Publications

siderophore-mediated iron dissolution from nontronites is controlled by mineral cristallochemistry.	bacteria living in oxic environments experience iron deficiency due to limited solubility and slow dissolution kinetics of iron-bearing minerals. to cope with iron deprivation, aerobic bacteria have evolved various strategies, including release of siderophores or other organic acids that scavenge external fe(iii) and deliver it to the cells. this research investigated the role of siderophores produced by pseudomonas aeruginosa in the acquisition of fe(iii) from two iron-bearing colloidal nontron ...	2016	27064911
the native microbiome of the nematode caenorhabditis elegans: gateway to a new host-microbiome model.	host-microbe associations underlie many key processes of host development, immunity, and life history. yet, none of the current research on the central model species caenorhabditis elegans considers the worm's natural microbiome. instead, almost all laboratories exclusively use the canonical strain n2 and derived mutants, maintained through routine bleach sterilization in monoxenic cultures with an e. coli strain as food. here, we characterize for the first time the native microbiome of c. elega ...	2016	27160191
potential of biological agents in decontamination of agricultural soil.	pesticides are widely used for the control of weeds, diseases, and pests of cultivated plants all over the world, mainly since the period after the second world war. the use of pesticides is very extensive to control harm of pests all over the globe. persistent nature of most of the synthetic pesticides causes serious environmental concerns. decontamination of these hazardous chemicals is very essential. this review paper elaborates the potential of various biological agents in decontamination o ...	2016	27293964
gcsr, a tyrr-like enhancer-binding protein, regulates expression of the glycine cleavage system in pseudomonas aeruginosa pao1.	glycine serves as a major source of single carbon units for biochemical reactions within bacterial cells. utilization of glycine is tightly regulated and revolves around a key group of proteins known as the glycine cleavage system (gcs). our lab previously identified the transcriptional regulator gcsr (pa2449) as being required for catabolism of glycine in the opportunistic pathogen pseudomonas aeruginosa pao1. in an effort to clarify and have an overall better understanding of the role of gcsr ...	2016	27303730
it all starts with a sandwich: identification of sialidases with trans-glycosylation activity.	sialidases (3.2.1.18) may exhibit trans-sialidase activity to catalyze sialylation of lactose if the active site topology is congruent with that of the trypanosoma cruzi trans-sialidase (ec 2.4.1.-). the present work was undertaken to test the hypothesis that a particular aromatic sandwich structure of two amino acids proximal to the active site of the t. cruzi trans-sialidase infers trans-sialidase activity. on this basis, four enzymes with putative trans-sialidase activity were identified thro ...	2016	27367145
impact of soil salinity on the structure of the bacterial endophytic community identified from the roots of caliph medic (medicago truncatula).	in addition to being a forage crop, caliph medic (medicago truncatula) is also a model legume plant and is used for research focusing on the molecular characterization of the interaction between rhizobia and plants. however, the endophytic microbiome in this plant is poorly defined. endophytic bacteria play a role in supplying plants with the basic requirements necessary for growth and development. moreover, these bacteria also play a role in the mechanism of salinity stress adaptation in plants ...	2016	27391592
the interaction between arbuscular mycorrhizal fungi and endophytic bacteria enhances plant growth of acacia gerrardii under salt stress.	microbes living symbiotically in plant tissues mutually cooperate with each other by providing nutrients for proliferation of the partner organism and have a beneficial effect on plant growth. however, few studies thus far have examined the interactive effect of endophytic bacteria and arbuscular mycorrhizal fungi (amf) in hostile conditions and their potential to improve plant stress tolerance. in this study, we investigated how the synergistic interactions of endophytic bacteria and amf affect ...	2016	27486442
novel m4c modification in type i restriction-modification systems.	we identify a new subgroup of type i restriction-modification enzymes that modify cytosine in one dna strand and adenine in the opposite strand for host protection. recognition specificity has been determined for ten systems using smrt sequencing and each recognizes a novel dna sequence motif. previously characterized type i systems use two identical copies of a single methyltransferase (mtase) subunit, with one bound at each half site of the specificity (s) subunit to form the mtase. the new m4 ...	2016	27580720
screen of non-annotated small secreted proteins of pseudomonas syringae reveals a virulence factor that inhibits tomato immune proteases.	pseudomonas syringae pv. tomato dc3000 (ptodc3000) is an extracellular model plant pathogen, yet its potential to produce secreted effectors that manipulate the apoplast has been under investigated. here we identified 131 candidate small, secreted, non-annotated proteins from the ptodc3000 genome, most of which are common to pseudomonas species and potentially expressed during apoplastic colonization. we produced 43 of these proteins through a custom-made gateway-compatible expression system for ...	2016	27603016
biodegradation of methyl tert-butyl ether by co-metabolism with a pseudomonas sp. strain.	co-metabolic bioremediation is supposed to be an impressive and promising approach in the elimination technology of methyl tert-butyl ether (mtbe), which was found to be a common pollutant worldwide in the ground or underground water in recent years. in this paper, bacterial strain dz13 (which can co-metabolically degrade mtbe) was isolated and named as pseudomonas sp. dz13 based on the result of 16s rrna gene sequencing analysis. strain dz13 could grow on n-alkanes (c₅-c₈), accompanied with the ...	2016	27608032
extremophiles in an antarctic marine ecosystem.	recent attempts to explore marine microbial diversity and the global marine microbiome have indicated a large proportion of previously unknown diversity. however, sequencing alone does not tell the whole story, as it relies heavily upon information that is already contained within sequence databases. in addition, microorganisms have been shown to present small-to-large scale biogeographical patterns worldwide, potentially making regional combinations of selection pressures unique. here, we focus ...	2016	27681902
protein domain architectures provide a fast, efficient and scalable alternative to sequence-based methods for comparative functional genomics.	a functional comparative genome analysis is essential to understand the mechanisms underlying bacterial evolution and adaptation. detection of functional orthologs using standard global sequence similarity methods faces several problems; the need for defining arbitrary acceptance thresholds for similarity and alignment length, lateral gene acquisition and the high computational cost for finding bi-directional best matches at a large scale. we investigated the use of protein domain architectures ...	2016	27703668
the isolation and functional identification on producing cellulase of pseudomonas mendocina.	the straw can be degraded efficiently into humus by powerful enzymes from microorganisms, resulting in the accelerated circulation of n,p,k and other effective elements in ecological system. we isolated a strain through screening the straw degradation strains from natural humic straw in the low temperature area in northeast of china, which can produce cellulase efficiently. the strain was identified as pseudomonas mendocina by using morphological, physiological, biochemical test, and molecular b ...	2016	27710430
pseudomonas mendocina native valve infective endocarditis: a case report.	gram-negative microorganisms are uncommon pathogens responsible for infective endocarditis. pseudomonas mendocina, a gram-negative water-borne and soil-borne bacterium, was first reported to cause human infection in 1992. since then, it has rarely been reported as a human pathogen in the literature. we describe the first case of native valve infective endocarditis due to p. mendocina in the usa.	2016	27716406
the diguanylate cyclase hsbd intersects with the hptb regulatory cascade to control pseudomonas aeruginosa biofilm and motility.	the molecular basis of second messenger signaling relies on an array of proteins that synthesize, degrade or bind the molecule to produce coherent functional outputs. cyclic di-gmp (c-di-gmp) has emerged as a eubacterial nucleotide second messenger regulating a plethora of key behaviors, like the transition from planktonic cells to biofilm communities. the striking multiplicity of c-di-gmp control modules and regulated cellular functions raised the question of signaling specificity. are c-di-gmp ...	2016	27792789
host-specific functional significance of caenorhabditis gut commensals.	the gut microbiota is an important contributor to host health and fitness. given its importance, microbiota composition should not be left to chance. however, what determines this composition is far from clear, with results supporting contributions of both environmental factors and host genetics. to gauge the relative contributions of host genetics and environment, specifically the microbial diversity, we characterized the gut microbiotas of caenorhabditis species spanning 200-300 million years ...	2016	27799924
molecular cloning, heterologous expression, and enzymatic characterization of lysoplasmalogen-specific phospholipase d from thermocrispum sp.	lysoplasmalogen (lypls)-specific phospholipase d (lypls-pld) is an enzyme that catalyses the hydrolytic cleavage of the phosphoester bond of lypls, releasing ethanolamine or choline, and 1-(1-alkenyl)-sn-glycero-3-phosphate (lysoplasmenic acid). little is known about lypls-pld and metabolic pathways of plasmalogen (pls). reportedly, pls levels in human serum/plasma correlate with several diseases such as alzheimer's disease and arteriosclerosis as well as a variety of biological processes includ ...	2016	27833852
the toxin-antitoxin system dartg catalyzes reversible adp-ribosylation of dna.	the discovery and study of toxin-antitoxin (ta) systems helps us advance our understanding of the strategies prokaryotes employ to regulate cellular processes related to the general stress response, such as defense against phages, growth control, biofilm formation, persistence, and programmed cell death. here we identify and characterize a ta system found in various bacteria, including the global pathogen mycobacterium tuberculosis. the toxin of the system (dart) is a domain of unknown function ...	2016	27939941
comparative investigation on a hexane-degrading strain with different cell surface hydrophobicities mediated by starch and chitosan.	bioremediation usually exhibits low removal efficiency toward hexane because of poor water solubility, which limits the mass transfer rate between the substrate and microorganism. this work aimed to enhance the hexane degradation rate by increasing cell surface hydrophobicity (csh) of the degrader, pseudomonas mendocina nx-1. the csh of p. mendocina nx-1 was manipulated by treatment with starch and chitosan solution of varied concentrations, reaching a maximum hydrophobicity of 52%. the biodegra ...	2017	28091789
phenotypic and genomic survey on organic acid utilization profile of pseudomonas mendocina strain s5.2, a vineyard soil isolate.	root exudates are chemical compounds that are released from living plant roots and provide significant energy, carbon, nitrogen and phosphorus sources for microbes inhabiting the rhizosphere. the exudates shape the microflora associated with the plant, as well as influences the plant health and productivity. therefore, a better understanding of the trophic link that is established between the plant and the associated bacteria is necessary. in this study, a comprehensive survey on the utilization ...	2017	28655216
pseudomonas mendocina: the first case of peritonitis on peritoneal dialysis.		2017	28655401
degradation and conversion of endosulfan by newly isolated pseudomonas mendocina zam1 strain.	endosulfan contamination is one of the major concerns of soil ecosystem, which causes detrimental effects not only to humans but also to animals and plants. therefore, the aim of this study was to isolate and identify a novel bacterial strain capable of degrading endosulfan in agriculture contaminated soils. a novel bacterial strain was isolated from the sugarcane field contaminated with endosulfan, and was named as zam1 strain. the zam1 bacterial strain was further identified as pseudomonas men ...	2017	28667651
biodegradation of p(3hb-co-4hb) powder by pseudomonas mendocina for preparation low-molecular-mass p(3hb-co-4hb).	poly(3-hydroxybutyrate-co-4-hydroxybutyrate) (p(3hb-co-4hb)) is a biodegradable plastic that is extensively utilized in many fields. in this work, p(3hb-co-4hb) powder was degraded by pseudomonas mendocina for the preparation of low-molecular-mass (lmw) p(3hb-co-4hb). after degradation, the remaining p(3hb-co-4hb) powder was analyzed via gel permeation chromatography (gpc), differential scanning calorimetry (dsc), x-ray powder diffraction (xrd), fourier transform infrared (ftir) spectroscopy, an ...	2017	28828288
diversity of culturable aerobic denitrifying bacteria in the sediment, water and biofilms in liangshui river of beijing, china.	aerobic denitrification is a process reducing the nitrate into gaseous nitrogen forms in the presence of oxygen gas, which makes the nitrification and denitrification performed simultaneously. however, little was known on the diversity of the culturable aerobic denitrifying bacteria in the surface water system. in this study, 116 strains of aerobic denitrifying bacteria were isolated from the sediment, water and biofilm samples in liangshui river of beijing. these bacteria were classified into 1 ...	2017	28855587