, we investigated the interactions between C. albicans and the bacterium Escherichia coli and unexpectedly observed that C. albicans enhances growth and proliferation of Escherichia coli strain K12 by facilitating its cell division. Importantly, we found, based on our genetic screens, that both fungus- and bacterium-derived factors, including the iron-responsive transcription factors Sef1 and Sfu1 in C. albicans and the siderophere enterobactin transporters FepD and FepG in E. coli, actively contribute to this transkingdom interaction. Deletion of SFU1 or SEF1 caused a dramatic reduction in growth enhancement of E. coli. Compared to the wild type E. coli, the enhanced growth of both fepD and fepG null mutants were largely dampened. However, the E. coli mutant lacking entB, a key enzyme catalyzing the biosynthesis of siderophore enterobactin, showed similar growth enhancement as the wild type when co-inoculated with C. albicans. C. albicans promotes growth and proliferation of the commensal bacterium E. coli and an iron-responsive signaling pathway appears to be required. C. albicans may act to supply a siderophere-like molecule that captures the environmental iron to promote the growth of E. coli. Our studies gave insight into a novel interacting mechanism operative in interspecies communication that occurs when bacteria and fungi co-exist.
Comparative transcriptomic analysis of Cerrena unicolor revealed differential expression of genes engaged in degradation of various kinds of wood Microbiol. Res. (IF 3.037) Pub Date : 2017-12-20 Grzegorz Janusz, Andrzej Mazur, Jerzy Wielbo, Piotr Koper, Kamil Żebracki, Anna Pawlik, Beata Ciołek, Andrzej Paszczyński, Agnieszka Kubik-Komar
To explore the number of enzymes engaged by Cerrena unicolor FCL139 for wood degradation, the transcriptomes of the fungus growing on birch, ash, maple sawdust and the control liquid medium were analyzed. Among 12,966 gene models predicted for the C. unicolor genome, 10,396 all-unigenes were detected, of which 9,567 were found to be expressed in each of the tested growth media. The highest number (107) of unique transcripts was detected during fungus growth in the control liquid medium, while the lowest number (11) – in the fungal culture comprising maple saw dust. Analysis of C. unicolor transcriptomes identified numerous genes whose expression differed substantially between the mycelia growing in control medium and each of the sawdust media used, with the highest number (828) of upregulated transcripts observed during the fungus growth on the ash medium. Among the 294 genes that were potentially engaged in wood degradation, the expression of 59 was significantly (p < .01) changed in the tested conditions. The transcripts of 37 of those genes were at least four times more abundant in the cells grown in all sawdust media when compared to the control medium. Upregulated genes coding for cellulases and, to a lower extent, hemicellulases predominated during fungus growth on sawdust. Transcripts encoding cellulolytic enzymes were the most abundant in mycelia grown on birch and maple while lower number of such transcripts was detected in fungus growing on ash. The expression pattern of lignolytic activities-coding genes was strongly dependent on the type of sawdust applied for fungus growth medium.
First report of a cross-kingdom pathogenic bacterium, Achromobacter xylosoxidans isolated from stipe-rot Coprinus comatus Microbiol. Res. (IF 3.037) Pub Date : 2017-12-19 Luona Ye, Mengpei Guo, Pengfei Ren, Gangzheng Wang, Yinbing Bian, Yang Xiao, Yan Zhou
Coprinus comatus is an edible mushroom widely cultivated in China as a delicious food. Various diseases have occurred on C. comatus with the cultivated area increasing. In this study, the pathogenic bacterium JTG-B1, identified as Achromobacter xylosoxidans by 16S rDNA and nrdA gene sequencing, was isolated from edible mushroom Coprinus comatus with serious rot disease on its stipe. A. xylosoxidans has been confirmed as an important opportunistic human pathogenic bacterium and has been isolated from respiratory samples from cystic fibrosis. It is widely distributed in the environment. Here, we first report that fungi can also serve as a host for A. xylosoxidans. We confirmed that it can cross-kingdom infect between animals (mice) and fungi (C. comatus). The results of pathogenicity tests, physiological, biochemical and genotyping analysis of A. xylosoxidans from different hosts suggested that different strain of A. xylosoxidans may have pathogenicity differentiation. A. xylosoxidans not only is pathogenic to C. comatus but also may threaten human health.
Could FlhF be a key element that controls Campylobacter jejuni flagella biosynthesis in the initial assembly stage? Microbiol. Res. (IF 3.037) Pub Date : 2017-12-19 Fangzhe Ren, Tianyao Lei, Zhaojun Song, Ting Yu, Qiuchun Li, Jinlin Huang, Xin-an Jiao
The disordered arrangement of flagella biosynthetic genes, combined with a simplified regulatory mechanism, has made elucidating the process of Campylobacter jejuni flagellation difficult. FlhF is a recently identified element that controls the assembly of the flagella, although its function mechanism and regulatory preference are not well defined at present. In this study, we found that inactivation of FlhF caused the transcription of most flagella genes down-regulated. The importance of FlhF was systematically evaluated by analyzing changes in the transcription profiles between wild-type and flhF mutant strains, which showed that FlhF affects late flagella genes obviously. FlhF is constitutively expressed during C. jejuni growth, demonstrating that it is a class I flagella element that participates in early flagella assembly. In addition, the early flagella component FlhB was not localized to the cell pole in the flhF mutant. Thus, flagella assembly was impeded at the initial stage. We propose a model in which FlhF helps target the early flagella components to the cell pole, functioning prior to the formation of the flagella export apparatus, and thus places FlhF at the top of the flagella regulatory cascade hierarchy. Inactivation of FlhF impeded flagella assembly at the initial stage and decreased transcription of flagella genes through a feed-back control mechanism, leading to FlhF having a significant influence on the expression of late flagella components and resulting in the aflagellate C. jejuni phenotype. Our present study has uncovered how FlhF influences C. jejuni flagella biosynthesis, which will be helpful in understanding the C. jejuni flagella biosynthetic pathway and bacterial flagellation in general.
Monitoring biocalcification potential of Lysinibacillus sp. isolated from alluvial soils for improved compressive strength of concrete Microbiol. Res. (IF 3.037) Pub Date : 2017-12-18 Rajneesh Vashisht, Sampan Attri, Deepak Sharma, Abhilash Shukla, Gunjan Goel
The present study reports the potential of newly isolated calcite precipitating bacteria isolated from alluvial soil to improve the strength and durability of concrete. A total of sixteen samples of alluvial soil and sewage were collected from the different locations of province Solan (India). For isolation, enrichment culture technique was used to enrich calcite precipitating strains in Urea broth. After enrichment, fourteen distinct bacterial strains were obtained on Urea agar. Based on qualitative and quantitative screening for urease activity, five isolates were obtained possessing higher calcite formation and urease activities (38–77 μmhos/cm) as compared with standard strain of Bacillus megaterium MTCC 1684 (77 μmhos/cm). An isolate I13 identified as Lysinibacillus sp. was selected for self healing property in the concrete mix of M20. An improved compressive strength of 1.5 fold was observed in concrete samples amended with Lysinibacillus sp. over the concrete amended with B. megaterium MTCC 1684 after 28 days of curing. The higher calcite precipitation activity was indicated in Lysinibacillus sp. by FE-SEM micrographs and EDX analysis.
A critical role for very long-chain fatty acid elongases in oleic acid-mediated Saccharomyces cerevisiae cytotoxicity Microbiol. Res. (IF 3.037) Pub Date : 2017-11-06 Qiao Wang, Xiuxiu Du, Ke Ma, Ping Shi, Wenbin Liu, Jing Sun, Min Peng, Zhiwei Huang
Elongases FEN1/ELO2 and SUR4/ELO3 are important enzymes involved in the elongation of long-chain fatty acids (LCFAs) to very long-chain fatty acids (VLCFAs) in Saccharomyces cerevisiae. The molecular mechanism of the involvement of these elongases in lipotoxicity is unclear. In the present study, we investigated the role of VLCFA elongases in oleic acid-mediated yeast cytotoxicity. The spot test showed that yeast strains with the deletion of ELO2 or ELO3 were strikingly sensitive to oleic acid, while there was no change on the growth of strain with deleted ELO1 which was involved in the elongation of C14 fatty acid (FA) to C16 FA. By using GC–MS, the unsaturation index was increased in elo2△ and elo3△ mutants after treatment with oleic acid (OLA). However, the proportion of VLCFAs was increased in response to OLA in the wild-type strain. The growth inhibition of elo2△ and elo3△ could be partially rescued by two commonly used antioxidant agents N-acetyl cysteine (NAC) and Ascorbic acid (VC). The further study showed that exposure to excess OLA led to an increase in the levels of reactive oxygen species (ROS) and thiobarbituric acid reactive substances (TBARS), and a decline in the quantity of reduced glutathione (GSH) in both the wild type and mutant strains. However, the antioxidant enzyme activities of superoxide dismutase (SOD) and catalase (CAT) were increased in the wild type and elo1△ strains, while they were significantly decreased in the mutants of elo2△ and elo3△ after treated with excess OLA. Thus, oxidative damage mainly contributed to the cell death induced by OLA in ole2△ and ole3△. Taken together, although disruption of ELO2 or ELO3 did not affect the cellular lipid unsaturation, they altered the distribution and propotion of cellular VLCFAs, leading to the cell membrane impairment, which augmented the ability of OLA to permeabilize the plasma membrane. The data suggest that the very long-chain fatty acids elongases ELO2 and ELO3 play important roles in lipotoxic cell death induced by OLA through maintaining a balanced FA composition in plasma membrane.
Diversity of cultivable bacterial endophytes in Paullinia cupana and their potential for plant growth promotion and phytopathogen control Microbiol. Res. (IF 3.037) Pub Date : 2017-11-01 Rhavena Graziela Liotti, Maria Isabela da Silva Figueiredo, Gilvan Ferreira da Silva, Elisabeth Aparecida Furtado de Mendonça, Marcos Antônio Soares
Endophytic bacteria occupy the same niche of phytopathogens and may produce metabolites that induce the host plant systemic resistance and growth. Host and environmental variables often determine the endophytic community’s structure and composition. In this study, we addressed whether the plant genotype, organ, and geographic location influence the structure, composition, and functionality of endophytic bacterial communities in Paullinia cupana. To characterize the communities and identify strains with potential application in agriculture, we analyzed two P. cupana genotypes cultivated in two cities of the State of Amazonas, Brazil. Endophytic bacteria were isolated from surface-disinfested root, leaf, and seed tissues through the fragmentation and maceration techniques. The colonization rate, number of bacteria, richness, diversity, and functional traits were determined. The plant growth-promoting ability of selected bacterial strains was assessed in Sorghum bicolor. We identified 95 bacterial species distributed in 29 genera and 3 phyla (Proteobacteria, Actinobacteria, and Firmicutes). The colonization rate, richness, diversity, and species composition varied across the plant organs; the last parameter also varied across the plant genotype and location. Some strains exhibited relevant plant growth-promoting traits and antagonistic traits against the main phytopathogens of P. cupana, but they were not separated by functional traits. The main bacterial strains with plant growth-promoting traits induced S. bicolor growth. Altogether, our findings open opportunities to study the application of isolated endophytic bacterial strains in the bioprospection of processes and products.
5-hydroxymethyl-2-furaldehyde from marine bacterium Bacillus subtilis inhibits biofilm and virulence of Candida albicans Microbiol. Res. (IF 3.037) Pub Date : 2017-11-08 Ganapathy Ashwinkumar Subramenium, Thirukannamangai Krishnan Swetha, Prasanth Mani Iyer, Krishnaswamy Balamurugan, Shunmugiah Karutha Pandian
Reactive oxygen species-independent apoptotic pathway by gold nanoparticles in Candida albicans Microbiol. Res. (IF 3.037) Pub Date : 2017-11-06 Minju Seong, Dong Gun Lee
Candida albicans is the most common pathogenic fungus in humans, causing cutaneous and life-threatening systemic infections. In this study, we confirmed using propidium iodide influx that gold nanoparticles (AuNPs), which are promising materials for use as antimicrobial agents, did not affect the membrane permeability of C. albicans. Thus, the fungal cell death mechanisms induced by AuNPs were assessed at intracellular levels including DNA damage, mitochondrial dysfunction, and reactive oxygen species (ROS) overproduction. AuNPs interacted with C. albicans DNA leading to increased nuclear condensation and DNA fragmentation. Changes in the mitochondria induced by AuNPs involving mass, Ca2+ concentrations, and membrane potential indicated dysfunction, though the level of intracellular and mitochondrial ROS were maintained. Although ROS signaling was not disrupted, DNA damage and mitochondrial dysfunction triggered the release of mitochondrial cytochrome c into the cytosol, metacaspase activation, and phosphatidylserine externalization. Additionally, the AuNPs-induced apoptotic pathway was not influenced by N-acetylcysteine, an ROS scavenger. This indicates that ROS signaling is not linked with the apoptosis. In conclusion, AuNPs induce ROS-independent apoptosis in C. albicans by causing DNA damage and mitochondria dysfunction.
Does plant—Microbe interaction confer stress tolerance in plants: A review? Microbiol. Res. (IF 3.037) Pub Date : 2017-11-09 Akhilesh Kumar, Jay Prakash Verma
The biotic and abiotic stresses are major constraints for crop yield, food quality and global food security. A number of parameters such as physiological, biochemical, molecular of plants are affected under stress condition. Since the use of inorganic fertilizers and pesticides in agriculture practices cause degradation of soil fertility and environmental pollutions. Hence it is necessary to develop safer and sustainable means for agriculture production. The application of plant growth promoting microbes (PGPM) and mycorrhizal fungi enhance plant growth, under such conditions. It offers an economically fascinating and ecologically sound ways for protecting plants against stress condition. PGPM may promote plant growth by regulating plant hormones, improve nutrition acquisition, siderophore production and enhance the antioxidant system. While acquired systemic resistance (ASR) and induced systemic resistance (ISR) effectively deal with biotic stress. Arbuscular mycorrhiza (AM) enhance the supply of nutrients and water during stress condition and increase tolerance to stress. This plant-microbe interaction is vital for sustainable agriculture and industrial purpose, because it depends on biological processes and replaces conventional agriculture practices. Therefore, microbes may play a key role as an ecological engineer to solve environmental stress problems. So, it is a feasible and potential technology in future to feed global population at available resources with reduced impact on environmental quality. In this review, we have attempted to explore about abiotic and biotic stress tolerant beneficial microorganisms and their modes of action to enhance the sustainable agricultural production.
Stress response of a clinical Enterococcus faecalis isolate subjected to a novel antimicrobial surface coating Microbiol. Res. (IF 3.037) Pub Date : 2017-11-12 Emanuel Clauss-Lendzian, Ankita Vaishampayan, Anne de Jong, Uwe Landau, Carsten Meyer, Jan Kok, Elisabeth Grohmann
Emerging antibiotic resistance among pathogenic bacteria, paired with their ability to form biofilms on medical and technical devices, represents a serious problem for effective and long-term decontamination in health-care environments and gives rise to an urgent need for new antimicrobial materials. Here we present the impact of AGXX®, a novel broad-spectrum antimicrobial surface coating consisting of micro-galvanic elements formed by silver and ruthenium, on the transcriptome of Enterococcus faecalis. A clinical E. faecalis isolate was subjected to metal stress by growing it for different periods in presence of the antimicrobial coating or silver-coated steel meshes. Subsequently, total RNA was isolated and next-generation RNA sequencing was performed to analyze variations in gene expression in presence of the antimicrobial materials with focus on known stress genes. Exposure to the antimicrobial coating had a large impact on the transcriptome of E. faecalis. After 24 min almost 1/5 of the E. faecalis genome displayed differential expression. At each time-point the cop operon was strongly up-regulated, providing indirect evidence for the presence of free Ag+-ions. Moreover, exposure to the antimicrobial coating induced a broad general stress response in E. faecalis. Genes coding for the chaperones GroEL and GroES and the Clp proteases, ClpE and ClpB, were among the top up-regulated heat shock genes. Differential expression of thioredoxin, superoxide dismutase and glutathione synthetase genes indicates a high level of oxidative stress. We postulate a mechanism of action where the combination of Ag+-ions and reactive oxygen species generated by AGXX® results in a synergistic antimicrobial effect, superior to that of conventional silver coatings.
A review on sustainable yeast biotechnological processes and applications Microbiol. Res. (IF 3.037) Pub Date : 2017-11-21 Subir Kumar Nandy, R.K. Srivastava
Yeast is very well known eukaryotic organism for its remarkable biodiversity and extensive industrial applications. Saccharomyces cerevisiae is one of the most widely used microorganisms in biotechnology with successful applications in the biochemical production. Biological conversion with the focus on the different utilization of renewable feedstocks into fuels and chemicals has been intensively investigated due to increasing concerns on sustainability issues worldwide. Compared with its counterparts, Saccharomyces cerevisiae, the baker’s yeast, is more industrially relevant due to known genetic and physiological background, the availability of a large collection of genetic tools, the compatibility of high-density and large-scale fermentation, and optimize the pathway for variety of products. Therefore, S. cerevisiae is one of the most popular cell factories and has been successfully used in the modern biotech industry to produce a wide variety of products such as ethanol, organic acids, amino acids, enzymes, and therapeutic proteins. This study explores how different sustainable solutions used to overcome various environmental effects on yeast. This work targets a broad matrix of current advances and future prospect in yeast biotechnology and discusses their application and potential in general.
Comparative analysis of gut bacterial communities of green turtles (Chelonia mydas) pre-hospitalization and post-rehabilitation by high-throughput sequencing of bacterial 16S rRNA gene Microbiol. Res. (IF 3.037) Pub Date : 2017-11-21 Md. Shamim Ahasan, Thomas B. Waltzek, Roger Huerlimann, Ellen Ariel
Stranded green turtles (Chelonia mydas) are often cared for in rehabilitation centers until they recover. Although the specific causal agents of diseases in stranded turtles are difficult to diagnose, we know that gut microbiota of green turtles play a vital role in health as well as a wide range of diseases. The objective of this study was to characterize and compare the gut bacterial communities between pre-hospitalization (PH) and post-rehabilitation (PR) stranded green turtles using high-throughput sequencing analysis targeting V1–V3 regions of the bacterial 16S rRNA gene. A total of eight cloacal swab samples were collected from four green turtles undergoing rehabilitation. Proteobacteria dominating in both PH and PR samples without any significant difference. Firmicutes was the second and Bacteroidetes was the third most abundant phylum in PH samples, while Bacteroidetes prevailed in PR samples, followed by Firmicutes. The predominance of the genus Bacteroides in both PH and PR samples indicates the importance of this genus in turtle gut health. At a class level, Epsilonproteobacteria was significantly (P < 0.05) associated with PH samples and Deltaproteobacteria predominated (P < 0.05) in PR samples. The significant abundance of Campylobacter fetus, Escherichia coli, Clostridium botulinum and Vibrio parahaemolyticus in PH samples indicate pathogenic associations with stranded green turtles with zoonotic potential. The presence of Salmonella enterica in only PR samples suggest possible acquisition of this bacteria during rehabilitation. In this study, all post-rehabilitation green turtles exhibited similar bacterial communities, irrespective of their microbial compositions at pre-hospitalization. The marked differences in the gut bacterial communities of PH and PR turtles indicate the outcome of dietary, management and environmental shift during rehabilitation. Therefore, it is important to address the process of restoring normal gut microbiota of recovered turtles prior to release back to their natural habitat.
Modulation in phenolic root exudate profile of Abelmoschus esculentus expressing activation of defense pathway Microbiol. Res. (IF 3.037) Pub Date : 2017-11-26 Shatrupa Ray, Sandhya Mishra, Kartikay Bisen, Surendra Singh, Birinchi Kumar Sarma, Harikesh Bahadur Singh
Phenolics play a key role in communication between plants and microbes in the rhizosphere. In this study, shikimic, gallic, fumaric, ferulic, vanillic acid and quercetin in root exudates of Abelmoschus esculentus act as chemoattractants of endophytic Alcaligenes faecalis strains, BHU 12, BHU 16 and BHU M7. In vitro chemotaxis assay showed that BHU 12 expressed highest chemotactic movement (CFU ∼50 × 1012) towards A.esculentus root exudates followed by BHU 16 and BHU M7 (CFU∼ 9 × 1012), thereby confirming their ability to colonize the host rhizoplane region. However, BHU 16 expressed highest biofilm formation ability followed by BHU 12 and BHU M7. Assessment of chemotactic and biofilm formation potential towards individual phenolic acids revealed BHU 12 to be maximally attracted towards 1 μM shikimic acid (2 × 1015) while BHU 16 towards 1 mM vanillic acid (6.5 × 1012) and BHU M7 towards 1 mM ferulic acid (3.5 × 1012), thereby confirming the phenolic acid components responsible for particularly attracting the endophytic isolates. Upon colonization, the endophytic isolates modified the phenolic profiles of root exudates in planta in a manner so as to plausibly attract more of the beneficial rhizospheric microbiota as well as self-fortification against pathogenic microbes. This hypothesis was verified by monitoring the changes in phenolic components of A. esculentus root exudate owing to S. rolfsii infection, a disastrous soil-borne pathogen. Thus, on the whole, the work provides intricate details of plant-endophyte interactions for biotic stress management through careful manipulation of root exudates, thereby aiding in sustainable agriculture.
Leptospirosis in human: Biomarkers in host immune responses Microbiol. Res. (IF 3.037) Pub Date : 2017-11-28 Chin VK, Lee TY, Lim WF, Wan Shahriman YWY, Syafinaz AN, Zamberi S, Maha A
Leptospirosis remains one of the most widespread zoonotic diseases caused by spirochetes of the genus Leptospira, which accounts for high morbidity and mortality globally. Leptospiral infections are often found in tropical and subtropical regions, with people exposed to contaminated environments or animal reservoirs are at high risk of getting the infection. Leptospirosis has a wide range of clinical manifestations with non-specific signs and symptoms and often misdiagnosed with other acute febrile illnesses at early stage of infection. Despite being one of the leading causes of zoonotic morbidity worldwide, there is still a gap between pathogenesis and human immune responses during leptospiral infection. It still remains obscure whether the severity of the infection is caused by the pathogenic properties of the Leptospira itself, or it is a consequence of imbalance host immune factors. Hence, in this review, we seek to summarize the past and present milestone findings on the biomarkers of host immune response aspects during human leptospiral infection, including cytokine and other immune mediators. A profound understanding of the interlink between virulence factors and host immune responses during human leptospirosis is imperative to identify potential biomarkers for diagnostic and prognostic applications as well as designing novel immunotherapeutic strategies in future.
The special existences: nanoRNA and nanoRNase Microbiol. Res. (IF 3.037) Pub Date : 2017-11-29 Hebin Liao, Mafeng Liu, Xiaolan Guo
To adapt to a wide range of nutritional and environmental changes, cells must adjust their gene expression profiles. This process is completed by the frequent transcription and rapid degradation of mRNA. mRNA decay is initiated by a series of endo- and exoribonucleases. These enzymes leave behind 2- to 5-nt-long oligoribonucleotides termed “nanoRNAs” that are degraded by specific nanoRNases; the degradation of nanoRNA is essential because nanoRNA can mediate the priming of transcription initiation that is harmful for the cell via an unknown mechanism. Identified nanoRNases include Orn in E. coli, NrnA and NrnB in B. subtilis, and NrnC in Bartonella. Even though these nanoRNases can degrade nanoRNA specifically into mononucleotides, the biochemical features, structural features and functional mechanisms of these enzymes are different. Sequence analysis has identified homologs of these nanoRNases in different bacteria, including Gammaproteobacteria, Betaproteobacteria, Alphaproteobacteria, Firmicutes and Cyanobacteria. However, there are several bacteria, such as those belonging to the class Thermolithobacteria, that do not have homologs of these nanoRNases. In this paper, the source of nanoRNA, the features of different kinds of nanoRNases and the distribution of these enzymes in prokaryotes are described in detail.
A glucanolytic Pseudomonas sp. associated with Smilax bona-nox L. displays strong activity against Phytophthora parasitica Microbiol. Res. (IF 3.037) Pub Date : 2017-12-01 Ashraf S.A. El-Sayed, Asma Akbar, Irum Iqrar, Robina Ali, David Norman, Mary Brennan, Gul Shad Ali
Biological control is an eco-friendly strategy for mitigating and controlling plant diseases with negligible effects on human health and environment. Biocontrol agents are mostly isolated from field crops, and microbiomes associated with wild native plants is underexplored. The main objective of this study was to characterize the bacterial isolates associated with Smilax bona-nox L, a successful wild plant with invasive growth habits. Forty morphologically distinct bacterial isolates were recovered from S. bona-nox. Based on 16S rRNA gene sequencing, these isolates belonged to 12 different genera namely Burkholderia, Pseudomonas, Xenophilus, Stenotrophomonas, Pantoea, Enterobactriaceae, Kosakonia, Microbacterium, Curtobacterium, Caulobacter, Lysinibacillus and Bacillus. Among them, Pseudomonas sp. EA6 and Pseudomonas sp. EA14 displayed the highest potential for inhibition of Phytophthora. Based on sequence analysis of rpoD gene, these isolates revealed a 97% identity with a Pseudomonas fluorescence strain. Bioactivity-driven assays for finding bioactive compounds revealed that crude proteins of Pseudomonas sp. EA6 inhibited mycelial growth of P. parasitica, whereas crude proteins of Pseudomonas sp. EA14 displayed negligible activity. Fractionation and enzymatic analyses revealed that the bioactivity of Pseudomonas sp. EA6 was mostly due to glucanolytic enzymes. Comparison of chromatographic profile and bioactivity assays indicated that the secreted glucanolytic enzymes consisted of β-1,3 and β-1,4 glucanases, which acted together in hydrolyzing Phytophthora cell walls. Since the biological activity of the crude glucanolytic extract was >60-fold higher than the purified β-1,3 glucanase, the glucanolytic enzyme system of Pseudomonas sp. EA6 likely acts synergistically in cell wall hydrolysis of P. parasitica.
Distribution of apple and blackcurrant microbiota in Lithuania and the Czech Republic Microbiol. Res. (IF 3.037) Pub Date : 2017-09-14 Iglė Vepštaitė-Monstavičė, Juliana Lukša, Ramunė Stanevičienė, Živilė Strazdaitė-Žielienė, Vyacheslav Yurchenko, Saulius Serva, Elena Servienė
The microbial assemblies on the surface of plants correlate with specific climatic features, suggesting a direct link between environmental conditions and microbial inhabitation patterns. At the same time however, microbial communities demonstrate distinct profiles depending on the plant species and region of origin. In this study, we report Next Generation Sequencing-based metagenomic analysis of microbial communities associated with apple and blackcurrant fruits harvested from Lithuania and the Czech Republic. Differences in the taxonomic composition of eukaryotic and prokaryotic microorganisms were observed between plant types. Our results revealed limited geographic differentiation between the bacterial and fungal communities associated with apples. In contrast, blackcurrant berries harvested from different regions demonstrated high diversity in both bacterial and fungal microbiota structures. Among fungal and bacterial microorganisms, we identified both potentially beneficial (Cryptococcus, Hanseniaspora, Massilia, Rhodotorula, Sphingomonas) and phytopathogenic microorganisms (Cladosporium, Pantoea, Phoma, Pseudomonas, Septoria, Taphrina) indicating their important roles in ecological and evolutionary processes.
Combination of amplified rDNA restriction analysis and high-throughput sequencing revealed the negative effect of colistin sulfate on the diversity of soil microorganisms Microbiol. Res. (IF 3.037) Pub Date : 2017-09-14 Tingli Fan, Yongxue Sun, Jinju Peng, Qun Wu, Yi Ma, Xiaohui Zhou
Colistin sulfate is widely used in both human and veterinary medicine. However, its effect on the microbial ecologyis unknown. In this study, we determined the effect of colistin sulfate on the diversity of soil microorganisms by amplified rDNA restriction analysis (ARDRA) and high-throughput sequencing.ARDRAshowed that the diversity of DNA from soil microorganisms was reduced after soil was treated with colistin sulfate, with the most dramatic reductionobserved after 35 days of treatment. High-throughput sequencing showed that the Chao1 and abundance-based coverage estimators (ACE) were reduced in the soils treated with colistin sulfate for 35 dayscompared to those treated with colistin sulfate for 7 days. Furthermore, Chao1 and ACE tended to be lower when higher concentration of colistin sulfate was used, suggesting that the microbial abundance is reduced by colistin sulfate in a dose-dependent manner. Shannon index showed that the diversity of soil microorganism was reduced upon treatment with colistin sulfate compared to the untreated control group. Following 7 days of treatment, Bacillus, Clostridiumand Sphingomonas were sensitive to all the concentration of colistin sulfate used in this study. Following 35 days of treatment, the abundance of Choroplast, Haliangium, Pseudomonas, Lactococcus, and Clostridium was significantly decreased. Our results demonstrated that colistin sulfate especially at high concentration (≥5 mg/kg) could alter the population structure of microorganisms and consequently the microbial community function in soil.
Isolation and characterisation of theobromine-degrading filamentous fungi Microbiol. Res. (IF 3.037) Pub Date : 2017-09-19 Daniel Oduro-Mensah, Augustine Ocloo, Sammy T. Lowor, Evelyn Y. Bonney, Laud K.N.A. Okine, Naa Ayikailey Adamafio
Strategies for achieving global food security include identification of alternative feedstock for use as animal feed, to contribute towards efforts at increasing livestock farming. The presence of theobromine in cocoa pod husks, a major agro-waste in cocoa-producing countries, hinders its utilisation for this purpose. Cheap treatment of cocoa pod husks to remove theobromine would allow largescale beneficial use of the millions of metric tonnes generated annually. The aim of this study was to isolate theobromine-degrading filamentous fungi that could serve as bioremediation agents for detheobromination of cocoa pod husks. Filamentous fungi were screened for ability to degrade theobromine. The most promising isolates were characterized with respect to optimal environmental conditions for theobromine degradation. Secretion of theobromine-degrading enzymes by the isolates was investigated. Theobromine degradation was monitored by HPLC. Of fourteen theobromine-degrading isolates collected and identified by rDNA 5.8S and ITS sequences, seven belonged to Aspergillus spp. and six were Talaromyces spp. Based on the extent of theobromine utilization, four isolates; Aspergillus niger, Talaromyces verruculosus and two Talaromyces marneffei, showed the best potential for use as bioagents for detheobromination. First-time evidence was found of the use of xanthine oxidase and theobromine oxidase in degradation of a methylxanthine by fungal isolates. Metabolism of theobromine involved initial demethylation at position 7 to form 3-methylxanthine, or initial oxidation at position 8 to form 3,7-dimethyuric acid. All four isolates degraded theobromine beyond uric acid. The data suggest that the four isolates can be applied to substrates, such as cocoa pod husks, for elimination of theobromine.
Klebsiella sp. confers enhanced tolerance to salinity and plant growth promotion in oat seedlings (Avena sativa) Microbiol. Res. (IF 3.037) Pub Date : 2017-09-23 Swapnil Sapre, Iti Gontia-Mishra, Sharad Tiwari
Plant growth and yield is adversely affected by soil salinity. Salt tolerant plant growth-promoting rhizobacteria (PGPR) strain IG 3 was isolated from rhizosphere of wheat plants. The isolate IG 3 was able to grow in presence of NaCl ranging from 0 to 20% in Luria Bertani medium. The present study was planned to evaluate the role of inoculation of PGPR strain IG 3 and its efficacy in augmenting salt tolerance in oat (Avena sativa) under NaCl stress (100 mM). The physiological parameter such as shoot length, root length, shoot dry weight, root dry weight and relative water content (RWC) were remarkably higher in IG 3 inoculated plants in comparison to un-inoculated plants under NaCl stress. Similarly, the biochemical parameters such as proline content, electrolyte leakage and malondialdehyde (MDA) content and activities of antioxidant enzymes were analyzed and found to be notably lesser in IG 3 inoculated oat plants in contrast to un-inoculated plants under salt stress. Inoculation of IG 3 strain to oat seedlings under salt stress positively modulated the expression profile of rbcL and WRKY1 genes. Root colonization of root surface and interior was demonstrated using scanning electron microscopy and tetrazolium staining, respectively. Due these outcomes, it could be implicated that inoculation of PGPR strain IG 3 enhanced plant growth under salt stress condition. This study demonstrates that PGPR play an imperative function in stimulating salt tolerance in plants and can be used as biofertilizer to enhance growth of crops in saline areas.
Screening of tropically derived, multi-trait plant growth- promoting rhizobacteria and evaluation of corn and soybean colonization ability Microbiol. Res. (IF 3.037) Pub Date : 2017-09-20 Bruna Durante Batista, Paulo Teixeira Lacava, Andrea Ferrari, Natalia Sousa Teixeira-Silva, Maria Letícia Bonatelli, Sarina Tsui, Mateus Mondin, Elliot Watanabe Kitajima, José Odair Pereira, João Lúcio Azevedo, Maria Carolina Quecine
The present study assessed the plant growth-promoting (PGP) traits and diversity of culturable rhizobacteria associated with guarana (Paullinia cupana), a typical tropical plant. Ninety-six bacteria were isolated, subjected to biochemical tests, and identified by partial or total 16S rDNA sequencing. Proteobacteria and Firmicutes were the dominant rhizospheric phyla found, and Burkholderia and Bacillus were the most abundant genera. Thirteen strains exhibited the four PGP traits evaluated, and most of them belonged to the genus Burkholderia. Two multi-trait PGP strains, RZ2MS9 (Bacillus sp.) and RZ2MS16 (Burkholderia ambifaria), expressively promoted corn and soybean growth under greenhouse conditions. Compared to the non-inoculated control, increases in corn root dry weight of 247.8 and 136.9% were obtained with RZ2MS9 and RZ2MS16 inoculation, respectively, at 60 days after seeding. The dry weights of corn and soybean shoots were significantly higher than those of non-inoculated plants, showing increases of more than 47% for both strains and crops. However, soybean root dry weight did not increased after bacterial inoculation with either strain. The colonization behavior of RZ2MS16 was assessed using GFP-labeling combined with fluorescence microscopy and a cultivation-based approach for quantification. RZ2MS16:gfp was able to colonize the roots and shoots of corn and soybean, revealing an endophytic behavior.
Characterization and assessment of two biocontrol bacteria against Pseudomonas syringae wilt in Solanum lycopersicum and its genetic responses Microbiol. Res. (IF 3.037) Pub Date : 2017-09-12 Kaliannan Durairaj, Palanivel Velmurugan, Jung-Hee Park, Woo-Suk Chang, Yool-Jin Park, Palaninaicker Senthilkumar, Kyung-Min Choi, Jeong-Ho Lee, Byung-Taek Oh
Pseudomonas and Bacillus species are attractive due to their potential bio-control application against plant bacterial pathogens. Pseudomonas aeruginosa strain D4 and Bacillus stratosphericus strain FW3 were isolated from mine tailings in South Korea. In these potent bacterial strains, we observed improved antagonistic activity against Pseudomonas syringae DC3000. These strains produced biocatalysts for plant growth promotion, and in vivo examination of Solanum lycopersicum included analysis of disease severity, ion leakage, chlorophyll content, and H2O2 detection. In addition, regulation of the defense genes pathogen-related protein 1a (PR1a) and phenylalanine ammonia lyase (PAL) was compared with treated plants and untreated control plants. The results suggest that these two bacterial strains provide protection against plant pathogens via direct and indirect modes of action and could be used as a bio-control agent.
A novel Burkholderia ambifaria strain able to degrade the mycotoxin fusaric acid and to inhibit Fusarium spp. growth Microbiol. Res. (IF 3.037) Pub Date : 2017-09-22 Ester Simonetti, Irma N. Roberts, Marcela S. Montecchia, Flavio H. Gutierrez-Boem, Federico M. Gomez, Jimena A. Ruiz
A comprehensive review of non-enterica subspecies of Salmonella enterica Microbiol. Res. (IF 3.037) Pub Date : 2017-10-07 Alexandre Lamas, José Manuel Miranda, Patricia Regal, Beatriz Vázquez, Carlos Manuel Franco, Alberto Cepeda
Salmonella is a major foodborne pathogen with a complex nomenclature. This genus is composed of two species, S. enterica and S. bongori. S. enterica is divided into six subspecies. S. enterica subspecies enterica is composed of more than 1500 serotypes with some of great importance, such as S. Typhimurium and S. Enteritidis. S. enterica subsp. enterica is responsible of more than 99% of human salmonellosis and therefore it is widely studied. However, the non-enterica subspecies of S. enterica have been little studied. These subspecies are considered to be related to cold-blooded animals and their pathogenicity is very limited. Phenotype and genotype information generated from different studies of non-enterica subspecies reveal poor ability to invade host cells and the absence or modification of important virulence factors. Also, the great majority of human infections due to non-enterica subspecies are related to a previous depressed immune system. Therefore, we propose to treat these subspecies only as opportunistic pathogens. For establish this premise, the present review evaluated, among other things, the genomic characteristics, prevalence, antimicrobial resistance and reported human cases of the non-enterica subspecies.
Pathogenic Labyrinthula associated with Australian seagrasses: Considerations for seagrass wasting disease in the southern hemisphere Microbiol. Res. (IF 3.037) Pub Date : 2017-10-09 Stacey M. Trevathan-Tackett, Brooke K. Sullivan, Katie Robinson, Osu Lilje, Peter I. Macreadie, Frank H. Gleason
Marine disease ecology is a growing field of research, particularly for host organisms negatively impacted by a changing climate and anthropogenic activities. A decrease in health and increase in susceptibility to disease has been hypothesised as the mechanism behind wide-spread seagrass die-offs related to wasting disease in the past. However, seagrass wasting disease and the causative pathogen, Labyrinthula, have been vastly understudied in the southern hemisphere. Our aim was to build on the current knowledge of Australian Labyrinthula descriptions and phylogeny, while also providing a first look at wasting disease ecology in Australia. Five seagrass species along a 750 km stretch of coastline in southeastern Australia were sampled. The resulting 38 Labyrinthula isolates represented a diversity of morphotypes and five haplotypes of varying phylogenetic clade positions and virulence. The haplotypes clustered with previously-described phylogenetic clades containing isolates from Asia, USA and Europe. Pathogenicity tests confirmed, for the first time, the presence of at least two pathogenic haplotypes in Australia. While historically there have been no reports of wasting disease-related seagrass habitat loss, the presence of pathogenic Labyrinthula highlights the need for disease monitoring and research to understand seagrass wasting disease ecology in Australia.
Transcription factors Atf1 and Sty1 promote stress tolerance under nitrosative stress in Schizosaccharomyces pombe Microbiol. Res. (IF 3.037) Pub Date : 2017-10-12 Puranjoy Kar, Pranjal Biswas, Sourav Kumar Patra, Sanjay Ghosh
Nitric Oxide (NO) and its associated reactive nitrogen species (RNS) produce nitrosative stress under various pathophysiological conditions in eukaryotes. The fission yeast Schizosaccharomyces pombe regulates stress response mainly through the Sty1-Atf1 MAP Kinase pathway. The present study deals with the role of transcription factor Atf1 and Sty1 in S. pombe under nitrosative stress. In this study, exposure to an NO donor resulted in S-phase slowdown with associated mitotic block in S. pombe. Deletion of sty1 and atf1 in S. pombe had differential growth sensitivity towards NO donor. Both Sty1 and Atf1 were involved in regulating mitotic slowdown in S. pombe under nitrosative stress. Experimental data obtained in this study reveals a novel role of Atf1 in initiating the replication slowdown in S. pombe under nitrosative stress. Both Sty1 and Atf1 were accumulated in the nucleus in S. pombe under nitrosative stress in a concentration and time dependent manner. Atf1 is also found to be nuclear delocalized under longer nitrosative stress.
SawR a new regulator controlling pyomelanin synthesis in Pseudomonas aeruginosa Microbiol. Res. (IF 3.037) Pub Date : 2017-10-13 Yossi Ben-David, Elena Zlotnik, Itzhak Zander, Gal Yerushalmi, Sivan Shoshani, Ehud Banin
Surface Acoustic Waves (SAW) were previously shown to inhibit biofilm formation, increase bacterial susceptibility to antibiotic treatment and alter the transcription pattern of Pseudomonas aeruginosa. Here we characterize one gene, sawR (PA3133), that is highly overexpressed when P. aeruginosa is exposed to SAW. SawR is a putative transcription factor belonging to the TetR regulator family. When overexpressed sawR causes numerous phenotypes, including the accumulation of a brown pigment which we identified as pyomelanin. In this study we describe how sawR regulates pyomelanin synthesis. We show that sawR down-regulates the expression levels of hmgA and this causes the accumulation of homogentisic acid which in turn undergoes oxidation and polymerization to pyomelanin. Using bioinformatics, we were able to identify a specific amino acid, arginine 23, which is found within the sawR DNA binding domain and is crucial for its regulatory activity. Our results indicate that sawR does not affect any other genes in the phenylalanine/tyrosine metabolic pathway and its repressive ability on hmgA is not mediated by the hmgA repressor PA2010 (i.e. hmgR). Taken together, our results shed light on the regulatory cascade controlling pyomelanin synthesis and uncover yet another unknown regulator involved in its regulation.
Endophytism or saprophytism: Decoding the lifestyle transition of the generalist fungus Phomopsis liquidambari Microbiol. Res. (IF 3.037) Pub Date : 2017-10-16 Jun Zhou, Xin Li, Peng-Wei Huang, Chuan-Chao Dai
Filamentous ascomycete Phomopsis sp. are common inhabitants of natural ecosystems and, as saprophytes, are largely responsible for the destructive decay of litterfall, promoting the carbon and nitrogen cycles. Phomopsis liquidambari B3 can establish mutualistic symbiosis with a broad spectrum of crop plants. Colonizing dynamics observations and a growth promotion assay of rice and Arabidopsis thaliana revealed that the B3 colonization strategy is host-adapted and resulted in different growth promotions influenced by N availability. However, the biochemical mechanisms and underlying genetics of the saprophyte transition to an endophyte are poorly understood. Here, the transcriptome features of generalist P. liquidambari and highlighted gene sets involved in the lifestyle transition from saprophytism to endophytism were reported. Most notable were genes for translation, ribosome biogenesis and MAPK signaling, several of which were only up-regulated in endophytic B3. Coordinated up-regulation of genes encoding enzymes involved in phenylalanine, tyrosine and tryptophan biosynthesis were preceded by secondary metabolite induction, which was encountered with host defense. Quantitative PCR validates the reliability of RNA-seq. Dissection at the molecular level facilitated a deeper understanding of P. liquidambari adaptation to hosts and the complex natural environment to play a role in sustainable agriculture and carbon and nitrogen cycles.
Phosphatidylcholine absence affects the secretion of lipodepsipeptide phytoxins in Pseudomonas syringae pv. syringae van Hall CFCC 1336 Microbiol. Res. (IF 3.037) Pub Date : 2017-10-16 Fang Cao, Min Xiong, Shunyi Li, Huawan Cai, Yufang Sun, Sheng Yang, Xin Liu, Rong Zhu, Xuejing Yu, Xingguo Wang
Pseudomonas syringae pv. syringae van Hall CFCC 1336 (Pss 1336) is the causal agent of bacterial disease of stone fruit trees, and also able to elicit hypersensitive response (HR) in non-host tobacco. It is known that this pathogen uses PCS-pathway to synthesize phosphatidylcholine (PC), and mutation of the pcs gene abolishes bacterial PC synthesis. Previous study also found that the 1336 pcs− mutant lacking PC in its membrane phospholipids was unable to secrete HrpZ harpin and elicit HR in non-host plants. In this study, we further analyzed virulence of lipodepsipeptide phytoxins of Pss 1336 wild type (pcs+), the 1336RM (pcs−/+) and the 1336 pcs− mutant, and found that the 1336 pcs− mutant was unable to cause necrosis of Chinese date fruits and inhibit fungal growth. HPLC analysis also showed that the 1336 pcs− mutant markedly reduced its secretion of lipodepsipeptide phytoxins. Analysis of semi-quantitative RT-PCR revealed that PC presence or absence did not affect gene expressions of SyrD, PseABC and PseEF efflux systems at transcriptional level. However, western blotting assays found that PseE and PseF present only in the cytoplasmic fractions but undetectable in the membrane extract of the 1336 pcs− mutant. PC absence obviously interrupted the translocation of two membrane-associated proteins PseE and PseF from cytoplasm to cell membranes to form an intact PseEF efflux system in bacterial membranes. Failure to form PseEF efflux system could be a major factor for less lipopeptide-phytoxin secretion. Our results demonstrate that PC in bacterial membrane phospholipids plays an important role in maintaining physiological functions of PseEF efflux system.
Composition of lactic acid bacteria during spontaneous curly kale (Brassica oleracea var. sabellica) fermentation Microbiol. Res. (IF 3.037) Pub Date : 2017-10-16 Magdalena Michalak, Klaudia Gustaw, Adam Waśko, Magdalena Polak-Berecka
The present work is the first report on spontaneous fermentation of curly kale and characteristics of autochthonous lactic acid bacteria (LAB). Our results indicate that curly kale fermentation is the new possibility of the technological use of this vegetable. Bacteria representing ten different species were isolated from three phases of curly kale fermentation and identified by MALDI-TOF mass spectrometry and 16S rRNA gene sequencing. Among them, four species were identified as Lactobacillus spp. (Lb. plantarum 332, Lb. paraplantarum G2114, Lb. brevis R413, Lb. curvatus 154), two as Weissella spp. (W. hellenica 152, W. cibaria G44), two as Pediococcus spp. (P. pentosaceus 45AN, P. acidilactici 2211), one as Leuconostoc mesenteroides 153, and one as Lactococcus lactis 37BN. The functional properties of isolates, i.e. acid, NaCl and bile salt tolerance, enzyme activities, adhesion to hydrocarbons, and antibiotic resistance, were examined. Among the tested strains, Lb. plantarum 332, Lb. paraplantarum G2114, P. pentosaceus 2211, and Lb. brevis R413 exhibited the best hydrophobicity value and high tolerance to bile salts, NaCl, and low pH.
Revitalization of plant growth promoting rhizobacteria for sustainable development in agriculture Microbiol. Res. (IF 3.037) Pub Date : 2017-10-17 Sushanto Gouda, Rout George Kerry, Gitishree Das, Spiros Paramithiotis, Han-Seung Shin, Jayanta Kumar Patra
The progression of life in all forms is not only dependent on agricultural and food security but also on the soil characteristics. The dynamic nature of soil is a direct manifestation of soil microbes, bio-mineralization, and synergistic co-evolution with plants. With the increase in world’s population the demand for agriculture yield has increased tremendously and thereby leading to large scale production of chemical fertilizers. Since the use of fertilizers and pesticides in the agricultural fields have caused degradation of soil quality and fertility, thus the expansion of agricultural land with fertile soil is near impossible, hence researchers and scientists have sifted their attention for a safer and productive means of agricultural practices. Plant growth promoting rhizobacteria (PGPR) has been functioning as a co-evolution between plants and microbes showing antagonistic and synergistic interactions with microorganisms and the soil. Microbial revitalization using plant growth promoters had been achieved through direct and indirect approaches like bio-fertilization, invigorating root growth, rhizoremediation, disease resistance etc. Although, there are a wide variety of PGPR and its allies, their role and usages for sustainable agriculture remains controversial and restricted. There is also variability in the performance of PGPR that may be due to various environmental factors that might affect their growth and proliferation in the plants. These gaps and limitations can be addressed through use of modern approaches and techniques such as nano-encapsulation and micro-encapsulation along with exploring multidisciplinary research that combines applications in biotechnology, nanotechnology, agro biotechnology, chemical engineering and material science and bringing together different ecological and functional biological approaches to provide new formulations and opportunities with immense potential.
Differential protein-DNA contacts for activation and repression by ArgP, a LysR-type (LTTR) transcriptional regulator in Escherichia coli Microbiol. Res. (IF 3.037) Pub Date : 2017-10-23 Phu Nguyen Le Minh, Cristina Velázquez Ruiz, Steven Vandermeeren, Pamella Abwoyo, Indra Bervoets, Daniel Charlier
ArgP is a LysR-type transcriptional regulator (LTTR) that operates with two effector molecules, lysine and arginine, to differentially regulate gene expression. Effector-free ArgP stimulates transcription of all investigated regulon members, except argO, whereas lysine abolishes this effect. Activation of argO, encoding an exporter for arginine and canavanine, is strictly dependent on arginine-bound ArgP. Lysine counteracts this effect and even though lysine-bound ArgP stimulates RNA polymerase recruitment at the argO promoter, the complex is non-productive. It is presently unclear what distinguishes argO from other ArgP targets and how binding of arginine and lysine translates in antagonistic effects on promoter activity. Here we generate high resolution contact maps of effector-free and effector-bound ArgP-DNA interactions and identify the sequence 5′-CTTAT as the consensus recognition motif for ArgP binding. argO is the only operator at which ArgP binding overlaps the −35 promoter element and binding of arginine results in a repositioning of the promoter proximal bound ArgP-arg subunits. This effect was mimicked by the generation of a 10 bp insertion mutant (ins-10) in the argO operator that renders its activation by ArgP arginine-independent. ArgP-induced DNA bending of the argO operator by approximately 60° was found to be effector independent. An ArgP:DNA binding stoichiometry of 4:1 indicates binding of four ArgP subunits even to DNA constructs that are truncated for one binding subsite (ΔABS). These results provide insight into the molecular mechanisms of ArgP-mediated regulation and a molecular explanation for the unique arginine-dependence of argO activation that distinguishes this particular ArgP target from all others.
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